Works about MOLECULAR dynamics

Results: 5000

Effect of Water on Local Structure and Dynamics in a Protic Ionic Liquid‐Based Electrolyte.

Published in:

ChemSusChem, 2025, v. 18, n. 13, p. 1, doi. 10.1002/cssc.202402753

By:

Lundin, Filippa;
Stettner, Timo;
Falus, Peter;
Balducci, Andrea;
Matic, Aleksandar

Publication type:

Article

Effects of Hydration Level and Hydrogen Bonds on Hydroxide Transport Mechanisms in Anion Exchange Membranes.

Published in:

ChemSusChem, 2025, v. 18, n. 13, p. 1, doi. 10.1002/cssc.202402660

By:

Ma, Lunliang;
Wang, Tao

Publication type:

Article

SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf308

By:

Motta, Stefano;
Callea, Lara;
Mulla, Shaziya Ismail;
Davoudkhani, Hamid;
Bonati, Laura;
Pandini, Alessandro

Publication type:

Article

VTX: real-time high-performance molecular structure and dynamics visualization software Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf295

By:

Maria, Maxime;
Guionnière, Simon;
Dacquay, Nicolas;
Plateau-Holleville, Cyprien;
Guillaume, Valentin;
Larroque, Vincent;
Lardé, Jean;
Naimi, Yassine;
Piquemal, Jean-Philip;
Levieux, Guillaume;
Lagarde, Nathalie;
Mérillou, Stéphane;
Montes, Matthieu

Publication type:

Article

ColBuilder: flexible structure generation of crosslinked collagen fibrils Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf278

By:

Monego, Debora;
Brosz, Matthias;
Buck, Johanna;
Viliuga, Vsevolod;
Greicius, Paulius;
Jung, Jaewoon;
Stuehn, Torsten;
Schmies, Matthias;
Sugita, Yuji;
Gräter, Frauke

Publication type:

Article

Discovery of Novel Potential Binders Targeting Norovirus 3CL Protease: A Machine Learning and Molecular Dynamics Approach.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 2, p. 257, doi. 10.1142/S2737416525500474

By:

Babaker, Manal A.;
Alatawi, Hanan Ali;
AlRashidi, Aljazi Abdullah;
Moglad, Ehssan;
Abdulhakim, Jawaher A.;
Afzal, Muhammad;
Babiker, M. A.;
Zeid, Isam M. Abu;
Altayb, Hisham N.

Publication type:

Article

Investigating the Anti-glioblastoma Potential of Alkaloids from the Solanaceae Family: A Multi-Targeted Approach Using Network Pharmacology and Molecular Modeling Approaches.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 2, p. 167, doi. 10.1142/S2737416525500425

By:

Alamri, Abdulaziz;
Jabir, Nasimudeen R.;
Firoz, Chelapram K.;
Alsolami, Khadeejah;
Khan, Mohd Shahnawaz;
Alhashmi, Mohammad Hassan;
Tabrez, Shams

Publication type:

Article

Systems Biology and Molecular Dynamics Approach for Identifying Synergistic Drug Combinations in Cancer Therapy.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 1, p. 125, doi. 10.1142/S2737416525500401

By:

Ullah, Ihsan;
Firoz, Ahmad;
Anwar, Yasir;
Alghamdi, Khalid M. S.

Publication type:

Article

Targeting Pathogenic Desulfovibrio Species with a Novel Multi-Epitope Vaccine: A Reverse Vaccinology and Computational Approach.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 1, p. 25, doi. 10.1142/S2737416525500334

By:

Attar, Roba M. S.;
Abbas, Basma;
Aldakheel, Fahad M.;
Aljohani, Waad;
Aldaiji, Leen A.;
Al-Megrin, Wafa Abdullah I.;
Allemailem, Khaled S.

Publication type:

Article

Towards a standardised methodology of radiation damage defect distributions for microstructure evolution models.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-05661-2

By:

Gutiérrez-Camacho, A.-C.;
Caturla, M. J.;
Sand, A. E.

Publication type:

Article

Comparative analysis of biodesulfurization of dibenzothiophene (DBT) and 4,6-dimethyl dibenzothiophene (4,6-DMDBT) by 4S pathway using molecular simulations.

