Works about MOLECULAR dynamics

Results: 5000

Computer Simulations to Study the Mechanisms of Cold Plasma-Induced Degradation of Amoxicillin.

Published in:

Plasma Chemistry & Plasma Processing, 2025, v. 45, n. 4, p. 1151, doi. 10.1007/s11090-025-10567-y

By:

Rajabov, Otamurot;
Zhang, Quan-Zhi;
Matyakubov, Nosir;
Zhang, Yuan-Tao;
Bogaerts, Annemie;
Yusupov, Maksudbek

Publication type:

Article

Molecular Dynamics Simulations of a Putative Novel Mechanism for UCP1‐Assisted FA Anion Transport.

Published in:

Acta Physiologica, 2025, v. 241, n. 7, p. 1, doi. 10.1111/apha.70068

By:

Vojvodić, Sanja;
Roticiani, Giorgia;
Vazdar, Mario;
Pohl, Elena E.

Publication type:

Article

Integrated experimental and computational analysis reveals amoxicillin binding dynamics to PBP1a in Staphylococcus aureus.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-07626-x

By:

Elabed, Seifeldin;
Ali, Mariam;
Hanafy, Shrouk;
Mostafa, Sohila;
Mamdouh, Momen;
Meselhi, Ayman

Publication type:

Article

Evolutionary and Structural Assessment of the Human Secreted Frizzled-Related Protein (SFRP) Family.

Published in:

Journal of Molecular Evolution, 2025, v. 93, n. 3, p. 350, doi. 10.1007/s00239-025-10249-5

By:

Mafakher, Ladan;
Rismani, Elham;
Teimoori-Toolabi, Ladan

Publication type:

Article

Performance and adsorption mechanism of microbial fuel cells in treating industrial wastewater with high salt and nitrogen content.

Published in:

Environmental Technology, 2025, v. 46, n. 17, p. 3438, doi. 10.1080/09593330.2025.2464980

By:

Liu, Ning;
Liu, Xinmin;
Guo, Qingjie

Publication type:

Article

Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00616-1

By:

Kamel, Emadeldin M.;
Allam, Ahmed A.;
Rudayni, Hassan A.;
Alshabrmi, Fahad M.;
Aba Alkhayl, Faris F.;
Lamsabhi, Al Mokhtar

Publication type:

Article

Dependence of the Vibrational Frequencies of a Graphene Sheet on the Ratio of Its Sides and the Number of Vacancy Defects.

Published in:

JETP Letters, 2025, v. 121, n. 9, p. 702, doi. 10.1134/S0021364024605438

By:

Akhmatov, Z. A.

Publication type:

Article

Identification and evaluation of a pinocembrin analog as a TRPV1 inhibitor with analgesic properties in murine pain models.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1585181

By:

Chen, Hanbin;
Li, Guanghong;
Deng, Lin;
Xu, Nan;
Lee, Simon Ming-Yuen;
Nie, Xiaowei;
Bian, Jin-Song

Publication type:

Article

Molecular simulation studies and systems biological approach to identify the target lead compound for the enzyme DNA gyrase.

Published in:

Journal of Applied Pharmaceutical Science, 2025, v. 15, n. 6, p. 216, doi. 10.7324/JAPS.2025.209927

By:

Karuppaiah, Rajakumari;
Parthiban, Brindha Devi;
Rishikesan, Shanmugapriya;
Munusamy, Balamugundan;
Kaliyamurthy, Aravind;
Himalanathan, Sundar

Publication type:

Article

Molecular docking and molecular dynamics simulation of glycyrrhizic acid in multitarget agents as potential inhibitors of respiratory influenza viruses.

Published in:

Journal of Applied Pharmaceutical Science, 2025, v. 15, n. 6, p. 190, doi. 10.7324/JAPS.2025.197023

By:

Supekar, Aarati Ramesh;
Bhujbal, Santosh;
Yadav, Rashmi

Publication type:

Article

Molecular docking and molecular dynamics simulations revealed interaction mechanism of acetylcholinesterase with organophosphorus pesticides and their alternatives.

