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Maria Fyta
Ins,tut für Computerphysik, Universität Stu<gart Stu<gart, Germany
Nuggets on mul,scale computa,onal schemes
Computa,onal Physics
Systems/proper,es
Methodology/accuracy
Time/length scales
Hierarchy of scales
length
cm
mm
μm
nm
ps ns μs ms time
electron
ic
structure
atom
ic
structure
mesoscopic
processes
con/nuum: connec/on to experiments
Coarse-‐graining (CG) • Reduce degrees of freedom • Computa,onal efficiency
Yethiraj group, U. Wisconsin-Madison
CG: more examples
Effect of glycosylation on protein folding
D. Shental-Bechor and Y. Levy, PNAS 105, 8256 (2008)
Knots in protein folding
E. Shakhnovich, Nat. Mater. 10, 84 (2011)
Modeling the nucleosome
C.W. Hsu, AM 250b, Harvard University (2011)
Hsu, et al, JCP 2012 model
DNA
Histone Core
Initial and relaxed configuration of a histone
The Scientist, March 1, 2011
Modeling the nucleosome
C.W. Hsu, AM 250b, Harvard University (2011)
Hsu, et al, JCP 2012 model
DNA
Histone Core
Initial and relaxed configuration of a histone
Mul,scale Computa,onal Schemes ➪ Single-‐scale
Quantum-‐mechanical/electronic structure (different levels of accuracy: CI, DFT)
Classical (Molecular Dynamics) Semi-‐empirical (Tight binding) Stochas,c (Monte-‐Carlo) Discre,zed schemes (FEM,LB)
➪ Mul/-‐scale ✽ Sequen,al
✽ Concurrent
I II III
I
II
III
Sophis/cated schemes and
powerful resources
Concurrent Mul/scale Schemes
Coupling different regions
Computational Chemistry Group, University of Amsterdam
Coupling different regions
M. Praprotnik, U. Ljubljana
3 scales:atomistic, mesoscopic, continuum
changing the number of molecular degrees of freedom on-the-fly thermodynamic equilibrium of all-atom with far simpler coarse-grained system
Crack propaga,on in Si
A concurrent computa,onal approach to the simula,on of crack propaga,on in silicon seamlessly unites quantum, atomis,c, and con,nuum descrip,ons of ma<er
Abraham, Broughton, Bernstein, Kaxiras, Computers in Physics (1998)
Metal contacts: Joule hea,ng
D. I. Irving et al, Model. Sim. Mater. Sci. Engin. 17, 015004 (2009)
Co-Al contacts
Molecular Dynamics coupled to heat-transport equation
Asperity contact geometry
Temperature contours
25ps MD simulations
"bo<om-‐up" design of novel molecular nano-‐electronic structures
Hexagonal phase found in NaCl
ab initio quantum mechanical calculations, molecular dynamics simulations with classical and reactive force fields, monte carlo simulations and mesoscale simulations
MSE, U. Michigan
QM/MM
Sierka Lab, FS U. Jena
J.B.Rommel and J. Kaestner, JACS 133, 10195 (2011)
Fragmentation–Recombination mechanism of the enzyme glutamate mutase
Biomolecular Simula,ons
Parallel mul,scale simula,ons of a brain aneurysm
L. Grinberg et al, J. Comput. Phys 244, 131 (2013)
Large scale flow features: Navier Stokes solver Blood rheology inside aneurysm: coarse-grained stochastic MD
brain vasculature
Multiscale approach for molecules moving in a fluid solvent:
– Molecular Dynamics (MD) (atomistic) for molecules
– Lattice Boltzmann (LB) (mesosopic) method for solvent
Coupling of LB to MD:
Ahlrichs and B. Duenweg, Int. J. Mod. Phys C, 9, 1429, (1998). MF, Melchionna, Kaxiras, Succi, Multisc. Model. & Sim.(2006)
u fluid velocity v bead velocity
€
Fpf = γ up −υ p( )
LB -‐ MD coupling scheme
particle (P) → grid (G)
time exchange dtMD=M·ΔtLB (M=5-10)
transfer of spatial information
grid (G) → particle (P)
1. G→ P interpolation of velocity
2. For m=1,M : advance molecular state (t → t+dt)
3. P → G extrapolation of forces
4. t → t+Δt : advance Boltzmann populations
Hemodynamics Model blood flow in human arterioles
Rybicki et al, Int. J. Cardiovasc. Imaging (2009) h<p://hemo.seas.harvard.edu
A concurrent coupling of Lacce-‐Boltzmann and Molecular Dynamics
DNA transloca,on through nanopores
a bead ~ 100-150 base-pairs
a bead ~ 1base
MF, S. Melchionna, E. Kaxiras, S. Succi
Sequen/al Mul/scale Schemes
Adsorp/ve processes for energy gas storage and CO2 capture in porous networks
Z. Xiang et al, Energy. Envir. Sci. 3, 1469 (2010)
Polymer-‐clay nanocomposites
A. Danani, SUPCI, CH
MD: obtain interaction energies among components (polymer, clay, surface modifier) DPD: interaction parameters between beads FEM: calculate properties (exfoliation, etc.)
Thermoelectric Materials
T. Gruhn, U. Bayreuth
Microphase separations in thermoelectric materials like Co(Ti,Mn)Sb occurs as the system is quenched in to the coexisting region (b). Dynamics and 3D structures are studied numerically with multiscale simulations.
DFT
Monte-Carlo Phase-field theory
Connect molecular scale to cellular processes
CMTS, U. Chicago
Barnett et al, J. Mater. Sci. (2007)
(a): Electronic states of bases/base pairs at various distances and angles
(c): Construc/on of effec/ve Hamiltonian for electron localiza/on along DNA
(b): Fron/er orbitals of stretched poly-‐CG Stretching
0%
30%
60%
90%
(a) (b) (c)
Electronic structure of stretched B-‐DNA
(a) (b)
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