Exploring effector protein dynamics and natural fungicidal potential in rice blast pathogen Magnaporthe oryzae. by Jannatul Ferdousy, Tanjin Barketullah Robin, Mst Sanjida Nasrin, Istiak Ahmed, Tawsif Hossain, Md Mehedi Hasan, Mehrab Hassan Soaeb, Md Ahsanul Tamim, Nusrat Jahan Yeasmin, Ummay Habiba, Nadim Ahmed, Nurul Amin Rani, Md Shishir Bhuyian, Suvarna N Vakare, Abu Tayab Moin, Rajesh B Patil, Mohammad Shahadat Hossain

“…Using molecular docking, we identified Hecogenin and Cucurbitacin E as strong binders to MAX40 and APIKL2A proteins, which are essential for the fungus's immune evasion and pathogenicity. Molecular dynamics simulations further confirmed that these compounds form stable, strong interactions with the target proteins, validating their potential as therapeutic agents. …”
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Sub-bandgap charge harvesting and energy up-conversion in metal halide perovskites: ab initio quantum dynamics by Bipeng Wang, Weibin Chu, Yifan Wu, Wissam A. Saidi, Oleg V. Prezhdo

“…By combining ab initio time-dependent density functional theory, nonadiabatic molecular dynamics and machine learning, we advance quantum dynamics simulation to nanosecond timescale and demonstrate that large fluctuations of MHP defect energy levels extend light absorption to longer wavelengths and enable trapped charges to escape into bands. …”
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Computational design of multi-epitope vaccine against Hepatitis C Virus infection using immunoinformatics techniques. by Sara Zubair, Fahed Parvaiz, Turki Abualait, Khalid Al-Regaiey, Tasneem Anwar, Mahnoor Zafar, Imdad Kaleem, Shahid Bashir

“…An adjuvant (β-defensin) was introduced to the N-terminus to increase the immunogenicity of the vaccine construct. Molecular dynamics simulation discloses the most stable structure of the proposed vaccine. …”
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A review on molecular simulation application in the field of coal macromolecular structure by Cong YANG, Peng XIA, Niuniu ZOU, Huan YANG, Yin YU, Biao ZHU

“…These techniques encompass molecular mechanics, molecular dynamics, and quantum mechanics. It also analyzes recent developments in classical coal macromolecular structure models and explores the potential applications of molecular simulation in this domain.…”
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Computational Perspectives into Plasmepsins Structure—Function Relationship: Implications to Inhibitors Design by Alejandro Gil L., Pedro A. Valiente, Pedro G. Pascutti, Tirso Pons

“…The high structural flexibility of plasmepsins, revealed by their X-ray structures and molecular dynamics simulations, made even more complicated the prediction of putative binding modes, and therefore, the use of common computational tools, like docking and free-energy calculations. …”
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Unraveling cerebroprotective potential of fenchone: A combined in vivo and in silico exploration of nitric oxide synthase modulation by Bangaru Mamatha, Anka Rao Areti, DSNBK Prasanth, Narender Malothu

“…This was validated through molecular dynamics simulations over a 100 ns time frame, demonstrating stability and favorable interaction profiles. …”
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Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery by Graham Lunt, Niloofar Hashemi, Subhamoy Mahajan, Tian Tang

“…Large-scale coarse-grained (CG) molecular dynamics simulations would facilitate the screening of gene carriers and understanding of the molecular mechanisms involved in pulmonary delivery. …”
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Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers by S. O. Yesylevskyy, A. P. Demchenko, S. Kraszewski, C. Ramseyer

“…The distribution of cholesterol in the highly curved asymmetric DOPC/DOPS lipid bilayer was investigated by the coarse-grained molecular dynamics simulations in the membrane patches with large aspect ratio. …”
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Role of Glass Composition on Mechanical Properties of Shape Memory Alloy-Metallic Glass Composites by Supat Chupradit, Indah Raya, Dinh Tran Ngoc Huy, Dmitry Bokov, Pham Van Tuan, Aravindhan Surendar, Doaa Alaa Lafta, Mustafa M. Kadhim, Olga Kravchenko, Yasser Fakri Mustafa, Zaid Hameed Mahmood, Sami Sajjadifar

“…In this work, the molecular dynamics (MD) simulation was applied to design a laminated composite structure comprised of the shape memory alloy (SMA) and Cu-Zr metallic glasses (MGs). …”
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Unveiling Cathepsin B inhibition with repurposed drugs for anticancer and anti-Alzheimer's drug discovery. by Mohammed Alrouji, Sabina Yasmin, Mohammed S Alshammari, Fahad A Alhumaydhi, Sharaf E Sharaf, Moyad Shahwan, Anas Shamsi