Published in:

Preparative Biochemistry & Biotechnology, 2025, v. 55, n. 6, p. 719, doi. 10.1080/10826068.2024.2448183

By:

Das, Pushpita;
Umesh;
Barbora, Lepakshi;
Moholkar, Vijayanand Suryakant

Publication type:

Article

Machine learning-driven molecular dynamics decodes thermal tuning in graphene foam composites.

Published in:

NPJ Computational Materials, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41524-025-01710-6

By:

Zhang, Pingyang;
Zhang, Shaodong;
Qin, Yihan;
Du, Tingting;
Wei, Lei;
Li, Xiangyu

Publication type:

Article

Combining Experiment and Theory to Understand the Corrosion Inhibition of Salicylamide and Sesamol Derivatives.

Published in:

Surface & Interface Analysis: SIA, 2025, v. 57, n. 8, p. 576, doi. 10.1002/sia.7417

By:

Ma, Yanheng;
Yan, Xuefeng;
Zhang, Linghui;
Yu, Liangmin;
Li, Xia

Publication type:

Article

Interaction of Three Flavonoids with α-Amylase and Their Effect on Its Stability.

Published in:

Journal of Chinese Institute of Food Science & Technology / Zhongguo Shipin Xuebao, 2025, v. 25, n. 5, p. 166, doi. 10.16429/j.1009-7848.2025.016

By:

LIU Yi;
SU Dongyu;
ZHANG Yingxin;
BAN Chenyu;
ZHOU Suzhen;
FAN Jinbo

Publication type:

Article

All‐In‐One Carbon Foam Evaporators for Efficient Co‐Generation of Freshwater and Electricity.

Published in:

Advanced Functional Materials, 2025, v. 35, n. 27, p. 1, doi. 10.1002/adfm.202423781

By:

Hu, Guixin;
Liu, Huajian;
Liu, Kuankuan;
Wang, Huiyue;
Wen, Xueying;
Liu, Lijie;
She, Yan;
Feng, Lingling;
Niu, Ran;
Gong, Jiang

Publication type:

Article

In situ XAFS study on the chemical states of transition-metal nanoparticle catalysts during single-walled carbon nanotube growth under conventional CVD conditions.

Published in:

Journal of Nanoparticle Research, 2025, v. 27, n. 6, p. 1, doi. 10.1007/s11051-025-06359-2

By:

Mizuno, Shinya;
Horiuchi, Jumpei;
Sharma, Kamal Prasad;
Saida, Takahiro;
Maruyama, Takahiro

Publication type:

Article

Thermodynamic properties of rhodium nanoparticles: size, shape, and temperature dependence.

Published in:

Journal of Nanoparticle Research, 2025, v. 27, n. 6, p. 1, doi. 10.1007/s11051-025-06350-x

By:

Tam, Nguyen Trong;
Hieu, Ho Khac

Publication type:

Article

Mechanical properties of crystalline and amorphous nickel nanoparticles: molecular dynamics simulation.

Published in:

Journal of Nanoparticle Research, 2025, v. 27, n. 6, p. 1, doi. 10.1007/s11051-025-06354-7

By:

Poletaev, Gennady;
Sannikov, Andrey;
Gafner, Yury;
Gafner, Svetlana;
Zorya, Irina

Publication type:

Article

Computational analysis of luteolin, apigenin and their derivatives from Allophylus africanus as potential inhibitors of plasmepsin II a malaria target.

Published in:

BMC Chemistry, 2025, v. 19, n. 1, p. 1, doi. 10.1186/s13065-025-01527-w

By:

Abubakari, Ismail;
Kwiyukwa, Lucas P.;
Paul, Lucas

Publication type:

Article

金刚石切削单晶镍纳米表面生成机理研究.

Published in:

China Mechanical Engineering, 2025, v. 36, n. 5, p. 963, doi. 10.3969/j.issn.l004-132X.2025.05.008

By:

郑江锋;
张国庆;
韩俊鸿;
赖志慧

Publication type:

Article

Subtractive proteomics and molecular docking identify therapeutic targets and drug candidates in drug resistant Klebsiella Michiganensis THO-011.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-08107-x

By:

Alanzi, Abdullah R.;
Alanazi, Ahmad Z.;
Alhazzani, Khalid;
Abbas, Munawar

Publication type:

Article

Synthesis, comprehensive in silico studies, and cytotoxicity evaluation of novel quinazolinone derivatives as potential anticancer agents.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-08062-7

By:

Haneen, David S. A.;
Abdalha, Abdelaal A.;
Alkhatib, Musaab M.;
Kamal, Mahmoud;
Youssef, Ahmed S. A.;
Abou-Elmagd, Wael S. I.;
Samir, Sandy S.

