A new approach was presented in this study to simulate a stable atom along with subatomic particles in it. Subatomic particles in an atom are treated as conventional particles, exhibiting attraction and repulsion between them, giving a stable atom simulation. This new approach leads to developing new potentials for subatomic particles to simulate a stable atom. Subatomic particle dynamics (SPD) simulations were developed for within-atom simulations that give a stable atom structure for infinite time and provide many insights into electron trajectories and atom properties like energies and radius of the atom. The effect of protons and neutrons movement in the nucleus on electron trajectories was captured in SPD. Hydrogen and Carbon atom SPD were reported in this study. The Pilot-wave theory was implemented in this study to simulate the wave nature of subatomic particles in an atom. Electrons motion was guided by the interference pattern produced by the electron’s aether medium waves in SPD. SPD was implemented on molecules, resulting in a stable molecular structure giving insights into electron trajectories shared by multiple atoms.

Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron-sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from DFT calculations. The distal cubane FeS-cluster has a three cysteine and one histidine coordination [Fe₄S₄](His)(Cys)₃ first ligation sphere. The reorganization energy (inner- and outer-sphere) is almost unchanged upon a histidine-to-cysteine substitution. Differences in rates of electron transfer between the wild-type enzyme and the all-cysteine mutant can be rationalized by a diminished electronic coupling between the donor and acceptor molecules in the [Fe₄S₄](Cys)₄ case. The fast and efficient electron transfer from the distal iron-sulfur cluster is realized by a fine-tuned protein environment which facilitates the flow of electrons. This study enables the design and control of electron transfer rates and pathways by protein engineering.

High-quality ionization injection methods for Wake Field Acceleration driven by lasers or charged beams (LWFA/PWFA) can be optimised so as to generate high-brightness electron beams with tuneable duration in the attosecond range. We present a model of the minimum bunch duration obtainable with low-emittance ionization injection schemes, by spotting the roles of the ionization pulse duration, of the wake field longitudinal shape and of the delay of the ionization pulse position with respect to the node of the accelerating field. The model is tested for the resonant multi-pulse ionization injection (ReMPI) scheme, showing that bunches having length of about 300as can be obtained with a ionization pulse having duration of 30fs FWHM

We investigate the production of an isolated attosecond pulse (IAP) via the phase-matching gating of high-harmonic generation by intense laser pulses. Our study is based on the integration of the propagation equation for the fundamental and generated fields with nonlinear polarisation found via the numerical solution of the time-dependent Schr\"odinger equation. We study the XUV energy as a function of the propagation distance (or the medium density) and find that the onset of the IAP production corresponds to the change from linear to quadratic dependence of this energy on the propagation distance (or density). Finally, we show that the upper limit of the fundamental pulse duration for which the IAP generation is feasible is defined by the temporal spreading of the fundamental pulse during the propagation. This nonlinear spreading is defined by the difference of the group velocities for the neutral and photoionised medium.

The theory of one-photon ionization and two-photon above-threshold ionization is formulated for applications to heavy atoms in attosecond science using the Dirac-Fock formalism. A direct comparison of the Wigner-Smith-Eisenbud delays for photoionization is made with delays from the Reconstruction of Attosecond Beating By Interference of Two-photon Transitions (RABBIT) method. Photoionization by an attosecond pulse train, consisting of monochromatic fields in the extreme ultraviolet range, is computed with many-body effects at the level of the Relativistic Random Phase Approximation (RRPA). Subsequent absorption and emission processes of infrared laser photons in RABBIT are evaluated using static ionic potentials as well as asymptotic properties of relativistic Coulomb functions. As expected, light elements, such as Argon, show negligible relativistic effects, while heavier elements, such a Krypton and Xenon, exhibit delays that depend on the fine-structure of the ionic target. The relativistic effects are notable close to ionization thresholds and Cooper minima with differences in fine-structure delays predicted to be as large as tens of attoseconds. The separability of relativistic RABBIT delays into a Wigner-Smith-Eisenbud delay and a universal continuum--continuum delay is studied with reasonable separability found for photoelectrons emitted along the laser polarization axis in agreement with prior non-relativistic results.

The attitude dynamics and orbit dynamics of large rigid space structures are coupled with each other under gravity gradient, which may affect the stability of the large rigid space structures. In this paper, the gravity gradient stability of a large rigid space structure is studied under both small and large disturbances. Based on the rigid body dynamics and orbit dynamics, an accurate dynamic model without any linearization of the large rigid space structure is established via the natural coordinate formulation (NCF), which is able to describe the large overall motions of the structures. By using the generalized-α algorithm, the gravity gradient stability of the large rigid space structure is simulated and analyzed via various examples, including the influence of large disturbance angles, the positions at the stabilization and unstabilization regions. Finally, the relationship between spinning stability and gravity gradient stability is also investigated via a large spinning space structure.

A U.S. government health agency conducted epidemiological studies to evaluate whether exposures to drinking water contaminated with volatile organic compounds at U.S. Marine Corps Base Camp Lejeune, North Carolina, were associated with increased health risks to children and adults. These health studies required knowledge of contaminant concentrations in drinking water—at monthly intervals—delivered to family housing, barracks, and other facilities within the study area. Because concentration data were limited or unavailable during much of the period of contamination (1950s–1985), the historical reconstruction process was used to quantify estimates of monthly mean contaminant-specific concentrations. This paper integrates many efforts, reports, and papers into a synthesis of the overall approach to, and results from, a drinking-water historical reconstruction study. Results show that at the Tarawa Terrace water treatment plant (WTP) reconstructed (simulated) tetrachloroethylene (PCE) concentrations reached a maximum monthly average value of 183 micrograms per liter (ug/L) compared to a one-time maximum measured value of 215 ug/L and exceeded the U.S. Environmental Protection Agency’s current maximum contaminant level (MCL) of 5 ug/L during the period November 1957–February 1987. At the Hadnot Point WTP, reconstructed trichloroethylene (TCE) concentrations reached a maximum monthly average value of 783 ug/L compared to a one-time maximum measured value of 1,400 ug/L during the period August 1953–December 1984. The Hadnot Point WTP also provided contaminated drinking water to the Holcomb Boulevard housing area continuously prior to June 1972, when the Holcomb Boulevard WTP came on line (maximum reconstructed TCE concentration of 32 ug/L) and intermittently during the period June 1972–February 1985 (maximum reconstructed TCE concentration of 66 ug/L). Applying the historical reconstruction process to quantify contaminant-specific monthly drinking-water concentrations is advantageous for epidemiological studies when compared to using the classical exposed versus unexposed approach.

The discrete element method (DEM) coupled with computational dynamics (CFD) has been considered one of the most sensitive ways of studying fluidized beds. This paper presents gas-solid fluidized bed simulations by use of CFD-DEM. The two-phase interaction is calculated in a way of decoupling. Within the effective neighborhood of the particles, the kernel approximation method is used to calculate the local porosity, thereby calculating the drag force on the particles. At the grid scale, the momentum exchange coefficient is calculated using a two fluid model based method, thereby calculating the source term of the phase interaction in the fluid control equation. The simulated form, size and motion process of the big bubble are all consistent with experimental observations. The simulated solid volume fraction and relative pressure averaged in a horizontal plane at 45 mm above the bottom are in reasonable agreement with the experimental data. The fluctuation of the simulated bed height over time is similar to the experimental measurement results. The reproduction of these qualitative and quantitative results indicates that the proposed method effectively improves simulation performance and accuracy.

It is well known that X-ray crystallography is based on X-ray diffraction (XRD) by atoms and molecules. The diffraction pattern arises as a result of scattering of incident radiation, which makes it possible to determine the structure of the scattering substance. With the advent of ultrashort radiation sources, the theory and interpretation of X-ray diffraction analysis remained the same. This work shows that when an attosecond laser pulse is scattered on a DNA molecule, including during its nicking and bending, the pulse duration is an important characteristic of the scattering. In this case, the diffraction pattern changes significantly compared to the previously known scattering theory. The results obtained must be used in XRD theory to study DNA structures, their mutations and damage, since the previously known theory can produce large errors and, therefore, the DNA structure can be “deciphered” incorrectly.

The Source Region of the Yellow River (SRYR), renowned as the "Water Tower of the Yellow River", serves as an important water conservation domain in the upper reaches of the Yellow River, significantly influencing water resources within the basin. Based on the Weather Research and Forecasting (WRF) Model Hydrological modeling system (WRF-Hydro) model, the key variables of the atmosphere-land-hydrology coupling processes over the SRYR during the 2013 rainy season are analyzed. The investigation involves a comparative analysis between the coupled WRF-Hydro and the standalone WRF simulations, focusing on the hydrological response to the atmosphere. The results reveal that the WRF-Hydro model's proficiency in depicting streamflow variations over the SRYR, yielding a Nash Efficiency Coefficient (NSE) of 0.44 and of  0.61 during the calibration and validation periods, respectively. Compared to the standalone WRF simulations, the coupled WRF-Hydro model demonstrates enhanced performance in soil heat fluxes simulations, reducing the mean Root Mean Square Error (RMSE) of surface soil temperature by 0.96 K and soil moisture by 0.01 m\textsuperscript{\textsuperscript{3}}/m\textsuperscript{\textsuperscript{3}}. Furthermore, the coupled model adeptly captures the streamflow variation characteristics with the NSE of 0.33. This underscores the significant potential of the coupled WRF-Hydro model for delineating coupled atmosphere-land-hydrology processes in regions characterized by cold climates and intricate topography.

This study investigates the stochastic dynamics of hepatitis B virus (HBV) infection using a newly proposed stochastic model. Contrary to deterministic models that fail to encapsulate the inherent randomness and fluctuations in biological processes, our stochastic model provides a more realistic representation of HBV infection dynamics. It incorporates random variability, thereby acknowledging the changes in viral and cellular populations and uncertainties in parameters such as infection rates and immune responses. We examine the solution's existence, uniqueness, and positivity for the proposed model, followed by a comprehensive stability analysis. We provide the necessary and sufficient conditions for local and global stability, offering deep insight into the infection dynamics. Furthermore, we utilize numerical simulations to corroborate our theoretical results. This research provides a robust tool for understanding the complex behavior of HBV dynamics, contributing significantly to the ongoing quest for more effective HBV control and prevention strategies.

Into the frame of the French TANDEM project (Tsunamis in the Atlantic and the English ChaNnel: Definition of the Effects through numerical Modelling) Principia has been working on the development and qualification of two in-house CFD software’s: the 2D EOLE-SV (Saint Venant) model for simulation of large scale tsunami propagation from the source up to coastal scale and the 3D EOLE-NS (Navier-Stokes) model dedicated to tsunami coastal impact modelling. This paper presents a large range of test cases carried out into the frame of the project and dedicated to the validation of numerical codes in various tsunami wave conditions. The main aspects of phenomena such as wave generation, propagation and coastal impact are investigated on academic situations. A real case simulation is concerned as well, the devastating 2011 Tohoku event which is compared with in-situ data.

Efficiency improvement is the new challenge in all fields of design. In this scenario the reduction of power losses is becoming more and more a main concern also in the design of power transmissions. Appropriate models to predict power losses are therefore from the earliest stages of the design phase. The aim of the project is to carry on lubrication simulations of several variants of a cylindrical-roller-bearing to understand the lubricant distribution and the related churning power losses. Several strategies to reduce the computational effort have been used. Among them the sectorial symmetry and three innovative meshing strategies (purely analytical with and without interfaces and analytical/subtractive) that have been implemented in the OpenFOAM® environment. The results of the different approaches were compared among them and with experimental observations showing good agreement and reasonable savings in terms of computational effort.

