Zika, Chikungunya, Dengue

The three names in the title designate viroses which are attributable to the dissemination through mosquitos of the species Aedes Aegypti.  Dengue is the oldest from the three diseases and, at least in Brazil, the first cases were reported between 1851 and 1853 with an epidemic episode in 1923. The name of the disease comes from one of the symptoms, joints pain, which leads people to walk with broken movements, like a puppet.

 Dengue was virtually extinct n Brazil during the campaign to eradicate Yellow Fever, which targeted the vector, by eliminating its habitat  n urban areas. Dengue returned to Brazil in the 1980's, probably by the dissemination of the vector from neighboring countries which had less success in eradicating it. At the time, however, I heard an alternative explanation: it stated that populations of the vector remained in the forest areas and that the advance of the urban areas (deforestation) lead to the reintroduction of the vector in the cities. Anyway, the mosquito returned and, with it, the Dengue fever. There is no vaccine (contrary to yellow fever) and so, the only way to control the disease is by controlling the vector.
Since the 1980's we "know" we cannot leave sources of still water exposed to the ambient, because these are preferred sites for reproduction of the mosquito. It is amazing. Last January I was  in the interior of the state of Bahia, an open water reservoir was filled by rain water and in the next day it was already swarming with mosquito larvae. This also shows why it is so difficult to solve the problem, I guarantee about 95% of the population takes the proper measures to avoid mosquito reproduction, the problem is the other 5%.
Dengue is usually not critical, it leads to severe fever (40°C), rashes in the skin, the already mentioned joint pain and some other symptoms, which are similar to influenza. The particularity, however, is that in a second infection there is the risk of development of the hemorrhagic dengue fever and this is very dangerous. There are vaccines in development, but none has been approved to date (as far as I know).
The development of a Dengue vaccine, however, would be no relief to the problem, because of the two other viroses, Chikungunya and Zika. As far as I know, Chikungunya is similar to Dengue (but the virus is different), Zika started as a third virose associated with the mosquito, but supposedly with less severity.
The situation escalated in the second half of 2015, when reports of an increase in cases of microcephaly in the northeast region of Brazil raised the suspicion the there was association with the development of Zika infection in the pregnant women in the first stages of the pregnancy. The brown press started to raise suspicion of relation with the introduction of transgenic mosquitos in the environment, this introduction was an attempt to control the vector.
Although it is possible, the relation between Zika and the microcephaly was not proven, I just read a report telling that only a fraction of pregnant women which had microcephalic babies reported Zika infection during pregnancy. There is the need to investigate this link, and, especially, to identify the mechanism by which a viral infection would affect a baby in the womb (as far as I understood, babies are protected against diseases in the mother). Any pregnant woman traveling through an affected area, however, should take extreme precaution against the mosquito bites.
An important question, however, is our vulnerability to viral infections. Bacterial infections can be combated by antibiotics, micoses can be successfully combated by medicines, even protozoa can be combated by other medicines, but the standard response of a physician to a person with a viral infections is: wait for the body to combat the illness. As we saw in the last Ebola outbreak in Africa, there are powerful antiviral medicines, but these are expensive and their collateral effects are severe.
Here in Brazil we keep trying to control the vector. The situation is critical, but not debilitating. People are not walking ill in the streets and, although the statistics are scaring, not everyone gets these diseases. The scientific community, however, should help, in particular the biologists and the biochemists, to investigate these viruses and their infection mechanisms, and the industry should work in the development of efficient medicines against viral infections.

Can graphite be ferromagnetic?

If people asked me this question last week, I would answer with an emphatic "No!", since then I discovered that my point of view about the matter was based on a prejudice based on an old article published by Heisenberg, which stated that only "d" or "f" electrons could spontaneously polarize. I learned this in the talk given by Prof. Pablo Esquinazi from the University of Leipzig, held in the 6th Workshop on Novel Methods for Electronic Structure Calculations, finished yesterday in La Plata, Argentina.

