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Protein Physics. Structural Change. Peptide Folding. Petascale Future. Movie Time. Molecular Mechanical. Quantum Mechanical. Computer Simulation - Basic Principles. Model System. or QM/MM Potential. Molecular Mechanics Potential. Simulation - exploring the energy landscape.

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Protein Physics

Structural Change

Peptide Folding

Petascale Future

Movie Time


Computer simulation basic principles

Molecular

Mechanical

Quantum

Mechanical

Computer Simulation - Basic Principles

Model System

or QM/MM

Potential

Molecular Mechanics Potential

Simulation -

exploring the energy landscape


Product

Reactant

Energy Landscape


ANDREEA GRUIA

Halorhodopsin - Chloride Pumping at Atomic Resolution



Structure13 617 (2005).


.

Spring-loaded throttle valve helps prevent chloride leakage

Valve Energy

= EI = 12 kcal/mol

Barrier without valve

= EII = 13 kcal/mol.

Sum = 25 kcal/mol

= no backflow.


Muscle contraction
Muscle Contraction

Thin filament

Thick filament


Atp hydrolysis by myosin

SONJA SCHWARZL

ATP Hydrolysis by Myosin

Biochemistry 45 5830 (2006)


Dynamics of muscle contraction

BJORN WINDSHUEGEL

Dynamics of Muscle Contraction.

MSBIO - Universität Heidelberg

PNAS 102 6873 (2005)


FRANK NOE

Large-Scale Functional

Conformational Transitions

product

reactant

s range

ns range


Ras p21

GTP-Bound Form (ON)

GDP-Bound Form (OFF)


Ras p21

GTP-Bound Form (ON)


FRANK NOE

Ras p21 trajectory


FRANK NOE

6

product

reactant

7

6

28

3

1

13

8

11

25

7

5

18

9

J. Chem. Phys. 126 155102 (2007)


Sampling: Uniform Distribution


Sampling:Exclusion of „Bad Structures“


Sampling:Fail-Fast Minimization


Sampling:Increase Density of Low-Energy Points


Transition Network:Edges between Neighbours


Temperature

Connectivity of Network of Best Paths


Ras Molecular Switch

ON - state

OFF - state


Spallation

Neutron

Source

Expensive

Toys

Cray

XT4


Cray

XT4

One Million Atoms –

Molecular Dynamics


Lars Meinhold

Zoe Cournia


Lignocellulosic biomass exhibits structural complexity
Lignocellulosic Biomass Exhibits Structural Complexity

Hemicellulose

Lignin

Cellulose


Spallation

Neutron

Source

Cray

XT4


Molecular simulation projects

Molecular Simulation Projects

Cellulose.

Lignin.

Lignocellulosic Biomass.

Cellulase Reaction Mechanism.

Cellulosomes (subsequent talk).


Now

5 years ago

Computer Power Improvement for Biological Molecular Dynamics Simulation

  • Gromacs with Reaction-Field

  • 5.4 million atoms, 175 atoms/core


Softwood Lignin & Cellulose

Cellulose Ib + 26 lignins

Probe for factors that might influence recalcitrance

  • cellulose accessible surface area

  • radii of gyration of lignins

Large-Scale Molecular Dynamics Simulation (1-3M atoms)

using 2008 DOE INCITE award on ORNL Cray XT4.


Cellulose:

Benjamin Lindner

Preliminary Findings


Crystalline/Amorphous

Crystalline

7 ns

1 ns


Collaborators
Collaborators

UT/ORNL Center for Molecular Biophysics

  • Maramuthu Krishnan (CMB, ORNL)

  • Loukas Petridis (CMB, ORNL)

  • Jiancong Xu (CMB, ORNL)

  • Roland Schulz (CMB, ORNL)

  • Benjamin Lindner (CMB, ORNL)

    External

  • Nicoleta Bondar (U. Cal Irvine)

  • Lars Meinhold, Ahmed Zewail (Caltech)

  • Kei Moritsugu (RIKEN)

  • Akio Kitao (U. Tokyo)

  • Stefan Fischer, Isabella Daidone (U. Heidelberg)

  • Torsten Becker (U. Bayreuth)

  • Frank Noe (Free University of Berlin).

  • Vandana Kurkal-Siebert (BASF, Ludwigshafen).

  • Franci Merzel (U. Ljubljana)

  • John Finney (U. London)

  • Roy Daniel (U. Waikato)

  • Andrea Amadei, Alfredo Di Nola (U. Rome “La Sapienza”)


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