Scalable molecular dynamics on CPU and GPU architectures with NAMD
Phillips, James C, Hardy, David J, Maia, Julio D C, Stone, John E, Ribeiro, João V, Bernardi, Rafael C, Buch, Ronak, Fiorin, Giacomo, Hénin, Jérôme, Jiang, Wei, McGreevy, Ryan, Melo, Marcelo C R, Radak, Brian K, Skeel, Robert D, Singharoy, Abhishek, Wang, Yi, Roux, Benoît, Aksimentiev, Aleksei, Luthey-Schulten, Zaida, Kalé, Laxmikant V, Schulten, Klaus, Chipot, Christophe, Tajkhorshid, Emad
Published in The Journal of chemical physics (28.07.2020)
Published in The Journal of chemical physics (28.07.2020)
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Journal Article
Comparative Study of Injury Models for Studying Muscle Regeneration in Mice
Hardy, David, Besnard, Aurore, Latil, Mathilde, Jouvion, Grégory, Briand, David, Thépenier, Cédric, Pascal, Quentin, Guguin, Aurélie, Gayraud-Morel, Barbara, Cavaillon, Jean-Marc, Tajbakhsh, Shahragim, Rocheteau, Pierre, Chrétien, Fabrice
Published in PloS one (01.01.2016)
Published in PloS one (01.01.2016)
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HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA)
Kinloch, Natalie N., Ren, Yanqin, Conce Alberto, Winiffer D., Dong, Winnie, Khadka, Pragya, Huang, Szu Han, Mota, Talia M., Wilson, Andrew, Shahid, Aniqa, Kirkby, Don, Harris, Marianne, Kovacs, Colin, Benko, Erika, Ostrowski, Mario A., Del Rio Estrada, Perla M., Wimpelberg, Avery, Cannon, Christopher, Hardy, W. David, MacLaren, Lynsay, Goldstein, Harris, Brumme, Chanson J., Lee, Guinevere Q., Lynch, Rebecca M., Brumme, Zabrina L., Jones, R. Brad
Published in Nature communications (08.01.2021)
Published in Nature communications (08.01.2021)
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Journal Article
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD
Vermaas, Josh V, Hardy, David J, Stone, John E, Tajkhorshid, Emad, Kohlmeyer, Axel
Published in Journal of chemical information and modeling (27.06.2016)
Published in Journal of chemical information and modeling (27.06.2016)
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Journal Article
GPU-accelerated molecular modeling coming of age
Stone, John E., Hardy, David J., Ufimtsev, Ivan S., Schulten, Klaus
Published in Journal of molecular graphics & modelling (01.09.2010)
Published in Journal of molecular graphics & modelling (01.09.2010)
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Journal Article
BCL-2 antagonism sensitizes cytotoxic T cell-resistant HIV reservoirs to elimination ex vivo
Ren, Yanqin, Huang, Szu Han, Patel, Shabnum, Alberto, Winiffer D Conce, Magat, Dean, Ahimovic, Dughan, Macedo, Amanda B, Durga, Ryan, Chan, Dora, Zale, Elizabeth, Mota, Talia M, Truong, Ronald, Rohwetter, Thomas, McCann, Chase D, Kovacs, Colin M, Benko, Erika, Wimpelberg, Avery, Cannon, Christopher, Hardy, W David, Bosque, Alberto, Bollard, Catherine M, Jones, R Brad
Published in The Journal of clinical investigation (01.05.2020)
Published in The Journal of clinical investigation (01.05.2020)
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Journal Article
Membrane protein extraction and purification using styrene-maleic acid (SMA) copolymer: effect of variations in polymer structure
Morrison, Kerrie A, Akram, Aneel, Mathews, Ashlyn, Khan, Zoeya A, Patel, Jaimin H, Zhou, Chumin, Hardy, David J, Moore-Kelly, Charles, Patel, Roshani, Odiba, Victor, Knowles, Tim J, Javed, Masood-Ul-Hassan, Chmel, Nikola P, Dafforn, Timothy R, Rothnie, Alice J
Published in Biochemical journal (01.12.2016)
Published in Biochemical journal (01.12.2016)
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Journal Article
py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD
Barhaghi, Mohammad Soroush, Crawford, Brad, Schwing, Gregory, Hardy, David J., Stone, John E., Schwiebert, Loren, Potoff, Jeffrey, Tajkhorshid, Emad
Published in Journal of chemical theory and computation (09.08.2022)
Published in Journal of chemical theory and computation (09.08.2022)
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Journal Article
Once-daily dolutegravir versus raltegravir in antiretroviral-naive adults with HIV-1 infection: 48 week results from the randomised, double-blind, non-inferiority SPRING-2 study
Raffi, Francois, Prof, Rachlis, Anita, Prof, Stellbrink, Hans-Jürgen, Prof, Hardy, W David, MD, Torti, Carlo, MD, Orkin, Chloe, MD, Bloch, Mark, MD, Podzamczer, Daniel, MD, Pokrovsky, Vadim, Prof, Pulido, Federico, MD, Almond, Steve, MMath, Margolis, David, MD, Brennan, Clare, DPT, Min, Sherene, MD
Published in The Lancet (British edition) (02.03.2013)
Published in The Lancet (British edition) (02.03.2013)
