Ecoles Thématiques de la Société Française de la Neutronique

Improvement of the ReaxFF Description for Functionalized Hydrocarbon/Water Weak Interactions in the Condensed Phase

Weiwei Zhang and Adri C. T. van Duin
The Journal of Physical Chemistry B 122 (14) 4083 (2018)
DOI: 10.1021/acs.jpcb.8b01127
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Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility in a Single Descriptor

Jerome G. P. Wicker and Richard I. Cooper
Journal of Chemical Information and Modeling 56 (12) 2347 (2016)
DOI: 10.1021/acs.jcim.6b00565
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Intracellular Delivery II

Deniz Meneksedag-Erol, Chongbo Sun, Tian Tang and Hasan Uludag
Fundamental Biomedical Technologies, Intracellular Delivery II 7 277 (2014)
DOI: 10.1007/978-94-017-8896-0_15
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A Simple Representation of Three-Dimensional Molecular Structure

Seth D. Axen, Xi-Ping Huang, Elena L. Cáceres, et al.
Journal of Medicinal Chemistry 60 (17) 7393 (2017)
DOI: 10.1021/acs.jmedchem.7b00696
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Design of novel cell penetrating peptides for the delivery of trehalose into mammalian cells

Yuping Wei, Chunlong Li, Liang Zhang and Xia Xu
Biochimica et Biophysica Acta (BBA) - Biomembranes 1838 (7) 1911 (2014)
DOI: 10.1016/j.bbamem.2014.02.011
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A Molecular Dynamics Simulation Study of Hydroxyls in Dioctahedral Phyllosilicates

Sangbo Son and Kideok D. Kwon
Journal of the mineralogical society of korea 29 (4) 209 (2016)
DOI: 10.9727/jmsk.2016.29.4.209
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Brain grants permission of access to Zika virus but denies entry to drugs: a molecular modeling perspective to infiltrate the boundary

Nikita Devnarain, Pritika Ramharack and Mahmoud E. Soliman
RSC Adv. 7 (75) 47416 (2017)
DOI: 10.1039/C7RA05918C
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Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials

David Dubbeldam, Krista S. Walton, Thijs J. H. Vlugt and Sofia Calero
Advanced Theory and Simulations 2 (11) 1900135 (2019)
DOI: 10.1002/adts.201900135
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Advances in modelling switchable mechanically interlocked molecular architectures

Gloria Bazargan and Karl Sohlberg
International Reviews in Physical Chemistry 37 (1) 1 (2018)
DOI: 10.1080/0144235X.2018.1419042
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Xanthine oxidoreductase inhibition – A review of computational aspect

Chao Dong, Milka Montes and Wael M. Al-Sawai
Journal of Theoretical and Computational Chemistry 19 (04) 2040008 (2020)
DOI: 10.1142/S0219633620400088
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The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)

Jiangfeng Du, Yaping Qin, Yahong Wu, et al.
Cell Communication and Signaling 16 (1) (2018)
DOI: 10.1186/s12964-018-0239-9
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A Review of Multiscale Computational Methods in Polymeric Materials

Ali Gooneie, Stephan Schuschnigg and Clemens Holzer
Polymers 9 (12) 16 (2017)
DOI: 10.3390/polym9010016
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Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

Hao Wang and Weitao Yang
The Journal of Chemical Physics 144 (22) 224107 (2016)
DOI: 10.1063/1.4953558
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Trends in therapeutic antibody affinity maturation: From in-vitro towards next-generation sequencing approaches

Maryam Tabasinezhad, Yeganeh Talebkhan, Wolfgang Wenzel, et al.
Immunology Letters 212 106 (2019)
DOI: 10.1016/j.imlet.2019.06.009
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Encyclopedia of Bioinformatics and Computational Biology

Marco Wiltgen
Encyclopedia of Bioinformatics and Computational Biology 38 (2019)
DOI: 10.1016/B978-0-12-809633-8.20484-6
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Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

Vikram Sundar, David Gelbwaser-Klimovsky and Alán Aspuru-Guzik
The Journal of Physical Chemistry Letters 9 (7) 1721 (2018)
DOI: 10.1021/acs.jpclett.7b03254
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MOF-Based Membranes for Gas Separations

Qihui Qian, Patrick A. Asinger, Moon Joo Lee, et al.
Chemical Reviews 120 (16) 8161 (2020)
DOI: 10.1021/acs.chemrev.0c00119
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Molecular dynamics-driven drug discovery: leaping forward with confidence

Aravindhan Ganesan, Michelle L. Coote and Khaled Barakat
Drug Discovery Today 22 (2) 249 (2017)
DOI: 10.1016/j.drudis.2016.11.001
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Mechanistic insights into the role of glycosaminoglycans in delivery of polymeric nucleic acid nanoparticles by molecular dynamics simulations

