Computational Biology The Computational Biology Capability in CCIM is focused on applying the CCIM Center capabilities in high-performance computing to problems in the biological sciences that are in the national interest. Much of the work is focused on developing and applying algorithms in massively parallel computing to problems spanning the range of computational biology areas: bioinformatics; molecular biophysics; systems biology. We pursue problems for DOE, DHS, and other governmental agencies and industrial customers. Areas of Research:

RuBisCo protein complex, site of CO2 fixation in Synechococcus and the focus of SNL lead Genomes to Life (GTL) project investigating mechanisms for carbon sequestration

• Molecular and Coarse-grained Particle Simulation Methods
  • Bio-inspired Fuel Cell Catalysts
    (Contact: Richard P. Muller)
  • CENTIPEDE: Protein Homology Modeler
    (Contact: Alexander Slepoy)
  • Chem Cell 3D
    (Contacts: Steven J. Plimpton and Alexander Slepoy)
  • Evaluation of Biological Force Fields
    (Contact: Marcus G. Martin)
  • Investigation of Rhodopsin - A Membrane Bound Protein
    (Contact: Paul S. Crozier)
  • LAMMPS: Large Atomic/Molecular Massively Parallel Simulator
    (Contact: Steven J. Plimpton)
  • MC Towhee - Tramonto Coupling Protein Structure with Sophisticated Hydration Model (Contacts: Laura J. D. Frink and Marcus G. Martin)
  • Modeling Bio Membranes
    (Contacts: Laura J. Frink and Steven J. Plimpton)
  • Molecular Physics Investigation of the RuBisCO Carbon Fixation Enzyme
    (Contact: Paul S. Crozier and Susan L. Rempe)
  • Motor Protein Simulation by Substructured Multibody MD
    (Contact: Paul S. Crozier)
  • Parallel Annealing
    (Contact: Mark P. Sears)
  • Quantum-Classical Couple Method for Solvation Modeling
    (Contacts: Susan L. Rempe and Mark P. Sears)
• Hydration and Solvation
  • FasTram
    (Contacts: Mark P. Sears and Laura J. D. Frink)
  • Modeling Bio Membranes
    (Contacts: Laura J. D. Frink and Steven J. Plimpton)
  • Quantum-Classical Couple Method for Solvation Modeling
    (Contacts: Susan L. Rempe and Mark P. Sears)
  • Tramonto: Classical Density Functional Theory - 3D equilibrium structure of inhomogeneous fluids
    (Contact: Laura J. D. Frink)
• Protein Structure Determination
  • CENTIPEDE: Protein Homology Modeler
    (Contact: Alexander Slepoy)
  • MC Towhee - Tramonto Coupling Protein Structure with Sophisticated Hydration Model (Contacts: Laura J. D. Frink and Marcus G. Martin)
• Metabolic, Regulatory and Signaling Networks
  • Chem Cell 3D
    (Contacts: Steven J. Plimpton and Alexander Slepoy)
  • Reverse Engineering of Bio Networks
    (Contact: Jean-Loup M. Faulon)
• Microarray Analysis
  • Gene Expression Analysis Using Supervised and Unsupervised Techniques
    including VxInsight (Graph Layout Algorithm), Support Vector Machines, Principal Component Analysis
    (Contacts: George S. Davidson and Shawn B. Martin)
• Structure-based Design
  • Structure Based Design: Inverse Quantitative Structure Activity Relations (iQSAR) (Contact: Jean-Loup M. Faulon)
• Circuit Models
  • A Parallel Circuit Simulator for Cellular Biology
    (Contact: Elebeoba E. May)
  • BioXyce
    (Contacts: Elebeoba E. May and Richard L. Schiek)
• Informatics
  • A Method of Evaluating Research Using New Innovation, Risk and Impact Indicators (Contact: Kevin W. Boyack)
  • DARPA Future Combat System - Decision Support System (DSS)
    (Contact: Kevin W. Boyack)
  • Detection and Reconstruction of Error Control Codes for Engineered and Biological Regulatory Systems
    (Contact: Elebeoba E. May)
  • The Effect of the WWW on Citation Networks
    (Contacts: Alejandro Backer and Kevin W. Boyack)
  • Evolutionary Ecology: Coexistence of Species and Vulnerabilities
    (Contact: Alejandro Backer)
  • Information Retrieval
    (Contact: Alejandro Backer)
  • Large Scale Clustering Using Graph Layout
    (Contacts: Shawn B. Martin and George S. Davidson)
  • The Memory of Science
    (Contacts: Alejandro Backer and Kevin W. Boyack)
  • Next Generation Intelligent Systems (NGIS) Grand Challenge
    (Contact: Kevin W. Boyack)
  • Protein-Protein Interaction Prediction Using Signature Support Vector Machines
    (Contacts: Jean-Loup M. Faulon and Shawn B. Martin)
• Neural Modeling
  • Analysis of Multiple Simultaneously Recorded Spike Trains
    (Contacts: Alejandro Backer and Elebeoba E. May)
  • Metrics for High Dimensional Datasets with Correlated Dimensions
    (Contact: Alejandro Backer)
  • Neural Networks for Recognition
    (Contact: Alejandro Backer)
• Reaction-diffusion Models
  • Microbial Cell Model
    (Contacts: Shawn Means and John Shadid)

Program Contacts: Mark D. (Danny) Rintoul and John B. Aidun

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