Conferences & Symposia

TMLS Conferences & Symposia are designed to uplift the goals of the initiative for its members and researchers with common interests in building theoretical frameworks for understanding living systems through presentations and discussion-driven panel formats.

Code of Conduct:
TMLS will not tolerate harassment of conference participants in any form at any conference venue, including talks, workshops, and social events, and on online media. Any conference participants violating this policy may be sanctioned or expelled from the conference without a refund at the discretion of the conference organizers.

Can we predict the diversity of real populations? August 18th & August 25th, 2020

"Can we predict the diversity of real populations?" 

Session 1: "What is linked selection doing to populations?"

(August 18th, 12:30-2:20pm EDT

About:

Natural selection affects not only selected alleles, but also indirectly affects all alleles linked to selected sites. An increasing body of evidence suggests that this linked selection is an important driver of allele frequency dynamics throughout the genomes of many species, implying that we need to substantially revise our basic understanding of molecular evolution and the tempo and mode of adaptation. This session brings together early-career researchers working towards a quantitative understanding of linked selection, bringing together data from many different systems as well as models of different forms of linked selection.                               

Speakers:         

Christelle Fraïsse (IST Austria/CNRS)
Derek Setter (U Edinburgh)
Kimberley Gilbert (U Lausanne/U Bern)
Ivana Cvijovic (Stanford U)

Schedule:

12:30-12:40: Introduction
12:40-1:00: Christelle Fraïsse (IST Austria/CNRS), "Multilocus Barriers To Introgression Between Hybridizing Species: Sex Chromosomes vs. Autosomes"
1:00-1:20: Derek Setter (U Edinburgh), "Sweeps in Time: Leveraging the Joint Distribution of Branch Lengths"
1:20-1:40: Kim Gilbert (U Lausanne/U Bern), "Drivers of Genetic Diversity in Regions of Low Recombination"
1:40-2:00: Ivana Cvijovic (Stanford U), "The Effect of Background Selection on Genetic Diversity"
2:00-2:20: Discussion

"Can we predict the diversity of real populations?" 

       Session 2: "What determines microbial diversity?"

(August 25th, TBD EDT

About:

Microbes make up the vast majority of the tree of life. While we know very little about most microbial species, large-scale sequencing is giving us glimpses of the diversity that exists both within species and in ecosystems. The challenge now is to find the patterns in this diversity and understand them. This session features provocative talks on attempts to meet that challenge.
 

Speakers:

Erik van Nimwegen (U Basel), "Bacterial phylogenies reflect complex patterns of recombination rates"
Jacopo Grilli (ICTP), "Laws of diversity and variation in microbial communities"
Maitreya Dunham (U Washington), "Microbial diversity between and within species in beer"
Nandita Garud (UCLA), "Evolution in the Human Gut Microbiome"

Schedule:

11:25-11:30: Introduction

11:30-12:00: Erik van Nimwegen (U Basel), "Bacterial Phylogenies Reflect Complex Patterns of Recombination Rates"

12:00-12:30: Jacopo Grilli (ICTP), "Laws of Diversity and Variation in Microbial Communities"

12:30-1:00: Maitreya Dunham (U Washington), "Microbial Diversity Between and Within Species in Beer"

1:00-1:30: Nandita Garud (UCLA), "Evolution in the Human Gut Microbiome"

1:30-1:50: Discussion

Registration:                                                                                 

 Registration is free. Please complete the form below: 

https://forms.gle/3K8PEht5SDK7aUpa7

How to participate?

We expect to broadcast the workshop live at the Emory TMLS YouTube channel, where you will be able to ask questions via the live chat (Google account required for Q&A):

https://www.youtube.com/watch?v=qZdAXtS-nZY (direct link to workshop live stream)
https://www.youtube.com/c/EmoryTMLS (TMLS main channel, if the live stream link doesn’t work for you)
We are making arrangements for an alternative broadcasting platform if YouTube Live fails us again. If there are any last-minute changes regarding how to access the workshop, these will be communicated via TMLS-WORKSHOP-L@listserv.cc.emory.edu and via Twitter at https://twitter.com/EmoryTMLS — please follow us there.

