Past

A growing plant is a fascinating system involving multiple fields. Biologically, it is a multi-cellular system controlled by bio-chemical networks. Physically, it is an example of an "active solid" whose element (cells) are active, performing mechanical work to drive the evolving geometry. Computationally, it is a distributed system, processing a multitude of local inputs into a coordinated developmental response. In this talk I will discuss how plants, a living information-processing organism, uses physical laws and biological mechanisms to alter its own shape, and negotiate its environment. Here I will focus on two examples reflecting the computational and mechanical aspects: (i) probing temporal integration in gravitropic responses reveals plants sum and subtract signals, (ii) the interplay between active growth-driven processes and passive mechanics.

We propose a unified theory of brain function called ‘Thermodynamics of Mind’ which provides a natural, parsimonious way to explain the underlying computational mechanisms. The theory uses tools from non-equilibrium thermodynamics to describe the hierarchical dynamics of brain states over time. Crucially, the theory combines correlative (model-free) measures with causal generative models to provide solid causal inference for the underlying brain mechanisms. The model-based framework is a powerful way to use regional neural dynamics within the hierarchical anatomical brain connectivity to understand the underlying mechanisms for shaping the temporal unfolding of whole-brain dynamics in brain states. As such this model-based framework fitted to empirical data can be exhaustively investigated to provide objectively strong causal evidence of the underlying brain mechanisms orchestrating brain states. 

My talk will have two parts. First, I will tell you how a single cell produces light to survive; then, I will explain how a huddle of chloroplasts in cells form glasses to optimize plant life. Part I: Bioluminescence (light generation in living organisms) has mesmerized humans since thousands of years ago. I will first go over the recent progress in experimental and mathematical biophysics of single-cell bioluminescence (PRL 125 (2), 028102, 2020) and then will go beyond and present a lab-scale experiment and a continuum model of bioluminescent breaking waves. Part II: To remain efficient during photosynthesis, plants can re-arrange the internal structure of cells by the active motion of chloroplasts. I will show that the chloroplasts can behave like a densely packed light-sensitive active matter, whose non-gaussian athermal fluctuations can lead to various self-organization scenarios, including glassy dynamics under dim lights (PNAS 120 (3), 2216497120, 2023). To this end, I will also present a simple model that captures the dynamic of these biological glasses.

Lightweight compliant surfaces are commonly used as roofs (awnings), filtration systems or propulsive appendages, that operate in a fluid environment. Their flexibility allows for shape to change in fluid flows, to better endure harsh or fluctuating conditions, or enhance flight performance of insect wings for example. The way the structure deforms is however key to fulfill its function, prompting the need for control levers. In this talk, we will consider two ways to tailor the deformation of surfaces in a flow, making use of the properties of origami (folded sheet) and kirigami (sheet with a network of cuts). Previous literature showed that the substructure of folds or cuts allows for sophisticated shape morphing, and produces tunable mechanical properties. We will discuss how those original features impact the way the structure interacts with a flow, through combined experiments and theory. We will notably show that a sheet with a symmetric cutting pattern can produce an asymmetric deformation, and study the underlying fluid-structure couplings to further program shape morphing through the cuts arrangement. We will also show that extreme shape reconfiguration through origami folding can cap fluid drag.

My group is developing a roadmap to replace bulky electric motors in miniature robots requiring large mechanical work output.

First, I will describe the mechanics of coiled muscles made by twisting nylon fishing lines, and how these actuators use internal strain energy to achieve a “record breaking” performance. Then I will describe intriguing hierarchical super-, and hyper-coiled artificial muscles which exploit the interplay between nonlinear mechanics and material microstructure. Next, I will describe their use to actuate the dynamic snapping of insect-scale jumping robots. The combination of strong but slow muscles with a fast-snapping beam gives rise to dynamic buckling cascade phenomena leading to effective robotic jumping mechanisms.

These examples shed light on the future of automation propelled by new bioinspired materials, nonlinear mechanics, and unusual manufacturing processes.