“…To further explore the binding mechanism and stability of the CatB-drug complexes, molecular dynamics (MD) simulations were conducted for 500 ns. …”
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Spontaneous curvature in two-dimensional van der Waals heterostructures by Yuxiang Gao, Fenglin Deng, Ri He, Zhicheng Zhong

“…Based on deep-learning-assisted large-scale molecular dynamics simulations, we observe significant out-of-plane displacements up to 3.8 Å in graphene/BN bilayers induced by curvature, producing a stable hexagonal moiré pattern, which agrees well with experimentally observations. …”
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Machine Learning-Assisted Drug Repurposing Framework for Discovery of Aurora Kinase B Inhibitors by George Nicolae Daniel Ion, George Mihai Nitulescu, Dragos Paul Mihai

“…<b>Methods:</b> This study introduces a machine learning-assisted drug repurposing framework integrating quantitative structure-activity relationship (QSAR) modeling, molecular fingerprints-based classification, molecular docking, and molecular dynamics (MD) simulations. Using this pipeline, we analyzed 4680 investigational and approved drugs from DrugBank database. …”
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Assessing nanobody interaction with SARS-CoV-2 Nsp9. by Gennaro Esposito, Yamanappa Hunashal, Mathias Percipalle, Federico Fogolari, Tomas Venit, Ainars Leonchiks, Kristin C Gunsalus, Fabio Piano, Piergiorgio Percipalle

“…The oligomerization state of Nsp9 was also analyzed by molecular dynamics simulations and both dimers and tetramers resulted plausible. …”
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Understanding Rifampicin Resistance in Tuberculosis through a Computational Approach by Satish Kumar, Lingaraja Jena

“…Subsequently, this was verified by molecular dynamics simulations. This in silico evidence may help us understand RIF resistance in rpoB mutant strains.…”
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Plants and fungi metabolites as novel autophagy inducers and senescence inhibitors by Rivka Ofir

“…New AI/SI can be identified using various approaches like hypothesis-driven approach for screening receptor agonists using an in-silico library of thousands of natural compounds; cheminformatics studies of phytochemicals using docking and molecular dynamics simulation, structure similarities/mimicry in vitro, “blind” high throughput screening (HTS) of libraries of natural metabolites against relevant models, and more. …”
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Unconventional ice nucleation pathway induced by irregular silver iodide surfaces by Yaochen Yu, Mingyi Chen, Yuefeng Lei, Haiyang Niu

“…Despite the acknowledged influence of factors like low lattice mismatch and surface dipole fields on the rapid freezing of water on AgI surfaces, one commonly neglects the impact of irregular surfaces on nucleation mechanisms. Using molecular dynamics simulations, we explore heterogeneous ice nucleation on irregular AgI surfaces. …”
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Unzipping of knotted DNA via nanopore translocation by Antonio Suma, Cristian Micheletti

“…DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA–enzyme interactions in biological systems. Here we use molecular dynamics simulations and a coarse-grained model of DNA to address the nanopore unzipping of DNA filaments that are knotted. …”
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Influence of crystallographic orientations and nanovoid on the plastic mechanism and damage behavior of single-crystal tungsten under shock by Ziyi Li, Wensheng Liu, Yunzhu Ma, Chaoping Liang

“…In this work, we investigated the shock response of single-crystal tungsten with pre-existing voids using nonequilibrium molecular dynamics simulations, considering four crystallographic orientations ([100], [110], [111], and [112]). …”
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A MD Simulation and Analysis for Aggregation Behaviors of Nanoscale Zero-Valent Iron Particles in Water via MS by Ying Zhao, Dongmei Liu, Huan Tang, Jing Lu, Fuyi Cui

“…NZVI are used widely in many fields resulting in more NZVI in water environment. Molecular dynamics simulations and Materials Studio software are used to investigate the microaggregation behaviors of NZVI particles. …”
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Optomechanical micro-rheology of complex fluids at ultra-high frequency by H. Neshasteh, I. Shlesinger, M. Ravaro, M. Gély, G. Jourdan, S. Hentz, I. Favero

“…UHF optomechanical micro-rheology provides direct mechanical access to the fast molecular dynamics in a liquid, in a quantitative manner and within a sub-millisecond measurement time.…”
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