Computational Modeling Workshop and Mini-Symposium

As with previous years, the MPSDC Computational Modeling core is hosting both a workshop and a mini-symposium dedicating to computational approaches. Please scroll down to see the mini-symposium information and schedule.

Computational Modeling and Simulation Workshop

Tuesday May 6th 2014, 8:30 AM to 3:00 PM
Knapp Center for Biomedical Discovery, room 3200
University of Chicago (directions)

Computational Modeling Workshop at the 2012 MPSDC Meeting, also held at the University of Chicago.

During the week of the Membrane Protein Structural Dynamics Consortium (MPSDC)’s Annual Meeting, a workshop specifically dedicated to Membrane Protein Modeling and Simulation will be held at the University of Chicago on Tuesday, May 6th. This workshop is designed to provide an introduction to the most important computational tools and techniques used in molecular dynamics simulations of membrane proteins, including utilization of the programs NAMD and VMD, as well as the CHARMM-GUI Membrane Builder. We will also cover the use of force field parameterization tools. The workshop will include a practical “hands-on” session.

The Workshop is co-organized by the Computational Modeling Core (CMC) of the MPSDC and the Computational Structural Biology and Molecular Biophysics (CSBMB) of the University of Illinois at Urbana-Champaign.

Laptop setup: the computational modeling and simulation workshop requires up-to-date hardware, operating systems, and software versions. Minimum requirements for laptops are provided in the following page. Configurations that provide less than the minimum requirements may function poorly, or not at all. Please visit this page to ensure that you meet the hardware and software requirements: link. Additionally, this page describes how workshop participants should set up their laptops for participation in workshop hands-on tutorial sessions: link.

Lecture Notes

Now that the workshop has passed, we are making the organizer’s lecture notes available for continued engagement with the materials presented in the workshop:


8:30 AM
Welcome and breakfast

9:00 AM – 9:45 AM
Emad Tajkhorshid from the University of Illinois at Urbana-Champaign
Molecular Dynamics Simulation I – Introduction and Examples

9:45 AM – 10:30 AM
Emad Tajkhorshid from the University of Illinois at Urbana-Champaign
Molecular Dynamics Simulation II – Biased Simulations and Force Fields

10:30 AM to 11:15 PM
Wonpil Im from Kansas University
Modeling and Simulation of Membrane Proteins

11:15 AM to 12:00 PM
Jeff Klauda from University of Maryland
Lipid Bilayer Simulations: Force fields, Simulation and Analysis

12:00 PM to 1:00 PM

1:00 PM to 3:00 PM
Hands on Workshop Session

Computational Modeling Mini-Symposium

Wednesday May 7th 2014, 8:15 AM to 3:50 PM
Gordon Center for Integrative Sciences, room 301
University of Chicago (directions)

Chair: Benoit Roux


8:15 Introduction: Benoit Roux
Methodologies and Their Applications
8:30 Wonpil Im, Kansas University
Updates in CHARMM-GUI for the Consortium
9:00 Yifei Qi, Kansas University
CHARMM-GUI PACE CG builder for solution, bilayer, micelle and vesicle simulations
9:20 Emad Tajkhorshid, UIUC
Extending the application of membrane mimetic models to transmembrane proteins
9:50 Zhe Wu, UIUC
Molecular Dynamics Simulations of Membrane with asymmetric charge distribution: New Application of Multilevel Summation Method
10:10 Ivan Teo, UIUC
Extending the Time Scale of Diffusion Simulations through MscS with a Kinetic Model
10:30 Aashish N Adhikari, Univ Chicago
A computational framework for insertion of lanthanide-binding tags onto membrane proteins
Voltage Gating
10:50 Kin Lam, UIUC
Molecular Basis of the Hodgin-Huxley Equation of Neuronal Signaling
11:10 Avisek Das, Univ Chicago 
Conformational transition in ATP-driven calcium pump SERCA
11:30 Abhi Singharoy, UIUC 
Resolution of Membrane Protein Structures with Data Guided MD Simulations: the Curious Cases of CiVSP and YidC
12:00 Lunch
Pumps and Transporters
1:00 Jeff Klauda, Univ of Maryland
Probing the Transport Cycle of Secondary Active Transporters with Atomistic Simulations
1:30 Sergei Noskov, University of Calgary
Mapping conformational states in vdac1 channel: gating control of mitochondrial metabolite transport
2:00 Shahid Islam Univ Chicago
EPR analysis of several transporter systems
2:30 Huan Rui, Univ Chicago
Ion binding to the NaK pump
3:00 Jing Li, UIC
Deciphering the ion-coupling mechanism in secondary transporters
3:20 Sundar Thangapandian, UIUC
Large-scale conformational changes in a neurotransmitter transporter
3:40 Closing: Benoit Roux
3:45 End of Mini-Symposium
4:00 Special Seminar, Rama Ranganathan, UT Southwest Room GCIS W301