A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the replicas which have reached the highest values along a chosen one-dimensional reaction coordinate. This reaction coordinate does not need to precisely describe all the metastabilities of the system for the method to give reliable results. An extension of the algorithm to compute transition times from one metastable state to another one is also presented. We demonstrate the interest of the method on two simple cases: A one-dimensional two-well potential and a two-dimensional potential exhibiting two channels to pass from one metastable state to another one.
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http://dx.doi.org/10.1063/1.3518708 | DOI Listing |
J Comput Chem
January 2025
Universidade de São Paulo, Instituto de Química, Departamento de Química Fundamental, São Paulo, Brazil.
Seventeen electronic states of the dication VH were characterized by the SA-CASSCF/icMRCI methodology using very extended basis sets; 11 were described for the first time. Potential energy curves were constructed and the associated spectroscopic parameters evaluated. Triplet and quintet states correlating with the V + H channel are thermodynamic stable.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Identifying transitional states is crucial for understanding protein conformational changes that underlie numerous biological processes. Markov state models (MSMs), built from Molecular Dynamics (MD) simulations, capture these dynamics through transitions among metastable conformational states, and have demonstrated success in studying protein conformational changes. However, MSMs face challenges in identifying transition states, as they partition MD conformations into discrete metastable states (or free energy minima), lacking description of transition states located at the free energy barriers.
View Article and Find Full Text PDFNat Commun
January 2025
Center for High Pressure Science and Technology Advanced Research, Beijing, 100093, China.
Due to the sulfur's atoms' propensity to form molecules and/or polymeric chains of various sizes and configuration, elemental sulfur possesses more allotropes and polymorphs than any other element at ambient conditions. This variability of the starting building blocks is partially responsible for its rich and fascinating phase diagram, with pressure and temperature changing the states of sulfur from insulating molecular rings and chains to semiconducting low- and high-density amorphous configurations to incommensurate superconducting metallic atomic phase. Here, using a fast compression technique, we demonstrate that the rapid pressurisation of liquid sulfur can effectively break the molecular ring structure, forming a glassy polymeric state of pure-chain molecules (Am-S).
View Article and Find Full Text PDFJ Phys Condens Matter
January 2025
Condensed Matter Physics, Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata 700 064, Kolkata, West Bengal, 700064, INDIA.
β-Mn-type chiral cubic CoxZnyMnz (x + y + z = 20) alloys present a intriguing platform for exploring topological magnetic orderings with promising spintronic potential. This study examines the magnetotransport properties of Co6.5Ru1.
View Article and Find Full Text PDFChaos
January 2025
Department of Cognitive Sciences, University of California, Irvine, California 92617, USA.
We propose a novel approach to investigate the brain mechanisms that support coordination of behavior between individuals. Brain states in single individuals defined by the patterns of functional connectivity between brain regions are used to create joint symbolic representations of brain states in two or more individuals to investigate symbolic dynamics that are related to interactive behaviors. We apply this approach to electroencephalographic data from pairs of subjects engaged in two different modes of finger-tapping coordination tasks (synchronization and syncopation) under different interaction conditions (uncoupled, leader-follower, and mutual) to explore the neural mechanisms of multi-person motor coordination.
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