physics (7)

COVID, and Math...

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Image Source: Link below

Topics: Biology, Chemistry, COVID-19, Mathematics, Physics

The year 2020 has been defined by the COVID-19 pandemic: The novel coronavirus responsible for it has infected millions of people and caused more than a million deaths. Like HIV, Zika, Ebola, and many influenza strains, the coronavirus made the evolutionary jump from animals to humans before wreaking widespread havoc. The battle to control it continues. When a disease outbreak is identified—usually through an anomalous spike in cases with similar symptoms—scientists rush to understand the new illness. What type of microbe causes the infection? Where did it come from? How does the infection spread? What are its symptoms? What drugs could treat it? In the current epidemic, science has proceeded at a frenetic pace. Virus genomes are quickly sequenced and analyzed, case and death numbers are visualized daily, and hundreds of preprints are shared every day.

Some scientists rush for their microscopes and lab coats to study a new infection; others leap for their calculators and code. A handful of metrics can characterize a new outbreak, guide public health responses, and inform complex models that can forecast the epidemic’s trajectory. Infectious disease epidemiologists, mathematical biologists, biostatisticians, and others with similar expertise try to answer several questions: How quickly is the infection spreading? What fraction of transmission must be blocked to control the spread? How long is someone infectious? How likely are infected people to be hospitalized or die?

Physics is often considered the most mathematical science, but theory and rigorous mathematical analysis also underlie ecology, evolutionary biology, and epidemiology.1 Ideas and people constantly flow between physics and those fields. In fact, the idea of using mathematics to understand infectious disease spread is older than germ theory itself. Daniel Bernoulli of fluid-mechanics fame devised a model to predict the benefit of smallpox inoculations2 in 1760, and Nobel Prize-winning physician Ronald Ross created mathematical models to encourage the use of mosquito control to reduce malaria transmission.3 Some of today’s most prolific infectious disease modelers originally trained as physicists, including Neil Ferguson of Imperial College London, an adviser to the UK government on its COVID-19 response, and Vittoria Colizza of Sorbonne University in Paris, a leader in network modeling of disease spread.

This article introduces the essential mathematical quantities that characterize an outbreak, summarizes how scientists calculate those numbers, and clarify the nuances in interpreting them. For COVID-19, estimates of those quantities are being shared, debated, and updated daily. Physicists are used to distilling real-world complexity into meaningful, parsimonious models, and they can serve as allies in communicating those ideas to the public.

The math behind epidemics, Alison Hill, Physics Today

Alison Hill is an assistant professor in the Institute for Computational Medicine and the infectious disease dynamics group at Johns Hopkins University in Baltimore, Maryland. She is also a visiting scholar at Harvard University in Cambridge, Massachusetts.

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#BlackInPhysics...

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Topics: African Americans, Diversity in Science, Physics

Throughout the week of 25 October, Black physicists, their allies, and the general public are invited to participate in #BlackInPhysics Week, a social media-based event dedicated to celebrating Black physicists and their contributions to the scientific community and to revealing a more complete picture of what a physicist looks like. Programming includes professional panels, a job fair, and an open mic night. If you are interested in learning more and registering for the events, check out blackinphysics.org or @BlackInPhysics on Twitter.

The lead organizers of #BlackInPhysics Week are Charles D. Brown II, an atomic and condensed-matter physicist; Jessica Esquivel, a particle physicist; and Eileen Gonzales, an astronomer studying brown dwarfs and exoplanets. Co-organizers include Jessica Tucker, a quantum information scientist; LaNell Williams, a biophysicist; Vanessa Sanders, a radiochemist; Bryan Ramson, a particle physicist; Xandria Quichocho, a physics education researcher; Marika Edwards, an astrophysicist, and engineer; Ashley Walker, an astrochemist; Cheyenne Polius, an astrophysicist; and Ciara Sivels, a nuclear engineer.

Brown, Esquivel, Gonzales, Quichocho, and Polius answered questions about #BlackInPhysics Week and described how physics became their passion.

Meet the organizers of #BlackInPhysics Week, Physics Today

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NEMS Photothermal Microscopy...

