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Efficiently obtaining atomic-scale thermodynamic parameters characterizing crystallization from solution is key to developing the modeling strategies needed in the quest for digital design strategies for industrial crystallization processes. Based on the thermodynamics of crystal nucleation in confined solutions, we develop a simulation framework to efficiently estimate the solubility and surface tension of organic crystals in solution from a few unbiased molecular dynamics simulations at a reference temperature. We then show that such a result can be extended with minimal computational overhead to capture the solubility curve. This enables an efficient and self-consistent estimate of the solubility and limit of solution stability associated with crystal nucleation in molecular systems from equilibrium molecular dynamics without the need for sophisticated free energy calculations. We apply our analysis to investigate the relative thermodynamic stability and aqueous solubility of the α and β polymorphs of l-glutamic acid. Our analysis enables an efficient appraisal of emergent ensemble properties associated with the thermodynamics of nucleation from solutions against experimental data, demonstrating that while the absolute solubility is still far from being quantitatively captured by an off-the-shelf point charge transferable force field, the relative polymorphic stability and solubility obtained from finite temperature simulation are consistent with the experimentally available information on glutamic acid. We foresee the ability to efficiently obtain solubility information from a limited number of computational experiments as a critical component of high-throughput polymorph screenings.
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http://dx.doi.org/10.1021/acs.iecr.4c02558 | DOI Listing |
Biochem J
September 2025
Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, 741246 Nadia, West Bengal, India.
Transcription initiation factor TFIID subunit 1 (TAF1) is a pivotal component of the TFIID complex, critical for RNA polymerase II-mediated transcription initiation. However, the molecular basis by which TAF1 recognizes and associates with chromatin remains incompletely understood. Here, we report that the tandem bromodomain module of TAF1 engages nucleosomal DNA through a distinct positively charged surface patch on the first bromodomain (BD1).
View Article and Find Full Text PDFVet Res Commun
September 2025
College of Veterinary Medicine, Vietnam National University of Agriculture, 100000, Hanoi, Vietnam.
African swine fever (ASF) is a contagious viral disease that affects domestic pigs and Eurasian wild boars, causing significant economic losses to the global pig industry. Since its first outbreak in February 2019, ASF has had a profound impact on the Vietnamese pig sector. This review presents a comprehensive analysis of ASF outbreaks in Vietnam from 2019 to 2024, focusing on outbreak dynamics, control strategies, economic impact, and key lessons learned.
View Article and Find Full Text PDFMol Divers
September 2025
Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al Kharj, Saudi Arabia.
Cyclin-dependent kinase 20 (CDK20), also known as cell cycle-related kinase (CCRK), plays a pivotal role in hepatocellular carcinoma (HCC) progression by regulating β-catenin signaling and promoting uncontrolled proliferation. Despite its emerging significance, selective small-molecule inhibitors of CDK20 remain unexplored. In this study, a known CDK20 inhibitor, ISM042-2-048, was employed as a reference to retrieve structurally similar compounds from the PubChem database using an 85% similarity threshold.
View Article and Find Full Text PDFMol Divers
September 2025
State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, Xinjiang, China.
Aurora kinases are a group of serine/threonine kinases essential for cell mitosis, comprising Aurora A, B, and C. However, the Aurora B is overexpressed in multiple tumors and the aurone has been proved to exhibit potent inhibitory activity against Aurora B kinase by our group. The indolinone was considered as an aurone scaffold hopping analog, and the indolinone-based Aurora B inhibitor library (3577 molecules) was constructed by FBDD strategy.
View Article and Find Full Text PDFJ Math Biol
September 2025
Department of Mathematics, University of Illinois Urbana-Champaign, Urbana, USA.
A fundamental question in the field of molecular computation is what computational tasks a biochemical system can carry out. In this work, we focus on the problem of finding the maximum likelihood estimate (MLE) for log-affine models. We revisit a construction due to Gopalkrishnan of a mass-action system with the MLE as its unique positive steady state, which is based on choosing a basis for the kernel of the design matrix of the model.
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