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Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…
In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamic simulations. In these models, the two…
We develop a stochastic theory that treats time-dependent exciton-exciton s-wave scattering and that accounts for dynamic Coulomb screening, which we describe within a mean-field limit. With this theory, we model excitation-induced…
Kinetics of collision-sticking processes between vapor molecules and molecular clusters of low volatile compounds facilitates the initial steps of atmospheric clustering. Conventional theoretical models are quite inaccurate due to the…
Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…
The recently developed Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and…
We investigate the convergence of solutions of a recently proposed diffuse interface/phase field model for cell blebbing by means of matched asymptotic expansions. It is a biological phenomenon that increasingly attracts attention by both…
We study the nonequilibrium phase transition in the one-dimensional contact process with quenched spatial disorder by means of large-scale Monte-Carlo simulations for times up to $10^9$ and system sizes up to $10^7$ sites. In agreement with…
Recently one has stated that temporal disorder constitutes a relevant perturbation in absorbing phase transitions for all dimensions. However, its effect for systems other than the standard contact process (CP), its competition with other…
Diffusion models have emerged as a leading framework in generative modeling, poised to transform the traditionally slow and costly process of drug discovery. This review provides a systematic comparison of their application in designing two…
We present simulation results for the contact process on regular, cubic networks that are composed of a one-dimensional lattice and a set of long edges with unbounded length. Networks with different sets of long edges are considered, that…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
In absence of advection, reaction-diffusion systems are able to organize into spatiotemporal patterns, in particular spiral and target waves. Whenever advection is present and can be parameterised in terms of effective or turbulent…
We present dynamic light scattering (DLS) measurements of soft polymethyl-methacrylate (PMMA) and polyacrylamide(PA) polymer gels prepared with trapped bodies (latex spheres or maghemite nanoparticles). We show that the anomalous…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…
We consider a general discrete model for heterogeneous semiflexible polymer chains. Both the thermal noise and the inhomogeneous character of the chain (the disorder) are modeled in terms of random rotations. We focus on the quenched…
Hydrodynamic interactions between particles confined in a liquid-filled linear channel are known to be screened beyond a distance comparable to the channel width. Using a simple analytical theory and lattice-Boltzmann simulations, we show…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…