Molecular Machines: the (Corona) Viruses Menace I

If you know the enemy and know yourself, you need not fear the result of a hundred battles. If you know yourself but not the enemy, for every victory gained you will also suffer a defeat. If you know neither the enemy nor yourself, you will succumb in every battle.”

SunTzu. The Art of War

A virus is life in the Bauhaus form: the minimalist reduction of an organism to its essential elements of functionality. More pragmatically, it is a container of genetic code A virus is the Bauhaus of the form of life: the minimalist reduction of an organism to its essential element of functionality. More pragmatically, it is a container of genetic code provided with a smart mechanism that allows it to invade a host cell of another organism. As a molecular machine, a virus can resemble in shape and destructive power the Death Star spaceship of Star War saga. Therefore, it is one kind of molecular machine that we do not definitively want to have within us! The recent outbreak of the Coronavirus influenza COVID-19 is the most recent case of a pandemic that is putting in danger the life of the human species on the planet. A resurge of a natural competition that let us recall that we are still just a brick in the natural world ecosystem of Gaia. However, even if it hard to believe, given the state of our planet, we are also the most intelligent form of life in the known universe. So it would be quite embarrassing to be defeated by an invisible enemy.

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The Particle in a Box I: the Schrödinger Equation in One-dimension

In 1926, the Austrian physicist Erwin Schrödinger (1887-1961) made a fundamental mathematical discovery that had a profound impact on the study of the molecular world (in 1933, Schrödinger was awarded with the Nobel prize in Physics just 7 years later his breakthrough discovery). He discovered that a state of a quantum system composed by particles (such as electrons and nucleons) can be described by postulating the existence of a function of the particle coordinates and time, called state function or wave function (\Psi, psi function). This function are solution of a wave equation: the so-called the Schrödinger equation (SE). Although the SE equation can be solved analytically only for relatively simple cases, the development of computer and numerical methods has made possible the application of SE to study complex molecular. 

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Buon Natale e Felice Anno Nuovo

Gentilissimi/e Lettori e Lettrici, Dear Reader, Sehr geehrte Leserinnen und Leser,

Grazie mille per aver fatto tappa durante le vostre peregrinazioni cibernautiche nel mio sito web e per dedicare un po’ del vostro tempo nel leggere i miei articoli. Spero che li avete trovati tanto interessanti e utili da continuate a tornare a leggermi.
Voglio anticipare alcune delle prossime pubblicazioni.
Tra breve usciranno nuovi titoli:

  • The Logistic Map and the Feigenbaum Constants: a Retro Programming Inspired Excursion.
  • L’integrazione numerica di equazioni differenziali, parte II: 50 anni fa l’uomo ha messo piede sulla Luna
  • Retro Programming: Acid-base Titration.
  • Retro Programming: Plant evolution.

Per il momento auguro a tutti voi di trascorrere con le vostri cari un felice Natale e di avere un nuovo anno pieno di buone notizie.

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A personal tribute to the founder of MD simulation of biological molecules: Prof Herman J.C. Berendsen (1934-2019)

On the 7 October 2019, Prof Dr Herman Johan Christiaan Berendsen passed away just shortly after his 85 birthday. Prof Berendsen is considered the founder of the molecular dynamics simulation of biological system: the area of theoretical research that also shaped my scientific career. He was working at the University of Groningen in the picturesque Northern part of the Netherlands. It was there that I meet him the first time as it allowed me to conduct research in his lab during the last year of my doctorate researches training at the University of Rome “La Sapienza”. After I completed my doctorate, Herman gave me the opportunity to continue working in his group with a postdoc position within the “Protein Folding” EU Training network. This happens just two years before his retirement and therefore I was also one of his last postdocs. After retirement, Herman dedicated himself to write two books that distillate all his experience in the area of molecular simulation [1] and in the education [2]. He stated in a project on the social scientific network Researchgate that “I am retired and work occasionally on methods for multiscale simulations.”