Published in:

Archives of Toxicology, 2025, v. 99, n. 6, p. 2433, doi. 10.1007/s00204-025-04020-4

By:

Yang, Jiawen;
Chen, Lin;
Wang, Shuo;
Zhao, Bing;
Wang, Ruige

Publication type:

Article

Modeling the Influence of Deposition Parameters on the Crystalline Degree in the Simulation of Polycrystalline Silicon.

Published in:

Physica Status Solidi (B), 2025, v. 262, n. 4, p. 1, doi. 10.1002/pssb.202400483

By:

Santonen, Mikael;
Lahti, Antti;
Srivastava, Divya;
Jahanshah Rad, Zahra;
Miettinen, Mikko;
Ebrahimzadeh, Masoud;
Laaksonen, Johanna;
Laukkanen, Pekka;
Punkkinen, Marko;
Kokko, Kalevi;
Kuronen, Antti;
Parkkinen, Katja;
Eklund, Markus

Publication type:

Article

Machine learning revealed giant thermal conductivity reduction by strong phonon localization in two-angle disordered twisted multilayer graphene.

Published in:

NPJ Computational Materials, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41524-025-01678-3

By:

Wang, Jingwen;
Zhu, Zheng;
Jiang, Tianran;
Chen, Ke

Publication type:

Article

An integrated approach based on FDA adverse event reporting system, network pharmacology, molecular docking, and molecular dynamics simulation analysis to study the cardiac adverse reactions and mechanism of action of osimertinib.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1619517

By:

Wang, Wenjuan;
Liu, Hong;
Wen, Yongqing;
Zhang, Yanhua;
Ma, Xu

Publication type:

Article

In silico insights into dual COX inhibition by fluoro‐substituted indole derivative using DFT, molecular docking, and MD simulation studies.

Published in:

Journal of the Chinese Chemical Society, 2025, v. 72, n. 6, p. 653, doi. 10.1002/jccs.70020

By:

Pal, Mamta;
Shukla, Raj;
Maurya, Anushree;
Siddiqui, Zohra;
Srivastava, Ruchi;
Pathak, Shilendra K.;
Shukla, Vikas K.;
Prasad, Onkar;
Sinha, Leena

Publication type:

Article

Understanding the N2/H2O/CO2 reactions mechanism in extreme conditions using reactive molecular dynamic simulations.

Published in:

Journal of the Chinese Chemical Society, 2025, v. 72, n. 6, p. 627, doi. 10.1002/jccs.70013

By:

Wang, Aibin;
Zhu, Simin;
Cao, Xinyu;
Li, Yong;
Li, Yinghui

Publication type:

Article

Plastic Deformation Mechanisms Regulated by Twin Boundary Spacing in Inverse Gradient Nanotwinned Copper.

Published in:

Physica Status Solidi. A: Applications & Materials Science, 2025, v. 222, n. 7, p. 1, doi. 10.1002/pssa.202400668

By:

Yang, Hongwei;
Du, Xinyu;
Yang, Qianqian

Publication type:

Article

Supramolecular Recognition of a DNA Four‐Way Junction by an M2L4 Metallo‐Cage, Inspired by a Simulation‐Guided Design Approach.

Published in:

Angewandte Chemie, 2025, v. 137, n. 26, p. 1, doi. 10.1002/ange.202504866

By:

Dettmer, Samuel J.;
Williams, Hugo D.;
Napier, Richard;
Beames, Joseph M.;
Walker‑Griffiths, Steffan;
Craggs, Timothy D.;
Hannon, Michael J.

Publication type:

Article

Porous Aromatic Frameworks Filler with Anion‐Constrained Centers in Composite Polymer Electrolyte for Lithium‐Ion Batteries.

Published in:

Angewandte Chemie, 2025, v. 137, n. 26, p. 1, doi. 10.1002/ange.202501412

By:

Ma, Tingting;
Fu, Bin;
Feng, Hua;
Li, Yunxuan;
Zhai, Yuhui;
Tian, Yuyang;
Li, Zhangnan;
Su, Zhong‐Min

Publication type:

Article

Solid‐State NMR‐Assisted Dynamic Characterization of two Isostructural Solvates of 5α‐Bromo‐6β,19‐Epoxy‐Androstan‐3β,17β‐Diol Diacetate.

