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Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for com- plex fluid, is widely employed in non-equilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization…
Nonadiabatic molecular dynamics simulations aim to describe the coupled electron-nuclear dynamics of molecules in excited electronic states. These simulations have been applied to understand a plethora of photochemical and photophysical…
Active materials with distinctive nonequilibrium properties have diverse materials science applications. Active systems are common in living matter, such as the filament network in the cell that is activated by molecular motors, and in…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
The glass transition, extensively studied in dense fluids, polymers, or colloids, corresponds to a dramatic evolution of equilibrium transport coefficients upon a modest change of control parameter, like temperature or pressure. A similar…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
Intracellular transport is mediated by molecular motors that pull cargos along cytoskeletal filaments. Many cargos move bidirectionally and are transported by two teams of motors which move into opposite directions along the filament. We…
Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density-density correlations in…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Instabilities in thermodynamic systems are often undesirable, as they can lead to loss of control or even catastrophic behavior. Yet, the same mechanisms can also generate rich nonequilibrium behavior and may play a constructive role in…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Molecular dynamics simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous…
Electrochemical kinetics at electrode-electrolyte interfaces are crucial to understand high-rate behavior of energy storage devices. Phase transformation of electrodes is typically treated under equilibrium thermodynamic conditions, while…
Spectroscopy is a crucial laboratory technique for understanding quantum systems through their interactions with electromagnetic radiation. Particularly, spectroscopy is capable of revealing the physical structure of molecules, leading to…
The main subject of this thesis rests on the study ---at different levels of description--- of instabilities in systems which are driven, i.e., maintained far from equilibrium by an external forcing. We focus here on two main classes,…
Controlling the non adiabatic dynamics of isolated quantum systems driven through a critical point is of interest in a variety of fields ranging from quantum simulation to finite-time thermodynamics. We briefly review the different methods…