Related papers: Virtual Molecular Dynamics
The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
This work describes a geometric framework on molecular reaction dynamics based on the variational principle, where the Schr{\"o}dinger equation must be solved to ``see'' how a reaction occurs. First, the mathematical preliminaries are given…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
The possibility to simulate the properties of many-body open quantum systems with a large number of degrees of freedom is the premise to the solution of several outstanding problems in quantum science and quantum information. The challenge…
Differential equations based on physical principals are used to represent complex dynamic systems in all fields of science and engineering. Through repeated use in both academics and industry, these equations have been shown to represent…
Locomotion is essential for living cells. It enables bacteria and algae to explore space for food, cancer to spread, and immune system to fight infections. Motile cells display trajectories of intriguing complexity, from regular (e.g.…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
Accurate modeling of ion-molecule reaction networks is essential for understanding the chemical evolution of planetary ionospheres, particularly for giant planets where proton-transfer chains drive atmospheric composition. However,…
A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte…
Non-adiabatic dynamics at molecule-metal interfaces govern diverse and technologically important phenomena, from heterogeneous catalysis to dye-sensitized solar energy conversion and charge transport across molecular junctions. Realistic…
A discrete time stochastic model for a multiagent system given in terms of a large collection of interacting Markov chains is studied. The evolution of the interacting particles is described through a time inhomogeneous transition…
Almost all Molecular Dynamics (MD) simulations are discrete dynamics with Newton's algorithm first published in 1687, and much later by L. Verlet in 1967. Discrete Newtonian dynamics has the same qualities as Newton's classical analytic…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Since its development, Stokesian Dynamics has been a leading approach for the dynamic simulation of suspensions of particles at arbitrary concentrations with full hydrodynamic interactions. Although originally developed for the simulation…
Generic open quantum dynamics can be described by two seemingly very distinct approaches: a top down approach by considering an (unknown) environment coupled to the system and affects the observed dynamics of the system; or a bottom up…
Recent advances in quantum technologies and related experiments have created a need for highly accurate, versatile, and computationally efficient simulation techniques for the dynamics of open quantum systems. Long-lived correlation effects…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…