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Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

Rudesh D Toofanny, Andrew M Simms, David AC Beck, Valerie Daggett
2011 BMC Bioinformatics  
We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts.  ...  Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time.  ...  Department of Energy under contract no. DE-AC02-05CH11231. We are also grateful for support from Microsoft for development of our database.  ... 
doi:10.1186/1471-2105-12-334 pmid:21831299 pmcid:PMC3166946 fatcat:ysiy4xz6anhxldhiqh4sad2t2m

An introduction to biomolecular simulations and docking

Cameron Mura, Charles E. McAnany
2014 Molecular Simulation  
to the diffusional dynamics and inter-molecular collisions in the early stages of formation of cellular-scale assemblies such as the ribosome.  ...  As a complement to experimentation, molecular simulation offers a uniquely powerful approach to analyze biomolecular structure, mechanism, and dynamics; this is possible because the molecular contacts  ...  Acknowledgements This work is dedicated to the memory of Aubin Mura. We thank RG Bryant, CT  ... 
doi:10.1080/08927022.2014.935372 fatcat:awr7ztftybc2zkylsoyz7f5sde

Towards possible opportunities in nuclear materials science and technology at an X-ray free electron laser research facility

A. Froideval, A. Badillo, J. Bertsch, S. Churakov, R. Dähn, C. Degueldre, T. Lind, D. Paladino, B.D. Patterson
2011 Journal of Nuclear Materials  
Spectroscopy and imaging of condensed matter have benefited greatly from the availability of intense Xray beams from synchrotron sources, both in terms of spatial resolution and of elemental specificity  ...  This article describes a selection of problems in nuclear materials science and technology that would directly benefit from this and similar X-ray FEL sources.  ...  Of ever increasing importance in the field of nuclear materials science and technology are numerical simulations of structure and dynamics at or close to the atomic-scale.  ... 
doi:10.1016/j.jnucmat.2011.01.124 fatcat:txylwfky3vb5he52yh4v4rgto4

Protein Function Analysis through Machine Learning

Chris Avery, John Patterson, Tyler Grear, Theodore Frater, Donald J. Jacobs
2022 Biomolecules  
We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function.  ...  The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein–ligand  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.  ... 
doi:10.3390/biom12091246 pmid:36139085 fatcat:yx37j5tyubhkrf5unj462mlvnm

2022 Review of Data-Driven Plasma Science [article]

Rushil Anirudh, Rick Archibald, M. Salman Asif, Markus M. Becker, Sadruddin Benkadda, Peer-Timo Bremer, Rick H.S. Budé, C.S. Chang, Lei Chen, R. M. Churchill, Jonathan Citrin, Jim A Gaffney (+51 others)
2022 arXiv   pre-print
A large amount of data and machine learning algorithms go hand in hand. Most plasma data, whether experimental, observational or computational, are generated or collected by machines today.  ...  Despite the recent impressive progress in applications of data science to plasma science and technology, the emerging field of DDPS is still in its infancy.  ...  In addition, spatial and time scales involved in those systems vary widely from the atomic scales to the manufacturing tool scales.  ... 
arXiv:2205.15832v1 fatcat:fxsl6gl3fncnhpoj76defxoc3a

GPU Computing

J.D. Owens, M. Houston, D. Luebke, S. Green, J.E. Stone, J.C. Phillips
2008 Proceedings of the IEEE  
The GPU's rapid increase in both programmability and capability has spawned a research community that has successfully mapped a broad range of computationally demanding, complex problems to the GPU.  ...  We describe the background, hardware, and programming model for GPU computing, summarize the state of the art in tools and techniques, and present four GPU computing successes in game physics and computational  ...  NAMD: Large-Scale Molecular Dynamics NAMD (nanoscale molecular dynamics) 3 is an awardwinning package for the classical molecular dynamics simulation of biomolecular systems on large parallel computers  ... 
doi:10.1109/jproc.2008.917757 fatcat:665l7t6lvzewvaqeky6j35mg6q

AbstractBook_OPTO2017.pdf

Michał Mikołajczyk
2017 Figshare  
The Book of Abstracts of the OPTO2017 Conference held in Warsaw  ...  With the simplicity of production it is a reasonable compromise In this article is presented hybrid diffractive structure consisting of phase encoded as a kinoform in the center and binary phase on the  ...  However, this coding method requires very large resolution and is tough to manufacture. We propose coding the area that is vulnerable for shadow effect with binary phase.  ... 
doi:10.6084/m9.figshare.5146993 fatcat:di5yptwolfa2hjypnxqmyemqby

AbstractBook_OPTO2017.pdf

Michał Mikołajczyk
2017 Figshare  
The Book of Abstracts of the OPTO2017 Conference held in Warsaw  ...  With the simplicity of production it is a reasonable compromise In this article is presented hybrid diffractive structure consisting of phase encoded as a kinoform in the center and binary phase on the  ...  However, this coding method requires very large resolution and is tough to manufacture. We propose coding the area that is vulnerable for shadow effect with binary phase.  ... 
doi:10.6084/m9.figshare.5146993.v1 fatcat:oaoupvmmgzbpboo32bs5775ypq

