Search results for " Dynamics"
showing 10 items of 4108 documents
Interpretation of the Ni K-edge EXAFS in nanocrystalline nickel oxide using molecular dynamics simulations
2011
Abstract Analysis of atomic structure at the nanoscale is a challenging task, complicated by relaxation phenomena and thermal disorder. In this work, the x-ray absorption spectroscopy at the Ni K-edge was used to address this problem in nanocrystalline NiO (nano-NiO) at 300 K. The analysis of the first two coordination shells using conventional two-shell single-scattering approximation allowed us to determine the expansion of the average lattice but contraction of the Ni―O bonds in the first coordination shell in nano-NiO in comparison with the bulk nickel oxide. The EXAFS signal generated within the first six coordination shells (up to ~ 6.5 A) was successfully interpreted using classical …
Reversible isomerization of metal nanoclusters induced by intermolecular interaction
2021
Most inorganic nanoparticles are directly surface-terminated (and -stabilized) by protecting ligands, which could greatly affect the atomic packing and physical/chemical properties of their inorganic cores. Here, we show that the intermolecular interactions between the adsorbed molecules and surface ligands can also affect the core structure of inorganic nanoparticles. Through the coupling/decoupling of cationic surfactants (cetyltrimethylammonium cations, CTA+) and anionic surface ligands (para-mercaptobenzoic acid, p-MBA) in the aqueous phase, we have achieved a reversible transformation between two isomers of [Au25(p-MBA)18]− nanoclusters. The interconversion process between the two isom…
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
2019
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …
Analysis of the U L3-edge X-ray absorption spectra in UO2 using molecular dynamics simulations
2017
This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s444. The resource allocation within the PSI share at CSCS and on the PSI compute cluster Merlin4 is also acknowledged. D. B. is grateful for a fellowship within the Sciex-NMS programme. A. K. was supported by Latvian Science Council Grant no. 187/2012.
Radiation from multi-GeV electrons and positrons in periodically bent silicon crystal
2014
A periodically bent Si crystal is shown to efficiently serve for producing highly monochromatic radiation in a gamma-ray energy spectral range. A short-period small-amplitude bending yields narrow undulator-type spectral peaks in radiation from multi-GeV electrons and positrons channeling through the crystal. Benchmark theoretical results on the undulator are obtained by simulations of the channeling with a full atomistic approach to the projectile-crystal interactions over the macroscopic propagation distances. The simulations are facilitated by employing the MBN Explorer package for molecular dynamics calculations on the meso-, bio- and nano-scales. The radiation from the ultra-relativist…
A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS
2019
Abstract The effect of the protonation state of the hydroxyl-ethylthiamin diphosphate intermediate, HEThDP, on the enzyme-substrate interactions and their consequences on the biosynthesis of R-phenylacetylcarbinol, R-PAC, by the acetohydroxy acid synthase, AHAS, is addressed by molecular dynamics simulations. It is found that the form of HEThDP, which favors the formation of R-PAC, is that having the 4-aminopyrimidine ring with the N1′ atom protonated and the N4′ atom as aminopyrimidinium ion. Under this form both active sites of AHAS have the ability to perform the catalysis, unlike that observed for the other possible protonation states of N1′ and N4′ atoms.
Data-based modeling of vehicle crash using adaptive neural-fuzzy inference system
2014
Vehicle crashes are considered to be events that are extremely complex to be analyzed from the mathematical point of view. In order to establish a mathematical model of a vehicle crash, one needs to consider various areas of research. For this reason, to simplify the analysis and improve the modeling process, in this paper, a novel adaptive neurofuzzy inference system (ANFIS-based) approach to reconstruct kinematics of colliding vehicles is presented. A typical five-layered ANFIS structure is trained to reproduce kinematics (acceleration, velocity, and displacement) of a vehicle involved in an oblique barrier collision. Subsequently, the same ANFIS structure is applied to simulate different…
Nonlinear coupling is absent in acute myocardial patients but not healthy subjects.
2008
We investigated whether autonomic nervous system imbalance imposed by pharmacological blockades and associated with acute myocardial infarction (AMI) is manifested as modifications of the nonlinear interactions in heart rate variability signal using a statistically based bispectrum method. The statistically based bispectrum method is an ideal approach for identifying nonlinear couplings in a system and overcomes the previous limitation of determining in an ad hoc way the presence of such interactions. Using the improved bispectrum method, we found significant nonlinear interactions in healthy young subjects, which were abolished by the administration of atropine but were still present afte…
Cognitive priming in sung and instrumental music: Activation of inferior frontal cortex
2006
Neural correlates of the processing of musical syntax-like structures have been investigated via expectancy violation due to musically unrelated (i.e., unexpected) events in musical contexts. Previous studies reported the implication of inferior frontal cortex in musical structure processing. However - due to the strong musical manipulations - activations might be explained by sensory deviance detection or repetition priming. Our present study investigated neural correlates of musical structure processing with subtle musical violations in a musical priming paradigm. Instrumental and sung sequences ended on related and less-related musical targets. The material controlled sensory priming com…
Modeling of Human Posturokinetic Movements by a Linear Feedback System: Relations among Feedback Coefficients
2002
This study describes a method of modeling human trunk and whole body backward bending and suggests a possible neural control strategy. The hypothesis was that the control system can be modeled as a linear feedback system, in which the torque acting at a given joint is a function of the state variables (angular positions and angular velocities). The linear system enabled representation of the feedback system by a gain matrix. The matrix was computed from the kinematics recorded by a movement analysis system and from the joint torques calculated by inverse dynamics. To validate the control model, a comparison was made between the angular kinematics yielded by the model and the experimental d…