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 Jesús A Izaguirre

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Average citations per article3.45
Citation Count76
Publication count22
Publication years1999-2012
Available for download7
Average downloads per article505.00
Downloads (cumulative)3,535
Downloads (12 Months)49
Downloads (6 Weeks)3
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22 results found Export Results: bibtexendnoteacmrefcsv

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1
October 2012 E-SCIENCE '12: Proceedings of the 2012 IEEE 8th International Conference on E-Science (e-Science)
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 0

Molecular modeling is a field that traditionally has large computational costs. Until recently, most simulation techniques relied on long trajectories, which inherently have poor scalability. A new class of methods is proposed that requires only a large number of short calculations, and for which minimal communication between computer nodes is ...
Keywords: Proteins,Catalogs,Computational modeling,Educational institutions,Heuristic algorithms,Servers,Graphics processing units

2
November 2011 CLOUDCOM '11: Proceedings of the 2011 IEEE Third International Conference on Cloud Computing Technology and Science
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 5

Over the past decade, high performance applications have embraced parallel programming and computing models. While parallel computing offers advantages such as good utilization of dedicated hardware resources, it also has several drawbacks such as poor fault-tolerance, scalability, and ability to harness available resources during run-time. The advent of cloud computing ...
Keywords: Elastic applications, cloud computing, distributed computing, high performance applications, replica exchange, molecular dynamics

3
February 2010 IEEE Transactions on Information Theory - Special issue on information theory in molecular biology and neuroscience: Volume 56 Issue 2, February 2010
Publisher: IEEE Press
Bibliometrics:
Citation Count: 1

In this paper, a novel framework is presented to estimate protein-protein interactions (PPIs) and domain-domain interactions (DDIs) based on a belief propagation estimation method that efficiently computes interaction probabilities. Experimental interactions, domain architecture, and gene ontology (GO) annotations are used to create a factor graph representation of the joint probability ...
Keywords: Bayesian networks, Belief propagation, Saccharomyces cerevisiae, belief propagation, sum–product algorithm (SPA), PPI inference, domain–domain interactions (DDIs), protein networks, domain-domain interactions (DDIs), protein–protein interactions (PPIs), protein-protein interactions (PPIs), sum-product algorithm (SPA)

4
December 2008 Bioinformatics: Volume 24 Issue 23, December 2008
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

An additional reference is needed in the article Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference . We include this reference as a matter of addendum. Contact: [email protected]

5
November 2008 Parallel Computing: Volume 34 Issue 11, November, 2008
Publisher: Elsevier Science Publishers B. V.
Bibliometrics:
Citation Count: 0

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, storage, organizational, and security challenges inherent to the wide-area computation and storage grid. PINS is presented as an effective and scalable scientific simulation framework ...
Keywords: High throughput computing, Computational biophysics, Distributed systems

6
October 2008 Bioinformatics: Volume 24 Issue 19, October 2008
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 1

Summary: Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain ...

7
July 2007 Computing in Science and Engineering: Volume 9 Issue 4, July 2007
Publisher: IEEE Educational Activities Department
Bibliometrics:
Citation Count: 3

To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.
Keywords: software engineering, simulation, modeling, computer applications, simulation, computer applications, modeling, software engineering

8
March 2007 ANSS '07: Proceedings of the 40th Annual Simulation Symposium
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 0

Molecular Dynamics (MD) involves solving Newton's equations of motion for a molecular system and propagating the system by time-dependent updates of atomic positions and velocities. As a severe limitation of molecular dynamics is the size of the timestep used for propagation, a key area of research is the development of ...

9
January 2007 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 4 Issue 1, January 2007
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 10
Downloads (6 Weeks): 1,   Downloads (12 Months): 8,   Downloads (Overall): 652

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One goal of contemporary proteome research is the elucidation of cellular protein interactions. Based on currently available protein-protein interaction and domain data, we introduce a novel method, Maximum Specificity Set Cover (MSSC), for the prediction of protein-protein interactions. In our approach, we map the relationship between interactions of proteins and ...
Keywords: Computations on discrete structures, graph algorithms, bioinformatics (genome or protein) databases, biology, genetics.

10
November 2005 SC '05: Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 6
Downloads (6 Weeks): 1,   Downloads (12 Months): 3,   Downloads (Overall): 258

Full text available: PDFPDF
Sharing data and storage space in a distributed system remains a difficult task for ordinary users, who are constrained to the fixed abstractions and resources provided by administrators. To remedy this situation, we introduce the concept of a tactical storage system (TSS) that separates storage abstractions from storage resources, leaving ...

