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public 01:34:53
public 43:08

James Colliander : Crowdmark presentation

  -   Presentations ( 327 Views )

public 01:14:52

Alan Guo : Affine semigroups and lattice points in polyhedra

  -   Colloquium ( 317 Views )

public 01:34:43

Bruce Donald : Some mathematical and computational challenges arising in structural molecular biology

  -   Applied Math and Analysis ( 304 Views )

Computational protein design is a transformative field with exciting prospects for advancing both basic science and translational medical research. New algorithms blend discrete and continuous mathematics to address the challenges of creating designer proteins. I will discuss recent progress in this area and some interesting open problems. I will motivate this talk by discussing how, by using continuous geometric representations within a discrete optimization framework, broadly-neutralizing anti-HIV-1 antibodies were computationally designed that are now being tested in humans - the designed antibodies are currently in eight clinical trials (See https://clinicaltrials.gov/ct2/results?cond=&term=VRC07&cntry=&state=&city=&dist= ), one of which is Phase 2a (NCT03721510). These continuous representations model the flexibility and dynamics of biological macromolecules, which are an important structural determinant of function. However, reconstruction of biomolecular dynamics from experimental observables requires the determination of a conformational probability distribution. These distributions are not fully constrained by the limited information from experiments, making the problem ill-posed in the sense of Hadamard. The ill-posed nature of the problem comes from the fact that it has no unique solution. Multiple or even an infinite number of solutions may exist. To avoid the ill-posed nature, the problem must be regularized by making (hopefully reasonable) assumptions. I will present new ways to both represent and visualize correlated inter-domain protein motions (See Figure). We use Bingham distributions, based on a quaternion fit to circular moments of a physics-based quadratic form. To find the optimal solution for the distribution, we designed an efficient, provable branch-and-bound algorithm that exploits the structure of analytical solutions to the trigonometric moment problem. Hence, continuous conformational PDFs can be determined directly from NMR measurements. The representation works especially well for multi-domain systems with broad conformational distributions. Ultimately, this method has parallels to other branches of applied mathematics that balance discrete and continuous representations, including physical geometric algorithms, robotics, computer vision, and robust optimization. I will advocate for using continuous distributions for protein modeling, and describe future work and open problems.

public 01:34:49

Camille Scalliet : When is the Gardner transition relevant?

  -   Nonlinear and Complex Systems ( 289 Views )

The idea that glasses can become marginally stable at a Gardner transition has attracted significant interest among the glass community. Yet, the situation is confusing: even at the theoretical level, renormalization group approaches provide contradictory results on whether the transition can exist in three dimensions. The Gardner transition was searched in only two experimental studies and few specific numerical models. These works lead to different conclusions for the existence of the transition, resulting in a poor understanding of the conditions under which a marginally stable phase can be observed. The very relevance of the Gardner transition for experimental glasses is at stake.

We study analytically and numerically the Weeks-Chandler-Andersen model. By changing external parameters, we continuously explore the phase diagram and regimes relevant to granular, colloidal, and molecular glasses. We revisit previous numerical studies and confirm their conclusions. We reconcile previous results and rationalise under which conditions a Gardner phase can be observed. We find that systems in the vicinity of a jamming transition possess a Gardner phase. Our findings confirm the relevance of a Gardner transition for colloidal and granular glasses, and encourage future experimental work in this direction. For molecular glasses, we find that no Gardner phase is present, but our studies reveal instead the presence of localised excitations presumably relevant for mechanical and vibrational properties of glasses.

public 01:34:42

Robert V. Kohn : A Variational Perspective on Wrinkling Patterns in Thin Elastic Sheets: What sets the patterns seen in geometry-driven wrinkling?

  -   Gergen Lectures ( 286 Views )

The wrinkling of thin elastic sheets is very familiar: our skin wrinkles, drapes have coarsening folds, and a sheet stretched over a round surface must wrinkle or fold.

What kind of mathematics is relevant? The stable configurations of a sheet are local minima of a variational problem with a rather special structure, involving a nonconvex membrane term (which favors isometry) and a higher-order bending term (which penalizes curvature). The bending term is a singular perturbation; its small coefficient is the sheet thickness squared. The patterns seen in thin sheets arise from energy minimization -- but not in the same way that minimal surfaces arise from area minimization. Rather, the analysis of wrinkling is an example of "energy-driven pattern formation," in which our goal is to understand the asymptotic character of the minimizers in a suitable limit (as the nondimensionalized sheet thickness tends to zero).

What kind of understanding is feasible? It has been fruitful to focus on how the minimum energy scales with sheet thickness, i.e. the "energy scaling law." This approach entails proving upper bounds and lower bounds that scale the same way. The upper bounds tend to be easier, since nature gives us a hint. The lower bounds are more subtle, since they must be ansatz-free; in many cases, the arguments used to prove the lower bounds help explain "why" we see particular patterns. A related but more ambitious goal is to identify the prefactor as well as the scaling law; Ian Tobasco's striking recent work on geometry-driven wrinkling has this character.

Lecture 1 will provide an overview of this topic (assuming no background in elasticity, thin sheets, or the calculus of variations). Lecture 2 will discuss some examples of tensile wrinkling, where identification of the energy scaling law is intimately linked to understanding the local length scale of the wrinkles. Lecture 3 will discuss our emerging undertanding of geometry-driven wrinkling, where (as Tobasco has shown) it is the prefactor not the scaling law that explains the patterns seen experimentally.