Search results for "molecular dynamics"
showing 10 items of 1075 documents
Spherical polymer brushes under good solvent conditions: molecular dynamics results compared to density functional theory.
2010
A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions, by Molecular Dynamics methods and density functional theory. With increasing chain length the monomer density profile exhibits a crossover to the star polymer limit. The distribution of polymer ends and the linear dimensions of individual polymer chains are obtained, while the inhomogeneous stretching of the chains is characterized by the local persistence lengths. The results on the structure factor of both single chain and full spherical brush as well as the range of applicability of the different theoretic…
Atomistic modeling of crystal structure of Ca1.67SiHx
2015
The atomic structure of calcium-silicate-hydrate (C-1.67-S-H-x) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three m…
The Importance of Intermediate Range Order in Silicates: Molecular Dynamics Simulation Studies
2003
We present the results of large scale computer simulations in which we investigate the structural and dynamic properties of silicate melts with the compositions (Na2O)2(SiO2) and (Al2O3)2(Si02). In order to treat such systems on a time scale of several nanoseconds and for system sizes of several thousand atoms it is necessary to use parallel supercomputers like the CRAY T3E. We show that the silicates under consideration exhibit additional intermediate range order as compared to silica (SiO2) where the characteristic intermediate length scales stem from the tetrahedral network structure. For the sodium silicate system it is demonstrated that the latter structural features are intimately con…
Quaternary structures of GroEL and naïve-Hsp60 chaperonins in solution: a combined SAXS-MD study
2015
The quaternary structures of bacterial GroEL and human naïve-Hsp60 chaperonins in physiological conditions have been investigated by an innovative approach based on a combination of synchrotron Small Angle X-ray Scattering (SAXS) in-solution experiments and molecular dynamics (MD) simulations. Low-resolution SAXS experiments over large and highly symmetric oligomers are analyzed on the basis of the high-resolution structure of the asymmetric protein monomers, provided by MD. The results reveal remarkable differences between the solution and the crystallographic structure of GroEL and between the solution structures of GroEL and of its human homologue Hsp60.
Modeling glass materials
2005
Abstract Structural and dynamic properties of silicate melts and glasses (SiO 2 and its mixtures with Na 2 O and Al 2 O 3 ) are derived from Molecular Dynamics simulations and compared to pertinent experimental data. It is shown that these mixtures exhibit additional intermediate order as compared to pure silica, where the characteristic length scales stem from the tetrahedral network structure. While sodium ions show much faster diffusion through percolating channels than the silicon and oxygen ions forming the surrounding network, aluminium ions are incorporated into the network (leading to tricluster formation) and do not show such an enhanced mobility.
Study of silicon crystal surface formation based on molecular dynamics simulation results
2014
Abstract The equilibrium shape of 〈 110 〉 -oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of { 111 } surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid–liquid interface was constructed using the same model of the shape as for the solid–vapor interface. The parameters describing solid–liquid interface shape were found using values of surface energies in low-index dir…
Aging as dynamics in configuration space
1999
The relaxation dynamics of many disordered systems, such as structural glasses, proteins, granular materials or spin glasses, is not completely frozen even at very low temperatures. This residual motion leads to a change of the properties of the material, a process commonly called aging. Despite recent advances in the theoretical description of such aging processes, the microscopic mechanisms leading to the aging dynamics are still a matter of dispute. In this Letter we investigate the aging dynamics of a simple glass former by means of molecular dynamics computer simulation. Using the concept of the inherent structure we give evidence that aging dynamics can be understood as a decrease of …
Structure of anisole derivatives by total neutron and X-ray scattering: Evidences of weak C–H⋯O and C–H⋯π interactions in the liquid state
2020
Abstract High resolution, total neutron and X-ray scattering data have been used in synergy with Molecular Dynamics simulations to access atomistic scale insight into the structure of anisole and 2,3,5-trimethylanisole, two aromatic compounds bearing an electron-donating methoxy group. A detailed description is provided for the main interactions occurring in these systems, including π-π stacking and weak hydrogen bonding correlations: C H⋯O and C H⋯π. The existence of preferential orientations of the first shell coordinating molecules and the specific nature of the interactions involving the π cloud and the polar methoxy group have been reported and discussed.
Negative thermal expansion of ScF 3 : first principles vs empirical molecular dynamics
2019
The calculations were performed on the Paul Scherrer Institute cluster Merlin4, HPC resources of the Swiss National Supercomputing Centre in Lugano (project ID s626) as well as at the Latvian SuperCluster (LASC). Authors are greatly indebted to S. Ali, D. Gryaznov, R.A. Evarestov, M. Isupova, A. Kalinko, V. Kashcheyevs, V. Pankratov, S. Piskunov, A. I. Popov, J. Purans, F. Rocca, L. Shirmane, P. Zˇguns, and Yu. F. Zhukovskii for many stimulating discussions. Financial support provided by project No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity “Post-doctoral research aid” realized at the Institute of Solid State Physics, University of Latvia is greatly acknowledged.
A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules
2019
We estimate the time- and temperature-evolution of spin energy levels in a metallopeptide by combining molecular dynamics with crystal field analysis. Fluctuations of tens of cm-1 for spin energy levels at fs times gradually average out at longer times. We confirm that local vibrations are key in spin dynamics.