Works matching Molecular dynamics

Results: 5000

小分子凝胶的分子动力学模拟和汉森溶解度参数研究进展.

Published in:

Chinese Journal of Applied Chemistry, 2022, v. 39, n. 12, p. 1803, doi. 10.19894/j.issn.1000-0518.220053

By:

张万年;
于芳;
赵杉林;
张志强;
何宇鹏

Publication type:

Article

Seamless coupling of molecular dynamics and material point method via smoothed molecular dynamics.

Published in:

International Journal for Numerical Methods in Engineering, 2017, v. 112, n. 4, p. 380, doi. 10.1002/nme.5543

By:

He, Nianfeng;
Liu, Yan;
Zhang, Xiong

Publication type:

Article

Molecular dynamics-smoothed molecular dynamics (MD-SMD) adaptive coupling method with seamless transition.

Published in:

International Journal for Numerical Methods in Engineering, 2016, v. 108, n. 3, p. 233, doi. 10.1002/nme.5224

By:

He, Nianfeng;
Liu, Yan;
Zhang, Xiong

Publication type:

Article

Molecular dynamics simulation and steered molecular dynamics simulation on irisin dimers.

Published in:

Journal of Molecular Modeling, 2018, v. 24, n. 4, p. 1, doi. 10.1007/s00894-018-3609-8

By:

Gao, Qi;
Lu, Chao;
Wang, Xiao-Wen;
Zhang, Jun-Wei;
Song, Youtao;
Xue, You-Lin

Publication type:

Article

Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study.

Published in:

Biomolecules (2218-273X), 2021, v. 11, n. 2, p. 334, doi. 10.3390/biom11020334

By:

Hong, Shih-Ting;
Su, Yu-Cheng;
Wang, Yu-Jen;
Cheng, Tian-Lu;
Wang, Yeng-Tseng

Publication type:

Article

Unified quantum molecular dynamics method based on centroid molecular dynamics and semiempirical molecular orbital theory.

Published in:

International Journal of Quantum Chemistry, 2003, v. 95, n. 4/5, p. 372, doi. 10.1002/qua.10619

By:

Ohta, Yasuhito;
Ohta, Koji;
Kinugawa, Kenichi

Publication type:

Article

大大豆中一种富含半胱氨酸蛋白性质的分子动力学模拟.

Published in:

Journal of Jilin University (Science Edition) / Jilin Daxue Xuebao (Lixue Ban), 2022, v. 60, n. 5, p. 1202, doi. 10.13413/j.cnki.jdxblxb.2021454

By:

李洋;
王科飞;
胡海燕;
王志超;
李延春

Publication type:

Article

An improved smoothed molecular dynamics method with high‐order shape function.

Published in:

International Journal for Numerical Methods in Engineering, 2021, v. 122, n. 13, p. 3300, doi. 10.1002/nme.6664

By:

Wang, Shuai;
Zhao, LeiYang;
Liu, Yan

Publication type:

Article

Electrochemical Oxidation of UV Filters: A First‐Principles Molecular Dynamics Study.

Published in:

Chemistry - A European Journal, 2024, v. 30, n. 71, p. 1, doi. 10.1002/chem.202402924

By:

Álvarez, Luis;
Frank, Irmgard

Publication type:

Article

Microextraction of steroidal hormones from urine samples using natural deep eutectic solvents: insights into chemical interactions using molecular dynamics simulations: Microextraction of steroidal hormones from urine samples using natural deep eutectic solvents: insights into chemical interactions using molecular dynamics simulations: D. C. de Andrade et al

Published in:

Analytical & Bioanalytical Chemistry, 2025, v. 417, n. 7, p. 1305, doi. 10.1007/s00216-024-05560-x

By:

de Andrade, Débora Coelho;
Monteiro, Sofia Aquino;
de Oliveira, Tiago Espinosa;
Merib, Josias

Publication type:

Article

Ab Initio Molecular Dynamics Studies of the Electric-Field-Induced Catalytic Effects on Liquids.

Published in:

Topics in Catalysis, 2022, v. 65, n. 1-4, p. 40, doi. 10.1007/s11244-021-01487-0

By:

Cassone, Giuseppe;
Sponer, Jiri;
Saija, Franz

Publication type:

Article

A Study of a Protein-Folding Machine: Transient Rotation of the Polypeptide Backbone Facilitates Rapid Folding of Protein Domains in All-Atom Molecular Dynamics Simulations.

Published in:

International Journal of Molecular Sciences, 2023, v. 24, n. 12, p. 10049, doi. 10.3390/ijms241210049

By:

Sahakyan, Harutyun;
Nazaryan, Karen;
Mushegian, Arcady;
Sorokina, Irina

Publication type:

Article

Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement.

