Статті в журналах з теми "MM simulations"
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de la Lande, Aurélien, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, et al. "Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review." Molecules 24, no. 9 (April 26, 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.
Повний текст джерелаField, Martin J. "An Algorithm for Adaptive QC/MM Simulations." Journal of Chemical Theory and Computation 13, no. 5 (April 6, 2017): 2342–51. http://dx.doi.org/10.1021/acs.jctc.7b00099.
Повний текст джерелаAlameldeen, A. R., and D. A. Wood. "Addressing workload variability in architectural simulations." IEEE Micro 23, no. 6 (November 2003): 94–98. http://dx.doi.org/10.1109/mm.2003.1261392.
Повний текст джерелаWymore, Troy, David W. Deerfield, Martin J. Field, John Hempel, and Hugh B. Nicholas. "Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations." Chemico-Biological Interactions 143-144 (February 2003): 75–84. http://dx.doi.org/10.1016/s0009-2797(02)00175-8.
Повний текст джерелаZurek, Jolanta, Anna L. Bowman, W. Andrzej Sokalski, and Adrian J. Mulholland. "MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations." Structural Chemistry 15, no. 5 (October 2004): 405–14. http://dx.doi.org/10.1023/b:stuc.0000037896.80027.2c.
Повний текст джерелаSuh, Donghyuk, Kwangho Nam, and Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.
Повний текст джерелаAnam, Muhammad Syaekhul, and S. Suwardi. "Hydration Structures and Dynamics of Ga3+ Ion Based on Molecular Mechanics Molecular Dynamics Simulation (Classical DM)." Indonesian Journal of Chemistry and Environment 4, no. 2 (March 10, 2022): 49–56. http://dx.doi.org/10.21831/ijoce.v4i2.48401.
Повний текст джерелаShimada, J., T. Sakuma, K. Nakata, T. Wasiho, and T. Takada. "3K1015 BioMolecular Simulations : MD and QM/MM calculations." Seibutsu Butsuri 42, supplement2 (2002): S180. http://dx.doi.org/10.2142/biophys.42.s180_2.
Повний текст джерелаSolt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, and Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations." Journal of Physical Chemistry B 113, no. 17 (April 30, 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.
Повний текст джерелаMorzan, Uriel N., Diego J. Alonso de Armiño, Nicolás O. Foglia, Francisco Ramírez, Mariano C. González Lebrero, Damián A. Scherlis, and Darío A. Estrin. "Spectroscopy in Complex Environments from QM–MM Simulations." Chemical Reviews 118, no. 7 (March 21, 2018): 4071–113. http://dx.doi.org/10.1021/acs.chemrev.8b00026.
Повний текст джерелаMartins Costa, M. T. C. "QM/MM simulations of polyols in aqueous solution." Journal of Molecular Structure: THEOCHEM 729, no. 1-2 (September 2005): 47–52. http://dx.doi.org/10.1016/j.theochem.2005.03.016.
Повний текст джерелаJász, Ádám, Ádám Rák, István Ladjánszki, Gábor János Tornai, and György Cserey. "Towards chemically accurate QM/MM simulations on GPUs." Journal of Molecular Graphics and Modelling 96 (May 2020): 107536. http://dx.doi.org/10.1016/j.jmgm.2020.107536.
Повний текст джерелаRiahi, Saleh, and Christopher N. Rowley. "QM/MM Simulations of Mg and Zn Solvation." Biophysical Journal 106, no. 2 (January 2014): 405a. http://dx.doi.org/10.1016/j.bpj.2013.11.2281.
Повний текст джерелаDohm, Sebastian, Eckhard Spohr, and Martin Korth. "Developing adaptive QM/MM computer simulations for electrochemistry." Journal of Computational Chemistry 38, no. 1 (October 28, 2016): 51–58. http://dx.doi.org/10.1002/jcc.24513.
Повний текст джерелаWatanabe, Hiroshi C., and Qiang Cui. "Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 15, no. 7 (May 16, 2019): 3917–28. http://dx.doi.org/10.1021/acs.jctc.9b00180.
Повний текст джерелаThelen, Bryce C., and Elisa Toulson. "A computational study on the effect of the orifice size on the performance of a turbulent jet ignition system." Proceedings of the Institution of Mechanical Engineers, Part D: Journal of Automobile Engineering 231, no. 4 (August 20, 2016): 536–54. http://dx.doi.org/10.1177/0954407016659199.
Повний текст джерелаKarstensen, Anders, Wei Fan, Fengchun Zhang, Jesper Ø. Nielsen, and Gert F. Pedersen. "Analysis of Simulated and Measured Indoor Channels for mm-Wave Beamforming Applications." International Journal of Antennas and Propagation 2018 (2018): 1–17. http://dx.doi.org/10.1155/2018/2642904.
Повний текст джерелаPeguiron, Anke, Lucio Colombi Ciacchi, Alessandro De Vita, James R. Kermode, and Gianpietro Moras. "Accuracy of buffered-force QM/MM simulations of silica." Journal of Chemical Physics 142, no. 6 (February 14, 2015): 064116. http://dx.doi.org/10.1063/1.4907786.
