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We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale simulations (more than 1 s), unavailable for conventional molecular dynamics. No preliminary information about the system's potential landscape is needed for the use of this technique. The optimal interatomic potential modification is automatically derived from the previous simulation steps. The average time between adjusted potential energy fluctuations provides an accurate evaluation of physical time during the hyperdynamics simulation. The main application of the presented hyperdynamics method is the study of thermal-induced defects arising in the middle-sized or relatively large atomic systems at low temperatures. To validate the presented method, we apply it to the C cage and its derivative CNH. Hyperdynamics leads to the same results as a conventional molecular dynamics, but the former possesses much higher performance and accuracy due to the wider temperature region. The coefficient of acceleration achieves 10 and more.
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http://dx.doi.org/10.1021/acs.jctc.9b01229 | DOI Listing |
Cell Rep Methods
July 2025
Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA; Consortium for Fibrosis Research & Translation, University of Colorado School of Medicine, Aurora, CO, USA. Electronic address:
Protein turnover is a critical component of gene expression regulation and cellular homeostasis, yet methods for measuring turnover rates that are scalable and applicable to different models are still needed. We introduce an improved DO (heavy water) labeling strategy to investigate the landscape of protein turnover in cell culture, with accurate calibration of per-residue deuterium incorporation in multiple cell types. Applying this method, we mapped the proteome-wide turnover landscape of pluripotent and differentiating human induced pluripotent stem cells (hiPSCs).
View Article and Find Full Text PDFFree Radic Biol Med
June 2025
Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, NY, USA; New York VA Health Care, Syracuse VA Medical Center, Syracuse, NY, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
Exfoliation Syndrome is an age-related systemic condition characterized by large aggregated fibrillar material deposition in the anterior eye tissues. This aggregate formation and deposition on the aqueous humor outflow pathway are significant risk factors for developing Exfoliation Glaucoma (XFG). XFG is a multifactorial late-onset disease that shares common features of neurodegenerative diseases, such as increased protein aggregation, impaired protein degradation, and oxidative and cellular stress.
View Article and Find Full Text PDFCell Mol Gastroenterol Hepatol
May 2025
Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. Electronic address:
Background & Aims: Portal hypertension (PHT) is the potentially deadly complication of liver cirrhosis. Intrahepatic vascular resistance and the splanchnic hyperdynamic circulation are 2 principal driving factors contributing to the maintenance and exacerbation of PHT. However, in the advanced stages of cirrhosis, the fibrotic process in the liver becomes irreversible, leading to persistent and intractable increases in intrahepatic vascular resistance.
View Article and Find Full Text PDFProtein Sci
March 2025
School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
Molecular dynamics (MD) simulation is an important tool for understanding protein dynamics and the thermodynamic properties of proteins. However, due to the high computational cost of MD simulations, it is still challenging to explore a wide conformational space. To solve this problem, a variety of accelerated MD (aMD) schemes have been proposed over the past few decades.
View Article and Find Full Text PDFLiver Int
November 2024
Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria.