Search results for "Free energies"

The ensemble switch method and related approaches to obtain interfacial free energies between coexisting phases from simulations: a brief review

2015

The accurate estimation of the excess free energy due to an interface between coexisting phases of a model system by computer simulation often is a challenging task. We review here two methods, whi...

Docking of indolo- and pyrrolo-pyrimidines to DNA. New DNA-interactive polycycles from amino-indoles/pyrroles and BMMA

2004

New indolo- and pyrrolo-pyrimidines of type 1-4 were studied for their ability to form stable complexes with DNA fragments. The calculated free energies of binding were found in the range -8.39 ÷ -16.72 Kcal/mol. The docking studies revealed a common binding mode with the chromophore intercalated between GC base pairs whereas the side chain lies along the minor groove.

Erratum: “Computing absolute free energies of disordered structures by molecular simulation” [J. Chem. Phys. 131, 231102 (2009)]

2011

Stable and metastable hard-sphere crystals in fundamental measure theory

2013

Using fully minimized fundamental measure functionals, we investigate free energies, vacancy concentrations and density distributions for bcc, fcc and hcp hard-sphere crystals. Results are complemented by an approach due to Stillinger which is based on expanding the crystal partition function in terms of the number n of free particles while the remaining particles are frozen at their ideal lattice positions. The free energies of fcc/hcp and one branch of bcc agree well with Stillinger's approach truncated at n=2. A second branch of bcc solutions features rather spread-out density distributions around lattice sites and large equilibrium vacancy concentrations and is presumably linked to the …

Positive Tolman Length in a Lattice Gas with Three-Body Interactions

2011

We present a new method to determine the curvature dependence of the interface tension between coexisting phases in a finite volume from free energies obtained by Monte Carlo simulations. For the example of a lattice gas on a 3D fcc lattice with nearest neighbor three-body interactions, we demonstrate how to calculate the equimolar radius ${R}_{e}$ as well as the radius ${R}_{s}$ of the surface of tension and thus the Tolman length $\ensuremath{\delta}({R}_{s})={R}_{e}\ensuremath{-}{R}_{s}$. Within the physically relevant range of radii, $\ensuremath{\delta}({R}_{s})$ shows a pronounced ${R}_{s}$ dependence, such that the simple Tolman parametrization for the interface tension is refutable.…

Logarithmic finite-size effects on interfacial free energies: Phenomenological theory and Monte Carlo studies

2014

The computation of interfacial free energies between coexisting phases (e.g.~saturated vapor and liquid) by computer simulation methods is still a challenging problem due to the difficulty of an atomistic identification of an interface, and due to interfacial fluctuations on all length scales. The approach to estimate the interfacial tension from the free energy excess of a system with interfaces relative to corresponding single-phase systems does not suffer from the first problem but still suffers from the latter. Considering $d$-dimensional systems with interfacial area $L^{d-1}$ and linear dimension $L_z$ in the direction perpendicular to the interface, it is argued that the interfacial …

Computing absolute free energies of disordered structures by molecular simulation

2009

We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect, we discuss several properties of the …

Nonequilibrium thermodynamics of the RNA-RNA interaction underlying a genetic transposition program

2021

Thermodynamic descriptions are powerful tools to formally study complex gene expression programs evolved in living cells on the basis of macromolecular interactions. While transcriptional regulations are often modeled in the equilibrium, other interactions that occur in the cell follow a more complex pattern. Here, we adopt a nonequilibrium thermodynamic scheme to explain the RNA-RNA interaction underlying IS10 transposition. We determine the energy landscape associated with such an interaction at the base-pair resolution, and we present an original scaling law for expression prediction that depends on different free energies characterizing that landscape. Then, we show that massive experim…

Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.

2014

The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine different inhibitors of HIV-1 RT, one of the three key proteins responsible for the virus replication, have been selected to develop and test a computational protocol that allows getting a deep insight into the inhibitors’ binding mechanism. The interaction between the inhibitors and the protein have been quantified by computing binding free energies through FEP calculations, while a more detailed characterization of the kind of inhibitor–protein interactions is based on …

Spinodal lines and Flory-Huggins free-energies for solutions of human hemoglobins HbS and HbA

1991

Gelation of deoxygenated solutions of sickle-cell human Hemoglobin (HbS) is of high theoretical interest and it has serious pathological consequences. For this reason HbS is probably the most studied protein capable of self-organization. This notwithstanding, the location in the T, c plane of the region of thermodynamic instability of solutions of deoxy-HbS (as bounded by the spinodal line and as distinct from the gelation region) has remained unknown, along with related values of Flory-Huggins enthalpies and entropies. In the present work this information is derived from experiments for the two cases of (deoxy) HbS and of human adult hemoglobin (HbA). Experiments also show critical exponen…