Published in:

Magnetic Resonance in Chemistry, 2025, v. 63, n. 5/6, p. 360, doi. 10.1002/mrc.5517

By:

Vazquez‐Chavez, Josué;
Navarro‐Huerta, Armando;
Flores‐Álamo, Marcos;
Rodríguez‐Molina, Braulio;
Iglesias‐Arteaga, Martín A.

Publication type:

Article

Simulation study of hardness via nanoindentation of polymer nanocomposites through molecular dynamics.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06403-x

By:

Naranjo-Adorno, Eduardo;
Castrejón-González, Edgar O.;
Alvarado, Juan F. J.;
Díaz-Ovalle, Christian O.;
Rico-Ramírez, Vicente

Publication type:

Article

A comprehensive review on structural insights through molecular visualization: tools, applications, and limitations.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06402-y

By:

Verma, Ved Vrat;
Vimal, Swapnil;
Mishra, Manoj Kumar;
Sharma, Varun Kumar

Publication type:

Article

Molecular dynamics simulation of TNT/PYRN cocrystal PBXs.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06394-9

By:

Han, Yu-hang;
Li, Xin-yi;
Ma, Zhong-liang;
Wang, Bao-guo;
Du, Ji-hang;
Yang, Yu;
Zhao, Hong-wei;
Jin, Qing-jun;
Bi, Peng-yu

Publication type:

Article

Influence of wetted micro/nano-structures on bubble nucleation in flow boiling: a molecular dynamics study.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06389-6

By:

Xiao, Chengdi;
Yu, Dalin;
Huang, Jiaxun;
Zhang, Haitao;
Rao, Xixin

Publication type:

Article

Study on efficient seawater desalination of Ti3C2 MXene nanochannels.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06386-9

By:

Zhang, Yixuan;
Liu, Jiaxin;
Yang, Xiaohong;
Yuan, Fanhang;
Zhang, Xinyu

Publication type:

Article

Synergistic in silico exploration of some pyrazole-based potential anticancer agents: a DFT, molecular docking, and molecular dynamics study.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06385-w

By:

Barukial, Pratyashee;
Nandi, Rajib;
Das, Nipu Kumar;
Barman, Rituraj;
Ahmed, Benzir;
Nagendraprasad, Gunolla;
Banerjee, Tamal;
Bezbaruah, Bipul

Publication type:

Article

Thermal decomposition behaviors of an ultralow-density porous ice stored with H2.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06383-y

By:

Kong, Jiajia;
Li, Dezhen;
Liu, Yuan;
Liu, Chang

Publication type:

Article

Differential molecular interactions between iberiotoxin and human SLO3 and SLO1 potassium channels.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06379-8

By:

Torres Juárez, Jorge Arturo;
Hernández Puga, Ana Gabriela;
Sánchez Tusie, Ana Alicia

Publication type:

Article

Axial compression–induced post-buckling of nanotube films on copper nanopillars: a molecular dynamics study.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06377-w

By:

Xu, Jing;
Li, Kang;
Yin, Hang

Publication type:

Article

A constant pH molecular dynamics and experimental study on the effect of different pH on the structure of urease from Sporosarcina pasteurii.

Published in:

Journal of Molecular Modeling, 2025, v. 31, n. 6, p. 1, doi. 10.1007/s00894-025-06369-w

By:

Zheng, Yifei;
Wu, Lingling;
Zhang, Qiucai;
Hu, Lin;
Tian, Yakun;
Wang, Min;
Zheng, Huaimiao;
Zhang, Zhijun

Publication type:

Article

Structural Elucidation, DFT Calculations, Hirshfeld Surface Analysis, Molecular Dynamics Simulation, ADMET Profiles, and Molecular Docking of Two Benzazocine Derivatives NAOP-12 and NEMKH-12.