Deniz Meneksedag-Erol, Tian Tang and Hasan Uludağ
Biomaterials 156 107 (2018)
DOI: 10.1016/j.biomaterials.2017.11.037
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CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

Seonghoon Kim, Jumin Lee, Sunhwan Jo, et al.
Journal of Computational Chemistry 38 (21) 1879 (2017)
DOI: 10.1002/jcc.24829
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Advances in Protein Chemistry and Structural Biology

Fernando D. Prieto-Martínez and José L. Medina-Franco
Advances in Protein Chemistry and Structural Biology 122 127 (2020)
DOI: 10.1016/bs.apcsb.2020.06.002
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Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble

Ivan Scivetti, Kakali Sen, Alin M. Elena and Ilian Todorov
The Journal of Physical Chemistry A 124 (37) 7585 (2020)
DOI: 10.1021/acs.jpca.0c05461
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An Evaluation of the Potential of NMR Spectroscopy and Computational Modelling Methods to Inform Biopharmaceutical Formulations

Akash Pandya, Mark Howard, Mire Zloh and Paul Dalby
Pharmaceutics 10 (4) 165 (2018)
DOI: 10.3390/pharmaceutics10040165
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Rising Up: Hierarchical Metal–Organic Frameworks in Experiments and Simulations

Yi Luo, Momin Ahmad, Alexander Schug and Manuel Tsotsalas
Advanced Materials 31 (26) 1901744 (2019)
DOI: 10.1002/adma.201901744
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Determination of confined fluid phase behavior using extended Peng-Robinson equation of state

Gang Yang, Zhaoqi Fan and Xiaoli Li
Chemical Engineering Journal 378 122032 (2019)
DOI: 10.1016/j.cej.2019.122032
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Efficient methods of X-ray diffraction pattern inversion

Ian Gregory Shuttleworth
Results in Physics 15 102605 (2019)
DOI: 10.1016/j.rinp.2019.102605
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Computational Modelling of Nanoparticles

Dean Sayle
Frontiers of Nanoscience, Computational Modelling of Nanoparticles 12 129 (2018)
DOI: 10.1016/B978-0-08-102232-0.00003-8
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Comparison of CHARMM and OPLS-aa forcefield predictions for components in one model asphalt mixture

Kolawole Sonibare, Lasantha Rathnayaka and Liqun Zhang
Construction and Building Materials 236 117577 (2020)
DOI: 10.1016/j.conbuildmat.2019.117577
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Atomic Force Microscopy

Fidan Sumbul and Felix Rico
Methods in Molecular Biology, Atomic Force Microscopy 1886 163 (2019)
DOI: 10.1007/978-1-4939-8894-5_9
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Homology Molecular Modeling - Perspectives and Applications [Working Title]

Jacob A. Bauer and Vladena Bauerová-Hlinková
Homology Molecular Modeling - Perspectives and Applications [Working Title] (2020)
DOI: 10.5772/intechopen.94139
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Cyanine dyes derived inhibition of insulin fibrillization

Kateryna Vus, Mykhailo Girych, Valeriya Trusova, et al.
Journal of Molecular Liquids 276 541 (2019)
DOI: 10.1016/j.molliq.2018.11.149
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A Classical Molecular Dynamics Study of the Mg²⁺ Coordination in Todorokite

Juhyeok Kim, Jin-Yong Lee and Kideok D. Kwon
Journal of the mineralogical society of korea 32 (3) 151 (2019)
DOI: 10.9727/jmsk.2019.32.3.151
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Modeling and Simulations of Polymers: A Roadmap

Thomas E. Gartner and Arthi Jayaraman
Macromolecules 52 (3) 755 (2019)
DOI: 10.1021/acs.macromol.8b01836
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Monoclonal Antibodies [Working Title]

Tania M. Manieri, Carolina G. Magalhaes, Daniela Y. Takata, João V. Batalha-Carvalho and Ana M. Moro
Monoclonal Antibodies [Working Title] (2020)
DOI: 10.5772/intechopen.94366
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In Silico Drug Design

Fernando D. Prieto-Martínez, Edgar López-López, K. Eurídice Juárez-Mercado and José L. Medina-Franco
In Silico Drug Design 19 (2019)
DOI: 10.1016/B978-0-12-816125-8.00002-X
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Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches

Paola Ruiz Puentes, María C. Henao, Carlos E. Torres, et al.
Antibiotics 9 (12) 854 (2020)
DOI: 10.3390/antibiotics9120854
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Interplay between synthetic conditions and micromorphology in poly(3,4-ethylenedioxythiophene):tosylate (PEDOT:Tos): an atomistic investigation

A. Cappai, A. Antidormi, A. Bosin, et al.
Physical Chemistry Chemical Physics 21 (16) 8580 (2019)
DOI: 10.1039/C9CP00970A
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An ab initio molecular dynamics method for cocrystal prediction: validation of the approach

