Related papers: Kinetic rates calculation via non-equilibrium dyna…
Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for…
Conventional kinesin is a dimeric motor protein that transports membranous organelles toward the plus-end of microtubules (MTs). Individual kinesin dimers show steadfast directionality and hundreds of consecutive steps, yetthe detailed…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
In this paper we present a new ultra efficient numerical method for solving kinetic equations. In this preliminary work, we present the scheme in the case of the BGK relaxation operator. The scheme, being based on a splitting technique…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Molecular dynamics simulations have become essential in many areas of atomistic modelling from drug discovery to materials science. They provide critical atomic-level insights into key dynamical events experiments cannot easily capture.…
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
We present a systematic account of recent developments of the relativistic Lattice Boltzmann method (RLBM) for dissipative hydrodynamics. We describe in full detail a unified, compact and dimension-independent procedure to design…
We derive the non-adiabatic ring polymer molecular dynamics (RPMD) approach in the phase space of the SU(N) Lie Group. This method, which we refer to as the spin mapping non-adiabatic RPMD (SM-NRPMD), is based on the spin-mapping formalism…
Quasiparticle dynamics in relativistic plasmas associated with hot, weakly-coupled gauge theories (such as QCD at asymptotically high temperature $T$) can be described by an effective kinetic theory, valid on sufficiently large time and…
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following…
In this thesis I generalize Ring Polymer Molecular Dynamics (RPMD) rate theory to electronically non-adiabatic systems, followed by application to two one-dimensional curve crossing models and a multidimensional spin-boson model.
A novel approach is presented for computing flexible body dynamics based on conventional structural dynamics models. This approach innovatively captures the rigid body motion component embedded within a flexible body's movement, generates…
Although the reverse non-equilibrium molecular dynamics (RNEMD) simulation method has been widely employed, the range of applicability is yet to be discussed. In this study, for the first time, we systematically examine the method against…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
Being able to effectively locate saddle (and other fixed) points in dynamical systems holds tremendous implications in a number of applications in engineering and science, among which the study of rare events in molecular simulations stands…
Simulating dynamics of open quantum systems is sometimes a significant challenge, despite the availability of various exact or approximate methods. Particularly when dealing with complex systems, the huge computational cost will largely…
An algorithm is proposed for finding numerical solutions of a kinetic equation that describes an infinite system of point articles placed in $\mathbb{R}^d (d \geq 1)$. The particles perform random jumps with pair wise repulsion, in the…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…