Related papers: Field theory of enzyme-substrate systems with rest…
Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…
Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding…
A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules.…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
A general approach to the design of accurate classical potentials for protein folding is described. It includes the introduction of a meaningful statistical measure of the differences between approximations of the same potential energy, the…
We calculate real-space static correlation functions related to basic entities of the one-dimensional Hubbard model, which emerge from the exact Bethe-ansatz solution. These entities involve complex rearrangements of the original electrons.…
The Self Consistent Random Phase Approximation (SCRPA) and a Direct Analytical (DA) method are proposed to solve the Extended Hubbard Model in 1D. We have considered an Extended Hubbard Model (EHM) including on-site and off-site…
Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, we push composites of circular…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…
Substrate modification networks are ubiquitous in living, biochemical systems. A higher-level hypergraph "skeleton" captures key information about which substrates are transformed in the presence of modification-specific enzymes. Many…
The effective interaction between two probe particles in a one-dimensional driven system is studied. The analysis is carried out using an asymmetric simple exclusion process with nearest-neighbor interactions. It is found that the driven…
Enzyme-enriched condensates can organize the spatial distribution of their substrates by catalyzing non-equilibrium reactions. Conversely, an inhomogeneous substrate distribution induces enzyme fluxes through substrate-enzyme interactions.…
We study the pinning of a two-dimensional membrane to a patterned substrate within elastic theory both in the bending rigidity and in the strain dominated regimes. We find that both the in-plane strains and the bending rigidity can lead to…
We complete the existing literature on the kinetic theory of systems with long-range interactions. Starting from the BBGKY hierarchy, or using projection operator technics or a quasilinear theory, a general kinetic equation can be derived…
The Lieb-Schultz-Mattis (LSM) theorem asserts that microscopic details of the system can impose non-trivial constraints on the system's low-energy properties. While traditionally applied to short-range interaction systems, where locality…