Related papers: ATP binding to a multisubunit enzyme: statistical …
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
For the system with inhomogeneous distribution of macroscopic parameters we obtain thermodynamic relation which depends on the spatial point (coordinate). In our approach, to obtain such a relation we use the basic ideas of the method of…
Mismatch repair is a critical step in DNA replication that occurs after base selection and proofreading, significantly increasing fidelity. However, the mechanism of mismatch recognition has not been established for any repair enzyme.…
In this paper we obtain the first general multi-component solution to thermodynamic perturbation theory for the case that molecules can participate in cyclic double bonds. In contrast to previous authors, we do not restrict double bonding…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
The extension of thermodynamic principles to active matter remains a challenge due to the non-equilibrium nature inherent to active systems. In this study, we introduce a framework to assess entropy in our minimal macroscopic experiment…
The past two decades have seen a revolution in statistical physics, generalizing it to apply to systems of arbitrary size, evolving while arbitrarily far from equilibrium. Many of these new results are based on analyzing the dynamics of the…
The paper moves a step towards the full integration of statistical mechanics and information theory. Starting from the assumption that the thermodynamical system is composed by particles whose quantized energies can be modelled as…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
Many dynamical systems consist of multiple, co-evolving subsystems (degrees of freedom). These subsystems often depend upon each other in a way that restricts the overall system's dynamics. How does this network of dependencies affect the…
Ability of dynamical systems to relax to equilibrium has been investigated since the invention of statistical mechanics, which establishes the connection between dynamics of many-body Hamiltonian systems and phenomenological thermodynamics.…
An ensemble of classical subsystems interacting with surrounding particles has been considered. In general case, a phase volume of the subsystems ensemble was shown to be a function of time. The evolutional equations of the ensemble are…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
Adaptive humoral immunity, from the physical perspective, can be regarded as the self-organization of the binding energy landscape of antibodies. In biological terms, the humoral immune system evolves and adapts its repertoire of antigen…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…