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NNadir

NNadir's Journal
NNadir's Journal
January 16, 2021

The next person that searches for Black women in computational biology...

There's a new scientific journal (like we needed more?) called Nature Computational Science .

For the inaugural issue which happens to be published inaugural week when decency is restored to the US Presidency, there is this wonderful article about the future we all desire, here at least: Connecting Black women in computational biology (Chirigati, F., Rastogi, A. Connecting Black women in computational biology. Nat Comput Sci 1, 11–13 (2021). )

It should be open sourced, but some excerpts from the interview with Jenea Adams, a second year PhD student who created the Black Women in Computational Biology Network:

I got my bachelor’s from the University of Dayton in biology, and I had a minor in computer science. After realizing that medical school was not for me, I was quite interested in blending my curiosity for mathematics and programming with my long-term excitement for biology. Initially, I did not know anyone in the field of computational biology, but I had mentors and advisors who pushed me in the direction of relevant resources, since the University of Dayton didn’t have a computational biology curriculum. By the time I completed a bioinformatics Research Experiences for Undergraduates (REU) program at the University of Pittsburgh, I realized that I wanted to pursue a PhD in this field, not only because it was an exciting field research-wise, but also due to the diversity in terms of people’s backgrounds. Eventually, this led me to the University of Pennsylvania, where I have been working with computational genomics...

...My main role model was Ivet Bahar from the University of Pittsburgh, who was my advisor during my REU program. I saw a really powerful woman leading an important department at the university and in computational science, and she inspired me to reach for more and think outside of my comfort zone. At the time, I didn’t know many women in the field, and I certainly didn’t know any women who looked like me in the field, so she was definitely inspiring to me...

... It was honestly a natural process. I decided to search for ‘number of Black women with degrees in computational biology’ on the Internet and found nothing. There was an editorial on women in the field, but nothing relevant to race or ethnicity demographics of the field. I didn’t put that much thought into it, but I knew that someone like me was going to really appreciate being able to find other Black women by doing a simple search...

... Now, we have a new website that is so much more and symbolizes our growth into a full organization. The next person that searches for Black women in computational biology will be able to find us...


I have no comment to add except kudos to Ms. (eventually "Dr." ) Adams


January 16, 2021

Exploration of the Plutonium/Plutonium Hydride Phase Diagram.

(Graphics in this and previous posts may not be visible in Google Chrome, but should show up in Microsoft Edge, Firefox and Android.)

The paper I'll discuss in this post is this one: Quantum Accurate Prediction of Plutonium–Plutonium Dihydride Phase Equilibrium Using a Lattice Gas Model (Ryan Gotchy Mullen and Nir Goldman, The Journal of Physical Chemistry C 2020 124 (38), 20881-20888).

Not so long ago in this space, I noted that in nuclear fission, some americium isotopes exhibit a very high yield of neutrons, called generally "multiplicity," and thus are capable of extraordinary breeding ratios: Electrochemical oxidation of 243Am(III) in nitric acid by a terpyridyl-derivatized electrode.

Although americium will always be produced in a fission nuclear reactor having any kind of fuel efficient high burn up, the reality is that, even though Am-241, the lightest commonly available americium isotope, exhibits high multiplicity in the fast neutron spectrum, it is still 3 mass units separated from its natural source, uranium-238. It is also true that there is not enough americium on the planet - even though inventories in used nuclear fuel are significant - to work toward the immediate elimination of dangerous fossil fuels while still preserving human development goals and the elimination of poverty.

There is, by contrast, enough plutonium available in used nuclear fuel to power all of the world's energy demand, roughly 600 EJ/year, by utilizing a type of nuclear reactor currently under commercial development by a number of companies and laboratories: The "Breed and Burn" type reactor, Sekimoto's "Candle Reactor" and variants thereof. This strategy would be sufficient to provide all of humanity's energy needs for centuries without operating a single energy mine of any kind anywhere on the planet using uranium already mined and isolated - including "depleted uranium" - as well as the thorium mined and dumped in order to serve the ridiculous so called "renewable" wind industry and other lanthanide dependent industries.

Light A Candle, An Innovative Burnup Strategy for Nuclear Reactors.

