KITP Conference: Modeling Soft Matter: Linking Multiple Length and Time Scales (June 4-8, 2012)
Coordinators: Paul Atzberger, Kurt Kremer, Mark Robbins

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Monday, June 04, 2012

Morning Session, Chair: Kurt Kremer (MPI-P)

10:00am Lars Bildsten (KITP Permanent Member) Welcome[Podcast][Aud][Cam]
10:15am Glenn Fredrickson (UCSB) Frontiers of Computational Polymer Field Theory[Slides][Podcast][Aud][Cam]
11:00am Mark Tuckerman (NYU) Exploring the Free Energy Landscapes of Complex Molecules and Crystalline Polymorphs[Slides][Podcast][Vid][Aud][Cam]
11:45am Friederike Schmid (JGU Mainz) Linking Scales with Molecular Fields[Slides][Podcast][Aud][Cam]
12:30pm Lunch Break

Afternoon Session, Chair: Philip Pincus (UCSB, MRL)

2:00pm Cameron Abrams (Drexel Univ.) Collective-Variable-Enhanced Biomolecular Simulations[Slides][Podcast][Aud][Cam]
2:45pm Athanassios Panagiotopoulos (Princeton Univ.) Coarse-grained Models for Oligomer-grafted Silica Nanoparticles[Slides][Podcast][Aud][Cam]
3:30pm Afternoon Break
4:00pm Gregory Rutledge (MIT) Density-Dependent Potentials and their Application to Self- Assembly[Slides][Podcast][Aud][Cam]
4:45pm Alexander Lyubartsev (Stockholm Univ.) Systematic Coarse-graining of Molecular Models by Inverse Monte Carlo: Theory, Practice and Software[Slides][Podcast][Aud][Cam]

Tuesday, June 05, 2012

Morning Session, Chair: Mark Robbins (JHU)

9:00am Christoph Dellago (Univ. Vienna) Challenges in the Simulation of Nucleation Processes: From Transition Pathways to Reaction Coordinates[Slides][Podcast][Aud][Cam]
9:45am Christoph Junghans (Los Alamos National Lab) Towards a Unified Framework for Coarse-graining Particle-based Simulations [Slides][Podcast][Aud][Cam]
10:30am Morning Break
11:00am Petros Koumoutsakos (ETH Zürich) Multiscale Simulations using Particles[Slides][Podcast][Aud][Cam]
11:45am Matej Praprotnik (Nat'l Inst. of Chem., Slovenia) Coupling Atomistic and Continuum Hydrodynamics[Slides][Podcast][Aud][Cam]
12:30pm Lunch Break

Afternoon Session, Chair: Paul Atzberger (UCSB)

2:00pm Xin Zhou (GU-CAS) Hierarchical Metastable States and Kinetic Transition Networks in Proteins: Trajectory Mapping and Clustering[Slides][Podcast][Aud][Cam]
2:45pm M. Scott Shell (UCSB) An Information-based Approach to Coarse-grained Models in Molecular Biophysics[Slides][Podcast][Aud][Cam]
3:30pm Afternoon Break
4:00pm Christof Schütte (Freie Univ. Berlin) Coarse Graining via Markov State Models[Podcast][Aud][Cam]
4:45pm Tom Mason (UCLA) Entropic Phase Behavior of Hard Regular Polygons

Wednesday, June 06, 2012

Morning Session, Chair: Michael Rubinstein (UNC, Chapel Hill)

9:00am Markus Deserno (Carnegie Mellon Univ.) A Novel Coarse-grained Force Field for Unbiased Protein- Membrane Simulations[Slides][Podcast][Aud][Cam]
9:45am Sarah Keller (Univ. Washington) Experimental Observations of Lipid Membranes in (roughly) 2D Influenced by Bulk Water in 3D[Slides][Podcast][Aud][Cam]
10:30am Morning Break
11:00am Axel Voigt (TU Dresden) Cell Motility - A Continuum Modeling Approach[Slides][Podcast][Aud][Cam]
11:45am Joan-Emma Shea (UCSB) Simulations of Protein Aggregation[Podcast][Aud][Cam]
1:15pm Lunch Break