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Journal Article
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
Jiang, Wei, Hardy, David J, Phillips, James C, MacKerell, Alexander D, Schulten, Klaus, Roux, Benoît
Published in The journal of physical chemistry letters (20.01.2011)
Published in The journal of physical chemistry letters (20.01.2011)
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Journal Article
Hidden Biomass of Intact Malaria Parasites in the Human Spleen
Kho, Steven, Qotrunnada, Labibah, Leonardo, Leo, Andries, Benediktus, Wardani, Putu A.I, Fricot, Aurelie, Henry, Benoit, Hardy, David, Margyaningsih, Nur I, Apriyanti, Dwi, Puspitasari, Agatha M, Prayoga, Pak, Trianty, Leily, Kenangalem, Enny, Chretien, Fabrice, Safeukui, Innocent, del Portillo, Hernando A, Fernandez-Becerra, Carmen, Meibalan, Elamaran, Marti, Matthias, Price, Ric N, Woodberry, Tonia, Ndour, Papa A, Russell, Bruce M, Yeo, Tsin W, Minigo, Gabriela, Noviyanti, Rintis, Poespoprodjo, Jeanne R, Siregar, Nurjati C, Buffet, Pierre A, Anstey, Nicholas M
Published in The New England journal of medicine (27.05.2021)
Published in The New England journal of medicine (27.05.2021)
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Journal Article
Experimental Investigation of a Novel Solar Micro-Channel Loop-Heat-Pipe Photovoltaic/Thermal (MC-LHP-PV/T) System for Heat and Power Generation
Yu, Min, Chen, Fucheng, Zheng, Siming, Zhou, Jinzhi, Zhao, Xudong, Wang, Zhangyuan, Li, Guiqiang, Li, Jing, Fan, Yi, Ji, Jie, Diallo, Theirno M.O., Hardy, David
Published in Applied energy (15.12.2019)
Published in Applied energy (15.12.2019)
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Journal Article
Contemporary management and natural history of aberrant right subclavian artery
Dong, Siwei, Alarhayem, Abdul Q., Meier, Garrett, Hardy, David M., Lyden, Sean P., Farivar, Behzad S.
Published in Journal of vascular surgery (01.04.2022)
Published in Journal of vascular surgery (01.04.2022)
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Journal Article
Brain and cognitive reserve: Mediator(s) and construct validity, a critique
Satz, Paul, Cole, Michael A., Hardy, David J., Rassovsky, Yuri
Published in Journal of clinical and experimental neuropsychology (01.01.2011)
Published in Journal of clinical and experimental neuropsychology (01.01.2011)
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Journal Article
Accelerating molecular modeling applications with graphics processors
Stone, John E, Phillips, James C, Freddolino, Peter L, Hardy, David J, Trabuco, Leonardo G, Schulten, Klaus
Published in Journal of computational chemistry (01.12.2007)
Published in Journal of computational chemistry (01.12.2007)
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Journal Article
Multilevel summation for periodic electrostatics using B-splines
Kaya, Hüseyin, Hardy, David J, Skeel, Robert D
Published in The Journal of chemical physics (14.04.2021)
Published in The Journal of chemical physics (14.04.2021)
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Evaluation of splenic accumulation and colocalization of immature reticulocytes and Plasmodium vivax in asymptomatic malaria: A prospective human splenectomy study
Kho, Steven, Qotrunnada, Labibah, Leonardo, Leo, Andries, Benediktus, Wardani, Putu A I, Fricot, Aurelie, Henry, Benoit, Hardy, David, Margyaningsih, Nur I, Apriyanti, Dwi, Puspitasari, Agatha M, Prayoga, Pak, Trianty, Leily, Kenangalem, Enny, Chretien, Fabrice, Brousse, Valentine, Safeukui, Innocent, Del Portillo, Hernando A, Fernandez-Becerra, Carmen, Meibalan, Elamaran, Marti, Matthias, Price, Ric N, Woodberry, Tonia, Ndour, Papa A, Russell, Bruce M, Yeo, Tsin W, Minigo, Gabriela, Noviyanti, Rintis, Poespoprodjo, Jeanne R, Siregar, Nurjati C, Buffet, Pierre A, Anstey, Nicholas M
Published in PLoS medicine (26.05.2021)
Published in PLoS medicine (26.05.2021)
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Journal Article
Dual vaccination against IL-4 and IL-13 protects against chronic allergic asthma in mice
Conde, Eva, Bertrand, Romain, Balbino, Bianca, Bonnefoy, Jonathan, Stackowicz, Julien, Caillot, Noémie, Colaone, Fabien, Hamdi, Samir, Houmadi, Raïssa, Loste, Alexia, Kamphuis, Jasper B. J., Huetz, François, Guilleminault, Laurent, Gaudenzio, Nicolas, Mougel, Aurélie, Hardy, David, Snouwaert, John N., Koller, Beverly H., Serra, Vincent, Bruhns, Pierre, Grouard-Vogel, Géraldine, Reber, Laurent L.
Published in Nature communications (11.05.2021)
Published in Nature communications (11.05.2021)
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