In order to assure that sufficient plutonium remains available for this purpose, as well as to provide for other uses for neutrons beyond fuel breeding, it is desirable to have as high a multiplicity as possible for plutonium. In the fast neutron spectrum, plutonium is always a breeder fuel, but how well it breeds is a function of the chemical form of the element, for example, whether it exist as oxides or nitrides or some other compound. Metallic plutonium, although it has a complex phase diagram, gives the highest multiplicity among these options. Very old literature, from the 1960's, indicates that the highest multiplicity ever observed in plutonium, giving a breeding ratio of over 1.5, is available in liquid plutonium. (cf. E.V. Evans, Editor, Fast Breeder Reactors, Proceedings of the London Conference on Fast Breeder Reactors, 17-19 May, 1966, Whitman, in "Fast Breeder Reactor Development in the United States, paper 3/2 pg. 286 )

I have been thinking about and studying the literature associated with liquid plutonium for a number of years now with particular attention to an experimental reactor that was being described in the 1966 reference just above, which operated at Los Alamos nearly sixty years ago, the LAMPRE reactor. This reactor utilized tantalum capsules to contain the plutonium, tantalum and tungsten being the only two metals that do not dissolve in liquid plutonium. Tantalum was selected because of the difficulty of machining and welding tungsten.

No device dependent on tantalum can be considered sustainable, since the element is a "critical element," one which is easily subject to depletion with rising use. In addition, it is a "conflict element," an element mined under appalling conditions often involving human slavery, where some of the slaves are children. (The main use for the element today is for supercapacitors in cell phones.)

It does seem to me that advances in materials science over the last 60 years may well eliminate the need for tantalum for the purpose for liquid plutonium, and that composite ceramics may be the key to solving this technical problem.

During operations of LAMPRE, it was noted that the surface of the liquid plutonium during operation became coated with a solid material. To my knowledge it was not chemically analyzed, but most likely it was metallic and contained fission products like the element strontium (which is insoluble in liquid plutonium and has a melting point of 777°C, higher than the LAMPRE operating temperature) as well as intermetallic phases like those between zirconium, a fission product, and plutonium.

(Plutonium Handbook, O.J. Wick Ed., M.D. Freshly, Vol 2, Chap 20 . pg 662-664, Gordon and Breach Scientific Publishers 1967. This offers a fairly illuminating, if brief, description of the irradiation of a liquid plutonium/iron eutectic in the LAMPRE reactor.)

Here is the phase binary diagram of the zirconium-plutonium system:



(cf. Plutonium Handbook, O.J. Wick Ed. Ellinger, Land and Gschneidner, Vol 1, Chap7. pg 227, Gordon and Breach Scientific Publishers 1967)

Although this binary phase diagram comes from a reference now 53 years old, it is essentially equivalent to the ATSM database version published in 2007 which includes more recent references, with the benefit that this older version is better labeled with allotropes as opposed to more arcane space groups accessed by keys in the ASM version. It is notable that the ASM version shows more completely the closing of the ellipsoid Zr solid + Pu liquid region at increasing Zr concentrations up to the melting point of zirconium, 1855°C, as one should well expect.

An aptly named review article from last year refers to this phase diagram as well as CALPHAD (Computer Coupling of Phase Diagrams and Thermochemistry) models and other updates: Experimental and Modeling Review of the Plutonium-Zirconium (Pu-Zr) System: Lost in Translation and Over Time? (Aurélien Perron & Patrice E. A. Turchi , ( J. Phase Equilib. Diffus. 41, 756–763 (2020))

In any case, this binary diagram is a vast over simplification of the putative nature of the solid phase on the LAMPRE fuel surface, but does indicate that it is possible to saturate liquid plutonium with zirconium. I have in my files, more complex ternary phase diagrams, for example, the iron zirconium plutonium system and the iron uranium zirconium system, but I will spare the reader these. Real systems are even more complex, given the plethora of elements in the periodic table present as fission products and/or structural materials.

Nevertheless, these complex systems suggest the possibility of peritectoid systems, in which solid phases crystallize out of solutions. It is a property of peritectics that on occasion they can represent inert coatings, since they are quasi-stable at the peritectoid point, with limitations in further penetrations of a given element into this system, something that was not likely explored very deeply half a century ago.

Although historically it was believed that compound formation was not involved in these phases, it seems that the modern interpretation is quite different and that several of the phases are indeed thought to be peritectoid in nature.



References 4 and 15, however, date from the 1960's.

Nevertheless one can look at something approximating a "synthetic peritectoid" of plutonium to moderate the rate of corrosion in the design of a nuclear reactor that is in fact, designed to eat through its fuel. Modern computational capabilities, not available in the period between 1960-1980 -when the bulk of our nuclear fleet much of which still operates today was designed and built - can certainly play a role in materials design that must be employed to allow nuclear energy to do what it must do to save the world from the ongoing disaster of climate change.