Publication type:

Article

Molecular underpinnings of hornwort CO2 concentrating mechanisms: subcellular localization of putative key molecular components in the model hornwort Anthoceros agrestis.

Published in:

New Phytologist, 2025, v. 247, n. 3, p. 1244, doi. 10.1111/nph.70167

By:

Ruaud, Stephanie;
Nötzold, Svenja I.;
Waller, Manuel;
Galbier, Florian;
Mousavi, Sabereh S.;
Charran, Mark;
Mateos, José María;
Zeeman, Samuel;
Baily, Aurélien;
Baroux, Célia;
Hippler, Michael;
Wicke, Susann;
Szövényi, Péter

Publication type:

Article

Characterization of a thermostable uricase derived from Thermoactinospora rubra YIM 77501T and its heat-resistant mechanism.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1615845

By:

Yan, Xin;
Tang, Lan-Xin;
Ortúzar, Maite;
Yang, Li-Quan;
Sang, Peng;
Jin, Na-Ying;
Li, Lin-Hua;
Yang, Zheng-Feng;
Wang, Yan-Wen;
Li, Wen-Jun;
Hu, Wei;
Yin, Yi-Rui

Publication type:

Article

Irreversible changes in amorphous C₃N₄ under pressure: loss of chemical order and graphite-like character.

Published in:

High Pressure Research, 2025, v. 45, n. 2, p. 124, doi. 10.1080/08957959.2025.2496647

By:

Durandurdu, Murat

Publication type:

Article

Nordihydroguaiaretic acid inhibits bladder cancer metastasis through suppression of α1,3-mannosyltransferase expression and LRFN4 N-glycosylation.

Published in:

Journal of Translational Medicine, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12967-025-06571-7

By:

Liu, Mulin;
Zhang, Jingyang;
Zhang, Tianya;
Zheng, Qin;
Li, Shijun

Publication type:

Article

Subtractive proteo-genomics and model-based druggability analyses prioritized nitrate reductase-A subunit-α as potential therapeutic target against MDR pneumonia; a homology-based approach.

Published in:

BMC Microbiology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12866-025-03883-y

By:

Begum, Kainat;
Aiman, Sara;
Khan, Asifullah;
Mumtaz, Mah Noor;
Ali, Fawad;
Hussain, Shaik Althaf;
Khan, Sara;
Shaik, Mohammed Rafi

Publication type:

Article

Deep learning-based dipeptidyl peptidase IV inhibitor screening, experimental validation, and GaMD/LiGaMD analysis.

Published in:

BMC Biology, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12915-025-02295-8

By:

He, Yi;
Zhang, Yan;
Liu, Minghao;
Li, Jiaying;
Li, Wannan;
Han, Weiwei

Publication type:

Article

Molecular dynamics in pharmaceutical nanotechnology: simulating interactions and advancing applications.

Published in:

Journal of Biomaterials Science -- Polymer Edition, 2025, v. 36, n. 10, p. 1502, doi. 10.1080/09205063.2025.2450150

By:

Mundada, Anand Badrivishal;
Pradhan, Pankaj;
Raju, Rajapandi;
Sujitha, Y. Sarah;
Kulkarni, Parag Arun;
Mundada, Pooja Anand;
Tiwari, Ruchi;
Sharma, Pankaj

Publication type:

Article

Experimental investigation and molecular dynamics simulations of plasma treatment on the interface properties of carbon fiber-reinforced PI resin composites.

Published in:

Composite Interfaces, 2025, v. 32, n. 7, p. 987, doi. 10.1080/09276440.2024.2448881

By:

Zhen, Guoqing;
Liu, Long;
Chen, Ping

Publication type:

Article

A single main-chain hydrogen bond required to keep GABAA receptors closed.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61447-0

By:

Borghese, Cecilia M.;
Galpin, Jason D.;
Eriksson Lidbrink, Samuel;
Zhuang, Yuxuan;
Desai, Netrang G.;
Howard, Rebecca J.;
Lindahl, Erik;
Ahern, Christopher A.;
Goldschen-Ohm, Marcel P.