Magnetic ordering in these cases is a result of unpaired spins related with vacancies (if you still didn't read my point-of-view on things that do not exist, read here). The effect was predicted in graphene, but cannot be experimentally realized. The reason is that not all vacancies may ferromagnetically polarize, only those siting in particular sublattices do and there is no way to create an array of vacancies in graphene sitting only on a particular sublattice, because they are symmetrically equivalent. In graphite the layered structure breaks the symmetry and then the vacancy formation energy becomes different in different sublattices.

But the effect is not restricted to carbon, SiC may present the effect, as well as ZnO. Strange enough, not all oxides present the phenomenon. The effect is very weak and the Curie temperatures reach about room temperature, but it is exciting producing megnetism without Fe, Co, Ni, Cr, Gd, Dy and Tb.

Talking about the event, it s a very sympathetic meeting, with a small number of participants, mostly coming from south american countries, but I was gratefully surprised with the quality of the presentations. I must say I learned something with every talk I watched.

The unbearable persistence of Nothing

Have you ever heard about Aether?  I'm not talking about the chemical compound. You probably heard this word as a footnote in some Physics lecture about the massless medium through which the ancient believed lightwaves propagate in the vacuum. Do you remember now? Well, if your teacher talked about this, moments later he (or she) told you light does not need a medium to propagate, it is an oscillatory perturbation in the electromagnetic field which may travel even in the absence of matter.

This idea, in our present days, is no longer weird. We receive our entertainment from electromagnetic perturbations, we talk to the other side of the world using electromagnetic perturbations and everybody already felt their arm hairs being attracted by a surface under the action of an electrostatic field, certainly no medium is needed for this attraction to happen, but still, this must have caused headaches to the ancients: light travels through nothing, and nothing has properties (it can be electrically and magnetically polarized! at least, there are two physical constants, the vacuum permitivity, and the vacuum permeability).

We, Materials Scientists, are used to the nothing with properties. We call it "Vacancies". Although they are surely occupied by something (in conductors, the free electrons), vacancies are defects created by the absence of atoms in crystal lattice positions. As I always teach my students, vacancies don't exist, what exist are the atoms. Nevertheless, vacancies have properties, they interact with dislocations (another thing that does not exist, but has properties) , they are responsible for diffusion in a solid and, therefore, they have velocity. We use to talk about "vacancy wind" in diffusion (i.e. a wind or nothing, spooky, isn't it?).

Another example of nothing with properties in materials science we have the "holes" in the valence band of the electronic structure in a semiconductor (well, critics will say this belongs to condensed matter physics, but I think we can share responsibility). Here the situation is weirder (as always, when quantum mechanics gets involved). Holes (the absence of electrons) have mass, carry a charge (positive) and even diffract, as every particle does. A particle of nothing!

As a final example of this ode to nothing, we have dark matter (and its cousin, the dark energy). Here at least it is assumed it is something, we just don't know what it is. It is weird to think that only 4,9% of the universe we see is composed by our regular matter, the rest is dark matter and dark energy. As far as we know, dark matter particles could be traveling through our body without our knowledge. Creepy, isn't it.

So, hail to nothing, we couldn't live without it (literally)

On the good ol' practice of writing academic text with LaTeX

I heard about LaTeX for the first time around 1993, when I was working with Prof. Diana Farkas on a manuscript we published in Acta Materialia. I fed her with my text contributions, just a few, since I was then just a master of sciences student. I watched her insert my text in the tex file and compile the source to produce the manuscript. I found that strange, since I was used with a text editor from an unknown company called Microsoft which was introduced just one or two years earlier in our university (we were late).

Then I forgot about that, I wrote my master dissertation using word (and suffering from compatibility problems related to fonts when I printed the text, there was no pdf at that time) and went to Düsseldorf to work in my doctoral thesis. Nobody used LaTeX there, so I wrote my thesis in Word too. I learned how to use the program, so it was less painful to print the text. And , of course, pdf already existed at that time.

I continued working with Word when I returned to Brazil in 1998, for my post-doc at USP. All my connections worked with word, so it seemed good to keep on using the program to write my manuscripts. Then I wrote a paper with Prof. Ryoichi Kikuchi, full of equations. When I received the proofs I noticed that many equations had strange typing errors which I didn't produce in the original manuscript. This was registered in my memory, I corrected the errors returning the proofs and kept using Word.

