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Parallel Biomolecular Computation: Models and Simulations
1999
Algorithmica
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Then we briefly discuss and compare Lipton and Adleman's biomolecular computation models and operations. ...
Here we propose an apparently more powerful abstract model of biomolecular computation, which we call the Parallel ...
Rankin, Arnold Reif, Steve Tate, Neil Tweedy, Hongyan Wang, and also Ken Robinson for his aid in preparation of the paper. ...
doi:10.1007/pl00008272
fatcat:jedz3g2sebd6rj6vp5u3hffbdy
Local parallel biomolecular computation
[chapter]
1999
DNA Based Computers III
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nite state automata simulation, and ngerprinting hashing a string. ...
Biomolecular ComputationBMC is computation at the molecular scale, using biotechnology engineering techniques. ...
Seeman gave us many v ery valuable and insightful suggestions on our assemblies and nano-fabrication techniques in general, particularly with respect to the geometry and DNA nano-construction of our tiles ...
doi:10.1090/dimacs/048/17
dblp:conf/dimacs/Reif97
fatcat:j37ygpgztzglfohaocajcgztyi
Parallel biomolecular simulation: Theory, algorithms and implementation
1997
Simulation Practice and Theory
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The essential goal of this work is the unified treatment of quantum mechanical and classical degrees of freedom in biomolecular simulation on all three levels: Theory, algorithms and implementation. ...
to the cut-off principle, the list of integrals to the pairlist and the computation of interaction matrix elements to the computation of pair forces. ...
Zinterhof at Salzburg University for both, having access to their DEC-alpha cluster and being supported strongly. ...
doi:10.1016/s0928-4869(97)00025-6
fatcat:rpvvdcj7gjgphaep3utw7xgmva
Biomolecular committor probability calculation enabled by processing in network storage
2008
Parallel Computing
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Computationally complex and data intensive atomic scale biomolecular simulation is enabled via processing in network storage (PINS): a novel distributed system framework to overcome bandwidth, compute, ...
Biomolecular simulation methods are correlated with the primary PINS components, including: client tools, hybrid database/file management service (GEMS), computation engine (Condor), virtual file system ...
Computational resources were made available by the Center for Research Computing and Department of Computer Science and Engineering at the University of Notre Dame. ...
doi:10.1016/j.parco.2008.08.001
fatcat:deadyt5gvvgfjhvwlbuwsfmd6a
RPYFMM: Parallel adaptive fast multipole method for Rotne–Prager–Yamakawa tensor in biomolecular hydrodynamics simulations
2018
Computer Physics Communications
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2017 pre-print arXiv:1711.02976v1 fatcat:yu3gxi65w5h4ddvqhqjezoo2fu
RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library [2, 3]. ...
RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. ...
David Keyes and Rio Yokota on different parallelization strategies for our solver. BZ was supported in part by National Science Foundation grant number ACI-1440396. ...
doi:10.1016/j.cpc.2018.02.005
pmid:30147116
pmcid:PMC6107314
fatcat:meukzaf5tjct7en2afnuzdkbdy
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads
2016
2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)
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We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-onchip multi-core CPUs ...
Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis ...
ACKNOWLEDGMENT The authors wish to acknowledge support of the CUDA Center of Excellence at the University of Illinois, and NIH funding through grants 9P41GM104601, 5R01GM098243-02 and PHS 5 T32 GM008276 ...
doi:10.1109/ipdpsw.2016.130
pmid:27516922
pmcid:PMC4978513
dblp:conf/ipps/StoneHPPLS16
fatcat:bs7d25eh5fhi7fxkliu4gkkfyu
Computational challenges for modeling and simulating biomacromolecular assemblies
2006
Journal of Physics, Conference Series
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time-frame molecular simulation, and implementation on massively parallel computing infrastructure. ...
Understanding the structure and dynamics of large biomolecular assemblies requires the development of new computational methods for (i) accurate structure prediction, (ii) molecular docking and (iii) long ...
The ORNL Computational Biology Program is focusing on the key steps necessary to build and simulate large molecular machines: (1) Computing Accurate Building Blocks: Building accurate models of molecular ...
doi:10.1088/1742-6596/46/1/043
fatcat:6i7tyii4cbbrxdqwwyavojyeeu
Hybrid Modeling and Simulation of Biomolecular Networks
[chapter]
2001
Lecture Notes in Computer Science
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Finally we describe our agenda for future work that includes the development of models and simulation for stochastic hybrid systems. 1 ...
We use two case studies to illustrate a modular approach to modeling such networks and describe the architectural and behavioral hierarchy in the underlying models. ...
In this paper we model and simulate examples of genetic and metabolic networks using a hybrid systems approach that combines concepts and tools from control theory and computer science. ...
doi:10.1007/3-540-45351-2_6
fatcat:bo47cwfsxze7vkl3aozkjznlzi
Steering in computational science: Mesoscale modelling and simulation
2003
Contemporary physics (Print)
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Lattice-Boltzmann mesoscale fluid simulations of binary and ternary amphiphilic fluids in two and three dimensions are used to illustrate the substantial improvements which computational steering offers ...