Published in:

International Journal of Molecular Sciences, 2023, v. 24, n. 4, p. 3596, doi. 10.3390/ijms24043596

By:

Menin, Silvia;
Pavan, Matteo;
Salmaso, Veronica;
Sturlese, Mattia;
Moro, Stefano

Publication type:

Article

Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations.

Published in:

International Journal of Molecular Sciences, 2019, v. 20, n. 15, p. 3780, doi. 10.3390/ijms20153780

By:

Yang, Ting;
Zhang, Wenying;
Cheng, Jie;
Nie, Yanhong;
Xin, Qi;
Yuan, Shuai;
Dou, Yusheng

Publication type:

Article

A Hamiltonian Replica Exchange Molecular Dynamics (MD) Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins.

Published in:

International Journal of Molecular Sciences, 2013, v. 14, n. 6, p. 12157, doi. 10.3390/ijms140612157

By:

Meli, Massimiliano;
Colombo, Giorgio

Publication type:

Article

Accelerating molecular dynamics simulations by a hybrid molecular dynamics-continuum mechanical approach.

Published in:

Soft Materials, 2022, v. 20, n. 4, p. 428, doi. 10.1080/1539445X.2022.2061513

By:

Bauer, Christof;
Ries, Maximilian;
Pfaller, Sebastian

Publication type:

Article

Theoretical Investigation of Interaction of Sorbitol Molecules with Alcohol Dehydrogenase in Aqueous Solution Using Molecular Dynamics Simulation.

Published in:

Cell Biochemistry & Biophysics, 2011, v. 59, n. 2, p. 79, doi. 10.1007/s12013-010-9116-x

By:

Bahrami, Homayoon;
Zahedi, Mansour;
Moosavi-Movahedi, Ali;
Azizian, Homa;
Amanlou, Massoud

Publication type:

Article

Diffusivity of CH 4 In Model Silica Nanopores: Molecular Dynamics and Quasichemical Mean Field Theory.

Published in:

Molecular Simulation, 2005, v. 31, n. 1, p. 57, doi. 10.1080/08927020512331325783

By:

Papadopoulos, George K.

Publication type:

Article

Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations.

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 7, p. 1135, doi. 10.1002/jcc.21144

By:

JI-LAI LI;
CAI-YUN GENG;
YUXIANG BU;
XU-RI HUANG;
CHIA-CHUNG SUN

Publication type:

Article

高磷赤铁矿直接还原过程中CaO脱磷机制的分子动力学模拟.

Published in:

Nonferrous Metals (Mineral Processing Section), 2022, n. 6, p. 35, doi. 10.3969/j.issn.1671-9492.2022.06.005

By:

李宗蔚;
寇珏;
孙体昌;
陈泽坤

Publication type:

Article

三种糖基化中间产物与小牛胸腺 DNA 相互作用的多光谱和分子动力学模拟.

Published in:

Journal of Nanchang University (Natural Science), 2023, v. 47, n. 3, p. 243

By:

吴健妹;
张国文

Publication type:

Article

Prediction of the Mechanism of Sodium Butyrate against Radiation-Induced Lung Injury in Non-Small Cell Lung Cancer Based on Network Pharmacology and Molecular Dynamic Simulations and Molecular Dynamic Simulations.

Published in:

Frontiers in Oncology, 2022, v. 12, p. 1, doi. 10.3389/fonc.2022.809772

By:

Zhang, Xiao-zhen;
Chen, Mao-jian;
Fan, Ping-ming;
Su, Ting-shi;
Liang, Shi-xiong;
Jiang, Wei

Publication type:

Article

Analysis of Influencing Factors on Cracking of SiO2 Materials Based on Molecular Dynamics Simulation at Ultralow Temperatures.

Published in:

Silicone Material, 2022, v. 36, n. 4, p. 593, doi. 10.14136/j.cnki.issn1673-2812.2022.04.008

By:

LV Shiming;
SHEN Caihua;
GUO Dan;
CHEN Wei;
LI Xuesong;
TANG Kai

Publication type:

Article

Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 11, p. 1181, doi. 10.1007/s10822-020-00338-6

By:

Atanasio, Silvia;
Deganutti, Giuseppe;
Reynolds, Christopher A.

Publication type:

Article

Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation.

Published in:

European Biophysics Journal, 2014, v. 43, n. 2/3, p. 81, doi. 10.1007/s00249-014-0942-4

By:

Sharma, Neeru;
Sonavane, Uddhavesh;
Joshi, Rajendra

Publication type:

Article

Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins.

Published in:

European Biophysics Journal, 2011, v. 40, n. 2, p. 181, doi. 10.1007/s00249-010-0638-3

By:

Kalikka, Janne;
Akola, Jaakko

Publication type:

Article

Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations.