Thus examination of the phase diagrams of plutonium with other elements always catch my eye. Hydrogen is moderating, of course, which precludes a "breed and burn" system, so it's not clear that this particular system would be useful as a containment strategy exploiting the benefits of liquid plutonium. But it is the process, and not the result, which is most important here.

From the introduction to the text:

The unique material properties of plutonium make it a possible source of heat to generate steam in power production or to power radioisotope thermoelectric generators for space probes and, once upon a time, in pacemakers.(1) However, even trace amounts of hydrogen gas or water vapor dissociatively absorb in plutonium because of the high inherent reactivity of the metal. Above a temperature-dependent solubility limit, the absorbed H atoms aggregate to form plutonium dihydride (PuH2) flakes or powder.(2) Plutonium hydride can further catalyze rapid, catastrophic oxidation or induce pyrophoricity,(3) generating toxic waste. As a result, understanding plutonium corrosion properties is of primary importance for its continued use in many application areas.

The complexities of plutonium hydriding can be illustrated by a comparison to hydriding in a more common metal, such as palladium. The critical temperature of the palladium–palladium hydride phase envelope is 550 K (277 °C), well below the palladium metal melting temperature of 1828 K (1555 °C).(4) In contrast, solid plutonium dihydride (PuH2) will crystallize from liquid Pu that is exposed to hydrogen gas.(5) In addition, hydriding in face-centered cubic (fcc) ?-Pu (of interest for engineering applications because of its high ductility(6)) induces a large volume expansion of 54%, compared to an expansion of only ?10% in palladium hydriding, resulting in flaking and the complete degradation of Pu-based materials because of this lattice mismatch. Finally, neutron diffraction reveals that H atoms randomly occupy interstitial octahedral (O) sites in palladium hydride.(7) In contrast, no neutron diffraction studies have been performed on ?-Pu or PuH2 to indicate how H atoms partition between O sites and tetrahedral (T) sites, though investigations of lanthanide hydrides show that O sites are not occupied until all available T sites are filled.(8)

Conducting experiments with plutonium is exceedingly difficult because of its toxicity and radioactivity. The lowest temperature at which the composition of the PuH2 phase has been reported is 773 K (500 °C).(5) Mulford and Sturdy additionally reported equilibrium pressures at 673 and 723 K (400 and 450 °C) but were unable to determine the equilibrium compositions at these temperatures, reporting that it took 20 h to equilibrate at each trial composition...


I have always known that plutonium is a very active metal, but the idea that hydrides are involved in the dissociative absorption of water into the metal is something I had not considered. This should have some implications in connection with the long term stability of nuclear weapons, reducing their reliability - a good thing - I would think if the core is not desiccated with regular maintenance to address saturation of the desiccant would further reduce their viability of weapons. (We need to do a "sword into ploughshares" kind of thing with plutonium, something with which VP Al Gore had notable success with negotiating with Russia in the 1990's with enriched uranium, pre-Putin of course.)

Later on, the introduction gives the paper's raison d’être:

...Conducting experiments with plutonium is exceedingly difficult because of its toxicity and radioactivity. The lowest temperature at which the composition of the PuH2 phase has been reported is 773 K (500 °C).(5) Mulford and Sturdy additionally reported equilibrium pressures at 673 and 723 K (400 and 450 °C) but were unable to determine the equilibrium compositions at these temperatures, reporting that it took 20 h to equilibrate at each trial composition. Allen(9) and Richmond et al.(10) both published equilibrium pressures but only determined the lower solubility limit of H in Ga-stabilized ?-Pu and not the upper limit in the PuH2 phase...


Ga-stabilized ?-Pu is the form of plutonium utilized in nuclear weapons. An interesting and fun bit of history is that the Russians and the Americans each figured out in the 1950's that they both were using this alloy in their weapons because the gallium/plutonium alloy was the only phase diagram that was consistently not published in the open scientific literature because it was regarded as "classified."

...This scarcity of experimental data for bulk plutonium hydriding makes computer model prediction particularly attractive for possible chemical and environmental studies. Recent efforts have utilized density functional theory (DFT) to assess the crystal structure, density, magnetization, conductivity, elasticity, and reactivity of plutonium(11?18) and plutonium hydrides.(19?22) These properties were computed from energy-minimized configurations at zero kelvin, which excludes potentially important thermal effects on the free energy as a function of composition...


