Boltzmann Transport Monte Carlo Code - BioMOCA

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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

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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.

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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/
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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

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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

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Transport Monte Carlo Particle Simulations

• 3D particle trajectories
• P3M
• Continuum background
• Implicit water
• Scattering
• Thermalizes ions
• Finite size of the ions

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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

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Complexity of Monte Carlo Simulations for Typical
Ion Channels

• Very large domains and very few particles

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Complexity Continued

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

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High Throughput Simulations

• IV curves
• Bias
• Ionic concentrations
• Ionic species
• Different protein configurations
• Crystallographic configurations
• Mutations
• etc

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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

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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
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MscS Continued
Biophysical Journal 903496-3510, 2006.
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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