SI2010 Special Topics on Emerging Technologies

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General Information

The track is geared towards researchers in the computational biology field, who are interested in multiscale modeling and applications in translational research. Examples will come from heart physiology and pathology, molecular electrostatics and diffusion, and computer aided drug discovery.

This track is a series of short presentations and hands on tutorials on emerging software tools, and algorithms in multiscale modeling, ranging from nano-, meso- to macro-scale, with an emphasis on integrative biomedical computation and translational research. The topics may include use of the FEniCS toolkit and adaptive finite element modeling in calcium signaling; the relaxed complex scheme and ensemble based virtual screening; use of GAMER in the generation of high quality mesh representation of subcellular structures; modeling of the T-tubular network in the simulation of CICR in cardiac myocytes.

Each session includes lectures and demonstrations or hands-on exercises.

Projected Outcome By the end of the sessions, the participants should be able to gain ideas about the ongoing research topics and emerging software tools from NBCR, with a preview of the tools ready for training in the regular tracks. Participants are encouraged to provide feedback and interact with the developers at the early stages of the tools development.

Instructors: Prof. Rommie Amaro; Riccardo Baron, Ph.D.; Prof. Zeyun Yu; Anushka Michailova, Ph.D.; Johan Hake, Ph.D.; Yi Wang, Ph.D; Cesar de Oliveira, Ph.D.; Barry Grant, Ph.D. Robert V. Swift, Ph.D.

Time M-Th, 2:00 pm to 5:30 pm, Aug 2-6, 2010

Location PFBH PC lab Room 161

Prerequisite Familiarity with Unix is recommended but NOT required.


  • Monday BD, aMD, and CADD
    Instructors: Rommie Amaro, Ph.D; Yi Wang, Ph.D; Cesar de Oliveira, Ph.D.
    Applications of molecular dynamics techniques in CADD: Rommie Amaro, Ph.D.
    Introduction to accelerated molecular dynamics, an enhanced sampling method: Yi Wang, Ph.D.
    Accelerated molecular dynamics simulations of Trypanosoma cruzi proline racemase: accessing long time scale conformational changes: Cesar de Oliveira, Ph.D.
  • Tuesday Molecular Motors & Electrostatics and Free Energy Approaches in Drug Design
    Instructors: Barry Grant, Ph.D.; Riccardo Baron, Ph.D.
    Molecular Motors & Electrostatic: Barry Grant, Ph.D.
    Free Energy Approaches in Drug Design: Riccardo Baron, Ph.D.
    Free energy is the key thermodynamic quantity describing the propensity of a biomolecular system to spontaneously undergo a given process. Often, chemistry and biochemistry of fundamental relevance are characterized by a delicate balance between a large change in enthalpy and a large opposite change in entropy, resulting in comparatively small free-energy differences. In recent years, the calculation of accurate free-energy differences by computer simulation has become feasible in practice. An introduction to state-of-the-art methods for free energy calculations for molecular recognition will be given:
    • General presentation of the use of free energy approaches in CADD
    • Key concepts involved: thermodynamic cycles and molecular physics contributions
    • The basics of three alternative methods: Thermodynamic Integration (TI), Independent-Trajectory TI (IT-TI), and Single Step Perturbation (SSP).
    The focus of this Special Topic is to describe how to exploit their robust features in biological recognition, association, and CADD. The future implementation of these methods in the NBCR pipeline framework will also be briefly described.
  • Wednesday, Application of FETK and FEniCS in Multiscale Biomedical Simulation
    Instructor: Johan Hake, Ph.D., Yuhui Cheng, Ph.D.
    Both of these talks will be followed by a hands on tutorial session. See instructions
    Mesh Generation:
    • Mesh improvement, using GAMer/FEtk, of segmented EM tomography data
    • slides
    Introduction to Finite Element Method:
    • FEniCS provides a high level interface to the Finite element method. This talk will be an introduction to FEM using FEniCS.
    • slides
  • Thursday, From Meshing to Model Building to Simulation of CICR using realistic models of cardiac myocytes
    Instructor: Zeyun Yu, Ph.D., Anushka Michailova, Ph.D., Yuhui Cheng, Ph.D.
    • Image Processing: contrast enhancement, noise reduction, segmentation, skeleton extraction slides
    • Mesh Generation: surface and volumetric meshing from molecules (PDB/PQR) and 3D images, and surface mesh quality improvement slides
    • Zeyun: Multi-scale geometric modeling of ventricular myocytes slides
    • Anushka: Finite element simulation of cardiac myocytes

Related Tracks from Previous SI

SI2008 Multiscale Image Analysis and Visualization

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