Related papers: Peptide Conformational Equilibria Computed via a S…
We present the nonequilibrium implementation of the two-particle self-consistent (TPSC) approach, which has been shown to provide a reliable equilibrium description of interacting lattice systems in the weak- and intermediate-correlation…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
We present and characterize a method to accelerate the relaxation of a Brownian object between two distinct equilibrium states. Instead of relying on a deterministic time-dependent control parameter, we use stochastic resetting to guide and…
Melting and solidification processes are often affected by natural convection of the liquid, posing a multi-physics problem involving fluid flow, convective and diffusive heat transfer, and phase-change reactions. Enthalpy methods formulate…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Accurate determination of the equation of state of dense hydrogen is essential for understanding gas giants. Currently, there is still no consensus on methods for calculating its entropy, which play a fundamental role and can result in…
We derive entropy conserving and entropy dissipative overlapping domain formulations for systems of nonlinear hyperbolic equations in conservation form, such as would be approximated by overset mesh methods. The entropy conserving…
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
We propose a method to experimentally study the equation of state of strongly interacting matter created at the early stage of nucleus--nucleus collisions. The method exploits the relation between relative entropy and energy fluctuations…
We extend the convergence analysis for methods solving PDE-constrained optimal control problems containing both discrete and continuous control decisions based on relaxation and rounding strategies to the class of first order semilinear…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We contemplate the pair of the purely imaginary delta-function potentials on a finite interval with Dirichlet boundary conditions. The two parameter model exhibits nicely the expected quantitative features of the unavoided level crossing…
We consider a finite element method for elliptic equation with heterogeneous and possibly high-contrast coefficients based on primal hybrid formulation. A space decomposition as in FETI and BDCC allows a sequential computations of the…
A Hamiltonian-based model of many harmonically interacting massive particles that are subject to linear friction and coupled to heat baths at different temperatures is used to study the dynamic approach to equilibrium and non-equilibrium…
We analyze the physics of optimal protocols to prepare a target state with high fidelity in a symmetrically coupled two-qubit system. By varying the protocol duration, we find a discontinuous phase transition, which is characterized by a…