The paper goes on to discuss the issue of computer time required to do various types of calculations associated with computer models, density function theory (DFT) for example and lattice gas models. On a simplistic level, these calculations should be expected to be computationally expensive given the fact that plutonium metal involves 94 electrons for each atom, but great strides have been made in the last 50 years in accessing meaningful data using approximations, a task that was initiated, among other places, with the Born-Oppenheimer approximation which assumed static nuclei. People with a college level background in quantum physics/chemistry will recall that exact solutions to energy calculations only exist for the (unbonded) hydrogen atom, and all other calculations in all other systems require iterative calculations that converge on solutions. These systems have become increasingly sophisticated and useful. Just one example is Orbital-free density functional theory which is an "electron gas" model for finding the solutions which the Kohn-Sham theorem predicts.

In the text a simplification utilized is to restrict hydrogen atoms in plutonium hydride to tetrahedral (T) and octahedral (O) sites in the lattice.

Some sample math porn from the paper:

The Hamiltonian of a PuHx lattice gas in the grand canonical ensemble is



where the configurational potential energy Econfig, the vibrational free energy Fvib, and number of hydrogen atoms NH are properties of the microstate while the chemical potential of a gas-phase hydrogen molecule ?H2, the number of plutonium atoms NPu, and the temperature T are held constant. Each absorbed H is treated as an independent quantum harmonic oscillator. Consequently, eq 1 contains the analytic free energy Fvib rather than a potential energy Evib and corresponding quantum degrees of freedom. A P?V term for H in the Pu lattice is not included in eq 1 because under the conditions studied here, its value is several orders of magnitude smaller than other terms. The impact of plutonium defects on Pu–PuH2 equilibrium is not considered in this work...

...Because of the likely strong screening effects of the intervening plutonium atoms, we parameterize the change in energy using only the number of occupied nearest neighbor sites surrounding an occupied O or T site. This results in three types of H–H structures: those comprised of hydrogens in neighboring T sites (ETT), those in neighboring O sites (EOO), and cross-interactions (EOT). As will be shown, all OO and OT structures are sufficiently energetically prohibitive as to be rare in either ?-Pu or PuH2 phases. Accordingly, we ignore the change in energy induced by an OO structure when OT structures are present because the latter increase the energy significantly more than the former. The configurational potential energy is



where ni is 1 if site i is occupied and 0 otherwise, and the function EOT accounts for H–H interactions between a hydrogen in an O site and the NiT hydrogens in the nearest neighbor T sites. ETT, EOO, and NiO are defined similarly. The number of occupied neighbors NiT and NiO are computed using periodic boundary conditions. The first sum is over T sites, the second sum is over O sites, and the Heaviside function ? (x) is 1 if x ? 0 and 0 otherwise.

Zero-point energies and entropic contributions from the vibration of light interstitials such as H in metals can be significant. Changes in the plutonium vibrational frequencies are not included because Pu atoms are much heavier than the absorbed H atoms. The insertion of a hydrogen atom, on the other hand, creates three vibrational modes that did not exist in the previous configuration. These modes are treated as quantum harmonic oscillators, with the following analytical free-energy expression

where ni is 1 if site i is occupied and 0 otherwise, and the function EOT accounts for H–H interactions between a hydrogen in an O site and the NiT hydrogens in the nearest neighbor T sites. ETT, EOO, and NiO are defined similarly. The number of occupied neighbors NiT and NiO are computed using periodic boundary conditions. The first sum is over T sites, the second sum is over O sites, and the Heaviside function ? (x) is 1 if x ? 0 and 0 otherwise.

Zero-point energies and entropic contributions from the vibration of light interstitials such as H in metals can be significant. Changes in the plutonium vibrational frequencies are not included because Pu atoms are much heavier than the absorbed H atoms. The insertion of a hydrogen atom, on the other hand, creates three vibrational modes that did not exist in the previous configuration. These modes are treated as quantum harmonic oscillators, with the following analytical free-energy expression



Here, ?ij is the vibrational temperature ℏ?ij/kB for frequency ?ij of a hydrogen in site i along normal mode j. We parameterized ?ij as a function of NiT to account for the decrease in ?ij as the plutonium lattice expands with the absorption of hydrogen...



Some pictures from the text:




The caption:

Figure 1. Snapshots of DFT-optimized PuHx configurations. Pu atoms are gray, H atoms in O sites are blue, and H atoms in T sites are red.




The caption:

Figure 2. Change in potential energy for inserting a hydrogen into a site with the specified number of occupied neighboring sites. Filled symbols indicate parameters computed from DFT energies while open symbols were determined from linear interpolation.




