BEGIN:VCALENDAR VERSION:2.0 PRODID:talks.ox.ac.uk BEGIN:VEVENT SUMMARY:Modelling infectious diseases within-host - Dr Ruth Bowness (Univ ersity of Bath) DTSTART;VALUE=DATE-TIME:20250523T110000 DTEND;VALUE=DATE-TIME:20250523T120000 UID:https://talks.ox.ac.uk/talks/id/696327c0-87e5-488c-9677-6a082ace7c9c/ DESCRIPTION:During the talk I will describe my research on host-pathogen i nteractions during lung infections. Various modelling approaches have been used\, including a hybrid multiscale individual-based model that we have developed\, which simulates pulmonary infection spread\, immune response a nd treatment within in a section of human lung. The model contains discret e agents which model the spatio-temporal interactions (migration\, binding \, killing etc.) of the pathogen and immune cells. Cytokine and oxygen dyn amics are also included\, as well as Pharmacokinetic/Pharmacodynamic model s\, which are incorporated via PDEs. I will also describe ongoing work to develop a continuum model\, comparing the spatial dynamics resulting from these different modelling approaches. I will focus in the most part on tw o infectious diseases: Tuberculosis and COVID-19.\nSpeakers:\nDr Ruth Bown ess (University of Bath) LOCATION:Mathematical Institute (L2)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/696327c0-87e5-488c-9677-6a082ace7c9c/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Modelling infectious diseases within-host - Dr Ruth Bown ess (University of Bath) TRIGGER:-PT1H END:VALARM END:VEVENT BEGIN:VEVENT SUMMARY:Modelling the rheology of biological tissue - Professor Suzanne Fi elding (Dept of Physics Durham University) DTSTART;VALUE=DATE-TIME:20250530T110000 DTEND;VALUE=DATE-TIME:20250530T120000 UID:https://talks.ox.ac.uk/talks/id/04efe1f8-8508-4aef-bd93-c161b845b615/ DESCRIPTION:The rheological (deformation and flow) properties of biologica l tissues \nare important in processes such as embryo development\, wound healing and \ntumour invasion. Indeed\, processes such as these spontaneou sly generate \nstresses within living tissue via active process at the sin gle cell level. \nTissues are also continually subject to external stresse s and deformations \nfrom surrounding tissues and organs. The success of n umerous physiological \nfunctions relies on the ability of cells to withst and stress under some \nconditions\, yet to flow collectively under others . Biological tissue is \nfurthermore inherently viscoelastic\, with a slow time-dependent mechanics. \nDespite this rich phenomenology\, the mechani sms that govern the \ntransmission of stress within biological tissue\, an d its response to bulk \ndeformation\, remain poorly understood to date.\n \nThis talk will describe three recent research projects in modelling the \nrheology of biological tissue. The first predicts a strain-induced \nsti ffening transition in a sheared tissue [1]. The second elucidates the \nin terplay of external deformations applied to a tissue as a whole with \nint ernal active stresses that arise locally at the cellular level\, and \nsho ws how this interplay leads to a host of fascinating rheological \nphenome na such as yielding\, shear thinning\, and continuous or \ndiscontinuous s hear thickening [2]. The third concerns the formulation of \na continuum c onstitutive model that captures several of these linear and\nnonlinear rhe ological phenomena [3].\n\n[1] J. Huang\, J. O. Cochran\, S. M. Fielding\, M. C. Marchetti and D. Bi\, \nPhysical Review Letters 128 (2022) 178001\n \n[2] M. J. Hertaeg\, S. M. Fielding and D. Bi\, Physical Review X 14 (202 4) \n011017.\n\n[3] S. M. Fielding\, J. O. Cochran\, J. Huang\, D. Bi\, M. C. Marchetti\, \nPhysical Review E (Letter) 108 (2023) L042602.