## Samuel Isaacson : Spatial Jump Process Models for Estimating Antibody-Antigen Interactions

- Mathematical Biology ( 38 Views )Surface Plasmon Resonance (SPR) assays are a standard approach for quantifying kinetic parameters in antibody-antigen binding reactions. Classical SPR approaches ignore the bivalent structure of antibodies, and use simplified ODE models to estimate effective reaction rates for such interactions. In this work we develop a new SPR protocol, coupling a model that explicitly accounts for the bivalent nature of such interactions and the limited spatial distance over which such interactions can occur, to a SPR assay that provides more features in the generated data. Our approach allows the estimation of bivalent binding kinetics and the spatial extent over which antibodies and antigens can interact, while also providing substantially more robust fits to experimental data compared to classical bivalent ODE models. I will present our new modeling and parameter estimation approach, and demonstrate how it is being used to study interactions between antibodies and spike protein. I will also explain how we make the overall parameter estimation problem computationally feasible via the construction of a surrogate approximation to the (computationally-expensive) particle model. The latter enables fitting of model parameters via standard optimization approaches.

## Leo Darrigade : Modelling G protein-coupled receptors (GPCRs) compartmentalized signaling

- Mathematical Biology ( 46 Views )G protein-coupled receptors (GPCRs) are membrane receptors that play a pivotal role in the regulation of reproduction and behavior in humans. Upon binding to specific ligands, they trigger a local cAMP production. Activated receptor are then internalized to different endosomal compartments where they can continue signaling before being recycled or destroyed. Recent studies showed that the different pools of cAMP have different effect on the cell.

In the first part of the talk, I will present a piecewise deterministic Markov process (PDMP) of intracellular signaling. The stochastic part of the model accounts for formation, coagulation, fragmentation and recycling of intracellular vesicles which contain the receptor, whereas the deterministic part of the model represents evolution of chemical reactions due to signaling activity of the receptor. We are interested in the existence of and convergence to a stationary measure. I will present different cases for which we were able to obtain results in this direction.

In the second part of the talk, I will present the numerical workflow (SBML, PEtab and PyPESTO) we use to fit ODEs model of GPCR signaling to longitudinal measure of chemical concentrations (BRET data).

## Louis Fostier : A model of oocyte population dynamics for fish oogenesis

- Mathematical Biology ( 44 Views )We introduce and analyze a size-structured oocyte population model, with non local nonlinearities on recruitment, growth and mortality rates to take into account interactions between cells. We pay special attention to the form of the recruitment term, and its influence on the asymptotic behavior of the cell population.

This model is well-suited for representing oocyte population dynamics within the fish ovary. The nonlocal nonlinearities enable us to capture the diverse feedback mechanisms acting on the growth of oocytes of varying sizes and on the recruitment of new oocytes.

We firstly investigate the existence and uniqueness of global bounded solutions by transforming the partial differential equation into an equivalent system of integral equations, which can be solved using the Contraction Mapping Principle.

In a second step, we investigate the asymptotic behavior of the model. Under an additional assumption regarding the form of the growth rate, we can, with the use of a classical time-scaling transformation, reduce the study to that of a equation with linear growth speed and nonlinear inflow boundary condition. Using arguments from the theory of abstract semilinear Cauchy problems, we investigate the local stability of stationary solutions of this equation by reducing it to a characteristic equation involving the eigenvalues of the linearized problem around equilibrium states.

When the mortality rate is zero, the study of existence and stability of stationary solutions is simplified. Explicit calculations can be carried out in certain interesting cases.

## Sean Lawley : Stochastics in medicine: Delaying menopause and missing drug doses

- Mathematical Biology ( 61 Views )Stochastic modeling and analysis can help answer pressing medical questions. In this talk, I will attempt to justify this claim by describing recent work on two problems in medicine. The first problem concerns ovarian tissue cryopreservation, which is a proven tool to preserve ovarian follicles prior to gonadotoxic treatments. Can this procedure be applied to healthy women to delay or eliminate menopause? How can it be optimized? The second problem concerns medication nonadherence. What should you do if you miss a dose of medication? How can physicians design dosing regimens that are robust to missed/late doses? I will describe (a) how stochastics theory offers insights into these questions and (b) the mathematical questions that emerge from this investigation. The first problem is based on joint work with Joshua Johnson (University of Colorado School of Medicine), John Emerson (Yale University), and Kutluk Oktay (Yale School of Medicine).

