Related papers: Atomistic simulations of rare events using gentles…
The theoretical investigation of gas adsorption, storage, separation, diffusion and related transport processes in porous materials relies on a detailed knowledge of the potential energy surface of molecules in a stationary environment. In…
We report the development of programs for on-the-fly surface hopping dynamics simulations in the gas and condensed phases on the potential energy surfaces computed by multistate multireference perturbation theory (XMS-CASPT2) with full…
The glass transition of supercooled fluids is a particular challenge for computer simulation, because the (longest) relaxation times increase by about 15 decades upon approaching the transition temperature T_g. Brute-force molecular…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
This work shows that applying Gradient Descent (GD) with a fixed step size to minimize a (possibly nonconvex) quadratic function is equivalent to running the Power Method (PM) on the gradients. The connection between GD with a fixed step…
Complex spectra of dissipative quantum systems may exhibit degeneracies known as exceptional points (EPs). At these points the systems' dynamics may undergo drastic changes. Phenomena associated with EPs and their applications have been…
We describe the newly written code GADGET which is suitable both for cosmological simulations of structure formation and for the simulation of interacting galaxies. GADGET evolves self-gravitating collisionless fluids with the traditional…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
Stochastic dynamical systems arise as models for fluid particle motion in geophysical flows with random velocity fields. Escape probability (from a fluid domain) and mean residence time (in a fluid domain) quantify fluid transport between…
We numerically study the potential energy landscape of a fragile glassy system and find that the dynamic crossover corresponding to the glass transition is actually the effect of an underlying geometric transition caused by a qualitative…
First conceived as a topological construction, Wada basins abound in dynamical systems. Basins of attraction showing the Wada property possess the particular feature that any small perturbation of an initial condition lying on the boundary…
Jumps between neighboring minima in the energy landscape of both homopolymeric and heteropolymeric chains are numerically investigated by determining the average escape time from different valleys. The numerical results are compared to the…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Facilitated spin models were introduced some decades ago to mimic systems characterized by a glass transition. Recent developments have shown that a class of facilitated spin models is also able to reproduce characteristic signatures of the…
Fault systems have geometrically complex structures in nature, such as stepovers, bends, branches, and roughness. Many geological and geophysical studies have shown that the geometrical complexity of fault systems in nature decisively…
Equilibration dynamics of hot oxygen atoms following O2 dissociation on Pd(100) and Pd(111) surfaces are investigated by molecular dynamics simulations based on a scalable neural network potential enabling first-principles description of O2…
Granular systems confined in vertically vibrated shallow horizontal boxes (quasi two-dimensional geometry) present a liquid to solid phase transition when the frequency of the periodic forcing is increased. An effective model, where grains…
Molecular dynamics simulations are used to generate an ensemble of saddles of the potential energy of a Lennard-Jones liquid. Classifying all extrema by their potential energy u and number of unstable directions k, a well defined relation…
We perform molecular dynamics simulation of a small number of particles in a box with periodic boundary conditions from a view point of chaotic dynamical systems. There is a transition at a critical energy E_c that each particle is confined…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…