blender in bio-/ quantum-chemistrydownload.blender.org/documentation/bc2011/thomas_haschka.pdf ·...
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Blender in Bio-/Quantum-chemistry
Thomas Haschka - Blenderconf 2011thomas.haschka@inserm.fr
Our Mission
• Academic research institution
• Mixed biology/chemistry/physics/informatics interdisciplinary environment
• Molecular dynamics / quantum chemistry etc.
• Building/using mathematical models to explain biological processes on a molecular level
What does it take to explain a biological
process?
• A biological process happens at different scales.
• Different scales require different kinds of treatments and careful linkage between them.
What are our Scales?
Continuum >10nm
Electrons
Proteins
Building Blocks:Entire Biological Molecule(Protein) 10000+ Atoms
Blocks of such a BiologicalMolecule
Methods:Mechanical ModelsFluid DynamicsLangevin/Brownian Dynamics
All Atoms ~0.1nmCoarse Grained
Electrons
Proteins
Building Blocks:AtomsAtom Assemblies
Methods:Molecular Dynamics SimulationsCG MD SimulationsLangevin/Brownian Dynamics
What is classical molecular dynamics?• Atoms have modeled interactions which
are trying to describe reality.
• Correctness vs (amount of data and computational effort)
Springs
electrostatics
0.1 nm > Quantum
Electrons
Proteins
Building Blocks:SubatomicElectrons - Wave function
Methods:Quantum Mechanical
Mixed Quantum/classical molecular dynamics simulations
Electronic Shell Evaluations
Why Blender ?
• Allows us to visualize our molecules in three dimensions.
• At all scales the molecule’s function is determined by its three dimensional structure.
• Visualizing a molecule thus means in many cases that you know how it actually works!
• Visualization further helps you to communicate your discoveries.
What else besides Blender?
• Different scales require different programs
• What we are using:
• Hand written code, various tools,...
• GROMACS - Molecular Dynamics
• GAUSSIAN - Quantum Mechanics
• VMD, PyMOL generate 3D VRML models
• Blender to show off our results!
WorkflowsThat’s how we do it!
Continuum Mechanics
Continuum Mechanics
Create a mathematical model of your
molecule
Create a visual model of your mathematical
model
Continuum Mechanics
Create a mathematical model of your
molecule
Create a visual model of your mathematical
model
Continuum Mechanics
Create a mathematical model of your
molecule
Simulate
Create a visual model of your mathematical
model
Continuum Mechanics
Create a mathematical model of your
molecule
Simulate
Create a visual model of your mathematical
model
Continuum Mechanics
Create a mathematical model of your
molecule
Simulate
Create a visual model of your mathematical
model
Animate your visual model
Continuum Mechanics
Create a mathematical model of your
molecule
Simulate
Create a visual model of your mathematical
model
Animate your visual model
Continuum Mechanics
Create a mathematical model of your
molecule
Simulate
Create a visual model of your mathematical
model
Animate your visual model Render
MD Simulations
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Create a visual model of your
structure.
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Create a visual model of your
structure.
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Analyze your simulations and interpret them.
Create a visual model of your
structure.
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Analyze your simulations and interpret them.
Create a visual model of your
structure.
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Analyze your simulations and interpret them.
Model features you find to be
important into the model of your
structure.
Create a visual model of your
structure.
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Analyze your simulations and interpret them.
Model features you find to be
important into the model of your
structure.
Create a visual model of your
structure.
MD SimulationsObtain / model a
structure of a Protein. Optionally generate a coarse
grained model
Simulate
Analyze your simulations and interpret them.
Model features you find to be
important into the model of your
structure. Render
Create a visual model of your
structure.
Quantum Chemistry
Obtain / model a structure of your
molecule
Calculate quantum features of your
molecule (like the electron density)
Generate volumetric data
from your obtained results
Render
Other Scientific TasksArbitrary Volume Data
Molecular Properties
Normal Mode Analyses
Function Plotting
Phase Space Visualization
Structural Alignment
Case Study:Thrombospondin
C-Terminal
TSP Model in Blender• Quickly modeled (like 20
minutes) in Blender using just spheres and Bezier curves.
• Allows us to point out different regions of the molecule, and those we are interested in.
• Works way better then hand drawn 2d schemes.
N-Terminal
C-Terminal/Signature
CC-Region
TSR1-Repeats
Signature Domain (Atomistic Level)
• Mesh has been generated in Pymol from a structure available in the Protein Data Bank
• Around 40, 50ns all atom simulations have been evaluated.
• We used blender to highlight main features of the structure known from literature.
• Further we used armatures to model major motions found by the MD simulations.
Stalk
Globe
Globe
CD-47 Binding Site
Calcium Ion
IntegrinBinding Site
Still Frame with Important Sites
Mov
e
Structural Alignment
Differentmembers of
the TSP familyshare the same
signature domain
DifferentMembers of
the TSP familyshare the same
Signature Domain
TSP-1TSP-2TSP-5
Quantum Mechanics• Many movements, biological processes can
not be described by the simplicity of classical molecular dynamics. In this cases we need to use data evaluated by the principles of quantum mechanics.
• In the case of thrombospondin the electron cloud around calcium binding sites was evaluated using GAUSSIAN.
• GAUSSIAN allows us to express its results in so called “cube” files, which essentially is voxel data.
• So far no classical molecular visualization software (VMD, PyMOL) allows us to visualize this data at an arbitrary precision.
GettingQuantumData into Blender
Input
GettingQuantumData into Blender
Input
GettingQuantumData into Blender
Gaussian/cubegenInput
GettingQuantumData into Blender
Gaussian/cubegenInput
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coords
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coords
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegen
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegen
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegen
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegen
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
raw
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
raw
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
raw blender
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
raw blender
cubes’
GettingQuantumData into Blender
Gaussian/cubegenInput cubes
cubealign
coordscubegencube2raw
raw blender images
cubes’
GettingQuantumData into Blender
-1 0 1 ... e-Potential in Atomic Units
Positive Calcium
Negative Oxygens
Negative Oxigens
Almost Neutralized
Oxygens
Amine
And we can actually make a movie how charge and electron density change as the calcium ion moves away
Everything Assembled Together!
The Thrombospondin Movie
Thanks to my French partners:
Reims:CNRS UMR 6237Manuel DauchezLaurent Martiny
CNRS UMR 6229Eric Henon
The Champagne Ardenne Computational Center
Romeo
Paris:INSERM UMRS 665Catherine Etchebest
The Champagne Ardenne region for funding my
work
9/10/10 12:14 PMhttp://upload.wikimedia.org/wikipedia/fr/0/0f/CNRS_fr_quadri.svg
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