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The First 150 Years of the Periodic Table of the Elements

That the nobility of man, acquired in a hundred centuries of trial and error, lay in making himself the conquerer of matter, and that I had enrolled in chemistry because I wanted to remain faithful to this nobility. That conquering matter is to understand it, and understanding matter is necessary to understanding the universe and ourselves: and that therefore Mendeleev’s Periodic Table, which just during those weeks we were laboriously learning to unravel, was poetry, loftier and more solemn than all the poetry we had swallowed down in liceo; and come to think of it, it even rhymed!

Primo Levi, The Periodic Table.

This year marks the 150th anniversary of the periodic table of the elements (TPE) which currently has 118 entries, the latest arrival (the Tennessine) was discovered 10 years ago (2009), and I feel obliged as a chemist to give some a small informative contribution to celebrate this important event.

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Retro programming nostalgia III: the MSX Microcomputer and the Orbit of the Planets in the Solar System

In a recent article, I have explained the Euler’s method for solving ordinary differential equations using as a motivation the fictionalized version in the film Hidden Figures of the scientific contribution of Katherine Goble and her two colleagues to the NASA space program. As an example of application, I have also shown a program written in the awk programming language for calculating the orbits of planets of the solar system. However, my interest in astrodynamics come back to my juvenile age, when still going to high school, my parents decided to gift me a more sophisticated microcomputer than my previous one (the celebrated Commodore VIC 20). So I became a programmer of a Philips MSX VG 8010 that I still jealously own in its original box. So, powered by the versatile Federico Faggin’s Zilog Z80 processor with a clock 3.58 MHz, with an impressive (for a previous owner of a VIC20 with a mere 3.583 kB!) memory of 32 kB RAM , 16kB of video RAM and a dedicated tape-record device as storage system, I started to write more sophisticated in MSX Basic. At that time, I was eagerly following the department “Ricreazioni al Computer” by the famous computer scientist A. K. Dewdney on the magazine “Le Scienze”, the Italian edition of Scientific American. The new microcomputer allowed me to experiment with the fascinating computational topics that Dewdney was offering every month. One of these topics was dedicated to the simulation of stars using the algorithm based on the Euler integration of the Newton equation. Following the instruction of Dewdney, I managed to write a small program in MSX basic and this was the starting of my interest in computational astronomy.

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L’Integrazione Numerica di Equazioni Differenziali: 50 anni fa l’ uomo ha messo piede sulla Luna

Nel giorno in cui ho iniziato a scrivere questo articolo ricorreva l’anniversario della prima esplorazione da parte dei cosmonauti americani Neil Armstrong, Michael Collins, Buzz Aldrin della nostra Luna. Anche se non ho una memoria diretta di questi eventi, le missioni delle progetto Apollo evocano in tutti noi una forte emozione rappresentando un momento unico ed epico nella storia della conquista dello spazio. Nessun altro uomo ha messo di nuovo piede sulla Luna dopo l’ultima missione Apollo 17 nel 1972, per cui i recenti annunci della NASA di nuove esplorazioni umane del nostro satellite rende l’anniversario ancora piu’ eccitante.

L’ immagine di copertina di questo articolo è stata creata da mio figlio per una sua ricerca scolastica sulle missioni Apollo ed è un collage d’immagini ottenute usando i programmi Google Earth e Sketchup. Nella figura si confrontano le dimensioni del razzo Saturno V con quelle della meravigliosa cattedrale di Lincoln in Gran Bretagna per dare un’idea dell’enorme grandezza del vettore spaziale. Il pensiero che l’uomo sia riuscito nel giro pochissimi anni in uno sforzo tecnologico e scientifico immenso a costruire questa cattedrale volante della tecnologia mi ha suscitato un senso di forte curiosità e non ho saputo trattenermi nel spiluccare tra la miriade di documenti disponibili sul sito della NASA sul programma Apollo.

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