Related papers: Applicability of molecular statics simulation to p…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
The cross-slip process of a screw $<$a$>$ dislocation from the basal to the prismatic plane in magnesium was studied using the density functional theory and the molecular dynamics calculations. An atomistic method for calculating the total…
Stationary electric transport in semiconductor nanostructures is studied by the method of nonequilibrium Green functions. In the case of sequential tunneling the results are compared with density matrix theory, providing almost identical…
Movements of molecular motors on cytoskeletal filaments are described by directed walks on a line. Detachment from this line is allowed to occur with a small probability. Motion in the surrounding fluid is described by symmetric random…
In this paper we describe the metastable behavior of solutions to a class of parabolic systems. In particular, we improve some results contained in \cite{MS} by using different techniques to describe the slow motion of the internal layers.…
(a+c) dislocations in hexagonal materials are typically observed to be dissociated into partial dislocations. Edge (a+c) dislocations are introduced into (0001) nitride semiconductor layers by the process of plastic relaxation. As there is…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
The atomic structure, mechanical and thermodynamic stability of vacancy clusters in Cu are studied by atomistic simulations. The most stable atomic configuration of small vacancy clusters is determined. The mechanical stability of the…
Screw dislocations in bcc metals display non-planar cores at zero temperature which result in high lattice friction and thermally activated strain rate behavior. In bcc W, electronic structure molecular statics calculations reveal a…
This work presents a finite element method for simulating dynamic processes that involve the coupled evolution of dislocation motion and crack propagation. The method numerically solves the Concurrent Atomistic-Continuum (CAC) formulation…
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…
Non-equilibrium Markov State Modeling (MSM) has recently been proposed [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach…
The Monge-Ampere-Kantorovich (MAK) reconstruction is tested against cosmological N-body simulations. Using only the present mass distribution sampled with particles, and the assumption of homogeneity of the primordial distribution, MAK…
The structural, electronic, and magnetic properties of (100)-oriented Co$_{2}$MnAl/MgO and Co$_{2}$MnAl/GaAs heterostructures are investigated using plane-wave pseudopotential density functional theory. For the Co$_{2}$MnAl/MgO, CoCo-MgMg,…
The collective structure of atomic nuclei intermediate between spherical and quadrupole deformed structure presents challenges to theoretical understanding. However, models have recently been proposed in terms of potentials which are soft…
The interrelation of dynamic processes active on separated time-scales in glasses and viscous liquids is investigated using a model displaying two time-scale bifurcations both between fast and secondary relaxation and between secondary and…
The experimental density dependence of gas (argon and nitrogen) permeability of partially densified silica aerogels in the Knudsen regime is quantitatively accounted for by a computer model. The model simulates both the structure of the…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…