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Parallel Biomolecular Computation: Models and Simulations

J. H. Reif
1999 Algorithmica  
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]

John Reif
1999 DNA Based Computers III  
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

O. Steinhauser, H. Schreiber, G. Löffler, W. Kleinert
1997 Simulation Practice and Theory  
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

P. Brenner, J.M. Wozniak, D. Thain, A. Striegel, J.W. Peng, J.A. Izaguirre
2008 Parallel Computing  
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

W. Guan, X. Cheng, J. Huang, G. Huber, W. Li, J.A. McCammon, B. Zhang
2018 Computer Physics Communications  
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

John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, Klaus Schulten
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
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

Ed Uberbacher, Philip LoCascio, Sergey Passovets, Pavan Ghattyvenkatakrishna, Pratul Agarwal, Nikita Arnold, Andrew Bordner, Andrey Gorin
2006 Journal of Physics, Conference Series  
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]

Rajeev Alur, Calin Belta, Franjo Ivančić, Vijay Kumar, Max Mintz, George J. Pappas, Harvey Rubin, Jonathan Schug
2001 Lecture Notes in Computer Science  
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

J Chin, J Harting, S Jha, PV Coveney, AR Porter, SM Pickles
2003 Contemporary physics (Print)  
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

P. Brenner, J. M. Wozniak, D. Thain, A. Striegel, J. W. Peng, J. A. Izaguirre
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
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

Violeta Mangourova, John Ringwood, Bruce Van Vliet
2011 Computer Methods and Programs in Biomedicine  
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

Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwal, Al Geist
2006 Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP '06  
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

Dominik Gront
2014 Biophysical Journal  
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

Guiyeom Kang, Claudio Márquez, Ana Barat, Annette T. Byrne, Jochen H.M. Prehn, Joan Sorribes, Eduardo César
2017 Future generations computer systems  
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

Sadaf R. Alam, Pratul K. Agarwal
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
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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