Past Industrial and Applied Mathematics Seminar

Capillary forces acting at the surface of a liquid drop can be strong enough to deform small objects and recent studies have provided several examples of elastic instabilities induced by surface tension. Inspired by the windlass mechanism in spider webs, we present a system where a liquid drop sits on a straight fiber and attracts the fiber which thereby coils inside the drop. We then introduce a 2D extension of the mechanism and build a membrane that can extend/contract by a factor of 20.

In order for artificial neural networks to learn a task, one must solve an inverse design problem. What network will produce the desired output? We have harnessed AI approaches to design physical systems to perform functions inspired by biology, such as protein allostery. But artificial neural networks require a computer in order to learn in top-down fashion by the global process of gradient descent on a cost function. By contrast, the brain learns by local rules on its own, with each neuron adjusting itself and its synapses without knowing what all the other neurons are doing, and without the aid of an external computer. But the brain is not the only biological system that learns by local rules; I will argue that the actin cortex and the amnioserosa during the dorsal closure stage of Drosophila development can also be viewed this way.

The key role of physical and mechanical interactions in cancer emerges from a very large variety of data sources and methods - from genomics to bioimaging, from proteomics to clinical records. Thus, learning physics-driven relational information is crucial to characterize its progression at different scales.

In this talk I will discuss how mathematical and computational tools allow for learning  and better understanding of  the mechano-biology of cancer,  thanks to the integration of  patient-specific data and physics-based models. I will present a few applications developed in the last decade in which the development of  digital twins,  empowered by ad-hoc learning tools,  allows us to test new hypotheses,  to assess the model predictions against biological and clinical data, and to aid decision-making in a clinical setting.

Funding from MUR - PRIN 2020, Progetto di Eccellenza 2023-2027 and Regione Lombardia (NEWMED Grant, ID: 117599, POR FESR 2014-2020) is gratefully acknowledged.

We formulate and solve a generalized inverse Navier–Stokes boundary value problem for velocity field reconstruction and simultaneous boundary segmentation of noisy Flow-MRI velocity images. We use a Bayesian framework that combines CFD, Gaussian processes, adjoint methods, and shape optimization in a unified and rigorous manner.
With this framework, we find the velocity field and flow boundaries (i.e. the digital twin) that are most likely to have produced a given noisy image. We also calculate the posterior covariances of the unknown parameters and thereby deduce the uncertainty in the reconstructed flow. First, we verify this method on synthetic noisy images of flows. Then we apply it to experimental phase contrast magnetic resonance (PC-MRI) images of an axisymmetric flow at low and high SNRs. We show that this method successfully reconstructs and segments the low SNR images, producing noiseless velocity fields that match the high SNR images, using 30 times less data.
This framework also provides additional flow information, such as the pressure field and wall shear stress, accurately and with known error bounds. We demonstrate this further on a 3-D in-vitro flow through a 3D-printed aorta and 3-D in-vivo flow through a carotid artery.

The classical model of evaporation of liquids hinges on Maxwell’s assumption that the air near the liquid’s surface is saturated. It allows one to find the evaporative flux without considering the interface separating liquid and air. Maxwell’s hypothesis is based on an implicit assumption that the vapour-emission capacity of the interface exceeds the throughput of air (i.e., its ability to pass the vapour on to infinity). If indeed so, the air adjacent to the liquid would get quickly saturated, justifying Maxwell’s hypothesis.

In the present paper, the so-called diffuse-interface model is used to account for the interfacial physics and, thus, derive a generalised version of Maxwell’s boundary condition for the near-interface vapour density. It is then applied to a spherical drop floating in air. It turns out that the vapour-emission capacity of the interface exceeds the throughput of air only if the drop’s radius is r_d ≳ 10μm, but for r_d ≈ 2μm, the two are comparable. For r_d ≲ 1μm, evaporation is interface-driven, and the resulting evaporation rate is noticeably smaller than that predicted by the classical model.

Over the years, I've often taught a first course in asymptotics and perturbation methods, even though I don't know much about the subject. In this talk, I'll discuss a textbook example of a singularly perturbed nonlinear boundary-value problem that has revealed delightful new surprises, every time I teach it. These include a pitchfork bifurcation in the number of solutions as one varies the small parameter, and transcendentally small terms in the solutions' initial conditions that can be calculated by elementary means.

