Hands-on Workshop on Computational Biophysics 2017

Dates: May 30 - June 2, 2017
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA

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Application Deadline: May 8
Early decision application deadline: April 24


Applications decisions have been finalized.  Please check your email.   

Accepted applicants, please check the updated housing information below.


HandsOn2015This workshop will cover a wide range of physical models and computational approaches for the simulation of biological systems at  multiple scales, using cutting edge technology including ProDy, NAMDVMD, iGNM and ANM.  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 (UIUC) 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.


See the tentative workshop agenda (subject to change).

Workshop Instructors:

Ivet Bahar (University of Pittsburgh)
Emad Tajkhorshid (UIUC)

Assistant Instructors:

Cihan Kaya (Carnegie Mellon University/University of Pittsburgh)
JiYoung Lee (University of Pittsburgh)
Hongchun Li (University of Pittsburgh)
Karolina Mikulska-Ruminska (University of Pittsburgh)
She (John) Zhang(Carnegie Mellon University/University of Pittsburgh)


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

Housing and directions

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.

Workshop provides triple or quad-occupancy apartment housing at the University of Pittsburgh’s apartment-style Bouquet Gardens J, 307 Oakland Avenue, Pittsburgh PA, 15213.  The residence hall has a Welcome Desk staffed around the clock.   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.  The workshop can neither fund nor arrange participant travel.

Check in and pick up your key at Panther Central, located in the lobby of Litchfield Towers at 3990 Fifth Avenue, Pittsburgh PA 15213.  Conference Services Staff is available at Panther Central 24/7, and they can be reached at 412.648.1100.  At check in, you will receive your room key card (Panther Utility Card) and a small Pitt welcome bag that includes a folder, pen, and notebook.  Be sure to bring valid photo identification for check in

The apartments are furnished and have air-conditioning, private bedrooms (triples and quadruples), semi-private bathrooms, fully equipped kitchens, wireless internet, and linen service.  Laundry facilities are located on the second and third floors of Bouquet Gardens.  Machines are card operated, and you may load funds onto your room access card (Panther Utility Card) at Panther Central.  The Campus Shuttle will accept your Panther Utility Card/room card for boarding.  Please note that the shuttle does not operate during the weekend.

You must return your room key at the conclusion of the workshop.  If you do not check out and leave your key at the Bouquet Gardens J Welcome Desk, you will be charged a lost key fee.  You may check in beginning at 3PM on Monday, May 29, 2017 and must check out by noon on Saturday, June 3,2017.

The workshop is held at the Pittsburgh Supercomputing Center (PSC), 300 South Craig Street, Room 103, Pittsburgh PA, 15213.  If you have trouble finding the building, call 412.268.4960.

A Pitt campus map is available here, a Carnegie Mellon campus map is available here, and directions from Bouquet Gardens to the Pittsburgh Supercomputing Center can be found via Google Maps. Pittsburgh Supercomputing Center is located in the same building as, and in between, Quiznos and Razzy Fresh.


Breakfast and lunch will be provided at the workshop, and ample evening restaurant options are available along Forbes Avenue and South Craig Street. Bouquet Gardens is also very close to a pleasant recreational area, Schenley Plaza and Schenley Park (shown in the Google Maps link).


There are several ground transportation options available to and from campus.  You may use bus service, specifically the 28X Airport Flyer, which will take you from Pittsburgh International Airport and drop you close to Bouquet Gardens (note times for the Oakland Forbes Ave at Atwood St stop).  Likewise, you can take this bus back to the airport.  Uber and Lyft are also options, but note you must have the app installed on your phone.  Taxi/shuttle service is also available by calling Yellow Cab/zTrip (412.321.8100) or Super Shuttle (1.800.258.3826).

There are several paid lots and garages in the Oakland area, should you need to obtain parking for your vehicle.  More details and maps are available here and here.  Parking is not provided as a part of workshop registration or housing services - if you may need a parking pass for your vehicle during your stay, please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for further details.  Be advised, you will need to provide payment for the parking pass.

Addresses and Contacts

Panther Central (Check In and General Assistance): 412.648.1100
Lobby, Litchfield Towers, 3990 Fifth Avenue, Pittsburgh PA 15213

Bouquet Gardens J (Housing)
307 Oakland Avenue, Pittsburgh PA, 15213

Pittsburgh Supercomputing Center (Workshop): 412.268.4960
300 South Craig Street, Room 103, Pittsburgh PA, 15213

University of Pittsburgh Campus Police: 412.624.2121
Jerome Cochran Public Safety Building, 3412 Forbes Avenue, Pittsburgh PA, 15260

You can also contact This email address is being protected from spambots. You need JavaScript enabled to view it. with any questions.