NIC Workshop 2006, From Computational Biophysics to Systems Biology, (2009)
Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, Jesús A. Izaguirre, Jan Meinke, ...
published in
Pathways into Large Parameter Search Spaces: Experiences with Molecular Hyperdynamics (2009)
Justin M. Wozniak, Santanu Chatterjee, Paul Brenner, Douglas Thain, Aaron Striegel, Jesús A. Izaguirre
A great deal of systems software is available to enable researchers to utilize complex computation and data grids to perform and visualise large batches of scientific jobs [1]–[6]. However, the...
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based (2009)
Nan Chen, James A. Glazier, Jesús A. Izaguirre
The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the...
MDL, A Domain-Specific Language for Molecular Dynamics (2008)
Trevor Cickovski, Chris Sweet, Jesús A. Izaguirre
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...
MDL, A Domain-Specific Language for Molecular Dynamics (2008)
Trevor Cickovski, Chris Sweet, Jesús A. Izaguirre
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...
BIOINFORMATICS BIOLOGO: A Domain-Specific Language For (2008)
Trevor Cickovski, M. H. Merks, Jesús A. Izaguirre
† to whom correspondence should be addressed
Bayesian Inference of Protein and Domain Interactions Using The Sum-Product Algorithm (2008)
Marcin Sikora, Faruck Morcos, Daniel J. Costello, Jesús A. Izaguirre
Abstract — In order to fully understand the functions of proteins in living organisms we must study their interactions and construct accurate interaction maps. Each protein can be composed of one...
Prediction of domain interactions in C. elegans (2008)
Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, Jesús A. Izaguirre
High throughput experiments and computational methods allow the elucidation of networks of protein-protein interactions (PPI) in several organisms. Since about 80 % of all proteins consist of...
MDSimAid: Automatic parameter optimization in fast electrostatic algorithms (2008)
Michael S. Crocker, Scott S. Hampton, Thierry Matthey, Jesús A. Izaguirre
MDSimAid is a recommender system that optimizes parallel Particle Mesh Ewald (PME) and both sequential and parallel multigrid (MG) summation fast electrostatic solvers. MDSimAid optimizes the running...
Backward error analysis of multiscale symplectic integrators and propagators. (2008)
Christopher R. Sweet, Jesús A. Izaguirre
Symplectic integrators are used in molecular dynamics simulations for their to excellent long term behavior, due to the existence of the associated shadow Hamiltonian. Improvements in the efficiency...
IMPROVED SAMPLING OF CONFIGURATION SPACE OF BIOMOLECULES (2007)
Jesús A. Izaguirre, Using Shadow, Hybrid Monte Carlo
by Scott S. Hampton Sampling the configuration space of complex biological molecules is an important and formidable problem. One major difficulty is the high dimensionality of this space, roughly 3N,...
Michael S. Crocker, Scott S. Hampton, Jesús A. Izaguirre
Once the paper is finished, we will add the abstract here. 1
MDSimAid: Automatic parameter optimization in fast electrostatic algorithms (2007)
Michael S. Crocker, Scott S. Hampton, Jesús A. Izaguirre
MDSimAid is a recommender system that generates nearly optimal parameters for Particle Mesh Ewald (PME) and multigrid (MG) summation fast electrostatic solvers. MDSimAid optimizes the running time of...
Nonlinear instability in multiple time stepping molecular dynamics (2007)
Qun Ma, Jesús A. Izaguirre, Robert D. Skeel
Nonlinear instability in multiple time stepping molecular dynamics This paper uncovers additional stability limitations of multiple time stepping (MTS) integrators for molecular dynamics (MD) that...
Chengbang Huang, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
The goal of contemporary proteome research is the elucidation of protein interactions in the cell. Based on cur-rently available protein-protein interaction and domain data of S. cerevisiae, we...
Trevor Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, Mark Alber, ...
2004 DRAFT IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2 We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogen-esis in different organisms....
Jesús A. Izaguirre, Thierry Matthey
An Θ(n) parallel multigrid summation method for the N-body problem is presented. The method works with vacuum or periodic boundary conditions. It is based on a hierarchical decomposition of...
targeted Langevin stabilization ∗ (2007)
Long time step molecular dynamics using
Predicting protein-protein interactions from protein domains using a set cover approach (2007)
Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
Abstract—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...
Trevor Cickovski, Kedar Aras, Maciej Swat, M. H. Merks, Tilmann Glimm, H. George E, ...
Scientific applications are typically developed using procedural languages such as C or Fortran to gain performance, but often at the cost of reduced flexibility. As software complexity increases,...
Predicting protein-protein interactions from protein domains using a set cover approach (2007)
Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
Abstract—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...
Optimal implementation of the Shadow Hybrid Monte (2006)
Carlo Method, Christopher R. Sweet, Scott S. Hampton, Jesús A. Izaguirre
Jesús A. Izaguirre, Trevor M. Cickovski, Kedar Aras, Chengbang Huang, Joseph Coffland
We present this user guide as a tool to detail both how to operate and use key features of the COM-PUCELL3D framework. COMPUCELL3D was designed to be a useful framework to run simulations of...
Parallel multigrid summation for the n-body problem (2005)
Jesús A. Izaguirre, Scott S. Hampton, Thierry Matthey
An Θ(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...
A framework for three-dimensional simulation of morphogenesis (2005)
Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George, E. Hentschel, ...
Abstract—We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering,...
CompuCell, a multimodel framework for simulation of morphogenesis (2004)
J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffl, G. Thomas, ...
Motivation: COMPUCELL 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...
Improved sampling for biological molecules using Shadow Hybrid Monte Carlo (2004)
Scott S. Hampton, Jesús A. Izaguirre
Abstract. Shadow Hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large biological molecules. It improves sampling by allowing larger time steps and system sizes in the...
Linearly scalable hybrid monte carlo method for conformational sampling of large biomolecules (2003)
Scott Hampton, Jesús A. Izaguirre
We present a variation on the hybrid Monte Carlo (HMC) algorithm that improves the sampling of phase space. This new algorithm, called Shadow Hybrid Monte Carlo (SHMC), achieves a nearly linear...
Alice N. Ko, Notre Dame, Jesús A. Izaguirre
by Alice N. Ko Molecular dynamics (MD) for modeling the behavior of biological molecules is an important but di#cult task. This thesis presents an approach that incorporates ideas from recommender...
Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method (2002)
Jesús A. Izaguirre, Qun Ma, Thierry Matthey, Jeremiah Willcock, Thomas Slabach, En Moore, ...
Abstract. The primary objective of this paper is to explain the derivation of symplectic mollified Verlet-I/r-RESPA (MOLLY) methods that overcome linear and nonlinear instabilities that arise as...
1 Introduction The Christian Idea of Work (2000)
In this brief document, I try to explore the question of the meaning of work in the light of
Normal mode partitioning of Langevin dynamics for biomolecules
Sweet, Christopher R., Petrone, Paula, Pande, Vijay S., Izaguirre, Jesús A.
We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a...