相关论文: Peptide Conformational Equilibria Computed via a S…

A two-dimensional system of differential equations with delay modelling the glucose-insulin interaction processes in the human body is considered. Sufficient conditions are derived for the unique positive equilibrium in the system to be…

A non-equilibrium steady state is characterized by a non-zero steady dissipation rate. Chemical reaction systems under suitable conditions may generate such states. We propose here a method that is able to distinguish states with identical…

We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…

Alternative approach for description of the non-equilibrium phenomena arising in solids at a severe external loading is analyzed. The approach is based on the new form of kinetic equations in terms of the internal and modified free energy.…

Analytical equations were found for interdigitated electrodes, which considered reversible electrode reactions and pure diffusion within confined spaces. A conformal transformation, obtained by the use of Jacobian elliptic functions, was…

The phase transitions in a realistic system with triplet pairing, dense neutron matter, have been investigated. The spectrum of phases of the $^3P_2-^3F_2$ model, which adequately describes pairing in this system, is analytically…

We consider systematic numerical approximation of a viscoelastic phase separation model that describes the demixing of a polymer solvent mixture. An unconditionally stable discretisation method is proposed based on a finite element…

A simultaneous variational principle is introduced that offers a novel avenue to the description of the equilibrium configurations, and at the same time of the elementary excitations, or undulations, of fluid lipid membranes, described by a…

We study the adsorption-desorption of fluid molecules on a solid substrate by introducing a schematic model in which the adsorption/desorption transition probabilities are given by irreversible kinetic constraints with a tunable violation…

The flexibility of the DPG methodology is exposed by solving the linear elasticity equations under different variational formulations, including some with non-symmetric functional settings (different infinite-dimensional trial and test…

We present an algorithm for recovering planted solutions in two well-known models, the stochastic block model and planted constraint satisfaction problems, via a common generalization in terms of random bipartite graphs. Our algorithm…

Differential equations (DE) constrained optimization plays a critical role in numerous scientific and engineering fields, including energy systems, aerospace engineering, ecology, and finance, where optimal configurations or control…

We consider the numerical solution of coupled volume-surface reaction-diffusion systems having a detailed balance equilibrium. Based on the conservation of mass, an appropriate quadratic entropy functional is identified and an…

This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…

Finding better solutions to combinatorial optimization problems could have a large positive impact on many real-world application areas, such as logistics. For this reason, significant efforts have been made to design novel optimisation…

It is known that binding energies calculated from the Bethe-Salpeter equation in ladder approximation can be reasonably well accounted for by an energy-dependent interaction, at least for the lowest states. It is also known that none of…

Microscopic formula to describe the entropy of biomolecular solutions are derived based on the Gibbs formula of entropy, and the generalized Langevin theory combined with the RISM/3D-RISM theory. Two formula are derived: one is concerned…

In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…

In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…

We introduce a new $hp$-adaptive strategy for self-adjoint elliptic boundary value problems that does not rely on using classical a posteriori error estimators. Instead, our approach is based on a generally applicable prediction strategy…