Some time later I decided to start using LaTeX, I must confess, it was pedantry, an ideologically motivated decision (I support free software since I first read about this in the heroic 1990' s). I believed I was not able to work with a tex file, so I started with LyX. Then the late Prof. Ibrahim (Himo) Ansara came to visit us. He saw me using LyX and told me he was a LaTeX adept. I asked what he used, and he said he edited the raw tex file, because LyX introduces many useless lines in the source. I thought "Is this possible"?

With the time, I discovered he was right. There is no problem using LyX to produce a letter, but if you try to produce a manuscript to be sent to a magazine you will end up with a lot of garbage in the preamble. By the way, soon after that, I discovered what were those errors in the proofs I mentioned before: missing backslashes in a LaTeX math formula. The publisher took my word file and converted it to LaTeX! Finally I started working with the tex file and I still do it today. In the present days I select magazines for my manuscripts based on whether they accept tex files or not, I primarily choose those who accept and use the "word-colonized" magazines only in a last case scenario.

I told all this only to show that the transition from the editor which carries its ultimate usefulness in the name (it is designed to be used in an office) to LaTeX is not easy, but can be done. As I told, I was ideologically motivated and took more than 10 years to make the transition. What bothers me is that my colleagues don' t even try it.

LaTeX is the better option to produce academic texts. Its ability to produce nice quality math equations cannot be even matched by any other text editor. The fact that you can edit the tex file in the raw version (it is ascii coded!) is also an advantage. Everybody who ever needed to insert an extra line in a matrix will agree with me that this is better performed editing the tex file rather than using the infamous "equation editor" of winword. Combined with gnuplot, LaTeX produces a manuscript with a professional look which allows you to publish your own manuscripts
if you want (and now, with ResearchGate, you can). My book was entirely typeset in LaTeX, in the final form, by me. The publisher had only to send it to the printing machines.

You don' t need to be a hardcore LaTeX user, though. Today there are plentiful tools to help generate tex files (and which does not generate garbage in the preamble). I  use Kile in a linux system. There are many useful resources, like autocompletion of commands and a previewer of equations which help a lot in finding mistakes in very complex formulas. I also used the Latex Editor when I have to work in a Windows system. I'm not implying these are the best tools, they are only the ones I use.

So, if you are a scientist, give LaTeX a try. It does not hurt, and you will enjoy the result.

The IASCC in Steels and the example of How Materials Science can support the Nuclear Development

A nuclear reactor is a very harmful environment for materials: neutrons with no electric charge can penetrate into alloys and crystalline networks promoting displacements of its atoms from equilibrium positions. This mechanism is responsible to change material's properties in which could result in a nuclear accident by failure of internal components. The task of choosing materials to operate and compose the structure of a nuclear reactor has paramount importance in nuclear activity, notwithstanding this is a major challenge.

Advanced Stainless Steels has been studied for nuclear reactors internal components because its good properties: relatively high strength, ductility, fracture and corrosion resistance. But in the middle of eighties, when IASCC (Irradiation-Assisted Stress Corrosion Cracking) was discovered and deeply studied, the steels were phased out in light water nuclear applications for safety reasons.

What is the IASCC? The scientific knowledge regarding Stress Corrosion Cracking (SCC) for materials operating in high- temperature and -pressure conditions depends on three main issues: high-stress, extreme harmful place and a susceptible material. As aforementioned, neutron can produce damage in materials by displacing atoms in equilibrium positions and the material will loose its ductility. The embrittlement caused by neutron irradiation will contribute to the evolution of crack tips in the material. So then IASCC is a mechanism of crack growth/formation in a corrosive environment assisted by neutron irradiation. Steels are aggressively affected by the IASCC [1].

Unfortunately, there are no data regarding crack evolution and growth mechanisms in Steels by the IASCC in nuclear reactors. Nowadays, failures of internal components are reported in nuclear reactors for fluences around 5E22 neutrons per centimetre-square and there is no strong correlation between IASCC and failure of PWR or BWR internal components. There is a lack in science and nuclear engineering here, therefore metallurgy and materials sciences should be more addressed to face  and solve problems in nuclear field: this will enhance the safety of nuclear materials in harmful environments and will improve the overall operation of a nuclear reactor.

