We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.
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http://dx.doi.org/10.1063/1.4921234 | DOI Listing |
Hepatology
January 2025
Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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View Article and Find Full Text PDFAnal Chem
January 2025
School of Molecular and Cellular Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, U.K.
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to interrogate protein structure and dynamics. With the ability to study almost any protein without a size limit, including intrinsically disordered ones, HDX-MS has shown fast growing importance as a complement to structural elucidation techniques. Current experiments compare two or more related conditions (sequences, interaction partners, excipients, conformational states, etc.
View Article and Find Full Text PDFSci Adv
January 2025
Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan.
Proc Natl Acad Sci U S A
February 2025
Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena 07740, Germany.
In mammals, the four subunit isoforms HCN1-4 assemble to form functional homotetrameric and heterotetrameric hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels. Despite the outstanding relevance of HCN channels for organisms, including generating electrical rhythmicity in cardiac pacemaker cells and diverse types of brain neurons, key channel properties are still elusive. In particular, the unitary conductance, of HCN channels is highly controversial.
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February 2025
Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom.
CaSiO[Formula: see text] perovskite (CaPv) is the last major mineral in the Earth's lower mantle whose elasticity remains largely unresolved. Here, we investigate the elasticity of CaPv using ab initio machine-learning force fields (MLFF). At room temperature, the elasticity of tetragonal CaPv determined by MLFF molecular dynamics (MD) agrees well with experimental measurements after considering temperature induced variations in the hydrostatic structure, proving the effectiveness of the method.
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