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Topics: Microscopy, Nanotechnology, NEMS, Physics, Research

Single-molecule microscopy has become an indispensable tool for biochemical analysis. The capability of characterizing distinct properties of individual molecules without averaging has provided us with a different perspective for the existing scientific issues and phenomena. Recently, super-resolution fluorescence microscopy techniques have overcome the optical diffraction limit by the localization of molecule positions. However, the labeling process can potentially modify the intermolecular dynamics. Based on the highly sensitive nanomechanical photothermal microscopy reported previously, we propose optimizations on this label-free microscopy technique toward localization microscopy. A localization precision of 3 Å is achieved with gold nanoparticles, and the detection of polarization-dependent absorption is demonstrated, which opens the door for further improvement with polarization modulation imaging.

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FIG. 2. (a) Schematic of the measurement setup. BE: beam expander. M: mirror. WP: waveplate. LP: linear polarizer. BS: beam splitter. PD: photodetector/power meter. DM: dichroic mirror. ID: iris diaphragm. CCD: charge-coupled device camera. APD: avalanche photodiode detector. (b) The transduction scheme of the trampoline resonator. (c) SEM image of the trampoline resonator.

J. Appl. Phys. 128, 134501 (2020); https://doi.org/10.1063/5.0014905

Nanoelectromechanical photothermal polarization microscopy with 3 Å localization precision, Miao-Hsuan Chien and Silvan Schmid, Journal of Applied Physics

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Nobel Prize in Physics...

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Nobel Prize in Physics, 2020

Topics: Nobel Laureate, Nobel Prize, Physics

The Nobel Prize in Physics 2020 was divided, one half awarded to Roger Penrose “for the discovery that black hole formation is a robust prediction of the general theory of relativity”, the other half jointly to Reinhard Genzel and Andrea Ghez “for the discovery of a supermassive compact object at the centre of our galaxy.”

The Nobel Prize in Physics 2020. NobelPrize.org. Nobel Media AB 2020. Tue. 6 Oct 2020. <https://www.nobelprize.org/prizes/physics/2020/summary/>

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Figure

The spike protein of the SARS-CoV-2 virus (gray) is shown with three small antibodies (pink) attached to its receptor binding domains. The spike attaches at the left to the viral membrane (not shown). DIAMOND LIGHT SOURCE

Topics: Chemistry, COVID-19, Physics, Research

As the world anxiously awaits development of one or more vaccines to tame the SARS-CoV-2 virus, other research continues at a feverish pace to find effective treatments for the disease it causes, COVID-19. That work, in which physicists and chemists are deeply involved, has made significant strides in the past several months and has turned up a few surprises. Researchers at the University of Alberta reported at the August virtual meeting of the American Crystallographic Association that a dipeptide-based protease inhibitor used to treat a fatal coronavirus infection in cats also blocks replication of the SARS-CoV-2 virus in samples of monkey lung tissue. Joanne Lemieux, a biochemist at the university, says the antiviral, known as GC373, works by blocking the function of the main protease (Mpro), an enzyme that cleaves the polyproteins translated from viral RNA into individual proteins once it enters human cells.

Lemieux says GC373 has been shown to have no toxic effects in cats. Anivive, a California company that develops pet medicines, has applied for US Food and Drug Administration approval to begin trials in humans. Lemieux’s group crystallized the Mpro in combination with the drug and produced three-dimensional images of how the drug binds strongly to the active pocket on the enzyme. Although GC373 should be effective in its current form, the group is planning further crystallography experiments at the Stanford Synchrotron Radiation Lightsource (SSRL) and the Canadian Light Source to see if a reformulation could optimize it for human use, she says.

Cats and llamas could offer a path to coronavirus therapies, David Kramer, Physics Today

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Dr. Peter Delfyett, Jr...

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Dr. Peter Delfyett, Jr., National Society of Black Physicists

Topics: Diversity, Diversity in Science, Laser, Physics, Semiconductors

Dr. Peter Delfyett, former NSBP President and NSBP fellow, is the 2020 winner of the William Streifer Scientific Achievement Award. The William Streifer Scientific Achievement Award was established to recognize an exceptional single scientific contribution which has had a significant impact in the field of lasers and electro-optics in the past ten years. Dr. Delfyett has been selected, "For pioneering contributions to semiconductor diode based ultrafast laser science and technology." The Award is endowed by Xerox Corp and Spectra Diode Labs. The Award consists of an honorarium of $2,500 and a medal. The presentation is made at the IEEE Photonics Conference.

