Bulletin of the American Physical Society
Mid-Atlantic Section Meeting 2021
Volume 66, Number 18
Friday–Sunday, December 3–5, 2021; Rutgers University, New Brunswick, New Jersey
Session E04: Biophysics III |
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Chair: Gyan Bhanot, Rutgers University Room: 202B |
Saturday, December 4, 2021 2:00PM - 2:36PM |
E04.00001: A spherical cow model of Covid-19 epidemiology and applications Invited Speaker: Gyan Bhanot In late 2019, a coronavirus called SARS-CoV-2 appeared in Wuhan, China. This virus has since caused a worldwide pandemic, which is still ongoing. The associated respiratory illness, called COVID-19, ranges in severity from a symptomless infection, to common-cold like symptoms, to viral pneumonia, organ failure, neurological complications and sometimes, death. While mortality rates from SARS-CoV-2 infections are significantly lower than from the earlier pandemic in 2003 from the SARS-CoV-1 virus, it has more favorable transmission characteristics, a higher reproduction number, and a long incubation period, when the patient may be asymptomatic but infective. Each country/region instituted varying measures to reduce the rates of infections using lockdown, quarantine, use of masks, reduced movement of people etc. In this paper, after a brief introduction to the origins and spread of the virus, I will describe a simple mathematical epidemiological SIR model for the pandemic, where S $=$ Susceptible, I $=$ Infected, R $=$ Removed: Recovered or Dead. This model accurately describes the initial rise of cases in a pandemic, up to and beyond the initial peak in daily cases. I will then discuss two applications of the model, using public data on caseloads and deaths. The first application was to understand daily caseloads and deaths in the United Kingdom and eight European counties: Norway, Sweden, Denmark, The Netherlands, Italy, France, Germany, and Spain. The results can be used to determine where mitigation effects worked and where they did not. In the second application I will show how to use Change of Address data to understand how the virus spread from its epicenter in the five boroughs of New York City into counties of the tri-state area of New Jersey, Connecticut and New York to cause a second wave in cases because of movements of households. This analysis shows that tracking household movements may be a simple way to predict where new cases are likely to appear. I will end with some caveats on the limitations of the model and prospects for future work. [Preview Abstract] |
Saturday, December 4, 2021 2:36PM - 3:12PM |
E04.00002: Stochastic Oscillations in Biology Invited Speaker: James MacLaurin Oscillations are ubiquitous in biology and are widely thought to play an essential functional role. Most biological systems are also inherently stochastic, and a key challenge for modelers is to understand how the function of the oscillation can remain robust despite significant noise. This talk has two main components. In the first component, I will outline a general method for studying the effect of noise on discrete chemical reaction networks with a large number of particles. Assuming that the averaged system (obtained by taking the large N limit) is oscillatory, I perform a phase reduction procedure to map the high dimensional stochastic system to a one-dimensional phase. I then outline an accurate approximation for the stochastic dynamics of the phase, and I bound the probability of the system leaving a neighborhood of the oscillation, showing that over timescales diverging in N, this is exponentially unlikely. In the second part of the talk I will touch on recent work to understand intracellular stochastic oscillations in calcium. This mechanism of oscillation is different, because the averaged system is not necessarily oscillatory, and stochastic fluctuations can play an essential role even in the large N limit. [Preview Abstract] |
Saturday, December 4, 2021 3:12PM - 3:24PM |
E04.00003: Helium-ion microscopy reveals an intra-cytoplasmic route suitable for SARS-CoV-2 cell-to-cell transmission Antonio Merolli, Leila Kasaei, Leonard Feldman The usual picture of SARS-CoV-2 transmission is extra-cytoplasmic. Virions (the basic virus complex when outside the cell) enter the host cell by docking their spike glycoproteins to the Angiotensin Converting Enzyme 2 (ACE2) on the host cell membrane. Newly replicated virions are then released outside the host cell to propagate the infection via the ACE2 docking mechanism. Antibodies may attack these extra-cellular virions, thus providing immunity. We used scanning Helium-ion microscopy to study the virion propagation in-vitro in a culture of Vero E6 cells prepared at the PHRI RU-Newark (Dr. Selvakumar Subbian). The unprecedented resolution of HeIM and its capacity to scan a large number of samples, showed the presence of: 1)-long tunneling nanotubes (TNT) that connect two or more cells; 2)-multiple cell fusion events; 3)- abundant extracellular vesicles (EV). TNT and cell fusion events are not significantly present in uninfected samples. These three ultrastructural features (TNT; cell fusion; EV) provide an intra-cytoplasmic modality to connect SARS-CoV-2 infected cells, and this may act as an alternative route of viral transmission. This finding may explain the ability of SARS- CoV-2 to survive the immune surveillance and the observation of the breakthrough infections. [Preview Abstract] |
Saturday, December 4, 2021 3:24PM - 3:36PM |
E04.00004: A Novel Micromethod for Measuring the Solubility of Sickle Hemoglobin Mark Fugate, Eli Worth, Frank Ferrone Sickle cell is a genetic disease wherein a point mutation in the hemoglobin amino acid chain allows the protein to polymerize into long fibers in anoxic conditions, deforming red blood cells and causing severe circulatory problems. The search for drug and gene therapeutics which destabilize these fibers is ongoing. Since solubility quantifies the thermodynamic stability of the fiber, measuring sickle hemoglobin solubility is of great importance in this research. Existing techniques for making such measurements are cumbersome and require several hundred milligrams of protein. We have devised a technique for measuring solubility which uses only a few milligrams of protein, prepared as a concentration gradient in a thin (10-20 $\mu m$) layer. We have modified an inverted microscope to measure laser light scattering and optical absorption simultaneously along the gradient, deducing the presence of polymers by detecting the light they scatter and measuring concentration by optical absorption spectroscopy. Solubility is inferred by noting the concentration at which scattering disappears. We will present our initial results along with specific details of the device’s construction, and discuss future directions. [Preview Abstract] |
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