Intermediate-luminosity-optical-transients (ILOTs) are stellar outbursts with luminosity between those of classical novae and supernovae. They are divided into a number of sub-groups depending on the erupting progenitor and the properties of the eruption. Many of the ILOTs sit on the slanted Optical Transient Stripe (OTS) in the Energy-Time Diagram (ETD) that shows their total energy vs. duration of their eruption. We describe the different kinds of ILOTs that populate the OTS and other parts of the ETD. We also stand on similarities between Planetary Nebulae (PN) to ILOTs, and suggest that some PNe were formed in an ILOT event. The high energy part of the OTS is reserved to the supernova impostors -- giant eruption of very massive stars. We show results of 3D hydrodynamical simulations of supernova impostors that expose the mechanism behind these giant eruptions, and present new models for recent ILOTs. We stand on the connection between different kinds of ILOTs, and suggest that they are powered by a similar source of energy -- gravitational energy released by mass transfer.

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can provide predictions, reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

In this paper we show how to efficiently implement parallel discrete simulations on Multi-Core and GPU architectures through a real example of application: a cellular automata model of laser dynamics. We describe the techniques employed to build and optimize the implementations using OpenMP and CUDA frameworks. We have evaluated the performance on two different hardware platforms that represent different target market segments: high-end platforms for scientific computing, using an Intel Xeon Platinum 8259CL server with48cores and also an NVIDIA Tesla6V100 GPU, both running on Amazon Web Server (AWS) Cloud, and on a consumer-oriented platform, using an Intel Core i9 9900k CPU and an NVIDIA GeForce GTX 1050 TI GPU. Performance results are compared and analysed in detail. We show that excellent performance and scalability can be obtained in both platforms, and we extract some important issues that imply a performance degradation for them. We also found that current Multi-Core CPUs with large core numbers can bring a performance very near to that of GPUs, even similar in some cases.

Polymers' controlled pyrolysis is an economical and environmentally friendly solution to prepare activated carbon. However, due to the experimental difficulty in measuring the dependence between tissues and pyrolysis parameters at high temperatures, the unknown pyrolysis mechanism hinders access to the target products with desirable morphologies and performances. In this study, we investigate the pyrolysis process of polystyrene under different heating rates and temperatures employing reactive molecular dynamics (ReaxFF-MD) simulations. A clear profile of the generation of pyrolysis products determined by the temperature and heating rate is constructed. It is found that the heating rate affects the type and amount of pyrolysis intermediates and their timing, and low-rate heating helps yield more diverse pyrolysis intermediates. While the temperature affects the pyrolytic tissues of the final equilibrium products, either too low or too high a target temperature is detrimental to generating large areas of graphitized tissue. The established theoretical evolution process matches experiments well, thus contributing to preparing target activated carbons by referring to the regulatory mechanism of pyrolytic tissues.

Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and a thereby be trafficked to specific locations. The description of curvature-sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations, given the right tools. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles, and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow the researcher to closely match the conditions of experimental studies of membrane curvatures.

Purification of biologically-derived therapeutics is a major cost contributor to the production of this rapidly growing class of pharmaceuticals. Monoclonal antibodies comprise a large percentage of these products therefore new antibody purification tools are needed. Small peptides, as opposed to traditional antibody affinity ligands such as Protein A, may have advantages in stability and production costs. Multiple heptapeptides that demonstrate Fc binding behavior that have been identified from a combinatorial peptide library using M13 Phage Display are presented herein. Seven unique peptide sequences of diverse hydrophobicity and charge were identified. All seven peptides showed strong binding to the four major human IgG isotypes, human IgM, as well as binding to canine, rat, and mouse IgG. These seven peptides were also shown to bind human IgG4 from DMEM cell culture media with 5% FCS and 5 g/L ovalbumin present. These peptides may be useful as surface ligands for antibody detection and purification purposes. Molecular docking and classical molecular dynamics (MD) simulations were conducted to elucidate the mechanisms and energetics for the binding of these peptides to the Fc region. The binding site was found to be located between the two glycan chains inside the Fc fragment. Both hydrogen bonding and hydrophobic interactions were found to be crucial for the binding interactions. Excellent agreement for the binding strength was obtained between experimental results and simulations.

Numerical models widely used for hydrocarbon phase behavior and compositional flow simulations are based on assumption of thermodynamic equilibrium. However, it is not uncommon for oil and gas-condensate reservoirs to exhibit essentially non-equilibrium phase behavior, e.g., in the processes of secondary recovery after pressure depletion below saturation pressure, or during gas injection, or for condensate evaporation at low pressures. In many cases the ability to match field data with equilibrium model depends on simulation scale. The only method to account for non-equilibrium phase behavior adopted by the majority of flow simulators is the option of limited rate of gas dissolution (condensate evaporation) in black oil models. For compositional simulations no practical yet thermodynamically consistent method has been presented so far except for some upscaling techniques in gas injection problems. Previously reported academic non-equilibrium formulations have a common drawback of doubling the number of flow equations and unknowns compared to the equilibrium formulation. In the paper a unified thermodynamically-consistent formulation for compositional flow simulations with non-equilibrium phase behavior model is presented. Same formulation and a special scale-up technique can be used for upscaling of an equilibrium or non-equilibrium model to a coarse-scale non-equilibrium model. A number of test cases for real oil and gas-condensate mixtures are given. Model implementation specifics in a flow simulator are discussed and illustrated with test simulations. A non-equilibrium constant volume depletion algorithm is presented to simulate condensate recovery at low pressures in gas-condensate reservoirs. Results of satisfactory model matching to field data are reported and discussed.

Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its recent prominence in Bio-medical Engineering for biopolymer materials has recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: A) Computer-aided design (CAD/CAM), B) Finite Element Analysis, and C) Molecular Dynamic Simulations. This review centers on Molecular Dynamics (MD) simulations in biopolymers, analyzing structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, generating spatial trajectories for each atom, providing insights into properties like water absorption on biopolymer surfaces and interactions with solid surfaces, crucial for biomaterial assessment. This review offers readers a comprehensive overview of the diverse applications of Molecular Dynamics (MD) simulations on biopolymers. Furthermore, it emphasizes the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.

X-rays production through betatron radiation emission from electron bunches is a valuable resource for several research fields. The EuAPS (EuPRAXIA Advanced Photon Sources) project, within the framework of the EuPRAXIA project, aims to provide 1-10 keV photons (soft X-rays) developing a compact plasma-based system designed to exploit self-injection processes that occur in highly nonlinear laser-plasma interaction (LWFA) to drive electron betatron oscillations. Since the emitted radiation spectrum, intensity, angular divergence, and possible coherence strongly depend on the properties of the self-injected beam, accurate preliminary simulations of the process are necessary to evaluate the optimal diagnostic device specifications. Dedicated tools for these tasks are under development: electron trajectories from particle-in-cell (PIC) simulations are currently undergoing numerical analysis through the calculation of retarded fields and spectra for various plasma and laser parameter combinations. At the same time, an analytical approach is being examined to obtain an expression for the emitted spectrum, assuming linear or quadratic electron energy variation. Code structure and some trajectories analysis results are presented.

Modeling the flow of polymer solutions requires knowledge at various length and time scales. The macroscopic behavior is described by the overall velocity, pressure and stress. The polymeric contribution to the stress requires knowledge of the evolution of polymer chains. In this work, we use a microscopic model, the finitely extensible nonlinear elastic (FENE) model, to capture the polymer behavior. The benefit of microscopic models is they remain faithful to the polymer dynamics without information loss via averaging. The downside is the computational cost needed to solve the thousands to millions of differential equations describing the microstructure. We thus describe a multiscale flow solver that utilizes GPUs for massively parallel, efficient simulations. We compare and contrast the microscopic model with its macroscopic counterpart under various flow conditions. In particular, significant differences are observed under nonlinear flow conditions, where the polymers become highly stretched and oriented.

Tsunami modeling and simulation has changed in the past few years more than it had in decades, especially so with respect to coastal inundation. Among other things, this change is supported by the approaching era of exa-scale computing, whether via GPU or more likely forms of hybrid computing whose presence is growing across the geosciences. For reasons identified across this review, exa-scale computing efforts will impact the on-shore, highly turbulent r\'egime to higher degree than the 2D shallow water equations used to model tsunami propagation in the open ocean. This short review describes the different approaches to tsunami modeling from generation to impact and underlines the limits of each model based on the flow r\'egime. Moreover, from the perspective of a future comprehensive multi-scale modeling infrastructure to simulate a full tsunami, we underline the current challenges associated with this approach and review the few efforts that are currently underway to achieve this goal. A table of existing tsunami software packages is provided along with an open Github repository to allow developers and model users to update the table with additional models as they are published and help with model discoverability.

In this study, a new structure is proposed based on the body-centered cubic (BCC) lattice structure: adding a cubic truss in the center of the BCC structure, which is denoted by TLC (Truss-lattice-cube). The different dimensions of the central cube can affect the mechanical properties of the lattice structure notably. With a fixed length (15mm) of a unit cell, the optimal size for the central cube is determined to be 5 mm. Quasi-static compressive tests are performed on specimens made of Polylactic Acid (PLA) using additive manufacturing technology. The deformation characteristics of the new structure is analyzed in detail by experiments and numerical simulations. Compared to the BCC structure, the mechanical properties of the TLC structure are significantly improved. The initial flow stress of the TLC has been increased by 122% at a strain of 0.1; the specific strength has been enhanced by 293% at a strain of 0.5; and the specific energy absorption has been improved by 312% at the strain of 0.6. Printing defects in the lattice structure could deteriorate the mechanical property remarkably. In this work, incorporation of microcracks into the finite element model makes the simulation capture the influence of printing defects and improve the predictive accuracy of simulation significantly.

Turbulent dissipation is a central issue in the star and galaxy formation process. Its fundamental property of space-time intermittency, well characterised in incompressible laboratory experiments, remains elusive in cosmic turbulence. Progress requires the combination of state-of-the-art modelling, numerical simulations and observations. The power of such a combination is illustrated here where the statistical method intended to locate extrema of velocity shears in a turbulent field is applied to numerical simulations of compressible magneto-hydrodynamical (MHD) turbulence dedicated to dissipation scales and to a nearby turbulent diffuse molecular cloud. We demonstrate that short-spacing increments of observables can detect strongly dissipative structures. In our simulations, we compute structure functions of various synthetic observables and show that they verify Extended Self-Similarity. This allows to compute their intermittency exponents and we show how they could help constraining some properties of the underlying three-dimensional turbulence. In observations of a turbulent cloud close to the Sun in our Galaxy, a remarkable coherent structure of velocity shear extremum is disclosed . At the location of the largest velocity shear, this coherent structure is found to foster 10 × more carbon monoxide molecules than standard diffuse molecular gas, an enrichment supported by models of non-equilibrium warm chemistry triggered by turbulent dissipation. The power of the combination between modelling and observations is also illustrated by observations of the CH+ cation that provide unique quantitative informations on the kinetic energy trail in the massive, multi-phase and turbulent circum-galactic medium of a galaxy group at redshift z = 2.8.

Shale gas and coalbed methane are energy sources that partly or even mainly consist of methane stored in an adsorbed state in the pores of the organic-rich rock and coal seams. In this study, the graphene nanoslit model is employed to model the nanometer slit pores in shale and coal. The Grand Canonical Monte Carlo (GCMC) and Molecular Dynamics (MD) modelling methods are used to investigate the mechanisms of adsorption and displacement of methane in the slit pore. It was found that the CVFF forcefield resulted in the largest adsorption amount, while the PCFF forcefield resulted in the least. The COMPASS and COMPASS II force fields led to similar results. As the width of the slit pore increases, the adsorption amount of gas molecules increases, and the number density profile of adsorbed methane molecules alters from a single adsorption layer to multi-adsorption layers. The minimum slit pore width at which methane molecules can penetrate the slit pore was found to be 0.7 nm. Moreover, it is demonstrated that by lowering the temperature, the adsorption rate of the methane increases since the adsorption is an exothermic process. Enhancing methane recovery was investigated by the injection of gases such as CO2 and N2 to displace the adsorbed methane. The comparison of adsorption isotherms of gas molecules provided the following order in terms of the amount of adsorption: CO2>CH4>N2.

