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Biophysical simulations

Signal hierarchical petri nets: Formal semantics of hierarchical regulatory control of biological systems

Eugênio Simão

published 21 Aug 2026

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Network pharmacology and molecular simulation study on the multi-target gene regulatory mechanism of Isatis indigotica against hepatic inflammation

XueRu Li, Yang Wang, HuiJun Cheng, Rong Chen, XiaoLu Chen

published 13 Aug 2026

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In silico identification and biophysical characterization of candidate antimicrobial peptides from the Indian marine microbiome targeting multidrug-resistant ESKAPE pathogens

Sreelakshmi K. V, Nasri Thaha, Budheswar Dehury

published 22 Jul 2026

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Microbial fuel cells for wastewater treatment and electricity production: A multi-platform simulation workflow

Muhammad Ali

published 07 May 2026

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QuPepFold: A python package for hybrid quantum-classical protein folding simulations with CVaR-optimized VQE

Akshay Uttarkar, Vidya Niranjan, Amit Saxena, Vinay Kumar

published 11 Feb 2026

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Calibration of discrete element parameters for cohesive soils at different moisture contents

Shixi Wei, Bing Li, Jinxia Yang, Dengsheng Cai, Wubin Xu, Zhaoyang Liu

published 09 Feb 2026

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Structure-based identification of bioactive compounds as trace amine-associated receptor 1 agonists for the therapeutic management of major depressive disorder

Abdelbaset Mohamed Elasbali, Ahmed S. Ali, Mohd Adnan, Taj Mohammad, Anas Shamsi, Md. Imtaiyaz Hassan

published 05 Aug 2025

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Consensus structure prediction of A. thaliana’s MCTP4 structure using prediction tools and coarse grained simulations of transmembrane domain dynamics

Sujith Sritharan, Raphaelle Versini, Jules D Petit, Emmanuelle E Bayer, Antoine Taly

published 15 Jul 2025

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Coarse-grained molecular dynamics investigation on the interaction between κ- and β-casein aggregates and curcumin

Jian Gao, Rong Dong, Shuailing Yang, Zhengtao Zhao, Ye-Wang Zhang

published 10 Jul 2025

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Development and validation of mass reduction prediction model during torrefaction using biomass chemical composition analysis

Sunyong Park, Kyeong Sik Kang, Kwang Cheol Oh, Seok Jun Kim, Paudel Padam Prasad, Seon Yeop Kim, Ha Eun Kim, Jae Youl Shin, DaeHyun Kim

published 23 May 2025

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Comparison of SPH and CEL methods for simulating the soil cutting process of a biomimetic digging shovel

Yunning Dong, Liangfei Fang, Kuan Qin, Shoujun Sun, Yue Gong

published 22 May 2025

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Cooperation in the face of disaster

Marijane Luistro Jonsson, Markus Jonsson

published 03 Apr 2025

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SMND-309 activates Nrf2 signaling to alleviate acetaminophen-induced hepatotoxicity and oxidative stress

Yao Dong, Ru Jia, Yujie Jiang, Qing Li, Lei Wang, Wensi Ding, Rui Yan, Yujie Qiu, Zhengjie Shi, Wenying Liu, Jing Wang, Sen Xu, Na Li

published 31 Mar 2025

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