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The field of synthetic active matter has, thus far, been led by efforts to create point-like, isolated (yet interacting) self-propelled objects (\emph{e.g.} colloids, droplets, microrobots) and understanding their collective dynamics. The…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
Complex fluids, such as polymer solutions and blends, colloids and gels, are of growing interest in fundamental and applied soft-condensed-matter science. A common feature of all such systems is the presence of a mesoscopic structural…
Exciton-exciton annihilation is a ubiquitous nonlinear dynamical phenomenon in materials hosting Frenkel excitons, that has been employed to probe exciton diffusion processes in conjugated polymeric materials. In this work, we investigate…
The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers depends on molecular motion over distances of the order of 1-2 nm. From the concentration dependence of the excimer photoemission curve, it is possible to derive a…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
The expulsion dynamics of the last liquid monolayer of molecules confined between two surfaces has been analyzed by solving the two-dimensional (2D) Navier-Stokes equation for a compressible liquid. We find that the squeeze-out is…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
We present a new and straightforward algorithm that simulates exact sample paths for a generalized stress-release process. The computation of the exact law of the joint interarrival times is detailed and used to derive this algorithm.…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
In this paper, we suggest a novel sampling method for Monte Carlo molecular simulations. In order to perform efficient sampling of molecular systems, it is advantageous to avoid extremely high energy configurations while also retaining the…
In recent years, pre-trained multimodal large models have attracted widespread attention due to their outstanding performance in various multimodal applications. Nonetheless, the extensive computational resources and vast datasets required…
We investigate the ejection dynamics of a ring polymer out of a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. The ejection dynamics for ring polymers shows two regimes like for…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Motivated by the experiments on DNA under torsion, we consider the problem of pulling a polymer out of a potential well by a force applied to one of its ends. If the force is less than a critical value, then the process is activated and has…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
We discuss the simulation methods and results for the crystal extraction experiments performed recently at the high energy accelerators. Possible future applications of the crystal channeling technique are considered.
The Gas-Kinetic Scheme (GKS), widely used in computational fluid dynamics for simulating hypersonic and other complicated flow phenomena, is extended in this work to electromagnetic problems by solving Maxwell's equations. In contrast to…