Search results for "molecular dynamics"
showing 10 items of 1075 documents
Computing bulk and shear viscosities from simulations of fluids with dissipative and stochastic interactions
2016
Exact values for bulk and shear viscosity are important to characterize a fluid and they are a necessary input for a continuum description. Here we present two novel methods to compute bulk viscosities by non-equilibrium molecular dynamics (NEMD) simulations of steady-state systems with periodic boundary conditions -- one based on frequent particle displacements and one based on the application of external bulk forces with an inhomogeneous force profile. In equilibrium simulations, viscosities can be determined from the stress tensor fluctuations via Green-Kubo relations; however, the correct incorporation of random and dissipative forces is not obvious. We discuss different expressions pro…
Self-consistent field theory based molecular dynamics with linear system-size scaling
2012
We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented …
Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials.…
1997
A new approach to carry out molecular dynamics simulations of chemical reactions in solution using combined density functional theory/molecular mechanics potentials is presented. We focus our attention on the analysis of reactive trajectories, dynamic solvent effects and transmission coefficient rather than on the evaluation of free energy which is another important topic that will be examined elsewhere. In a previous paper we have described the generalities of this hybrid molecular dynamics method and it has been employed to investigate low energy barrier proton transfer process in water. The study of processes with activation energies larger than a few kT requires the use of specific tech…
Combining Molecular Dynamics with Lattice-Boltzmann: A Hybrid Method for the Simulation of (Charged) Colloidal Systems
2005
We present a hybrid method for the simulation of colloidal systems, that combines molecular dynamics (MD) with the Lattice-Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the hydrodynamic mass and momentum transport through the solvent. The colloidal particles are propagated via MD and they are coupled to the LB fluid by viscous forces. With respect to the LB fluid, the colloids are represented by uniformly distributed points on a sphere. Each such point (with a velocity V(r) at any off-lattice position r is interacting with the neighboring eight LB nodes by a frictional force F=\xi_0(V(r)-u(r)) with \xi_0 being a friction force and u(r)…
Approximate Modeling of Spherical Membrane
2010
Spherical symmetry is ubiquitous in nature. It's therefore unfortunate that spherical system simulations are so hard, and require complete spheres with millions of interacting particles. Here we introduce an approach to model spherical systems, using revised periodic boundary conditions adapted to spherical symmetry. Method reduces computational costs by orders of magnitude, and is applicable for both solid and liquid membranes, provided the curvature is sufficiently small. We demonstrate the method by calculating the bending and Gaussian curvature moduli of single- and multi-layer graphene. Method works with any interaction (ab initio, classical interactions), with any approach (molecular …
Lattice Boltzmann versus Molecular Dynamics simulations of nanoscale hydrodynamic flows
2006
A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the appropriate mapping of length and time units from LB to MD, the velocity field as obtained from MD is quantitatively reproduced by LB. The implications of this finding for prospective LB-MD multiscale applications are discussed.
Quantum Creep and Quantum-Creep Transitions in 1D Sine-Gordon Chains
2003
Discrete sine-Gordon (SG) chains are studied with path-integral molecular dynamics. Chains commensurate with the substrate show the transition from collective quantum creep to pinning at bead masses slightly larger than those predicted from the continuous SG model. Within the creep regime, a field-driven transition from creep to complete depinning is identified. The effects of disorder in the external potential on the chain's dynamics depend on the potential's roughness exponent $H$, i.e., quantum and classical fluctuations affect the current self-correlation functions differently for $H = 1/2$.
Plenty of motion at the bottom: atomically thin liquid gold membrane
2015
The discovery of graphene some ten years ago was the first proof of a free-standing two-dimensional (2D) solid phase. Here, using quantum molecular dynamics simulations of nanoscale gold patches suspended in graphene pores, we predict the existence of an atomically thin, free-standing 2D liquid phase. The liquid phase, enabled by the exceptional planar stability of gold due to relativistic effects, demonstrates extreme fluxionality of metal nanostructures and opens possibilities for a variety of nanoscale phenomena.
Anomalous magneto-transport in disordered structures: classical edge-state percolation
2015
By event-driven molecular dynamics simulations we investigate magneto-transport in a two-dimensional model with randomly distributed scatterers close to the field-induced localization transition. This transition is generated by percolating skipping orbits along the edges of obstacle clusters. The dynamic exponents differ significantly from those of the conventional transport problem on percolating systems, thus establishing a new dynamic universality class. This difference is tentatively attributed to a weak-link scenario, which emerges naturally due to barely overlapping edge trajectories. We make predictions for the frequency-dependent conductivity and discuss implications for active coll…
Dynamic Self-assembly of Non-Brownian Spheres.
2017
International audience; Granular self-assembly of confined non-Brownian spheres under gravity is studied by Molecular Dynamics simulations. Starting from a disordered phase, dry or cohesive spheres organize, by vibrational an-nealing into BCT or FCC structures, respectively. During the self-assembling process, isothermal and isodense points are observed. The existence of such points indicates that both granular temperature and packing fraction undergo an inversion process. Around the isothermal point, a sudden growth of beads having the maximum coordination number takes place. We show by a density fluctuation analysis that a transition form a disordered phase to a crystalline structure may …