Periodic patterns in environmental light, physiology and behaviour: Measurement, modelling and evaluation of diurnal and circadian phenomena in biology

18 and 19 November, 
Virtual meeting via Zoom

​Organised by: Manuel Spitschan, Ben Lambert, Helen Byrne (University of Oxford) and Nayantara Santhi (Northumbria University)

​Overview

Temporal organization is a fundamental aspect of biology that acts on multiple time scales and is orchestrated by complex interactions between internal clock mechanisms and external factors. Circadian rhythmicity is ubiquitous and tightly bound to the 24h solar day. In mammals, circadian rhythms are generated by a set of core ‘clock’ genes and synchronised by neural and endocrine pathways originating from a master clock (the suprachiasmatic nucleus), located in the hypothalamus. The master clock sets internal time using temporal cues or ‘zeitgebers’, which are external stimuli such as patterns of light and darkness given by solar radiation and, more recently, artificial illumination. One of the most observable consequences of circadian organisation is the sleep-wake cycle, which delineates periods of sleep from periods of wakefulness. Traditionally, laboratory studies have been used to examine circadian rhythms including the sleep-wake cycle, but the field is now increasingly using wearable technology to design ‘real world’ studies. 

Currently, the approach that is most widely used to collect “outside laboratory” data is actigraphy: continuous measurements of wrist or ankle movement during a 24h period, as a proxy for the diurnal ‘rest-activity’ or ‘sleep-wake’ cycle. Techniques to extract circadian rhythmicity from these data are still at an early stage of development. In this workshop, we will focus on the interface between circadian biology, physics and mathematical modelling and explore novel ways of describing this periodic phenomenon.

Who should attend?

The workshop is designed to be accessible to academics from a wide range of disciplines and career stages, with a specific aim being to encourage an “outsider” perspective on circadian data. The goal of the workshop is to integrate knowledge from physics, mathematical modelling and human circadian biology in novel and innovative ways.

Format

The workshop, which will be held between 10 am and 4 pm across two days, will focus the following themes:

Theme 1: Non-visual effects of light: from physics to physiology
In addition to vision, light affects human physiology and behaviour via the pathway that connects melanopsin-containing retinal ganglion eye cells with the circadian clock in the brain. To examine processing of light by the circadian clock, different aspects of light such as its intensity, duration and spectral composition are manipulated and the consequent impact on physiology studied. The goal of this session is to bring together physicists, optical engineers working on sculpting and crafting light, and  circadian biologists to better characterise the non-visual effects of light on physiology and behaviour.

​Theme 2: Modelling periodic phenomena in circadian biology
At present, large amounts of data are generated using actigraphy. However, a variety of analyses are used to extract circadian rhythmicity from these data, including parametric and non-parametric techniques. Increasingly, algorithms are being applied to actigraphy data to distinguish ‘rest-activity’ classifications and ‘sleep-wake ‘classifications, the latter with varying degrees of success. The goal of this session is to explore the analysis of biological rest-activity data through the lens of a physicist and to develop a shared understanding of the best practices for data analysis.

Audience engagement 

​Poster session: We will invite attendees to submit posters for presentation during virtual poster sessions, in which each presenter gets 5 minutes to present their poster.
 
Data challenge and contest: In advance of the meeting, we will distribute an actigraphy data set to teams of registrees. The data set will already be publicly available or be made available on a public GitHub repository. Workshop participants will be invited to analyse this data set and specifically to derive novel and interpretable metrics that describe it. There will be no restrictions on how the data set can be analysed, but possible questions/analytic directions will be distributed as part of the announcement and invitation. Participants will be able to opt into the data challenge and contest at registration and will, at a later stage, confirm that they can present their results in a special session on Day 1 of the workshop. An independent jury comprised of five people will then judge the contributions of the contestants. There will be two specific categories: “Most innovative visualisation” and “Most innovative analysis”. The winner in each category will receive a £200 prize (voucher), and the runners-up will receive £100 each in each category. The rules of the participation will be written in advance; one of the key features is that analysis scripts will have to be made available under an open-source license to qualify.
 
“Bring your data" brainstorming and hackathon: We will invite participants (from a circadian biology background) to put forward a selected data set that they have collected which they are uncertain of how best to analyse. Attendees will then sign up for brainstorming sessions in which novel ideas of data analysis will be discussed. In small groups, participants will work together to analyse the data using Zoom breakout rooms.
 