Published in:

European Biophysics Journal, 2009, v. 38, n. 2, p. 185, doi. 10.1007/s00249-008-0369-x

By:

Peräkylä, Mikael

Publication type:

Article

Exploration of the activation pathway of Δα-Chymotrypsin with molecular dynamics simulations and correlation with kinetic experiments.

Published in:

European Biophysics Journal, 2008, v. 38, n. 1, p. 13, doi. 10.1007/s00249-008-0348-2

By:

Mätrai, Janka;
Jonckheer, Abel;
Joris, Eddy;
Krüger, Peter;
Carpenter, Eric;
Tuszynski, Jack;
De Maeyer, Marc;
Engelborghs, Yves

Publication type:

Article

Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations.

Published in:

Polymers (20734360), 2020, v. 12, n. 10, p. 2235, doi. 10.3390/polym12102235

By:

Lin, Wen-Wei;
Wang, Yu-Jen;
Ko, Cheng-Wen;
Cheng, Tain-Lu;
Wang, Yeng-Tseng

Publication type:

Article

Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality.

Published in:

Nanomaterials (2079-4991), 2023, v. 13, n. 13, p. 1905, doi. 10.3390/nano13131905

By:

Bystrov, Vladimir;
Likhachev, Ilya;
Filippov, Sergey;
Paramonova, Ekaterina

Publication type:

Article

Molecular dynamics-based insight of VEGFR-2 kinase domain: a combined study of pharmacophore modeling and molecular docking and dynamics.

Published in:

Journal of Molecular Modeling, 2023, v. 29, n. 1, p. 1, doi. 10.1007/s00894-022-05427-x

By:

Parves, Md. Rimon;
Riza, Yasir Mohamed;
Alam, Sanjida;
Jaman, Sadia

Publication type:

Article

Structural and electronic structure differences due to the O–H···O and O–H···S bond formation in selected benzamide derivatives: a first-principles molecular dynamics study.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2009, v. 124, n. 5/6, p. 319, doi. 10.1007/s00214-009-0612-2

By:

Jezierska, Aneta;
Panek, Jarosław J.;
Mazzarello, Riccardo

Publication type:

Article

Double Lattice Potential for Molecular Dynamics Simulation of Silicon with Demonstrated Validity.

Published in:

Journal of Materials Science & Engineering (1673-2812), 2022, v. 40, n. 6, p. 974, doi. 10.14136/j.cnki.issn1673-2812.2022.06.009

By:

WEI Chongyang;
ZHANG Hui;
LIU Zhongwu;
ZHONG Xiehun;
JIAO Dongling;
QIU Wanqi;
YU Hongya

Publication type:

Article

Implementation of the replica‐exchange molecular dynamics method for rigid bodies.

Published in:

International Journal of Quantum Chemistry, 2006, v. 106, n. 10, p. 2208, doi. 10.1002/qua.20940

By:

Moskovsky, A. A.;
Vanovschi, V. V.;
Konyukhov, S. S.;
Nemukhin, A. V.

Publication type:

Article

Chemical Reaction Dynamics of PeCB and TCDD Decomposition: A Tight-Binding Quantum Chemical Molecular Dynamics Study with First-Principles Parameterization.

Published in:

International Journal of Quantum Chemistry, 2005, v. 102, n. 3, p. 318, doi. 10.1002/qua.20396

By:

Suzuki, Ai;
Selvam, Parasuraman;
Kusagaya, Tomonori;
Takami, Seiichi;
Kubo, Momoji;
Imamura, Akira;
Miyamoto, Akira

Publication type:

Article

Transparent interface between classical molecular dynamics and first-principles molecular dynamics.

Published in:

International Journal of Quantum Chemistry, 2003, v. 93, n. 1, p. 1, doi. 10.1002/qua.10480

By:

Du, Mao‐Hua;
Cheng, Hai‐Ping

Publication type:

Article

Molecular dynamics simulations provide molecular insights into the role of HLA‐B51 in Behçet's disease pathogenesis.

Published in:

Chemical Biology & Drug Design, 2020, v. 96, n. 1, p. 644, doi. 10.1111/cbdd.13658

By:

Gur, Mert;
Golcuk, Mert;
Gul, Ahmet;
Erman, Burak

Publication type:

Article

Experimental Investigation and Molecular Dynamics Modeling of the Effects of K 2 O on the Structure and Viscosity of SiO 2 -CaO-Al 2 O 3 -MgO-K 2 O Slags at High Temperatures.