\n\nSpeake rs:\nProfessor Suzanne Fielding (Dept of Physics Durham University) LOCATION:Mathematical Institute (L4)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/04efe1f8-8508-4aef-bd93-c161b845b615/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Modelling the rheology of biological tissue - Professor S uzanne Fielding (Dept of Physics Durham University) TRIGGER:-PT1H END:VALARM END:VEVENT BEGIN:VEVENT SUMMARY:Combining computational modelling\, deep generative learning and i maging to infer new biology - Prof Simon Walker-Samuel (UCL) DTSTART;VALUE=DATE-TIME:20250124T110000Z DTEND;VALUE=DATE-TIME:20250124T120000Z UID:https://talks.ox.ac.uk/talks/id/f1d6ab53-5252-4e53-b467-1bf7ff04fe53/ DESCRIPTION:Deep learning algorithms provide unprecedented opportunities t o characterise complex structure in large data\, but typically in a manner that cannot easily be interpreted beyond the 'black box'. We are developi ng methods to leverage the benefits of deep generative learning and comput ational modelling (e.g. fluid dynamics\, solid mechanics\, biochemistry)\, particularly in conjunction with biomedical imaging\, to enable new insig hts into disease to be made. In this talk\, I will describe our applicatio ns in several areas\, including modelling drug delivery in cancer and reti nal blood vessel loss in diabetes\, and how this is leading us into the de velopment of personalised digital twins.\nSpeakers:\nProf Simon Walker-Sam uel (UCL) LOCATION:Mathematical Institute (L4)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/f1d6ab53-5252-4e53-b467-1bf7ff04fe53/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Combining computational modelling\, deep generative learn ing and imaging to infer new biology - Prof Simon Walker-Samuel (UCL) TRIGGER:-PT1H END:VALARM END:VEVENT BEGIN:VEVENT SUMMARY:Engineering Biology for Robust Turing Patterns - Prof Robert Endr es (Imperial College London) DTSTART;VALUE=DATE-TIME:20241025T110000 DTEND;VALUE=DATE-TIME:20241025T120000 UID:https://talks.ox.ac.uk/talks/id/d6713d44-bca6-48e6-9567-6dd8eec77e43/ DESCRIPTION:Turing patterns have long been proposed as a mechanism for spa tial organization in biology\, but their relevance remains controversial d ue to the stringent fine-tuning often required. In this talk\, I will pres ent recent efforts to engineer synthetic Turing systems in bacterial colon ies\, highlighting both successes and limitations. While our three-node ge ne circuit generates patterns\, challenges remain in extending these resul ts to broader contexts. Additionally\, I will discuss our exploration of m achine learning methods to address the inverse problem of pattern formatio n\, helping the design process down the road. This work addresses the ongo ing task in translating theory into robust biological applications\, offer ing insights into both current capabilities and future directions.\nSpeake rs:\nProf Robert Endres (Imperial College London) LOCATION:Mathematical Institute (L5)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/d6713d44-bca6-48e6-9567-6dd8eec77e43/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Engineering Biology for Robust Turing Patterns - Prof Ro bert Endres (Imperial College London) TRIGGER:-PT1H END:VALARM END:VEVENT BEGIN:VEVENT SUMMARY:Cytoneme-mediated morphogenesis - Prof Paul Bressloff (Dept of Mat hematics\, Imperial College\, London) DTSTART;VALUE=DATE-TIME:20240531T140000 DTEND;VALUE=DATE-TIME:20240531T150000 UID:https://talks.ox.ac.uk/talks/id/5a481226-6078-4299-b051-7e7287289947/ DESCRIPTION:Morphogen protein gradients play an essential role in the spat ial regulation of patterning during embryonic development. The most commo nly accepted mechanism of protein gradient formation involves the diffusio n and degradation of morphogens from a localized source. Recently\, an alt ernative mechanism has been proposed\, which is based on cell-to-cell tran sport via thin\, actin-rich cellular extensions known as cytonemes. It has been hypothesized that cytonemes find their targets via a random search p rocess based on alternating periods of retraction and growth\, perhaps med iated by some chemoattractant. This is an actin-based analog of the search -and-capture model of microtubules of the mitotic spindle searching for cy tochrome binding sites (kinetochores) prior to separation of cytochrome pa irs. In this talk\, we introduce a search-and-capture model of cytoneme-ba sed morphogenesis\, in which nucleating cytonemes from a source cell dynam ically grow and shrink until making contact with a target cell and deliver ing a burst of morphogen. We model the latter as a one-dimensional search process with stochastic resetting\, finite returns times and refractory pe riods. We use a renewal method to calculate the splitting probabilities an d conditional mean first passage times (MFPTs) for the cytoneme to be capt ured by a given target cell. We show how multiple rounds of search-and-cap ture\, morphogen delivery\, cytoneme retraction and nucleation events lead to the formation of a morphogen gradient. We proceed by formulating the m orphogen bursting model as a queuing process\, analogous to the study of t ranslational bursting in gene networks. We end by briefly discussing curre nt work on a model of cytoneme-mediated within-host viral spread.