Understanding research culture participatory workshop: In a participatory workshop, we will explore structures, mechanisms and barriers to collaboration. In many ways, physics is much more advanced in collaborative and open science practices than, e.g. neuroscience. For example, posting preprints and large-scale collaborations are much more common and have a much longer history than in biomedical research. We want to understand factors that might hinder cross-disciplinary research in a participatory workshop. This could be facilitated, e.g., by the interactive platform Mentimeter.

Programme

Day 1	Wednesday 10 April
13.00	​Registration
Session 1	Noise Driven Systems
14.00	Stefano Bo, Can microscopic system exploit noise? The case of driven anisotropic diffusion at boundaries
14.30	Grant Rotskoff, Nonequilibrium importance sampling with a driven dynamics
15.00	Alexandre Lazarescu, Large deviations and dynamical phase transitions in stochastic chemical networks
15.30	​​Break
Session 2	Active Polymers
16.00	Tom Ouldridge, Biological copying of polymers: a necessarily non-equilibrium process​
16.30	Aleksandre Japaridze, The role of spatial confinement in DNA organization: From single molecules to bacterial chromosomes
17.00	Luca Tubiana, Title TBC
17.30	Jan Smrek, Active-passive polymer mixtures in relation to chromatin conformation and dynamics​
Day Two	Thursday ​11 April
Session 3	Topology
9.30	Lucia Coronel, Dynamics of supercoiled knotted DNA: large-scale rearrangements and persistent multi-strand interlocking
10.00	​Amin Doostmohammadi, Active Thin Structures
10.30	Dan Pearce, Controlling active matter with curvature and topology ​
11.00	Break
Session 4	​​Rheology
11.30	​​Nicoletta  Gnan,The microscopic role of deformation in the dynamics of soft colloids
12.00	​Jan Meibohm, Catastrophes and Large deviations in turbulent aerosols
12.30	Romain Mari, Dynamic vorticity banding in discontinuously shear thickening suspensions ​
13.00	​Lunch
​Session 5	​​Slow Relaxation
14.00	Beatriz Seoane, Spin-glass-like dynamics in highly compressed colloidal and granular glasses
14.30	​​Misaki  Ozawa, Numerical Investigation of Ideal Glass Transition in Glass-Forming Liquids
15.00	Elisabeth Agoritsas, Out-of-equilibrium dynamics of particle systems in infinite dimension
15.30	​​Francesco Turci, Structural-dynamical correlations and rigid response
16.00-17.30	Poster Session/Social Event​
Day Three	Friday 12 April
​Session 6 ​	​Swimmers​
9.30	​Raphael Jeanneret, Pairing in planktonic elongated diatoms, or how synchronized-sinking favors cell encounter for sexual reproduction​
10.00	​Fanlong Meng, Magnetic swimmers in a microfluidic channel​
10.30	​​​Joakim Stenhammar, Correlations and collective behaviours in suspensions of swimming microorganisms
11.00	​​Break ​
Session 7	​Physics of Motion​
​11.30	Kirsty Wan, Non-equilibrium and critical behaviour in biological microswimmers​
12.00	Demian Levis, Activity induced synchronization in chiral active matter
12.30	Ariana Bottinelli, Predicting collective motion in high-density crowds ​
13.00	​Lunch
Session 8	​Tissues and Biofilms​
14.00	​Diana  Khoromskaia, Active surface models for cell and tissue morphogenesis
14.30	​Ananyo Maitra, Unusual stability of oriented active suspensions on substrates
​15.00	Silke Henkes, Universal motion patterns in confluent cell monolayers​
15.30-17.30	​​Poster Session/Social Event
Day Four	​Saturday 13 April
Session 9	Ecology and Evolution​
9.30	Andrea Giometto, Mechanical interactions reduce the power of natural selection in growing yeast colonies
10.00	​Hye Jin Park, Population size and interaction structure driven by mutant interactors​
​10.30	​Matthieu Barbier, Are complex ecosystems ever simple? Disorder in competition experiments
11.00	​Break ​
Session 10	​Inference and Optimisation
11.30	​​Barbara Bravi, Characterizing and inferring epistasis via direct evolutionary couplings in models of allostery
12.00	​Caterina De Bacco, A physical model for efficient ranking in networks
	​​Silvia Zaoli, Trip Centrality: walking on a temporal multiplex with non-instantaneous link travel time
13.00	​Workshop Close

​Registration 

Please complete the registration in order to insure your place for the Workshop. Please note that there is a registration fee of £10, contributing to the cost of lunch and refreshments during the breaks. Accommodation for this event should be arranged separately. Please note, there are limited spaces available for this event. Registration will close as soon as capacity has been reached. For any enquiries relating to this event, please email: k.h.baker@dur.ac.uk.