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Microscopic surface diffusivity theory based on atomic ionization energy concept is developed to explain the variations of the atomic and displacement polarizations with respect to the surface diffusion activation energy of adatoms in the…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
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,…
Small-amplitude dynamic atomic force microscopy (dynamic-AFM) in a simple nonpolar liquid was studied through molecular dynamics simulations. We find that within linear dynamics regime, the contact stiffness and damping of the confined film…
Quantum-mechanical van der Waals dispersion interactions play an essential role for both intra-protein and protein-water interactions -- the two main driving forces for the structure and dynamics of proteins in aqueous solution. Typically,…
We carry out a comprehensive linear stability analysis of active Brownian particle systems around a constant homogeneous state. These scalar models, being important prototypes for the continuous description of active matter, are…
Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not…
We use state-of-the-art molecular dynamics simulations to study the effects of annealed disorder on the phase separating kinetics and aging phenomena of a segregating binary fluid mixture. In the presence of disorder, we observe a dramatic…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
It has been experimentally established in numerous cases that precipitation of monodispersed colloids from homogeneous solutions is a complex process. Specifically, it was found that in many systems nuclei, produced rapidly in a…
The control of biofilm formation is a challenging goal that has not been reached yet in many aspects. One is the role of van der Waals forces and another the importance of mutual interactions between the adsorbing and the adsorbed…
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed…
We consider a suspension of active rigid particles (swimmers) in a steady Stokes flow, where particles are distributed according to a stationary ergodic random process, and we study its homogenization in the macroscopic limit. A key point…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Colloidal nanoparticles, used for applications from catalysis and energy applications to cosmetics, are typically embedded in matrixes or dispersed in solutions. The entire particle surface, which is where reactions are expected to occur,…
Understanding the crystallization pathways of water-rich ammonia-water (NH3-H2O) solutions and the stability of ammonia hydrates is key to unraveling the behavior of complex hydrogen-bonding networks as well as for planetary interior…