Links :  UCR Interdisciplinary Center for Data-driven Modeling in Biology

     UCR Math Department seminar

               PDE and Applied Math Seminar

The format of the seminar can be either in-person or online. If on zoom, please contact Dr. Jia Gou (jia.gou@ucr.edu)  for the zoom link.

Fall 2026 

Sep 29, 2:00 PM, Dr. Rohan Mehta, Elmhurst University

Oct 06, 2:00 PM, Dr. Jing Chen ,Virginia Tech 

Oct 13, 2:00 PM, Dr. Chunyan Li, University of South Carolina

Oct 20, 10:00 AM, Dr. Albert Goldbeter , Université libre de Bruxelles 

Oct 27, 2:00 PM, Dr. Wenzheng Shi, Allen Institute

Nov 03, 2:00 PM, Dr. Therese Basa Landry, UCSB (in person)

Nov 10, 2:00 PM, 

Nov 17, 2:00 PM, Dr. Jennifer Rangel Ambriz, City of Hope (in person)

Nov 24, 2:00 PM, 

Dec 01, 2:00 PM, Dr. Sarafa Adewale Iyaniwura, Fred Hutchinson Cancer Center

Upcoming talks:

Tuesday, October 06, 2026, 02:00 PM - 03:00 PM Pacific Time

Dr. Jing Chen, Virginia Tech

Title: Sticking with two poles: Energetic principles of bipolar spindle formation

Abstract: Accurate chromosome segregation depends on bipolar mitotic spindles, each pole of which is normally organized by a centrosome. Centrosome defects can produce abnormal monopolar or multipolar spindles. Remarkably, cells can often

recover bipolarity by separating centrosomes in monopolar spindles or clustering them in multipolar spindles. To investigate the physical basis of this robustness, we developed a parsimonious energy-based model in which the key mechanical forces

of spindle assembly are represented by effective potentials calibrated against experimental measurements. The model identifies general biophysical factors, such as cell size and geometry, that are essential for robust bipolarization of spindles that start monopolar or multipolar. Consistent with these predictions, our experiments in tetraploid cancer cells with supernumerary centrosomes show that small cell volume and aspect ratio promote bipolar clustering of centrosomes. The model also accounts for several previously reported observations, providing a unifying energetic framework and revealing fundamental physical principles for bipolar spindle formation.

Bio: Dr. Jing Chen is an associate professor of Biological Sciences at Virginia Tech. Her research focuses on mathematical modeling of cellular dynamics, particularly the coupling of spatiotemporal, mechanical, and chemical processes in cellular mechanisms. Working closely with experimental collaborators, she studies a broad range of biological systems, including mitotic signaling and spindle assembly, bacterial motility and control, viral dynamics, circadian clocks, and RNA expression control. She received a B.S. in Biology from Fudan University, an M.S. in Mathematics in Bioscience from the Technical University of Munich, and a PhD in Biophysics from UC Berkeley, followed by postdoctoral training in theoretical cellular biophysics at NIH. She serves on the editorial boards of Biophysical Journal and PLoS Computational Biology.

Tuesday, October 20, 2026, 10:00 AM - 11:00 AM Pacific Time

Dr. Albert Goldbeter, Université libre de Bruxelles

Title: The cell cycle and the circadian clock: Dynamics of two coupled cellular rhythms

Abstract: Rhythmic behavior occurs at all levels of biological organization. After a brief review of biochemical and cellular rhythms, I will examine the oscillatory dynamics of the major regulatory networks that control, respectively, the circadian clock and the cell cycle. Models show how circadian rhythms occur in constant environmental conditions in the form of limit cycle oscillations, which can be entrained by the light-dark cycle. The model for the mammalian circadian clock accounts for the occurrence of different types of human sleep disorder. On the other hand, an experimentally based model for the mammalian cell cycle shows how the ordered progression through the successive cell cycle phases is driven by oscillations in the activity of a network of cyclin-dependent kinases. Experiments indicate that the circadian clock and the cell cycle are linked through bidirectional coupling. The dynamical consequences of such coupling have been studied by merging models for the mammalian circadian clock and for the network of cyclin-dependent kinases that drives the mammalian cell cycle. Compared to unidirectional coupling, which results in the entrainment of one oscillator by the other, bidirectional coupling enhances the robust synchronization of the two cellular rhythms. The model further predicts the possibility of multi-synchronization, i.e., the coexistence between multiple modes of synchronized oscillations characterized by different amplitudes and periods.