I’m excited to share with everyone some new, unpublished work that we are just in the process of wrapping up and could use everyone’s reactions. It is a reconciliation of evolutionary game theory and ecological dynamics that I have wrestled with since I moved from an evolution program into an ecology-heavy department. It always seemed like, depending on the problem I was thinking about, I had to change my perspective and approach it as either an evolutionary game theorist, or an ecologist; and yet I had this nagging feeling that, at its core, the problem was often one and the same, and therefore one theoretical framework should suffice. So when should one write down an n-type replicator equation and when should one write down an n-species Lotka-Volterra system; and what does it mean mathematically and biologically when one has made such a choice? In the process of reconciling, I also got a deeper appreciation of what is and is not a proper game, such as a Prisoner’s Dilemma. These findings can help shed light on previously puzzling empirical findings.

Metal forming involves permanently deforming metal into a required shape.  Many forms of metal forming are used in industry: rolling, stamping, pressing, drawing, etc; for example, 99% of steel produced globally is first rolled before any subsequent processing.  Most theoretical studies of metal forming use Finite Elements, which is not fast enough for real-time control of metal forming processes, and gives little extra insight.  As an example of how little is known, it is currently unknown whether a sheet of metal that is squashed between a large and a small roller should curve towards the larger roller, or towards the smaller roller.  In this talk, I will give a brief overview of metal forming, and then some progress my group have been making on some very simplified models of cold sheet rolling in particular.  The mathematics involved will include some modelling and asymptotics, multiple scales, and possibly a matrix Wiener-Hopf problem if time permits.

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.

It is well known that stochasticity can play a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be adequately modeled by Markov processes and, for such systems, methods such as Gillespie’s algorithm are typically employed. While such schemes are easy to implement and are exact, the computational cost of simulating such systems can become prohibitive as the frequency of the reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation for systems where all reactants are present in large concentrations, the approximation breaks down when the fast chemical species exist in small concentrations, giving rise to significant errors in the simulation. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as computing observables of cell cycle models. In this talk, we present a hybrid scheme for simulating well-mixed stochastic kinetics, using Gillespie–type dynamics to simulate the network in regions of low reactant concentration, and chemical Langevin dynamics when the concentrations of all species are large. These two regimes are coupled via an intermediate region in which a “blended” jump-diffusion model is introduced. Examples of gene regulatory networks involving reactions occurring at multiple scales, as well as a cell-cycle model are simulated, using the exact and hybrid scheme, and compared, both in terms of weak error, as well as computational cost. If there is time, we will also discuss the extension of these methods for simulating spatial reaction kinetics models, blending together partial differential equation with compartment based approaches, as well as compartment based approaches with individual particle models.

This is joint work with Andrew Duncan (Imperial), Radek Erban (Oxford), Kit Yates (Bath), Adam George (Bath), Cameron Smith (Bath), Armand Jordana (New York )

Bacteria represent the major component of the world’s biomass. A number of these bacteria are motile and swim with the use of flagellar filaments, which are slender helical appendages attached to a cell body by a flexible hook. Low Reynolds number hydrodynamics is the key for flagella to generate propulsion at a microscale [1]. In this talk I will discuss two projects related to swimming of a model bacterium Escherichia coli (E. coli).

E. coli has many flagellar filaments that are wrapped in a bundle and rotate in a counterclockwise fashion (if viewed from behind the cell) during the so-called ‘runs’, wherein the cell moves steadily forward. In between runs, the cell undergoes quick ‘tumble’ events, during which at least one flagellum reverses its rotation direction and separates from the bundle, resulting in erratic motion in place. Alternating between runs and tumbles allows cells to sample space by stochastically changing their propulsion direction after each tumble. In the first part of the talk, I will discuss how cells reorient during tumble and the mechanical forces at play and show the predominant role of hydrodynamics in setting the reorientation angle [2].