Повний текст джерелаMessner, Christoph B., Günther K. Bonn, and Thomas S. Hofer. "QM/MM MD simulations of La(iii)–phosphopeptide complexes." Molecular BioSystems 11, no. 1 (2015): 232–38. http://dx.doi.org/10.1039/c4mb00424h.
Повний текст джерелаWang, Meiting, Ye Mei, and Ulf Ryde. "Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations." Journal of Chemical Theory and Computation 14, no. 12 (October 26, 2018): 6613–22. http://dx.doi.org/10.1021/acs.jctc.8b00685.
Повний текст джерелаBulo, Rosa E., Bernd Ensing, Jetze Sikkema, and Lucas Visscher. "Toward a Practical Method for Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 5, no. 9 (July 30, 2009): 2212–21. http://dx.doi.org/10.1021/ct900148e.
Повний текст джерелаFogolari, Federico, Alessandro Brigo, and Henriette Molinari. "Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins." Biophysical Journal 85, no. 1 (July 2003): 159–66. http://dx.doi.org/10.1016/s0006-3495(03)74462-2.
Повний текст джерелаLu, Xiya, Dong Fang, Shingo Ito, Yuko Okamoto, Victor Ovchinnikov, and Qiang Cui. "QM/MM free energy simulations: recent progress and challenges." Molecular Simulation 42, no. 13 (July 5, 2016): 1056–78. http://dx.doi.org/10.1080/08927022.2015.1132317.
Повний текст джерелаCooper, April M., and Johannes Kästner. "Averaging Techniques for Reaction Barriers in QM/MM Simulations." ChemPhysChem 15, no. 15 (September 5, 2014): 3264–69. http://dx.doi.org/10.1002/cphc.201402382.
Повний текст джерелаKim, Wan-Il, Se-Hoon Kim, and Kwang-Cheol Ko. "Investigation of the Optimum Diameter of the Ring Reflector for an Axial Virtual Cathode Oscillator." Electronics 11, no. 13 (June 26, 2022): 2002. http://dx.doi.org/10.3390/electronics11132002.
Повний текст джерелаYang, Wei, Ryan Bitetti-Putzer, and Martin Karplus. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials." Journal of Chemical Physics 120, no. 20 (May 22, 2004): 9450–53. http://dx.doi.org/10.1063/1.1738106.
Повний текст джерелаXia, Shu-Hua, Ganglong Cui, Wei-Hai Fang, and Walter Thiel. "How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations." Angewandte Chemie 128, no. 6 (January 6, 2016): 2107–12. http://dx.doi.org/10.1002/ange.201509622.
Повний текст джерелаXia, Shu-Hua, Ganglong Cui, Wei-Hai Fang, and Walter Thiel. "How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations." Angewandte Chemie International Edition 55, no. 6 (January 6, 2016): 2067–72. http://dx.doi.org/10.1002/anie.201509622.
Повний текст джерелаMiranda, Sebastião, Jonas Feldt, Frederico Pratas, Ricardo A. Mata, Nuno Roma, and Pedro Tomás. "Efficient parallelization of perturbative Monte Carlo QM/MM simulations in heterogeneous platforms." International Journal of High Performance Computing Applications 31, no. 6 (July 27, 2016): 499–516. http://dx.doi.org/10.1177/1094342016649420.
Повний текст джерелаSusanto, Tri Nugroho Hadi. "COMPUTATIONAL FLUID DYNAMICS SIMULATION OF KARTINI REACTOR FUELED PLATE." Indonesian Journal of Physics and Nuclear Applications 4, no. 2 (June 30, 2019): 33–38. http://dx.doi.org/10.24246/ijpna.v4i2.33-38.
Повний текст джерелаSchwenk, C. F., and B. M. Rode. "Ab initio QM/MM MD simulations of the hydrated Ca2+ ion." Pure and Applied Chemistry 76, no. 1 (January 1, 2004): 37–47. http://dx.doi.org/10.1351/pac200476010037.
Повний текст джерелаChalmet, S., D. Rinaldi, and M. F. Ruiz-López. "A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations." International Journal of Quantum Chemistry 84, no. 5 (2001): 559–64. http://dx.doi.org/10.1002/qua.1410.
Повний текст джерелаWilliams, Christopher R. "How Much Attenuation Extinguishes mm-Wave Vertically Pointing Radar Return Signals?" Remote Sensing 14, no. 6 (March 8, 2022): 1305. http://dx.doi.org/10.3390/rs14061305.
Повний текст джерелаKulkarni, Prajakta U., Harshil Shah, and Vivek K. Vyas. "Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery." Mini-Reviews in Medicinal Chemistry 22, no. 8 (May 2022): 1096–107. http://dx.doi.org/10.2174/1389557521666211007115250.
