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Probing Biomolecular Machines with Graphics Processors

James C Phillips, John E. Stone
2009 Queue  
The DNA of every cell contains both data (the amino acid sequences of every protein required for life) and metadata (large stretches of "junk" DNA that inter-Probing Biomolecular Machines with Graphics  ...  In 2007 we began working with the Nvidia CUDA (Compute Unified Device Architecture) system for general-purpose graphics processor programming to bring the power of many-core computing to practical scientific  ...  and graphics workstations.  ... 
doi:10.1145/1626135.1629155 fatcat:ded6hyp5wfdgbhukhfvgsgrnqu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone
2009 Communications of the ACM  
The DNA of every cell contains both data (the amino acid sequences of every protein required for life) and metadata (large stretches of "junk" DNA that inter-Probing Biomolecular Machines with Graphics  ...  In 2007 we began working with the Nvidia CUDA (Compute Unified Device Architecture) system for general-purpose graphics processor programming to bring the power of many-core computing to practical scientific  ...  and graphics workstations.  ... 
doi:10.1145/1562764.1562780 fatcat:sdn2bizd5bcovpv3bbtvqurzra

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Ramu Anandakrishnan, Tom R.W. Scogland, Andrew T. Fenley, John C. Gordon, Wu-chun Feng, Alexey V. Onufriev
2010 Journal of Molecular Graphics and Modelling  
Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function.  ...  Two commonly used techniques to speed-up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors.  ...  Acknowledgments This work was supported in part by NIH R01 grant GM076121 and by NSF I/UCRC grant IIP-0804155 with support from AMD.  ... 
doi:10.1016/j.jmgm.2010.04.001 pmid:20452792 pmcid:PMC2907926 fatcat:lmxvebf4gvbdbkihn4ajx6hpmm

On the design of distributed autonomous embedded systems for biomedical applications

Jose Germano, Rui Ramalho, Leonel Sousa
2009 Proceedings of the 3d International ICST Conference on Pervasive Computing Technologies for Healthcare  
Two embedded systems have been developed based on this platform, a simple system for movement monitoring, and another for biomolecular recognition detection.  ...  Therefore, the actual embedded systems for biomedical applications have to be designed with low power communication sub-systems and, on the other hand, have to be easily integrated with more general distributed  ...  If the probe and target strands are complementary, a biomolecular reaction (hybridization) occurs binding the two strands.  ... 
doi:10.4108/icst.pervasivehealth2009.5966 dblp:conf/ph/GermanoRS09 fatcat:7wrx5io2pravlhbao7jig4bfrq

Artificial intelligence—cogito, ergo sum

Gregory W. Auner, Ehsan Majidi
2021 Cancer Metastasis Review  
By 2011, the speed and memory of graphical processor units (GPUs) had increased significantly.  ...  These biomolecular signatures can clearly differentiate normal from cancerous tissue but become subtle at the tumor boundary.  ... 
doi:10.1007/s10555-021-09975-1 pmid:34031763 fatcat:wgclanffovhvvilsnsbnax3hum

Scalable molecular dynamics with NAMD

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten
2005 Journal of Computational Chemistry  
The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory  ...  Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting  ...  Free energy calculation development with C. Chipot was aided by a CNRS/UIUC collaborative grant.  ... 
doi:10.1002/jcc.20289 pmid:16222654 pmcid:PMC2486339 fatcat:ltac7t3jtrbkngvn33tkmemmta

BioExcel Deliverable D2.4 - Final Release of Workflows and Modular Tools for User Services

Adam Hospital, Anna Montras, Josep Lluís Gelpí, Daniele Lezzi, Rosa Maria Badia, Steven Newhouse, Jose Antonio Dianes, Pau Andrio, Luís Jordà, Stian Soiland-Reyes, Darren J White, Adam Carter (+3 others)
2019 Zenodo  
The current implementation for each of the project pilot use cases is detailed, with special focus on the workflows behind them, availability and feedback.  ...  A summary of the software development process adopted, following a set of best practices promoted by ELIXIR, is exposed together with examples of working implementations.  ...  CTE-POWER, with IBM Power9 processors).  ... 
doi:10.5281/zenodo.3236256 fatcat:vdacumustjaafbozovyktxtdnm

Adapting a message-driven parallel application to GPU-accelerated clusters

J.C. Phillips, J.E. Stone, K. Schulten
2008 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis  
Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility of GPU hardware, and due to the availability  ...  We describe strategies for the decomposition and scheduling of computation among CPU cores and GPUs, and techniques for overlapping communication and CPU computation with GPU kernel execution.  ...  After the resulting forces are copied to the CPU, the CUDA stream continues with a second force kernel invocation for on-processor patches while a CUDA event timer probe in the Charm++ message loop triggers  ... 
doi:10.1109/sc.2008.5214716 dblp:conf/sc/PhillipsSS08 fatcat:kzunlcf7wbexfnjxij55pcsr2y

Biophysical experiments and biomolecular simulations: A perfect match?