In the second part, I will talk about hydrodynamics of bacteria near walls in visco-elastic fluids. Flagellar motility next to surfaces in such fluids is crucial for bacterial transport and biofilm formation. In Newtonian fluids, bacteria are known to accumulate near walls where they swim in circles [3,4], while experimental results from our collaborators at the Wu Lab (Chinese University of Hong Kong) show that in polymeric liquids this accumulation is significantly reduced. We use a combination of analytical and numerical models to propose that this reduction is due to a viscoelastic lift directed away from the plane wall induced by flagellar rotation. This viscoelastic lift force weakens hydrodynamic interaction between flagellated swimmers and nearby surfaces, which results in a decrease in surface accumulation for the cells. 

References

[1] Lauga, Eric. "Bacterial hydrodynamics." Annual Review of Fluid Mechanics 48 (2016): 105-130.

[2] Dvoriashyna, Mariia, and Eric Lauga. "Hydrodynamics and direction change of tumbling bacteria." Plos one 16.7 (2021): e0254551.

[3] Berke, Allison P., et al. "Hydrodynamic attraction of swimming microorganisms by surfaces." Physical Review Letters 101.3 (2008): 038102.

[4] Lauga, Eric, et al. "Swimming in circles: motion of bacteria near solid boundaries." Biophysical journal 90.2 (2006): 400-412.

Macroscopic Transport in Heterogeneous Porous Materials

Lucy Auton

Solute transport in porous materials is a key physical process in a wide variety of situations, including contaminant transport, filtration, lithium-ion batteries, hydrogeological systems, biofilms, bones and soils. Despite the prevalence of solute transport in porous materials, the effect of microstructure on flow and transport remains poorly understood and improving our understanding of this remains a major challenge.  In this presentation, I consider a two-dimensional microstructure comprising an array of obstacles of smooth but arbitrary shape, the size and spacing of which can vary along the length of the porous medium, allowing for anisotropy.  I use a nontrivial extension to classical homogenisation theory via the method of multiple scales to rigorously upscale the novel problem involving cells of varying area. This results in simple effective continuum equations for macroscale flow and transport where the effect of the microscale geometry on the macroscopic transport and removal is encoded within these simple macroscale equations via effective parameters such as an effective local anisotropic diffusivity and an effective local adsorption rate.  For a simple example geometry I exploit the two degrees of microstructural freedom in this problem, obstacle size and obstacle spacing, to investigate scenarios of uniform porosity but heterogenous microstructure, noting the impact this heterogeneity has on filter efficiency. 

This model constitutes the development of the core framework required to consider other crucial problems such as solute transport within soft porous materials for which there does not currently exist a simple macroscale model where the effective diffusivity and removal depend on the microstructure. Further, via this methodology I will  derive a  bespoke model for fluoride and arsenic removal filters. With this model I will be able to optimise the design of fluoride-removal filters which are being deployed across rural India. The design optimisation will both increase filter lifespan and reduce filter cost, enabling more people to access safe drinking water

Averaged interface conditions: evaporation fronts in porous media

Ellen Luckins

Homogenisation methods are powerful tools for deriving effective PDE models for processes incorporating multiple length-scales. For physical systems in which interface processes are crucial to the overall system, we might ask how the microstructure impacts the effective interface conditions, in addition to the PDEs in the bulk. In this talk we derive an effective model for the motion of an evaporation front through porous media, combining homogenisation and boundary layer analysis to derive averaged interface conditions at the evaporation front. Our analysis results in a new effective parameter in the boundary conditions, which encodes how the shape and speed of the porescale evaporating interfaces impact the overall drying process.

