Name: Dynamics of Biomolecular Processes: From Atomistic Representations to Coarse-Grained Models
Start: 2012-02-27T08:00:00+01:00
End: 2012-03-23T18:00:00+01:00
Location: Nordita

Monday, February 27, 2012

8:30 AM Welcome breakfast & Registration
Welcome breakfast & Registration
8:30 AM - 9:15 AM
Room: 132:028

9:15 AM

9:15 AM - 9:30 AM
Room: 132:028
9:30 AM Biomolecular force fields I - David van der Spoel (Uppsala University)
Biomolecular force fields I
- David van der Spoel (Uppsala University)
9:30 AM - 11:30 AM
Room: 132:028 Classical non-polarizable force fields. Computing physical properties that can be compared to experiment. Introducing quantum corrections.
1:00 PM Advanced Monte Carlo Methods - Ulrich Hansmann (Department of Chemistry and Biochemistry, University of Oklahoma)
Advanced Monte Carlo Methods
- Ulrich Hansmann (Department of Chemistry and Biochemistry, University of Oklahoma)
1:00 PM - 3:00 PM
Room: 132:028 Ensemble averages vs. time averages, improved updates; reweighting techniques; generalized ensembles, parallel tempering techniques, optimization techniques, recent applications, limitations and future directions.
3:00 PM Coffee
Coffee
3:00 PM - 3:30 PM
Room: 132:028
3:30 PM DNA and DNA-protein interaction - Richard Lavery (BMSSI, CNRS / Univ. Lyon I)
DNA and DNA-protein interaction
- Richard Lavery (BMSSI, CNRS / Univ. Lyon I)
3:30 PM - 5:30 PM
Room: 132:028 All-atom molecular dynamics applied to DNA and DNA-protein complexes.
Tuesday, February 28, 2012
9:30 AM Biomolecular force fields II - David van der Spoel (Uppsala University)
Biomolecular force fields II
- David van der Spoel (Uppsala University)
9:30 AM - 11:30 AM
Room: 132:028 State-of-the-art in protein force fields and simulation. Comparison of long simulations with different force fields. Large and long simulations of biomolecules.
1:00 PM Coarse-grained models for proteins I - Adam Liwo (University of Gdansk)
Coarse-grained models for proteins I
- Adam Liwo (University of Gdansk)
1:00 PM - 3:00 PM
Room: 132:028 1. Purpose and overview of history and applications of coarse-grained force fields for proteins. 2. Representation of polypeptide chains in coarse-grained force fields. 3. Connection between statistical mechanics and coarse-grained force field 4. Types of potentials (physics-based, statistical, structure-based, engineered, elastic network). 5. Coarse-grained force fields from potentials of mean force: emergence and role of multibody terms. 6. Equations of motion with coarse-grained force field and algorithms for their solving. 7. Generalized-ensemble sampling with coarse-grained force field. 8. Examples (UNRES, CABS, MARTINI).
3:00 PM Coffee
Coffee
3:00 PM - 3:30 PM
Room: 132:028
3:30 PM Long-Timescale Molecular Dynamics Simulations of Protein Folding and Dynamics - Kresten Lindorff-Larsen (Copenhagen University)
Long-Timescale Molecular Dynamics Simulations of Protein Folding and Dynamics
- Kresten Lindorff-Larsen (Copenhagen University)
3:30 PM - 5:30 PM
Room: 132:028 Simulations of protein folding. Testing force fields with folding simulations. Comparison of simulations and experiments. Long-timescale motions in folded proteins. Conformational clustering. Dynamics in unfolded proteins.
Wednesday, February 29, 2012
9:30 AM Parameterisation aspects of atomistic and coarse-grained models of biomolecules - Alessandra Villa (Karolinska Institutet)
Parameterisation aspects of atomistic and coarse-grained models of biomolecules
- Alessandra Villa (Karolinska Institutet)
9:30 AM - 11:30 AM
Room: 132:028 Parametrization strategy in biomolecular atomistic force field. Design strategies to build a coarse grained model (mapping scheme, potentials, solvent description). Approach used to parametrize CG potentials (with attention to non-bonded interactions). Backmapping. Transferability problems. Example from a fragment-based coarse grained model for peptide. Brief introduction of possible approach to access multi-scale modeling.
1:00 PM Nucleation in peptide systems - Stefan Auer (Centre for Molecular Nanoscience, University of Leeds)
Nucleation in peptide systems
- Stefan Auer (Centre for Molecular Nanoscience, University of Leeds)
1:00 PM - 3:00 PM
Room: 132:028 Calculation of the peptide phase diagram (J. Chem. Phys. 135, 175103 (2011)). Introduce the tube model and the Monte Carlo simulations related to determine the solubility diagram. Nucleation. Numerical work. Application of atomistic nucleation theory to describe amyloid nucleation.
3:00 PM Coffee
Coffee
3:00 PM - 3:30 PM
Room: 132:028
3:30 PM Coarse-grained models for proteins II - Adam Liwo (University of Gdansk)
Coarse-grained models for proteins II
- Adam Liwo (University of Gdansk)
3:30 PM - 5:30 PM
Room: 132:028 continued
Thursday, March 1, 2012
9:30 AM The internal dynamics of proteins I - Cristian Micheletti (SISSA)
The internal dynamics of proteins I
- Cristian Micheletti (SISSA)
9:30 AM - 11:30 AM
Room: 132:028 Coarse-grained modelling of proteins' internal dynamics. Generalities about functionally-oriented large-scale structural fluctuations in proteins. Modeling proteins' internal dynamics using elastic network models (ENMs): Stochastic diffusion of a free particle. Stochastic motion of an harmonic oscillator.
1:00 PM The internal dynamics of proteins II - Cristian Micheletti (SISSA)
The internal dynamics of proteins II
- Cristian Micheletti (SISSA)
1:00 PM - 3:00 PM
Room: 132:028 Stochastic motion of a set of coupled harmonic oscillators. Applications to proteins' internal dynamics. Principal component analysis of MD trajectories.
3:00 PM Coffee
Coffee
3:00 PM - 3:30 PM
Room: 132:028
3:30 PM Hydrodynamic and mesoscopic simulations I - Jens Harting (TU Eindhoven)
Hydrodynamic and mesoscopic simulations I
- Jens Harting (TU Eindhoven)
3:30 PM - 5:30 PM
Room: 132:028 Hybrid methods including molecular dynamics for solved particles/molecules and (mesoscopic) methods for hydrodynamic solvent interactions. Examples for the latter are Dissipative Particle Dynamics, Multi Particle Collision Dynamics, Lattice Boltzmann. The methods will be introduced and advanced applications including for example multiphase solvents or complex particle interactions will be explained.
6:00 PM Reception
Reception
6:00 PM - 8:00 PM
Room: 132:028
Friday, March 2, 2012
9:30 AM The internal dynamics of proteins III - Cristian Micheletti (SISSA)
The internal dynamics of proteins III
- Cristian Micheletti (SISSA)
9:30 AM - 11:30 AM
Room: 132:028 Comparing the internal dynamics of proteins with different fold: dynamics-based protein alignment.
1:00 PM Hydrodynamic and mesoscopic simulations II - Jens Harting (TU Eindhoven)
Hydrodynamic and mesoscopic simulations II
- Jens Harting (TU Eindhoven)
1:00 PM - 3:00 PM
Room: 132:028 continued
3:00 PM

3:00 PM - 3:15 PM
Room: 132:028
Saturday, March 3, 2012
Sunday, March 4, 2012