Related papers: Selection originating from protein foldability: I.…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We propose a replica-exchange method (REM) which does not use pseudo random numbers. For this purpose, we first give a conditional probability for Gibbs sampling replica-exchange method (GSREM) based on the heat bath method. In GSREM,…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Exploiting the similarity between the bunched single-particle energy levels of nuclei and of random distributions around the Fermi surface, pairing properties of the latter are calculated to establish statistically-based bounds on the basic…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Accurately predicting protein melting temperature changes (Delta Tm) is fundamental for assessing protein stability and guiding protein engineering. Leveraging multi-modal protein representations has shown great promise in capturing the…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
Many of the existing stochastic models of gene expression contain the first-order decay reaction term that may describe active protein degradation or dilution. If the model variable is interpreted as the molecule number, and not…
It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside…
Protein Folding is concerned with the reasons and mechanism behind a protein's tertiary structure. The thermodynamic hypothesis of Anfinsen postulates an universal energy function (UEF) characterizing the tertiary structure, defined…
Exact and approximate expressions for thermodynamic characteristics of heated matter, which consists of particles with finite mass-widths, are constructed. They are expressed in terms of Fermi/Bose distributions and spectral functions,…
A possible approach to the statistical description of granular assemblies starts from Edwards' assumption that all blocked states occupying the same volume are equally probable (S.F. Edwards, R. Oakeshott, Physica A 157, 1080 (1989)). We…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Temperature of a finite-sized system fluctuates due to the thermal fluctuations. However, a systematic mathematical framework for measuring or estimating the temperature is still underdeveloped. Here, we incorporate the estimation theory in…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…