Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session L42: Physics of LifeInvited
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Sponsoring Units: DMP FED GSNP Chair: Nitin Samarth, Pennsylvania State Univ Room: LACC 502B |
Wednesday, March 7, 2018 11:15AM - 11:51AM |
L42.00001: Using networks to model cell behaviors Invited Speaker: Reka Albert The Biology of 21st century increasingly relies on cross-disciplinary collaboration. My group at Penn State is collaborating with wet-bench biologists to develop and validate predictive models of various biological systems. Over the years we found that logic-based modeling is very useful in synthesizing qualitative interaction information into a predictive model. The dynamic attractors of these models can be directly related to the real system’s phenotypes and behaviors. This allows connecting a lower-level (e.g. molecular) interaction network to a higher-level (e.g. cellular) phenotype. We recently developed an efficient method to determine the attractor repertoire of a dynamic model based on an integration of the regulatory network and logic into an expanded network. Specific strongly connected components of this expanded network, called stable motifs, can maintain an associated state regardless of the rest of the network, and thus represent points of no return in the dynamics of the system. Control of (a subset of) these stable motifs can guide the system into a desired attractor. I will illustrate stable motifs and their control on our model of epithelial to mesenchymal transition (the first step toward cancer metastasis). Attractor control can form the foundation of therapeutic strategies on a wide application domain. |
Wednesday, March 7, 2018 11:51AM - 12:27PM |
L42.00002: The physics of brain network architecture, function, and control Invited Speaker: Danielle Bassett The human brain is a complex organ characterized by a heterogeneous pattern of structural connections that supports long-range functional interactions. New non-invasive imaging techniques now allow for these patterns to be carefully and comprehensively mapped in individual humans, paving the way for a better understanding of how the complex network architecture of structural wiring supports our thought processes. While a large body of work now focuses on descriptive statistics to characterize these wiring patterns, a critical open question lies in how the organization of these networks constrains the potential repertoire of brain dynamics. In this talk, I will describe an approach for understanding how perturbations to brain dynamics propagate through complex wiring patterns, driving the brain into new states of activity. Drawing on a range of disciplinary tools – from graph theory to network control theory and optimization – I will identify control points in brain networks, characterize trajectories of brain activity states following perturbation to those points, and propose a mechanism for how network control evolves in our brains as we grow from children into adults. Finally, I will describe how these computational tools and approaches can be used to better understand how the brain controls its own dynamics (and we in turn control our own behavior), and also how we can inform stimulation devices to control abnormal brain dynamics, for example in patients with severe epilepsy. |
Wednesday, March 7, 2018 12:27PM - 1:03PM |
L42.00003: Is there universality in biology? Invited Speaker: Nigel Goldenfeld It is sometimes said that there are two reasons why physics is so successful as a science. One is that it deals with very simple problems. The other is that it attempts to account only for universal aspects of systems at a desired level of description, with lower level phenomena subsumed into a small number of adjustable parameters. It is a widespread belief that this approach seems unlikely to be useful in biology, which is intimidatingly complex, where "everything has an exception", and where there are a huge number of undetermined parameters. I will try to argue, nonetheless, that there are important, experimentally-testable aspects of biology that can best be tackled from a physics perspective, and that this can lead to useful new insights into the existence and universal characteristics of living systems. |
Wednesday, March 7, 2018 1:03PM - 1:39PM |
L42.00004: Insights from Insects: Emergent Dynamics in the Physics of Animal Locomotion. Invited Speaker: Simon Sponberg Animals, including ourselves, move through complex and uncertain environments with an ease and agility we find hard to recreate in engineered systems. Indeed the ability to move is a trait of all animals. The physics of organisms is maturing given a convergence of non-linear dynamics, soft active matter, and biophysics of complex systems, along with associated computational tools, time-resolved imaging methods, and rapid prototyping particularly in robotics. There is a long history of considering the organism in physics. Yet it remains challenging to capture the relevant details necessary to identify the interesting, often simple, dynamics that emerge at the level of the organism without just revealing in their complexity. We are making progress faster than ever, especially in understanding the physical and physiological mechanisms of locomotion. High-speed x-ray diffraction through living muscles is connecting active matter principles to the macroscopic material dynamics of this versatile actuator. The brains of small flapping insects are still complex, containing 105-106 neurons. Despite this complexity, we find that they control wingstroke dynamics with as little as 101 bits/wingstroke, mostly through precise timing that takes advantage of muscle’s nonlinearities. Analyzing and manipulating feedback pathways in animals through virtual reality is enabling a dynamic systems description of locomotion that can be surprisingly low dimensional and linear. Using robots as experimental tools to get at biophysical mechanisms, we are discovering how animals’ visual systems can adjust to light levels that vary by 7 orders of magnitude from early afternoon to late dusk. We cannot yet emulate the motility seen in nature, nor derive all behaviors, but for the physicist interested in the workings of nature’s most versatile systems, the neuromechanics of animal locomotion is an exciting opportunity. |
Wednesday, March 7, 2018 1:39PM - 2:15PM |
L42.00005: Physical Biology of Living Embryos Invited Speaker: Hernan Garcia An abiding mystery in biology is how a single cell develops into a multicellular organism. Despite great advances in identifying the molecular players of developmental programs, the quantitative prediction of gene expression patterns from knowledge of DNA regulatory sequence has proven elusive. Technological limitations have kept us in the dark about the dynamics of these regulatory decisions, a necessary first step towards the predictive understanding of developmental response. In this talk I present new technologies and theoretical methods to access and predict developmental decisions in living fruit fly embryos at the single nucleus level. Using this approach we can measure where, when and how fast nuclei express a gene in response to an input morphogen and bridge these dynamics to the resulting macroscopic domains of gene expression that arise throughout the embryo and that lead to the specification of future body parts. In contradiction with the standard picture of gene regulation, we discovered that transcription factors can regulate gene activity in three seemingly decoupled ways. First, they determine a random subset of nuclei that is able to participate in the regulatory game. Second, for those promoters that are randomly turned on, transcription factors also dictate the dynamics with which mRNA is produced in bursts. Finally, transcription factors also regulate the length of time each promoter will partake in gene expression. All of these modes of regulation are necessary in order to create sharp boundaries in the embryo. This work provides a framework to predictively understand and control developmental response by identifying the different regulatory strategies employed by the fly in the generation of patterns of gene expression. |
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