Topological data analysis (TDA) comprises a set of techniques of computational topology that has had enormous growth in the last decade, with applications to a wide variety of fields, such as images,  biological data, meteorology, materials science, time-dependent data, economics, etc. In this talk, we will first have a walk through a typical pipeline in TDA, to move later to its adaptation to a specific context: the topological characterization of the spatial distribution of regions in a segmented image

By definition, planktonic organisms drift with the water flows. But these millimetric organisms are not necessarily passive; many can swim and can sense the surrounding flow through mechanosensory hairs. But how useful can be flow sensing in a turbulent environment? To address this question, we show two examples of smart planktonic behavior: (1) we develop a model where plantkters choose a swimming direction as a function of the velocity gradient to "surf on turbulence" and move efficiently upwards; (2) we show how a plankter measuring the velocity gradient may track the position of a swimming target from its hydrodynamic signature. 

Ernst Haeckel, Kunstformen der Natur (1904), Copepoda 

In this presentation, I will discuss the construction and results of numerical simulations quantifying flows around several species of soft corals. In the first project, the flows near the tentacles of xeniid soft corals are quantified for the first time. Their active pulsations are thought to enhance their symbionts' photosynthetic rates by up to an order of magnitude. These polyps are approximately 1 cm in diameter and pulse at frequencies between approximately 0.5 and 1 Hz. As a result, the frequency-based Reynolds number calculated using the tentacle length and pulse frequency is on the order of 10 and rapidly decays as with distance from the polyp. This introduces the question of how these corals minimize the reversibility of the flow and bring in new volumes of fluid during each pulse. We estimate the Péclet number of the bulk flow generated by the coral as being on the order of 100–1000 whereas the flow between the bristles of the tentacles is on the order of 10. This illustrates the importance of advective transport in removing oxygen waste. In the second project, the flows through the elaborate branching structures of gorgonian colonies are considered.  As water moves through the elaborate branches, it is slowed, and recirculation zones can form downstream of the colony. At the smaller scale, individual polyps that emerge from the branches expand their tentacles, further slowing the flow. At the smallest scale, the tentacles are covered in tiny pinnules where exchange occurs. We quantified the gap to diameter ratios for various gorgonians at the scale of the branches, the polyp tentacles and the pinnules. We then used computational fluid dynamics to determine the flow patterns at all three levels of branching. We quantified the leakiness between the branches, tentacles and pinnules over the biologically relevant range of Reynolds numbers and gap-to-diameter ratios, and found that the branches and tentacles can act as either leaky rakes or solid plates depending upon these dimensionless parameters. The pinnules, in contrast, mostly impede the flow. Using an agent-based modeling framework, we quantified plankton capture as a function of the gap-to diameter ratio of the branches and the Reynolds number. We found that the capture rate depends critically on both morphology and Reynolds number. 

Andrea Giudici: Multiple shapes from one elastomer sheet

Active soft materials, such as Liquid Crystal Elastomers (LCEs), possess a unique property: the ability to change shape in response to thermal or optical stimuli. This makes them attractive for various applications, including bioengineering, biomimetics, and soft robotics. The classic example of a shape change in LCEs is the transformation of a flat sheet into a complex curved surface through the imprinting of a spatially varying deformation field. Despite its effectiveness, this approach has one important limitation: once the deformation field is imprinted in the material, it cannot be amended, hindering the ability to achieve multiple target shapes.

In this talk, I present a solution to this challenge and discuss how modulating the degree of actuation using light intensity offers a route towards programming multiple shapes. Moreover, I introduce a theoretical framework that allows us to sculpt any surface of revolution using light.

Edwina Yeo: Modelling the onset of arterial blood clotting

Arterial blood clot formation (thrombosis) is the leading cause of both stroke and heart attack. The blood protein Von Willebrand Factor (VWF) is critical in facilitating arterial thrombosis. At pathologically high shear rates the protein unfolds and rapidly captures platelets from the flow.

I will present two pieces of modelling to predict the location of clot formation in a diseased artery. Firstly a continuum model to describe the mechanosensitive protein VWF and secondly a model for platelet transport and deposition to VWF. We interface this model with in vitro data of thrombosis in a long, thin rectangular microfluidic geometry. Using a reduced model, the unknown model parameters which determine platelet deposition can be calibrated.

We explore the dynamics of a compressible fluid bubble surrounded by an incompressible fluid of infinite extent in three-dimensions, constructing bubble solutions with finite time blowup under this framework when the equation of state relating pressure and volume is soft (e.g., with volume singularities that are locally weaker than that in the Boyle-Mariotte law), resulting in a finite time blowup of the surrounding incompressible fluid, as well. We focus on two families of solutions, corresponding to a soft polytropic process (with the bubble decreasing in size until eventual collapse, resulting in velocity and pressure blowup) and a cavitation equation of state (with the bubble expanding until it reaches a critical cavitation volume, at which pressure blows up to negative infinity, indicating a vacuum). Interestingly, the kinetic energy of these solutions remains bounded up to the finite blowup time, making these solutions more physically plausible than those developing infinite energy. For all cases considered, we construct exact solutions for specific parameter sets, as well as analytical and numerical solutions which show the robustness of the qualitative blowup behaviors for more generic parameter sets. Our approach suggests novel -- and perhaps physical -- routes to the finite time blowup of fluid equations.

Biological systems achieve their complexity by processing and exploiting information stored in molecular copolymers such as DNA, RNA and proteins. Despite the ubiquity and power of this approach in natural systems, our ability to implement similar functionality in synthetic systems is very limited. In this talk, we will first outline a new mathematical framework for analysing general models of colymerisation for infinitely long polymers. For a given model of copolymerisation, this approach allows for the extraction of key quantities such as the sequence distribution, speed of polymerisation and the rate of molecular fuel consumption without resorting to simulation. Subsequently, we will explore mechanisms that allow for reliable copying of the information stored in finite-length template copolymers, before touching on recent experimental work in which these ideas are put into practice.  

This talk will explore a series of topics and example applications at the interface of graph theory and dynamics, from synchronization and diffusion dynamics on networks, to graph-based data clustering, to graph convolutional neural networks. The underlying links are provided by concepts in spectral graph theory.

ife forms have devised impressive and subtle ways to exploit fluid flows. I’ll talk about birds as flying machines whose behaviors can give surprising insights into flow physics. One story explains how flocking interactions can help to bring flapping flyers into orderly formations. A second story involves the more subtle role of aerodynamics in the highly efficient breathing of birds, which is thought to be critical to their ability to fly.

Hypergraphs for multiscale cycles in structured data

Iris Yoon

Understanding the spatial structure of data from complex systems is a challenge of rapidly increasing importance. Even when data is restricted to curves in three-dimensional space, the spatial structure of data provides valuable insight into many scientific disciplines, including finance, neuroscience, ecology, biophysics, and biology. Motivated by concrete examples arising in nature, I will introduce hyperTDA, a topological pipeline for analyzing the structure of spatial curves that combines persistent homology, hypergraph theory, and network science. I will show that the method highlights important segments and structural units of the data. I will demonstrate hyperTDA on both simulated and experimental data. This is joint work with Agnese Barbensi, Christian Degnbol Madsen, Deborah O. Ajayi, Michael Stumpf, and Heather Harrington.

Minmax Connectivity and Persistent Homology 

Ambrose Yim

We give a pipeline for extracting features measuring the connectivity between two points in a porous material. For a material represented by a density field f, we derive persistent homology related features by exploiting the relationship between dimension zero persistent homology of the density field and the min-max connectivity between two points. We measure how the min-max connectivity varies when spurious topological features of the porous material are removed under persistent homology guided topological simplification. Furthermore, we show how dimension one persistent homology encodes a relaxed notion of min-max connectivity, and demonstrate how we can summarise the multiplicity of connections between a pair of points by associating to the pair a sub-diagram of the dimension one persistence diagram.