"(What) can soft matter physics teach us about biological function?” - July 31st, 2020

"(What) can soft matter physics teach us about biological function?

 

(Friday July 31, 2020 10am – 1pm EDT) 

About:

The “soft, active, and living matter” community has grown tremendously in recent years, conducting exciting research at the interface between soft matter and biological systems. But are all living systems also soft matter systems? Do the ideas of function (or purpose) in biological systems require us to introduce deep new ideas into the framework of soft matter theories? Does the (often) qualitatively different character of data in biological experiments require us to change the types of experiments we conduct and the goals of our theoretical treatments? Eight speakers will anchor the workshop, exploring these questions across a range of biological system scales. Each speaker will deliver a 10-minute talk with another 10 minutes set aside for moderated questions/discussion. We expect the talks to be broad, bold, and provocative, discussing both the nature of the theoretical tools and experimental techniques we have at present and also those we think we will ultimately need to answer deep questions at the interface of soft matter and biology.                                       

Speakers:         

Michael Brenner (Harvard University)
Eleni Katifori (University of Pennsylvania)
Cristina Marchetti (University of California, Santa Barbara)
Chase Broedersz (Ludwig Maximilian University)
Joshua Shaevitz (Princeton University)
Michael Murrell  (Yale University)
Symone Alexander (Georgia Tech)
Orit Peleg (CU Boulder)

Organizers: Jennifer Rieser (Georgia Tech) & Daniel Sussman (Emory University)

Schedule:

10:00 - 10:05 Daniel Sussman - Introduction To Session 1 
10:05 - 10:25 Chase Broedersz - Dynamics and Interactions Of Confined Cell Migration”
10:25 - 10:45 Michael Murrell - “Capillarity and Wetting in Active Systems”
10:45 - 11:05 Cristina Marchetti - “Symmetry Breaking, Geometry and Topology in Biology”
11:05 - 11:25 Joshua Shaevitz - “Active and Passive Dewetting In Biological Systems From Molecules To Populations”
11:25 - 11:35 Break
11:35 - 11:40 Jennifer Rieser - Introduction To Session 2  
11:40 - 12:00 Michael Brenner - “Towards Living Synthetic Matter”
12:00 - 12:20 Eleni Katifori - “Fluid Interactions and Information Flows”
12:20 - 12:40 Symone Alexander - “Multifunctional Materials Designed and Inspired By Nature"
12:40 - 01:00 Orit Peleg - On Growth and Form of Dense Insect Aggregations”

Registration:                                                                                 

 Registration is free. Please complete the form below: 

https://tinyurl.com/tmlsbiosoft

How to participate?

We expect to broadcast the workshop live at the Emory TMLS YouTube channel, where you will be able to ask questions via the live chat (Google account required for Q&A):

https://www.youtube.com/watch?v=qZdAXtS-nZY (direct link to workshop live stream)
https://www.youtube.com/c/EmoryTMLS (TMLS main channel, if the live stream link doesn’t work for you)
We are making arrangements for an alternative broadcasting platform if YouTube Live fails us again. If there are any last-minute changes regarding how to access the workshop, these will be communicated via TMLS-WORKSHOP-L@listserv.cc.emory.edu and via Twitter at https://twitter.com/EmoryTMLS — please follow us there.

Inaugural Simons-Emory Symposium On Motor Control June 26th, 2020

Inaugural Simons-Emory Symposium On Motor Control

(June 26th, 2020 - 10:00am - 1pm EST) 
"What tools are we missing to understand motor control?
What could we learn if we had them?”

                                       

Speakers:         

Amy Bastian (Kennedy Krieger Institute)
Rui Costa (Columbia)
Amy Orsborn (University of Washington)
Chethan Pandarinath (Emory and Georgia Tech)
Abigail Person (University of Colorado)
Andrew Pruszynski (Western University)
Flip Sabes (UCSF and Neuralink)
Lena Ting (Emory and Georgia Tech)
Discussants:
*Gordon Berman (Emory)
Megan Carey (Champalimaud)
Ilya Nemenman (Emory)
*Sam Sober (Emory)
*Moderators

Registration:                                                                                 

 Registration is free. Please complete the form below: 

internationalmotorcontrol.org/symposium.html

How to participate?