Refs.:

[1] O.K. Chopra, A.S. Rao, A review of irradiation effects on LWR core internal materials – IASCC susceptibility and crack growth rates of austenitic stainless steels, Journal of Nuclear Materials, Volume 409, Issue 3, 28 February 2011, Pages 235-256.

Living and learning: there is a g-index!

Recently I published a post on the h-index, so, you see, I am concerned about the issues of science production evaluation. Today I was surfing on another publication listing service (google scholar) and I discovered a link to something called "g-index". I investigated and discovered it is the following: you place all your publications in a list ordered by decreasing citations, then you calculate the cumulative number of citations. Your g index is the rank g of the publication for which this cumulative number is just smaller than g squared.

The theory behind this is in the article by Leo Egghe in Scientometrics. There is nothing metaphysical about the square of g, as Egghe shows, a researcher with a given h-index should receive at least h squared citations for the most quoted works.  The author argues that this index corrects the inability of the h-index to evaluate the "power" of the highly cited works. Indeed, once a work entered the list of the most quoted, any new citations will not affect the h-index of that author. Egghe also showed, mathematically, that h <= g.

I calculated mine and it is, indeed, nine units larger than my h-index. I detected a problem, though, suppose a given researcher has many works piled up below the h threshold with exactly h citations (this situation happens with me), his g-index will most probably be smaller than the one of a similar researcher, who has many low cited works below the h threshold (and will accumulate citations slower).

Anyway, it is a new measure of research production. Probably, as always, the evaluation of a production quality will never depend on a single parameter. This one has the advantage to result in larger numbers (I know many people frustrated about low h values). This can power the researcher's ego.

Isopleths and phase diagrams

I work with phase diagrams in materials science. More specifically, I calculate phase diagrams using ab initio methods. In many occasions in the past, I came across the term "isopleth". to designate a projection of a high order phase diagram in the form of a composition - temperature diagram in which all composition variables are kept constant except one (of course two if we consider the base "solvent"). The diagram below is an example, it shows the 20 wt% Cr isopleth in system Fe-Cr-C as calculated using the Thermo-Calc program with the solid solution 2.0 database.

Those who are familiar with the Fe-C diagram will recognize some familiar points, like something which resembles the eutectic reaction and something which resembles the peritectic reaction, this familiarity is useful in interpreting the phase relations in this complex phase diagram. This diagram may also be used to understand basic phase relations in some special grades of ferritic stainless steels.
I wished to use this concept in my own language, this would lead to "isopletas" in a simple, literal, translation. I already discussed with my colleagues of the Brazilian Materials Phase Diagram Committee in the past, and although many of them meant this was "allowed", no one was really quite sure of it. Today I decided to investigate.
I did a google search for the term "isopleth" and discovered some interesting facts. First the word is derived from Greek (as I already suspected), through iso + pleth(os), which means equal + large number (or quantity). Most references in phase diagram literature conform the definition I knew (reproduced at the beginning of this post), but in formal online dictionaries I found only one reference to this definition. I found out, on the contrary, that the term is quite used in physical geography to denote contour lines of a given quantity (wind velocity is often mentioned) in a map. I searched for the term "isopleta" and discovered that this meaning (contour line) is also used in Portuguese geographical literature.
Comparing with the suggested etymology this makes sense, it seems to me that the original meaning of a synonym for isolines is the correct one. What about the term in phase diagram literature? It looks to me the the term was "borrowed" without much care and designates something quite different.
In summary, I believe it is safe to use the term "isopleta" in Portuguese to designate the same thing as the English specialized literature does. One has to consider this has a quite different meaning in Physical Geography and Cartography. The safer solution would be to look after some other word to designate these special projections in phase diagram. One thing is, however, clear. The term cannot be used to designate any composition temperature section of a multicomponent phase diagram, only those in which all other components are kept constant deserve this name.