Learning Collective Variables and Coarse Grained Models Poster Session

Presenter: Matteo Carli (Harvard University, Cambridge)
Collaborator(s): Aldo Glielmo, Alex Rodriguex, Alessandro Laio
Title: Nonparametric free energy estimation in high dimensional spaces

Presenter: Yaoyi Chen (Free University of Berlin and Zuse Institute Berlin)
Collaborator(s): Yaoyi Chen, Jonas Köhler, Andreas Krämer, Aleksander Durumeric, Nick Charron, Frank Noé, Cecilia Clementi
Title: Enhancing Data Efficiency in Coarse-Grained Force Field Parameterization with Machine Learning

Presenter: Luke Evans (Flatiron Institute)
Collaborator(s): Lars Dingeldein, David Silva-Sanchez, Edoardo D’Imprima, Nikolaus Grigorieff, Roberto Covino, Pilar Cossio
Title: Amortized Inference for Biomolecular Conformations in Cryo-EM using Simulation-based Inference

Presenter: Abhik Ghosh Moulick (CUNY – College of Staten Island)
Collaborator(s): Prabir Khatua, Rutika Patel, Augustine Onyema, Sharon Loverde
Title: Comparative Exploration of nucleosome dynamics using All-atom and Coarse-Grain Approaches

Presenter: Andrea Guljas (Free University of Berlin and Zuse Institute Berlin)
Collaborator(s): Yaoyi Chen, Nicholas E. Charron, Felix Musil, Andreas Krämer, Frank Noé, Cecilia Clementi
Title: Machine Learned Molecular Coarse-Graining of Protein Folding and Aggregation

Presenter: Spencer Guo (University of Chicago)
Collaborator(s): John Strahan, Chatipat Lorpaiboon, Aaron Dinner, Jonathan Weare
Title: Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction

Presenter: Carl Gustav Henning Hansen (University of Copenhagen)
Collaborator(s): Simone Orioli, Kresten Lindorff-Larsen
Title: Combining Molecular Simulations and Time-Resolved Experimental Data using the Fokker-Planck Equation and Maximum Entropy Reweighting

Presenter: Mike S Jones (University of Chicago)
Collaborator(s): Smayan Khanna, Andrew Ferguson
Title: A Flow-matching Approach for Generative Backmapping of Biomolecules

Presenter: Chatipat Lorpaiboon (University of Chicago)
Collaborator(s): Jonathan Weare, Aaron R. Dinner
Title: Dimensionality reduction for transient and metastable systems using restrained VAMPnets

Presenter: John Charlie Maier (University of Illinois at Urbana-Champaign)
Collaborator(s): Chun-I Wang, Nicholas Jackson
Title: Designing Target-Optimized Coarse-Grained Representations for Soft Materials Using Attentive Message-Passing

Presenter: Juno Nam (Massachusetts Institute of Technology (MIT))
Collaborator(s): Rafael Gomez-Bombarelli
Title: Revealing hidden alchemical degrees of freedom in machine learning interatomic potentials

Presenter: Rutika Patel (CUNY – City University of New York (CUNY))
Title: Conformational Dynamics of Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations and Markov State Model

Presenter: Adolfo Poma (Institute of Fundamental Technological Research Polish Academy of Sciences)
Collaborator(s): Luis F. Cofas-Vargas
Title: GōMartini 3: A Computational Tool to Elucidate Conformational Changes in Proteins

Presenter: Subarna Sasmal (New York University)
Title: Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Atomic Positions

Presenter: Shashank Sule (University of Maryland)
Collaborator(s): Maria Cameron, Jiaxin Yuan
Title: Learning collective variables for quantifiably good representations of molecular dynamics

Presenter: Soojung Yang (Massachusetts Institute of Technology (MIT))
Collaborator(s): Juno Nam, Johannes C. B. Dietschreit, Rafael Gómez-Bombarelli
Title: Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation