Browse
Submit Data
Databases
API
Help

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Computing inelastic neutron scattering spectra from molecular dynamics trajectories.

ABSTRACT: Inelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation method that is frequently used to simulate semicrystalline/amorphous materials. We illustrate the technique by analyzing spectra of a well-studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) and conclude that our technique provides improved volume and structural variety, but that the classical force field requires improvement before the morphology can be accurately interpreted.

SUBMITTER: Harrelson TF

PROVIDER: S-EPMC8041884 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Computing inelastic neutron scattering spectra from molecular dynamics trajectories.

Harrelson Thomas F TF Dettmann Makena M Scherer Christoph C Andrienko Denis D Moulé Adam J AJ Faller Roland R

Scientific reports 20210412 1

Inelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation met ...[more]

PMID: 33846390

Similar Datasets

A database of synthetic inelastic neutron scattering spectra from molecules and crystals.

Project description:Inelastic neutron scattering (INS) is a powerful tool to study the vibrational dynamics in a material. The analysis and interpretation of the INS spectra, however, are often nontrivial. Unlike diffraction, for which one can quickly calculate the scattering pattern from the structure, the calculation of INS spectra from the structure involves multiple steps requiring significant experience and computational resources. To overcome this barrier, a database of INS spectra consisting of commonly seen materials will be a valuable reference, and it will also lay the foundation of advanced data-driven analysis and interpretation of INS spectra. Here we report such a database compiled for over 20,000 organic molecules and over 10,000 inorganic crystals. The INS spectra are obtained from a streamlined workflow, and the synthetic INS spectra are also verified by available experimental data. The database is expected to greatly facilitate INS data analysis, and it can also enable the utilization of advanced analytics such as data mining and machine learning.Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ).

| S-EPMC9873913 | biostudies-literature

Optimization and inference of bin widths for histogramming inelastic neutron scattering spectra.

Project description:A data-driven bin-width optimization for the histograms of measured data sets based on inhomogeneous Poisson processes was developed in a neurophysiology study [Shimazaki & Shinomoto (2007). Neural Comput. 19, 1503-1527], and a subsequent study [Muto, Sakamoto, Matsuura, Arima & Okada (2019). J. Phys. Soc. Jpn, 88, 044002] proposed its application to inelastic neutron scattering (INS) data. In the present study, the results of the method on experimental INS time-of-flight data collected under different measurement conditions from a copper single crystal are validated. The extrapolation of the statistics on a given data set to other data sets with different total counts precisely infers the optimal bin widths on the latter. The histograms with the optimized bin widths statistically verify two fine-spectral-feature examples in the energy and momentum transfer cross sections: (i) the existence of phonon band gaps; and (ii) the number of plural phonon branches located close to each other. This indicates that the applied method helps in the efficient and rigorous observation of spectral structures important in physics and materials science like novel forms of magnetic excitation and phonon states correlated to thermal conductivities.

| S-EPMC9172031 | biostudies-literature

Computing Resonant Inelastic X-Ray Scattering Spectra Using The Density Matrix Renormalization Group Method.

Project description:We present a method for computing the resonant inelastic x-ray scattering (RIXS) spectra in one-dimensional systems using the density matrix renormalization group (DMRG) method. By using DMRG to address this problem, we shift the computational bottleneck from the memory requirements associated with exact diagonalization (ED) calculations to the computational time associated with the DMRG algorithm. This approach is then used to obtain RIXS spectra on cluster sizes well beyond state-of-the-art ED techniques. Using this new procedure, we compute the low-energy magnetic excitations observed in Cu L-edge RIXS for the challenging corner shared CuO4 chains, both for large multi-orbital clusters and downfolded t-J chains. We are able to directly compare results obtained from both models defined in clusters with identical momentum resolution. In the strong coupling limit, we find that the downfolded t-J model captures the main features of the magnetic excitations probed by RIXS only after a uniform scaling of the spectra is made.

| S-EPMC6056525 | biostudies-literature

Portraying entanglement between molecular qubits with four-dimensional inelastic neutron scattering.

Project description:Entanglement is a crucial resource for quantum information processing and its detection and quantification is of paramount importance in many areas of current research. Weakly coupled molecular nanomagnets provide an ideal test bed for investigating entanglement between complex spin systems. However, entanglement in these systems has only been experimentally demonstrated rather indirectly by macroscopic techniques or by fitting trial model Hamiltonians to experimental data. Here we show that four-dimensional inelastic neutron scattering enables us to portray entanglement in weakly coupled molecular qubits and to quantify it. We exploit a prototype (Cr7Ni)2 supramolecular dimer as a benchmark to demonstrate the potential of this approach, which allows one to extract the concurrence in eigenstates of a dimer of molecular qubits without diagonalizing its full Hamiltonian.

| S-EPMC5321722 | biostudies-literature

Vibrational Dynamics in crystalline 4-(dimethylamino) benzaldehyde: Inelastic Neutron Scattering and Periodic DFT Study.

