A simple and efficient internal-coordinate importance sampling protocol for the Monte Carlo computation of (up to fourth-order) virial coefficients ̅B(n) of atomic systems is proposed. The key feature is a multivariate sampling distribution that mimics the product structure of the dominating pairwise-additive parts of the ̅B(n). This scheme is shown to be competitive over routine numerical methods and, as a proof of principle, applied to neon: The second, third, and fourth virial coefficients of neon as well as equation-of-state data are computed from ab initio two- and three-body potentials; four-body contributions are found to be insignificant. Kirkwood-Wigner quantum corrections to first order are found to be crucial to the observed agreement with recent ab initio and experimental reference data sets but are likely inadequate at very low temperatures.
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http://dx.doi.org/10.1063/1.4731344 | DOI Listing |
J Phys Chem Lett
December 2024
Discovery Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States.
Nonspecific protein-protein interactions (PPIs) are key to understanding the behavior of proteins in solutions. However, experimentally measuring anisotropic PPIs as a function of orientation and distance has been challenging. Here, we propose to measure a new parameter, the generalized second virial coefficient, (), to address this challenge.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Institut für Thermodynamik, Helmut-Schmidt-Universität/Universität der Bundeswehr Hamburg, Holstenhofweg 85, 22043 Hamburg, Germany.
We apply the methodology of Lustig, with which rigorous expressions for all thermodynamic properties can be derived in any statistical ensemble, to derive expressions for the calculation of thermodynamic properties in the path integral formulation of the quantum-mechanical isobaric-isothermal (NpT) ensemble. With the derived expressions, thermodynamic properties such as the density, speed of sound, or Joule-Thomson coefficient can be calculated in path integral Monte Carlo simulations, fully incorporating quantum effects without uncontrolled approximations within the well-known isomorphism between the quantum-mechanical partition function and a classical system of ring polymers. The derived expressions are verified by simulations of supercritical helium above the vapor-liquid critical point at selected state points using recent highly accurate ab initio potentials for pairwise and nonadditive three-body interactions.
View Article and Find Full Text PDFACS Nano
December 2024
Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States.
Electrostatically stabilized nanocrystals (NCs) and, in particular, quantum dots (QDs) hold promise for forming strongly coupled superlattices due to their compact and electronically conductive surface ligands. However, studies of the colloidal dispersion and interparticle interactions of electrostatically stabilized sub-10 nm NCs have been limited, hindering the optimization of their colloidal stability and self-assembly. In this study, we employed small-angle X-ray scattering (SAXS) experiments to investigate the interparticle interactions and arrangement of PbS QDs with thiostannate ligands (PbS-SnS) in polar solvents.
View Article and Find Full Text PDFPhysica A
June 2024
Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA.
We present a method, FMAPS(q), for calculating the structure factor, , of a protein solution, by extending our ast Fourier transform-based odeling of tomistic rotein-protein interactions (FMAP) approach. The interaction energy consists of steric, nonpolar attractive, and electrostatic terms that are additive among all pairs of atoms between two protein molecules. In the present version, we invoke the free-rotation approximation, such that the structure factor is given by the Fourier transform of the protein center-center distribution function .
View Article and Find Full Text PDFJ Chem Theory Comput
November 2024
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
Sugar molecules play important roles as mediators of biomolecular interactions in cellular functions, disease, and infections. Molecular dynamics simulations are an indispensable tool to explore these interactions at the molecular level. The large time and length scales involved frequently necessitate the use of coarse-grained representations, which heavily depend on the parametrization of sugar-protein interactions.
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