This study explores wind energy resources in different locations through the Gulf of Oman and also their future variability due climate change impacts. In this regard, EC-EARTH near-surface wind outputs obtained from CORDEX-MENA simulations are used for historical and future projection of the energy. The ERA5 wind data are employed to assess the suitability of the climate model. Moreover, the ERA5 wave data over the study area are applied to compute sea surface roughness as an important variable for converting near-surface wind speeds to those of wind speed at turbine hub height. Considering the power distribution, bathymetry and distance from the coats, some spots as tentative energy hotspots to provide a detailed assessment of directional and temporal variability and also to investigate climate change impact studies. RCP8.5 is a common climatic scenario is used to project and extract future variation of the energy in the selected sites. The results of this study demonstrate that the selected locations have a suitable potential for wind power turbine plans and constructions.

This study has developed a Matlab application for simulating statistical models project (SMp) probabilistic distributions that are similar to binomial and Poisson, which were created by mathematical procedures. The simulated distributions are graphically compared with these popular distributions. The application allows to obtain many probabilistic distributions, and shows the trend (τ ) for n trials with success probability p, i.e. the maximum probability as τ=np. While the Poisson distribution PD(x;µ) is a unique probabilistic distribution, where PD=0 in x=+∞, the application simulates many SMp(x;µ,Xmax) distributions, where µ is the Poisson parameter and value of x with generally the maximum probability, and Xmax is the upper limit of x with SMp(x;µ,Xmax) ≥ 0 and limit of the stochastic region of a random discrete variable. It is shown that by simulation via, one can get many and better probabilistic distributions than by mathematical one.

This study has developed a Matlab application for simulating statistical models project (SMp) probabilistic distributions that are similar to binomial and Poisson, which were created by mathematical procedures. The simulated distributions are graphically compared with these legendary distributions. The application allows to obtain many probabilistic distributions, and shows the trend (τ ) for n trials with success probability p, i.e. the maximum probability as τ=np. While the Poisson distribution PD(x;µ) is a unique probabilistic distribution, where PD=0 in x=+∞, the application simulates many SMp(x;µ,Xmax) distributions, where µ is the Poisson parameter and value of x with generally the maximum probability, and Xmax is upper limit of x with SMp(x;µ,Xmax) ≥ 0 and limit of the stochastic region of the random discrete variable X. It is shown that by simulation via, one can get many and better probabilistic distributions than by mathematical one.

Transient analysis of gas flow in pipeline was studied. Finite Element Method based on ANSYS FLOTRAN was used to account for changes in pressure, temperature and flow rate. Compressibility factor function of temperature and pressure was considered. For non-isothermal transient results, the pressure and the flowrate gave wave propagation as a result of slow transients created by demand condition at the outlet end of custody transfer. Results obtained were in agreement with the demand restrictions at the outlet end of custody transfer indicating that the predictions are accurate and reliable. The results demonstrated that the Finite Element Method gave accurate prediction of pressure, temperature and flowrate in transient gas studies. For steady state non-isothermal model, results showed that the magnitude of the average pressure drop was higher when pressure was predicted with constant compressibility factor, but the same average pressure drop was reduced when the pressure was predicted with variable compressibility factor, z. Since compressibility factor is a function of temperature and pressure, the above findings signifies that in the case when gas temperature does not stabilize, the prediction of pressure with isothermal model and constant compressibility factor will lead to significant errors.

It is always a difficult task to assign the peaks recorded from vibrational spectrum. Herein we explored a new pathway of density functional theory (DFT) simulation to present three kinds of spectra of ice XIV and can be referenced as inelastic neutron scattering (INS), IR, and Raman experimental spectrum. The INS spectrum is proportional to phonon density of states (PDOS) while the photon scattering signals reflect the normal vibration frequencies near the Brillouin zone (BZ) center. Based on good agreements with experimental data, we identified the relative frequency and made scientific assignments by normal vibration modes analysis. The debating two hydrogen bond (H-bond) peaks among ice phases from INS have been discussed and the dynamic process of H-bond vibrations were found to be classified into two basic modes. we deduce that two H-bond modes are a general rule among ice family and more works are ongoing to investigate this subject.

Biomass gasification acquired great interest over the past decades as an effective and trustable technology to produce energy and fuels with net-zero carbon emissions. Moreover, using biomass waste as feedstock enables to recycle organic wastes and to fit the circular economy goals thus reducing the environmental impacts of waste management. Even if many studies have been already carried on, this kind of process must still be investigated and optimized with the final aim to develop industrial plants for different applications, from the hydrogen production to net-negative emission strategies. Modeling and developing of process simulations became an important tool to investigate the chemical and physical behavior of the plant, allowing to make a first raw optimization of the process and to define heat and material balances of the plant as well as to define optimal geometrical parameters with cost and time effective approaches. The present review paper focuses on the main literature models developed until now to describe biomass gasification process, and in particular on kinetic models, thermodynamic models, and computational fluid dynamic models. The aim of this study is to point out the strengths and the weakness of those models, comparing them and indicating in which situation is better to use an approach instead of another. Moreover, theoretical shortcut models and software simulations, not explicitly addressed by prior reviews, are taken into account. For researchers and designers this review provides a detailed methodology characterization as a guide to develop innovative study or project.

Background and motivation: Combining Deep Reinforcement Learning (Deep RL) and Health Systems Simulations has significant potential, for both research into improving Deep RL performance and safety, and in operational practice. While individual toolkits exist for Deep RL and Health Systems Simulations, no framework to integrate the two has been established. Aim: Provide a framework for integrating Deep RL Networks with Health System Simulations, and to ensure this framework is compatible with Deep RL agents that have been developed and tested using OpenAI Gym. Methods: We developed our framework based on the OpenAI Gym framework, and demonstrate its use on a simple hospital bed capacity model. We built the Deep RL agents using PyTorch, and the Hospital Simulation using SimPy. Results: We demonstrate example models using a Double Deep Q Network or a Duelling Double Deep Q Network as the Deep RL agent. Conclusion: SimPy may be used to create Health System Simulations that are compatible with agents developed and tested on OpenAI Gym environments. GitHub repository of code: https://github.com/MichaelAllen1966/learninghospital

Blazars are highly variable and display complex characteristics. A key characteristic is the flux distribution or flux PDF whose shape depends upon the form of the underlying physical process driving variability. The BL Lacertae, Mrk 421 is one of the brightest and most variable blazars across the electromagnetic spectrum. It has been reported to show hints of lognormality across the spectrum from observed histograms of radio to gamma-ray fluxes. This would imply that the underlying mechanisms may not conform to the "standard" additive, multi-zone picture, but could potentially have multiplicative processes. This is investigated by testing the observed lightcurves at different wavelengths with time-series simulations. We find that the simulations reveal a more complex scenario, than a single lognormal distribution explaining the multiwavelength lightcurves of Mrk 421.

G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. There is evidence that some ligands that bind to the GPCRs activate different downstream signaling pathways. G protein activation or -arrestin biased signaling involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. Molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions between receptors and ligands. Here, we highlight recent simulation studies and methods used to study biased G protein-coupled receptor signaling and their conformational dynamics. We also highlight applications of MD simulations to drug discovery.

Computational simulations of three-dimensional flow around a NACA 0018 wing with an aspect ratio of AR=5 are carried out using the Unsteady Reynolds-Averaged Navier-Stokes (URANS) equations with the Shear-Stress Transport turbulence model closure. Simulations were performed to capture the aerodynamic stall hysteresis using a developed Pseudo-Transient Continuation (PTC) method based on a dual time step approach in the CFD code OpenFOAM. The flow was characterized by an incompressible Mach number of M=0.12 and a moderate Reynolds number Re=0.67×10^6. The results obtained indicate the presence of a noticeable aerodynamic hysteresis in the static dependencies of the force and moment coefficients, as well as the manifestation of bi-stable flow separation patterns, accompanied by the development of asymmetry in the stall zone. The URANS simulation results are in good agreement with the experimental data obtained for the NACA 0018 finite aspect ratio wing from the low-speed wind tunnel under the same test conditions. A new phenomenological bifurcation model of aerodynamic stall hysteresis under static and dynamic conditions is formulated, which is proven to be able to closely match the experimental data.

Fires are complex multi-physics problems that span wide spatial scale ranges. Capturing this complexity in computationally affordable numerical simulations for process studies and “outer-loop” techniques (e.g., optimization and uncertainty quantification) is a fundamental challenge in reacting flow research. Further complications arise for propagating fires where a priori knowledge of the fire spread rate and direction is typically not available. In such cases, static mesh refinement at all possible fire locations is a computationally inefficient approach to bridging the wide range of spatial scales relevant to fire behavior. In the present study, we address this challenge by incorporating adaptive mesh refinement (AMR) in fireFoam, an OpenFOAM solver for simulations of complex fire phenomena involving pyrolyzing solid surfaces. The AMR functionality in the extended solver, called fireDyMFoam, is load balanced, models gas, solid, and liquid phases, and allows us to dynamically track regions of interest, thus avoiding inefficient over-resolution of areas far from a propagating flame. We demonstrate the AMR capability and computational efficiency for fire spread on vertical panels, showing that the AMR solver reproduces results obtained using much larger statically refined meshes, but at a substantially reduced computational cost. We then leverage the computational efficiency of the AMR solver to demonstrate an optimization framework for fire suppression based on the open-source Dakota toolkit.

Drilling operation is the major cost factor for the industry. Appropriately designed operations are essential for successful drilling. Optimized drilling operations also allow enhanced drilling performance and reduce the drilling cost. This is achieved by increasing the bit life (minimizing premature bit wear), drilling faster that allows reducing drilling time, and also reducing tripping operations. The paper presents two parts. The first part compares the parametric physic-based swab and surge simulation results obtained from Bingham Plastic, Power Law, and Robertson and Stiff models. The aim is to show how the model predictions deviate from each other. Two 80-20 Oil Water ratios (OWR) and two 90-10 OWR oil-based drilling fluids with 1.96 sg and 2.0 sg were considered in vertical- and deviated wells. Simulation results analysis revealed that the deviations depend on the drilling fluid’s physical and rheological parameters as well as the well trajectory. Moreover, the model’s predictions were inconsistent. Data-driven machine learning (ML) modeling makes up the second section. Data-driven modeling was done using both software-generated datasets and field datasets. Results show that the Random Forest Regressor (RF), Artificial Neural Network (ANN), Long Short-Term Memory (LSTM), LightGBM, XGboost, and Multivariate regression models predict the training and test datasets with higher R-squared and minimum root means square values. Deploying the ML model in real-time applications and the planning phase would have the potential application of artificial intelligence for well planning and optimization processes.

Large office buildings are responsible for a substantial portion of energy consumption in urban districts. However, thorough assessments regarding the Nordic countries are still lacking. In this paper we analyse the largest dataset to date for a Nordic office building, by considering a case study located in Stockholm, Sweden, that is occupied by nearly a thousand employees.Distinguishing the lighting and occupants’ appliances energy use from heating and cooling, we can estimate the impact of occupancy without any schedule data. A standard frequentist analysis is compared with Bayesian inference, and the according regression formulas are listed in tables that are easy to implement into building performance simulations (BPS). Monthly as well as seasonal correlations are addressed, showing the critical importance of occupancy.A simple method, grounded on the power drain measurements aimed at generating boundary conditions for the BPS, is also introduced; it shows how, for this type of data and number of occupants, no more complexities are needed in order to obtain reliable predictions. For an average year, we overestimate the measured cumulative consumption by only 4.7%. The model can be easily generalised to a variety of datasets.

