Related papers: Finite-temperature local protein sequence alignmen…
The critical point is a fixed point in finite-size scaling. To quantify the behaviour of such a fixed point, we define, at a given temperature and scaling exponent ratio, the width of scaled observables for different sizes. The minimum of…
We consider the statistical mechanics of a classical particle in a one-dimensional box subjected to a random potential which constitutes a Wiener process on the coordinate axis. The distribution of the free energy and all correlation…
In Stochastic Thermodynamics, heat is a random variable with a probability distribution associated. Studies of the distribution of heat are mostly in the overdamped regime and in one dimension. Here we solve the heat distribution in the…
The optimal design of power converters requires accurate knowledge of the dissipation elements of its system to achieve the desired performance and security requirements. Calorimetric methods have surpassed classical electrical methods for…
A dynamic linear thermo-poroelasticity model, containing inertial and relaxation terms with second-order time derivatives, is investigated in this paper. The mathematical and numerical analysis of this model is performed in the frequency…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Some lattice models having two conservation laws may display an equilibrium phase transition from a homogeneous (positive temperature - PT) to a condensed (negative temperature) phase, where a finite fraction of the energy is localized in a…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…
The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density…
We suggest that if a localized phase at nonzero temperature $T>0$ exists for strongly disordered and weakly interacting electrons, as recently argued, it will also occur when both disorder and interactions are strong and $T$ is very high.…
We present a massively parallel algorithm for calculating the self-energy in self-consistent finite temperature perturbation theory for lattice models. The algorithm uses analytic functions with appropriate asymptotic high frequency…
In this study, internal energy (U), electric field (E) and particle number (N) which specify the system quantities i.e. thermodynamical quantities for the proteins. In the frame of thermodynamical formalism, the relation between the heat…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…
Long linear polymers in dilute solutions are known to undergo a collapse transition from a random coil (expand itself) to a compact ball (fold itself up) when the temperature is lowered, or the solvent quality deteriorates. A natural model…
Exact free energy minimization is a convex optimization problem that is usually approximated with stochastic sampling methods. Deterministic approximations have been less successful because many desirable properties have been difficult to…
We provide a rigorous and asymptotically exact expression of the mutual information of translationally invariant free fermionic lattice systems in a Gibbs state. In order to arrive at this result, we introduce a novel frameworkfor computing…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…