Sandro Bottaro, Kresten Lindorff-Larsen
2018 Science  
These developments are enabling detailed studies of complex biomolecular assemblies.  ...  Progress has been made through an increasingly tight integration of experiments and simulations, with experiments being used to refine simulations and simulations used to interpret experiments.  ...  Machine-learning approaches, particularly neural networks, make it possible to train simple potentials with QM-level accuracy (21) .  ... 
doi:10.1126/science.aat4010 pmid:30049874 fatcat:qhvu4i33ujapzomdonac5dd2m4

Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor

Manuel Wahle, Willy Wriggers, Arthur Olson
2015 PLoS Computational Biology  
We describe a paradigm shift currently under way in computer graphics towards the use of more realistic global illumination models, and we apply the so-called ambient occlusion approach to our opensource  ...  The modeling of large biomolecular assemblies relies on an efficient rendering of their hierarchical architecture across a wide range of spatial level of detail.  ...  Although special purpose graphics hardware was available since the early 1980s, it was not until the early 1990s that 3D graphics rendering, actively performed by a processor on a graphics card, became  ... 
doi:10.1371/journal.pcbi.1004516 pmid:26505203 pmcid:PMC4623981 fatcat:4jdi24hyp5fdxjb27vxkkhubfe

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

Tamar Schlick
2009 F1000 Biology Reports  
changes along with chemical dynamics behavior.  ...  While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov  ...  MD, with variations and extensions, has become a universal tool for probing relationships among biomolecular structure, flexibility, and function.  ... 
doi:10.3410/b1-51 pmid:20948633 pmcid:PMC2948272 fatcat:c5dragh2gvhifgx2sh3mhmfrvu

Perspectives on Structural Molecular Biology Visualization: From Past to Present

Arthur J. Olson
2018 Journal of Molecular Biology  
Pauling, who helped develop the CPK model and adopted the use of physical models throughout his career, used the simple process of folding a paper with a drawing of a polypeptide chain, coupled with his  ...  Conversely over this time, the field of structural biology has helped to drive development and commercialization of computer graphics and visualization technologies.  ...  Acknowledgements I would like to acknowledge the past and present members of the Molecular Graphics Laboratory at The Scripps Research Institute, for their creativity, talent and hard work.  ... 
doi:10.1016/j.jmb.2018.07.009 pmid:30009769 pmcid:PMC6186497 fatcat:4oxdbckyhbf6bh5dqgyfef4bra

A high-speed magnetic tweezer beyond 10,000 frames per second

Bob M. Lansdorp, Shawn J. Tabrizi, Andrew Dittmore, Omar A. Saleh
2013 Review of Scientific Instruments  
Here we have introduced superluminescent diode illumination and high-speed camera detection to the magnetic tweezer, with graphics processing unit-accelerated particle tracking for high-speed analysis  ...  We have demonstrated the ability of the high-speed magnetic tweezer to resolve particle position to within 1 Å at 100 Hz, and to measure the extension of a 1566 bp DNA with 1 nm precision at 100 Hz in  ...  Video-based images of probe particles are sent to a computer processor to convert images into threedimensional positions. 8, 18 A.  ... 
doi:10.1063/1.4802678 pmid:23635212 fatcat:b5hz35xvufd3hdrzwdj3zgp43i

Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems

Yan Xie, Tiantian Liu, Bin Tu, Benzhuo Lu, Linbo Zhang
2016 Communications in Computational Physics  
A bisection method is used for the mesh refinements according to the molecular PDB or PQR file which describes the biomolecular region.  ...  graphics programs.  ...  as the number of processors grows.  ... 
doi:10.4208/cicp.161114.021015a fatcat:7gyxj65ydzgabjt75uwxaowht4

Biomolecular NMR: Past and future

John L. Markley, William Milo Westler
2017 Archives of Biochemistry and Biophysics  
The editors of this special volume suggested this topic, presumably because of the perspective lent by our combined >90-year association with biomolecular NMR.  ...  Our group's association with the Biological Magnetic Resonance data Bank (BMRB) and with the Worldwide Protein Data Bank (wwPDB) has also been rewarding.  ...  The seamless interoperability of biomolecular NMR software packages under a virtual machine [54] is likely to become more refined through the NMRbox project (https://www.nmrbox.org/).  ... 
doi:10.1016/j.abb.2017.05.003 pmid:28495511 pmcid:PMC5701516 fatcat:2aw6oo3wcfa3peq3prb76ananq
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