We expect to broadcast the workshop live at the Emory TMLS YouTube channel, where you will be able to ask questions via the live chat (Google account required for Q&A):

https://www.youtube.com/watch?v=qZdAXtS-nZY (direct link to workshop live stream)
https://www.youtube.com/c/EmoryTMLS (TMLS main channel, if the live stream link doesn’t work for you)
We are making arrangements for an alternative broadcasting platform if YouTube Live fails us again. If there are any last-minute changes regarding how to access the workshop, these will be communicated via TMLS-WORKSHOP-L@listserv.cc.emory.edu and via Twitter at https://twitter.com/EmoryTMLS — please follow us there.

"Learning New Physics with Machine Learning Virtual Workshop" -June 4th, 2020

Learning New Physics with Machine Learning (June 4th, 2020 - 9:45am - 1pm EDT) 

"Can machine learning learn new physics, or do we need to put it in by hand?"

 

The Emory Theory and Modeling of Living Systems initiative is organizing a series of online workshops to explore the future of our field, and to retain a sense of community at the interface of physics, biology, and statistical inference. Our next workshop is "Can machine learning learn new physics, or do we need to put it in by hand?" 
 
There has been a surge of publications on using machine learning (ML) on experimental data from physical systems: social, biological, statistical, and quantum. However, can these methods discover fundamentally new physics? It can be that their biggest impact is in better data preprocessing, while inferring new physics is unrealistic without specifically adapting the learning machine to find what we are looking for — that is, without the “intuition” — and hence without having a good a priori guess about what we will find.
 
Is machine learning a useful tool for physics discovery? Which minimal knowledge should we endow the machines with to make them useful in such tasks? How do we do this? Eight speakers below will anchor the workshop, exploring these questions in contexts of diverse systems (from quantum to biological), and from general theoretical advances to specific applications. Each speaker will deliver a 10 min talk with another 10 minutes set aside for moderated questions/discussion. We expect the talks to be broad, bold, and provocative, discussing where the field is heading, and what is needed to get us there.


                                       

Program:         

9:45-9:50 Ilya Nemenman (Emory University) - Introduction to The Workshop
9:50-11:10 Session 1
9:50-10:10 Aleksandra Walczak (CNRS/ENS Paris) - Generative Models of Immune Repertoires
10:10-10:30 David Schwab (CUNY) - Renormalizing Data
10:30-10:50 Sam Greydanus (Google Brain) - Nature’s Cost Function
10:50-11:10 Max Tegmark (MIT) - Symbolic Regression & Pregression
11:10-11:25 BREAK 
11:25-13:00 Session 2
11:25-11:45 Bryan Daniels (Arizona State University) - Inferring Logic, Not Just Dynamical Models
11:45-12:05 Andrea Liu (University of Pennsylvania) - Doing "Statistical Mechanics" with Big Data
12:05-12:25 Roger Melko (University of Waterloo) - Machine Learning And The Complexity of Quantum Simulation
12:25-12:45 Lucy Colwell (Cambridge University) - Using Simple Models To Explore The Sequence Plasticity of Viral Capsids
12:45-13:00 Panel Discussion

Registration:                                                                                 

 Registration is free. Please complete the form below: 

https://bit.ly/3fC9uxr

How to participate?

We expect to broadcast the workshop live at the Emory TMLS YouTube channel, where you will be able to ask questions via the live chat (Google account required for Q&A):

https://www.youtube.com/watch?v=DRh1OlGlRxo (direct link to workshop live stream)
https://www.youtube.com/c/EmoryTMLS (TMLS main channel, if the live stream link doesn’t work for you)
We are making arrangements for an alternative broadcasting platform if YouTube Live fails us again. If there are any last-minute changes regarding how to access the workshop, these will be communicated via TMLS-WORKSHOP-L@listserv.cc.emory.edu and via Twitter at https://twitter.com/EmoryTMLS — please follow us there.

"Physics of Behavior Virtual Workshop" - April 30th, 2020

Title                                                                                         

Physics of Behavior Virtual Workshop (April 30th, 2020 - 10am - 1pm ) 
If we can track (most) everything, what should we do with the data?

