Related papers: A Formulation of the Ring Polymer Molecular Dynami…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
In this combined experimental and simulation study, we utilize bond-order topology to quantitatively match particle volume fraction in mechanically uniformly compressed colloidal suspensions with temperature in atomistic simulations. The…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Mobile robotic manipulators (MRMs), which integrate mobility and manipulation capabilities, present significant control challenges due to their nonlinear dynamics, underactuation, and coupling between the base and manipulator subsystems.…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
Reaction-nonlinear diffusion (RND) partial differential equations are a fruitful playground to model the formation of sharp travelling fronts, a fundamental pattern in nature. In this work, we demonstrate the utility and scope of…
We propose a parametrization for the generalized parton distributions (GPDs) which is based on representation of parton distributions as an infinite series of t-channel exchanges. The entire generalized parton distribution is given as an…
Control co-design (CCD) is a technique for improving the closed-loop performance of systems through the coordinated design of both plant parameters and an optimal control policy. While model predictive control (MPC) is an attractive control…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
Polymerization of C60 molecular crystal under high pressure and high temperature is simulated by using linear scaling tight binding molecular dynamics (TBMD) with Graphic Processing Unit (GPU) as a computational accelerator for…
We present the construction of molecular force fields for small molecules (less than 25 atoms) using the recently developed symmetrized gradient-domain machine learning (sGDML) approach [Chmiela et al., Nat. Commun. 9, 3887 (2018); Sci.…
Rapidly rotating spherical kinematic dynamos are computed using the combination of a quasi geostrophic (QG) model for the velocity field and a classical spectral 3D code for the magnetic field. On one hand, the QG flow is computed in the…
In order to investigate relativistic effects we compare the transverse flow calculated by using the four versions of the QMD approaches with that of the full covariant RQMD approach. From the comparison we conclude that the simplified RQMD…
It was shown recently that smooth and continuous "Matsubara" phase-space loops follow a quantum-Boltzmann-conserving classical dynamics when decoupled from non-smooth distributions, which was suggested as the reason that many dynamical…
We introduce EChemDID, a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and…
Wave packet molecular dynamics (WPMD) has recently received a lot of attention as a computationally fast tool to study dynamical processes in warm dense matter beyond the Born-Oppenheimer approximation. These techniques, typically, employ…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
The transport of molecules for chemical reactions is critically important in various cellular biological processes. Despite thermal diffusion being prevalent in many biochemical processes, it is unreliable for any sort of directed transport…
We present a new time integrator for articulated body dynamics. We formulate the governing equations of the dynamics using only the position variables and recast the position-based articulated dynamics as an optimization problem. Our…
Basic problems of the semiclassical microscopic modelling of strongly interactingsystems are discussed within the framework of Quantum Molecular Dynamics (QMD). This model allows to study the influence of several types of nucleonic…