Harsh Barua, Anilkumar Gunnam, Balvant Yadav, Ashwini Nangia and Nalini R. Shastri
CrystEngComm 21 (47) 7233 (2019)
DOI: 10.1039/C9CE01436E
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A computational and experimental approach to develop minocycline-imprinted hydrogels and determination of their drug delivery performances

Büsra Eroglu, Dilek Dalgakiran, Tugce Inan, Ozge Kurkcuoglu and F. Seniha Güner
Journal of Polymer Research 25 (12) (2018)
DOI: 10.1007/s10965-018-1647-7
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Interaction study between M-Phenylenediamine, Trimesoyl Chloride and Nylon 66 using Molecular Dynamic Simulation

W Z A W Jusoh, S A Rahman, A L Ahmad and N M Mokhtar
IOP Conference Series: Materials Science and Engineering 702 012030 (2019)
DOI: 10.1088/1757-899X/702/1/012030
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Peptide science: A “rule model” for new generations of peptidomimetics

Hannah R. Reese, Calvin C. Shanahan, Caroline Proulx and Stefano Menegatti
Acta Biomaterialia 102 35 (2020)
DOI: 10.1016/j.actbio.2019.10.045
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Classical molecular dynamics on graphics processing unit architectures

Ádám Jász, Ádám Rák, István Ladjánszki and György Cserey
WIREs Computational Molecular Science 10 (2) (2020)
DOI: 10.1002/wcms.1444
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Invited Review: Modern Methods for Accurately Simulating the Terahertz Spectra of Solids

Michael T. Ruggiero
Journal of Infrared, Millimeter, and Terahertz Waves 41 (5) 491 (2020)
DOI: 10.1007/s10762-019-00648-3
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Principal mode of Syndecan‐4 mechanotransduction for the endothelial glycocalyx is a scissor‐like dimer motion

Xi Zhuo Jiang, Kai H. Luo and Yiannis Ventikos
Acta Physiologica 228 (3) (2020)
DOI: 10.1111/apha.13376
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A review of atomistic simulation methods for surface physical-chemistry phenomena applied to froth flotation

Y. Foucaud, M. Badawi, L. Filippov, I. Filippova and S. Lebègue
Minerals Engineering 143 106020 (2019)
DOI: 10.1016/j.mineng.2019.106020
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Benchmark assessment of molecular geometries and energies from small molecule force fields

Victoria T. Lim, David F. Hahn, Gary Tresadern, Christopher I. Bayly and David L. Mobley
F1000Research 9 1390 (2020)
DOI: 10.12688/f1000research.27141.1
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Investigation of tetracosane thermal transport in presence of graphene and carbon nanotube fillers––A molecular dynamics study

Hossein Tafrishi, Sadegh Sadeghzadeh, Rouhollah Ahmadi, et al.
Journal of Energy Storage 29 101321 (2020)
DOI: 10.1016/j.est.2020.101321
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Development of Density Functional Tight-Binding Parameters Using Relative Energy Fitting and Particle Swarm Optimization

Néstor F. Aguirre, Amanda Morgenstern, M. J. Cawkwell, Enrique R. Batista and Ping Yang
Journal of Chemical Theory and Computation 16 (3) 1469 (2020)
DOI: 10.1021/acs.jctc.9b00880
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Thermophysical Properties of Amorphous‐Paracrystalline Celluloses by Molecular Dynamics

Jurgen Lange Bregado, Frederico Wanderley Tavares, Argimiro Resende Secchi and Iuri Soter Viana Segtovich
Macromolecular Theory and Simulations 29 (4) 2000007 (2020)
DOI: 10.1002/mats.202000007
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SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

Martin Amezcua, Léa El Khoury and David L. Mobley
Journal of Computer-Aided Molecular Design (2021)
DOI: 10.1007/s10822-020-00363-5
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Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase

Olivier Sheik Amamuddy, Thommas Mutemi Musyoka, Rita Afriyie Boateng, Sophakama Zabo and Özlem Tastan Bishop
Computational and Structural Biotechnology Journal 18 1103 (2020)
DOI: 10.1016/j.csbj.2020.05.009
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A critical study of the parameters governing molecular dynamics simulations of nanostructured materials

A.R. Alian and S.A. Meguid
Computational Materials Science 153 183 (2018)
DOI: 10.1016/j.commatsci.2018.06.028
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QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface

Prasanth B. Ganta, Oliver Kühn and Ashour A. Ahmed
Frontiers in Forests and Global Change 3 (2020)
DOI: 10.3389/ffgc.2020.00071
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Geo-Measures: A PyMOL plugin for protein structure ensembles analysis

Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres and Vera Lucia Eifler-Lima
Computational Biology and Chemistry 87 107322 (2020)
DOI: 10.1016/j.compbiolchem.2020.107322
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Force fields and molecular dynamics simulations

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