Related papers: A Rotational/Roto-translational Constraint Method …
We computationally demonstrate a new method for coherently controlling the rotation-axis direction in asymmetric top molecules with an optical centrifuge. Appropriately chosen electric-field strengths and the centrifuge's acceleration rate…
Classical molecular dynamics simulations are based on solving Newton's equations of motion. Using a small timestep, numerical integrators such as Verlet generate trajectories of particles as solutions to Newton's equations. We introduce…
Droplet motion over a surface with wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics. GROMACS and Visual Molecular Dynamics (VMD) were used for simulation and intermittent…
We present a cut-cell method for the simulation of 2D incompressible flows past obstacles. It consists in using the MAC scheme on cartesian grids and imposing Dirchlet boundary conditions for the velocity field on the boundary of solid…
A very simple explicit integrator for the rotational motion of rigid linear molecules is presented which can preserve the rigidity of the molecules without requiring any constraint force. The integrator is time-reversible and symplectic,…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations, and is limited in accuracy…
Our ability to numerically model and understand the complex flow behavior of solid-bearing suspensions has increased significantly over the last couple of years, partly due to direct numerical simulations that compute flow around individual…
We apply two different monotonically convergent optimization algorithms to the control of molecular rotational dynamics by laser pulses. This example represents a quantum control problem where the interaction of the system with the external…
Fluctuating hydrodynamics based techniques have been developed in recent years for the simulation of Brownian motion of particles. These mesoscale simulation tools are viable approaches for problems where molecular dynamics simulations may…
Numerical simulations are a key tool to decipher the dynamics of gravitation. Yet, they fail to spatially reproduce the Universe we observe, limiting comparison between observations and simulations to a statistical level. This is highly…
Little is known about the coupling of rotation and translation in dense systems. Here, we report results of confocal fluorescence microscopy where simultaneous recording of translational and rotational particle trajectories from a…
Accurate computer simulations of the rotational dynamics of linear molecules solvated in He clusters indicate that the large-size (nano-droplet) regime is attained quickly for light rotors (HCN, CO) and slowly for heavy ones (OCS, N$_2$O,…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
Recent experiments have demonstrated direct cooling and trapping of diatomic and triatomic molecules in magneto-optical traps (MOTs). However, even the best molecular MOTs to date still have density $10^{-5}$ times smaller than in typical…
We present a revision to the well known Stormer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate…
This paper deals with an implicit Newton-like inertial dynamical system governed by a maximally comonotone inclusion problem in a Hilbert space. Under suitable conditions, we establish not only pointwise estimates and integral estimates for…
We experimentally demonstrate that the rotation of molecules embedded in helium nanodroplets can be controlled with an optical centrifuge, allowing for the study of molecular dynamics inside the strongly interacting many-body environment of…