Bio: Albert Goldbeter is honorary professor in the Faculty of Sciences at Université Libre de Bruxelles (ULB), Brussels, Belgium. His research primarily pertains to modeling the mechanism of a variety of biochemical and cellular rhythms, including glycolytic oscillations, oscillations in Calcium and cyclic AMP signaling, the segmentation clock, circadian rhythms, and the cell cycle. Albert Goldbeter held visiting research professorships at the University of California at Berkeley (Miller Institute), the Universities of Paris VI and Paris-Sud Orsay, Fudan University (Shanghai), Nanjing Agricultural University, and Soochow University (Suzhou). He is author of the books Biochemical Oscillations and Cellular Rhythms. The molecular bases of periodic and chaotic behaviour (Cambridge University Press, 1996), and Oscillatory Life. Mechanisms and functions of biological rhythms (Springer, 2027, in press).

Tuesday, October 27, 2026, 02:00 PM - 03:00 PM Pacific Time

Dr. Wenzheng Shi, Allen Institute

Title: Actin based cell chirality emerging at the boundary of 2D-microtissue directs chiral multicellular pattern formation

Abstract: The mechanisms underlying both the establishment of mirror (reflection) symmetry and deviations from it in the development of bilateral multicellular organisms remain insufficiently understood. Actin cytoskeletons of individual cells exhibit intrinsic chirality, and a strong correlation exists between single-cell actin fibres’ chiral organisation and the collective alignment of cells confined to rectangular adhesive islands (2D-microtissues). Here, we demonstrate how multicellular chiral patterns can be inferred from the chiral behaviour of actin fibres in individual cells. By analysing chiral actin systems in cells with elliptical and semicircular shapes, representing inner and boundary positions within 2D-microtissues, we defined the rules of chiral motile behaviour and formulated two models of cell alignment: (i) chiral rotation of inner cells and (ii) chiral tilting of boundary cells relative to island edges. In both models, neighbouring cells are mutually aligned. Systematic variation of island area and aspect ratio, combined with dynamic observations, revealed the primary role of boundary cells. Chiral order first emerged at tissue boundaries and then propagated inward. This outside-in mechanism also explains how intrinsically chiral cells can build mirror-symmetric tissues in bilateral organisms: either by reversing cell chirality in one half or by enlarging the tissue to minimise boundary influence.

Bio: Wenzheng Shi is a Scientist at the Allen Institute in Seattle. An applied mathematician by training, he works at the interface between mathematical modeling and experimental cell biology, developing theory and computational methods that recover the hidden mechanics of living cells from the way they move.

His research spans scales. At the molecular scale, he showed how septin proteins sense membrane curvature as an emergent property of their multiscale assembly. At the cellular scale, he reconstructed a full nonlinear model of a migrating cell's leading edge, recovering reaction rates, forces, and feedbacks directly from unperturbed imaging data. At the tissue scale, he explained how the handedness of single cells propagates into left-right order across a whole tissue. He also develops machine-learning methods for recovering stochastic differential equations from trajectory data, a general engine for the inference problems that recur throughout his biological work.

Shi earned his Ph.D. in Applied Physics from the University of North Carolina at Chapel Hill, and before joining the Allen Institute he was a Courant Instructor and Assistant Professor at the Courant Institute of Mathematical Sciences at New York University.

Tuesday, November 03, 2026, 02:00 PM - 03:00 PM Pacific Time

Dr. Therese Basa Landry, UCSB

Title: Hack's Law, Erosion, and Optimal Transport: Developing Mathematical Models and Computational Methods

Abstract: Hack's Law says that the length of the main river in a river basin scales with the area of the river basin to the power 0.58, thereby prompting speculation on whether there exist optimality principles governing natural processes like channel formation.  Identification of such principles and their continued mathematical development could lead to the formulation of a theoretical framework which supports study not only of fluvial landscape evolution, but other geomorphological processes as well.  Erosion is nature's process of ``moving dirt." In 1781, Monge initiated the theory of optimal transport with the question, ``Given a pile of sand and a pit of equal volume, how can one optimally transport the sand into the pit?"  Building on earlier work by Birnir, Merchant, Smith, Cattan, and Rowlett, we aim to extend optimal transport theory to develop mathematical models and computational methods for studying erosion.  

Via optimal transport theory, we prove the existence of unique global weak solutions to equations describing the sediment flow in the evolution of fluvial land surfaces, with constant water depth.   While an earlier existence theory result by Birnir and Landry demonstrates that the slopes, or gradients of the surface, are moved optimally, our current work proves that erosion does what Monge proposed: move sediment optimally from the mountainside to the river.  Next steps include improvements in robustness and efficiency to existing numerical methods, faster-running models, and application of optimal transport models to sediment transport.  This is joint work with Bjorn Birnir.