 

Please catch the playback of this workshop

below: https://www.youtube.com/watch?v=xSwWAgp2VdU

 

About                                                                                         

With the cancellation of the March Meeting and most of our summer conferences and travel, we were hoping to retain a sense of community amongst all of us studying questions at the interface of physics and animal behavior.  Accordingly, we thought it would be fun to host a virtual workshop where we could at least get a sense for current research directions, see each other, and devote time to thinking about the non-virus-related science that we all care about.  Thus, we have organized a virtual workshop on the Physics of Behavior, to be held on April 30th from 10am - 1pm Eastern Daylight Time over Zoom (RSVP information below).

We both agreed that typical workshop formats wouldn’t necessarily translate well to the virtual domain and thought to organize around one question: “Now that we can track (most) everything, what can we do with the data?”  Given the recent dramatic advances in technology, we now have behavioral data sets with orders of magnitude more accuracy, dimensionality, diversity, and size than we had even a few years ago.  That being said, there is still little agreement as to what theoretical frameworks can inform our understanding of these data sets and suggest new experiments we can perform.  We hope that after this workshop we’ll see a variety of new ideas and perhaps gain some inspiration.

We have invited eight speakers, each studying different systems, scales, and topics, to provide 10 minute presentations focused on the above question, with another 10 minutes set aside for questions/discussions (moderated by the two of us).  Although we naturally expect speakers to include aspects of their own work, we have encouraged all of them to think broadly and provocatively.  We are also hoping to organize some breakout sessions after the talks so that we can have some more expanded discussions about topics arising during the meeting.  
 
 

 

Speakers         

Andre Brown (Imperial College)
William Bialek (Princeton University)
Ann Kennedy (California Institute of Technology)
Ugne Klibaite (Harvard University)
Alexander Mathis (Harvard University)
Nicholas Ouellette (Stanford University)
Samuel Reiter (Okinawa Institute of Science and Technology)
Ariana Strandburg-Peshkin (University of Konstanz)

Registration                                                                                 

To avoid Zoom-bombing and other nascent perils of our time, we are asking that all potential participants RSVP at the link herehttps://forms.gle/kg1jpFebr343jdq16 .  We will forward Zoom invites to all registered participants at some time within a day or two of the workshop. 

 

 

"Theoretical Biophysics Workshop" - January 16th - 18th, 2019

Title                                                                                         

What is Theoretical Biological Physics in The Age of Quantitative Biology and Big Data?

About                                                                                         

With the advent of Big Data, machine learning, and large-scale simulations, the boundaries of what constitutes theoretical biophysics have become unclear. It is even unclear if the theoretical physics mindset has much to offer to a modern way of understanding life: in modern quantitative biology, one can measure more and more in the quest to measure everything, computers simulate things fast, and deep networks are better at finding correlations in these data than we are (after all, our theories are just a way to summarize correlations we expect in data). It remains uncommon for theoretical approaches to help formulate better questions and guide design of experiments — we are often in the regime where experiments are done, and we are being asked to make sense of them a posteriori, or where experiments disambiguate between a few related models of the system.

While there are clear overlaps, and we must — and want to! — interact effectively with biologists and learn from them, theoretical physics of living systems is not the same as quantitative biology. Is it also not the same as soft condensed matter, or dynamical systems or control theories — living systems are interesting precisely because they are alive, and live and act autonomously with a purpose. It is also not medical physics, just like condensed matter physics is not electrical engineering. Our questions can be (and maybe should be) different from those of biologists.

Attendees at this workshop will think together about what defines our field, how to explain it to ourselves and others, and how to promote it. They will attempt to articulate a vision of what role theoretical physicists (or, more generally, the theoretical physics diaspora) should/could play in scientific discoveries in biological systems moving forward, without being insular, but also preserving the sense of our field.

