相关论文: Equilibrium study of Protein/DNA Complexes from Cr…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
We consider the relationship between thermodynamics, fitness, and Darwinian selection in autocatalytic molecular replicators. We uncover a thermodynamic bound that relates fitness, replication rate, and thermodynamic affinity of…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…
The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
A number of successful theoretical models of hardness have been developed recently. A thermodynamic model of hardness, which supposes the intrinsic character of correlation between hardness and thermodynamic properties of solids, allows one…
The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The…
Conventional methods to calculate the thermodynamics of crystals evaluate the harmonic phonon spectra and therefore do not work in frequent and important situations where the crystal structure is unstable in the harmonic approximation, such…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in…
To sample rare events, dissipation-corrected targeted molecular dynamics (dcTMD) applies a constant velocity constraint along a one-dimensional reaction coordinate $s$, which drives an atomistic system from an initial state into a target…
In this study, we propose a theoretical framework to investigate the interactions between flexible polymer chains, specifically polyelectrolytes (PEs). By calculating the system's free energy while considering position-dependent mutual…
We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind…
When we consider five-dimensional warped Taub-NUT/Bolt AdS black string with minimally coupled massive scalar field, we calculate entropy by using the brick wall method. It is found that they are proportional to being quadratically…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the…
For classical discrete systems under constant composition, a set of microscopic state dominantly contributing to thermodynamically equilibrium structure should depend on temperature and energy through Boltzmann factor, exp(-bE). Despite…