Повний текст джерелаDoll, K., and T. Jacob. "QM/MM description of periodic systems." Journal of Theoretical and Computational Chemistry 14, no. 07 (November 2015): 1550054. http://dx.doi.org/10.1142/s0219633615500546.
Повний текст джерелаLiang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers, and Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations." Physical Chemistry Chemical Physics 20, no. 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.
Повний текст джерелаSaito, Toru, and Yu Takano. "QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease." Journal of Physical Chemistry B 126, no. 10 (March 3, 2022): 2087–97. http://dx.doi.org/10.1021/acs.jpcb.1c10200.
Повний текст джерелаCurchod, Basile F. E., Pabloc Campomanes, Andrey Laktionov, Marilisa Neri, Thomas J. Penfold, Stefano Vanni, Ivano Tavernelli, and Ursula Rothlisberger. "Mechanical (QM/MM) Simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena." CHIMIA International Journal for Chemistry 65, no. 5 (May 26, 2011): 330–33. http://dx.doi.org/10.2533/chimia.2011.330.
Повний текст джерелаAcevedo, Orlando, and William L. Jorgensen. "Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations." Journal of the American Chemical Society 128, no. 18 (May 2006): 6141–46. http://dx.doi.org/10.1021/ja057523x.
Повний текст джерелаRiccardi, Demian, Guohui Li, and Qiang Cui. "Importance of van der Waals Interactions in QM/MM Simulations." Journal of Physical Chemistry B 108, no. 20 (May 2004): 6467–78. http://dx.doi.org/10.1021/jp037992q.
Повний текст джерелаHudson, Phillip S., H. Lee Woodcock, and Stefan Boresch. "Use of Interaction Energies in QM/MM Free Energy Simulations." Journal of Chemical Theory and Computation 15, no. 8 (May 29, 2019): 4632–45. http://dx.doi.org/10.1021/acs.jctc.9b00084.
Повний текст джерелаSieffert, Nicolas, Michael Bühl, Marie-Pierre Gaigeot, and Carole A. Morrison. "Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations." Journal of Chemical Theory and Computation 9, no. 1 (October 30, 2012): 106–18. http://dx.doi.org/10.1021/ct300784x.
Повний текст джерелаGovender, Krishna K., and Kevin J. Naidoo. "Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations." Journal of Chemical Theory and Computation 10, no. 10 (September 18, 2014): 4708–17. http://dx.doi.org/10.1021/ct500373p.
Повний текст джерелаLambros, Eleftherios, Filippo Lipparini, Gerardo Andrés Cisneros, and Francesco Paesani. "A Many-Body, Fully Polarizable Approach to QM/MM Simulations." Journal of Chemical Theory and Computation 16, no. 12 (November 19, 2020): 7462–72. http://dx.doi.org/10.1021/acs.jctc.0c00932.
Повний текст джерелаDifley, Seth, Lee-Ping Wang, Sina Yeganeh, Shane R. Yost, and Troy Van Voorhis. "Electronic Properties of Disordered Organic Semiconductors via QM/MM Simulations." Accounts of Chemical Research 43, no. 7 (July 20, 2010): 995–1004. http://dx.doi.org/10.1021/ar900246s.
Повний текст джерелаJo, Ye-Joon, Jun-Seok Choi, Jin Kim, Hyo-Joon Kim, and Seong-Yong Moon. "Virtual Reality (VR) Simulation and Augmented Reality (AR) Navigation in Orthognathic Surgery: A Case Report." Applied Sciences 11, no. 12 (June 18, 2021): 5673. http://dx.doi.org/10.3390/app11125673.
Повний текст джерелаQian, Ping, Li-Nan Lu, and Zhong-Zhi Yang. "Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model." Canadian Journal of Chemistry 87, no. 12 (December 2009): 1738–46. http://dx.doi.org/10.1139/v09-134.
Повний текст джерелаKim, Se-Hoon, Chang-Jin Lee, Wan-Il Kim, and Kwang-Cheol Ko. "Experimental Investigation into the Optimum Position of a Ring Reflector for an Axial Virtual Cathode Oscillator." Electronics 10, no. 16 (August 5, 2021): 1878. http://dx.doi.org/10.3390/electronics10161878.
Повний текст джерелаDavis, C. P., K. F. Evans, S. A. Buehler, D. L. Wu, and H. C. Pumphrey. "3-D polarised simulations of space-borne passive mm/sub-mm midlatitude cirrus observations: a case study." Atmospheric Chemistry and Physics Discussions 6, no. 6 (December 6, 2006): 12701–28. http://dx.doi.org/10.5194/acpd-6-12701-2006.
Повний текст джерелаDavis, C. P., K. F. Evans, S. A. Buehler, D. L. Wu, and H. C. Pumphrey. "3-D polarised simulations of space-borne passive mm/sub-mm midlatitude cirrus observations: a case study." Atmospheric Chemistry and Physics 7, no. 15 (August 7, 2007): 4149–58. http://dx.doi.org/10.5194/acp-7-4149-2007.
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