The caption:

Figure 3. (Left) 2D free energy projected onto the number of hydrogen atoms in O sites NHO and in T sites NHT at 673 K for a system of NPu = 32 and reweighted to . Dashed lines show the boundaries of integration for determining . (Right) ?-Pu, PuH2, and metastable multiphase configurations. The corresponding location of each configuration on the free-energy surface is indicated by an arrow. Pu atoms are gray, H atoms in O sites are blue, and H atoms in T sites are red.




The caption:

Figure 4. (a) Free energy normalized by NPu projected onto the ratio of hydrogen-to-plutonium atoms at temperature 673 K for systems of NPu = 4 (light blue), 32 (black), 108, 256, and 500 (dark blue) and reweighted to the equilibrium chemical potential. (b) Equilibrium chemical potential as a function of system size. Error bars are smaller than the symbol size.





The caption:

Figure 5. Free energy projected onto the ratio of hydrogen-to-plutonium atoms for a system of NPu = 32 at temperatures 298, 373, 473, 573, 673, 723, and 773 K and reweighted to the equilibrium chemical potential for (a) the ?-Pu basin and (b) the PuH2 basin. The gray arrow shows the direction of increasing temperature. (c) Van’t Hoff plot of equilibrium pressures from experiment (red triangles,(5) blue squares,(9) and green filled circles(10)), and simulation (black open circles). Error bars on simulation data are smaller than the symbol size.


From the conclusion to the paper:

Our lattice gas approach accounts for H–H interactions in nearest neighbor O and T sites and leverages a tractable number of energies computed via DFT. This allows for the calculation of accurate Pu–PuH2 phase envelopes at a fraction of the cost of standard quantum mechanical approaches. Our results yield quantitative agreement with direct experimental measurements of the solubility limits of hydrogen in plutonium at high temperatures but are higher than previous extrapolations to room-temperature solubilities by six orders of magnitude. We predict the heat of formation of PuH2 to within 7–16 kJ/mol of the experimental range of results...

...We anticipate that our lattice gas model could be parameterized to examine the hydride phase envelopes of other fcc actinides, rare earth metals, or transition metals (e.g., thorium, cerium, and palladium). Overall, our predictions provide a baseline to guide future plutonium experiments...


I'm not shy in offering my opinion that if we are to save the world, we should definitely have lots and lots of "future plutonium experiments"

I trust you're having a nice and safe weekend, as we all look forward to having a real President of the United States again in this coming week.
January 16, 2021

Large Scale Continuous Flow Synthesis En Route to the Synthesis of the Antiviral Remsdesivir.

The paper to which I'll briefly refer (it's open sourced) to make a point relevant to our current situation is this one: Development of a Large-Scale Cyanation Process Using Continuous Flow Chemistry En Route to the Synthesis of Remdesivir (Tiago Vieira, Andrew C. Stevens, Andrei Chtchemelinine, Detian Gao, Pavel Badalov, and Lars Heumann Organic Process Research & Development 2020 24 (10), 2113-2121)

Today, between normal duties, I took a little time out to attend some lectures put together by my section of the ACS and hosted by Professor Spencer Knapp of Rutgers, on Zoom: 2021 Synthesis on Scale Symposium One of the speakers was Lars Heumann of Gilead, who described beautifully the total synthesis of Remdesivir.

I know...I know...I know...

I'm used to hearing all the time about how "evil" Gilead is because their making a ton of money on the antiviral remdesivir which is a controversial and marginally effective drug in the treatment of Covid-19.

I know...I know...I know...

Donald Rumsfeld had a position in Gilead.

The pharmaceutical industry is evil...I know...I know...I know...

I guess it would be too much to appreciate all the hard work that goes into producing a drug after its discovered. The task of the medicinal chemist is to simply make molecules by the most effective quick route for the purpose of screening. It is rare that the syntheses in this context can be economically or viably scaled up to production levels.

Although I'm no longer actively as engaged as I once was in process chemistry support, I remember very well the period in which the scale up of HIV drugs was at the forefront of the industry. I was a foot soldier in a veritable army of scientists who solved incredible problems, coordinating logistics from all over the world, quite literally, to bring those drugs to market.

Dr. Heumann's lecture reminded be of those days.

Remsdesivir was developed for the treatment of Ebola, where it is clearly effective. It was done in an extremely high pressure environment, with the synthesis going from milligrams to kilograms (to support early clinical trials) in a matter of months. Making the drug on a ton scale was also required in a matter of months.

The drug is a nucleoside mimetic which interferes with viral reverse transcription from viral RNA to active DNA utilized for the synthesis of viral particles.