A pivotal strategy in decarbonizing the transport sector is by transitioning from internal combustion engine vehicles (ICEVs) to electric vehicles (EVs), especially if they are charged with renewable energy. To provide an incentive to the common populace to switch to EVs, cities should set up - or enable or even encourage the private sector to do so - electric vehicle charging stations (EVCS) at multiple and suitably accessible locations. This paper aims to present a digitaltwin-enabled methodology study for selecting the most suitable possible locations to establish EVCS with consideration of the low voltage (LV) network operation in terms of power losses, active and reactive power in EV charging demand and the effect of the EVCS on the transformers, based on examples in Newcastle upon Tyne (England, UK). It also evaluates the most suitable type of charger that could be installed at these locations by studying the estimated traffic, cost and impact of the EVCS on the power grid, both at peak and off hours. This paper demonstrates how digitaltwin technologies, such as the web-based tool AutoDesign by Northern Powergrid and EA Technology and open source Pandapower can be used for identifying the most viable and cost-effective locations to connect EVCSs to a Distribution Network Operators (DNO)’s LV network. The results of the analysis indicate that with the installation of the most suitable type of EVCS in a particular location, the local power grid would not be significantly affected at any hour of the day.

3D bioprinting, like 3D printing, is a process that builds structures by depositing material layer by layer. In the specific case of bioprinting, these layers are composed of a biocompatible material together with living cells, allowing the creation of three-dimensional structures that recreate functional tissues and organs. Bioprinting cell-laden structures is complicated by the high rate of cell damage and stress that occurs during the process, caused by the high pressures and stresses to which they are subjected. To minimise damage during the process, it is important to study and optimise certain bioprinting conditions beforehand and to analyse how they affect the cells by means of computational simulations. In this review, both quantitative and qualitative data are collected to improve the nozzle geometry through computational simulation studies. Optimal ranges for nozzle diameter (0.2-1mm) and length (8-10mm; 300-900μm) have been defined, and recommendations for improving nozzle performance during bioprinting, such as the provision of an inner angle of 20-30°, an inner EDTA coating and a shear stress of less than 10kPa, have been gathered. Finally, based on the data collected, a design of experiments is proposed to obtain an optimal bioprinting configuration for a particular bioink.

This study investigates the magnetization of Cobalt (Co) nanoparticles with two different crystal structures: a centered cubic (fcc) and an hexagonal close packed (hcp), under the magnetic field of the Earth. For that reason, the hysteresis loops of the two material samples are exported and compared with the corresponding value by experimental procedure in the laboratory under the Earth’s magnetization. For both samples, the nanoparticle number variation and the nearest neighbor distance effect, in the Co hysteresis loop are investigated, structural information that is useful for the sample preparation. For the simulations the Finite Element Method (FEM) was used, while experiments are conducted using a measurement set-up based on fluxgate magnetometers. From the simulation, it is proven that, for both samples, the nanoparticle number effect does not change the hysteresis loop. In contrast, when the distance between the nanoparticles increases, the magnetization obtains smaller value. This study aims to build a novel, simple and economical measurement arrangement enabling in situ magnetic measurements for ferromagnetic nano-material characterization. As the need for continuous knowledge of the condition and the phase of ferromagnetic nanoparticles that is crucial in many applications, like catalytic processes, this work aims to introduce an alternative approach that will add another dimension to conventional chemical reaction engineering this of the magnetic state of the material resolved in time and space and to contribute in the field of the monitoring and the early fault diagnosis of nanoparticle materials.

Air pollution is responsible for any adverse effects on human beings. Thermal discomfort, on the other hand, is able to overload the human body and eventually provoke health implications due to the heat imbalance. Methods: The aim of the present work is to study the behavior of two bio-climatic indexes and statistical characteristics of the air quality index for Sofia city - the capital of Bulgaria for the period 2008 - 2014. The study is based on WRF-CMAQ model system simula-tions with a spatial resolution of 1 kilometer. The air quality is estimated by the air quality index, taking into account the influence of different pollutants and the thermal conditions by two indi-ces, respectively, for hot and cold weather. Results: It was found that half of the heat and cold index categories are present in the simulations. Their distribution has some spatial features. All air quality categories are present in the domain, with dominance only of the O3 and PM10. Conclu-sions: It was found that Sofia is not so hot and air polluted place, but in some situations, people have to have some concerns when intend to be outdoors for a prolonged time.

The availability of high quality surface observations of precipitation and volume observations by polarimetric operational radars make it possible to constrain, evaluate and validate numerical models with a wide variety of microphysical schemes. In this article, a novel particle-based Monte-Carlo microphysical model (called “McSnow”) is used to simulate the outer rain bands of Hurricane Dorian which traversed the densely instrumented precipitation research facility operated by NASA at Wallops Island, Virginia. The rain bands showed steady stratiform vertical profiles with radar signature of dendritic growth layers near −15 °C and peak reflectivity in the bright band of 55 dBZ along with polarimetric signatures of wet snow with sizes inferred to exceed 15 mm. A 2D-video disdrometer measured frequent occurrences of large drops >5 mm and combined with an optical array probe the drop size distribution was well-documented in spite of uncertainty for drops <0.5 mm due to high wind gusts and turbulence. The 1D McSnow control run and four numerical “experiments” were conducted and compared with observations. One of the main findings is that even at the moderate rain rate of 10 mm/h collisional breakup is essential for the shape of the drop size distribution.

In this manuscript, an automated framework dedicated to design space exploration and design optimization studies is presented. The framework integrates a set of numerical simulation, computer-aided design, numerical optimization, and data analytics tools using scripting capabilities. The tools used are open-source and freeware, and can be deployed on any platform. The main feature of the proposed methodology is the use of a cloud-based parametrical computer-aided design application, which allows the user to change any parametric variable defined in the solid model. We demonstrate the capabilities and flexibility of the framework using computational fluid dynamics applications; however, the same workflow can be used with any numerical simulation tool (e.g., a structural solver or a spread-sheet) that is able to interact via a command line interface or using scripting languages. We conduct design space exploration and design optimization studies using quantitative and qualitative metrics, and to reduce the high computing times and computational resources intrinsic to these kinds of studies, concurrent simulations and surrogate-based optimization are used.

The present studies deliver the computational investigations of a 10 MW turbine with a diameter of 205.8 m developed within the framework of the AVATAR (Advanced Aerodynamic Tools for Large Rotors) project. The simulations were carried out using two methods with different fidelity levels, namely the computational fluid dynamics (CFD) and blade element and momentum (BEM) approaches. For this purpose, a new BEM code namely B-GO was developed employing several correction terms and three different polar and spatial interpolation options. Several flow conditions were considered in the simulations, ranging from the design condition to the off-design condition where massive flow separation takes place, challenging the validity of the BEM approach. An excellent agreement is obtained between the BEM computations and the 3D CFD results for all blade regions, even when massive flow separation occurs on the blade inboard area. The results demonstrate that the selection of the polar data can influence the accuracy of the BEM results significantly, where the 3D polar datasets extracted from the CFD simulations are considered the best. The BEM prediction depends on the interpolation order and the blade segment discretization.

The total enthalpies of the 16 different spin configurations that can be realized in the unit cell of the archetype spin crossover complex [Fe(phen)₂(NCS)₂] (phen=1,2-phenanthroline) were calculated applying periodic density functional theory combined with the Hubbard model and the Grimme-D2 dispersion correction (DFT+U/D2). The obtained enthalpy differences between the individual spin configurations were used to determine spin couplings of an Ising-like model and subsequent Monte Carlo simulations for this model allowed to estimate the phenomenological interaction parameter Г of the Slichter-Drickamer model, which is commonly used to describe the cooperativity of the spin transition. The calculational procedure described here, which led to an estimate of about 3 kJ/mol⁻¹ for Г, in good agreement with experiment, may be used to predict from first principles how modifications of spin crossover complexes can change the character of the spin transition from gradual to abrupt and vice versa.

Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this mini-review, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions and, on other hand, highly simplified structure-based Elastic Network Models of protein flexibility. In contrast to classical Molecular Dynamics the modeling strategies discussed here allow quite accurate modeling of much larger systems and longer time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.

Point defects induced by doping rare earth elements RE (Nd, Er) into the magnesium oxide host were investigated by classical atomistic simulations utilising the General Utility Lattice Program (GULP). Formation and association energies were calculated for the potential defect structures. Both isolated defects and defect complexes were considered. The most energetically favourable structures of defect complexes were found for rare earth doped and Li co-doped systems. The correlation between the association energy and the structure of the defect complex was investigated. The influences of Li were revealed with respect to energy and structure. The simulation results contribute to the understanding of the point defects of doped MgO and how Li influences the doping of rare earth elements in the MgO host.

In a previous companion study, satellite data were used to describe peculiar characteristics of ocean surface wave fields, generated by two extra-tropical cyclones (ETCs) rapidly propagating in the North Atlantic. Based on a 2D parametric wave model, further details are now provided to analyse and interpret the spatio-temporal evolution of ETC very intense generated waves. Significant wave height and wavelength values are shown to reach extreme values, 18 m and 500 m, respectively. Resulting energetic swell systems waves then radiate in the whole eastern part of North Atlantic, and more particularly in the Norwegian sea region. Moving to higher latitudes, wind forcing characteristics of ETCs evolve, with the shape of the wind field changing from quasi-cyclonic to "air jets/Icelandic lows". In this paper, the resulting swell generation and propagation, after the deformation of an individual ETC, are studied, as well. Confirmed with comparisons with multi-satellite observations, the application of the parametric-2D wave-ray model is demonstrated to provide robust and highly detailed information on wave generation under very complex wind regime changes.

Formation in soccer is among the most important tactical choices for a successful match.Herein, the simulations of 420000 match-plays have been performed varying the formation, the number of opponents that are actively pressing the team, the speed of the opponents in attempting a pass interception. Dribbling has been neglected. The match-play ends either with a successful series of passes from a central back to the line of the strikers or with the opponents that steal the ball. In this work, I demonstrate that 3-4-3 formation, which is among the most employed formations, relates to the highest probability of success.

In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial physics, droplet evaporation, super hydrophobic surfaces, and wettability etc.

A common reactor type in the chemical and process industry is the fixed-bed reactor. Accurate modeling can be achieved with particle-resolved Computational Fluid Dynamic (CFD) simulations. However, the underlying bed morphology plays a paramount role. Synthetic bed-generation methods are much more flexible and faster than image-based approaches. In this study, we look critically at the two different bed generation methods: Discrete Element Method (DEM) (in the commercial software STAR-CCM+) and the rigid-body model (in the open-source software Blender). The two approaches are compared in terms of synthetically generated beds with experimental data of overall and radial porosity, particle orientation, as well as radial velocities. Both models show accurate agreement for the porosity. However, only Blender shows similar particle orientation than the experimental results. The main drawback of the DEM is the long calculation time and the shape approximation with composite particles.

