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It is well known that energy dissipation and finite size can deeply affect the dynamics of granular matter, often making usual hydrodynamic approaches problematic. Here we report on the experi-mental investigation of a small model system,…
A funnel transformation is introduced, which acts recursively from higher towards lower temperatures. It biases the a-priori probabilities of a canonical or generalized ensemble Metropolis simulation, so that they zoom in on the global…
The rotating-wave approximation to light-matter interactions is widely used in the quantum electrodynamics Hamiltonian; however, its validity has long been a matter of debate. In this article, we explore the impact of the rotating-wave…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
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…
A generic algorithm for the extraction of probabilistic (Bayesian) information about model parameters from data is presented. The algorithm propagates an ensemble of particles in the product space of model parameters and outputs. Each…
A reliable and efficient computation of the entire single-particle spectrum of correlated molecules is an outstanding challenge in the field of quantum chemistry, with standard density functional theory approaches often giving an inadequate…
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be…
The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semi-volatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed…
We propose a very simple scheme to slow down the usual exponential decay of upper state population in an atomic two level system considerably. The scheme makes use of an additional intense field with frequency lower than the total decay…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior of macromolecules in solution or…
The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The…
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at biochemical and morphological levels. A…
Quantum annealing is a promising technique which leverages quantum mechanics to solve hard optimization problems. Considerable progress has been made in the development of a physical quantum annealer, motivating the study of methods to…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…