Hands-on Workshop on Computational Biophysics 2016

Dates: June 6 - 10, 2016
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA



HandsOn2015This workshop will cover a wide range of physical models and computational approaches for the simulation of biological systems including ProDy, NAMD and VMD.  The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.

It will be presented by members of the Theoretical and Computational Biophysics Group (www.ks.uiuc.edu) from the University of Illinois at Urbana-Champaign and the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh.

The workshop is designed for students and researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations.

Participants are encouraged to bring their own laptops for use in workshop tutorial sessions but computer workstations are also available.


A tentative workshop agenda (subject to change) is available.

Workshop Instructors:

Klaus Schulten (UIUC)
Ivet Bahar (University of Pittsburgh)
Zan Luthey-Schulten (UIUC)
Dan Zuckerman (University of Pittsburgh)

Assistant Instructors:

Cihan Kaya (University of Pittsburgh)
Karolina Mikulska-Ruminska (University of Pittsburgh)
JiYoung Lee
She Zhang
Adam Pratt 
Ali Saglam<
Justin Spiriti
Ernesto Suarez



The application deadline May 9, 2016.  Due to space constraints, the workshop will be limited to 25 participants.

Housing and fees

Registration fee for accepted participants*: $150 fee for students; $250 non-student academics; $350 all others. The fee is non-refundable.

Housing in three person apartments* at the University of Pittsburgh Bouquet Gardens (check-in May 31; check-out June 5) and all course materials will be provided. The workshop can neither fund nor arrange participant travel.

*Workshop provides triple-occupancy apartment housing for workshop participants only. Those preferring a single room or any other arrangements (e.g., early arrival or late departure) need to arrange and pay for their own housing. Participants are responsible for any incidental charges related to their stay in the residence hall.

Visa or waiver holders must provide documentation of their status so that hotel costs can be covered. Please consult our visa page for more information.  

Please contact Pat Sudac at This email address is being protected from spambots. You need JavaScript enabled to view it. for any questions.