Starting up in September 2020, we're proud to introduce our monthly Physics of Life Seminar Series. We'll be hosting top speakers from across the globe, presenting on all topics from fundamental theory to cutting edge experiments. At least initially, seminars will be hosted remotely and everyone is welcome, whether you are a member of College or not. If you're interested, please sign up to our network mailing list for regular updates on speakers; our full schedule is shown below, and you can find details about how to watch live by clicking on the event links.  Recordings of previous talks can be found in the video playlist below (the full playlist can also be accessed here).

If you'd like to suggest a speaker, please do so using this form.

Events

Recorded Seminars

Prof Margaret Gardel

Mechanical Homeostasis in the Actin Cytoskeleton

My lab studies the design principles of cytoskeletal materials the drive cellular morphogenesis, with a focus on contractile machinery in adherent cells. In addition to force generation, a key feature of these materials are distributed force sensors which allow for rapid assembly, adaptation, repair and disintegration. Here I will describe how optogenetic control of RhoA GTPase is a powerful and versatile force spectroscopy approach of cytoskeletal assemblies and its recent use to probe repair response in actomyosin stress fibers. I will also describe our recent identification of 18 proteins from the zyxin, paxillin, Tes and Enigma families with mechanosensitive LIM (Lin11, Isl- 1 & Mec-3) domains that bind exclusively to mechanically stressed actin filaments. Our results suggest that the evolutionary emergence of contractile F-actin machinery coincided with, or required, proteins that could report on the stresses present there to maintain homeostasis of actively stressed networks.

Mechanical Homeostasis in the Actin Cytoskeleton

Prof Margaret Gardel

Mechanical Homeostasis in the Actin Cytoskeleton

Mechanical Homeostasis in the Actin Cytoskeleton

My lab studies the design principles of cytoskeletal materials the drive cellular morphogenesis, with a focus on contractile machinery in adherent cells. In addition to force generation, a key feature of these materials are distributed force sensors which allow for rapid assembly, adaptation, repair and disintegration. Here I will describe how optogenetic control of RhoA GTPase is a powerful and versatile force spectroscopy approach of cytoskeletal assemblies and its recent use to probe repair response in actomyosin stress fibers. I will also describe our recent identification of 18 proteins from the zyxin, paxillin, Tes and Enigma families with mechanosensitive LIM (Lin11, Isl- 1 & Mec-3) domains that bind exclusively to mechanically stressed actin filaments. Our results suggest that the evolutionary emergence of contractile F-actin machinery coincided with, or required, proteins that could report on the stresses present there to maintain homeostasis of actively stressed networks.

RNA-driven phase separation from cells to SARS

Prof Amy Gladfelter

RNA-driven phase separation from cells to SARS

RNA-driven phase separation from cells to SARS

Biomolecular condensation is a mechanism for controlling cell organization. Many condensates are rich in nuclei acids such as RNA. The role of specific RNA sequences and structures in promoting the molecular identity of condensates formed for cell polarity and division and by the SARS CoV-2 virus will be discussed.

Is there Universality in Biology?

Prof Nigel Goldenfeld

Is there Universality in Biology?

Is there Universality in Biology?

It is sometimes said that there are two reasons why physics is so successful as a science. One is that it deals with very simple problems. The other is that it attempts to account only for universal aspects of systems at a desired level of description, with lower level phenomena subsumed into a small number of adjustable parameters. It is a widespread belief that this approach seems unlikely to be useful in biology, which is intimidatingly complex, where “everything has an exception”, and where there are a huge number of undetermined parameters.

I will try to argue, nonetheless, that there are important, experimentally-testable aspects of biology that exhibit universality, and should be amenable to being tackled from a physics perspective. My suggestion is that this can lead to useful new insights into the existence and universal characteristics of living systems. I will try to justify this point of view by contrasting the goals and practices of the field of condensed matter physics with materials science, and then by extension, the goals and practices of the newly emerging field of “Physics of Living Systems” with biology.

Anatomical decision-making by cellular collectives

Prof Michael Levin

Anatomical decision-making by cellular collectives

Anatomical decision-making by cellular collectives: Bioelectrical pattern memories, regeneration, and synthetic living organisms

It is sometimes said that there are two reasons why physics is so successful as a science. One is that it deals with very simple problems. The other is that it attempts to account only for universal aspects of systems at a desired level of description, with lower level phenomena subsumed into a small number of adjustable parameters. It is a widespread belief that this approach seems unlikely to be useful in biology, which is intimidatingly complex, where “everything has an exception”, and where there are a huge number of undetermined parameters.

