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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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Presentation Transcript
slide1

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

slide3

Product

Reactant

Energy Landscape

slide4

ANDREEA GRUIA

Halorhodopsin - Chloride Pumping at Atomic Resolution

slide7

.

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)

slide12

FRANK NOE

Large-Scale Functional

Conformational Transitions

product

reactant

s range

ns range

slide13

Ras p21

GTP-Bound Form (ON)

GDP-Bound Form (OFF)

slide14

Ras p21

GTP-Bound Form (ON)

slide15

FRANK NOE

Ras p21 trajectory

slide16

FRANK NOE

6

product

reactant

7

6

28

3

1

13

8

11

25

7

5

18

9

J. Chem. Phys. 126 155102 (2007)

slide22

Temperature

Connectivity of Network of Best Paths

slide23

Ras Molecular Switch

ON - state

OFF - state

slide24

Spallation

Neutron

Source

Expensive

Toys

Cray

XT4

slide25

Cray

XT4

One Million Atoms –

Molecular Dynamics

slide26

Lars Meinhold

Zoe Cournia

slide28

Spallation

Neutron

Source

Cray

XT4

molecular simulation projects

Molecular Simulation Projects

Cellulose.

Lignin.

Lignocellulosic Biomass.

Cellulase Reaction Mechanism.

Cellulosomes (subsequent talk).

slide30

Now

5 years ago

Computer Power Improvement for Biological Molecular Dynamics Simulation

  • Gromacs with Reaction-Field
  • 5.4 million atoms, 175 atoms/core
slide31

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.

slide32

Cellulose:

Benjamin Lindner

Preliminary Findings

slide33

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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