Published in:

Orbital: The Electronic Journal of Chemistry, 2025, v. 17, n. 1, p. 35, doi. 10.17807/orbital.v17i1.20314

By:

Hasan, Tanveer;
Ghalib, Raza Murad;
Mehdi, Sayed Hasan;
Tazeem;
Kazmi, Nazia

Publication type:

Article

K36-based inhibitor analogs as potential therapeutics against SARS-CoV-2 main protease (Mpro): a computational investigation.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-06676-5

By:

AbouYoussef, Mohamed L.;
Aboelnga, Mohamed M.;
Hanafy, Nemany A;
El-Kelany, Khaled E.

Publication type:

Article

Mitigating the Oncogenic Roles of miR‑629‑5p and miR‑660‑5p Through Direct Binding by Two Potential Drug Targets for Colorectal Cancer Prevention.

Published in:

International Journal of Preventive Medicine, 2025, v. 16, p. 1, doi. 10.4103/ijpvm.ijpvm_277_24

By:

Poorbaferani, Fariborz;
Bolandi, Soheil;
Abdolvand, Mohammad;
Aghaie‑Kheyrabadi, Fatemeh;
Farhadian, Nooshin;
Abdolvand, Shirin;
Maghool, Fatemeh;
Emami, Mohammad H.;
Fahim, Alireza;
Rahimi, Hojjatolah;
Amjadi, Elham;
Bon, Fatemeh D. N.;
Hemati, Simin;
Salehi, Mansoor

Publication type:

Article

A Kinematics Based Evolutionary Approach for Molecular Conformational Search.

Published in:

Computer-Aided Design & Applications, 2011, v. 8, n. 1, p. 23, doi. 10.3722/cadaps.2011.23-36

By:

Brintaki, Athina N.;
Lai-Yuen, Susana K.;
Nikolos, Ioannis K.

Publication type:

Article

Effect of basicity on the structure and viscosity properties of HIsmelt slag: A molecular dynamics simulation.

Published in:

Canadian Metallurgical Quarterly, 2025, v. 64, n. 3, p. 799, doi. 10.1080/00084433.2024.2367925

By:

Zhang, Shushi;
Zhang, Jianliang;
Wang, Zhenyang;
Jiang, Dewen;
Liang, Zeng;
Zhang, Song

Publication type:

Article

Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer.

Published in:

Vietnam Journal of Chemistry, 2024, v. 62, n. 5, p. 624, doi. 10.1002/vjch.202300313

By:

Joshi, Sravani;
Srivastava, Ruby

Publication type:

Article

Toxicological Mechanism of Triptolide‐Induced Liver Injury.

Published in:

Journal of Biochemical & Molecular Toxicology, 2025, v. 39, n. 6, p. 1, doi. 10.1002/jbt.70319

By:

Hang, Sirui;
Xu, Liu;
Wang, Jin;
Zhang, Caiqun;
Cao, Chenxi

Publication type:

Article

Enhancing SO3 hydrolysis and nucleation: the role of formic sulfuric anhydride.

Published in:

Atmospheric Chemistry & Physics, 2025, v. 25, n. 11, p. 5695, doi. 10.5194/acp-25-5695-2025

By:

Wang, Rui;
Li, Rongrong;
Chen, Shasha;
Mu, Ruxue;
Zhang, Changming;
Ma, Xiaohui;
Khan, Majid;
Zhang, Tianlei

Publication type:

Article

High-throughput atomistic modeling of nanocrystalline structure and mechanics of calcium aluminate silicate hydrate.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60631-6

By:

Li, Yunjian;
Chen, Cheng;
Li, Zhenning;
Li, Zongjin

Publication type:

Article

Hexafluorophosphate additive enables durable seawater oxidation at ampere-level current density.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60413-0

By:

He, Xun;
Yao, Yongchao;
Zhang, Limei;
Wang, Hefeng;
Tang, Hong;
Jiang, Wenlong;
Ren, Yuchun;
Nan, Jue;
Luo, Yongsong;
Wu, Tongwei;
Luo, Fengming;
Tang, Bo;
Sun, Xuping

Publication type:

Article

Kinetic modelling and reactivity of liquid nitromethane under detonation conditions.

