chemistry (11)

COVID, and Math...


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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Nobel Prize in Chemistry...


Topics: Chemistry, Nobel Laureate, Nobel Prize

The Nobel Prize in Chemistry 2020 was awarded jointly to Emmanuelle Charpentier and Jennifer A. Doudna "for the development of a method for genome editing."

The Nobel Prize in Chemistry 2020. Nobel Media AB 2020. Wed. 7 Oct 2020. <>

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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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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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Dr. Moddie Taylor...

Dr. Moddie Taylor, Smithsonian


Topics: African Americans, Chemistry, Diversity in Science, Nanotechnology

Moddie Taylor was born on this date March 3, 1912. He was an African American chemist.

From Nymph, Alabama, Moddie Daniel Taylor was the son of Herbert L. Taylor and Celeste (Oliver) Taylor. His father worked as a postal clerk in St. Louis, Missouri, and it was there that Taylor went to school, graduating from the Charles H. Sumner High School in 1931. He then attended Lincoln University in Jefferson City, Missouri, and graduated with a B.S. in chemistry in 1935 as valedictorian and as a summa cum laude student. He began his teaching career in 1935, working as an instructor until 1939 and then as an assistant professor from 1939 to 1941 at Lincoln University, while also enrolled in the University of Chicago's graduate program in chemistry. He received his M.S. in 1939 and his Ph.D. in 1943.

Taylor married Vivian Ellis on September 8, 1937, and they had one son, Herbert Moddie Taylor. It was during 1945 that Taylor began his two years as an associate chemist for the top-secret Manhattan Project based at the University of Chicago. Taylor's research interest was in rare earth metals (elements which are the products of oxidized metals and which have special properties and several important industrial uses); his chemical contributions to the nation's atomic energy research earned him a Certificate of Merit from the Secretary of War. After the war, he returned to Lincoln University until 1948 when he joined Howard University as an associate professor of chemistry, becoming a full professor in 1959 and head of the chemistry department in 1969.

In 1960, Taylor's First Principles of Chemistry was published; also in that year the Manufacturing Chemists Association as one of the nation’s six top college chemistry teachers selected him. In 1972, Taylor was also awarded an Honor Scroll from the Washington Institute of Chemists for his contributions to research and teaching. Taylor was a member of the American Chemical Society, the American Association for the Advancement of Science, the National Institute of Science, the American Society for Testing Materials, the New York Academy of Sciences, Sigma Xi, and Beta Kappa Chi, and was a fellow of the American Institute of Chemists and the Washington Academy for the Advancement of Science. Taylor retired as a professor emeritus of chemistry from Howard University on April 1, 1976, and died of cancer in Washington, D.C., on September 15, 1976.


African American Registry: Dr. Moddie Taylor

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John E. Hodge...

John E. Hodge, African American Registry (link below)

Topics: African Americans, Chemistry, Diversity in Science, Nanotechnology

John Edward Hodge was born on this date (October 12) in 1914. He was an African American chemist.

From Kansas City, Kansas he was the son of Anna Belle Jackson and John Alfred Hodge. His active mind found certain games and sports to be a challenge. He won a number of model airplane contests in Kansas City. He became an expert at billiards in college, and later in Peoria. Chess was another fascination for John, his father, John Alfred, and his son, John Laurent. He graduated from Sumner High School in 1932 and got his A.B. degree in 1936. Hodge received his M.A. in 1940 from the University of Kansas where he was elected to the PI-ii Beta Kappa scholastic society and the Pi Mu Epsilon honorary mathematics organization. He did his postgraduate studies at Bradley University between 1946 and 1960 and received a diploma from the Federal Executive Institute, Charlottesville, VA in 1971.

Hodges career began as oil chemist in Topeka, Kansas at the Department of Inspections. He was also a professor of chemistry at Western University, Quindaro, KS. In 1941 he began nearly 40 years of service at the USDA Nonhem Regional Research Center in Peoria, IL; where he retired in 1980. During that time (1972) he was visiting professor of chemistry at the University of Campinas, Sao Paulo, Brazil. He also received a Superior Service Award at Washington, D.C., from the U.S. Department of Agriculture in 1953, and two research team awards also. He was chairman of the Division of Carbohydrate Chemistry of the American Chemical Society in 1964, and was an active member of the cereal chemists and other scientific organizations. After retirement Hodge was an adjunct chemistry professor at Bradley University in 1984-85.

Hodge encouraged young black college students to study chemistry. He made tours of historically Black colleges in the South to assess their laboratory capabilities, and recruited summer interns for research experiences. Hodge was on the board of directors of Carver Community Center from 1952 to 1958. In 1953 he was secretary of the Citizens Committee for Peoria Public Schools; as well as secretary for the Mayor's Commission for Senior Citizens, 1982-85. Hodge was an advisory board member at the Central Illinois Agency for the Aging in 1975. John Hodge died on January 3, 1996.


