Reading List

Date Paper Presenter Notes, slides, etc.
Dec. 02
  • The Chemical Basis of Morphogenesis
    		•  Matt Rissler mrissler.pdf
    Nov. 30
  • A Mathematical Model for Outgrowth and Spatial Patterning of the Vertebrate Limb Bud
    		•  Anthony Schorer aschorer.pdf
    Nov. 23
  • BioLogo: A Domain Specific Language for Morphogenesis
    		•  Trevor Cickovski tcickovs2.ppt
    Nov. 18
  • A Framework for 3-Dimensional Simulation of Morphogenesis
    		•  Scott Christley schristley.pdf
    Nov. 11
  • The Anatomy of the Grid: Enabling Scalable Virtual Organizations
    		•  Xiarong Xiang xxiang.pdf
    Nov. 09
  • The Pfam Protein Families Database
    		•  Simon Kanaan skanaan.ppt
    Nov. 04
  • Hidden Markov Models in Computational Biology: Applications to Protein modeling UCSC-CRL-93-32
    		•  Open Slides.pdf
    Nov. 02
  • SCOP: A Structural Classification of Proteins Database
    		•  Open Slides.pdf
    Oct. 28
  • Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction
    		•  Trevor Cickovski tcickovs.ppt
    Oct. 26
  • The Protein Threading Problem with Sequence Amino Acid Interaction Preferences is NP-Complete
    		•  Chengang Huang chuang.ppt
    Oct. 07
  • Fast Algorithms for Classical Physics
  • Multiscale Fast Summation of Long-Range Charge and Dipolar Interactions
    		•  Paul Brenner pbrenner2.pdf
    Oct. 05
  • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
  • Molecular Dyanmics Simulations of Biomolecules: Long-Range Electrostatic Effects
    		•  David Cieslak dcieslak.ppt
    Sep. 30
  • Protein Flexibility and drug design: How to Hit a Moving Target
  • FlexE: Efficient Molecular Docking Considering Protein Structure Variations
    		•  Santanu Chatterjee schatter2.pdf
    Sep. 28
  • A Single-Molecule Study of RNA Catalysis and Folding
  • "New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations
    		•  Joe Lammersfeld jlammers.pdf
    Sep. 23
  • Novel Methods of Sampling Phase Space in the Simulation of Biological Systems
  • Shadow Hybrid Monte Carlo: an Efficient Propagator in Phase Space of Macromolecules
    		•  David Salyers dsalyers.pdf
    Sep. 21
  • Ab Initio Protein Structure Prediction
  • Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
    		•  John Tan jtan1.pdf
    Sep. 16
  • ProtoMol, an Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics
  • NAMD2: Greater Scalability for Parallel Molecular Dynamics
    		•  Santanu Chatterjee schatter.pdf
    Sep. 14
  • Force Evaluators, Integrators and Propagators
  • Long time step molecular dynamics using targeted Langevin stabilization
    		•  Paul Brenner pbrenner.pdf
    Sep. 09
  • Validation of Molecular Dynamics Simulation
  • Assesing Equilibration and Convergence in Biomolecular Simulations
    		•  Kedar Aras karas.pdf
    Sep. 02
  • A Test Set for Molecular Dynamics Algorithms
  • Molecular Dynamics Simulations
    		•  Scott Hampton shampton.pdf