11
October 2005 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 2 Issue 4, October 2005
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 10
Downloads (6 Weeks): 1,   Downloads (12 Months): 8,   Downloads (Overall): 843

Full text available: PDFPDF
We present CompuCell3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. CompuCell3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. CompuCell3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have ...
Keywords: Cellular Potts Model (CPM), biological development, reaction-diffusion, cellular automata, morphogenesis, Extensible Markup Language (XML).

12
August 2005 Journal of Parallel and Distributed Computing: Volume 65 Issue 8, August 2005
Publisher: Academic Press, Inc.
Bibliometrics:
Citation Count: 4

An @Q(n) parallel multigrid summation method (MG) for the N-body problem is presented. The method was originally devised for vacuum boundary conditions. Here, it is extended to periodic boundary conditions and implemented in parallel using force decomposition and MPI. MG is based on a hierarchical decomposition of computational kernels on ...
Keywords: Fast electrostatic solvers, particle mesh-Ewald, Multigrid summation, Parallel N-body solvers

13
July 2005 HPDC '05: Proceedings of the High Performance Distributed Computing, 2005. HPDC-14. Proceedings. 14th IEEE International Symposium
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 4

Biomolecular simulations produce more output data than can be managed effectively by traditional computing systems. Researchers need distributed systems that allow the pooling of resources, the sharing of simulation data, and the reliable publication of both tentative and final results. To address this need, we have designed GEMS, a system ...

14
April 2005 ANSS '05: Proceedings of the 38th annual Symposium on Simulation
Publisher: IEEE Computer Society
Bibliometrics:
Citation Count: 4
Downloads (6 Weeks): 0,   Downloads (12 Months): 5,   Downloads (Overall): 169

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Although the grid allows the researcher to tap a vast amount of resources, the complexity involved in utilizing this power can make it unwieldy and time-consuming. The Grid Interface for Parameter Sweeps and Exploration (GIPSE) 1 toolset aims to solve this issue by freeing users from script debugging, storage issues, ...

15
November 2004 Journal of Computational Physics: Volume 200 Issue 2, November 2004
Publisher: Academic Press Professional, Inc.
Bibliometrics:
Citation Count: 8

Shadow hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large molecules, particularly biological molecules. It improves sampling of hybrid Monte Carlo (HMC) by allowing larger time steps and system sizes in the molecular dynamics (MD) step. The acceptance rate of HMC decreases exponentially with ...
Keywords: conformational sampling, hybrid Monte Carlo, symplectic integrator, modified Hamiltonian, sampling methods

16 published by ACM
September 2004 ACM Transactions on Mathematical Software (TOMS): Volume 30 Issue 3, September 2004
Publisher: ACM
Bibliometrics:
Citation Count: 8
Downloads (6 Weeks): 0,   Downloads (12 Months): 15,   Downloads (Overall): 1,052

Full text available: PDFPDF
ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to ...
Keywords: incremental parallelism, multigrid, multiple time-stepping integration, object-oriented framework., Fast electrostatic methods, molecular dynamics

17
May 2004 Bioinformatics: Volume 20 Issue 7, May 2004
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 7

Motivation: C ompu C ell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic ...

18
June 2003 ICCS'03: Proceedings of the 2003 international conference on Computational science: PartIII
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 2

Early development of multicellular organisms (morphogenesis) is a complex phenomenon. We present COMPUCELL, a multi-model software framework for simulations of morphogenesis. As an example, we simulate the formation of the skeletal pattern in the avian limb bud, which requires simulations based on interactions of the genetic regulatory network with generic ...

19
June 2003 ICCS'03: Proceedings of the 2003 international conference on Computational science: PartIII
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 1

This paper describes the design and evaluation of ProtoMol, a high performance object-oriented software framework for molecular dynamics (MD). The main objective of the framework is to provide an efficient implementation that is extensible and allows the prototyping of novel algorithms. This is achieved through a combination of generic and ...

20 published by ACM
March 2003 SAC '03: Proceedings of the 2003 ACM symposium on Applied computing
Publisher: ACM
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 0,   Downloads (12 Months): 4,   Downloads (Overall): 248

Full text available: PDFPDF
This paper discusses additional stability limitations of multiple time stepping (MTS) integrators for molecular dynamics (MD) that attempt to bridge time scales. In particular, it is shown that when constant-energy (NVE) simulations of Newton's equations of motion are attempted using the Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the longest step ...
Keywords: multiple time stepping, linear instability, Verlet-I/r-RESPA/Impulse, long molecular dynamics simulations, nonlinear instability



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