Related papers: Predicting binding free energies in solution
We show that the Random Energy Model has interesting rejuvenation properties in its frozen phase. Different `susceptibilities' to temperature changes, for the free-energy and for other (`magnetic') observables, can be computed exactly.…
A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of…
This work provides a self-consistent extension of the recently proposed density-based basis-set correction method for wave-function electronic-structure calculations [J. Chem. Phys. 149, 194301 (2018)]. In contrast to the previously used…
The first-principles calculation of contributions of phonon and electron excitations to free formation, binding, and migration energies of defects is illustrated in the case of bcc-Fe. First of all, the ground state properties of the…
A large collaboration carefully benchmarks 20 first principles many-body electronic structure methods on a test set of 7 transition metal atoms, and their ions and monoxides. Good agreement is attained between the 3 systematically converged…
Reported here are theoretical calculations on the triflic acid and water, establishing molecular scale information necessary to modeling of the structure, thermodynamics, and ionic transport of Nafion membranes. To characterize side chain…
Free energies of molecules can be calculated by quantum computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic…
The variation of energies associated with soft matter interfaces where surface inhomogeneities are present. These energies include the total bending and splay energy, the variable surface tension energy, a coupling energy between the total…
A method for increasing the accuracy of configuration interaction (CI) calculations of molecules and other electronic systems is proposed. The energy defect of a given calculation is associated with the electron pair origin of…
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…
The problem of determining lower bounds for the energy cost of a given nanoscale design is addressed via a complexity theory-based approach. This paper provides a theoretical framework that is able to assess the trade-offs existing in…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
In this PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
A phenomenological formula based on liquid drop model has been proposed for ground state binding energies of nuclei. The effect due to bunching of single particle levels has been incorporated through a term resembling the one-body…
How much free energy is irreversibly lost during a thermodynamic process? For deterministic protocols, lower bounds on energy dissipation arise from the thermodynamic friction associated with pushing a system out of equilibrium in finite…
A new mathematical model for non-equilibrium evaporation/condensation including boiling effect is proposed. A simplified differential-algebraic system of equations is obtained. A code to solve numerically this differential-algebraic system…
Gluon and quark contributions to the thermodynamic potential (free energy) of a (2+1)-dimensional QCD model at finite temperature in the background of a constant homogeneous chromomagnetic field H combined with A_0 condensate are…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…
We investigate the thermal and electronic collective fluctuations that contribute to the finite-temperature adsorption properties of flexible adsorbates on surfaces on the example of the molecular switch azobenzene C$_{12}$H$_{10}$N$_{2}$…