Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session G36: Delbruck Prize SessionInvited Prize/Award
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Sponsoring Units: DBIO Chair: Phil Nelson, University of Pennsylvania Room: 601/603 |
Tuesday, March 3, 2020 11:15AM - 11:51AM |
G36.00001: Synthetic Biology: Physical Biology by Design Invited Speaker: James Collins Synthetic biology is bringing together physicists and biologists to model, design and construct biological circuits out of proteins, genes and other bits of DNA, and to use these circuits to rewire and reprogram organisms. These re-engineered organisms are going to change our lives in the coming years, leading to cheaper drugs, rapid diagnostic tests, and synthetic probiotics to treat infections and a range of complex diseases. In this talk, we highlight recent efforts to create synthetic gene networks and programmable cells, and discuss a variety of synthetic biology applications in biotechnology and biomedicine. |
Tuesday, March 3, 2020 11:51AM - 12:27PM |
G36.00002: Physical principles from evolutionary synthetic biology Invited Speaker: Gabor Balazsi Synthetic biology designs and builds artificial biological systems, using principles from engineering, mathematics and physics. Just like engineering was crucial for many traditional physics discoveries over the past centuries, synthetic biology can advance biological physics by providing sensors, switches, oscillators, control knobs and other tools for quantitatively monitoring and perturbing living cells. Moreover, synthetic biological devices can serve as simple model systems to elucidate complex biophysical processes. For example, synthetic biological devices evolve along with the cells that carry them, providing new opportunities to investigate cellular and molecular evolution. I will present examples of how evolving synthetic gene circuits can provide deeper understanding of evolutionary processes, specifically of gene networks mediating the adaptation of cell populations. |
Tuesday, March 3, 2020 12:27PM - 1:03PM |
G36.00003: Synthetic Biology: Building to learn so that we might learn to build Invited Speaker: Jeff Hasty Synthetic Biology can be broadly parsed into the “top-down creation” of entire genomes and the “bottom-up engineering” of relatively small genetic circuits. A defining component of the gene circuit approach is the development of theory that can serve as the foundation for a new type of cellular engineering. This talk will be anchored by my quest to build genetic oscillators in cells, with a particular focus on the utility of mathematical modeling in determining general design principles. I’ll first describe the design and construction of an intracellular circuit that cycles over a wide range of environmental conditions (http://biodynamics.ucsd.edu/Intracellular.mov). The large space of observed oscillatory behavior drove a revision of model equations that revealed unanticipated coupling of the clock to native cellular processes. More generally, the necessity of the model revision led to our ongoing exploration of biochemical networks that act as queues that can be balanced at a type of critical point. In terms of engineering, the clock was not of the Swiss variety; the period and amplitude exhibited large intracellular variability. However, viewed through the lens of dynamical systems theory, the noisy oscillator provided a benchmark for the development of general synchronization strategies that can restore determinism. This led to three studies describing (i) how quorum sensing can be used to couple clocks between cells (biodynamics.ucsd.edu/Intercellular.mov), (ii) how redox signaling can combine with quorum sensing to couple colonies at centimeter length scales (biodynamics.ucsd.edu/Intercolony.mov), and (iii) how intra- and inter-cellular dynamics can be rapidly coupled and used to encode information (biodynamics.ucsd.edu/Multiplexing.mp4). I’ll conclude with a brief description of current applications that have arisen from our progress in traversing the scales from mathematical design in single cells to observable dynamics at the macroscopic level. |
Tuesday, March 3, 2020 1:03PM - 1:39PM |
G36.00004: Context dependence of biological circuits: Predictive models and engineering solutions Invited Speaker: Domitilla Del Vecchio Engineering biology has tremendous potential to impact a number of applications, from energy, to environment, to health. As the sophistication of engineered biological circuits increases, the ability to predict system behavior becomes more limited. In fact, while a system’s component may be well characterized in isolation, the salient properties of this component often change in surprising ways once it interacts with other components in the cell. This context-dependence of biological circuits makes it difficult to perform rational design and often leads to lengthy, combinatorial, design procedures where each component is re-designed ad hoc when other parts are added to a system. In this talk, I will review some causes of context-dependence. I will then focus on problems of resource loading and describe a design-oriented mathematical model that accounts for it. I will introduce a general engineering framework, grounded on control theoretic concepts, that can serve as a basis for creating devices that mitigate context-dependence. Example devices will be introduced that mitigate context-dependence due to resource loading in both bacterial and mammalian genetic circuits. These solutions support rational and modular design of sophisticated genetic circuits and can serve for engineering biological circuits that are more reliable and predictable. |
Tuesday, March 3, 2020 1:39PM - 2:15PM |
G36.00005: Universality in Cardiac Dynamics Invited Speaker: Leon Glass Cardiac dynamics displays universal features that stem from similarities in the underlying molecules and structures in the hearts of different species. But the universality can also be considered from the context of nonlinear dynamics. Nonlinear dynamical processes of wave initiation, wave propagation and wave collision prevail over diverse organisms and experimental preparations. Concepts such as period-doubling bifurcations, Cantor sets, and circle maps arise naturally. Application of these concepts provides a physical perspective to the classification of cardiac arrhythmias by cardiologists. Determining the factors that facilitate or impede the persistence of cardiac arrhythmias offer potential directions for improving therapy. I will illustrate these ideas with examples derived from theory, experiment and clinical data with emphasis on paroxysmal rhythms that start and stop suddenly. I will mention several different cardiac arrhythmias including "palpitations", heart block, atrial fibrillation, ventricular tachycardia. The talk may be personally relevant if you (or a close friend or relative) have experienced one of these common arrhythmias. |
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