Attendees                                                                                         

Sena Agezo, Emory University Kanishk Jain, Emory University Ilya Nemenman, Emory University
Brent Allman, Emory University
Yi Jiang, Georgia State University Bertrand Ottino-Loffler, Massachusetts Institute of Technology
Rustom Antia, Emory University Mehran Kardar, Massachusetts Institute of Technology Katherine Overman, Emory University
Dani Bassett, University of Pennsylvania Shella Keilholz, Emory University Itai Pinkoviezky, Emory University
Robert Batterman, University of Pittsburgh Minsu Kim, Emory University Mahajabin Rahman, Emory University
Gordon Berman, Emory University Maria Kochugaeva, Yale University Gautam Reddy, The University of California - San Diego
Jeremie Breda, University of Basel Katia Koelle, Emory University Jennifer Rieser, Georgia Institute of Technology
Josuan Calderon, Emory University Andre Levchenko, Yale University Carlos Rodriguez, Emory University
Shivesh Chaudhary, Georgia Institute of Technology Herbert Levine, Rice University Ahmed Roman, Emory University
Bryce Chung, Emory University Andrea Liu, University of Pennsylvania Ishan Saran, Emory University
Rachel Conn-Barker, Emory University Luis Maria Lopes da Fonseca, Emory University David Schwab, The City University of New York
Daniel Coombs, University of British Columbia Hang Lu, Georgia Institute of Technology Perrin Schiebel, Georgia Institute of Technology
David Cutler, Emory University Christopher Lynn, University of Pennsylvania Audrey Sederberg, Georgia Institute of Technology
Noah DeTal, Georgia Institute of Technology Tzuhsuan Ma, University of Texas - Austin Hong-Yan Shih, University of Illinois - Urbana-Champaign
Ila Fiete, Massachusetts Institute of Technology Natalia Maksymchuk, Georgia State University David Stockton, Emory University
Gregory Gabadadze, NYU/Simons Foundation Jacopo Marchi, Ecole Normale Superieure Daniel Sussman, Syracuse University
Xiangxi Gao, Emory University Robert Marsland, Boston University Arabind Swain, Emory University
Nigel Goldenfeld, University of Illinois - Urbana-Champaign Michael Martini, Emory University Erik Van Nimwegen, University of Basel
Haejun HanGeorgia Institute of Technology Pankaj Mehta, Boston University Aleksandra Walczak, Ecole Normale Superieure
Jeremy Haris, Emory University Leenoy Meshulam, Massachusetts Institute of Technology Daniel Weissman, Emory University
David Hofmann, Emory University Leonid Mirny, Massachusetts Institute of Technology Jim Wu, Princeton University
Zachary Jackson, Georgia Institute of Technology Joseph Natale, Emory University Veronika Zarnitsyna, Emory University
Farshid Jafarpour, University of Pennsylvania Jacob Neal, University of Pittsburgh Baohua Zhou, Emory University

 

Schedule                                                                                         

1/16/2019
Day 1- Opening Banquet
6:00 - 6:05 pm
Michael Elliott, ECAS Dean Welcome
6:05 - 7:15 pm
Dinner
7:15 - 8:00 pm
Ilya Nemenman Is There a Place for Theoretical Biophysics?

1/17/2019

Day 2 - Talks Describing Recent Advances in Theoretical Biophysics Emory Conference Center & Hotel

8:00 - 9:00 am Breakfast
Session 1 Moderator: Michael Martini
9:00 - 9:25 am Mehran Kardar Genome Organization by Loop Extrusion
9:25 - 9:50 am Yi Jiang Epigenetic Landscape: Statics, Dynamics, and Stochasticity
9:50 - 10:15 am Andre Levchenko Complex Optimization on Complex Landscapes in Biological Function
10:15 - 10:45 am Break
Session 2
Moderator: Bertrand Ottino-Loffler
10:45 -
11:10 am
Rustom Antia How Have Mathematical Models Contributed to our Understanding of the Basic Principles of Immunology?
11:10 - 11:35 am
Aleks Walczak Prediction in Biological Systems
11:35 am -12:00 pm
Daniel Weissman New Approaches to Microbial Evolutionary Genetics
12:00 - 2:00 pm
Lunch
Session 3 Moderator: Audrey Sederberg
2:00 - 2:25 pm
David Schwab Biologically Plausible Learning Algorithms
2:25 - 2:50 pm
Ila Fiete The Rheory that Launches a Thousand Boats: Neural Computation with Discrete and Continuous Attractors
2:50 - 3:15 pm
Leonid Mirny Folding and Self-Assembly
3:15 - 3:45 pm
Break
Session 4 Moderator: Itai Pinkoviezky
3:45 - 4:10 pm
Herbert Levine Phenotypic Exploration as a Response to Cellular Stress
4:10 - 4:45 pm
Lightning Session
5:00 - 6:30 pm
Poster Session & Reception A listing of the posters being presented can be found on the program abstracts sheet.
1/18/2019