Computational Fluid Dynamics (CFD) simulations, based on Reynolds Averaged Navier Stokes (RANS) models, are a useful tool for a wide range of coastal and offshore applications, providing a high fidelity representation of the underlying hydrodynamic processes. Generating input waves in the CFD simulation is performed by a numerical wavemaker (NWM), with a variety of different NWM methods existing for this task. While NWMs, based on impulse source methods, have been widely applied for wave generation in depth averaged, shallow water models, they have not seen the same level of adoption in the more general RANS based CFD simulations, due to difficulties in relating the required impulse source function to the resulting free surface elevation for non-shallow water cases. This paper presents an implementation of an impulse source wavemaker, which is able to self-calibrate the impulse source function to produce a desired wave series in deep or shallow water at a specific point in time and space. Example applications are presented, for a numerical wave tank (NWT), based on the opensource CFD software OpenFOAM, for wave packets in deep and shallow water, highlighting the correct calibration of phase and amplitude. Also, the suitability for cases requiring very low reflection from NWT boundaries is demonstrated. Possible issues in the use of the method are discussed and guidance for good application is given.

β-dicalcium silicate (β-Ca₂SiO₄, or β-C₂S in cement chemistry notation) is one of the most important minerals in cement. An improvement of its hydration rate would be the key point for developing environmentally friendly cements with lower energy consumption and CO₂ emissions. However, there is a lack of fundamental understanding on the water/β-C₂S surface interactions. In this work we aim to evaluate the water adsorption on three β-C₂S surfaces at the atomic scale using density functional theory (DFT) calculations. Our results indicate that thermodynamically favorable water adsorption takes place in several surface sites, with a broad range of adsorption energies (−0.78 to −1.48 eV), depending on the particular mineral surface and adsorption site. To clarify the key factor governing the adsorption, the electronic properties of water at the surface were analyzed. The partial density of states (DOS), charge analysis, and electron density difference analyses suggest a dual interaction of water with β-C₂S (100) surface: a nucleophilic interaction of the water oxygen lone pair with surface calcium atoms, and an electrophilic interaction (hydrogen bond) of one water hydrogen with surface oxygen atoms. Despite the elucidation of the adsorption mechanism, no correlation was found between the electronic structure and the adsorption energies.

In this study, we introduce the dynamics of a Hepatitis B virus (HBV) model with the class of asymptomatic carriers and conduct a comprehensive analysis to explore its theoretical aspects and examine the crossover effect within the HBV model. To investigate the crossover behavior of the operators, we divide the study interval into two subintervals. In the first interval, the classical derivative is employed to study the qualitative properties of the proposed system, while in the second interval, we utilize the ABC fractional differential operator. Consequently, the study is initiated using the piecewise Atangana-Baleanu derivative framework for the systems. The HBV model is then analyzed to determine the existence, Hyers-Ulam (HU) stability, and disease-free equilibrium point of the model. Moreover, we showcase the application of an Adams-type predictor-corrector (PC) technique for Atangana-Baleanu derivatives and an extended Adams-Bashforth-Moulton (ABM) method for Caputo derivatives through numerical results. Subsequently, we employ computational methods to numerically solve the models and visually present the obtained outcomes using different fractional-order values. This network is designed to provide more precise information for disease modeling, considering that communities often interact with one another, and the rate of disease spread is influenced by this factor.

The successive steps of the oxidation mechanism of crocin, major compound of saffron, by the free OH• radical are investigated by the pulse radiolysis, steady-state (gamma) radiolysis methods and molecular simulations. The optical absorption properties of the transient species and their reaction rate constants are determined. The absorption spectrum of the oxidized radical of crocin resulting from the H-abstraction presents a maximum at 678 nm and a band at 441 nm, almost as intense as that of crocin. The spectrum of the covalent dimer of this radical contains an intense band at 441 nm and a weaker one at 330 nm. The final oxidized crocin, issued from radical disproportionation, absorbs weaker with a maximum at 330 nm. The molecular simulation results suggest that the OH• radical is electrostatically attracted by the terminal sugar and is scavenged predominantly by the neighbor methyl site of the polyene chain as in a sugar-driven mechanism. Based on detailed experimental and theoretical investigations, the antioxidant properties of crocin are highlighted.

Molecular Dynamics (MD) simulations model motion of molecules in atomistic detail and aid in drug design. While simulations on large systems may require several days to complete, analysis of terabytes of data generated in the process could also be time consuming. Recent studies captured exciting and dramatic drug-receptor interactions under cell-like complex conditions. Such advances make simulations of biomolecular interactions more realistic, insightful, and informative and have potential to make drug design more realistic. However, currently available resources and techniques do not provide, in reasonable time, a comprehensive understanding of events seen in simulations. We demonstrate that big data approach results in significant speedups, and provides rapid insights into simulations performed. Advancing this improvement, we propose a scalable, self-tuning, and responsive framework based on Cloud-infrastructure to accomplish the best possible MD studies with given priorities and within available resources.

The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling disordered protein interactions and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein-peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein-peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution and studies of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.

Despite being small and simple structured in comparison to their victims, virus particles have the potential to harm severly and even kill highly developed species such as humans. To face upcoming virus pandemics, detailed quantitative biophysical understanding of intracellular virus replication mechanisms is inevitable. Unveiling the relationship of form and function might allow to determine putative attack points relevant for the systematic development of direct antiviral agents (DAA) and potent vaccines. Biophysical investigations of spatio-temporal dynamics of intracellular virus replication so far are rare. We are developing a framework to allow for fully spatio-temporal resolved virus replication dynamics simulations based on partial differential equations models (PDE) and evaluated with advanced numerical mathematical methods on leading supercomputers. This study presents an advanced highly nonlinear model of the genome replication cycle of a specific RNA virus, the Hepatitis C virus (HCV). The diffusion-reaction model mimics the interplay of the major components of the viral RNA (vRNA) cycle, namely non structural viral proteins (NSP), vRNA and a generic host factor. Technically, we couple surface PDEs (sufPDEs) on the 3D embedded 2D Endoplasmatic Reticulum (ER) manifold with PDEs in the 3D membranous web (MW) and cytosol volume. (The MWs are the replication factories growing on the ER induced by NSPs.) The sufPDE/PDE model is evaluated at realistic reconstructed cell geometries which are based on experimental data. The simulations couple the effects of NSPs which are restricted to the ER surface with effects appearing in the volume. The volume effects include the host factor supply from the cytosol and the MW dynamics. Special emphasis is put to the exchange of components between ER surface, MWs and cytosol volume. As the vRNA spatial properties are not fully understood so far in experiment, the model allows for vRNA both restricted to the ER and moving in the cytosol. The visualization of the simulation resembles a look into some sort of fully 3D resolved “in silico microscopes” to mirror and complement in vitro / in vivo experiments for the intracellular vRNA cycle dynamics. The output data are quantitatively consistent with experimental data and provoke advanced experimental studies to validate the model.

Water conflicts have been a significant issue in Brazil, especially in the Sao Francisco River basin. Subseasonal forecasts, up to a 60-day forecast range, can provide information to support decision-makers in managing water resources in the river basin, especially before drought events. Predictability in the subseasonal forecasts range is a research topic as this range contains mixed dependence on weather and seasonal phenomena. Numerical models may inherit this mixed dependence on their skills. The objective of this paper is to evaluate the Eta Model simulations to reproduce the drought events between the years 2011 and 2016. Two sets of 60-day simulations were produced; one started in September (SO) and the other in January (JF) each year. These months were chosen to evaluate the model skill to reproduce the onset and the middle of the rainy seasons in Central Brazil, where the Upper Sao Francisco River is located. The SO simulations reproduced the observed spatial distribution of precipitation but underestimated the amounts. Precipitation errors exhibit large variability across the subbasins. The JF simulations also reproduced the observed precipitation distribution but overestimated it in the Upper and Lower subbasins. The JF simulations better captured the interannual variability of precipitation. The 60-day simulations were discretized in six 10-day accumulations to assess the intra-monthly variability. They showed that simulations can capture the onset of the rainy season and the small amounts of the rainy months that occurred in these severe drought years.

In this study, we investigate the structural changes, electronic properties, and charge redistribution within azo-bithiophene (Azo-BT) chemisorbed monolayers under different light stimuli using density functional theory and molecular dynamics simulations. We consider two types of switches, Azo-BT and BT-Azo, with different arrangements of the Azo and BT blocks counting from the anchor thiol group. The chemisorbed monolayers of pure cis- and trans-isomers with a surface concentration of approximately 2.7 molecules per nm2 are modeled on a gold surface using classical all-atom molecular dynamics. Our results reveal significant shrinkage of the BT-Azo layer under UV illumination, whereas the thicknesses of the Azo-BT layer remain comparable for both isomers. This difference in behavior is attributed to the ordering of the trans-molecules in the layers, which is more pronounced for Azo-BT, leading to a narrow distribution of the inclination angle to the gold surface. Conversely, both layers consisting of cis-switches exhibit disorder, resulting in similar brush heights. To study charge transfer within the immobilized layers, we analyze each snapshot of the layer and calculate mean charge transfer integrals using Nelsen’s algorithm for a number of interacting neighboring molecules. Combining these integrals with reorganization energies defined for the isolated molecules, we evaluate the charge transfer rates and mobilities for electron and hole hopping within the layers at room temperature based on Marcus’ theory. This research offers new perspectives for the innovative design of electrode surface modifications and provides insights into controlling charge transfer within immobilized layers using light triggers. Additionally, we identify molecular properties that are enhanced through specific molecular design, which contributes to the development of more efficient molecular switches for various electronic applications.

Landform Evolution Modelling (LEM) provides an avenue for simulating how a landscape may evolve over extended time periods of thousands of years. The CAESAR-Lisflood LEM that includes a hydrologic model (TOPMODEL) and a hydraulic model (Lisflood) can be used to assess the proposed final landform morphology of a mine site by simulating how the mine landform and the landscape would evolve over a 1,000-year period. The accuracy of future simulations depends on the calibration and validation of the model to the past and present events. Calibration and validation of the model involves finding a combination of parameters of the model which when applied and simulated gives model outputs similar to those observed for the real site scenario for corresponding input data. Calibrating the sediment output of the CAESAR-Lisflood model at the catchment level and using it for studying the equilibrium conditions of the landform is an area yet to be explored. Therefore, the aim of this study was to calibrate the CAESAR-Lisflood model and then validate it. To achieve this, the model was run for a rainfall event with a set of parameters, plus discharge and sediment data for the input point of the catchment, to analyze how similar the model output would behave when compared with the discharge and sediment data for the output point of the catchment. The model parameters were then adjusted until the model closely approximate the real site values of the catchment. It was then validated by running the model for a different set of events and checking that the model gave similar results to the real site values. The outcomes demonstrated that while the model can be calibrated to a greater extent for hydrology (discharge output) throughout the year, the sediment output calibration may be slightly improved by having the ability to change parameters to take into account the seasonal vegetation growth during the start and end of the wet season. This study is important for designing and testing post-mining rehabilitated landscape systems that assess hydrology and sediment movement in seasonal biomes.

Particle layers employing conductive transition metal nitrides have been proposed as possible alternative plasmonic materials for photovoltaic applications due to their reduced losses compared to metal nanostructures. We critically compare the photocurrent gain due to an additional layer made of nanopillars of nitrides with other material classes obtained in an already highly optimized doped c-Si baseline solar cell with accurate doping profile from measurements. A relative photocurrent gain with respect to the baseline cell of on average 5% to 10% is observed, with a few cases achieving around 30% gain. While the local field enhancement is moderate resonances for nitrides spread over the whole UV-VIS range. For some nitrides, the shading effect remains a problem similar as for metals, but others behave more like dielectric scatterers with high photocurrent gain.

2-Hydroxypropyl-β-cyclodextrin (HPβCD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. Understanding of the structural properties of HPβCD and its derivatives based on the number of 2-hydroxypropyl (HP) substituents at the a-D-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution called as 6-HPβCDs and 2,6-HPβCDs, respectively. The results show that glucose subunits in both 6-HPβCDs and 2,6-HPβCDs have lower chance to flip than in βCD. Also, HP groups are occasionally blocking the hydrophobic cavity of HPβCDs, thus hindering the drug inclusion. We found that HPβCDs with high number of HP-substitutions are more likely to be blocked, while HPβCDs with double-sided HP-substitution are even more probable to be blocked. Overall, 6-HPβCDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation based on our conformational analyses such as structural distortion, radius of gyration, circularity and cavity self-closure of the HPβCDs.

