Simons Center for Computational Physical Chemistry

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Simons Symposium: Challenges in Biomolecular Simulations

May 6, 2024 - May 8, 2024

Organizers

Tamar Schlick 
New York University
schlick@nyu.edu

Rommie Amaro
Univ. of California, San Diego
ramaro@ucsd.edu

The Simons Center for Computational Physical Chemistry at NYU shall host this Symposium which aims to provide a broad perspective on the history and state-of-the-art in biomolecular simulations and discuss anticipated progress and challenges for the future.  This 3-day event will be  held in-person at New York University’s Kimmel Center, 60 Washington Square.  The event features Invited Talks by leading researchers in the field, a Poster Session, Contributed Talks, and networking opportunities throughout.

 

Symposium Schedule

All talks take place in the Kimmel Center, 60 Washington Square, Shorin Lecture Hall, Room 802.  

Click here for a pdf of the Symposium Program

Click here to view a listing of Posters Session presentations.

Monday, May 6  
Time   Event Presenter
9:30 AM    Arrival, Check-in, Coffee
    Session Ia Chair:  Tamar Schlick
10:00 AM   Welcome Antonio Merlo, New York University Dean of Arts and Science
       
10:10 AM     J. Andrew McCammon, University of California, San Diego
Protein Dynamics Zoo: Gating and Channeling
       
10:45 AM     Emad Tajkhorshid, University of Illinois at Urbana-Champaign
Challenges in Modeling and Simulation of cell-scale systems
11:20 AM   Break   
    Session Ib Chair:  Tamar Schlick
11:45 AM     Yuji Sugita, RIKEN
Multi-scale molecular dynamics simulations of liquid-liquid phase separation and macromolecular crowding effects
       
12:20 PM     Jeremy Smith, Oak Ridge National Laboratory/University of Tennessee, Knoxville
Molecular Simulation in the Circular Bioeconomy
       
12:55 PM   Lunch & Poster Session
Room 905-907
       
    Session IIa Chair: Rommie Amaro
2:15 PM     Cecilia Clementi, Free University of Berlin
Understanding protein dynamics by combining simulation, experimental data, and machine learning
       
2:50 PM     Pilar Cossio, Flatiron Institute
Exploring conformational landscapes with molecular simulations and single-particle cryo-EM
3:25 PM   Break   
    Session IIb  Chair:  Rommie Amaro
3:50 PM     Jodi Hadden-Perilla, University of Delaware
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD
       
4:02 PM     Glen Hocky, New York University
Good rates from bad coordinates: the exponential average time-dependent rate method (EATR)
       
4:14 PM     Shuting Yan, New York University
Multiple transition pathways between two pseudoknots of the SARS-CoV-2 frameshift element shed insight on viral mechanism
       
4:26 PM     Konstantin Roeder, King’s College London
Investigation of structural heterogeneity in RNA through energy landscape explorations
4:38 PM   Break  
    Session IIc  Chair:  Tamar Schlick
4:45 PM     David Shaw, DE Shaw Research
Biomolecular Simulation in our Lab:  Progress, Problems and Prospects
5:20 PM   Adjourn  
       
Tuesday, May 7  
Time   Event Presenter
9:30 AM    Arrival, Coffee  
    Session IIIa Chair:  Tamar Schlick
10:00 AM     Modesto Orozco, IRB Barcelona
Multiscale simulation of nucleic acids
       
10:35 AM     José Onuchic, Rice University
Unraveling Chromatin Architecture and Dynamics Through Physical Modeling and Large-Scale Simulations
11:10 AM   Break   
    Session IIIb Chair:  Jeremy Smith
11:30 AM     Jessica Swanson, University of Utah
Challenges in multiscale kinetic modeling: Capturing the roles of kinetic selection and electrochemically-driven charge transport
       
11:42 AM     Ivan Coluzza, Rice University
The Role of Charges and Solvent in Protein Folding and Aggregation: A Computational Insight
       
11:54 AM     Rajitha Tatikonda, University of Tennessee/Oak Ridge National Laboratory
TCR-H: Machine Learning Prediction of T-cell Receptor Epitope Binding on Unseen Datasets
       
12:06 PM     Daniele Di Marino, Polytechnic University of Marche
Structural basis of dimerization of chemokine receptors CCR5 and CXCR4
12:18 PM   Break  
    Session IIIc Chair:  Rommie Amaro
12:25 PM     Syma Khalid, University of Oxford
Large scale MD simulations of bacterial membranes
1:00 PM   Adjourn  
       
Wednesday, May 8
Time   Event Presenter
9:00 AM    Coffee  
    Session IVa Chair:  Karissa Sanbonmatsu
9:30 AM     Abhishek Singharoy, Arizona State University
Path integral approaches to study molecular complexity in Latent spaces
       
10:05 AM     Adrian Mulholland, University of Bristol
Dynamical-Nonequilibrium Molecular Dynamics Simulations for Enzyme Design, Evolution and Drug Resistance
10:40 AM   Break   
    Session IVb Chair:  Karissa Sanbonmatsu
11:00 AM     David S. Cerutti, Psivant Therapeutics
Scaling Small Problems to Modern GPUs in the STORMM Code Base
       
11:12 AM     Yinghao Wu, Albert Einstein College of Medicine
Understanding how tumor necrosis factor activates the signaling of its different receptors through multiscale simulations
       
11:24 AM     Tomek Wlodarski, Intitute of Biochemistry and Biophysics PAS
Co-translational protein folding in the light of ribosome evolution
       
11:36 AM     Rongmei Judy Wei, City University of New York
Electron Transfer Directionality in Type II Photosynthetic Reaction Centers
11:48 AM   Break   
    Session IVc Chair:  Karissa Sanbonmatsu
12:10 PM     Martin Vögele, Schrödinger, Inc.
Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding?
       
12:22 PM     Gehan Ranepura, City College of New York
Inhomogenous Broadening of Antenna Protein Chorophyll Site Energies due to Side Chain Conformational and Protonation States determined by Monte Carly Microstate Analysis
       
12:34 PM     Pinchen Xie, Princeton University
Dynamically consistent coarse-graining with multi-dimensional generalized Langevin equation
12:46 PM   Adjourn  

 

Plan your Visit 

 

The event will be held at NYU’s Kimmel Center, 60 Washington Square, New York, NY.

Hotel accommodations within walking distance of the Kimmel Center include:

Washington Square Hotel, 103 Waverly Place

The Marlton Hotel, 5 West 8th Street

The Standard, East Village, 25 Cooper Square

 

Getting to Kimmel Center via public transportation:

From JFK: Take the AirTrain towards Howard Beach.  Transfer at Howard Beach for the A Train towards Manhattan.  Get off at W. 4th Street.

– or –

Take the AirTrain towards Jamaica.  Transfer at Jamaica for the E Train towards Manhattan.  Get off at W. 4th Street.

  
From LGA: Take the Q70-SBS buss to Roosevelt Av/74th St (1 stop).  Walk to Roosevelt Ave, and take the F train toward Manhattan.  Get off at W. 4th St.
From EWR: Take the AirTrain to Newwark Liberty International Airport Station.  Transfer to any NJ Transit train to Manhattan.  Get off at New York Penn Station (not to be confused with Newark Penn Station).  Take any downtown A, C or E subway train to W. 4th Street.
From New York’s
Penn Station:		 Take any downtown A, C or E subway train to W. 4th Street.

 

Details

Start:
May 6, 2024
End:
May 8, 2024