Related papers: Simultaneous identification of multiple binding si…
Doublon-holon dynamics is investigated in a pumped one-dimensional Hubbard model with a staggered on?site Coulomb interaction at half-filling. When the system parameters are set to be in the Mott insulating regime the equilibrium sublattice…
We present a nonlocal statistical field theory of a dilute electrolyte solution with small additive of dipolar particles. We postulate that every dipolar particle is associated with an arbitrary probability distribution function (PDF) of…
Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is dominated by long range hydro(phobic/philic)…
We study stability of superflow of Bose gases in optical lattices by analyzing the Bose-Hubbard model within the Gutzwiller mean-field approximation. We calculate the excitation spectra of the homogeneous Bose-Hubbard model at unit filling…
We examine the spectral structure and many-body dynamics of two and three repulsively interacting bosons trapped in a one-dimensional double-well, for variable barrier height, inter-particle interaction strength, and initial conditions. By…
The dynamics of dry active matter have implications for a diverse collection of biological phenomena spanning a range of length and time scales, such as animal flocking, cell tissue dynamics, and swarming of inserts and bacteria. Uniting…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
We study the statistical properties of hydrophobic/polar model sequences with unique native states on the square lattice. It is shown that this ensemble of sequences differs from random sequences in significant ways in terms of both the…
We study, by Monte Carlo simulations, a coarse-grained model of a water monolayer between hydrophobic walls at partial hydration, with a wall-to-wall distance of about 0.5 nm. We analyze how the diffusion constant parallel to the walls,…
Recent experimental advances in realizing degenerate quantum dipolar gases in optical lattices and the flexibility of experimental setups in attaining various geometries offer the opportunity to explore exotic quantum many-body phases…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
The standard Poisson-Boltzmann model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL)…
Colloidal aggregation could be implemented in various fields ranging from purely colloidal thermodynamics to protein interactions, their stability, and maybe folding. Indeed, colloidal aggregation is closely linked to the so-called…
We use lattice Boltzmann simulations, in conjunction with Ewald summation methods, to investigate the role of hydrodynamic interactions in colloidal suspensions of dipolar particles, such as ferrofluids. Our work addresses volume fractions…