Equal-Channel Angular Pressing (ECAP) is a method used to introduce severe plastic deformation into a metallic billet without changing its geometry. In special cases strain localization occurs and a pattern consisting of regions with high and low deformation (so-called shear and matrix bands) can emerge. This paper studies this phenomenon numerically adopting two-dimensional finite element simulations of one ECAP pass. The mechanical behavior of aluminum is modeled using phenomenological plasticity theory with isotropic or kinematic hardening. The effects of the two different strain hardening types are investigated numerically by systematic parameter studies: While isotropic hardening only causes minor fluctuations in the plastic strain fields, a material with high initial hardening rate and sufficient strain hardening capacity can exhibit pronounced localized deformation after ECAP. The corresponding finite element simulation results show a regular pattern of shear and matrix bands. This result is confirmed experimentally by ECAP-processing of AA6060 material in a severely cold worked condition, where microstructural analysis also reveals the formation of shear and matrix bands. Excellent agreement is found between the experimental and numerical results in terms of shear and matrix band width and length scale. The simulations provide additional insights regarding the evolution of the strain and stress states in shear and matrix bands.

In numerical simulations, achieving high accuracy without significantly increasing computational costs is often challenging. To address this, this paper presents an improved finite volume weighted essentially non-oscillatory (WENO) scheme tailored for applicability in computational fluid dynamics (CFD) and implemented in the flow solver NUAA-Turbo for simulating turbomachinery flows using both RANS and RANS/LES coupling. Firstly, the new WENO scheme is validated against classic numerical test cases to assess its stability and reliability in handling discontinuities, the Double problem, and Raleigh-Taylor (RT) instability issues. Compared to the original format, this enhanced finite volume WENO scheme demonstrates superior stability near discontinuities and resolves flow features with the same grid resolution more effectively. Next, for engineering applications related to turbomachinery, such as compressor and turbine characteristics, computations are performed using RANS, and the results obtained using WENO-ZQ3 and WENO-JS3 are compared. Finally, the new fifth-order WENO scheme is applied to RANS/LES coupled simulations of turbine wakes and film cooling. The results show that the enhanced finite volume WENO scheme offers improved stability and accuracy in engineering applications, allowing for high-precision calculations with fewer grid points to capture more detailed flow physics, thereby reducing computational costs in aerodynamic applications.

Managing sidelobe levels (SLLs) in metasurface-driven beam-steering antennas poses a significant challenge due to intrinsic factors leading to grating lobes. Our proposed method employs an equivalent model to optimize large periodic metasurfaces efficiently. This model predicts complete metasurface performance, accounting for mutual coupling between patches. We introduce an evolutionary optimization algorithm based on the Cross Entropy (CE) method to enhance PGM-based beam-steering antennas and suppress sidelobes. Two strategies were employed: first is to optimize the patch dimensions for a sidelobe-free pattern and the second is to maintain the PGM dimensions while optimizing feed array amplitudes. Both strategies effectively suppressed sidelobes, offering insights into the CE method's applicability and effectiveness for CPU-intensive electromagnetic optimization challenges. The proposed CE method variant retains its simplicity while improving monitoring capabilities, addressing this limitation. Smaller generations yield better improvements per evaluation

The fluorinated organic compounds have superior physicochemical properties than general organic compounds due to the strong C-F single bond, and widely used in medicine, biology, pesticides, and materials science. In order to gain a deeper understanding of the physicochemical properties of fluorinated organic compounds, fluorinated aromatic compounds have been investigated by various spectroscopic techniques. 2-Fluorobenzonitrile and 3-fluorobenzonitrile are important fine chemical intermediates, and their excited state S1 and cationic ground state D0 vibrational features remain unknown. In this paper, we used two-color resonance two photon ionization (2-color REMPI) and mass analyzed threshold ionization (MATI) spectroscopy to study S1 and D0 states vibrational features of 2-fluorobenzonitrile and 3-fluorobenzonitrile. The precise excitation energy (band origin) and adiabatic ionization energy were determined to be 36028 2 cm-1 and 78650 5 cm-1 for 2-fluorobenzonitrile; and 35989 2 cm-1 and 78873 5 cm-1 for 3-fluorobenzonitrile, respectively. The density functional theory (DFT) at the levels of RB3LYP/aug-cc-pvtz, TD-B3LYP/aug-cc-pvtz, and UB3LYP/aug-cc-pvtz were used to calculate the stable structures and vibrational frequencies for the ground states S0, excited state S1, and cationic ground state D0, respectively. Franck-Condon spectral simulations for transitions of S1 S0 and D0 S1 were performed based on above DFT calculations. The theoretical and experimental results are in good agreement. The observed vibrational features in S1 and D0 states are assigned according to the simulated spectra and the comparison with structurally similar molecules. Several experimental findings and molecular features were discussed in detail.

This study analyzes the potential response of the seasonal cycle of heatwave (HWDI), dry (CDD) and wet (CWD) spells indices over West Africa for the near (2031-2060) and the far (2071-2100) future periods, under RCP4.5 and RCP8.5 scenarios using CORDEX simulations. Although some relative biases during the historical period (1976-2005), the CORDEX simulations and their ensemble mean outperform the seasonal variability of the above indices over three defined sub-regions of West Africa (i.e., Guinea gulf, west and east Sahel). They have shown significant correlation coefficients and less RMSE. They project an increase in heatwave days for both near and far future periods over whole west Africa region under both RCP scenarios. In addition, the Sahel regions will face to a decrease in wet spells days from March to November, whereas, the Gulf of Guinea will face to a decrease during all the year, except CCCLM simulation which indicates an increase during the retreat phase of the monsoon (October to December). The results also have shown an increase in dry spells over Sahel regions, more pronounced during March-November period, whereas, over Guinea gulf, the increase is observed over the entire year. On the other hand, the months of increasing dry spells and decreasing wet spells coincide, suggesting that countries in these regions could be exposed simultaneously to dry season associated with a high risk of drought and heatwave under future climate conditions.

Neuromorphic computing, reconfigurable optical metamaterials operational over a wide spectral range, holographic and nonvolatile displays of extremely high resolution, integrated smart photonics and many other applications need phase-change materials (PCMs) of the next generation with better energy efficiency, wider temperature and spectral range for reliable operation compared to current flagship PCMs as Ge2Sb2Te5 or doped Sb2Te. Gallium tellurides are promising candidates to achieve the necessary requirements because of higher melting and crystallization temperatures, combined with a low switching power and fast switching rate. At the same time, Ga2Te3 and non-stoichiometric alloys appear to be atypical PCMs, characterized by regular tetrahedral structure and the absence of metavalent bonding. The sp3 gallium hybridization in cubic and amorphous Ga2Te3 is also different from conventional p-bonding in flagship PCMs, raising a question of the phase-change mechanism. Besides, gallium tellurides exhibit a number of unexpected and highly unusual phenomena as nanotectonic compression or viscosity anomaly just above melting. Using high-energy X-ray diffraction, supported by first-principles simulations, we will unravel the atomic structure of amorphous Ga2Te5 PLD films, compare it with the crystal structure of tetragonal gallium pentatelluride, and investigate electrical, optical and thermal properties of these two materials to estimate their potential for memory applications as well as for other fields.

In this study, the unsteady Reynolds-averaged Navier-Stokes (URANS) equations are employed in conjunction with the Menter Shear Stress Transport (SST)-Scale-Adaptive Simulation (SAS) turbulence model in compressible flow, unstructured mesh and complex geometry. Whereas, other scale-resolving approaches in space and time, such as Direct Numerical Simulation (DNS) and Large-Eddy Simulation (LES), supply more comprehensive information about the turbulent energy spectra of the fluctuating component of the flow; however, previously mentioned avenues imply computationally intensive situations, usually performed over structured meshes and relatively simply geometries. In contrast, the SAS approach is designed according to “physically” prescribed length scales of the flow. More precisely, it operates by locally comparing the length scale of the modelled turbulence to the von Karman length scale (which is prescribed according to local fluid velocity derivatives and depends on the grid point distribution in the computational domain). This length scale ratio allows the flow to dynamically adjust the local eddy viscosity in order to better capture the large scale motions (LSM) in unsteady regions of URANS simulations. While SAS may be constrained to model only low flow frequencies or waivenumbers (i.e., LSM), its versatility and computational low-cost make it attractive to obtain a quick first insight of the flow physics; particularly, in those situations dominated by strong flow unsteadiness. The selected numerical application is the well-known M219 three-dimensional rectangular acoustic cavity from the literature at two different freestream Mach numbers, M∞ (0.85 and 1.35) and a length-to-depth ratio of 5:1. Thus, we consider the “deep configuration" in experiments by Henshaw. The SST-SAS model has demonstrated a satisfactory compromise between simplicity, accuracy and flow physics description.

This paper summaries the main findings from the full-scale CFD analyses conducted at SINTEF Ocean on the case of MV REGAL, which is one of the benchmark vessels studied in the ongoing joint industry project JoRes. The numerical approach is described in detail, and comparative results are presented regarding the propeller open water characteristics, ship towing resistance, and ship self-propulsion performance. The focus of numerical investigations is on the assessment of the existing simulation best practices applied to a ship scale case in a blind simulation exercise, and performance of thereof with different turbulence modelling methods. The results are compared directly with full-scale performance predictions based on model tests conducted at SINTEF Ocean and sea trails data obtained in the JoRes project.

Manufacturers of photovoltaic modules do not provide all the information necessary to predict their performance under different climatic conditions. This forces the development of mathematical models of behavior and the application of mathematical methods for the calculation of their associated parameters. A toolbox called PVMSim implemented in MATLAB/GUI is proposed in this paper. PVMSIm provides models allowing the simulation of photovoltaic modules. A two-diode model is used to represent the effect of irradiance and temperature on the V-I and V-P characteristic curves. The accuracy of PVMSim has been vaildated by applying the models to two mono-crystalline and multi-crystalline solar modules of different power ratings and manufacturers. The model PVMSim model accuracy was verified against the manufacturer’s datasheet. This paper shows that this tool is useful for designers and professionals who require an intuitive graphical interface for fast and accurate modeling, simulation and sizing of photovoltaic systems.

Porcelain tile manufacturing is an energy-intensive industry that is in dire need of increasing productivity, minimizing costs, and reducing CO2 emissions, while keeping the product quality intact to remain competitive in today’s environment. In this contribution, alternative processing parameters for the porcelain tile production sequence were proposed based on simulation-based process optimization. Flowsheet simulations in the Dyssol framework were used to study the impact of milling and firing process parameters on the electrical and thermal energy consumption, final product quality, and productivity of the entire processing sequence. For this, a new model of gas flow consumption in the sintering stage was proposed and implemented. During optimization, the primary condition was to maintain the product quality by keeping the final open porosity of the tile within the specified industrial range. The proposed simulation methodology proved to be effective in predicting the influence of processing parameters on the intermediate and final products of the manufacturing sequence, as well as in estimating production costs for the Brazilian and Spanish economic conditions. This approach has shown great potential to promote digitalization and establish digital twins in ceramic tile manufacturing for further in-line process control.