Latent Dirichlet Allocation (LDA) is capable of analyzing thousands of documents in a short time and highlighting important elements, recurrences and anomalies. It is generally used in linguistics to study natural language: its word analysis reveals the theme(s) of a document, each theme being identified by a specific vocabulary or, more precisely, by a particular statistical distribution of word frequency.
In the climatologists' use of LDA, the document is a daily weather map and the word is a pixel of the map. The theme with its corpus of words can become a cyclone or an anticyclone and, more generally, a 'pattern'  that the scientists term motif. Artificial intelligence – a sort of incredibly fast robot meteorologist – looks for correlations both between different places on the same map, and between successive maps over time. In a sense, it 'notices' that a particular location is often correlated with another location, recurrently throughout the database, and this set of correlated locations constitutes a specific pattern.
The algorithm performs statistical analyses at two distinct levels: at the word or pixel level of the map, LDA defines a motif, by assigning a certain weight to each pixel, and thus defines the shape and position of the motif;  LDA breaks down a daily weather map into all these motifs, each of which is assigned a certain weight.
In concrete terms, the basic data are the daily weather maps between 1948 and nowadays over the North Atlantic basin and Europe. LDA identifies a dozen or so spatially defined motifs, many of which are familiar meteorological patterns such as the Azores High, the Genoa Low or even the Scandinavian Blocking. A small combination of those motifs can then be used to describe all the maps. These motifs and the statistical analyses associated with them allow researchers to study weather phenomena such as extreme events, as well as longer-term climate trends, and possibly to understand their mechanisms in order to better predict them in the future.

The preprint of the study is available as:
 Lucas Fery, Berengere Dubrulle, Berengere Podvin, Flavio Pons, Davide Faranda. Learning a weather dictionary of atmospheric patterns using Latent Dirichlet Allocation. 2021. ⟨hal-03258523⟩ https://hal-enpc.archives-ouvertes.fr/X-DEP-MECA/hal-03258523v1
 

Statics and dynamics of droplets on lubricated surfaces

Zhaohe Dai

The abstract is "Slippery liquid infused porous surfaces are formed by coating surface with a thin layer of oil lubricant. This thin layer prevents other droplets from reaching the solid surface and allows such deposited droplets to move with ultra-low friction, leading to a range of applications. In this talk, we will discuss the static and dynamic behaviour of droplets placed on lubricated surfaces. We will show that the layer thickness and the size of the substrate are key parameters in determining the final equilibrium. However, the evolution towards the equilibrium is extremely slow (on the order of days for typical experimental parameter values). As a result, we suggest that most previous experiments with oil films lubricating smooth substrates are likely to have been in an evolving, albeit slowly evolving, transient state.

Modeling and Design Optimization for Pleated Membrane Filters

Yixuan Sun

Membrane filtration is widely used in many applications, ranging from industrial processes to everyday living activities. With growing interest from both industrial and academic sectors in understanding the various types of filtration processes in use, and in improving filter performance, the past few decades have seen significant research activity in this area. Experimental studies can be very valuable, but are expensive and time-consuming, therefore theoretical studies offer potential as a cost-effective and predictive way to improve on current filter designs. In this work, mathematical models, derived from first principles and simplified using asymptotic analysis, are proposed for pleated membrane filters, where the macroscale flow problem of Darcy flow through a pleated porous medium is coupled to the microscale fouling problem of particle transport and deposition within individual pores of the membrane. Asymptotically-simplified models are used to describe and evaluate the membrane performance numerically and filter design optimization problems are formulated and solved for industrially-relevant scenarios. This study demonstrates the potential of such modeling to guide industrial membrane filter design for a range of applications involving purification and separation.

Motivated by the desire to automate classification of neuron morphologies, we designed a topological signature, the Topological Morphology Descriptor (TMD),  that assigns a so-called “barcode" to any geometric tree (i.e, any finite binary tree embedded in R^3). We showed that the TMD effectively determines  reliable clusterings of random and neuronal trees. Moreover, using the TMD we performed an objective, stable classification of pyramidal cells in the rat neocortex, based only on the shape of their dendrites.

We have also reverse-engineered the TMD, in order to digitally synthesize dendrites, to compensate for the relatively small number of available biological reconstructions. The algorithm we developed, called Topological Neuron Synthesis (TNS), stochastically generates a geometric tree from a barcode, in a biologically grounded manner. The synthesized neurons are statistically indistinguishable from real neurons of the same type, in terms of morpho-electrical properties and  connectivity. We synthesized networks of structurally altered neurons, revealing principles linking branching properties to the structure of large-scale networks.  We have also successfully applied these classification and synthesis techniques to microglia and astrocytes, two other types of cells that populate the brain.

In this talk I will provide an overview of the TMD and the TNS and then describe the results of our theoretical and computational analysis of their behavior and properties.

