State of the art in mesoscale and multiscale modeling May 29, 2017 - June 01, 2017 CECAM-IRL Ignacio Pagonabarraga CECAM EPFL, Switzerland Vladimir Lobaskin University College Dublin, Ireland Donal Mac Kernan University College Dublin, Ireland https://www.cecam.org/workshop-8-1487.html Program Day 1 – 29 May, 2017 UCD School of Physics Science North Room 232 - shuttle bus (departs hotel at 9.30 for UCD) max 16 passangers google map link https://goo.gl/maps/LQ9pTNMtYKv •10:00 to 11:00 - Didactic Lecture I methodologies of systematic static coarse- graining •11:00 to 11:30 - Coffee Break •11:30 to 12:30 - Burkhard Duenweg Introduction to the Mori-Zwanzig formalism •12:30 to 13:30 - Lunch •13:30 to 14:10 - Overview Talk on mesoscale/hybrid approaches (KREMER) •14:10 to 14:30 - Christian Holm Influence of the permittivity gradient on static and dynamic properties of charged macromolecules •14:30 to 14:50 - Burkhard Duenweg Monte Carlo approach to Fluctuating Lattice Boltzmann •14:50 to 15:10 - Matej Praprotnik Adaptive resolution simulations of supramolecular water •15:10 to 15:30 - Pietro Lio Multiscale computational approaches in modeling biological data integration and molecular communication •15:30 to 16:00 - Coffee Break •16:00 to 16:20 - Pierre Cazade Multi-scale modelling of Large Biomolecular Complexes •16:20 to 16:40 - Focused/Question specific talk 5 on mesoscale/hybrid approaches •16:40 to 17:00 - Jason Reese Best of Both Worlds? Hybrid Fluid Simulations for Multiscale Engineering •17:00 to 17:20 - Gerhard Jung Iterative Reconstruction of Memory Kernels •17:20 to 18:20 - Roundtable on current challenges for hybrid approaches, inclusion of ab- initio description (moderator Kremer) •18:20 to 19:50 - Reception-welcome-poster session (Physics Lounge) Day 2 – 30 May, 2017 UCD School of Physics Science North Room 232 shuttle bus departs hotel at 9.0 & 9.15 for UCD max 16 passangers •09:30 to 10:10 - Overview on non-equilibrium processes and heterogeneous systems (RIEGER) •10:10 to 10:30 - Julija Zavadlav Multiscale Simulations of DNA Arrays •10:30 to 10:50 - Aleksandar Donev Coupling a nano-particle with fluctuating hydrodynamics •10:50 to 11:20 - Coffee Break •11:20 to 11:40 - David Cheung Coarse-grain modeling of polymer nanostructures •11:40 to 12:30 - Roundtable on non-equilibrium processes (moderator Reiger) •12:30 to 13:30 - Lunch •13:30 to 14:10 - Overview on Coarse Graining (MUELLER) •14:10 to 14:30 - Alexander Lyubartsev Multiscale modelling by systematic structure-based coarse-graining •14:30 to 14:50 - Agur Sevink Automated multi-scaling with Stochastic Quasi-Newton (S-QN) •14:50 to 15:10 - Pep Español Non-isothermal coarse-graining of complex molecules •15:10 to 15:30 - Denis Andrienko Many-body effects in systematic coarse graining •15:30 to 15:50 - Nicolae-Viorel Buchete Coarse-Grained Kinetic Models of Protein Folding and Binding Networks •15:50 to 16:20 - Coffee Break •16:20 to 17:00 - Overview on connecting to continuum/engineering level descriptions (Casciola) •17:00 to 17:20 - Pietro Asinari Multi-Scale Modelling of Nanoparticle Suspensions •17:20 to 17:40 - Serafim Kalliadasis From the nano- to the macroscale: bridging scales for the moving contact line problem •17:40 to 18:40 - Roundtable on connecting to continuum/engineering level descriptions (moderator O'REILLY) •19:45 to 22:00 - Workshop Dinner on Canal Boat (lapeniche.ie) Day 3 – 31 May, 2017 UCD School of Physics Science North Room 232 shuttle bus departs hotel at 9.0 & 9.15 for UCD max 16 passangers •09:30 to 10:10 - Overview on Software packages (SEATON) •10:10 to 10:30 - Kevin Stratford Performance portability in coarse-grained mesoscale complex fluids •10:30 to 10:50 - Danny Perez Long-timescale Simulations with Accelerated Molecular Dynamics and the EXAALT package •10:50 to 11:20 - Coffee Break •Moderated roundtable on software solutions and their limitations: H2020 funding opportunities (ASINARI) •12:30 to 13:30 - Lunch •13:30 to 14:10 - Additional Research talks/AOB •14:10 to 15:10 - Denis Andrienko Systematic coarse-graining with VOTCA •15:10 to 15:40 - Coffee Break •15:40 to 16:40 - Didactic Lecture on continuum/engineering level descriptions 3 Abstracts Introduction to the Mori-Zwanzig formalism Burkhard Duenweg[1] Max Planck Institute for Polymer Research Mainz The lecture will outline the basic steps to derive the Mori-Zwanzig memory equation, and illustrate its application to derive some well-known Green-Kubo relations. If time permits, the method of multiple time scale expansion (aka Chapman-Enskog expansion within the framework of the kinetic theory of gases) will be outlined as well. Both approaches have in common that they aim at deriving effective equations of motion for slow degrees of freedom, which often involves