In this work, we augment the approximate density functional method SCC-DFTB (DFTB3) with the chemical-potential equalization (CPE) approach in order to improve the performance for molecular electronic polarizabilities. The CPE method, originally implemented for the NDDO type of methods by Giese and York, has been shown to significantly emend minimal basis methods with respect to the response properties and has been applied to SCC-DFTB recently. CPE allows this inherent limitation of minimal basis methods to be overcome by supplying an additional response density. The systematic underestimation is thereby corrected quantitatively without the need to extend the atomic orbital basis (i.e., without increasing the overall computational cost significantly). The dependency of polarizability as a function of the molecular charge state, especially, was significantly improved from the CPE extension of DFTB3. The empirical parameters introduced by the CPE approach were optimized for 172 organic molecules in order to match the results from density functional theory methods using large basis sets. However, the first-order derivatives of molecular polarizabilities (e.g., required to compute Raman activities) are not improved by the current CPE implementation (i.e., Raman spectra are not improved).
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http://dx.doi.org/10.1021/jp306239c | DOI Listing |
J Chem Phys
January 2025
Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
Nucleosomes are fundamental units of chromatin in which a length of genomic DNA is wrapped around a histone octamer spool in a left-handed superhelix. Large-scale nucleosome maps show a wide distribution of DNA wrapping lengths, which in some cases are tens of base pairs (bp) shorter than the 147 bp canonical wrapping length observed in nucleosome crystal structures. Here, we develop a thermodynamic model that assumes a constant free energy cost of unwrapping a nucleosomal bp.
View Article and Find Full Text PDFMacromolecules
November 2024
Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States.
Particle and field-theoretic simulations are both commonly used methods to study the equilibrium properties of polymeric materials. Yet despite the formal equivalence of the two methods, no comprehensive comparisons of particle and field-theoretic simulations exist in the literature. In this work, we seek to fill this gap by performing a systematic and quantitative comparison of particle and field-theoretic simulations.
View Article and Find Full Text PDFPhys Rev Lett
September 2024
Université Bordeaux, CNRS, LOMA, UMR 5798, F-33400 Talence, France.
Single-file diffusion is a paradigmatic model for the transport of Brownian colloidal particles in narrow one-dimensional channels, such as those found in certain porous media, where the particles cannot cross each other. We consider a system where a different external uniform potential is present to the right and left of an origin. For example, this is the case when two channels meeting at the origin have different radii.
View Article and Find Full Text PDFJ Chem Phys
August 2024
Ioffe Institute, 26 Polytechnicheskaya, St. Petersburg 194021, Russia.
A field-supported multiphase kinetic Monte Carlo method previously applied to self-assembled trimesic acid molecular layers [Ustinov et al., Phys. Chem.
View Article and Find Full Text PDFPhys Rev Lett
June 2024
State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
A unitary Fermi gas in an isotropic harmonic trap is predicted to show scale and conformal symmetry that have important consequences in its thermodynamic and dynamical properties. By experimentally realizing a unitary Fermi gas in an isotropic harmonic trap, we demonstrate its universal expansion dynamics along each direction and at different temperatures. We show that as a consequence of SO(2,1) symmetry, the measured release energy is equal to that of the trapping energy.
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