This talk is based on work in collaborations led by Lida Kanari at the Blue Brain Project.

This is a preparatory study for our ultimate goal of understanding the various instabilities associated with an electrodes-coated dielectric membrane that is subject to mechanical stretching and electric loading. Leaving out electric loading for the moment, we consider bifurcations from the homogeneous solution of a circular or square hyperelastic sheet that is subjected to equibiaxial stretching under either force- or displacement-controlled edge conditions. We derive the condition for axisymmetric necking and show, for the class of strain-energy functions considered, that the critical stretch for necking is greater than the critical stretch for the Treloar-Kearsley (TK) instability and less than the critical stretch for the limiting-point instability. Abaqus simulations are conducted to verify the bifurcation conditions and the expectation that the TK instability should occur first under force control, but when the edge displacement is controlled the TK instability is suppressed, and it is the necking instability that will be observed. It is also demonstrated that axisymmetric necking follows a growth/propagation process typical of all such localization problems.

Connectivity and percolation are two well studied phenomena in random graphs. 

In this talk we will discuss higher-dimensional analogues of connectivity and percolation that occur in random simplicial complexes.

Simplicial complexes are a natural generalization of graphs that consist of vertices, edges, triangles, tetrahedra, and higher dimensional simplexes.

We will mainly focus on random geometric complexes. These complexes are generated by taking the vertices to be a random point process, and adding simplexes according to their geometric configuration.

Our generalized notions of connectivity and percolation use the language of homology - an algebraic-topological structure representing cycles of different dimensions.

In this talk we will discuss recent results analyzing phase transitions related to these topological phenomena. 

The placenta is the essential organ of maternal-fetal interactions, where nutrient, oxygen, and waste exchange occur. In recent studies, differences in the morphology of the placental chorionic surface vascular network (PCSVN) have been associated with developmental disorders such as autism. This suggests that the PCSVN could potentially serve as a biomarker for the early diagnosis and treatment of autism. Studying PCSVN features in large cohorts requires a reliable and automated mechanism to extract the vascular networks. In this talk, we present a method for PCSVN extraction. Our algorithm builds upon a directional multiscale mathematical framework based on a combination of shearlets and Laplacian eigenmaps and can isolate vessels with high success in high-contrast images such as those produced in CT scans. 

The experimental evidence of the existence of a feedback between growth and stress in tumors poses challenging questions. First, the rheological properties (the constitutive equations) of aggregates of malignant cells are to identified. Secondly, the feedback law (the "growth law") that relates stress and mitotic and apoptotic rate should be understood. We address these questions on the basis of a theoretical analysis of in vitro experiments that involve the growth of tumor spheroids. We show that solid tumors exhibit several mechanical features of a poroelastic material, where the cellular component behaves like an elastic solid. When the solid component of the spheroid is loaded at the boundary, the cellular aggregate grows up to an asymptotic volume that depends on the exerted compression.
Residual stress shows up when solid tumors are radially cut, highlighting a peculiar tensional pattern.
The features of the mechanobiological system can be explained in terms of a feedback of mechanics on the cell proliferation rate as modulated by the availability of nutrient, that is radially damped by the balance between diffusion and consumption. The volumetric growth profiles and the pattern of residual stress can be theoretically reproduced assuming a dependence of the target stress on the concentration of nutrient which is specific of the malignant tissue.

Symmetrically Colored Gaussian Graphical Models with Toric Vanishing Ideals

Jane Coons

Gaussian graphical models are multivariate Gaussian statistical models in which a graph encodes conditional independence relations among the random variables. Adding colors to this graph allows us to describe situations where some entries in the concentration matrices in the model are assumed to be equal. In this talk, we focus on RCOP models, in which this coloring is obtained from the orbits of a subgroup of the automorphism group of the underlying graph. We show that when the underlying block graph is a one-clique-sum of complete graphs, the Zariski closure of the set of concentration matrices of an RCOP model on this graph is a toric variety. We also give a Markov basis for the vanishing ideal of this variety in these cases.

