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The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution…
It is now well accepted that cellular responses to materials in a biological medium reflect greatly the adsorbed biomolecular layer, rather than the material itself. Here, we study by molecular dynamic simulations the competitive protein…
Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a…
An ultra-strong photovoltaic effect has recently been reported for electrons trapped on a liquid Helium surface under a microwave excitation tuned at intersubband resonance [D. Konstantinov et. al. : J. Phys. Soc. Jpn. 81, 093601 (2012) ].…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
We investigate the quantum dynamics of ultra-long-range trilobite molecules exposed to homogeneous electric fields. A trilobite molecule consists of a Rydberg atom and a ground-state atom, which is trapped at large internuclear distances in…
A multiple-image method is developed to accurately calculate the electrostatic interaction between neutral dielectric particles and a uniformly charged dielectric substrate. The difference in dielectric constants between the particle and…
The ab-initio computational treatment of electrochemical systems requires an appropriate treatment of the solid/liquid interfaces. A fully quantum mechanical treatment of the interface is computationally demanding due to the large number of…
Classical theory of the electric double layer is based on the fundamental assumption of a dilute solution of point ions. There are a number of situations such as high applied voltages, high concentration of electrolytes, systems with…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…
A model for ionic and electronic grain boundary transport through thin films, scales or membranes with columnar grain structure is introduced. The grain structure is idealized as a lattice of identical hexagonal cells - a honeycomb pattern.…
While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…
We address the problem of proteasomal protein translocation and introduce a new stochastic model of the proteasomal digestion (cleavage) of proteins. In this model we account for the protein translocation and the positioning of cleavage…
The electronic conductance of a molecule making contact to electrodes is determined by the coupling of discrete molecular states to the continuum electrode density of states. Interactions between bound states and continua can be modeled…
Finding the "ideal" catalyst is a matter of great interest in the communities of chemists and material scientists, partly because of its wide spectrum of industrial applications. Information regarding a physical parameter termed "adsorption…