Search Results (71)

In addition to investigations of the three-dimensional protein structure, information on the dynamical properties of proteins is indispensable for an understanding of protein function in general. Correlations between protein dynamics and function are typically anticipated when both molecular mobility and function are concurrently affected under specific temperatures or hydration conditions. In contrast, excitation energy transfer within the major photosynthetic light-harvesting complex II (LHC II) presents an atypical case, as it remains fully operational even at cryogenic temperatures, primarily depending on the interactions between electronic states and involving harmonic protein vibrations only. This review summarizes recent work on vibrational and conformational protein dynamics of LHC II and directly relates these findings to its light-harvesting function. In addition, we give a comprehensive introduction into the use of neutron spectroscopy and molecular dynamics simulations to investigate the protein dynamics of photosynthetic protein complexes in solution, which is information complementary to that obtained by protein crystallography. Full article

This paper presents a combined analysis of muon neutrino and antineutrino charged-current cross sections at kinematics of relevance for the T2K, MINERvA and MicroBooNE experiments. We analyze the sum, difference and asymmetry of neutrino versus antineutrino cross sections in order to get a better understanding of the nuclear effects involved in these processes. Nuclear models based on the superscaling behavior and the relativistic mean field theory are applied, covering a wide range of kinematics, from hundreds of MeV to several GeV, and the relevant nuclear regimes, i.e., from quasileastic reactions to deep inelastic scattering processes. The NEUT neutrino-interaction event generator, used in neutrino oscillation experiments, is also applied to the analysis of the quasielastic channel via local Fermi gas and spectral function approaches. Full article

Besides a well-adapted structure, proteins often require a specific dynamical flexibility to undergo conformational changes in order to carry out their function. The latter dynamics can be directly measured by quasielastic neutron scattering as demonstrated here for three variants of the orange carotenoid protein (OCP), which plays a pivotal role in the protection of the cyanobacterial photosynthetic apparatus against photodamage. We investigate the dynamics of the structurally compact, dark-adapted wild type of OCP (OCP^wt) in comparison with that of two mutant forms. The latter two mutants differ preferentially in their structures. The orange mutant OCP-W288A is assumed to have a compact structure and to preferentially bind the pigment echinenone, while the pink mutant OCP-W288A appears to represent the more elongated structure of the red active state of OCP binding the carotenoid canthaxanthin, respectively. The study reveals three major findings: (a) the dynamics of the red active state of OCP is significantly enhanced due to a larger number of protein residues being exposed to the solvent at the surface of the protein; (b) the dynamics of all OCP forms appear to be suppressed upon the freezing of the solvent, which is most likely due to an ice-induced aggregation of the proteins; and (c) the wild type and the compact mutant exhibit different dynamics attributed to a missing H-bond between the pigment and protein, resulting a destabilization of the surrounding protein. Full article

The fundamental theory of nuclear interactions, Quantum Chromodynamics (QCD), operates in terms of quarks and gluons at higher resolution. At low resolution the relevant degrees of freedom are nucleons. Two-nucleon Short-Range Correlations (SRC) help to interconnect these two descriptions. SRCs are temporary fluctuations of strongly interacting close pairs of nucleons. The distance between the two nucleons is comparable to their radii and their relative momenta are larger than the fermi sea level. According to the electron scattering experiments held in the last decade, SRCs have far-reaching impacts on many-body systems, the nucleon-nucleon interactions, and nuclear substructure. The modern experiments with ion beams and cryogenic liquid hydrogen target make it possible to study properties of the nuclear fragments after quasi-elastic knockout of a single nucleon or an SRC pair. Here we review the status and perspectives of the SRC program in so-called inverse kinematics at JINR (Dubna, Russia). The first SRC experiment at the BM@N spectrometer (2018) with 4 GeV/c/nucleon carbon beam has shown that detection of an intact 11B nucleus after interaction selects out the quasi-elastic knockout reaction with minimal contribution of initial- and final-state interactions. Also, 25 events of SRC-breakups showed agreement in SRC properties as known from electron beam experiments. The analysis of the second measurement of SRC at BM@N held in 2022 with an improved setup is currently ongoing. The SRC project at JINR moved to a new experimental area in 2023, where the next measurement is being planned in terms of experimental setup and physics goals. Full article

Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes scattering patterns from simulations with good single-core performance and support for parallelization. In this work, the existing program Sassena is used as a potent solution to this requirement for a range of scattering methods, covering pico- to nanosecond dynamics, as well as the structure from some Ångströms to hundreds of nanometers. In the case of nanometer-level structures, the finite size of the simulation box, which is referred to as the finite size effect, has to be factored into the computations for which a method is described and implemented into Sassena. Additionally, the single-core and parallelization performance of Sassena is investigated, and several improvements are introduced. Full article

Polarisation analysis for neutron scattering experiments is a powerful tool suitable for a wide variety of studies, including soft-matter samples which have no bulk magnetic behaviour and/or a significant hydrogen content. Here, we describe a method to leverage the versatility and spin-polarisation capabilities of a cold triple-axis spectrometer to perform a measurement to separate coherent and incoherent neutron scattering for a non-magnetic sample in the quasielastic neutron scattering (QENS) regime. Such measurements are complementary to unpolarised QENS measurements, which may typically be performed on a backscattering or time-of-flight spectrometer instrument where polarisation analysis can be significantly more difficult to achieve, and utilise the strengths of each type of instrument. Full article

The dynamics of water and agarose molecules in an agarose aqueous solution has been studied by means of quasielastic neutron scattering (QENS). The dynamic structure factor S (Q,E) of the agarose aqueous solution was fitted well to the sum of the Lorentz and delta function. The former is attributed to the diffusive motion of water molecules and the latter to the local vibrational motion of agarose molecules. The self-diffusion coefficient D of water molecules was obtained from the Q-dependence of the width of the Lorentz function, while the mean square displacement <u²> of agarose molecules was obtained from the Q-dependence of the intensity of the delta term. In the cooling direction, both D and <u²> decreased with decreasing temperature and showed discontinuous changes around the thermal gelation temperature (around 314 K). In the heating direction, however, D and <u²> did not show the obvious change below 343 K, indicating a large hysteresis effect. The present results of <u²> and D revealed that the thermal gelation suppresses the motion of the polymer and accelerates the diffusion of water molecules. The activation energy E_a of the diffusion of water in the sol state is the same as that of bulk water, but the E_a in the gel state is clearly smaller than that of bulk water. Full article

DUNE’s Argon time-projecting chambers (TPC) detectors will allow us to conduct precise studies about phenomena that have, until now, seemed too challenging to measure, like tau neutrino $\left({\nu }_{\tau }\right)$ interactions. Cross section measurements are needed to understand how accurate our neutrino-nucleus interaction models are and how accurately we can use them to reconstruct neutrino energy. Quasi-elastic scattering (QE), $\Delta$ resonance production (RES), and deep inelastic scattering (DIS) processes are known to provide dominant contributions in the medium and high neutrino energy to the total cross-section of ${\nu }_{\tau }$(N) and ${\overline{\nu }}_{\tau }$(N). These cross-sections have large systematic uncertainties compared to the ones measured for ${\nu }_{\mu }$ and ${\nu }_e$ and their antiparticles. Studies point out that the reason for these differences is due to the model dependence of the ${\nu }_{\tau }$(N) cross-sections in treating the nuclear medium effects described by the nucleon structure functions, $F_{1N,\cdots ,3N}(x,Q^2)$ for ${\nu }_{\mu }$ and ${\nu }_e$. These proceedings show the semi-theoretical and experimental approach to the estimation of the ${\nu }_{\tau }$(N) and ${\overline{\nu }}_{\tau }$(N) cross-sections in DUNE for the DIS region. We will check the contributions of the additional nucleon structure functions $F_{4N}(x,Q^2)$ and $F_{5N}(x,Q^2)$ and their dependence on Q² and Bjorken-x scale. Full article

