Related papers: Selection originating from protein foldability: I.…
We used statistical thermodynamics of conformational fluctuations and the elements of algebraic graph theory together with data from 2000 protein crystal structures, and showed that folded native proteins with harmonic interactions exhibit…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
We propose a new formulation of the fluctuating lattice Boltzmann equation that is consistent with both equilibrium statististical mechanics and fluctuating hydrodynamics. The formalism is based on a generalized lattice-gas model, with each…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
The change of the vibrational energy within a molecule after collisions with another molecule plays an essential role in the evolution of molecular internal energy distributions, which is also the limiting process in the relaxation of the…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
Experimental studies of the glassy slowdown in molecular liquids indicate that the high-temperature activation energy $E_{\infty}$ of glass-forming liquids is directly related to their glass transition temperature $T_{\text{g}}$. To further…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
During the synthesis of integral membrane proteins (IMPs), the hydrophobic amino acids of the polypeptide sequence are partitioned mostly into the membrane interior and hydrophilic amino acids mostly into the aqueous exterior. We analyze…
We examine the relaxation of the Kob-Andersen Lennard-Jones binary mixture using Brownian dynamics computer simulations. We find that in accordance with mode-coupling theory the self-diffusion coefficient and the relaxation time show…
The experimental calorimetric two-state criterion requires the van't Hoff enthalpy $\Delta H_{\rm vH}$ around the folding/unfolding transition midpoint to be equal or very close to the calorimetric enthalpy $\Delta H_{\rm cal}$ of the…
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
Atom-molecule equilibrium for molecular formation processes is discussed for boson-fermion, fermion-fermion, and boson-boson mixtures of ultracold atomic gases in the framework of quasichemical equilibrium theory. After presentation of the…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
The issue of the thermodynamics of a system of distinguishable particles is discussed in this paper. In constructing the statistical mechanics of distinguishable particles from the definition of Boltzmann entropy, it is found that the…
Observational entropy -- a quantity that unifies Boltzmann's entropy, Gibbs' entropy, von Neumann's macroscopic entropy, and the diagonal entropy -- has recently been argued to play a key role in a modern formulation of statistical…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…