Day 3 - Address Questions that are Understudied

Emory Conference Center & Hotel
8:00 - 9:00 am
Breakfast
Session 5
Farshid Jafarpor & David Hofmann
9:00 - 9:25 am
Danielle Bassett Human Learning of Relational Patterns
9:25 - 9:50 am
Robert Batterman Multiscale Modeling and Universality
9:50 - 10:15 am
Pankaj Mehta Taking High-Dimensions Seriously in Biology
10:15 - 10:40 am
Erik van Nimwegen Identifying Phenomenological Laws is an Underappreciated Theoretical Activity
10:40 - 11:15 am
Break
Session 6 Robert Marsland & Leenoy Meshulam
11:15 - 11:40 am
Gordon Berman Building Long Time Scales in Genes, Neurons, and Behavior
11:40 am - 12:05 pm
Andrea Liu Topological Nature of Structure-Function Relation in Flow and Mechanical Networks
12:05 - 12:30 pm
Nigel Goldenfeld Is the Phenomenon of Life an Inevitable Consequence of the Laws of Physics? And Why This Actually Matters!
12:30 - 2:30 pm
Lunch/Discussion

Abstracts                                                                                        

For a full list of the abstracts being presented at the workshop, please click here.

Lodging                                                                                         

Conference participants will be able to stay at the Emory Conference Center & Hotel while space is available (1615 Clifton Rd, Atlanta, GA 30329). To reserve your room, email TMLS Program Manager Davonte Biggers directly with your request including your full name.

The deadline to reserve a room was December 20th, 2018.

Registration                                                                                 

Registration for this workshop closed on December 15th, 2018.


Contact                                                                                         

Organizing Committee:

Ilya Nemenman, TMLS Co-Director Katia Koelle, TMLS Co-Director
Gordon Berman, TMLS Faculty Daniel Weissman, TMLS Faculty
Davonte Biggers, TMLS Program Manager

"Emerging Structure from Collective Interactions" - April 24th, 2018

The theme for this symposium is "Emerging Structure from Collective Interactions." It will be held on April 24th, 2018 from 9:30 a.m. - 1 p.m. in the Woodruff Library - Jones Room (Room 301) (540 Asbury Circle, Atlanta, GA 30307).

This event is free of charge and parking is available in the Fishburne Parking Deck.

For more information on the symposium, please contact Katia Koelle at katia.koelle@emory.edu.


         Schedule of Events

9:30 a.m. Breakfast - Introduction
Session 1 Emergent behavior from collective interactions in neuroscience
10:00 a.m. Gordon Berman, The emergent dynamics of behavioral repertoires
10:15 a.m. Astrid Prinz, Interactions in small neural circuits and their effect on circuit stability
10:30 a.m. Discussion led by Dieter Jaeger
Session 2 Emergent behavior from collective interactions in population biology, ecology, and evolution
10:45 a.m. Daniel Weissman, The collective effect of sweeps in space
11:00 a.m. Rustom Antia, Interactions between antibodies and virus, with implications for flu vaccine development
11:15 a.m. Discussion led by Katia Koelle
Session 3 Emergent behavior from collective interactions in medicine and molecules
11:30 a.m. Alessandro Veneziani, Emergent challenges in translational mathematics: from the computer lab to the clinics (and back)
11:45 a.m. James Kindt, Collective effects in dynamics and permeation near the melting point of a lipid bilayer
12:00 p.m. Discussion led by Ilya Nemenman
12:15 p.m. Lunch and broader discussion on TMLS
1:00 p.m. Conclusion