Here is a total synthesis of remdesivir, a variant of which, on scale, Dr. Heumann walked us through today:



It is described, also open sourced here: Discovery and Synthesis of a Phosphoramidate Prodrug of a Pyrrolo[2,1-f[triazin-4-amino] Adenine C-Nucleoside (GS-5734) for the Treatment of Ebola and Emerging Viruses] (Dustin Siegel, Hon C. Hui, Edward Doerffler, Michael O. Clarke, Kwon Chun, Lijun Zhang, Sean Neville, Ernest Carra, Willard Lew, Bruce Ross, Queenie Wang, Lydia Wolfe, Robert Jordan, Veronica Soloveva, John Knox, Jason Perry, Michel Perron, Kirsten M. Stray, Ona Barauskas, Joy Y. Feng, Yili Xu, Gary Lee, Arnold L. Rheingold, Adrian S. Ray, Roy Bannister, Robert Strickley, Swami Swaminathan, William A. Lee, Sina Bavari, Tomas Cihlar, Michael K. Lo, Travis K. Warren, and Richard L. Mackman
Journal of Medicinal Chemistry 2017 60 (5), 1648-1661)

The length of the list of authors should give some insight to how much work went into this project. When one considers all of the training that went into the education of this authors, one's mind should be blown.

I know...I know...I know...Donald Rumsfeld...profits....gasp.

The final industrial synthesis, is similar.

What is beautiful about the synthesis, as is described in the paper linked at the outset is that this process is a continuous flow process, as opposed to a batch process.

Continuous flow processes are cleaner, safer, more reliable, and generally cheaper than batch processes. Since there was a risk of generating hydrogen cyanide gas in the reaction, this was a big deal. Dr. Heumann's lecture featured some photographs of chemists and chemical operators in full protective suits with oxygen tanks and handy cyanide antidotes, during one step in the synthesis.

These people quite literally risked their lives to make this drug.

That matters.

I don't think people can really grasp that, understand that. They think that drugs come out of a magic faucet somehow, I think.

I cannot tell you what goes into scale up of drugs and vaccines in a brief post, but it does involve incredible sacrifice, and we should appreciate that on some level it can be heroic.

Here is a photograph, from a recent news section of Nature of reactors in which the Covid-Vaccines are being prepared:



How COVID unlocked the power of RNA vaccines (Elie Dolgin, Nature News January 12, 2021.)

Have a nice weekend.

January 16, 2021

Science on Saturday lecture: How to Recognize AI Snake Oil.

PPPL's science on Saturday lecture tomorrow morning by Princeton University Professor Arvind Narayanan is entitled "How to Recognize AI Snake Oil."

Sign up here:

Science on Saturday, on Zoom

Dr. Narayanan spoke a few years back when Science on Saturday was being held live at PPPL. I recall it as being quite interesting. (It's very, very, very rare when a PPPL Science on Saturday is not interesting.)

As the talks have moved to Zoom, they are now accessible around the world. They are held at 9:30 am EST, with a Q&A session after the talks ending usually by 11:30. The talks themselves are about an hour generally.

January 15, 2021

A New Type of Niobium Phosphate Compositing Carbon Nanotube Used as Anode Material...

I came across this paper in the journal ACS Sustainable Chemistry & Engineering:

P4Nb2O15@CNTs: A New Type of Niobium Phosphate Compositing Carbon Nanotube Used as Anode Material for High-Rate Lithium Storage (Peng Hei, Shanshan Luo, Kuo Wei, Junshuang Zhou, Yufeng Zhao, and Faming Gao ACS Sustainable Chemistry & Engineering 2021 9 (1), 216-223)

One of the great technical tragedies of our age is the pernicious belief that energy storage is both "green" and "sustainable." It is not.

Another is to confuse these magical terms, "green," and "sustainable" with human justice.

The great tragedy of lithium batteries, about which I often rale, is the dependence on cobalt, which is mined under horrendous conditions in Central Africa, conditions that should - but somehow doesn't - appall anyone concerned with human rights.

(Don't worry; be happy. Elon Musk says his cobalt is "fair trade." He's full of shit, but we have to believe him, because he's Elon Musk, Ayn Randian hero of everything.)

The authors of this paper have an idea. Let's replace cobalt with, um, niobium.

Niobium is a cogener of tantalum. Tantalum is widely used in cell phones and other electronic devices, which is also a conflict metal mine mined "under horrendous conditions in Central Africa, conditions that should - but somehow doesn't - appall anyone concerned with human rights." All tantalum ores are also niobium ores.