Scaling the Power Wall: A Path to Exascale

Oreste Villa, Daniel R. Johnson, Mike Oconnor, Evgeny Bolotin, David Nellans, Justin Luitjens, Nikolai Sakharnykh, Peng Wang, Paulius Micikevicius, Anthony Scudiero, Stephen W. Keckler, William J. Dally
2014 SC14: International Conference for High Performance Computing, Networking, Storage and Analysis  
A combination of architectural improvements, circuit design, and manufacturing technologies must provide over a 20× improvement in energy efficiency.  ...  In this paper, we present some of the progress NVIDIA Research is making toward the design of Exascale systems by tailoring features to address the scaling challenges of performance and energy efficiency  ...  CoMD CoMD is a proxy-app for molecular dynamics simulations which represent a significant fraction of the DoE workloads [12] .  ... 
doi:10.1109/sc.2014.73 dblp:conf/sc/VillaJOBNLSWMSKD14 fatcat:63yyeyb5jrhqpp6mypnn5hz44m

Mechanics of Carbon Nanotubes [chapter]

Wing Liu, Gregory Wagner, Dong Qian, Min-Feng Yu, Rodney Ruoff
2002 Electrical Engineering Handbook  
and structural perfection-could make them ideal for a wealth of technological applications.  ...  We also outline the computational approaches that have been taken, including ab initio quantum mechanical simulations, classical molecular dynamics, and continuum models.  ...  His research interests include nano-scale modeling, simulation and applications, meshfree methods, and development of multiscale methods in solid mechanics.  ... 
doi:10.1201/9781420040623.ch19 fatcat:zg2euwv6dbd35a4myc4xbfxwni

Mechanics of Carbon Nanotubes1 [chapter]

Wing Kam Liu, Gregory Wagner, Dong Qian, Rodney Ruoff, Min-Feng Yu
2007 Handbook of Nanoscience, Engineering, and Technology, Second Edition  
and structural perfection-could make them ideal for a wealth of technological applications.  ...  We also outline the computational approaches that have been taken, including ab initio quantum mechanical simulations, classical molecular dynamics, and continuum models.  ...  His research interests include nano-scale modeling, simulation and applications, meshfree methods, and development of multiscale methods in solid mechanics.  ... 
doi:10.1201/9781420007848.ch23 fatcat:plkalbykzvf7toh4cf5zdffjc4

Roadmap on biosensing and photonics with advanced nano-optical methods

Enzo Di Fabrizio, Sebastian Schlücker, Jérôme Wenger, Raju Regmi, Hervé Rigneault, Giuseppe Calafiore, Melanie West, Stefano Cabrini, Monika Fleischer, Niek F van Hulst, Maria F Garcia-Parajo, Annemarie Pucci (+3 others)
2016 Journal of Optics  
The materials used for detection include nanoparticles and nanostructures fabricated with different 2D and 3D lithographic methods.  ...  It is shown that sensitivity to a single molecule is already accessible whether the system under study is a single cell or a multitude of cells in a molecular mixture.  ...  Acknowledgments I thank the members of the nanobiophotonics lab at the UDE in Essen, Germany, for many stimulating discussions and the German Science Foundation (DFG) for financial support.  ... 
doi:10.1088/2040-8978/18/6/063003 fatcat:cnxom4yofjfvrpeqigcltqeioe

The 2017 Plasma Roadmap: Low temperature plasma science and technology

I Adamovich, S D Baalrud, A Bogaerts, P J Bruggeman, M Cappelli, V Colombo, U Czarnetzki, U Ebert, J G Eden, P Favia, D B Graves, S Hamaguchi (+26 others)
2017 Journal of Physics D: Applied Physics  
In fact, modelling coherent structures is generally a challenge [169] . The large dynamic range of time/ spatial scales and physical phenomena continues to challenge the field.  ...  nanometer scale roughness of a processed surface may be analyzed by atomic-scale PMI simulations.  ... 
doi:10.1088/1361-6463/aa76f5 fatcat:76umn2qaovaxzhiyypql5kxrai

Key Topics in Molecular Docking for Drug Design

Pedro H. M. Torres, Ana C. R. Sodero, Paula Jofily, Floriano P. Silva-Jr
2019 International Journal of Molecular Sciences  
Nevertheless, new approaches continue to be developed and the volume of published works grows at a rapid pace.  ...  Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings.  ...  Examples are energy minimisation methods and molecular dynamics (MD) simulations.  ... 
doi:10.3390/ijms20184574 pmid:31540192 pmcid:PMC6769580 fatcat:ye5rdnonofc3jjaizbncrdx2yu

De novo and inverse folding predictions of protein structure and dynamics

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
1993 Journal of Computer-Aided Molecular Design  
In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein  ...  Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3-4 A. from native.  ...  For example, long full atom molecular dynamics (MD) simulations run for 100 ns or so, whereas proteins fold in the millisecond to second regime.  ... 
doi:10.1007/bf02337559 pmid:8229093 fatcat:eo5brg46ljfo7p54zvbsb32kv4
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