Dimensionality reduction techniques for molecular dynamics

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Dimensionality reduction techniques for molecular dynamics

 02 - 06 Jun 2025

ICMS, Bayes Centre, Edinburgh

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 Enquiries

Scientific Organisers:

  • Lucie Delemotte, KTH Royal Institute of Technology
  • Andrew Ferguson, University of Chicago
  • Stefan Klus, Heriot-Watt University
  • Benedict Leimkuhler, University of Edinburgh
  • Edina Rosta, University College London
  • Gabriel Stoltz, Ecole des Ponts

About:

The focus of the proposed workshop is the mathematical analysis of models used to learn low-dimensional em-beddings and dynamical projections of molecular dynamical systems. The workshop will convene mathematicians, statisticians, theoretical chemists, and biophysicists to discuss theoretical and numerical techniques, to define open challenges and pressing needs in the field, and to establish new disciplinary bridges and collaboration opportunities. Although primarily mathematical in nature, the history of this field has taught us that the most challenging questions can only be tackled by a synthesis of interdisciplinary methods and tools. The workshop will promote participation of early-career and female researchers. Successful outcomes of the workshop will include a freely available online workshop report and the establishment of new collaborations, and the definition of set of open questions to guide future work in the field.

Participation:

Applications to attend this workshop have now closed. Late submissions will not be accepted.

All applicants have been contacted by ICMS. Please check your junk/spam inbox before getting in touch.

Public Lecture:

Andrew Ferguson will deliver the public lecture ChatGPT for proteins: Designing molecular machines using natural language text prompts on Tuesday 3 June, 18.00 BST. Further details can be found here.

Seats will be reserved for workshop participants, there is no need to register separately.

Resources

Programme

MONDAY 2 JUNE
09.00 - 09.45 Registration and refreshments
09.45 - 10.00 Welcome and housekeeping
10.00 - 12.00 Marina Meila, University of Washington Tutorial - Manifold learning from the user's perspective
12.00 - 13.30 Lunch
13.30 - 15.30 Andrew Ferguson, University of Chicago Tutorial - Talk Title TBC
15.30 - 16.00 Lightning talks
16.00 - 17.30 Poster session and welcome reception, hosted at ICMS
TUESDAY 3 JUNE
09.15 - 10.00 Jutta Rogal, Flatiron Institute
10.00 - 10.45 Hao Wu, Shanghai Jiao Tong University
10.45 - 11.15 Refreshments
11.15 - 12.00 Christof Schütte, Zuse Institute Berlin Learning Collective Variables for Complex Systems: A Theoretical and Practical Perspective
12.00 - 12.45 Pilar Cossio, Flatiron Institute Cryo-electron microscopy images are low-dimensional
12.45 - 14.00 Lunch break
14.00 - 14.45 Paraskevi Gkeka, Sanofi R&D Enhancing Sampling in Molecular Dynamics: Integrating Autoencoders and Linear Discriminant Analysis for the identification of collective variables
14.45 - 15.30 Mauro Maggionni, Johns Hopkins University
15.30 - 16.00 Refreshments
16.00 - 16.45 Feliks Nüske, Max-Planck-Institute DCTS Magdeburg Kinetically Consistent Coarse Graining using Kernel-based Extended Dynamic Mode Decomposition
18.00 - 19.00 Public Lecture, Andrew Ferguson, University of Chicago ChatGPT for proteins: Designing molecular machines using text prompts
WEDNESDAY 4 JUNE
09.15 - 10.00 Carsten Hartmann, BTU Cottbus-Senftenberg Coarse graining of diffusion processes in the absence of time scale separation
10.00 - 10.45 Maria Cameron, University of Maryland Learning collective variables for accurate transition rate estimation
10.45 - 11.15 Refreshments
11.15 - 12.00 Bernd Ensing, University of Amsterdam
12.00 - 12.45 Jérôme Hénin, CNRS
12.45 - 14.00 Lunch break
14.00 - 14.45 Tiffany Vlaar, University of Glasgow
14.45 - 15.30 Vitaliy Kurlin, University of Liverpool The Principle of Molecular Rigidity
19.00 Workshop dinner
THURSDAY 5 JUNE
09.15 - 10.00 Simon Cotter, University of Manchester
10.00 - 10.45 Thomas Pigeon, IFPEN Approximating committor functions: Objective functions and training data sampling
10.45 - 11.15 Refreshments
11.15 - 12.00 Wei Zhang, Zuse Institute Berlin Mathematical aspects of deep-learning techniques for identifying collective variables of molecular dynamics
12.00 - 12.45 Neelanjana Sengupta, Indian Institute of Science Education and Research (IISER) Kolkata Effectiveness of Machine Learned Collective Variable Projection in Bio-molecular Energy Landscapes
12.45 - 14.00 Lunch break
14.00 - 14.45 Antonia Mey, University of Edinburgh
14.45 - 15.30 Grigorios Pavliotis, Imperial College London Clustering for interacting particle systems with short range attractive potentials
FRIDAY 6 JUNE
09.15 - 10.00 Sapna Sarupria, University of Minnesota Seeing the invisible: Learning Pathways to Polymorphs through machine learning analysis of atomic trajectories
10.00 - 10.45 Hong Duong, University of Birmingham
10.45 - 11.00 Refreshments
11.00 - 11.45 Gareth Tribello, Queen's University Belfast Reconnaissance metadynamics Rides Again
11.45 Lunch and end of workshop

Sponsors and Funders:

  • ICMS
  • CCPBioSim