相关论文: Peptide Conformational Equilibria Computed via a S…
Nonequilibrium systems, in particular living organisms, are maintained by irreversible transformations of energy that drive diverse functions. Quantifying their irreversibility, as measured by energy dissipation, is essential for…
Using the Gaussian Ansatz for the monomer-monomer correlation functions we derive a set of the self-consistent equations for determination of the conformational state in the bead-and-spring copolymer model. The latter is based on the…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
We provide a complete thermodynamic solution of a 1D hopping model in the presence of a random potential by obtaining the density of states. Since the partition function is related to the density of states by a Laplace transform, the…
We present analytical results for the time-dependent information entropy in exactly solvable two-state (qubit) models. The first model describes dephasing (decoherence) in a qubit coupled to a bath of harmonic oscillators. The entropy…
A binary liquid near its consolute point exhibits critical fluctuations of the local composition; the diverging correlation length has always challenged simulations. The method of choice for the calculation of critical points in the phase…
Two identities in statistical mechanics involving entropy differences (or ratios of density of states) at constant energy are derived. The first provides a nontrivial extension of the Jarzynski equality to the microcanonical ensemble [C.…
Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using…
We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are…
Predicting changes in binding free energy ($\Delta\Delta G$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $\Delta\Delta…
To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a…
This work inspects the thermally activated transfer of solute particles across the interface between two interstitial solid solution phases that equilibrate internally by fast diffusion on conserved arrays of sites. When each phase is…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
Molecular computing promises massive parallelization to explore solution spaces, but so far practical implementations remain limited due to off-target binding and exponential proliferation of competing structures. Here, we investigate the…
Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
A lattice based model of a protein is used to study the dimerization equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to determine the free energy of both the monomeric and dimeric forms as a function of…
In this paper we study a problem of looking for an optimal solution of a system of the differential equations with a control and an optimized function. The system of differential equations is changed for two systems with the upper and lower…
We numerically study the finite-size droplet condensation-evaporation transition in two dimensions. We consider and compare two orthogonal approaches, namely at fixed temperature and at fixed density, making use of parallel multicanonical…
A method of the self-consistent calculation of the thermodynamical and correlation functions is presented. This approach is based on the GRPA (generalized random phase approximation) scheme with the inclusion of the mean field corrections.…