## Dean Bottino : Evaluating Strategies for Overcoming Rituximab (R) Resistance Using a Quantitative Systems Pharmacology (QSP) model of Antibody-Dependent Cell-mediated Cytotoxicity & Phagocytosis (ADCC & ADCP): An Academic/Industrial Collaboration

- Mathematical Biology ( 56 Views )Despite the impressive performance of rituximab (R) containing regimens like R-CHOP in CD20+ Non-Hodgkin’s Lymphoma (NHL), 30-60% of R-naïve NHL patients are estimated to be resistant, and approximately 60% of those patients will not respond to subsequent single agent R treatment. Given that antibody dependent cell mediated cytotoxicity (ADCC) and phagocytosis (ADCP) are thought to be the major mechanisms of action of Rituximab, increasing the activation levels of natural killer (NK) and macrophage (MP) cells may be one strategy for overcoming R resistance.

During (and after) the Fields Institute Industrial Problem Solving Workshop in August 2019, academic participants and industry mentors developed and calibrated to literature data a quantitative systems pharmacology (QSP) model of ADCC/ADCP to interrogate which mechanisms of R resistance could be overcome by increased NK or MP activation, and how much effector cell activation would be required to overcome a given degree and mechanism of R resistance.

This work was motivated by a real-world pharmaceutical drug development question, and the academic-industry interactions during and after the workshop resulted in sharknado plots as well as a published QSP model (presented at American Association of Cancer Research Annual Meeting, 2021) that was able to address some of the key questions around overcoming R resistance. The published model was then incorporated into an in-house QSP model supporting the development of a Takeda investigational drug which is being developed to restore R sensitivity in an R-resistant patient population.

## Chun-Hung Liu : Assouad-Nagata dimension of minor-closed metrics

- Mathematical Biology ( 78 Views )Assouad-Nagata dimension addresses both large-scale and small-scale behaviors of metric spaces and is a refinement of Gromov’s asymptotic dimension. A metric space is a minor-closed metric if it is defined by the distance function on the vertices of an edge-weighted graph that satisfies a fixed graph property preserved under vertex-deletion, edge-deletion, and edge-contraction. In this talk, we determine the Assouad-Nagata dimension of every minor-closed metric. It is a common generalization of known results about the asymptotic dimension of H-minor free unweighted graphs, about the Assouad-Nagata dimension of complete Riemannian surfaces with finite Euler genus, and about their corollaries on weak diameter coloring of minor-closed families of graphs and asymptotic dimension of minor-excluded groups.

## Jesse Zhang : Geodesic complexity of convex polyhedra

- Mathematical Biology ( 102 Views )Geodesic complexity of the d-dimensional boundary S of a convex polytope of dimension d+1 is intimately related to the combinatorics of nonoverlapping unfolding of S into a Euclidean space R^d following Miller and Pak (2008). This combinatorics is based on facet sequences, which are lists of adjacent facets traversed by geodesics in S. Our main result bounds the geodesic complexity of S from above by the number of distinct maximal facet sequences traversed by shortest paths in S. For d=2, results from the literature on nonoverlapping unfolding imply that this bound is polynomial in the number of facets. In arbitrary dimension d, a reinterpretation of conjectures by Miller and Pak (2008) leads to the conjecture that the geodesic complexity of S is polynomial in the number of facets. The theory and results developed here hold more generally for convex polyhedral complexes. This is joint work with Ezra Miller.

## Stephan Huckemann : Statistical challenges in shape prediction of biomolecules

- Mathematical Biology ( 164 Views )The three-dimensional higher-order structure of biomolecules
determines their functionality. While assessing primary structure is
fairly easily accessible, reconstruction of higher order structure is
costly. It often requires elaborate correction of atomic clashes,
frequently not fully successful. Using RNA data, we describe a purely
statistical method, learning error correction, drawing power from a
two-scale approach. Our microscopic scale describes single suites by
dihedral angles of individual atom bonds; here, addressing the
challenge of torus principal component analysis (PCA) leads to a
fundamentally new approach to PCA building on principal nested spheres
by Jung et al. (2012). Based on an observed relationship with a
mesoscopic scale, landmarks describing several suites, we use Fréchet
means for angular shape and size-and-shape, correcting
within-suite-backbone-to-backbone clashes. We validate this method by
comparison to reconstructions obtained from simulations approximating
biophysical chemistry and illustrate its power by the RNA example of
SARS-CoV-2.

This is joint work with Benjamin Eltzner, Kanti V. Mardia and Henrik
Wiechers.

Literature:

Eltzner, B., Huckemann, S. F., Mardia, K. V. (2018):
Torus principal component analysis with applications to RNA
structure. Ann. Appl. Statist. 12(2), 1332?1359.

