Nuggets on coarse- graining and mul,scale computa,onal schemes Maria Fyta Ins,tut für Computerphysik, Universität Stu<gart Stu<gart, Germany

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7 Nuggets on coarse- graining and mul,scale computa,onal schemes Maria Fyta Ins,tut für Computerphysik, Universität Stu<gart Stu<gart, Germany

8 Computa,onal Physics Systems/ proper,es Time/length scales Methodology/ accuracy

9 Hierarchy of scales length cm mesoscopic processes con/nuum: connec/on to experiments mm μm electronic structure atomic structure nm ps ns μs ms time

10 Coarse- graining (CG) Reduce degrees of freedom Computa,onal efficiency Yethiraj group, U. Wisconsin-Madison

11 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)

12 Modeling the nucleosome model Hsu, et al, JCP 2012 DNA Histone Core Initial and relaxed configuration of a histone The Scientist, C.W. Hsu, March AM 1, 250b, 2011 Harvard University (2011)

13 Modeling the nucleosome model Hsu, et al, JCP 2012 DNA Histone Core Initial and relaxed configuration of a histone The Scientist, C.W. Hsu, March AM 1, 250b, 2011 Harvard University (2011)

14 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 I II III Concurrent I II III Sophis/cated schemes and powerful resources

15 Concurrent Mul/scale Schemes

16 Coupling different regions Computational Chemistry Group, University of Amsterdam

17 Coupling different regions changing the number of molecular degrees of freedom on-the-fly thermodynamic equilibrium of all-atom with far simpler coarse-grained system 3 scales:atomistic, mesoscopic, continuum M. Praprotnik, U. Ljubljana

18 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)

19 Metal contacts: Joule hea,ng Co-Al contacts Asperity contact geometry Temperature contours 25ps MD simulations Molecular Dynamics coupled to heat-transport equation D. I. Irving et al, Model. Sim. Mater. Sci. Engin. 17, (2009)

20 "bo<om- up" design of novel molecular nano- electronic structures Hexagonal phase found in NaCl MSE, U. Michigan ab initio quantum mechanical calculations, molecular dynamics simulations with classical and reactive force fields, monte carlo simulations and mesoscale simulations

21 QM/MM Sierka Lab, FS U. Jena J.B.Rommel and J. Kaestner, JACS 133, (2011) Fragmentation Recombination mechanism of the enzyme glutamate mutase

22 Biomolecular Simula,ons

23 Parallel mul,scale simula,ons of a brain aneurysm brain vasculature Large scale flow features: Navier Stokes solver Blood rheology inside aneurysm: coarse-grained stochastic MD L. Grinberg et al, J. Comput. Phys 244, 131 (2013)

24 Coupling Molecular Dynamics (molecules) with lattice Boltzmann (solvent) 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 time exchange dt MD =M Δt LB (M=5-10) transfer of spatial information Coupling: F p f = γ( u p υ ) p u fluid velocity v bead velocity grid (G) particle (P) particle (P) grid (G) Ahlrichs and B. Duenweg, Int. J. Mod. Phys C, (1998) MF, Melchionna, Kaxiras, Succi, Multisc. Model. & Sim.(2006)

25 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

26 DNA transloca,on through nanopores a bead ~ base-pairs a bead ~ 1base MF, S. Melchionna, E. Kaxiras, S. Succi

27 Sequen/al Mul/scale Schemes

28 Adsorp/ve processes for energy gas storage and CO 2 capture in porous networks Z. Xiang et al, Energy. Envir. Sci. 3, 1469 (2010)

29 Polymer- clay nanocomposites MD: obtain interaction energies among components (polymer, clay, surface modifier) DPD: interaction parameters between beads FEM: calculate properties (exfoliation, etc.) A. Danani, SUPCI, CH

30 Thermoelectric Materials DFT Monte-Carlo Phase-field theory 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. T. Gruhn, U. Bayreuth

31 Connect molecular scale to cellular processes CMTS, U. Chicago

32 Electronic structure of stretched B- DNA (a): Electronic states of bases/base pairs at various distances and angles (a) (b) (a) (b) (c) (b): Fron/er orbitals of stretched poly- CG Stretching 0% 30% (c): Construc/on of effec/ve Hamiltonian for electron localiza/on along DNA 60% 90% Barnett et al, J. Mater. Sci. (2007)