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We recently introduced a wave-mechanical model for quasi-elastic neutron scattering (QENS) in proteins. We call the model ELM for "Energy Landscape Model". We postulate that the spectrum of the scattered neutrons consists of lines of…
We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…
A novel formulation of the electron energy relaxation terms is presented here, which is applicable to plasma flows and discharges wherein the electron temperature could be higher or lower than the gas temperature. It is demonstrated that…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
The soft diffraction phenomena in the elastic proton-proton scattering are reviewed from the viewpoint of experiments at the LHC (TOTEM and ATLAS collaboration). In the framework of the High Energy Generalized Structure (HEGS) model the…
Employing a recently-developed dispersive optical model (DOM) which allows a complete description of experimental data both above (up to 200 MeV) and below the Fermi energy in $^{40}$Ca, we demonstrate that elastic nucleon-nucleus…
Recently a variety of studies have shown the importance of including non-locality in the description of reactions. The goal of this work is to revisit the phenomenological approach to determining non-local optical potentials from elastic…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
It is widely held that the Random Energy Model (REM) describes the freezing transition of a variety of types of heteropolymers. We demonstrate that the hallmark property of REM, statistical independence of the energies of states over…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
Elastic scattering data gained for proton-proton collisions at high energies are being analyzed at the present practically only with the help of purely phenomenological mathematical models. And the question exists whether in the impact…
Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally…
Based on the behavior of the elastic scattering data, we introduce an almost model-independent parametrization for the imaginary part of the scattering amplitude, with the energy and momentum transfer dependences inferred on empirical basis…
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…