المؤلفون: Li, Junhao, Kumar, Amit, Långström, Bengt, Nordberg, Agneta, Ågren, Hans

المصدر: ACS Chemical Neuroscience. 14(18):3528-3539

مصطلحات موضوعية: 4R tau fibrils, metadynamics, positron emission tomography tracer, free energy surface, Alzheimer disease, molecular dynamics

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-511105
https://doi.org/10.1021/acschemneuro.3c00437
https://uu.diva-portal.org/smash/get/diva2:1795211/FULLTEXT01.pdf

المؤلفون: Timothy J. Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M. York

مصطلحات موضوعية: Molecular Biology, Physiology, Statistics, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, whereas approaches like, umbrella potential placement, free energy profile, efficiently optimize low, dimensional reaction pathways, >- transphosphorylation reaction, expensive quantum mechanical, previous string iterations, modified string method, accelerated string method, free energy surface, current best estimate, aggregate sampling obtained, synthetic images used, string method, sampling obtained, tautomeric reaction, molecular mechanical, images used, sampling performed, perform sampling, available sampling, three algorithms

Relation: https://figshare.com/articles/journal_contribution/Surface-Accelerated_String_Method_for_Locating_Minimum_Free_Energy_Paths/25238357

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01401.s001
https://figshare.com/articles/journal_contribution/Surface-Accelerated_String_Method_for_Locating_Minimum_Free_Energy_Paths/25238357

المؤلفون: Costil, Romain, Sterling, Alistair J, Duarte, Fernanda, Clayden, Jonathan

المصدر: Angewandte Chemie International Edition. 59(42)

مصطلحات موضوعية: atropisomers, diarylamines, dynamic stereochemistry, free energy surface, molecular dynamics, Chemical Sciences, Organic Chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/4nd019vh
https://escholarship.org/content/qt4nd019vh/qt4nd019vh.pdf

المؤلفون: Zhou, Yang, Li, Jonhao, Nordberg, Agneta, Ågren, Hans

المصدر: ACS Chemical Neuroscience. 12(18):3487-3496

مصطلحات موضوعية: Corticobasal degeneration, metadynamics, positron emission tomography tracer, free energy surface, Alzheimer disease, binding profile

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-456927
https://doi.org/10.1021/acschemneuro.1c00536
https://uu.diva-portal.org/smash/get/diva2:1605812/FULLTEXT01.pdf

المؤلفون: Briccolani‐bandini, Lorenzo, Brémond, Eric, Pagliai, Marco, Cardini, Gianni, Ciofini, Ilaria, Adamo, Carlo

المساهمون: Interfaces, Traitements, Organisation et Dynamique des Systèmes (ITODYS (UMR_7086)), Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institute of Chemistry for Life and Health Sciences (iCLeHS), Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS)

المصدر: ISSN: 0192-8651.

مصطلحات موضوعية: Ab initio molecular dynamics density functional theory free energy surface proton transfer, Ab initio molecular dynamics, density functional theory, free energy surface, proton transfer, [CHIM]Chemical Sciences

Relation: hal-04288470; https://hal.science/hal-04288470; https://hal.science/hal-04288470/document; https://hal.science/hal-04288470/file/Bricco_et_alREV2.pdf

الاتاحة: https://hal.science/hal-04288470
https://hal.science/hal-04288470/document
https://hal.science/hal-04288470/file/Bricco_et_alREV2.pdf
https://doi.org/10.1002/jcc.27198

المؤلفون: ZhongTing Zhang, ZhouYu Fang, HengAn Wu, YinBo Zhu

مصطلحات موضوعية: Biophysics, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, recent experiments extend, reaction path along, free energy surface, free energy gradient, corresponding local minima, atomically disordered diamonds, range order realized, formed inherently different, dependent paracrystalline nucleation, tetrahedral amorphous carbons, real experimental temperatures, amorphous carbons, paracrystalline diamond, narrow range, different temperatures, using metadynamics, shed light, related methods, performed atomistic, inappropriate temperatures, easily hindered, current understanding, based simulations, atomic disorder, arrhenius framework

Relation: https://figshare.com/articles/journal_contribution/Temperature-Dependent_Paracrystalline_Nucleation_in_Atomically_Disordered_Diamonds/24898022

الاتاحة: https://doi.org/10.1021/acs.nanolett.3c04037.s001
https://figshare.com/articles/journal_contribution/Temperature-Dependent_Paracrystalline_Nucleation_in_Atomically_Disordered_Diamonds/24898022

المؤلفون: Massimo Bocus (7246757), Louis Vanduyfhuys (1951726), Frank De Proft (7474127), Bert M. Weckhuysen (1317540), Veronique Van Speybroeck (7359878)

مصطلحات موضوعية: Biophysics, Biochemistry, Evolutionary Biology, Infectious Diseases, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, rate enhancement disappears, protic guest molecules, hydronium ion occurs, fully solvated regime, free energy surface, despite extensive research, realistic operating conditions, elusive arenium ion, important industrial reaction, aromatic electrophilic substitution, catalyzed benzene ethylation, benzene ethylation, reaction conditions, elusive intermediates, electrophilic attack, aromatic ring, benzene ring, reaction mechanism, reaction intermediates, key reaction, wheland complex