African American Registry: John E. Hodge

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Dr. Bettye Washington Greene...

Science History Institute: Dr. Bettye Washington Greene


Topics: African Americans, Chemistry, Diversity in Science, Nanotechnology, Women in Science


American Chemical Society: Nanotechnology

Bettye Greene was born on March 20, 1935 in Fort Worth, Texas and earned her B.S. from the Tuskegee Institute in 1955 and her Ph.D. from Wayne State University in 1962, studying under Wilfred Heller. She began working for Dow in 1965 in the E.C. Britton Lab, where she specialized in Latex products. According to her former colleague, Rudolph Lindsey, Dr. Greene served as a Consultant on Polymers issues in the Saran Research Laboratory and the Styrene Butadiene (SB) Latex group often utilized her expertise and knowledge. In 1970, Dr. Greene was promoted to the position of senior research chemist. She was subsequently promoted to the position of senior research specialist in 1975.

In addition to her work at Dow, Bettye Greene was active in community service in Midland and was a founding member of the Delta Sigma Theta Sorority, Inc., a national service group for African-American women (actually, more likely one of the alumni chapters). Greene retired from Dow in 1990 and passed away in Midland on June 16, 1995. [1]



Her doctoral dissertation, "Determination of particle size distributions in emulsions by light scattering" was published in 1965.


4968740: Latex-based adhesive prepared by emulsion polymerization
4609434: Composite sheet prepared with stable latexes containing phosphorus surface groups
4506057: Stable latexes containing phosphorus surface groups [2]

Spouse: Veteran Air Force Captain William Miller Greene in 1955, she attended Wayne State University in Detroit, where she earned her Ph.D. in physical chemistry working with Wilfred Heller.

Children: Willetta Greene Johnson, Victor M. Greene; Lisa Kianne Greene [2]


1. Science History Institute Digital Collections: Dr. Bettye Washington Greene
2. Wikipedia/Bettye_Washington_Greene

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No Planet B...



Topics: Chemistry, Climate Change, Economy, Global Warming, Green Tech, Jobs

This week will be historic. In over 150 countries, people are stepping up to support young climate strikers and demand an end to the age of fossil fuels. The climate crisis won’t wait, so neither will we. Source: Global Climate Strike dot net

As with the Parkland demonstrations on mass shootings, young people are leading us - actually, PULLING us over the line to DO something about both important matters.
This is not about being "woke": it's about being aware. The extreme avarice causing this societal division and economic stratification could be just the petard humanity hoists itself with* to extinction. I'm glad you all know that, because old, fossilized wealthy (men mostly) can't see beyond the next quarter; that their wealth also falls to dust if the planet fails beneath them. As far as the youth, this is THEIR planet as those above septuagenarians and octogenarians are exiting it. The very least adults can do is use our ashes to fertilize trees for more oxygen (my personal plans). We should leave something for them to live out their lives and dreams. To do less is the height of arrogance, self-destruction and egomania.

Shakespeare's phrase, *"hoist with his own petard", is an idiom that means "to be harmed by one's own plan to harm someone else" or "to fall into one's own trap", implying that one could be lifted (blown) upward by one's own bomb, or in other words, be foiled by one's own plan. Source: Wikipedia


Black, gooey, greasy oil is the starting material for more than just transportation fuel. It's also the source of dozens of petrochemicals that companies transform into versatile and valued materials for modern life: gleaming paints, tough and moldable plastics, pesticides, and detergents. Industrial processes produce something like beauty out of the ooze. By breaking the hydrocarbons in oil and natural gas into simpler compounds and then assembling those building blocks, scientists long ago learned to construct molecules of exquisite complexity.

Fossil fuels aren't just the feedstock for those reactions; they also provide the heat and pressure that drive them. As a result, industrial chemistry's use of petroleum accounts for 14% of all greenhouse gas emissions. Now, growing numbers of scientists and, more important, companies think the same final compounds could be made by harnessing renewable energy instead of digging up and rearranging hydrocarbons and spewing waste carbon dioxide (CO2) into the air. First, renewable electricity would split abundant molecules such as CO2, water, oxygen (O2), and nitrogen into reactive fragments. Then, more renewable electricity would help stitch those chemical pieces together to create the products that modern society relies on and is unlikely to give up.

Chemists in academia, at startups, and even at industrial giants are testing processes—even prototype plants—that use solar and wind energy, plus air and water, as feedstocks. "We're turning electrons into chemicals," says Nicholas Flanders, CEO of one contender, a startup called Opus 12. The company, located in a low-slung office park in Berkeley, has designed a washing machine–size device that uses electricity to convert water and CO2 from the air into fuels and other molecules, with no need for oil. At the other end of the commercial scale is Siemens, the manufacturing conglomerate based in Munich, Germany. That company is selling large-scale electrolyzers that use electricity to split water into O2 and hydrogen (H2), which can serve as a fuel or chemical feedstock. Even petroleum companies such as Shell and Chevron are looking for ways to turn renewable power into fuels.

