scholarly journals Computing inelastic neutron scattering spectra from molecular dynamics trajectories

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Thomas F. Harrelson ◽  
Makena Dettmann ◽  
Christoph Scherer ◽  
Denis Andrienko ◽  
Adam J. Moulé ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Amorphous Materials ◽  
Inelastic Neutron Scattering ◽  
Computational Cost ◽  
Simulation Method ◽  
Inelastic Neutron ◽  
Phonon Modes ◽  
Structural Variety ◽  
Dynamics Simulations

AbstractInelastic 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.

scholarly journals Correlation of the dynamics of native human acetylcholinesterase and its inhibited huperzine A counterpart from sub-picoseconds to nanoseconds

2014 ◽  
Vol 11 (97) ◽  
pp. 20140372 ◽  
Author(s):  
M. Trapp ◽  
M. Tehei ◽  
M. Trovaslet ◽  
F. Nachon ◽  
N. Martinez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Inelastic Neutron Scattering ◽  
Thermal Fluctuations ◽  
Inelastic Neutron ◽  
Huperzine A ◽  
Relaxation Dynamics ◽  
Elastic Neutron ◽  
Dynamics Simulations

It is a long debated question whether catalytic activities of enzymes, which lie on the millisecond timescale, are possibly already reflected in variations in atomic thermal fluctuations on the pico- to nanosecond timescale. To shed light on this puzzle, the enzyme human acetylcholinesterase in its wild-type form and complexed with the inhibitor huperzine A were investigated by various neutron scattering techniques and molecular dynamics simulations. Previous results on elastic neutron scattering at various timescales and simulations suggest that dynamical processes are not affected on average by the presence of the ligand within the considered time ranges between 10 ps and 1 ns. In the work presented here, the focus was laid on quasi-elastic (QENS) and inelastic neutron scattering (INS). These techniques give access to different kinds of individual diffusive motions and to the density of states of collective motions at the sub-picoseconds timescale. Hence, they permit going beyond the first approach of looking at mean square displacements. For both samples, the autocorrelation function was well described by a stretched-exponential function indicating a linkage between the timescales of fast and slow functional relaxation dynamics. The findings of the QENS and INS investigation are discussed in relation to the results of our earlier elastic incoherent neutron scattering and molecular dynamics simulations.

Inelastic neutron scattering and molecular dynamics studies on low-frequency modes of clathrate hydrates

2003 ◽  
Vol 81 (1-2) ◽  
pp. 493-501 ◽  
Author(s):  
H Itoh ◽  
B Chazallon ◽  
H Schober ◽  
K Kawamura ◽  
W F Kuhs
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Inelastic Neutron Scattering ◽  
Low Frequency ◽  
Inelastic Neutron ◽  
Host Lattice ◽  
Clathrate Hydrates ◽  
Type I ◽  
Dynamics Simulations

Low-frequency modes of gas hydrates with Xe, Ar, O2, and N2 atoms/molecules have been studied by inelastic neutron-scattering and molecular dynamics simulations. Type I and type II clathrate hydrates show some small but significant differences of the low-frequency host contribution to the density of states. Both differ markedly from that of ice Ih and depend only weakly on the guest. The vibrational modes associated with Xe atoms were observed at 2.2, 2.9, and 4.0 meV (T = 100 K). They are in good agreement with predictions from molecular dynamics simulations. In the case of N2 hydrate we found a well-defined peak at about 2 meV, which shows a remarkable shift to higher frequency with increasing temperature. This peak and a broad peak that is overlapped with the host lattice modes (6.5 and 10.5 meV) are assigned to the vibration of N2 molecules in the large and small cages, respectively. The calculated vibrational spectra of N2 molecules in doubly occupied large cages show a significant distinct spectral distribution. The anharmonic shift of the guest atoms in large cages is significantly less pronounced in Xe hydrates suggesting that guest-host interactions can vary considerably from one system to another. PACS Nos.: 82.75-z, 78.70N, 71.15Pd, 63

An inelastic neutron scattering, Raman, far-infrared, and molecular dynamics study of the intermolecular dynamics of two ionic liquids

2020 ◽  
Vol 22 (16) ◽  
pp. 9074-9085 ◽  
Author(s):  
Thamires A. Lima ◽  
Vitor H. Paschoal ◽  
Rafael S. Freitas ◽  
Luiz F. O. Faria ◽  
Zhixia Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Power Spectrum ◽  
Neutron Scattering ◽  
Inelastic Neutron Scattering ◽  
Far Infrared ◽  
Md Simulations ◽  
Inelastic Neutron ◽  
Tetraalkylammonium Cations

The THz dynamics of ionic liquids based on tetraalkylammonium cations were investigated by a combined usage of inelastic neutron scattering (INS), Raman, and far-infrared (FIR) spectroscopies and the power spectrum calculated by molecular dynamics (MD) simulations.

Molecular dynamics in gaseous and solid methane studied by the inelastic neutron scattering method

Physica ◽  
1969 ◽  
Vol 41 (3) ◽  
pp. 397-408 ◽  
Author(s):  
A. Bajorek ◽  
I. Natkaniec ◽  
K. Parliński ◽  
M. Sudnik-Hrynkiewicz ◽  
J.A. Janik ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Inelastic Neutron Scattering ◽  
Inelastic Neutron ◽  
Scattering Method ◽  
Solid Methane
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