Topological persistence for multi-scale terrain profiling and feature detection in drylands hydrology

Gillian Grindstaff

With the growing availability of remote sensing products and computational resources, an increasing amount of landscape data is available, and with it, increasing demand for automated feature detection and useful morphological summaries. Topological data analysis, and in particular, persistent homology, has been applied successfully to detect landslides and characterize soil pores, but its application to hydrology is currently still limited. We demonstrate how persistent homology of a real-valued function on a two-dimensional domain can be used to summarize critical points and shape in a landscape simultaneously across all scales, and how that data can be used to automatically detect features of hydrological interest, such as: experimental conditions in a rainfall simulator, boundary conditions of landscape evolution models, and earthen berms and stock ponds, placed historically to alter natural runoff patterns in the American southwest.

 In this talk, we show some recent results related to the study of mechanical instabilities in slender structures. First, we propose a model of metamaterial sheets inspired by the pellicle of Euglenids, unicellular organisms capable of swimming due to their ability of changing their shape. These structures are composed of interlocking elastic rods which can freely slide along their edges. We characterize the kinematics and the mechanics of these structures using the special Cosserat theory of rods and by assuming axisymmetric deformations of the tubular assembly. We also characterize the mechanics of a single elastic beam constrained to smoothly slide along a rigid support, where the distance between the rod midline and the constraint is fixed and finite. In the presence of a straight support, the rod can deform into shapes exhibiting helices and perversions, namely transition zones connecting together two helices with opposite chirality.

Finally, we develop a mathematical model of damaged axons based on the theory of continuum mechanics and nonlinear elasticity. In several pathological conditions, such as coronavirus infections, multiple sclerosis, Alzheimer's and Parkinson's diseases, the physiological shape of axons is altered and a periodic sequence of bulges appears. The axon is described as a cylinder composed of an inner passive part, called axoplasm, and an outer active cortex, composed mainly of F-actin and able to contract thanks to myosin-II motors. Through a linear stability analysis, we show that, as the shear modulus of the axoplasm diminishes due to the disruption of the cytoskeleton, the active contraction of the cortex makes the cylindrical configuration unstable to axisymmetric perturbations, leading to a beading pattern.

The complexity of biological systems necessitates that we develop mathematical models to further our understanding of these systems. Mathematical models of these systems are generally based on heterogeneous sets of experimental data, resulting in a seemingly heterogeneous collection of models that ostensibly represent the same system. To understand the system, and to reveal underlying design principles, we therefore need to understand how the different models are related to each other with a view to obtaining a unified mathematical description. This goal is complicated by the number of distinct mathematical formalisms that may be employed to represent the same system, making direct comparison of the models very difficult. In this talk I will discuss two general methodologies, namely comparison by distance and comparison by equivalence, that allow us to compare model structures in a systematic way by representing models as labelled simplicial complexes. The distance can be obtained either directly from the simplicial complexes, or from the persistence intervals obtained by employing persistent homology with a flat filtration. Model equivalence is used to determine the conceptual similarity of models and can be automated by using group actions on the simplicial complexes. We apply our methodology for model comparison to demonstrate a particular equivalence between a positional-information model and a Turing-pattern model from developmental biology, which constitutes a novel observation for two classes of models that were previously regarded as unrelated. We also discuss an alternative framework for model comparison by representing models as groups, which allows for the application of group-theoretic techniques within our model comparison methodology.

Microscopic green algae show great diversity in structural complexity, and successfully evolved efficient swimming strategies at low Reynolds numbers. Gonium is one of the simplest multicellular algae, with only 16 cells arranged in a flat plate. If the swimming of unicellular organisms, like Chlamydomonas, is nowadays widely studied, it is less clear how a colony made of independent Chlamydomonas-like cells performs coordinated motion. This simple algae is therefore a key organism to model the evolution from single-celled to multicellular locomotion.

In the absence of central communication, how can each cell adapt its individual photoresponse to efficiently reorient the whole algae? How crucial is the distinctive Gonium squared structure?

In this talk, I will present experiments investigating the shape and the phototactic swimming of Gonium, using trajectory tracking and micro-pipette techniques. I will explain our model linking the individual flagella response to the colony trajectory. This eventually emphasises the importance of biological noise for efficient swimming.