A detailed comprehension of protein function requires information on the spatial structure of the protein, which is often gathered from X-ray crystallography. However, conformational dynamics often also plays an important functional role in proteins and can be directly investigated by complementary quasielastic neutron scattering. A classic example for dynamics–function correlations is Photosystem II, which is a multimeric pigment–protein complex responsible for catalyzing the light-induced photosynthetic water splitting into protons and oxygen. Several functional subprocesses of photosynthetic electron transfer and water splitting are strongly dependent on temperature and hydration, two factors also known to affect protein dynamics. Photosystem II is often investigated in the form of membrane fragments, where the protein complex remains embedded into its native lipid environment. However, experiments on protein function are often carried out in solution state, while direct investigations of molecular dynamics by quasielastic neutron scattering are mainly performed using specifically hydrated membrane fragments only. The present study provides the first quasielastic neutron scattering investigation of the molecular dynamics of Photosystem II membrane fragments (PSIImf) in solution over a wide temperature range from 50 to 300 K. At physiological temperatures above the melting point of water, we observed that the dynamics of PSIImf are significantly activated, leading to larger atomic mean square displacement values compared to those of specifically hydrated membrane stacks. The QENS data can be described by two dynamical components: a fast one, most probably corresponding to methyl group rotation; and a slower one, representing localized conformational dynamics. The latter component could be fitted by a jump-diffusion model at 300 K. The dynamics observed characterize the level of flexibility necessary for the proper PS II functionality under physiological conditions. In contrast, we observe a severe restriction of molecular dynamics upon freezing of the solvent below ~276 K. We associate this unexpected suppression of dynamics with a substantial aggregation of PSIImf caused by ice formation. Full article

We introduce a method for consistently incorporating meson-exchange currents (MEC) within the superscaling analysis with relativistic effective mass, featuring a new scaling variable, ${\psi }^{*}$, and single-nucleon cross-sections derived from the relativistic mean field (RMF) model of nuclear matter. The single-nucleon prefactor is obtained from the 1p1h matrix element of the one-body current, combined with the two-body current, averaged over a momentum distribution of Fermi kind. The approach is applied to selected quasielastic cross-sectional data on ${}^{12}$C. The results reveal a departure from scaling behavior, yet, intriguingly, the data collapse into a discernible band that is parametrized using a simple function of ${\psi }^{*}$. This calculation, as developed, is not intended to provide pinpoint precision in extracting nuclear responses. Instead, it offers a global description of the quasielastic data with a considerable level of uncertainty. However, this approach effectively captures the overall trends of the quasielastic data beyond the Fermi gas model with a minimal number of parameters. The model incorporates partially transverse enhancement of the response, as embedded within the relativistic mean field framework. However, it does not account for enhancements attributed to the combined effects of tensor correlations and MEC, given that the initial RMF model lacks these correlations. A potential avenue for improvement involves starting with a correlated Fermi gas model to incorporate additional enhancements into single-nucleon responses. This study serves as a practical demonstration of implementing such corrections. Full article

This review paper emphasizes the significance of microscopic calculations with quantified theoretical error estimates in studying lepton–nucleus interactions and their implications for electron scattering and accelerator neutrino oscillation measurements. We investigate two approaches: Green’s Function Monte Carlo and the extended factorization scheme, utilizing realistic nuclear target spectral functions. In our study, we include relativistic effects in Green’s Function Monte Carlo and validate the inclusive electron scattering cross section on carbon using available data. We compare the flux-folded cross sections for neutrino-carbon scattering with T2K and MINER$\nu$A experiments, noting the substantial impact of relativistic effects in reducing the theoretical curve strength when compared to MINER$\nu$A data. Additionally, we demonstrate that quantum Monte Carlo-based spectral functions accurately reproduce the quasi-elastic region in electron scattering data and T2K flux-folded cross sections. By comparing results from Green’s Function Monte Carlo and the spectral function approach, which share a similar initial target state description, we quantify errors associated with approximations in the factorization scheme and the relativistic treatment of kinematics in Green’s Function Monte Carlo. Full article

The MicroBooNE liquid argon time projection chamber experiment is pursuing a broad range of neutrino physics measurements, including some of the first high-statistics results for neutrino–argon scattering cross-sections. At the neutrino energies relevant for MicroBooNE and its companion experiments in the Fermilab Short-Baseline Neutrino program, the dominant event topology involves mesonless final states containing one or more protons. A complete description of these events requires modeling the contributions of quasielastic and two-particle, two-hole neutrino interactions, as well as more inelastic reaction modes in which final state pions are reabsorbed by the residual nucleus. Refinements to the current understanding of these processes, informed by new neutrino cross-section data, will enable a precise and reliable interpretation of future measurements of neutrino oscillations and searches for exotic physics processes involving neutrinos. This proceeding presents the first double-differential cross-section results from MicroBooNE for mesonless charged current scattering of muon neutrinos on argon. Full article