Jung, S., Dryden, I. L., Marron, J. S. (2012):
Analysis of principal nested spheres. Biometrika, 99 (3), 551-568

Mardia, K. V., Wiechers, H., Eltzner, B., Huckemann, S. F. (2022).
Principal component analysis and clustering on manifolds. Journal of
Multivariate Analysis, 188, 104862,
https://www.sciencedirect.com/science/article/pii/S0047259X21001408

Wiechers, H., Eltzner, B., Mardia, K. V., Huckemann, S. F. (2021).
Learning torus PCA based classification for multiscale RNA backbone
structure correction with application to SARS-CoV-2. To appear in the
Journal of the Royal Statistical Society, Series C,
bioRxiv https://doi.org/10.1101/2021.08.06.455406

## Casey Diekman : Data Assimilation and Dynamical Systems Analysis of Circadian Rhythmicity and Entrainment

- Mathematical Biology ( 116 Views )Circadian rhythms are biological oscillations that align our physiology and behavior with the 24-hour environmental cycles conferred by the Earth’s rotation. In this talk, I will discuss two projects that focus on circadian clock cells in the brain and the entrainment of circadian rhythms to the light-dark cycle. Most of what we know about the electrical activity of circadian clock neurons comes from studies of nocturnal (night-active) rodents, hindering the translation of this knowledge to diurnal (day-active) humans. In the first part of the talk, we use data assimilation and patch-clamp recordings from the diurnal rodent Rhabdomys pumilio to build the first mathematical models of the electrophysiology of circadian neurons in a day-active species. We find that the electrical activity of circadian neurons is similar overall between nocturnal and diurnal rodents but that there are some interesting differences in their responses to inhibition. In the second part of the talk, we use tools from dynamical systems theory to study the reentrainment of a model of the human circadian pacemaker following perturbations that simulate jet lag. We show that the reentrainment dynamics are organized by invariant manifolds of fixed points of a 24-hour stroboscopic map and use these manifolds to explain a rapid reentrainment phenomenon that occurs under certain jet lag scenarios.

## Elliot Cartee : Control-Theoretic Models of Environmental Crime

- Mathematical Biology ( 180 Views )We present two models of perpetrators' decision-making in extracting resources from a protected area. It is assumed that the authorities conduct surveillance to counter the extraction activities, and that perpetrators choose their post-extraction paths to balance the time/hardship of travel against the expected losses from a possible detection. In our first model, the authorities are assumed to use ground patrols and the protected resources are confiscated as soon as the extractor is observed with them. The perpetrators' path-planning is modeled using the optimal control of randomly-terminated process. In our second model, the authorities use aerial patrols, with the apprehension of perpetrators and confiscation of resources delayed until their exit from the protected area. In this case the path-planning is based on multi-objective dynamic programming. Our efficient numerical methods are illustrated on several examples with complicated geometry and terrain of protected areas, non-uniform distribution of protected resources, and spatially non-uniform detection rates due to aerial or ground patrols.

## Sharon Lubkin : Notochord eccentricity and its relation to cell packing

- Mathematical Biology ( 237 Views )The notochord, the defining feature of chordates, is a pressurized tube which actuates elongation of the chordate embryo. The zebrafish notochord consists of large vacuolated cells surrounded by a thin sheath. We characterized the patterns of the cells’ packing, and their relationship to the known regular patterns from the study of foams, and irregular patterns in a gel bead system. Disruption of the wild type packing pattern leads to developmental defects. We characterize the bifurcations between the relevant regular patterns in terms of nondimensional geometrical and mechanical ratios, and suggest an important developmental role for the eccentric "staircase" pattern.

## John Gemmer : Nature’s Forms are Frilly, Flexible and Functional

- Mathematical Biology ( 253 Views )Many patterns in Nature and industry arise from the system minimizing an appropriate energy. Torn plastic sheets and growing leaves provide striking examples of pattern forming systems which can transition from single wavelength geometries (leaves) to complex fractal-like shapes (lettuce). These fractal-like patterns seem to have many length scales, i.e. the same amount of extra detail can be seen when looking closer (“statistical self-similarity”). It is a mystery how such complex patterns could arise from energy minimization alone. In this talk I will address this puzzle by showing that such patterns naturally arise from the sheet adopting a hyperbolic non-Euclidean geometry. However, there are many different hyperbolic geometries that the growing leaf could select. I will show using techniques from analysis, differential geometry and numerical optimization that the fractal like patterns are indeed the natural minimizers for the system. I will also discuss the implications of our work to developing shape changing soft matter which can be implemented in soft machines.