Related papers: Guessing the upper bound free-energy difference be…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
New definitions of the structural susceptibilities based on the fluctuations of distances to the native state of toy protein models are proposed. The calculation of such susceptibilities does not require the basin of native state and the…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
An approach to implementing variational Bayesian inference in biological systems is considered, under which the thermodynamic free energy of a system directly encodes its variational free energy. In the case of the brain, this assumption…
The thermodynamic properties of superconducting electrons are usually studied by means of the quasi-particles distribution; but in this approach, the ground state energy and the dependence of the chemical potential on the electron density…
A bound state problem in a topologically massive quantum electrodynamics is investigated by using a non-perturbative method. We formulate the Bethe- Salpeter equation for scalar bound states composed of massive fermion and anti-fermion pair…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
We divide the free energy near the critical point into two parts. One is the regular part, the other is the singular part. The singular part is assumed to be a concrete possible form. The singular part in this form is different from Widom…
We introduce an effective thermodynamics for multipartite entangled pure states and derive an upper bound on extractable energy with feedback control from a subsystem under a local Hamiltonian. The inequality that gives the upper bound…
This work explores fundamental statistical and thermodynamic properties of short-and long-range-interacting systems. The purpose of this study is twofold. Firstly, we rigorously prove that the probability distribution of arbitrary few-body…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…
It is possible to formulate the thermodynamics of a glass forming system in terms of the properties of inherent structures, which correspond to the minima of the potential energy and build up the potential energy landscape in the…
We study Derrida's generalized random energy model in the presence of uniform external field. We compute the fluctuations of the ground state and of the partition function in the thermodynamic limit for all admissible values of parameters.…
We present an exact treatment of the thermodynamics of physical systems in the framework of the generalized uncertainty principle (GUP). Our purpose is to study and compare the consequences of two GUPs that one implies a minimal length…
The thermodynamics for a system with given temperature, density, and volume is described by the Canonical ensemble. The thermodynamics for a corresponding system with the same temperature, volume, and average density is described by the…
In this work we show that there is a direct relationship between a graph's topology and the free energy of a spin system on the graph. We develop a method of separating topological and enthalpic contributions to the free energy, and find…