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Boltzmann Transport Monte Carlo Code - BioMOCA

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Adaptation of the Monte Carlo approach used for solid-state device simulation. Germane to Brownian Dynamics with implicit water description, but interaction ... – PowerPoint PPT presentation

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Title: Boltzmann Transport Monte Carlo Code - BioMOCA


1
Boltzmann Transport Monte Carlo Code - BioMOCA
Reza Toghraee and Umberto Ravaioli Beckman
Institute ECE Department University of Illinois
at Urban-Champaign
  • NIH Nanomedicine Center for Design of Biomimetic
    Nanoconductors
  • Network for Computational Nanotechnology (NCN)
    NanoHUB

2
BioMOCA code
  • Adaptation of the Monte Carlo approach used for
    solid-state device simulation.
  • Germane to Brownian Dynamics with implicit water
    description, but interaction between ions and
    water is resolved using a scattering process.
  • BioMOCA code - developed by Trudy van der
    Straaten, Gulzar Kathawala, Reza Toghraee, and
    Umberto Ravaioli at the University of Illinois.
  • Development funded by DARPA and NSF Network for
    Computational Nanotechnology.

3
Ion Channels
  • Biological membranes are made out of lipids to
    protect the valuable interior contents of the
    cell
  • Membrane proteins are embedded in the membrane
    bilayer lipid
  • Ion channels answer the need for transport system
  • Highly specific filters
  • For instance, ion channels play a key role in
    heart pulsing, neuron and muscle cells, toxins,
    and are related to many diseases

http//www.rsc.org/chemsoc/
4
Motivations
  • Engineers trying to model channels similar to
    devices
  • In particular we are interested in bio-inspired
    structures, to realize
  • sensors
  • artificial organs
  • nano batteries
  • etc

5
Computational Goals and Methods
  • Quantum Chemistry
  • Very few particles
  • Molecular Dynamics
  • Extremely costly
  • Limited time intervals
  • Ion traversal is a rare lucky event
  • A large number of ion crossings must be detected
  • Monte Carlo / Brownian Dynamics
  • BioMOCA is based on Transport Mante Carlo
  • Continuum Models

6
Transport Monte Carlo Particle Simulations
  • 3D particle trajectories
  • P3M
  • Continuum background
  • Implicit water
  • Scattering
  • Thermalizes ions
  • Finite size of the ions

7
initialize ( t 0 ) grid, protein
charges calculate ?fixed
Lennard Jones 6-12 potential

rions? ?ions
solve POISSON update E
P3M
t ? t dt
short range forces
Move ions (E FLJ) scattering with
water scattering off protein/lipid update rions
LJ

8
Complexity of Monte Carlo Simulations for Typical
Ion Channels
  • Very large domains and very few particles

9
Complexity Continued
  • Very large simulation times
  • Time multi-scale problem
  • Ergodicity
  • MOCA is based on random numbers

10
High Throughput Simulations
  • IV curves
  • Bias
  • Ionic concentrations
  • Ionic species
  • Different protein configurations
  • Crystallographic configurations
  • Mutations
  • etc

11
NanoHUB and Grid Application
  • How we use Grid
  • i.e. OSG, or TeraGrid
  • NCN account (nanoHUB)
  • Demo version of Rappturized BioMOCA
  • Coupling nanoHUB with the Grid
  • Automatic access and job lunching for non-experts

12
Recent Application
Periplasm
  • Simulation of the Mechanosensitive
  • Channel of Small Conductance (MscS)
  • Impractical with Molecular Dynamics
  • In collaboration with Prof. Klaus Schultens
    group, Theoretical and Computational Biophysics
    (TCB) at Beckman Institute, UIUC.

Cytoplasm
13
MscS Continued
Biophysical Journal 903496-3510, 2006.
14
OSG Experience with BioMOCA
  • Several protein configurations of MscS channel
  • Truncated protein
  • Hydrated lipid
  • 1800 runs on OSG
  • i.e.
  • Truncated protein without lipid hydration
  • KCl- at 100, 200, 500 milli molar
    concentrations
  • Filter selectivity
  • 100 milli molar / 100 milli volts
  • K L-gtR 0 R-gtL 5
  • Cl- L-gtR 75 R-gtL 1
  • Total current of 79 electron charges during 72
    nano seconds
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