We discuss details of our current steering implementations and describe their future outlook with the advent of computational grids. ...
Computer Services for Academic Research (CSAR), Manchester, UK. ...
doi:10.1080/00107510310001605046
fatcat:lswqecd2bra3npje6udsc7rsum
Biomolecular Path Sampling Enabled by Processing in Network Storage
2007
2007 IEEE International Parallel and Distributed Processing Symposium
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Computationally complex and data intensive atomic scale biomolecular simulation is enabled via Processing in Network Storage (PINS): a novel distributed system framework to overcome bandwidth, compute, ...
Biomolecular simulation methods are correlated with the client tools, hybrid database/file server (GEMS), computation engine (Condor), virtual file system adapter (Parrot), and local file servers (Chirp ...
Introduction Computationally complex and highly parallel biomolecular sampling methods such as Folding@home [8] have been successfully mapped to grid resources in order to overcome computational resource ...
doi:10.1109/ipdps.2007.370446
dblp:conf/ipps/BrennerWTSPI07
fatcat:ihb5q7wzqfchfnqetnazgkga6i
Graphical simulation environments for modelling and simulation of integrative physiology
2011
Computer Methods and Programs in Biomedicine
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This paper discusses the issues in the selection of a suitable platform, together with a number of current possibilities, and suggests a graphical computing environment for modelling and simulation. ...
However, though new research has added significantly to the knowledge represented by Guyton's model, and significant advances have been made in computing and simulation software, an accepted common platform ...
The authors would also like to thank Jean-Pierre Montani for providing the diagrams and Fortran code of the 1992 version of Guyton's model. r e f e r e n c e s ...
doi:10.1016/j.cmpb.2010.05.001
pmid:20576310
fatcat:wjvvvuvb45cfxdbifcaa6uks7y
Performance characterization of molecular dynamics techniques for biomolecular simulations
2006
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP '06
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Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. ...
It is well known that simulations of biological events at native time and length scales requires computing power several orders of magnitude beyond today's commonly available systems. ...
Acknowledgments The authors would like to thank Buddy Bland and other staff of the National Center for Computational Sciences (NCCS), Carlos Sosa of IBM, and MCS division at Argonne National Laboratory ...
doi:10.1145/1122971.1122983
dblp:conf/ppopp/AlamVAG06
fatcat:gb65colchrfmbiv4robentasdm
Modular Platform for Biomolecular Modeling and Simulations
2014
Biophysical Journal
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Board B48 Modular Platform for Biomolecular Modeling and Simulations Computational software has been a cornerstone of many biological sciences such as biophysics, bioinformatics or biomolecular modelling ...
Here we present the design, implementation and functionality of BioShell[1,2] software -a versatile package for biomolecular modelling. ...
-Pos Board B47 A Molecular Dynamics Simulation Study of Outer
3320-Pos Board B48 Modular Platform for Biomolecular Modeling and Simulations Dominik Gront. ...
doi:10.1016/j.bpj.2013.11.3633
fatcat:crkk6swcabci7jqcs2q7nhbkee
Colorectal tumour simulation using agent based modelling and high performance computing
2017
Future generations computer systems
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Colorectal tumour simulation using agent based modelling and high performance computing, Future Generation Computer Systems (2016), http://dx.Abstract 450,000 European citizens are diagnosed every year ...
For this reason, signif-* *Manuscript Click here to view linked References based simulation software platform (FLAME) with autotuning capabilities and optimisation strategies for the current tumour model ...
Colorectal)Tumour)Simulation)using)Agent)Based)Modelling)and)High)Performance) Computing) ) •! Colorectal)tumour)modelling)and)simulation) •! Parallel)agent)based)modelling)and)simulation)(ABMS)) •! ...
doi:10.1016/j.future.2016.03.026
fatcat:fve3zhmlovhuzpbks33adztnue
On the Path to Enable Multi-scale Biomolecular Simulations on PetaFLOPS Supercomputer with Multi-core Processors
2007
2007 IEEE International Parallel and Distributed Processing Symposium
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1 Biological processes occurring inside cell involve multiple scales of time and length; many popular theoretical and computational multi-scale techniques utilize biomolecular simulations based on molecular ...
In this preliminary study, we attempt to characterize computation, communication and memory efficiencies of bio-molecular simulations on a Cray XT3 system, which has recently been upgraded to dual-core ...
Acknowledgements The authors would like to thank National Center for Computational Sciences (NCCS) for access to Cray XT3 and support (INCITE award). ...
doi:10.1109/ipdps.2007.370443
dblp:conf/ipps/AlamA07
fatcat:uvkoel2jkvf6pfmr73pjxagwqe
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