Published in:

Metals (2075-4701), 2025, v. 15, n. 6, p. 590, doi. 10.3390/met15060590

By:

Yang, Fan;
Xue, Qingguo;
Zuo, Haibin;
Liu, Yu;
Wang, Jingsong

Publication type:

Article

Molecular dynamics of vegetable oil extraction and degumming: Analysis of micelles and phospholipid bilayers in different solvents.

Published in:

Journal of the American Oil Chemists' Society (JAOCS), 2024, v. 101, n. 2, p. 205, doi. 10.1002/aocs.12731

By:

Biasi, Lilian Caroline Kramer;
Rodrigues, Christianne Elisabete da Costa;
Pessoa Filho, Pedro de Alcântara

Publication type:

Article

NORMAL MODE ANALYSIS OF A SINGLE-WALLED CARBON NANOTUBE BASED ON MOLECULAR DYNAMIC:: A SINGULAR VALUE DECOMPOSITION STUDY.

Published in:

International Journal of Nanoscience, 2010, v. 9, n. 5, p. 471, doi. 10.1142/S0219581X10007125

By:

NEGI, S.;
CHATURVEDI, S.

Publication type:

Article

STUDY ON NANOMETRIC CUTTING MECHANISM AND BURR FORMATION USING MOLECULAR DYNAMICS SIMULATION.

Published in:

International Journal of Nanoscience, 2006, v. 5, n. 4/5, p. 547, doi. 10.1142/S0219581X06004772

By:

WU, H.;
FANG, F. Z.;
PEI, Q. X.

Publication type:

Article

Morphology and Crystal Planes Effects on Supercapacitance of CeO2 Nanostructures: Electrochemical and Molecular Dynamics Studies.

Published in:

Particle & Particle Systems Characterization, 2018, v. 35, n. 10, p. N.PAG, doi. 10.1002/ppsc.201800176

By:

Jeyaranjan, Aadithya;
Sakthivel, Tamil Selvan;
Molinari, Marco;
Sayle, Dean C.;
Seal, Sudipta

Publication type:

Article

Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes.

Published in:

Photosynthesis Research, 2011, v. 110, n. 1, p. 25, doi. 10.1007/s11120-011-9689-2

By:

Vassiliev, Serguei;
Mahboob, Abdullah;
Bruce, Doug

Publication type:

Article

Dissolution behavior and molecular dynamics study of cellulose in quaternary ammonium hydroxide/ethylenediamine solvent system.

Published in:

Cellulose, 2025, v. 32, n. 8, p. 4725, doi. 10.1007/s10570-025-06568-x

By:

Zhang, Haopeng;
Liu, Miaoqing;
Zhao, Xiaoying;
Zhang, Lifeng;
Yin, Xuewen;
Lu, Jianjun

Publication type:

Article

Recrystallization and size distribution of dislocated segments in cellulose microfibrils—a molecular dynamics perspective.

Published in:

Cellulose, 2021, v. 28, n. 10, p. 6007, doi. 10.1007/s10570-021-03906-7

By:

Khodayari, Ali;
Hirn, Ulrich;
Spirk, Stefan;
Van Vuure, Aart W.;
Seveno, David

Publication type:

Article

High-temperature decomposition of the cellulose molecule: a stochastic molecular dynamics study.

Published in:

Cellulose, 2017, v. 24, n. 7, p. 2713, doi. 10.1007/s10570-017-1325-7

By:

Paajanen, Antti;
Vaari, Jukka

Publication type:

Article

Molecular Dynamics Analysis of Thermalization of a Microcanonical Ensemble.

Published in:

Fluid Dynamics, 2024, v. 59, n. 8, p. 2487, doi. 10.1134/S0015462824605230

By:

Surzhikov, S. T.

Publication type:

Article

Adsorption of Oxygen and Nitrogen Atoms on the SiO2 Surface: Molecular Dynamics Calculation Based on the Quantum-Mechanical Potential.

Published in:

Fluid Dynamics, 2024, v. 59, n. 4, p. 924, doi. 10.1134/S0015462824602675

By:

Kroupnov, A. A.;
Pogosbekian, M. Ju.

Publication type:

Article

Antoine Equation Coefficients for Novichok Agents (A230, A232, and A234) via Molecular Dynamics Simulations.

Published in:

Physchem, 2023, v. 3, n. 2, p. 244, doi. 10.3390/physchem3020017

By:

Chalaris, Michail;
Koufou, Antonios

Publication type:

Article

Molecular Dynamics Simulation Study of Stabilizer Association with the Val122Ile Transthyretin Variant.

Published in:

Biophysica, 2025, v. 5, n. 2, p. 16, doi. 10.3390/biophysica5020016

By:

Morris, Kevin;
DeSalvo, John;
Deanparvar, Iman;
Schneider, Lucus;
Leach, Kaleigh;
George Jr., Matthew;
Fang, Yayin

Publication type:

Article