I will try to argue, nonetheless, that there are important, experimentally-testable aspects of biology that exhibit universality, and should be amenable to being tackled from a physics perspective. My suggestion is that this can lead to useful new insights into the existence and universal characteristics of living systems. I will try to justify this point of view by contrasting the goals and practices of the field of condensed matter physics with materials science, and then by extension, the goals and practices of the newly emerging field of “Physics of Living Systems” with biology.

How do single cells program collective behavior

Prof Lisa Manning

How do single cells program collective behavior

How do single cells program collective behavior at the scale of tissues?

In multicellular organisms, properly programmed collective cell motion is required to form tissues and organs, and this programming breaks down in diseases like cancer. Recent experimental work highlights that some organisms tune the global mechanical properties of a tissue across a fluid-solid transition. In the “fluid” phase, cells change neighbors and the global shape of the tissue deforms, while in the “solid” phase cell motion is prohibited and the tissue responds elastically via stretching and buckling. What is the physical origin of such rigidity transitions and how do cells control them? I will discuss our theoretical and computational work to understand what causes these transitions, and demonstrate that our theoretical predictions with no fit parameters explain detailed features of body axis elongation in the fruit fly and the architecture and dynamics of epithelial cell culture. I will also discuss possible biochemical pathways and cellular processes that individual cells may utilize to alter mechanical properties at the tissue scale.

Neural network like collective dynamics in molecules

Prof Arvind Murugan

Neural network like collective dynamics in molecules

Neural network like collective dynamics in molecules

Neural networks can learn and recognize subtle correlations in high dimensional inputs. However, neural networks are simply many-body systems with strong non-linearities and disordered interactions. Hence, many-body physical systems with similar interactions should be able to show neural network-like behavior. Here we show neural network-like behavior in the nucleation dynamics of promiscuously interacting molecules with multiple stable crystalline phases. Using a combination of theory and experiments, we show how the physics of the system dictates relationships between the difficulty of the pattern recognition task solved, time taken and accuracy. This work shows that high dimensional pattern recognition and learning are not special to software algorithms but can be achieved by the collective dynamics of sufficiently disordered molecular systems.

Energy landscapes, order and disorder

Prof Jose Onuchic

Energy landscapes, order and disorder

Energy landscapes, order and disorder, and protein sequence coevolution: From proteins to chromosome structure

In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (the minimal chromatin model) explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data is presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. This model was generalized by utilizing a neural network to infer these chromatin types using epigenetic marks present at a locus, as assayed by ChIP-Seq. The ensemble of structures resulting from these simulations completely agree with HI-C data and exhibits unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories. Although this theoretical methodology was trained in one cell line, the human GM12878 lymphoblastoid cells, it has successfully predicted the structural ensembles of multiple human cell lines. Finally, going beyond Hi-C, our predicted structures are also consistent with microscopy measurements. Analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. For gene active segments, the vast majority of genes appear clustered in the linker region of the chromatin segment, allowing us to speculate possible mechanisms by which chromatin structure and dynamics may be involved in controlling gene expression.

 

* Supported by the NS

Emergent Behaviour III.1

Emergent Behaviour III.1

Physics of Emergent Behaviour III: from origin of life to multicellularity (part 1)

Physics of Emergent Behaviour III: from origin of life to multicellularity, 2nd July 2021 (part 1)

 
In Part 1 of this thought-provoking conference, we discussed the origin of life in terms of thermodynamics at a molecular scale. Besides short talks delivered by esteemed international speakers from the biological physics community, a significant portion of the meeting was dedicated to open discussion. This exciting meeting was supported by the Physics of Life Network of Excellence at Imperial College London and the Biological Physics Group of the Institute of Physics (IOP).
 