Changing the lifeblood of industrial chemistry from fossil fuels to renewable electricity "will not happen in 1 to 2 years," says Maximilian Fleischer, chief expert in energy technology at Siemens. Renewable energy is still too scarce and intermittent for now. However, he adds, "It's a general trend that is accepted by everybody" in the chemical industry.

I repeat:
Tee Public: I'm going to buy this shirt


Can the world make the chemicals it needs without oil?
Robert F. Service, Science Magazine

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Boiling Superconductivity...

Under pressure: calculated structure of lithium magnesium hydride. Lithium atoms appear in green, magnesium in blue and hydrogen in red. (Courtesy: Ying Sun et al/Phys. Rev. Lett.)


Topics: Chemistry, Materials Science, Nanotechnology, Superconductors

A material that remains a superconductor when heated to the boiling point of water has been predicted by physicists in China. Hanyu Liu, Yanming Ma and colleagues at Jilin University have calculated that lithium magnesium hydride will superconduct at temperatures as high as 473 K (200 °C).

The catch is that the hydrogen-rich material must be crushed at 250 GPa, which is on par with pressures at the center of the Earth. While such a pressure could be achieved in the lab, it would be very difficult to perform an experiment to verify the prediction. The team’s research could, however, lead to the discovery of more practical high-temperature superconductors.

Superconductors are materials that, when cooled below a critical temperature, will conduct electricity with zero resistance. Most superconductors need to be chilled to very low temperatures, so the holy grail of superconductivity research is to find a substance that will superconduct at room temperature. This would result in lossless electricity transmission and boost technologies that rely on the generation or detection of magnetic fields.


Superconductivity at the boiling temperature of water is possible, say physicists
Hamish Johnston, Physics World

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A carbon nanocone includes nitrogen atoms around the periphery to improve the material’s solubility. Carbon atoms are shown in gray; hydrogen in white; nitrogen in blue; and oxygen in red.


Topics: Applied Physics, Chemistry, Graphene, Nanotechnology

Graphene, buckyballs, and carbon nanotubes now have a new family member, the nanocone, adding to the types of all-carbon nanostructures with remarkable electronic and optical characteristics and bringing its own promising properties. (J. Am. Chem. Soc., 2019, DOI: 10.1021/jacs.9b06617) Such molecules could be useful for developing efficient organic solar cells or as sensor molecules.

Organic chemist Frank Würthner and postdoctoral researcher Kazutaka Shoyama of the University of Würzburg came up with the method for synthesizing the nanocones, which are 1.68 nm in diameter and 0.432 nm tall. A five-atom ring of carbons forms the cone’s tip. The team used a cross-coupling annulation cascade to add hexagons around the edges of the ring until the molecule grew to 80 carbons. The team added five nitrogen atoms around the periphery of the cone, increasing the crystal’s solubility.


Nanocones extend the graphene toolbox, Neil Savage, Chemical & Engineering News

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From left to right, precursor molecule C24O6, intermediates C22O4 and C20O2 and the final product cyclo [18]carbon C18 created on surface by dissociating CO masking groups using atom manipulation. The bottom row shows atomic force microscopy (AFM) data using a CO functionalized tip. Credit: IBM Research


Topics: Applied Physics, Atomic Force Microscopy, Chemistry, Nanotechnology, Research

A team of researchers from Oxford University and IBM Research has for the first time successfully synthesized the ring-shaped multi-carbon compound cyclocarbon. In their paper published in the journal Science, the group describes the process they used and what they learned about the bonds that hold a cyclocarbon together.

Carbon is one of the most abundant elements, and has been found to exist in many forms, including diamonds and graphene. The researchers with this new effort note that much research has been conducted into the more familiar forms (allotropes) how they are bonded. They further note that less well-known types of carbon have not received nearly as much attention. One of these, called cyclocarbon, has even been the topic of debate. Are the two-neighbor forms bonded by the same length bonds, or are there alternating bonds of shorter and longer lengths? The answer to this question has been difficult to find due to the high reactivity of such forms. The researchers with this new effort set themselves the task of finding the answer once and for all.

The team's approach involved creating a precursor molecule and then whittling it down to the desired form. To that end, they used atomic force microscopy to create linear lines of carbon atoms atop a copper substrate that was covered with salt to prevent the carbon atoms from bonding with the subsurface. They then joined the lines of atoms to form the carbon oxide precursor C24O6, a triangle-shaped form. Next, the team applied high voltage through the AFM to shear off one of the corners of the triangle, resulting in a C22O4 form. They then did the same with the other two corners. The result was a C18 ring—an 18-atom cyclocarbon. After creating the ring, the researchers found that the bonds holding it together were the alternating long- and short-type bonds that had been previously suggested.


Ring-shaped multi-carbon compound cyclocarbon synthesized, Bob Yirka ,

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