Publication type:

Article

Effect of solvent-induced packing transitions on N-capped diphenylalanine peptide crystal growth.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61331-x

By:

Dan, Yoav;
Arnon, Zohar A.;
Tang, Yiming;
Kravikass, Mathar;
Zhou, Yun;
Misra, Rajkumar;
Tiwari, Om Shanker;
Shimon, Linda J. W.;
Beck, Roy;
Gazit, Ehud;
Wei, Guanghong;
Adler-Abramovich, Lihi

Publication type:

Article

Machine Learning simulations reveal oxygen's phase diagram and thermal properties at conditions relevant to white dwarfs.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61390-0

By:

Wang, Yunlong;
Shi, Jiuyang;
Liang, Zhixin;
Huang, Tianheng;
Wang, Junjie;
Ding, Chi;
Pickard, Chris J.;
Wang, Hui-Tian;
Xing, Dingyu;
Ni, Dongdong;
Sun, Jian

Publication type:

Article

Preference of negatively charged membranes in magnesium and lithium separation by nanofiltration.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61336-6

By:

Liu, Lulu;
Lin, Shihong;
Xu, Xinyi;
Wan, Yinhua;
Song, Weijie;
Luo, Jianquan

Publication type:

Article

Paschen–Back effect modulation of SO42- hydration in magnetized electrolyte toward dendrite-free Zn-ion batteries.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61310-2

By:

Yao, Xiayan;
Wang, Zhi;
Guo, Jianwei;
Qian, Guoyu;
Wang, Hongchen;
Gong, Xuzhong;
Wang, Dong

Publication type:

Article

Structural and functional insights of AmpG in muropeptide transport and multiple β-lactam antibiotics resistance.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61169-3

By:

Chang, Nienping;
Kim, Hoyoung;
Kim, Uijin;
Cho, Yongju;
Yoo, Youngki;
Lee, Hyunsook;
Kim, Ji Won;
Kim, Min Sung;
Lee, Jaeho;
Cho, Young-Lag;
Kim, Kitae;
Yong, Dongeun;
Cho, Hyun-Soo

Publication type:

Article

Bridging cell morphological behaviors and molecular dynamics in multi-modal spatial omics with MorphLink.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61142-0

By:

Huang, Jing;
Yuan, Chenyang;
Jiang, Jiahui;
Chen, Jianfeng;
Badve, Sunil S.;
Gokmen-Polar, Yesim;
Segura, Rossana L.;
Yan, Xinmiao;
Lazar, Alexander;
Gao, Jianjun;
Yao, Bing;
Epstein, Michael;
Wang, Linghua;
Hu, Jian

Publication type:

Article

An O-glycopeptide participates in the formation of distinct Aβ42 fibril structures and attenuates Aβ42 neurotoxicity.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60978-w

By:

Wei, Qijia;
Liu, Dangliang;
Xia, Wencheng;
Wang, Fengzhang;
Huang, Lu;
Zhang, Jun;
Wang, Xiaoya;
Xu, Zhongxin;
He, Changdong;
Li, Wenzhe;
Shi, Xiaomeng;
Wang, Chu;
Liu, Yuan;
Liu, Cong;
Dong, Suwei

Publication type:

Article

Nuclear quantum effects in molecular liquids across chemical space.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60850-x

By:

Ugur, Baris E.;
Webb, Michael A.

Publication type:

Article

An adaptive peptide-binding site in ubiquitin receptor hRpn13 revealed by structural studies.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60843-w

By:

Hassan, Bakar;
Chandravanshi, Monika;
Ng, Martin Y.;
Negi, Hitendra;
Wilson, Brice A. P.;
Walters, Kylie J.