Conference start[Robert Endres]
0:02 Welcome and intro Life in molecules
 
[Chair: Robert Endres]
11:20 Joana C. Xavier (University College London)
29:00 Sara Walker (Arizona State University)
51:33 Dieter Braun (LMU Munich)
1:11:52 Panel discussion
 
Defying 2nd law of thermodynamics [Chair: Sara Walker]
1:51:48 Udo Seifert (University of Stuttgart)
2:14:13 Jeremy England (Georgia Tech & GlaxoSmithKline)
2:38:05 Pablo Sartori (Instituto Gulbenkian de Ciencia)
2:59:25 Panel discussion
 
Organising committee:
Robert Endres (Imperial College London)
Chiu Fan Lee (Imperial College London)
Hélène de Maleprade (IRPHÉ, Marseille)
Sara Imari Walker (Arizona State University & Santa Fe Institute & Blue Marble Space Institute of Science)
Emergent Behaviour III.2

Emergent Behaviour III.2

Physics of Emergent Behaviour III: from origin of life to multicellularity (part 2)

Physics of Emergent Behaviour III: from origin of life to multicellularity, 2nd July 2021 (part 2)

 
In Part 2 of this thought-provoking conference, we discussed the emergence of order and multicellularity. Besides short talks delivered by esteemed international speakers from the interface of physics and biology, a significant portion of the meeting was dedicated to open discussion. This exciting meeting was supported by the “Physics of Life” Network of Excellence at Imperial College London and the Biological Physics Group of the Institute of Physics (IOP).
 
 
Emergence of order [Chair: Chiu Fan Lee]
1:25 Suriyanarayanan Vaikuntanathan (University of Chicago)
20:30 James Sethna (Cornell University)
42:16 Nigel Goldenfeld (University of Illinois at Urbana-Champaign)
1:05:15 Panel discussion
 
Cells and beyond [Chair: Hélène de Maleprade]
1:32:27 Ricard Solé (Catalan Institute for Research and Advanced Studies)
1:54:40 William Ratcliff (Georgia Tech)
2:16:57 Peter Yunker (Georgia Tech)
2:50:50 General Q&A
2:56:50 Jessica Flack (Santa Fe Institute)
3:28:25 Closing of conference
 
Organising committee:
Robert Endres (Imperial College London)
Chiu Fan Lee (Imperial College London)
Hélène de Maleprade (IRPHÉ, Marseille)
Sara Imari Walker (Arizona State University & Santa Fe Institute & Blue Marble Space Institute of Science)
Theory, reimagined

Prof Greg Stephens

Theory, reimagined

Theory, reimagined

Physics offers countless examples for which theoretical predictions are astonishingly powerful. But it’s hard to imagine a similar precision in complex systems where the number and interdependencies between components simply prohibits a first-principles approach, look no further than the challenge of the billions of neurons and trillions of connections within our own brains. In such settings how do we even identify the important theoretical questions? We describe a systems-scale perspective in which we integrate information theory, dynamical systems and statistical physics to extract understanding directly from measurements. We demonstrate our approach with a reconstructed state space of the behavior of the nematode C. elegans, revealing a chaotic attractor with symmetric Lyapunov spectrum and a novel perspective of motor control. We then outline a maximally predictive coarse-graining in which nonlinear dynamics are subsumed into a linear, ensemble evolution to obtain a simple yet accurate model on multiple scales. With this coarse-graining we identify long timescales and collective states in the Langevin dynamics of a double-well potential, the Lorenz system and in worm behavior. We suggest that such an “inverse’’ approach offers an emergent, quantitative framework in which to seek rather than impose effective organizing principles of complex systems.

Physics and the Origin of Life, from Chirality to Membranes

Prof Jack Szostak

Physics and the Origin of Life, from Chirality to Membranes to Information

Physics and the Origin of Life, from Chirality to Membranes to Information

Diverse physical processes played important roles in the origin of life. I will review the origin of molecular homochirality, the growth of protocell membranes, and potential roles for liquid-liquid phase separation. I will then discuss the concept of functional information and its quantitative relationship with molecular function.

Magic numbers in protein phase transitions

Prof Ned Wingreen

Magic numbers in protein phase transitions

Magic numbers in protein phase transitions

Biologists have recently come to appreciate that eukaryotic cells are home to a multiplicity of non-membrane bound compartments, many of which form and dissolve as needed for the cell to function. These dynamical “condensates” enable many central cellular functions – from ribosome assembly, to RNA regulation and storage, to signaling and metabolism. While it is clear that these compartments represent a type of separated phase, what controls their formation, how specific biological components are included or excluded, and how these structures influence physiological and biochemical processes remain largely mysterious. I will discuss recent experiments on phase separated condensates both in vitro and in vivo, and will present theoretical results that highlight a novel “magic number” effect relevant to the formation and control of two-component phase separated condensates.