Bio: Dr. Therese Basa Landry is a UC President's Postdoctoral Fellow at the University of California, Santa Barbara.  Previously, she was a Visiting Scholar at the Center for Complex and Nonlinear Science at the University of California, Santa Barbara.  From January 2022 through December 2025, Dr. Landry was a Visiting Assistant Professor at the University of California, Santa Barbara.  She was a Postdoctoral Fellow in the Non-Commutative Optimal Transport Program at the Institute for Pure and Applied Mathematics (IPAM).  She was also a Postdoctoral Fellow in the Thematic Program on Nonsmooth Riemannian and Lorentzian Geometry at the Fields Institute, as well as the Analysis and Geometry of Random Spaces Program at the Mathematical Sciences Research Institute (MSRI, now the Simons Laufer Mathematical Sciences Institute).  Part of the funding for Dr. Landry's fellowship at the Fields Institute was provided by George Elliott's NSERC grant.  Dr. Landry earned a PhD in noncommutative fractal geometry from the University of California, Riverside, under the direction of Michel Lapidus.

Tuesday, December 01, 2026, 02:00 PM - 03:00 PM Pacific Time

Dr. Sarafa Adewale Iyaniwura, Fred Hutchinson Cancer Center

Title: A Multiscale, Multiclass Mechanistic Model of Vaccine-Induced B Cell Dynamics

Abstract: Vaccine-induced humoral immunity involves coordinated B-cell expansion and antibody production following immunogen exposure in a competitive environment. To understand how different B-cell classes compete and subsequently produce antibodies during the humoral immune response to vaccination, we present a multiscale mechanistic mathematical model integrating vaccination regimen features, immunogen kinetics, multiclass B-cell dynamics, and germinal center processes. Calibrated to data from an HIV vaccine trial testing eOD-GT8, a promising immunogen designed to induce VRC01-class B cells, precursors of broadly neutralizing antibodies, the model reproduced key features of the observed B-cell and antibody responses. We examined competition among B-cell classes in the germinal center and found that competition is stronger within classes than between them. Our analysis further revealed heterogeneity in the activation rates of naïve and memory B cells, and across B-cell classes, highlighting the role of class-specific differences in activation and competition in shaping targeted humoral responses to HIV vaccines. More broadly, the model provides a quantitative framework for interpreting multiclass B-cell and antibody responses to vaccination and for evaluating how immunogen exposure and vaccination regimens shape humoral immunity.

Bio: Sarafa Iyaniwura is an Associate Research Scientist at the Vaccine and Immunology Statistical Center (VISC) within the Vaccine and Infectious Disease Division (VIDD) at the Fred Hutchinson Cancer Center, and an MGB-SIAM Early Career Fellow (2024–2026). His research develops data-driven mathematical modeling frameworks for studying complex biological systems, with an emphasis on infectious diseases and immunology. He received his Ph.D. in Applied Mathematics from the University of British Columbia in 2021, after which he completed a postdoctoral fellowship in the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory (2021–2024), developing mathematical theory for the in vivo kinetics of HIV, SARS-CoV-2, hepatitis B, and hepatitis C, among other viruses. His current research develops mechanistic frameworks to study and optimize HIV germline-targeting and sequential immunization strategies, bridging mathematical theory with clinical trial data to inform HIV vaccine design.

Previous talks:

Tuesday, September 29, 2026, 02:00 PM - 03:00 PM Pacific Time

Dr. Rohan Mehta, Elmhurst University

Title: Losing part of yourself to save the rest: eco-evolutionary dynamics of autotomy and offspring abandonment

Abstract: Organisms sometimes use extreme strategies to avoid predation. One such strategy is autotomy, the act of losing a body part on purpose in order to increase the chance of escaping a predator. This strategy has dramatic costs as well as dramatic benefits. Here, we study evolutionary game-theoretical and ecological models of the autotomy strategy and find that organisms can get "stuck" performing autotomy when it would otherwise be beneficial not to. We also find ecological conditions under which we expect autotomy to be seen. Finally, we extend the model to an even more dramatic strategy: abandoning offspring upon predator approach, and derive conditions for when this strategy is favored.

Bio: Dr. Rohan Mehta is an Assistant Professor of Biological Sciences at Elmhurst University. He uses mathematical models to study a wide variety of interacting biological systems, including predator-prey dynamics, diseae-behavior dynamics, and horizontal gene transfer in bacteria.