It has been known for some time that the contact sets between
self-avoiding idealised tubes (i.e. with exactly circular, normal
cross-sections) in various highly compact, tight structures comprise
double lines of contact. I will re-visit those results for two canonical
examples, namely the orthogonal clasp and the ideal trefoil knot. I will
then show experimental and 3D FEM simulation data for deformable elastic
tubes (obtained within the group of Pedro Reis at the EPFL) which
reveals that the ideal contact set lines bound (in a non-rigorous sense)
the actual contact patches that arise in reality.

[1] The shapes of physical trefoil knots, P. Johanns, P. Grandgeorge, C.
Baek, T.G. Sano, J.H. Maddocks, P.M. Reis, Extreme Mechanics Letters 43
(2021), p. 101172, DOI:10.1016/j.eml.2021.101172
[2]  Mechanics of two filaments in tight orthogonal contact, P.
Grandgeorge, C. Baek, H. Singh, P. Johanns, T.G. Sano, A. Flynn, J.H.
Maddocks, and P.M. Reis, Proceedings of the National Academy of Sciences
of the United States of America 118, no. 15 (2021), p. e2021684118
DOI:10.1073/pnas.2021684118

What sets the size and form of living organisms is still, by large, an open question. During this talk, I will illustrate how we are addressing this question by examining the links between spatial scales, from subcellular to organ, both experimentally and theoretically. First, I will present how we are deriving continuous plant growth mechanical models using homogenisation. Second, I will discuss how directionality of organ growth emerges from cell level. Last, I will present predictions of fluctuations at multiple scales and experimental tests of these predictions, by developing a data analysis approach that is broadly relevant to geometrically disordered materials.

The applied, numerical and asymptotic analysis of acoustic, electromagnetic and elastic scattering by smooth scatterers (e.g. a cylinder or a sphere) is a classical topic in applied mathematics. However, many real-world applications involve highly non-smooth scatterers with geometric structure on multiple length scales. Examples include acoustic scattering by trees and other vegetation in the modelling of urban noise propagation, electromagnetic scattering by snowflakes and ice crystal aggregates in climate modelling and weather prediction, and elastic scattering by cracks and other interfaces in seismic imaging and hydrocarbon exploration. In such situations it may be more appropriate to model the scatterer not by a smooth surface but by a fractal, a geometric object with self-similarity properties and detail on every length scale. Well-known examples include the Cantor set, Sierpinski triangle and the Koch snowflake. In this talk I will give an overview of our recent research into acoustic scattering by such fractal structures. So far our work has focussed on establishing well-posedness of the scattering problem and integral equation reformulations of it, and developing and analysing numerical methods for obtaining approximate solutions. However, there remain interesting open questions about the high frequency (short wavelength) asymptotic behaviour of solutions, and whether the self-similarity of the scatterer can be exploited to derive more efficient approximation techniques.

Many microorganisms must navigate strange biological environments whose physics are unique and counter-intuitive, with wide-ranging consequences for evolutionary biology and human health. Mucus, for instance, behaves like both a fluid and an elastic solid. This can affect locomotion dramatically, which can be highly beneficial (e.g. for mammalian spermatozoa swimming through cervical fluid) or extremely problematic (e.g. the Lyme disease spirochete B. burgdorferi swimming through the extracellular matrix of human skin). Mathematical modeling and numerical simulations continue to provide new fundamental insights about the biological world in and around us and point toward new possibilities in biomedical engineering. These complex fluid phenomena can either enhance or retard a microorganism's swimming speed, and can even change the direction of swimming, depending on the body geometry and the properties of the fluid. We will discuss analytical and numerical insights into swimming through model viscoelastic (Oldroyd-B) and liquid-crystalline (Ericksen-Leslie) fluids, with a special focus on the important and in some cases dominant roles played by the presence of nearby boundaries.