Project description:The structure and dynamics of crystalline 4-(dimethylamino) benzaldehyde, 4DMAB, are assessed through INS spectroscopy combined with periodic DFT calculations. The excellent agreement between experimental and calculated spectra is the basis for a reliable assignment of INS bands. The external phonon modes of crystalline 4DMAB are quite well described by the simulated spectrum, as well as the modes involving low-frequency molecular vibrations. Crystal field splitting is predicted and observed for the modes assigned to the dimethylamino group. Concerning the torsional motion of methyl groups, four individual bands are identified and assigned to specific methyl groups in the asymmetric unit. The torsional frequencies of the four methyl groups in the asymmetric unit fall in a region of ca. 190 ± 20 cm-1, close to the range of values observed for methyl groups bonding to unsaturated carbon atoms. The hybridization state of the X atom in X-CH3 seems to play a key role in determining the methyl torsional frequency.

| S-EPMC8780805 | biostudies-literature

Inelastic electron scattering induced quantum coherence in molecular dynamics.

Project description:Quantum coherence is pivotal in various applications ranging from chemical control to quantum computing. An example of its manifestation in molecular dynamics is inversion symmetry breaking in the photodissociation of homonuclear diatomic molecules. On the other hand, the dissociative attachment of an incoherent electron also induces such coherent dynamics. However, these processes are resonant and occur for projectiles with a specific energy. Here we present the most general scenario of non-resonant inelastic electron scattering inducing such a quantum coherence in molecular dynamics. The ion-pair formation (H+ + H─) that proceeds after the electron impact excitation of H2 shows a forward-backward asymmetry about the incoming electron beam. Simultaneous transfer of multiple angular momentum quanta during the electron collision induces the underlying coherence in the system. The non-resonant nature of this process makes this effect generic and points to its possible prevalent role in particle collision processes, including electron-induced chemistry.

| S-EPMC10183011 | biostudies-literature

New Insights about CuO Nanoparticles from Inelastic Neutron Scattering.

Project description:Inelastic Neutron Scattering (INS) spectroscopy has provided a unique insight into the magnetodymanics of nanoscale copper (II) oxide (CuO). We present evidence for the propagation of magnons in the directions of the ordering vectors of both the commensurate and helically modulated incommensurate antiferromagnetic phases of CuO. The temperature dependency of the magnon spin-wave intensity (in the accessible energy-range of the experiment) conforms to the Bose population of states at low temperatures (T ≤ 100 K), as expected for bosons, then intensity significantly increases, with maximum at about 225 K (close to TN), and decreases at higher temperatures. The obtained results can be related to gradual softening of the dispersion curves of magnon spin-waves and decreasing the spin gap with temperature approaching TN on heating, and slow dissipation of the short-range dynamic spin correlations at higher temperatures. However, the intensity of the magnon signal was found to be particle size dependent, and increases with decreasing particle size. This "reverse size effect" is believed to be related to either creation of single-domain particles at the nanoscale, or "superferromagnetism effect" and the formation of collective particle states.

| S-EPMC6473763 | biostudies-literature

The interpretation of polycrystalline coherent inelastic neutron scattering from aluminium.

Project description:A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available.

| S-EPMC3831299 | biostudies-literature

Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

Project description:Hydration effects on protein dynamics were investigated by comparing the frequency dependence of the calculated neutron scattering spectra between full and minimal hydration states at temperatures between 100 and 300 K. The protein boson peak is observed in the frequency range 1-4 meV at 100 K in both states. The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state. Protein motions with a frequency higher than 4 meV were shown to undergo almost harmonic motion in both states at all temperatures simulated, whereas those with a frequency lower than 1 meV dominate the total fluctuations above 220 K and contribute to the origin of the glass-like transition. At 300 K, the boson peak becomes buried in the quasielastic contributions in the full hydration state but is still observed in the minimal hydration state. The boson peak is observed when protein dynamics are trapped within a local minimum of its energy surface. Protein motions, which contribute to the boson peak, are distributed throughout the whole protein. The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (< approximately 20 microeV) is developed in the near future.

| S-EPMC2480692 | biostudies-literature

Unveiling phonons in a molecular qubit with four-dimensional inelastic neutron scattering and density functional theory.

Project description:Phonons are the main source of relaxation in molecular nanomagnets, and different mechanisms have been proposed in order to explain the wealth of experimental findings. However, very limited experimental investigations on phonons in these systems have been performed so far, yielding no information about their dispersions. Here we exploit state-of-the-art single-crystal inelastic neutron scattering to directly measure for the first time phonon dispersions in a prototypical molecular qubit. Both acoustic and optical branches are detected in crystals of [VO(acac)[Formula: see text]] along different directions in the reciprocal space. Using energies and polarisation vectors calculated with state-of-the-art Density Functional Theory, we reproduce important qualitative features of [VO(acac)[Formula: see text]] phonon modes, such as the presence of low-lying optical branches. Moreover, we evidence phonon anti-crossings involving acoustic and optical branches, yielding significant transfers of the spin-phonon coupling strength between the different modes.

| S-EPMC7145838 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data