Relation: https://figshare.com/articles/journal_contribution/Mechanistic_Characterization_of_Zeolite-Catalyzed_Aromatic_Electrophilic_Substitution_at_Realistic_Operating_Conditions/19115901

الاتاحة: https://doi.org/10.1021/jacsau.1c00544.s001

المؤلفون: Annalisa Cardellini, Francesco Maria Bellussi, Edoardo Rossi, Lorenzo Chiavarini, Claude Becker, David Cant, Pietro Asinari, Marco Sebastiani

المصدر: Materials & Design, Vol 208, Iss , Pp 109902- (2021)

مصطلحات موضوعية: Low-free-energy surface design, Surface characterization, Molecular dynamics, Contact angle, XPS, Materials of engineering and construction. Mechanics of materials, TA401-492

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S026412752100455X; https://doaj.org/toc/0264-1275

URL الوصول: https://doaj.org/article/6f329903b9e440488501408760aba7dc

المؤلفون: Hu, Zheyao, Martí Rabassa, Jordi

المساهمون: Universitat Politècnica de Catalunya. Doctorat en Física Computacional i Aplicada, Universitat Politècnica de Catalunya. Departament de Física, Universitat Politècnica de Catalunya. CCQM - Condensed, Complex and Quantum Matter Group

مصطلحات موضوعية: Àrees temàtiques de la UPC::Física, Drugs -- Research, Drug prototype, Derivatives, KRAS-G12D, Well-tempered metadynamics, Free-energy surface, Farmàcia--Investigació

وصف الملف: application/pdf

Relation: Hu, Z.; Marti, J. In silico drug derivatives for KRAS-G12D: free-energy surfaces in aqueous solution by well-tempered metadynamics simulations. "Molecular physics", 15 Febrer 2024; http://hdl.handle.net/2117/403331

الاتاحة: http://hdl.handle.net/2117/403331
https://doi.org/10.1080/00268976.2024.2316883

المؤلفون: Salah Uddin, K. M.

المساهمون: Kassel, Universität Kassel, Fachbereich Bauingenieur- und Umweltingenieurwesen, Middendorf, Bernhard (Prof. Dr.), Koenders, Eduardus (Prof. Dr.)

مصطلحات موضوعية: Hydration mechanism of Portland Cement, dissolution of C3S and C2S, reactivity of different surfaces, homogeneous nucleation, molecular dynamic simulation, Reactive Force Field theory (ReaxFF), metadynamics, free energy surface, carbonation mechanism of Portlandite, relative humidity, Hydratationsmechanismus von Portlandzement, Auflösung von C3S und C2S, Reaktivität verschiedener Oberflächen, homogene Keimbildung, Molekulardynamiksimulation, Reaktive Kraftfeldtheorie (ReaxFF), Metadynamik, Freie-Energie-Oberfläche, Karbonatisierungsmechanismus von Portlandit, relative Feuchte, ddc:500, ddc:690, swd:Hydratisierung, swd:Portlandzement, swd:Auflösung, swd:Alit, swd:Reaktivität, swd:Molekulardynamik, swd:Freie Oberfläche, swd:Carbonatisierung

Relation: http://doi.org/doi:10.17170/kobra-202009211835

الاتاحة: https://doi.org/10.17170/kobra-202009211835

المؤلفون: Xiangda Peng (2792242), Michael Baxa (11868425), Nabil Faruk (1458574), Joseph R. Sachleben (2217997), Sebastian Pintscher (1300281), Isabelle A. Gagnon (11868428), Scott Houliston (468620), Cheryl H. Arrowsmith (246847), Karl F. Freed (181039), Gabriel J. Rocklin (5585783), Tobin R. Sosnick (181042)

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Biotechnology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, underlying physiochemical interactions, two naturally occurring, partial unfolding event, ongoing challenges faced, free energy surface, energy function using, two designed proteins, stable native states, calculating accurate fess, rare states, native ensemble, folding proteins, upside <, scale openings, resulting increase, protein ’, protein stability, protein including, properly encoded, powerful measurement

Relation: https://figshare.com/articles/journal_contribution/Prediction_and_Validation_of_a_Protein_s_Free_Energy_Surface_Using_Hydrogen_Exchange_and_Importantly_Its_Denaturant_Dependence/17397242

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00960.s001

المؤلفون: Jérôme Hénin (1334514)

مصطلحات موضوعية: Medicine, Biotechnology, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, variance reduction schemes, poisson equation formalism, perform helmholtz decomposition, low intrinsic dimension, lelie ́ vre, hidden barriers due, free energy surface, enhanced sampling methods, collective variables module, adaptive biasing force, thermodynamic integration family, system variant eabf, portable c ++, umbrella sampling simulations, noisy gradient estimates, based analysis toolchain, poisson integration algorithm, umbrella integration, eabf simulations, portable implementation, standalone tool, slower exploration, simple cases

Relation: https://figshare.com/articles/journal_contribution/Fast_and_Accurate_Multidimensional_Free_Energy_Integration/16834410