Transition between free-surface and pressurized flows is an crucial phenomenon in many hydraulic systems, including water distribution systems, urban drainage systems, etc. During the transition, the force exerted on the structures changes drastically, thus it is meaningful to simulate this process. However, severe numerical oscillations are widely observed behind filling-bores, causing unphysical pressure variations and even computation failure. In this paper, some oscillation-suppressing approaches are reviewed and evaluated on a benchmark model. Then a new oscillation-suppressing approach is proposed to admit numerical viscosity when the water surface is at proximity of conduct roof which has first order accuracy. This approach adds numerical viscosity when water surface is at the proximity of conduct roof. It can sufficiently suppress numerical oscillations under an acoustic wave speed of 1000m/s and is simple to apply. In comparison with two experiments, the simulation results of this method show good agreement and little numerical oscillations. The results in this paper can help readers to choose an appropriate oscillation-suppressing method to improve the robustness and accuracy of flow regime transition simulations.

Single-molecule fluorescence detection (SMFD) experiments are useful in distinguishing sub-populations of molecular species when measuring heterogeneous samples. One experimental platform for SMFD is based on a confocal microscope, where molecules randomly traverse an effective detection volume. The non-uniformity of the excitation profile and the random nature of Brownian motion, produce fluctuating fluorescence signals. For these signals to be distinguished from the background, burst analysis is frequently used. Yet, the relation between the results of burst analyses and the underlying information of the diffusing molecules is still obscure and requires systematic assessment. In this work we performed three-dimensional Brownian motion simulations of SMFD, and tested the positions at which molecules emitted photons that passed the burst analysis criteria for different values of burst analysis parameters. The results of this work verify which of the burst analysis parameters and experimental conditions influence both the position of molecules in space when fluorescence is detected and taken into account, and whether these bursts of photons arise purely from single molecules, or not entirely. Finally, we show, as an example, the effect of bursts that are not purely from a single molecule on the accuracy in single-molecule Förster resonance energy transfer measurements.

The World Health Organization (WHO) documents malaria as one of the leading causes of high morbidity and mortality worldwide. The disease affects millions and kills thousands of people annually. Efforts to reduce the global burden of malaria have prompted WHO to recommend prevention strategies like using anti-malarial drugs. However, these strategies have been ineffective because of anti-malarial drug resistance. The only efficacious malaria treatment is Artemisinin-based Combination Therapy (ACT). However, the extended ACTs clearance times, linked to the emergence of artemisinin monotherapy resistance recorded most recently in Africa and the Great Mekong region, pose a danger to its efficacy. Therefore, better efficacious malaria drugs are required. Since P. falciparum heat shock protein 90 (PfHsp90) is a well-characterized malaria drugs target, this study uses it to discover more efficacious malaria drugs. An in-silico approach was used to discover PfHsp90 inhibitors with pharmacological properties against Plasmodium malaria using molecular dynamics simulation (MDS) and hierarchical virtual screening. Geldanamycin (GDM), a well-known anti-PfHsp90 compound, was used to identify PfHsp90 inhibitors with pharmacological properties against Plasmodium malaria by screening it against the ZINC database via the ZINCPHARMER web server. This virtual screening process resulted in 17 hits. These ZINCPHARMER hits were subjected to drug-likeness and pharmacokinetics properties analysis in the SwissADME web server, and 9 of them satisfied the requirements. The 9 ZINC compounds were docked with PfHsp90 using the PyRx software to understand their interactions. From the molecular docking results, ZINC09060002 (-8.2 kcal/mol), ZINC72133064 (-7.8 kcal/mol), ZINC72163401 (-7.7 kcal/mol), ZINC72358537 (-8.1 kcal/mol), and ZINC72358557 (-7.6 kcal/mol) had better binding affinities to PfHsp90 than GDM (-7.5 kcal/mol). The stability of these molecularly docked protein-inhibitor complexes was assessed through MDS using GROMACS 2022. ZINC72163401, ZINC72358537, and ZINC72358557 formed stable complexes with PfHsp90. The lead compounds were subjected to in vitro validation for their inhibitory capability. They showed promising inhibition of parasite growth with IC50 values ranging between 200 – 400 ng/ml. In this regard, the three PfHsp90 inhibitors can be used as anti-malarial drugs. However, further structural optimization studies and clinical (in vivo) tests are necessary to ascertain the antimalarial activity of these compounds in humans.

Breaching and liquefaction are two types of coastal flow slides proposed in the literature. While their final results are similar, liquefaction and breaching failure are two different processes, with breaching failure characterized by a different progression and sand movement mechanisms. In densely packed sand, breaching causes delayed sand grain discharge and negative excess pore pressures. Liquefaction, when a mass of soil suddenly behaves like a liquid, flow out over overly gentle slopes. Flow slides typically go unnoticed until the slope fails above ground because they start below the water. Without modern technology, diving equipment, risk assessment, and probabilistic and sensitivity assessments, flow slides inherently challenging. The authors developed a new sensitivity index to detect the susceptibility of coastal flow slides. It was established a sophisticated hybrid model that accommodates flow slides in sync with unpredictable variables employed in this new sensitivity index. Innovative hybrid model has three distinctive models. The Hybrid Hydrodynamic Model addresses wave, wind, current, climate change, and sediment transfer. The Monte Carlo Simulation analyses sensitivity, and the Bayesian Network calculates joint probability of coastal flow slide parameters of this new index that includes environmental characteristics, including climate change. With the assistance of these three models, researchers aim at a) presenting a methodology for coupling coastal flow slide projections with outcomes; b) distinguishing two flow slides; c) examining variables influencing flow slides. The use of such a hybrid model and risk index offers a robust and computationally efficient approach to evaluating the critical angle slope for breaching failure.

It has been known that the performance of the High-Pressure Grinding Rolls (HPGR) varies as a function of method used to confine laterally the rolls, their diameter/length (aspect) ratio as well as their condition, if new or worn. However, quantifying these effects through direct experimentation in machines with reasonably large dimensions is not straightforward given the challenge, among others, of guaranteeing that the feed material remains unchanged. The present work couples the discrete element method (DEM) to multibody dynamics (MBD) and a novel particle replacement model (PRM) to simulate the performance of pilot-scale HPGRs grinding pellet feed. It shows that rotating side plates, in particular when fitted with studs, allow reaching more uniform forces along the bed, which also translates in a more constant product size along the rolls as well as higher throughput. It also shows that the edge effect is relatively constant with roll length, leading to substantially larger proportional edge regions for high-aspect ratio rolls. On the other hand, the product from the center region of such rolls was found to be finer when pressed at identical specific forces. Finally, rolls were found to have higher throughput, but generate a coarser product when worn following the commonly observed trapezoidal profile. The approach used in industry to compensate for roller wear by increasing the specific force and roll speed has then been demonstrated to be effective to maintain and potentially even increase product fineness and throughput, as long as the minimum safety gap is not reached.

Subgrid scale models for unresolved turbulent fluxes are investigated with a focus on combustion for space propulsion applications. An extension to the gradient model is proposed, introducing a dependency on the local burning regime. The dynamic behavior of the model's coefficients is investigated, and scaling laws are studied. The discussed models are validated using a DNS database of a high-pressure turbulent fuel-rich methane-oxygen diffusion flame. The operating point and turbulence characteristics are selected to resemble those of modern combustors for space propulsion applications to support the future usage of the devised model in this context.

The rational fabrication of low-dimensional materials with a well-defined topology and functions is an incredibly important aspect of nanotechnology. In particular, the on-surface synthesis (OSS) methods based on the bottom-up approach enable facile construction of sophisticated molecular architectures unattainable by traditional methods of wet chemistry. Among such supramolecular constructs especially interesting are surface-supported metal-organic networks (SMONs), composed of low-coordinated metal atoms and π-aromatic bridging linkers differing in size, shape and functionalization scheme. In this work, the lattice Monte Carlo (MC) simulation technique was used to extract the chemical information encoded in a family of Y-shaped positional isomers coadsorbed with trivalent metal atoms on a flat metallic surface with (111) geometry. For this purpose the investigated tritopic molecules/metal atoms were carefully mapped on a triangular lattice as interconnected/isolated segments with appropriatelly embedded anisotropic interactions. Depending on the intramolecular distribution of active centers (functional groups) within the simulated molecular bricks, we observed the metal-directed self-assembly of two-dimensional (2D) openwork patterns, aperiodic mosaics and metal-organic ladders. The obtained theoretical findings could be especially relevant for the scanning tunneling microscopy (STM) experimentalists interested in a surface-assisted construction of complex nanomaterials stabilized by directional coordination bonds.

Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological systems. However, of the excellent results that the technique has arrogated, this approach remains computationally expensive, but with the emergence of the new supercomputing technologies bases on graphics processing units graphical processing units-based systems GPUs, the perspective has changed. The GPUs allow performing large and complex simulations at a significantly reduced time. In this work, we present recent innovations in the acceleration of molecular dynamics in GPUs to simulate non-Hamiltonian systems. In particular, we show the performance of measure-preserving geometric integrator in the canonical ensemble, that is, at constant temperature. We provide a validation and performance evaluation of the code by calculating the thermodynamic properties of a Lennard-Jones fluid. Our results are in excellent agreement with reported data reported from literature, which were calculated with CPUs. The scope and limitations for performing simulations of high-throughput MD under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.

This study explores the potential of natural compounds, including Daidzin, Luteolin, and Silibinin, as inhibitors of human monoamine oxidase B (MAO-B) for the treatment of Parkinson's disease. Docking simulations were performed using Autodock Vina with Pyrx program to evaluate the binding affinities of these compounds with MAO-B. Results indicate that Daidzin, Luteolin, and Silibinin exhibit promising binding affinities with MAO-B, with Daidzin demonstrating the highest affinity. Toxicity parameters were further predicted using the PkCSM Server, confirming the low toxicity of these compounds. Overall, the findings suggest that Daidzin, Luteolin, and Silibinin have the potential to be effective and safe treatments for Parkinson's disease through their inhibition of MAO-B. Further experimental validation is warranted to support their therapeutic efficacy in clinical settings.

Renewable energy research becomes increasingly necessary as it grows in importance. Wind turbines are an excellent method of harnessing wind energy, which is one of the most important renewable energy sources. In light of the importance of studying wind turbine performance, this study describes the background and principles of wind turbine operation. Computational fluid dynamics (CFD) was used to evaluate the hydrodynamic performance of two types of offshore and onshore wind turbines. Mechanical power and thrust force are calculated using the CFD model for both types of turbines in a steady state based on the number of blades and rotors. The results of three-dimensional simulations are compared with those of experimental testing. Based on the method and assumptions used, the offshore turbine's mechanical torque showed an average deviation of about 4%. Increased wind speed increased mechanical power and thrust, while turbulence caused irregular pressure distributions on surfaces as a result of turbulence intensity. Furthermore, as the free wind speed increases, the blade tip and hub speed will also increase, expanding the vortices created by that flow.

It is imperative to examine the performance of wind turbines both in steady and unsteady states due to their significant role in generating renewable energy by utilizing wind power. The computational fluid dynamics method (CFD) is one of the most efficient tools in this field, and the unsteady state has a great deal of importance when predicting turbine performance. Using the CFD method, the hydrodynamic performance of two types of offshore and onshore horizontal-axis wind turbines in the unsteady state was examined. Offshore wind turbines were modeled using the SST turbulence model and onshore wind turbines were modeled using the large eddy simulation (LES). Three-dimensional results of the simulation were compared and validated with experimental results, and good agreement between the two results indicates that the assumptions and method were accurate. Vortices were also studied in relation to the blade tip and their formation and development. Increasing the number of blades results in a reduction in torque, as well as a rise in vortices caused by the tips of the rotor blades. Due to the intensity of turbulence, the distribution of pressure on the surfaces will become irregular as the wind speed increases.

