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We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins such as human serum albumin (HSA) or lysozyme with linear…
Two models for energy and charge transport and storage in biomolecules are considered. A model based on the discrete nonlinear Schrodinger equation with long-range dispersive interactions (LRI's) between base pairs of DNA is offered for the…
Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…
Increasing the size of a Transformer does not always lead to enhanced performance. This phenomenon cannot be explained by the empirical scaling laws. Furthermore, the model's enhanced performance is closely associated with its memorization…
Under many conditions, biomolecules and nanoparticles associate by means of attractive bonds, due to hydrophobic attraction. Extracting the microscopic association or dissociation rates from experimental data is complicated by the…
Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling…
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…
Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction…
Mechanical loading generally weakens adhesive structures and eventually leads to their rupture. However, biological systems can adapt to loads by strengthening adhesions, which is essential for maintaining the integrity of tissue and whole…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
We use quantum and classical adiabatic capture theories to study the chemical reaction Li + CaH -> LiH + Ca. Using a recently developed ab initio potential energy surface, which provides an accurate representation of long-range interactions…
Molecular adhesion plays a central role in many biological systems, yet existing methods to quantify adhesive strength often struggle to bridge the gap between single-molecule resolution and biologically relevant environments. Here, we…
The Gibbs free energy of transferring a solute at infinite dilution between two solvents quantifies differences in solute-solvent interactions $-$ if the transfer takes place at constant molarity of the solute. Yet, many calculation…
One strategy to scale up ML-driven science is to increase wet lab experiments' information density. We present a method based on a neural extension of compressed sensing to function space. We measure the activity of multiple different…
We discuss the relaxation kinetics of a one-dimensional dimer adsorption model as recently proposed for the binding of biological dimers like kinesin on microtubules. The non-equilibrium dynamics shows several regimes: irreversible…
The first LHC results at 7-8 TeV, with the discovery of a candidate Higgs boson and the non observation of new particles or exotic phenomena, have made a big step towards completing the experimental confirmation of the Standard Model (SM)…
In the first part of this paper we give a short review of the hierarchy of stochastic models, related to physical chemistry. In the basement of this hierarchy there are two models --- stochastic chemical kinetics and the Kac model for…
Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these responses come about and how they can be harnessed, we develop…
In order to get insight into the connection between the vibrational dynamics and the atomic level Green-Kubo stress correlation function in liquids we consider this connection in a model crystal instead. Of course, vibrational dynamics in…
The fundamental law for protein folding is the Thermodynamic Principle: the amino acid sequence of a protein determines its native structure and the native structure has the minimum Gibbs free energy. If all chemical problems can be…