to study the system not only on large time scales, but on large length scales as well. Influence of the permittivity gradient on static and dynamic properties of charged macromolecules Christian Holm[1] Institut für Computerphysik, Universität Stuttgart, Stuttgart, Germany Dissolved ions can alter the local permittivity of water, nevertheless most theories and simulations ignore this fact. We present a novel algorithm for treating spatial and temporal variations in the permittivity, and show several examples where this leads to large qualitative and quantitative differences. A dynamic example is the equivalent conductivity of a salt-free polyelectrolyte solution. Our new approach quantitatively reproduces experimental results unlike simulations with a constant permittivity that even qualitatively fail to describe the data. We can relate this success to a change in the ion distribution close to the polymer due to the built-up of a permittivity gradient. F. Fahrenberger, O.A. Hickey, J. Smiatek, C. Holm, „The influence of charged-induced variations in the local permittivity on the static and dynamic properties of polyelectrolyte solutions“. J. Chem. Phys. 143, 243140, (2015). F. Fahrenberger, O.A. Hickey, J. Smiatek, C. Holm, „Importance of Varying Permittivity on the Conductivity of Polyelectrolyte Solutions“, Phys. Rev. Lett.115, 118301 (2015). F. Fahrenberger, C. Holm, „Computing the Coulomb interaction in inhomogeneous dielectric media via a local electrostatics lattice algorithm“ Phys. Rev. E 90, 063304, (2014). F. Fahrenberger, Z. Xu, C. Holm, „Simulation of electric double layers around charged colloids in aqueous solution of variable permittivity“, J. Chem. Phys. 141 064902 (2014) Monte Carlo approach to Fluctuating Lattice Boltzmann Burkhard Duenweg[1], Thomas Balles, Benjamin Pampel Max Planck Institute for Polymer Research Mainz TU Darmstadt We explore possibilities to sample the populations of a Fluctuating Lattice Boltzmann algorithm according to the correct Boltzmann distribution instead of the usually-applied Gaussian approximation thereof. Since there is no straightforward method to generate the needed random variables directly, we use Markov Chain Monte Carlo methods instead. Adaptive resolution simulations of supramolecular water Matej Praprotnik[1] National Institute of Chemistry, Ljubljana, Slovenia We present adaptive resolution molecular dynamics simulations of water using coarse-grained molecular models that are compatible with the MARTINI force field [1,2]. The solvent molecules change their resolution back and forth between the atomistic and coarse-grained representations according to their positions in the system. The difficulties that arise from coupling to a coarse-grained model with a supramolecular mapping are successfully circumvented by using bundled water models. We discuss the advantages and limitations of this multiscale approach on several examples, e.g., coupling of atomistic water with polarizable [3] and non-polarizable [4] coarse-grained water models. To overcome the limitations of the bundled water models we then intruduce a dynamic clustering algorithm SWINGER [5] that can concurrently assemble, disassemble, and reassemble water bundles, consisting of several water molecules. It allows for a seamless coupling between standard atomistic and supramolecular water models in adaptive resolution simulations. SWINGER paves the way for efficient multiscale simulations of biomolecular systems without compromising the accuracy of atomistic water models. [1] J. Zavadlav, M. N. Melo, S. J. Marrink, M. Praprotnik, J. Chem. Phys. 140, 054114, 2014. [2] J. Zavadlav, R. Podgornik, M. N. Melo, S. J. Marrink, M. Praprotnik, Eur. Phys. J. Special Topics 225, 1595-1607, 2016. [3] J. Zavadlav, M. N. Melo, S. J. Marrink, M. Praprotnik, J. Chem. Phys. 142, 244118, 2015. [4] J. Zavadlav, M. N. Melo, A. V. Cunha, A. H. de Vries, S. J. Marrink, M. Praprotnik, J. Chem. Theory Comput. 10, 2591-2598, 2014. [5] J. Zavadlav, S. J. Marrink, M. Praprotnik, J. Chem. Theory Comput. 12, 4138-4145, 2016. Multiscale computational approaches in modeling biological data integration and molecular communication Pietro Lio[1] University of Cambridge I have developed multiscale data integration computational approaches based on hierarchical block matrices [1], multilayer networks [2,3], cross-modal convolution networks [4], matrix factorisation and tri-factorisation. These methodologies (implemented in software tools used by a large community) combine clinical data from longitudinal studies and multidimensional molecular data (genomics, metabolomics, proteomics, metagenomics and epigenomics) with systems biomedicine approaches (network modeling, survival analysis, immune system simulations) to identify meaningful