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Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
The adhesion of biological membranes is controlled by various types of receptor and ligand molecules. In this letter, we present a statistical-mechanical model for membranes that interact via receptor/ligand bonds of two different lengths.…
Multisite protein modification is a ubiquitous mechanism utilized by cells to control protein functions. We have recently proposed a dynamical description of multisite protein modification which embodies all the essential features of the…
Doped free carriers can substantially renormalize electronic self-energy and quasiparticle band gaps of two-dimensional (2D) materials. However, it is still challenging to quantitatively calculate this many-electron effect, particularly at…
In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamic simulations. In these models, the two…
We devise a method for predicting certain receptor-ligand binding behaviors, based on stochastic dynamical modelling. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform…
The field of protein-ligand pose prediction has seen significant advances in recent years, with machine learning-based methods now being commonly used in lieu of classical docking methods or even to predict all-atom protein-ligand complex…
The increased complexity of infrastructure systems has resulted in critical interdependencies between multiple networks---communication systems require electricity, while the normal functioning of the power grid relies on communication…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
We introduce a derangement model of ligand-receptor binding that allows us to quantitatively frame the question "How can ligands seek out and bind to their optimal receptor sites in a sea of other competing ligands and suboptimal receptor…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
We formulate an analytical recursive method to generate the wave function of doped short-range resonating valence bond (RVB) states as a tool to efficiently estimate multisite entanglement as well as other physical quantities in doped…
Single receptor-ligand bonds have finite lifetimes, so that biological systems can dynamically react to changes in their environment. In cell adhesion, adhesion bonds usually act cooperatively in adhesion clusters. Outside the cellular…
We show that multiplexing allows to control noise-induced dynamics of multilayer networks in the regime of stochastic resonance. We illustrate this effect on an example of two- and multi-layer networks of bistable overdamped oscillators. In…
A very stable binding site for the interaction between an pentameric oligothiophene and an amyloid-$\beta$(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an…
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic…
Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a…
Biological sensory systems generally operate out of equilibrium, which often leads to their improved performance. Here, we study the sensitivity of ligand concentration for a general receptor model, which is generally in the non-equilibrium…
It is rigorously shown that the fluctuation formula, which is used in simulations to calculate the dielectric constant of interaction site models, corresponds to the reaction field with an individual site cut-off rather than with the usual…