ND1 subunit possesses the majority of the inhibitor binding domain of the human MRC-I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, some metabolites from Annona muricata called acetogenins have important biological activities such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine MRC-I by bis-THF acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human MRC-I. In this work, we evaluate the molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, QM optimizations, MD simulations and MM/PBSA analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known MRC-I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger BFE compared to the rotenone complex. Detailed analysis of the BFE shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of MRC-I.

The effect of river fronts on oil slick transport has been demonstrated using high resolution forcing models and a fully fledged oil drift model, OpenOil. The model system is used to simulate the 2010 DeepWater Horizon oil spill. Metocean forcing data are taken from the GoM-HYCOM 1/50° ocean model with realistic river input and ECMWF global forecast products of wind and wave parameters with 1/8° resolution. The simulations are initialized from satellite observations of the surface oil patch. OpenOil includes most of the relevant processes, such as emulsification, evaporation, wave entrainment, stranding and droplet formation. The model takes account of the actual oil type and properties, using the ADIOS oil weathering database of NOAA. The effect of using a newly developed parameterization for oil droplet size distribution is studied and compared to a traditional algorithm. Although the algorithms provide different distributions for a single wave breaking event, it is found that the net difference after long simulations is negligible, indicating that the outcome is robust regarding the choice of parameterization. That indicates that the wave entrainment, vertical mixing and re-surfacing mechanisms that are part of OpenOil are more important for determining the final droplet size spectrum than the spectrum prescribed for individual wave breaking events. In both cases, the size of the droplets controls how much oil is present at the surface and hence are subject to wind and Stokes drift. The effect of removing river outflow in the ocean model is investigated in order to showcase effects of river induced fronts on oil spreading. A consistent effect on the amount and location of stranded oil is found, and considerable impact of river induced fronts is seen on the location of the surface oil patch. During a case with large river outflow (May 20-27, 2010), the total amount of stranded oil is reduced by about 50% in the simulation with no river input. The results compares well with satellite observations of the surface oil patch.

Integrating a grid-connected battery into a Renewable Energy Community boosts Collective-Self-Consumption of photovoltaic produced energy and allow to perform Energy Arbitrage in the day-ahead and intraday electricity market. However, is it a cost-effective investment? The proposed analysis relay on Net Present Value assessment. Ageing affects are integrated and sensitivity analyses are conducted: considering community customers number, electricity mar-ket prices, battery cost, size and the decision to engage in energy arbitrage. Each scenario under-goes a 20-year hourly simulation using an ageing aware rolling-horizon 24-hours-looking-ahead scheduling, optimized with Mixed-integer linear Programming. Forecast errors, provid-ing of ancillary services, real time control and grid constrains are not taken into account. Simulations conducted on the Italian market indicates that a battery dedicated solely to collec-tive self-consumption is not economically appealing. However, integrating Energy Arbitrage, despite impact on battery lifespan, halves the payback period and enhances the attractiveness of larger battery investments. The Net Present Value is contingent upon battery size, customer number and market prices. However, if battery cost does not exceed 200 €/kWh the investment become cost-effective across all scenarios.

The ubiquitous deployment of Li-ion batteries (LIBs) in more demanding applications has reinforced the need to understand root-causes of thermal runaway. Herein we perform a forensic simulation of a real-case failure scenario, using localised heating of Li(Ni0.5Mn0.3Co0.2)O2 versus graphite 18650 cylindrical cells. This study determined the localised temperatures that would lead to venting and thermal runaway of these cells, as well as correlating the gases produced as a function of degradation pathway. Catastrophic failure, involving melting (with internal cell temperatures exceeding 1085°C), deformation and ejection of cell componentry, was induced by locally applying 200 °C and 250 °C to a fully charged cell. Conversely, catastrophic failure was not observed when the same temperatures were applied to the cells at lower state of charge (SOC). This work highlights the importance of SOC, chemistry and heat in driving the thermal failure mode of Ni-rich LIB cells, allowing for a better understanding of battery safety and associated design improvements.

This study evaluated the potential of ERA5 reanalysis as a reference dataset for snow water equivalent (SWE) modeling in 16 Alpine basins of varying catchment sizes using the semi-distributed snow model (TOPMELT) in the Upper Adige river basin in the Eastern Italian Alps. The study aimed to identify errors in ERA5 meteorological variables and assess their impact on SWE computation from 1992 to 2019. The findings revealed that ERA5 precipitation overestimated low-intensity rainfall (drizzle problem) and underestimated high-intensity rainfall, while ERA5 temperature underestimated observations. The overestimation of low-intensity rainfall created fictitious low-intensity snowfall events, which, when combined with colder ERA5 temperature, resulted in delayed snowmelt and increased fictitious snow cover days over the study area. The Quantile Mapping (QM) technique was used to remove errors in ERA5 variables. For precipitation, a monthly correction factor accounting the calibration period (1992-2005) was considered to correct the entire period. Temperature errors were corrected individually for calibration and validation periods. The corrected ERA5 SWE simulation showed improved performance, with a decrease in fictitious snow cover days. The study also highlighted the importance of temperature correction over precipitation correction in SWE simulation, particularly for smaller basins, while considering the monthly moving mean to remove seasonality.

We develop a machine learning (ML) approach for improving the accuracy of the horizontal dis-tribution of the aerosol optical depth (AOD) simulated by the CHIMERE chemistry-transport model over Northern Africa using Moderate-Resolution Imaging Spectroradiometer (MODIS) AOD satellite observations. These observations are used during the training phase of the ML method for deriving a regional bias correction of AODs simulated by CHIMERE. The results are daily maps of regional bias corrected AODs with full horizontal coverage over Northern Africa. We test four types of ML models: multiple linear regression (MLR), random forests (RF), gradi-ent boosting (XGB), and multiple layer perceptron networks (NN). We perform comparisons with satellite and independent ground-based observations of AOD that are not used in the training phase. They suggest that all models have overall comparable performances with a slight advantage of the RF model which expresses less spatial artifacts. While the method slightly underestimates the very high AODs, it significantly reduces biases and absolute errors, and clearly enhances linear correlations with respect to independent observations. This im-provement for deriving the AOD is particularly relevant for high dust pollution regions like the Sahara Desert, which dramatically lack ground-based measurements for validations of chemis-try-transport modeling which currently remains challenging and imprecise.

Nuclear export of viral mRNAs, is an essential step in the HIV replication cycle. This role is played by a small regulatory protein of HIV-1 called Rev.The N-terminal region of Rev contains an arginine-rich sequence. The arginine-rich motif (ARM) is located between amino acids 38-50 and forms an alpha-helical secondary structure. Expression of the structural proteins of human immunodeficiency virus type 1 requires the direct interaction of multiple copies of the viral Rev protein with its highly structured RNA target sequence, the Rev Response element (RRE). The major viral proteins are not produced if this transport of RNA is stopped. Therefore, knowledge of Rev structure is essential for understanding of its cooperative binding to the RRE, for understanding the mechanism of HIV infection and for the development of antiviral drugs that interfere with Rev’s essential functions and for acknowledgment of good candidate drugs for treatment of AIDS. To understand how REV interact with RRE element of HIV-RNA and its formation of oligomeric complex it is better to characterize the domain wise structure of REV with regard in function of each domain. Due to lack of structural data on Rev no single compound is reported as inhibitor of REV expect antiviral drugs. Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev Protein is much more important. The ARM is a highly specific sequence which allows for the multimerization of Rev and also binding of REV with RNA. Here we are first time exploring the structural characteristics of REV protein both in free form and in complex with RNA at domain function level especially explore the role of ARM motif in REV HIV-1 protein as RNA binding sites by molecular dynamics (MD) simulation and homology modeling studies. Results indicate that the arginine-rich motif (ARM) is crucial in stability of this complex. The residues ARG38, 39, 41, 43, 44, 48, 50, and ASN40 are most interacting with nucleobases of RRE in Crystal structure of Rev and Rev-response-element RNA complex. Our study plays a major role in elaboration of binding of RNA with REV and pave the way for further investigation for therapeutically agent for HIV.

Experiments to measure a single molecule/particle, i.e. an individual molecule/particle, at room temperature or under physiological conditions without immobilization, for example on a surface, or without significant hydrodynamic flow have so far failed. This failure has given impetus to the underlying theory of Brownian molecular motion towards its stochastic due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a live cell (cytoplasm) show that the tracks of individual single molecules are localized in Brownian motion, while there is fanning out in fractal diffusion (anomalous diffusion).

Abstract: Although experimental attempts to measure a single molecule/particle at room temperature or under physiological conditions without immobilization, for example on a surface, or without hydrodynamic flow have so far failed, this failure has given impetus to the underlying theory of Brownian motion towards its stochastic due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a live cell (cytoplasm) show that the tracks of individual single molecules are localized in Brownian motion, while there is fanning out in fractal diffusion (anomalous diffusion).

This study employs molecular docking simulations using Autodock Vina with the Pyrx program to investigate the binding interactions between Human prostate-specific antigen (PSA) and natural compounds, namely Amentoflavone, Ginketin, Rutin, and Hypericin. The evaluation reveals excellent binding energy values, averaging around -10 kcal/mol, suggesting robust and favorable interactions between the selected compounds and PSA. The results provide valuable insights into the potential therapeutic applications of these natural compounds in the context of prostate cancer treatment or management. Further experimental validation is warranted to confirm these findings and explore the viability of these compounds as promising candidates for innovative therapeutic strategies. This research contributes to the growing body of knowledge in the field of molecular docking and its applications in drug discovery and bioinformatics.

We use COMSOL Multiphysics software to model optical processes in media and the effects of light propagation in whispering gallery mode resonators (WGMRs). Although plane wave irradiating on resonator does not create resonances, it was shown that they can be obtained when focused tangentially on the perimeter of the resonator. We demonstrate that resonances can be excited in resonators by prism coupling when the incident angle of the light is larger than the angle of total internal reflection. We determined the optimal distance between the prism and the resonator to get the strongest resonances. Bio-sensing principle of WGMRs is shown by demonstrating that the shift of resonances increases with a larger number of "bio-molecules" attached to the surface of WGMR. Surface functionalization and surface roughness were explored.

We used ab initio molecular dynamics simulations to compare the activation of 2-propanol on the low index Co3O4 (111), (110) and (001) surfaces in dry conditions. The thermal and surface assisted decomposition of a film of 2-propanol to 2-propoxide on the B-termination of each surface was monitored and analyzed. The investigations suggest an activity order of Co3O4 (111) > (110) > (001). On the B-terminated (111) surface, full dissociation of all 2-propanol molecules at the interface is observed, accompanied by a Mars-van Krevelen-type mechanism upon hydroxylation of the surface. On the (110) surface, 2-propanol dissociation is driven by temperature, which activates the two-fold coordinatively unsaturated surface oxygens. The (001) surface on which almost no dissociation occurs is the least active. No formation of acetone is observed in the simulations conditions.

As the first time, 0D-1D-3D and fully 3D steady-state aero-thermo-fluid simulations of a structural oil-to-air Fan Outlet Guide Vane Cooler (FOGVC) in a jet engine are presented. Using the commercial softwares Ansys Fluent, the thermo-mechanical module of Ansys and the 1D fluid solver Flownex, 5 simulation types (3D fully conjugate heat transfer with and without a thin wall model, 3D with a thin wall model, 1D-3D coupled, 1D and 0D) corresponding to 4 levels of simplification in 3 possible domains (oil, oil-metal and oil-metal-air) have been compared to provide selection criteria when a determined level of accuracy in the simulations without prohibited computational times is desired. The methodologies are applied to two different oil internal cavities: an inverted U with rectangular cross section and a coil internal cavity with a circular cross section. The obtained results show that depending on the scope of the research (outlet oil temperature, dissipated heat rate or oil pressure drop) and the accuracy of the results, one method or the other may be used. Experimental data would be needed to validate the numerical results by all employed methodologies and geometries.