Learn more about this award and its previous winners.

Peter Delfyett wins the 2020 William Streifer Scientific Achievement Award, NSBP

#P4TC links:

Diaspora, 13 February 2012

Reducing the Impact of Negative Stereotypes on the Careers of Minority and Women Scientists, November 25, 2010

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Dilemma...

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Green Book Blog: The Technology Dilemma, Zoë Dowling

 

Topics: Biology, Chemistry, COVID-19, Nanotechnology, Physics, Research, STEM


As the coronavirus outbreak roils university campuses across the world, early-career scientists are facing several dilemmas. Many are worrying about the survival of cell cultures, laboratory animals, and other projects critical to their career success. And some are reporting feeling unwelcome pressure to report to their laboratories—even if they don’t think it’s a good idea, given that any gathering can increase the risk of spreading the virus.

It’s unclear exactly how common these concerns are, but social media posts reveal numerous graduate students expressing stress and frustration at requests to come to work. “Just emailed adviser to say I am not comfortable breaking self isolation to come to lab this week. They emailed … saying I have to come in. What do I do?” tweeted an anonymous Ph.D. student on 16 March who doesn’t have essential lab work scheduled. “My health & safety should NOT be subject to the whims of 1 person. It should NOT be this scary/hard to stand up for myself.”

Many universities, including Harvard, have moved to shut down all lab activities except for those that are deemed “essential,” such as maintaining costly cell lines, laboratory equipment, live animals, and in some cases, research relating to COVID-19. But others have yet to ban nonessential research entirely.

 

Amid coronavirus shutdowns, some grad students feel pressure to report to their labs
Michael Price, Science Magazine, AAAS

I feel their pain.


The Scientific Method is very simple in concept:

Problem research - This involves gathering data in the form of previous written papers, published and peer-reviewed; writing notes (for yourself), summaries and reviews.

Hypothesis - This is your question asked from all the research, discussion with your adviser, especially if it's a valid question to ask or research to pursue.

Test the hypothesis - Design of experiment (s) to verify the hypothesis.

Data analysis - Usually with a software package, and a lot of statistical analysis.

Conclusion - Does it support the hypothesis?

- If so, retest several times, to plot an R squared fit of the data, so predictions can be made.

- If not, form another hypothesis and start over.

Often, conclusions are written up for peer review to be considered for journal publication. No one ever gets in on first submission - get used to rejection. Conclusions will be challenged by subject matter experts that may suggest other factors to consider, or another way to phrase something. Eventually, you get published. You can then submit an abstract to present a poster and a talk at a national conference.

Meeting Cancellation

It is with deep regret that we are informing you of the cancellation of the 2020 APS March Meeting in Denver, Colorado. APS leadership has been monitoring the spread of the coronavirus disease (COVID-19) constantly. The decision to cancel was based on the latest scientific data being reported, and the fact that a large number of attendees at this meeting are coming from outside the US, including countries where the CDC upgraded its warning to level 3 as recently as Saturday, February 29.

 

APS Physics: March.APS/about/coronavirus/


Update on Coronavirus

The health and safety of MRS members, attendees, staff, and community are our top priority. For this reason, we are canceling the 2020 MRS Spring Meeting scheduled for April 13-17, 2020, in Phoenix.

With our volunteers, we are exploring options for rescheduling programming to an upcoming event. We will share more information as soon as it becomes available.

 

MRS: Materials Research Society/2020-Spring Meeting


Social distancing and "shelter-in-place" slows the scientific enterprise. Science is in-person and worked out with other humans in labs and libraries. However, I am in support of this action and reducing the impact on the healthcare industry that on normal days are dealing with broken bones, gunshot wounds; cancer and childbirth surgeries with anxious, expectant mothers.

The dilemma is the forces that would reject the science behind this pandemic (and most science in any endeavor), would have us all "go back to work" after two weeks. The curve we're trying to flatten could sharply spike. The infection rates would increase and otherwise healthy people would be stricken. Immunodeficient groups would start getting sick again ...dying again. Our infrastructure is not designed for that many sick or dead people. Science continues with our survival and societal stability.

The persons with the solutions might be chomping-at-the-bit at home for now. Survival insures science will continue ...someday.
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