The MicroBooNE detector is a liquid argon time projection chamber (LArTPC) with an 85 ton active mass that receives flux from the Booster Neutrino and the Nutrinos from the Main Injector (NuMI) beams, providing excellent spatial resolution of the reconstructed final-state particles. Since 2015, MicroBooNE has accumulated many neutrino and anti-neutrino scattering events with argon nuclei enabling searches for rare interaction channels. The Cabibbo-suppressed production of hyperons in anti-neutrino–nucleus interactions provides sensitivity to a range of effects, including second-class currents, SU(3) symmetry violations and reinteractions between the hyperon and the nuclear remnant. This channel exclusively involves anti-neutrinos, offering an unambiguous constraint on wrong-sign contamination. The effects of nucleon structure and final state interactions are distinct from those affecting the quasielastic channel and modify the $\Lambda$ and $\Sigma$ production cross sections in different ways, providing new information that could help to break their degeneracy. Few measurements of this channel have been made, primarily in older experiments such as Gargamelle. We present the sensitivity of the MicroBooNE experiment to the cross section for direct (Cabibbo-suppressed) $\Lambda$ production in muon anti-neutrino interactions, using anti-neutrinos from the off-axis NuMI beam. Full article

We present a short summary of a phenomenological analysis of all available electron scattering data on ${}^{12}\mathrm{C}$ (about 6600 differential cross-section measurements) and on ${}^{16}\mathrm{O}$ (about 250 measurements) within the framework of the quasielastic (QE) superscaling model (including Pauli blocking). All QE and inelastic cross-section measurements are included down to the lowest momentum transfer 3-vector $\mathbf{q}$ (including photo-production data). We find that there is enhancement of the transverse QE response function ($R_T^{QE}$) and quenching of the QE longitudinal response function ($R_L^{QE}$) at low $\mathbf{q}$ (in addition to Pauli blocking). We extract parameterizations of a $multiplicative$ low $\mathbf{q}$ “longitudinal quenching factor” and an $additive$ “transverse enhancement” contribution. The fit can be used as a proxy to validate the modeling of cross sections in Monte Carlo event generators for electron and neutrino (${\nu }_{e,\mu }$) scattering. Additionally, we find that the excitation of nuclear states contributes significantly (up to 30%) to the Coulomb sum rule $SL\left(\mathbf{q}\right)$. We extract the most accurate determination of $SL\left(\mathbf{q}\right)$ to date and find it to be in disagreement with random phase approximation (RPA) based calculations but in reasonable agreement with recent theoretical calculations, such as “first-principle Green’s function Monte Carlo”. Full article

Recently, it was reported that chitin and chitosan exhibited high-proton conductivity and function as an electrolyte in fuel cells. In particular, it is noteworthy that proton conductivity in the hydrated chitin becomes 30 times higher than that in the hydrated chitosan. Since higher proton conductivity is necessary for the fuel cell electrolyte, it is significantly important to clarify the key factor for the realization of higher proton conduction from a microscopic viewpoint for the future development of fuel cells. Therefore, we have measured proton dynamics in the hydrated chitin using quasi-elastic neutron scattering (QENS) from the microscopic viewpoint and compared the proton conduction mechanism between hydrated chitin and chitosan. QENS results exhibited that a part of hydrogen atoms and hydration water in chitin are mobile even at 238 K, and the mobile hydrogen atoms and their diffusion increase with increasing temperature. It was found that the diffusion constant of mobile protons is two times larger and that the residence time is two times faster in chitin than that in chitosan. In addition, it is revealed from the experimental results that the transition process of dissociable hydrogen atoms between chitin and chitosan is different. To realize proton conduction in the hydrated chitosan, the hydrogen atoms of the hydronium ions (H₃O⁺) should be transferred to another hydration water. By contrast, in hydrated chitin, the hydrogen atoms can transfer directly to the proton acceptors of neighboring chitin. It is deduced that higher proton conductivity in the hydrated chitin compared with that in the hydrated chitosan is yielded by the difference of diffusion constant and the residence time by hydrogen-atom dynamics and the location and number of proton acceptors. Full article