How anyone can call this substitution "sustainable" is beyond me.

Sorry to get "political" about "science," but these things almost drive me insane.

In these times, reality is defined by marketing and nothing else.

History will not forgive us nor should it.

January 14, 2021

"It was the last meaningful election we ever had. We chose unity and we got dictatorship."

Garry Kasparov opinion piece on CNN:

...History teaches us the cost of well-meaning but shortsighted attempts to sacrifice justice for unity. Russians learned this in the hardest possible way after the fall of the Soviet Union. As I discussed at length in my book, Winter Is Coming, they declined to root out the KGB security state in the interest of national harmony. It would be too traumatic, our leaders said, to expose the countless atrocities the Soviet security forces committed and to punish their authors.

A feeble truth commission was quickly abandoned by President Boris Yeltsin, and soon even the Soviet archives were closed, although not before researchers like Vladimir Bukovsky revealed some of the KGB's atrocities. The KGB's name was changed to the FSB and its members quietly stayed in touch and intact. The result? A mere nine years after the Soviet Union collapsed in 1991, Russia elected a former KGB lieutenant colonel, Vladimir Putin, to the presidency. It was the last meaningful election we ever had. We chose unity and we got dictatorship.

America should not make a similar mistake. The truth may hurt, but lies will do far greater damage in the end. Americans should be prepared for a long fight against these anti-democratic forces. The attack on the Capitol has opened every eye; there can be no more feigned ignorance of the crisis...


Full text:

Garry Kasparov: What happens next
January 13, 2021

I just watched "1917."


My grandfather was a terrible alcoholic who used to beat my Grandmother, and my father, his brother and his sisters.

He'd disappear for years at a time, come home on a bender, get violent.

The last time my father saw his father alive, he threw him down the stairs and told him never to set foot in the house again. My grandfather was trying to burn my grandmother's face off with a hot iron.

Two or three weeks later, they dragged my grandfather's body out of the East River, full of stab holes with live eels eating them. My father, then in his late teens or early 20's, identified the body. The cops never looked for the murderer.

They were going to bury him in Potter's field in NYC, but someone contacted the British Government, who in light of his combat experience and medals in the Scottish Black Watch, buried him with full military honors in soil transported from Scotland. The funeral was so elaborate, it was the only time in my father's life that my father was proud of his.

The last time I saw my Aunt, we took her to a restaurant. She was a loquacious but in her own way elegant woman, gracious to a fault. Thinking it might be the last time I saw her - it was - I asked her about her father, my grandfather, of whom I'd only heard stories, none of the them flattering. My aunt, then in her late 80's, began cursing like a sailor, right in the Restaurant, so loudly that my wife and I wanted to crawl under the table.

Surprisingly, my grandmother continued to love him for decades after his death. All she would say of him was "He was a nice man until he got that silver plate in his head."

"Until he got that silver plate in his head..." It happened during the war, of course. A piece of his skull was blown away.

My cousins and I used to laugh when she said that, "He was a nice man until..."

Of course, this was a time when no one discussed PTSD.

The Second World War was the First, restarted after an interlude. The first changed my life, I think, as much as the Second, of which my father was a veteran.

This movie, "1917," made understand something about my family.

It's a very powerful film.

January 12, 2021

Environmental Inequality Deepened During the COVID-19 in the Developing World

The "Scientific Opinion" paper to which I refer in this post is this one: Environmental Inequality Deepened During the COVID-19 in the Developing World (Yilin Chen, Niru Senthilkumar, Huizhong Shen, and Guofeng Shen Environmental Science & Technology 2021 55 (1), 7-8)

Like all Covid papers, this brief paper is open sourced, and can be read in full at the link.

Some excerpts:

Air pollution is a significant environmental risk factor affecting human health. In many developing countries around the world, exposure to severe air pollution has been associated with thousands to millions of premature deaths every year from cardiovascular diseases, respiratory diseases, etc. Sources of air pollution are complex, but major sources include transportation, industrial, and energy production emissions, primarily from the burning of fossil fuels and biomass. Unequal exposure to air pollutants is often linked with disparities in socioeconomic status (SES). For example, low SES communities often reside closer to major sources of emissions including highways, power plants, and industrial facilities, and experience higher exposure levels of particulate matter (PM2.5) and gas precursors such as nitrogen oxides (NOx), sulfate dioxide (SO2), and volatile organic compounds (VOCs).(1) In rural areas in many developing countries, low SES communities may experience enhanced PM2.5 exposure from biomass and solid fuel combustion for heating and cooking.(2)

The arrival of the COVID-19 pandemic has resulted in swift and radical changes in human activities, including a dramatic reduction in transportation emissions during strict lockdown periods. As a result, NO2 was found to decline during the quarantine period over multiple countries hit by the pandemic.(3) Aside from that, the impact of the pandemic on air quality is mixed...

