Royal Society of Chemistry

Molecular simulations and visualization: introduction and overview

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,9-22
DOI: 10.1039/C4FD90024C, PaperJonathan D. Hirst, David R. Glowacki, Marc Baaden
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Virtual and augmented reality immersive molecular simulations: general discussion

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,143-166
DOI: 10.1039/C4FD90019G, Discussion
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3D molecular models of whole HIV-1 virions generated with cellPACK

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,23-44
DOI: 10.1039/C4FD00017J, PaperGraham T. Johnson, David S. Goodsell, Ludovic Autin, Stefano Forli, Michel F. Sanner, Arthur J. Olson
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Impressions by a dinosaur - summary of Faraday discussion 169: molecular simulations and visualization

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,521-527
DOI: 10.1039/C4FD00130C, PaperFrederick P. Brooks, Jr
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Visual analysis for space-time aggregation of biomolecular simulations

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,167-178
DOI: 10.1039/C3FD00156C, PaperThomas Ertl, Michael Krone, Stefan Kesselheim, Katrin Scharnowski, Guido Reina, Christian Holm
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Immune Attack players perform better on a test of cellular immunology and self confidence than their classmates who play a control video game

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,403-423
DOI: 10.1039/C4FD00014E, PaperMelanie Stegman
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Density based visualization for molecular simulation

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,225-243
DOI: 10.1039/C3FD00124E, PaperOpen Access Open Access Creative Commons Licence&nbsp This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.Dmitri Rozmanov, Svetlana Baoukina, D. Peter Tieleman
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Exploring genomes with a game engine

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,443-453
DOI: 10.1039/C3FD00152K, PaperJeremiah J. Shepherd, Lingxi Zhou, William Arndt, Yan Zhang, W. Jim Zheng, Jijun Tang
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A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,63-87
DOI: 10.1039/C4FD00008K, PaperOpen Access Open Access Creative Commons Licence&nbsp This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.David R. Glowacki, Michael O'Connor, Gaetano Calabro, James Price, Philip Tew, Thomas Mitchell, Joseph Hyde, David P. Tew, David J. Coughtrie, Simon McIntosh-Smith
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GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,265-283
DOI: 10.1039/C4FD00005F, PaperJohn E. Stone, Ryan McGreevy, Barry Isralewitz, Klaus Schulten
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Haptic-driven, interactive drug design: implementing a GPU-based approach to evaluate the induced fit effect

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,323-342
DOI: 10.1039/C3FD00139C, PaperAthanasios Anthopoulos, Gaia Pasqualetto, Ian Grimstead, Andrea Brancale
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NRas slows the rate at which a model lipid bilayer phase separates

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,209-223
DOI: 10.1039/C3FD00131H, PaperOpen Access Open Access Creative Commons Licence&nbsp This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.Elizabeth Jefferys, Mark S. P. Sansom, Philip W. Fowler
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Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,455-475
DOI: 10.1039/C3FD00145H, PaperMatthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E. Stone, Bruno Jobard, Mark S. P. Sansom
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Visualising intrinsic disorder and conformational variation in protein ensembles

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,179-193
DOI: 10.1039/C3FD00138E, PaperJulian Heinrich, Michael Krone, Sean I. O'Donoghue, Daniel Weiskopf
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ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,119-142
DOI: 10.1039/C3FD00142C, PaperMatthieu Dreher, Jessica Prevoteau-Jonquet, Mikael Trellet, Marc Piuzzi, Marc Baaden, Bruno Raffin, Nicolas Ferey, Sophie Robert, Sebastien Limet
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Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,45-62
DOI: 10.1039/C3FD00134B, PaperA.-E. Molza, N. Ferey, M. Czjzek, E. Le Rumeur, J.-F. Hubert, A. Tek, B. Laurent, M. Baaden, O. Delalande
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Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, 169,285-302
DOI: 10.1039/C3FD00159H, PaperEvgen Pavlov, Makoto Taiji, Arturs Scukins, Anton Markesteijn, Sergey Karabasov, Dmitry Nerukh
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FD 178: Ultrafast dynamics of nanoplasmonic stopped-light lasing

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, Accepted Manuscript
DOI: 10.1039/C4FD00181H, PaperSebastian Wuestner, Tim Pickering, Joachim M Hamm, A Freddie Page, Andreas Pusch, Ortwin Hess
We study the spatio-temporal dynamics of coherent amplification and lasing in planar gain-enhanced nanoplasmonic structures and show that a singularity in the density of optical states leads to a stopped-light...
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FD 178: Ultimate limit of field confinement by surface plasmon polaritons

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, Accepted Manuscript
DOI: 10.1039/C4FD00193A, PaperJacob Khurgin
We show that electric field confinement in surface plasmon polaritons propagating at the metal/dielectric interfaces enhances the loss due to Landau damping and which effectively limits the degree of confinement...
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FD 178: Relaxation dynamics of a quantum emitter resonantly coupled to a coherent state of localized surface plasmon

Faraday Disc. - 24 October, 2014 - 07:54
Faraday Discuss., 2014, Accepted Manuscript
DOI: 10.1039/C4FD00165F, PaperKhachatur V Nerkararyan, Sergey Bozhevolnyi
We investigate relaxation dynamics of a quantum dipole emitter (QDE), e.g., a molecule or quantum dot, located near a metal nanoparticle (MNP) exhibiting a dipolar localized surface plasmon (LSP) resonance...
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