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Achieving thermodynamic faithfulness and transferability across state points is an outstanding challenge in the bottom-up coarse graining of molecular models, with many efforts focusing on augmenting the form of coarse-grained interaction potentials to improve transferability. Here, we revisit the critical role of the simulation ensemble and the possibility that even simple models can be made more predictive through a smarter choice of ensemble. We highlight the efficacy of coarse graining from ensembles where variables conjugate to the thermodynamic quantities of interest are forced to respond to applied perturbations. For example, to learn activity coefficients, it is natural to coarse grain from ensembles with spatially varying external potentials applied to one species to force local composition variations and fluctuations. We apply this strategy to coarse grain both an atomistic model of water and methanol and a binary mixture of spheres interacting via Gaussian repulsions and demonstrate near-quantitative capture of activity coefficients across the whole composition range. Furthermore, the approach is able to do so without explicitly measuring and targeting activity coefficients during the coarse graining process; activity coefficients are only computed after-the-fact to assess accuracy. We hypothesize that ensembles with applied thermodynamic potentials are more "thermodynamically informative." We quantify this notion of informativeness using the Fisher information metric, which enables the systematic design of optimal bias potentials that promote the learning of thermodynamically faithful models. The Fisher information is related to variances of structural variables, highlighting the physical basis underlying the Fisher information's utility in improving coarse-grained models.
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http://dx.doi.org/10.1063/5.0022808 | DOI Listing |
ACS Electrochem
September 2025
Liquid Sunlight Alliance, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.
Reaction rate coefficients for electron-transfer processes at the electrode-electrolyte interface are commonly estimated by using the Butler-Volmer equation, but their values are inaccurate beyond a few tenths of volts of overpotential. The Marcus-Hush-Chidsey (MHC) formalism yields correct asymptotic behavior of the rate coefficients vs applied overpotential but has complex dependencies on the redox system's intrinsic parameters, which can be difficult to model or measure. In this work, we bridge the two kinetics formalisms to estimate the reorganization energy, one of the important parameters for the MHC formalism, and investigate its dependence on other intrinsic parameters such as activation barriers, electronic coupling strength, and the density of states of the electrode surface.
View Article and Find Full Text PDFRev Cardiovasc Med
August 2025
Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, 100029 Beijing, China.
Background: Coagulation disorders are potentially one of the most important pathogeneses of acute respiratory distress syndrome (ARDS) following acute type A aortic dissection (ATAAD). This study aimed to determine whether aortic dissection singularly and cardiopulmonary bypass (CPB) surgery can activate coagulation pathways, promoting ARDS development in patients with ATAAD.
Methods: A total of 450 patients who received treatment at Beijing Anzhen Hospital, Capital Medical University, between March 2023 and February 2024 were consecutively enrolled in this prospective cohort study.
Bioinform Adv
August 2025
Department of CSE, BUET, Dhaka 1000, Bangladesh.
Motivation: Heavy usage of synthetic nitrogen fertilizers to satisfy the increasing demands for food has led to severe environmental impacts like decreasing crop yields and eutrophication. One promising alternative is using nitrogen-fixing microorganisms as biofertilizers, which use the nitrogenase enzyme. This could also be achieved by expressing a functional nitrogenase enzyme in the cells of the cereal crops.
View Article and Find Full Text PDFTemperature (Austin)
June 2025
Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
Sweating is a vital thermoregulatory mechanism in humans for maintaining thermal balance during exercise and exposure to hot environments. The development of models that predict sweat rate based on body temperature has been ongoing for over half a century. Here, we compared predicted water loss rates (WLR) from these models to actual observations collected during 780 participant-exposures in three independent laboratory-based experiments.
View Article and Find Full Text PDFFEBS Lett
September 2025
Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Minsk, Belarus.
Genetic variants of various cytochrome P450 (CYP) enzymes significantly impact pharmacokinetics. The highly polymorphic hepatic CYP2C9 metabolizes ~ 15% of clinically used drugs. This study aimed to characterize the ligand-binding properties of the understudied CYP2C9.
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