...Wu and colleagues (2020)(7) fitted negative binomial mixed models using COVID-19 deaths and PM2.5 at the county level in the U.S. as the outcome and exposure, respectively. After adjusting several confounding factors, they found that an increase of 1 ?g/m3 in PM2.5 was associated with an increase of 5% (2–15% as 95% CI) in the COVID-19 death rate. Similar links between ambient air pollution exposure and COVID-19 incidence and mortality was also reported in China,(8,9,11) India,(3) Pakistan,(11) and Indonesia.(11) It has been suggested that the ambient aerosols facilitate the transmission of the virus.(8)...

...As the pandemic goes on, COVID-19 gets widely spreading in rural areas in developing countries. The observed positive relationship between enhanced air pollutant exposures and COVID-19 deaths indicates that the pandemic may be further deepening environmental inequality. Over half of the population in the developing world still rely on solid fuel as their household energy source, exposing to a high level of PM2.5 daily. Besides previous chronic exposure to ambient NO2 and PM2.5, indoor air pollution exposure in developing countries would increase during quarantine, especially in those households heavily relying on solid fuels.(14) As a known leading environmental risk factor for many diseases and premature death, household solid-fuel use may increase the risk to develop severe symptoms among the infected population in the developing world...


I have no additional comment; it speaks for itself.
January 12, 2021

Bright side of the Covid Crisis: Princeton Plasma Physics Labs "Science on Saturday" now on Zoom!

There's really nothing like attending the lectures live, the donuts - especially the donuts - the fun conversations before and after the talks, but this year's are on Zoom. Not quite the same, but then again, people logged in from all over the world.

These lectures, only a few of which each year are about plasma physics and fusion energy, are purely wonderful; I've been attending them for years. They are hosted by Andrew Zweicker, a physicist at the lab responsible for community outreach who also holds a second job as Democratic Assemblyman in the NJ assembly.

It's fun; it's free; and now everyone can "be there," without being there:

Register and sign in on Saturday morning: PPPL Ron Hatcher Science on Saturday.

Last week's was on the revival of the Stellator concept in fusion reactors.

The program:

January 9, 2021

Forbes: We Will Assume That Any Company Hiring a Trump Spokesperson Is Lying In Anything Reported.

This article is written by the Chief Content Editor of the business magazine Forbes, Randall Lane:

A Truth Reckoning: Why We’re Holding Those Who Lied For Trump Accountable

Forbes will assume that any business that hires these people is engaged in fraud and lying.

An excerpt:

Yesterday’s insurrection was rooted in lies. That a fair election was stolen. That a significant defeat was actually a landslide victory. That the world’s oldest democracy, ingeniously insulated via autonomous state voting regimens, is a rigged system. Such lies-upon-lies, repeated frequently and fervently, provided the kindling, the spark, the gasoline.


That Donald Trump devolved from commander-in-chief to liar-in-chief didn’t surprise Forbes: As we’ve chronicled early and often, for all his billions and Barnum-like abilities, he’s been shamelessly exaggerating and prevaricating to our faces for almost four decades. More astonishing: the number of people willing to lend credence to that obvious mendacity on his behalf.

In this time of transition – and pain – reinvigorating democracy requires a reckoning. A truth reckoning. Starting with the people paid by the People to inform the People.

As someone in the business of facts, it’s been especially painful to watch President Trump’s press secretaries debase themselves. Yes, as with their political bosses, spins and omissions and exaggerations are part of the game. But ultimately in PR, core credibility is the coin of the realm.

From Day One at the Trump White House, up has been down, yes has been no, failure has been success. Sean Spicer set the tone with the inauguration crowd size – the worst kind of whopper, as it demanded that people disbelieve their own eyes. The next day, Kellyanne Conway defended Spicer’s lie with a new term, “alternative facts.” Spicer’s successor, Sarah Huckabee Sanders lied at scale, from smearing those who accused Trump of sexual harassment to conjuring jobs statistics. Her successor, Stephanie Grisham, over the course of a year, never even held a press conference, though the BS continued unabated across friendly outlets. And finally, Kayleigh McEnany, Harvard Law graduate, a propaganda prodigy at 32 who makes smiling falsehood an art form...

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