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00593.s001

المؤلفون: Fabian Dingfelder (3933965), Iuri Macocco (11128663), Stephan Benke (1736266), Daniel Nettels (1362219), Pietro Faccioli (319367), Benjamin Schuler (220257)

مصطلحات موضوعية: Biophysics, Biochemistry, Molecular Biology, Evolutionary Biology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, stopped-flow, origin, Pore-Forming Toxin Cytolysin, trap, kinetic, Slow Escape, helical content, path-sampling approach, single-molecule, nonnative topology, transfer, glimpse, Molecular dynamics simulations, nanosecond, microfluidic, Helical Misfolded State, hundred, α- helical monomer, ClyA monomer, protomer conformation, free-energy surface, spectroscopy

Relation: https://figshare.com/articles/journal_contribution/Slow_Escape_from_a_Helical_Misfolded_State_of_the_Pore-Forming_Toxin_Cytolysin_A/14977642

الاتاحة: https://doi.org/10.1021/jacsau.1c00175.s001

المؤلفون: Lara Callea (10921551), Laura Bonati (420068), Stefano Motta (4216600)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Immunology, Infectious Diseases, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, SMD, unbinding pathways, entrance pathway, PCV, binding cavity, Metadynamics-Based Approaches, free-energy surface, ligand binding processes, CV, elucidating ligand binding processes, Hypoxia-Inducible Factor 2α Ligand ., binding affinity scale, binding processes

Relation: https://figshare.com/articles/journal_contribution/Metadynamics-Based_Approaches_for_Modeling_the_Hypoxia-Inducible_Factor_2_Ligand_Binding_Process/14729898

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00114.s001

المؤلفون: Florian E. Blanc (10450756), Marco Cecchini (358268)

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, rotaxane, Symmetric Molecular Machine, design principle, Asymmetric Mechanism, free-energy calculations, transition path optimizations, free-energy surface, analysis, sequential mechanism, free-energy landscape

Relation: https://figshare.com/articles/journal_contribution/An_Asymmetric_Mechanism_in_a_Symmetric_Molecular_Machine/14308729

الاتاحة: https://doi.org/10.1021/acs.jpclett.1c00404.s001

المؤلفون: Szmitek, Jakub

المساهمون: Heard, Christopher James, Loi, Federico, Erlebach, Andreas

مصطلحات موضوعية: Diffusion, Cluster, Zeolite, Catalyst, Free Energy Surface, Molecular Dynamics, Enhanced Sampling, Machine Learning, Neural network potentials, Difúze, klastry, zeolity, katalyzátory, povrch volné energie, molekulová dynamika, vylepšené vzorkování, strojové učení, sítě neuronových potenciálů

وصف الملف: application/pdf

Relation: http://hdl.handle.net/20.500.11956/194209; 253057

الاتاحة: https://hdl.handle.net/20.500.11956/194209

المؤلفون: Chiavazzo, Eliodoro, Covino, Roberto, Coifman, Ronald R., Gear, C. William, Georgiou, Anastasia S., Hummer, Gerhard, Kevrekidis, Ioannis G.

المصدر: Proceedings of the National Academy of Sciences of the United States of America, 2017 Jul 01. 114(28), E5494-E5503.

URL الوصول: https://www.jstor.org/stable/26486494

المؤلفون: Nomura, Kentaro, Kaneko, Toshihiro, Bai, Jaeil, Francisco, Joseph S., Yasuoka, Kenji, Zeng, Xiao Cheng

المصدر: Proceedings of the National Academy of Sciences of the United States of America, 2017 Apr . 114(16), 4066-4071.

URL الوصول: https://www.jstor.org/stable/26480407

المؤلفون: Yang, Mingfeng, Teplow, David B

المصدر: Journal of Molecular Biology. 384(2)

مصطلحات موضوعية: Brain Disorders, Neurosciences, Neurodegenerative, Aging, Alzheimer's Disease, Dementia, Acquired Cognitive Impairment, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Amino Acid Sequence, Amyloid beta-Peptides, Aspartic Acid, Computer Simulation, Hydrogen Bonding, Molecular Sequence Data, Motion, Peptide Fragments, Protein Folding, Protein Isoforms, Protein Structure, Secondary, Protein Structure, Tertiary, Surface Properties, Thermodynamics, Alzheimer's disease, amyloid beta-protein, protein folding, molecular dynamics, free-energy surface, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Microbiology, Biochemistry & Molecular Biology

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/1qk432jv

المؤلفون: Yang, Mingfeng, Teplow, David B

المصدر: Journal of molecular biology. 384(2)

مصطلحات موضوعية: Aspartic Acid, Peptide Fragments, Protein Isoforms, Amino Acid Sequence, Protein Structure, Secondary, Protein Structure, Tertiary, Protein Folding, Hydrogen Bonding, Surface Properties, Motion, Thermodynamics, Computer Simulation, Molecular Sequence Data, Amyloid beta-Peptides, Alzheimer's disease, amyloid beta-protein, protein folding, molecular dynamics, free-energy surface, Biochemistry & Molecular Biology, Biochemistry and Cell Biology, Medicinal and Biomolecular Chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/1qk432jv