\nSpeaker s:\nProf Paul Bressloff (Dept of Mathematics\, Imperial College\, London) LOCATION:Mathematical Institute (L3)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/5a481226-6078-4299-b051-7e7287289947/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Cytoneme-mediated morphogenesis - Prof Paul Bressloff (De pt of Mathematics\, Imperial College\, London) TRIGGER:-PT1H END:VALARM END:VEVENT BEGIN:VEVENT SUMMARY:Some consequences of phenotypic heterogeneity in living active mat ter - Dr Philip Pearce (Dept of Mathematics\, UCL) DTSTART;VALUE=DATE-TIME:20240517T140000 DTEND;VALUE=DATE-TIME:20240517T150000 UID:https://talks.ox.ac.uk/talks/id/42f8eeaf-e288-4b9b-bbe7-b97a7cd1ce41/ DESCRIPTION:In this talk I will discuss how phenotypic heterogeneity affec ts emergent pattern formation in living active matter with chemical commun ication between cells. In doing so\, I will explore how the emergent dynam ics of multicellular communities are qualitatively different in comparison to the dynamics of isolated or non-interacting cells. I will focus on two specific projects. First\, I will show how genetic regulation of chemical communication affects motility-induced phase separation in cell populatio ns. Second\, I will demonstrate how chemotaxis along self-generated signal gradients affects cell populations undergoing 3D morphogenesis.\nSpeakers :\nDr Philip Pearce (Dept of Mathematics\, UCL) LOCATION:Mathematical Institute (L3)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/42f8eeaf-e288-4b9b-bbe7-b97a7cd1ce41/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Some consequences of phenotypic heterogeneity in living a ctive matter - Dr Philip Pearce (Dept of Mathematics\, UCL) TRIGGER:-PT1H END:VALARM END:VEVENT BEGIN:VEVENT SUMMARY:Emergent spatial patterning in engineered bacteria - Dr Neil Dalch au (Microsoft Research Cambridge) DTSTART;VALUE=DATE-TIME:20191115T140000Z DTEND;VALUE=DATE-TIME:20191115T150000Z UID:https://talks.ox.ac.uk/talks/id/71f49466-277f-429a-9725-9119dbcb396c/ DESCRIPTION:The spatial coordination of cellular differentiation enables f unctional organogenesis. How coordination results in specific patterns of differentiation in a robust manner is a fundamental question for all devel opmental systems in biology. Theoreticians such as Turing and Wolpert have proposed the importance of specific mechanisms that enable certain types of patterns to emerge\, but these mechanisms are often difficult to identi fy in natural systems. Therefore\, we have started using synthetic biology to ask whether specific mechanisms of pattern formation can be engineered into a simple cellular background. In this talk\, I will show several exa mples of emergent spatial patterning that results from the insertion of sy nthetic signalling pathways and transcriptional logic into E. coli. In all cases\, we use computational modelling to initially design circuits with a desired outcome\, and improve the selection of biological components (DN A sub-sequences) that achieve this outcome according to a quantifiable mea sure. In the specific case of Turing patterns\, we have yet to produce a f unctional system in vivo\, but I will describe new analytical tools that a re helping to guide the design of synthetic circuits that can produce a Tu ring instability.\nSpeakers:\nDr Neil Dalchau (Microsoft Research Cambridg e) LOCATION:Mathematical Institute (L3)\, Woodstock Road OX2 6GG TZID:Europe/London URL:https://talks.ox.ac.uk/talks/id/71f49466-277f-429a-9725-9119dbcb396c/ BEGIN:VALARM ACTION:display DESCRIPTION:Talk:Emergent spatial patterning in engineered bacteria - Dr N eil Dalchau (Microsoft Research Cambridge) TRIGGER:-PT1H END:VALARM END:VEVENT END:VCALENDAR