Related papers: First principles molecular dynamics without self-c…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
The dynamical phase-space of axisymmetric Canham-Helfrich (CH) cells is constructed from a Hamiltonian field recapitulating membrane curvature-elasticity and systemic restrictions. Guiding principles are reparametrization to convert a…
We report a computationally tractable approach to first principles investigation of time-dependent current of molecular devices under a step-like pulse. For molecular devices, all the resonant states below Fermi level contribute to the…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
Numerical algorithms are proposed for simulating the Brownian dynamics of charged particles in an external magnetic field, taking into account the Brownian motion of charged particles, damping effect and the effect of magnetic field…
The constraint of time-integrated zero-area on the laser field is a fundamental, both theoretical and experimental requirement in the control of molecular dynamics. By using techniques of local and optimal control theory, we show how to…
While Born-Oppenheimer molecular dynamics (BOMD) has been widely studied by resorting to powerful methods in mathematical analysis, this paper presents a geometric formulation in terms of Hamilton's variational principle and…
Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations is adapted to the most recent shadow potential formulations of extended Lagrangian Born-Oppenheimer molecular dynamics, including…
A new fully kinetic system is proposed for modeling collisionless magnetic reconnection. The formulation relies on fundamental principles in Lagrangian dynamics, in which the inertia of the electron mean flow is neglected in the expression…
A description of non-collinear magnetism in the framework of spin-density functional theory is presented for the exact exchange energy functional which depends explicitly on two-component spinor orbitals. The equations for the effective…
Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
We show that following the standard mantra of quantum chemistry and diagonalizing the Born-Oppenheimer (BO) Hamiltonian $\hat H_{\rm BO}(\bm R)$ is not the optimal means to construct potential energy surfaces. A better approach is to…
A shadow molecular dynamics scheme for flexible charge models is presented, where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential,…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
A variational method is used to derive a self-consistent macro-particle model for relativistic electromagnetic kinetic plasma simulations. Extending earlier work [E. G. Evstatiev and B. A. Shadwick, J. Comput. Phys., vol. 245, pp. 376-398,…
In this paper, we review some recent work on amorphous materials using current "first principles" electronic structure/molecular dynamics techniques. The main theme of the paper is to emphasize new directions in the use of such ab initio…
We examine stability properties of primal-dual gradient flow dynamics for composite convex optimization problems with multiple, possibly nonsmooth, terms in the objective function under the generalized consensus constraint. The proposed…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear…