Transcript here - BITS Embryo

BITS Embryo Lecture
Multi-scale modeling and molecular
simulations of materials and biological
systems
Arthi Jayaraman
Post Doc, University of Illinois Urbana Champaign
Ph.D. North Carolina State University 2006
B.E. Hons (Chemical Engineering) BITS Pilani 2000
1
Outline
• What is molecular simulation?
• Why do we need multi-scale modeling and
simulations?
• Steps involved in modeling and simulations
• Types of models
• Brief overview of simulation methods
• Examples of systems from
– material science
– biological science
2
What is molecular simulation?
• Molecular simulations use computer models to describe
chemical systems at an atomic level of detail
• In a computer simulation
– Provide individual positions and orientations of every
atom or molecule
– Place atoms and molecules in a simulation cell
– Let them interact with each other through a potential
– Let the system evolve according to some simulation
algorithm.
3
What is molecular simulation? (contd.)
Example: A gaseous mixture of monoatomic molecules
Components of the system
atom A
atom B
atom C
i-j interaction between
species i and j
A-C
B-B
A-A
A-B
B-C
C-C
4
What is multiscale modeling and
molecular simulation?
time
Milli sec
micro sec
nano sec
length
pico sec
1 A
100 nm
1 μm
5
Kremer and Delle Site, Development of methods
Why do we need modeling and simulation?
• Experiments
– cannot study systems at some length scales and time scales
– require very expensive equipments to study systems at
certain conditions
• Modeling and Simulations
– allow us to study systems at varying length scales and time
scales
– are cheaper (computers!)
– give us the ability to isolate the effect of each and every
parameter involved in the system
6
Steps involved in modeling and simulations
• 1: What is the system and what do we want to investigate?
– How to model the different components of the system
– What length scale to use
• 2: What are interactions between the different components of
the system?
– What force fields and potentials to use
• 3: Do we want to study system dynamics or equilibrium
thermodynamics?
– What simulation method to use
– What time scale to use
• 4: Analysis of the results
7
Types of models
• Atomistic
– Explicitly represent every atom in the molecule
C
H
• Coarse grained
– Group of atoms combined together
8
Intermolecular forces and potential
•
Contributions to potential energy (U) of a system with N molecules
U (r N )  U str  U bend  U tors  U cross  U vdW  U el  U pol
Intramolecular only
Intra- and Inter(between atoms within a molecule) molecular only
• Ustr - stretch
• UvdW - van der Waals
• Ubend - bend
• Uel - electrostatic + - - +
• Utors - torsion
• Upol - polarization + - + -
Repulsion
Attraction
• Ucross - cross
Dr. D. A. Kofke’s lectures on Molecular Simulation, SUNY Buffalo
http://www.eng.buffalo.edu/~kofke/ce530/index.html
9
Brief overview of simulation methods
Monte Carlo
Specify the initial positions of
all molecules
Generate random moves for
the molecules
Sample with probability  exp(-U/kT)
Molecular Dynamics
Specify the initial positions ri(0),
and velocities vi(0) of all
molecules
Solve Newton’s equations Fi = mi ai
Calculate ri(t), vi(t)
Take averages
Obtain equilibrium properties
Take averages
Dr. Keith Gubbins lectures, NCSU
Obtain equilibrium and
non-equilibrium
properties
10
Monte Carlo (MC) versus Molecular Dynamics (MD)
• MD gives information about dynamical behavior and equilibrium,
thermodynamic properties
so transport properties can be calculated.
MC can only give static, equilibrium properties
• In MD the motions of the molecules are natural
(follow newton’s law)
In MC the motions are artificial
(random moves)
11
Dr. Keith Gubbins lectures, NCSU
Brief Overview of Simulation Methods
(contd.)
• Other simulation methods
– Brownian dynamics simulation
– Quantum Mechanics-Molecular Mechanics
(QM/MM)
– Dissipative Particle Dynamics Simulation
• Suggested Reading:
– A. R. Leach, Molecular Modelling, Longman, London (1996)
– D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed.,
Academic Press (2002)
– M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford (1987)
12
Challenges
• pick the right model
– How much detail is required to represent the system
accurately and yet have reasonable simulation time ?
(note: too much detail in the model will slow down the
simulations tremendously)
• pick the right simulation method
– Which method would be able to simulate the complete
phenomena we are interested in ?
(note: often in some simulation methods the system simply will
not equilibrate)
13
Modeling and simulation of confined polymers
A bulk of copolymers confined between surfaces
A12B12 copolymer
A-sA
Attractive interaction
B-sB
Attractive interaction
A12B12
Using experiments
difficult to make these patterned surfaces (nanometer size patterns)
difficult to study how the polymer organize on these patterned surfaces
(observe the organized at the molecular level)
Q. Wang et al. Macromolecules, 33, 4512 (2000);
14
Modeling and simulation of confined polymers
• Similar structures found in experiments and simulations
Experiment2
Simulation1
A12B12 copolymer
polystyrene-bpolymethylmethacrylate copolymer
• Simulation is able to predict other structures depending on pattern spacing LS
1) Q. Wang et al. Macromolecules, 33, 4512 (2000);
2) L. Rockford et al. Phys. Rev. Lett. 82, 2602(1999)
15
Protein folding
Proteins are large organic compounds made of a sequence of amino acids.
sidechain
amine group
carboxyl group
Before proteins can carry out their important functions, they assemble
themselves, or fold
When proteins do not fold correctly (i.e. "misfold"), there can be serious
consequences, including many well known diseases, such as Alzheimer's,
Mad Cow (BSE), Huntington's, Parkinson's disease, etc.
16
Modeling and simulation of protein
folding
Experimental determination of the folded structure is a lengthy and complicated
process, involving methods like X-ray crystallography and NMR.
Simulations are trying to predict structures based on the amino acid sequence
There are many ways to model proteins:
H
Atomistic
H
United atom
H
c
c
H
N
c
H
O
Coarse-grained
Carol Hall’s group, NCSU
side group
17
backbone
Modeling and simulation of proteins
Two most commonly found motifs in folded proteins
a-helix
b-hairpin
b-turn
Structure of the protein is very complex
Modeling and simulations can be very useful
in predicting these complex structures
18
Dr. Stefan Franzen’s lectures NCSU
Summary
• Modeling and simulation are a useful tool in understanding
the molecular phenomena underlying complex processes in
– Material science
• Confined polymers, pattern recognition in polymers*
micelle formation, phase transitions in materials,
colloidal systems, etc.
– Biological science
• Structure of proteins, DNA and other biopolymers;
assembly of proteins; recognition in DNA microarrays*
DNA-protein binding, drug design, etc.
• Modeling and simulations complement experiments by
predicting phenomena that are difficult to study
experimentally.
19
* My PhD thesis http://turbo.che.ncsu.edu/arthi