In this talk I will discuss our recent work on two problems. The first problem concerns with capillary rise between rough structures, a fundamental wetting phenomenon that is functionalised in biological organisms and prevalent in geological or man-made materials. Predicting the liquid rise height is more complex than currently considered in the literature because it is necessary to couple two wetting phenomena: capillary rise and hemiwicking. Experiments, simulations and analytic theory demonstrate how this coupling challenges our conventional understanding and intuitions of wetting and roughness. For example, the critical contact angle for hemiwicking becomes separation-dependent so that hemiwicking can vanish for even highly wetting liquids. The rise heights for perfectly wetting liquids can also be different in smooth and rough systems. The second problem concerns with droplets (or condensates) formed via a liquid-liquid phase separation process in biological cells. Despite the widespread importance of surface tension for the interactions between these droplets and other cellular components, there is currently no reliable technique for their measurement in live cells. To address this, we develop a high-throughput flicker spectroscopy technique. Applying it to a class of cellular droplets known as stress granules, we find their interface fluctuations cannot be described by surface tension alone. It is necessary to consider elastic bending deformation and a non-spherical base shape, suggesting that stress granules are viscoelastic droplets with a structured interface, rather than simple Newtonian liquids. Moreover, given the broad distributions of surface tension and bending rigidity observed, different types of stress granules can only be differentiated via large-scale surveys, which was not possible previously and our technique now enables.

We present a framework to generate and evaluate thematic recommendations based on multilayer network representations of knowledge graphs (KGs).  We represent the relative importance of different types of connections (e.g., Directing/acting) with an intuitive salience matrix that can be learnt from data, tuned to incorporate domain knowledge, address different use cases, or respect business logic. We apply an adaptation of the personalised PageRank algorithm to multilayer network models of KGs to generate item-item recommendations. These recommendations reflect the knowledge we hold about the content, and are suitable for thematic or cold-start settings.

Evaluating thematic recommendations from user data presents unique challenges. Our method only recommends items that are 'thematically' related; that is, easily reachable following connections in the KG. We develop a variant of the widely-used Normalised Discounted Cumulative Gain (NDCG) to evaluate recommendations based on user-item ratings, respecting their thematic nature.

We apply our methods to a KG of the movie industry and MovieLens ratings and in an internal AB test. We learn the salience matrix and demonstrate that our approach outperforms existing thematic recommendation methods and is competitive with collaborative filtering approaches.

Numerous applications in geometric, visual, and scientific computing rely on the ability to nicely distribute points in space according to a repulsive potential.  In contrast, there has been relatively little work on equidistribution of higher-dimensional geometry like curves and surfaces—which in many contexts must not pass through themselves or each other.  This talk explores methods for optimization of curve and surface geometry while avoiding (self-)collision. The starting point is the tangent-point energy of Buck & Orloff, which penalizes pairs of points that are close in space but distant with respect to geodesic distance. We develop a discretization of this energy, and introduce a novel preconditioning scheme based on a fractional Sobolev inner product.  We further accelerate this scheme via hierarchical approximation, and describe how to incorporate into a constrained optimization framework. Finally, we explore how this machinery can be applied to problems in mathematical visualization, geometric modeling, and geometry processing.

Consider the injection of a fluid onto an impermeable surface for an infinite length of time... Does the injected fluid reach a finite height, or does it keep on growing forever? The classical theory of gravity currents suggests that the height remains finite, causing the radius to grow outwards like the square root of time. When the fluid resides within a porous medium, the same is thought to be true. However, recently I used some small scale experiments and numerical simulations, spanning 12 orders of magnitude in dimensionless time, to demonstrate that the height actually grows very slowly, at a rate ~t^(1/7)*(log(t))^(1/2). This strange behaviour can be explained by analysing the flow in a narrow "inner region" close to the source, in which there are significant vertical velocities and non-hydrostatic pressures. Analytical scalings are derived which match closely with both numerics and experiments, suggesting that the blob of fluid is in fact ever-growing, and therefore becomes unbounded with time.