Related papers: ATP binding to a multisubunit enzyme: statistical …
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
In traditional thermodynamical and statistical-mechanical approaches one has (some) detailed knowledge of the principles governing the microdynamics of a system. However in many instances we may not have a Hamiltonian or good information…
We consider viscous, heat conducting mixtures of molecularly miscible chemical species forming a fluid in which the constituents can undergo chemical reactions. Assuming a common temperature for all components, we derive a closed system of…
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in…
We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple…
Predicting ATP-Protein Binding sites in genes is of great significance in the field of Biology and Medicine. The majority of research in this field has been conducted through time- and resource-intensive 'wet experiments' in laboratories.…
The paper is devoted to further development of the new approach in equilibrium statistical mechanics the basis of which was worked out in a series of articles by the author. The approach proceeds on the use of a hierarchy of equations for…
We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
We consider a Brownian particle confined by an external potential and subject to stochastic resetting to the origin. Motivated by the repetitive nature of the dynamics, we describe the process as a thermodynamic cycle of thermal expansion…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
The Fermi liquid theory may provide a good description of the thermodynamic properties of an interacting particle system when the interaction between the particles contributes to the total energy of the system with a quantity which may…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
We develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…
Quantitative models of associative learning that explain the behavior of real animals with high precision have turned out very difficult to construct. We do this in the context of the dynamics of the thermal preference of C. elegans. For…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
Some deterministic cellular automata have been observed to follow the pattern of the second law of thermodynamics: starting from a partially disordered state, the system evolves towards a state of equilibrium characterized by maximal…
We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of…
Entropy is one of the key thermodynamic variables reflecting changes in the state of matter. Unlike other thermodynamic variables, it is well-defined also for nonequilibrium steady states through its relation to information. Applying this…