Published in:

Communications Chemistry, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42004-025-01582-3

By:

Zhang, Teng;
Chen, Lang;
Yang, Kun;
Zhang, Bin;
Yang, Tuo;
Long, Yao;
Lu, Jianying;
Liu, Danyang;
Chen, Jun

Publication type:

Article

Optimised nanobody-based quenchbodies for enhanced protein detection.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08359-3

By:

Cater, Jordan H.;
El Salamouni, Nehad S.;
Mansour, Ghada H.;
Hutchinson, Sebastian;
Mc Guinness, Conall;
Mueller, Stefan H.;
Spinks, Richard R.;
Shanmugam, Nirukshan;
Pichard-Kostuch, Adeline;
Zahoransky, Viktor;
Ghodke, Harshad;
Ribezzi-Crivellari, Marco;
Yu, Haibo;
van Oijen, Antoine M.;
Griffiths, Andrew D.;
Spenkelink, Lisanne M.

Publication type:

Article

Simulating the Effects of the Native Oxide Layer During Kinetic Spraying of Tantalum Particles Using a Deep Learning Interatomic Potential.

Published in:

Journal of Thermal Spray Technology, 2025, v. 34, n. 5, p. 1666, doi. 10.1007/s11666-025-01991-9

By:

Bierschenk, Stephen G.;
Becker, Michael F.;
Kovar, Desiderio

Publication type:

Article

Effect of depositional nanoparticles on heat transfer at the solid–liquid interface using molecular dynamics simulations.

Published in:

Journal of Non-Equilibrium Thermodynamics, 2025, v. 50, n. 3, p. 391, doi. 10.1515/jnet-2024-0080

By:

Yin, Xunyan;
Li, Congzheng;
Kou, Zhihai;
Zhang, Ran;
Zhou, Hailun

Publication type:

Article

4D-QSAR Analyses for EGFR Inhibitors Based on CDDA-OPS-GA Method.

Published in:

Journal of the Chemical Society of Pakistan, 2025, v. 47, n. 3, p. 204

By:

Cai, Biying;
Zhao, Tiansheng;
Qin, Daogang;
Tu, Guogang

Publication type:

Article

Computational design and evaluation of multiepitope vaccines against herpes simplex virus type 1.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1581571

By:

Zhao, Zibo;
Wang, Weixiong;
Pang, Jiaping;
Zhou, Bei;
Li, Xin;
Wang, Yifei;
Zheng, Kai;
Ren, Zhe

Publication type:

Article

Effect of twin boundary spacing on mechanical and structural properties of nano polycrystalline bulk Au element.

Published in:

Applied Physics A: Materials Science & Processing, 2025, v. 131, n. 6, p. 1, doi. 10.1007/s00339-025-08600-0

By:

Kazanc, Sefa;
Baykara, Oktay

Publication type:

Article

Tension–compression asymmetry of HCP CoCrFeMnNi high entropy alloy nanowires.

Published in:

Applied Physics A: Materials Science & Processing, 2025, v. 131, n. 6, p. 1, doi. 10.1007/s00339-025-08588-7

By:

Liu, Xuepeng;
Xie, Kaixin

Publication type:

Article

Tension-compression asymmetry in nanoporous metallic glasses: insights from molecular dynamics simulations.

Published in:

Applied Physics A: Materials Science & Processing, 2025, v. 131, n. 6, p. 1, doi. 10.1007/s00339-025-08575-y

By:

Amigo, Nicolás;
Valencia, Felipe J.

Publication type:

Article

Deep learning molecular dynamics for large-scale insights into yttrium's structural, thermal and diffusion properties.

Published in:

Applied Physics A: Materials Science & Processing, 2025, v. 131, n. 6, p. 1, doi. 10.1007/s00339-025-08560-5

By:

Ma, Li;
Wang, Haowen;
Wu, Yongzhi;
Chen, Keyuan;
Zhang, Haoxiang;
Zhang, Xingkao;
Rong, Ju;
Sui, Yudong;
Yu, Xiaohua;
Feng, Jing

Publication type:

Article