Publication type:

Article

Structure-based discovery and experimental validation of HIT101481851 as a potential PKMYT1 inhibitor for pancreatic cancer.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1605741

By:

Wang, Ting;
Wang, Jingyu;
Yao, Gongxiong;
Zhang, Hongchao;
Song, Chenghui;
Ao, Xueren

Publication type:

Article

The processed Sanguisorba officinalis L. triterpenoids prevent colon cancer through the TNF- α /NF-κB signaling pathway, combined with network pharmacology, molecular simulation dynamics and experimental verification.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1605326

By:

Gan, Chunli;
Mu, Yuanqiu;
Ali, Shah Syed Faizan;
Shi, Xuepeng;
Jiang, Shuang;
Wang, Zhengyang;
Wu, Xiaotian;
Wang, Xiaotong;
Wang, Zhibin;
Zhang, Shulu;
Feng, Zheng;
Yang, Chunjuan

Publication type:

Article

A small molecule enhances arrestin-3 binding to the β2-adrenergic receptor.

Published in:

Communications Chemistry, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42004-025-01581-4

By:

Kurt, Han;
Akyol, Ali;
Son, Cagdas Devrim;
Zheng, Chen;
Gado, Irene;
Meli, Massimiliano;
Ferrandi, Erica Elisa;
Bassanini, Ivan;
Vasile, Francesca;
Gurevich, Vsevolod V.;
Nebol, Aylin;
Cagavi, Esra;
Morra, Giulia;
Sensoy, Ozge

Publication type:

Article

Stability of colloidal gas aphrons based on polymer-surfactant formulations and molecular dynamics insights.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-08100-4

By:

Amankeldiyeva, Ayaulym;
Kaumbekova, Samal;
Khalidulliyeva, Aigerim;
Salimova, Zhanat;
Ibrayeva, Aizhan;
Cochennec, Maxime;
Colombano, Stéfan;
Amanbek, Yerlan;
Wang, Yanwei;
Omirbekov, Sagyn

Publication type:

Article

Lablab purpureus phytochemicals demonstrate potential anticancer activity as evidenced through experimental and computational analysis.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-06992-w

By:

Bhat, Smitha S.;
Jahagirdar, Sushma;
Dharmashekar, Chandan;
Lumsangkul, Chompunut;
Sommano, Sarana Rose;
Ahmad, Sheikh F.;
Al-Mazroua, Haneen A.;
Azimi, Iman;
Shivamallu, Chandan;
Prasad, Shashanka K.

Publication type:

Article

Chiral pyrimidinyl-piperazine carboxamide derivatives as potent yeast α-glucosidase inhibitors.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-06104-8

By:

Herfindo, Noval;
Mikled, Pirun;
Frimayanti, Neni;
Rungrotmongkol, Thanyada;
Chavasiri, Warinthorn

Publication type:

Article

Effect of physical properties of liquid phase by MD simulation on NaCl separation behavior during the phase transition of molten salt chloride slag.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-05909-x

By:

Guo, Yufeng;
Wen, Yuekai;
Chen, Feng;
Zheng, Yu;
Wang, Shuai;
Yang, Lingzhi;
Zhang, Meng

Publication type:

Article

Pressure induced irreversible phase transformation in an ordered high-entropy alloy.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-05327-z

By:

Pope, Andrew D.;
Xie, Bijun;
Sereika, Raimundas;
Yang, Wuxian;
Chen, Wen;
Chen, Hangman;
Cao, Penghui;
Vohra, Yogesh K.

Publication type:

Article

CO2 capture with hydrophobic halogen‐free natural deep eutectic solvents: Perturbed‐Chain Statistical Associating Fluid Theory modeling and molecular insights.

Published in:

AIChE Journal, 2025, v. 71, n. 8, p. 1, doi. 10.1002/aic.18878

By:

Yu, Gangqiang;
Fu, Yuxuan;
Mu, Wenbo;
Wang, Nan;
Jovein, Iman Bahrabadi;
Chen, Biaohua;
Sadowski, Gabriele;
Ji, Xiaoyan;
Held, Christoph

Publication type:

Article

π‐Electron‐driven ionic liquids to enhance lithium recovery from spent batteries: Experimental and mechanistic insights.

Published in:

AIChE Journal, 2025, v. 71, n. 8, p. 1, doi. 10.1002/aic.18860

By:

Guo, Yu;
Zhang, Xinhe;
Chen, Biaohua;
Sadowski, Gabriele;
Held, Christoph;
Yu, Gangqiang

Publication type:

Article