Thursday, June 07, 2012

Morning Session, Chair: Gary Leal (UCSB)

9:00am Ronald Miller (Carleton Univ.) Modeling the Solid State with Coupled Atomistic/Continuum Methods: An Overview of Recent Developments[Slides][Podcast][Aud][Cam]
9:45am Mitchell Luskin (Univ. Minnesota) Theory and Computation of Parallel Replica Dynamics[Slides][Podcast][Aud][Cam]
10:30am Morning Break
11:00am Masao Doi (Toyota Research Inst.) Dynamical Coarse Graining - Principle and Applications[Slides][Podcast][Aud][Cam]
11:45am Peter Gumbsch (IWM Fraunhofer) Transferability of Interatomic Potentials in Strong Solids - What Properties Can Actually Be Represented[Podcast][Aud][Cam]
12:30pm Lunch Break

Afternoon Session, Chair: Alexander Grosberg (NYU)

2:00pm William Noid (Penn State Univ.) Coarse-graining Entropy, Forces, and Structure[Slides][Podcast][Aud][Cam]
2:45pm Christine Peter (MPI-P) Transferability of Coarse Grained Models: Multiscale Simulations of Liquid Crystalline Phase Transitions[Slides][Podcast][Aud][Cam]
3:30pm Afternoon Break
4:00pm John Crocker (UPenn) Binary Colloidal Crystals Using DNA Handshaking Interactions[Slides][Podcast][Aud][Cam]
4:45pm Megan Valentine (UCSB) Microrheology of Entangled and Crosslinked Microtubule Networks[Podcast][Aud][Cam]

Friday, June 08, 2012

Morning Session, Chair: Gary Grest (Sandia Nat'l Labs)

9:00am Ryoichi Yamamoto (Kyoto Univ.) Multiscale Simulations for Polymeric Flow: MD/CFD Hybrid Modeling[Slides][Podcast][Aud][Cam]
9:45am Mark Wilson (Durham Univ.) Modeling Allosteric Signaling in Protein Homodimers[Slides][Podcast][Aud][Cam]
10:30am Morning Break
11:00am Hans Andersen (Stanford Univ.) Algorithms and Principles for Multiscale Coarse-Graining[Slides][Podcast][Aud][Cam]
11:45am Anna Balazs (Univ. Pittsburgh) Modeling the Interaction of Active Cilia with Species in Solution: From Chemical Reagents to Microscopic Particles[Slides][Podcast][Vid][Aud][Cam]
12:30pm Lunch Break


  All Poster Presenters POSTER SESSION[Podcast][Aud][Cam]
  Shengfeng Cheng (Sandia Nat'l Lab) Simulations and Theory of Model Microtubule Self-Assembly
  Jacob Davidson (Univ. Michigan) A Complex Network Analysis of Crosslinked Polymers[Poster]
  Michael Graham (Univ. Wisconsin - Madison) Mechanistic Insights Into Flow-induced Segregation in Blood and Other Multicomponent Suspensions
  Mitchell Luskin (Univ. Minnesota) Blended Atomistic-to-Continuum Methods
  Alexander Mirzoev (Stockholm Univ.) MagiC: A Software Package for Systematic Structure-based Coarse-graining
  Lars Pastewka (JHU) Seamless Elastic Boundaries for Atomistic Calculations
  Jörg Rottler (UBC) Modeling Atomic-scale Structure and Dynamics of Interfaces on Diffusive Timescales
  Jon Karl Sigurdsson (UCSB) Fluctuating Lipid Bilayer Membranes with Diffusing Protein Inclusions : Hybrid Continuum-Particle Model[Poster]
  Mark Thachuk (UBC) Suitability of the MARTINI Force Field For Use With Gas-Phase Protein Complexes[Poster]
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