Related papers: Cooperative Function with Thermal Fluctuations in …
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Metal to insulator transitions (MITs) driven by strong electronic correlations are common in condensed matter systems, and are associated with some of the most remarkable collective phenomena in solids, including superconductivity and…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
In this note we discuss a paradigmatic example of interacting particles subject to non conservative external forces and to the action of thermostats consisting of external (finite) reservoirs of particles. We then consider a model of…
We report the results of molecular dynamics simulations of the protein myosin carried out with an elastic network model. Quenching the system, we observe glassy behavior of a density correlation function and a density response function that…
We study mesoscopic fluctuations of the conductance through a quantum dot at the wings of the Coulomb blokade peaks. At low temperatures, the main mechanism of conduction is the elastic cotunneling. The conductance strongly fluctuates with…
Colloidal gel networks are disordered elastic solids that can form even in extremely dilute particle suspensions. With interaction strengths comparable to the thermal energy, their stress-bearing network can locally restructure via breaking…
We examine a biomolecular machine involving a driven, observable process coupled to a hidden process in a kinetically cooperative manner. A stochastic thermodynamics framework is employed to analyze a fluctuation theorem for the…
We report a theoretical study of the thermopower of single-molecule junctions, with focus on phenyl-based molecular junctions. In contrast to prior studies, thermal fluctuations of the torsional angle between the phenyl rings and variations…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
We study how the degree of ordering depends on the strength of the thermal and quantum fluctuations in frustrated systems by investigating the correlation function of the order parameter. Concretely, we compare the equilibrium spin…
From synthetic active devices such as self-propelling Janus colloids to micro-organisms like bacteria, micro-algae, living cells in tissues, active fluctuations are ubiquitous. Thermodynamics of small systems involving thermal as well as…
We study the origin of the cooperative nature of spin crossover (SC) between low spin (LS) and high spin (HS) states from the view point of elastic interactions among molecules. As the size of each molecule changes depending on its spin…
In this article, addressing large $n$ systems, we report that in numerous systems hosting long and short range interactions, multiple correlation lengths may appear. The largest correlation lengths often monotonically increase with…
Elastic metamaterials are often designed for a single permanent function. We explore the possibility of altering a material's function repeatedly through a self-organization, "training" process, controlled by applied strains. We show that…
The concept of communicability is introduced for complex socio-economic networks. The communicability function expresses how an impact propagates from one place to another in the network. This function is used to define unambiguously the…
In this paper, we applied a deep neural network to study the issue of knowledge transferability between statistical mechanics models. The following computer experiment was conducted. A convolutional neural network was trained to solve the…
Vitrimers, an important subset of dynamically crosslinked polymer networks, have many technological applications for their excellent properties, and the ability to be re-processed through plastic flow above the so-called vitrification…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…