Related papers: Efficient multiple time scale molecular dynamics: …
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
We present our study on the emergent states of two interacting nonlinear systems with differing dynamical time scales. We find that the inability of the interacting systems to fall in step leads to difference in phase as well as change in…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
Thermodynamics of nanoscale devices is an active area of research. Despite their noisy surrounding they often produce mechanical work (e.g. micro-heat engines), display rectified Brownian motion (e.g. molecular motors). This invokes…
Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…
A new configurational temperature thermostat suitable for molecules with holonomic constraints is derived. This thermostat has a simple set of motion equations, can generate the canonical ensemble in both position and momentum space, acts…
Time-resolved studies have so far relied on rapidly triggering a photo-induced dynamic in chemical or biological ions or molecules and subsequently probing them with a beam of fast moving photons or electrons that crosses the studied…
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a…
Finite-dimensional dissipative dynamical systems with multiple time-scales are obtained when modeling chemical reaction kinetics with ordinary differential equations. Such stiff systems are computationally hard to solve and therefore,…
Kinetic equations model distributions of particles in position-velocity phase space. Often, one is interested in studying the long-time behavior of particles in high-collisional regimes in which an approximate (advection)-diffusion model…
Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework…
The design of quantum control methods has been shown to greatly improve the performance of many evolving quantum technologies. To this end, the usage of adiabatic dynamics to drive quantum systems is seriously limited by the action of…
This paper presents Space-Time MultiGrid (STMG) methods which are suitable for performing topology optimisation of transient heat conduction problems. The proposed methods use a pointwise smoother and uniform Cartesian space-time meshes.…
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…
We present a mechanism to steer the sampling diversity of denoising diffusion and flow matching models, allowing users to sample from a sharper or broader distribution than the training distribution. We build on the observation that these…
Thermoacoustic instabilities in gas turbines and aeroengine combustors falls within the category of complex systems. They can be described phenomenologically using nonlinear stochastic differential equations, which constitute the grounds…
This paper introduces an adaptive time splitting technique for the solution of stiff evolutionary PDEs that guarantees an effective error control of the simulation, independent of the fastest physical time scale for highly unsteady…
Measuring fluctuations in matter's low energy excitations is the key to unveil the nature of the nonequilibrium response of materials. A promising outlook in this respect is offered by spectroscopic methods that address matter fluctuations…
We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest…