April 4, 2012

PASI 2012 PROGRAM





Workshop on Multiscale Modeling and Simulation
2012 NSF Pan American Advanced Studies Institute (PASI)


SUNDAY SEPTEMBER 2
Morning, Early afternoon – arrival

04:00 pm - 04:30 pm Workshop registration and check-in (conference hotel)
04:30 pm - 05:00 pm Opening Remarks (C. Abrams, S. Pantano, J. Pfaendtner)
05:00 pm - 07:00 pm Giovanni Bussi: Intro to MD and Thermostats
07:00 pm - 08:00 pm Get Together Party with refreshments @ Intercity Hotel

MONDAY SEPTEMBER 3
09:00 am - 10:00 am Giovanni Bussi: Crooks and Jarzynski/ Intro to rare events and CVs
10:00 am - 11:00 am Massimiliano Bonomi: Theory of simulated tempering and replica exchange
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Max Bonomi: Theory of umbrella sampling and SMD
12:30 pm - 02:00 pm Lunch
02:00 pm - 05:00 pm Hands-on workshop: PLUMED, monitoring CVs, PT, umbrella sampling and steered MD

TUESDAY SEPTEMBER 4 - - - WORKSHOP - - -
09:00 am - 09:30 am G. Bussi – research highlights
09:30 am - 10:00 amM. Bonomi – research highlights
10:00 am - 10:30 am S. Pantano – research highlights
10:30 am - 11:00 am Coffee Break
11:00 am - 12:00 pm J. Pfaendtner  – research highlights 
12:00 pm - 12:30 pmB. Peters – research highlights
12:30 pm - 02:00 pm Lunch
02:00 pm - 03:00 pm Keynote Lecture 1: M. Parrinello
03:00 pm - 03:30 pm Coffee Break  
03:30 pm - 04:00 pm C. Abrams – research highlights
04:00 pm - 04:30 pm M. Skaf – research highlights

WEDNESDAY SEPTEMBER 5
09:00 am - 10:00 am Leandro Martinez: Packmol
10:00 am - 11:00 am Baron Peters: Rare event and rate theory
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 am Keynote Lecture 2: Michele Parrinello
12:30 pm CULTURAL EXCURSION - Bouza Wine cellar


THURSDAY SEPTEMBER 6
09:00 am - 10:00 am Giovanni Bussi: Metadynamics from direct to well-tempered and flexible hills
10:00 am - 11:00 am Massimiliano Bonomi: Multiple walkers and combination of metadynamics with replica exchange methods
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 am Massimilano Bonomi: Path collective variables
12:30 pm - 02:00 pm Lunch
02:00 pm - 05:00 pm Hands-on workshop: Advanced PLUMED

FRIDAY SEPTEMBER 7
09:00 am - 11:00 am Baron Peters: Rare event and rate theory
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Leandro Martinez: Robust optimization strategies for the analysis of protein dynamics and model fitting
12:30 pm - 02:00 pm Lunch
02:00 pm – 05:00 pm Hands-on workshop: Baron Peters

SATURDAY SEPTEMBER 8
09:00 am - 10:00 am Leandro Martinez: The microscopic complexity of ligand binding dynamics and its implications to drug design
10:00 am - 11:00 am Sergio Pantano: SIRAH: a CG force field for biomolecular simulations
11:00 am - 11:30 am Coffee Break
11:30 am – 12:30 pm CFA: Getting and using your XSEDE account
12:30 pm - 02:30 pm BARBECUE AT IP MONTEVIDEO
02:30 pm – 04:30 pm Open discussion on Enhanced Sampling and Rates:
picking the right method for your problem
04:30 pm – 18:00 pm Coffee Break - Poster session and refreshments

MONDAY SEPTEMBER 10
09:00 am – 11:00 am SIRAH tutorial
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Monica Lamm: Force matching fundamentals
12:30 pm - 02:00 pm Lunch
02:00 pm - 05:00 pm Monica Lamm - Hands-on Workshop: Force matching

TUESDAY SEPTEMBER 11
09:00 am - 11:00 am Poster Session II 
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Monica Lamm: Evaluating coarse-grain mapping schemes
12:30 pm - CULTURAL EXCURSION Walk around the old town and Lunch at
MERCADO DEL PUERTO”

WEDNESDAY SEPTEMBER 12
09:00 am - 10:00 am Monica Lamm: Obtaining accurate dynamics from simulation with CG models
10:00 am - 11:00 am Roland Faller: Fundamentals of the Iterative Boltzmann Inversion (IBI)
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Faller/Lamm Research group highlights:
12:30 pm - 02:00 pm Lunch
02:00 pm - 03:00 pm Jim Pfaendtner/Alex Morriss-Andrews: Coarse-grained simulations of protein folding and aggregation
04:00 pm - 05:30 Hands-On Workshop on Coarse Grain

THURSDAY SEPTEMBER 13
09:00 am - 10:00 am Eric Vanden-Eijnden: Rare Events Theory
10:00 am - 11:00 am Roland Faller: Developing numerical potentials and their state point dependence
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Eric Vanden-Eijnden: Rare Events Numerical Implementation
12:30 pm - 02:00 pm Lunch
02:00 pm - 05:00 pm Hands-on workshop: EVE workshop

FRIDAY SEPTEMBER 14
09:00 am - 10:00 am Eric Vanden-Eijnden: Rare Events Applications
10:00 am - 11:00 am Roland Faller: Using the IBI for polymers
11:00 am - 11:30 am Coffee Break
11:30 am - 12:30 pm Eric Vanden-Eijnden:EVE
12:30 pm - 02:00 pm Lunch
02:00 pm - 05:30 pm Roland Faller: Hands-On Workshop
05:30 pm - 06:00 pm Closing

PASI: Molecular-based Multiscale Modeling and Simulation website