The Father Secchi’s Sundial of Alatri

Alatri is a picturesque town in the province of Frosinone, 80 km southeast of Rome. Located in the heart of Ciociaria, it overlooks the Sacco Valley from the highest point on top of a hill. Among other important attractions, the historical center of the city treasures one of the best-preserved megalithic constructions in Ciociaria. Megalithic architecture is characterized by imposing stonework (also called megalithic or Cyclopean ruins). The one in Alatri is an impressive perimeter wall. The wall, known as the polygonal walls, is built around the highest point of the town, the acropolis. It was constructed for fortification and ritual worship purposes. The megalithic civilization reached the highest level of stone masonry during the Neolithic period. Major centers existed in different Italian regions and throughout Europe from Greece to England. Alatri is just one of the megalithic towns of Ciociaria. Other nearby impressive remains can be found in Ferentino and Veroli.

I will write more about megalithic architecture in another article. In this context, I will describe a more recent but still beautiful architectural embellishment. This embellishment has a practical function. It is prominently visible in the Piazza Santa Maria Maggiore, the town’s central square. I am referring to the beautiful sundial (OROLOGIO SOLARE in italiano, see photo below). It was built in 1867 on the facade of the Palazzo Conti Gentili. The architect Giuseppe Olivieri constructed it based on accurate calculations by Padre Angelo Secchi. He was a renowned Jesuit and astronomer. A photo of the sundial is reported below. In Italian, the sundial is translated as orologio solare, as written in the image.

Figure 1: Photo of the Secchi’s sundial located in Piazza Santa Maria Maggiore of Alatri.

The analysis of this sundial gave me the opportunity to introduce the principles used to build it. I also learned a bit more about astronomical calculations. Therefore, I want to share with the reader my findings.

What is a sundial?

The sundial (also called meridian) is a time-measuring device based on the regular rotation of the Earth. The Sun’s apparent position in the sky changes the shadow’s projection cast by the dial. This shadow falls on a surface that has been time marked. As a result, the surface can have different orientations and shapes. The Secchi’s sundial is a vertical type with orientation North-South. The title on the top states this: The Secchi’s sundial shows the real time. It also shows the average time (OROLOGIO SOLARE A TEMPO VERO E MEDIO). The calligraphic text on the bottom indicates the geographic coordinates of the sundial.

The latitude and longitude indicate the location of the bell tower. It is part of the cathedral of Alatri (duomo di Alatri o Basilica di San Paolo). As reference meridian (the prime meridian) was consider the one passing for the city of Rome. In particular, it is the meridian that passes through the Collegio Romano observatory. Secchi was the director there at the time of the sundial’s construction. The international adoption of the prime meridian passing through London was agreed upon during an international geographic conference. This conference was organized in the same city in October 1884. Before this date, country were used to adopt their own prime meridian, usually passing for the capital. So it is not surprising that Sacchi used as reference meridian the one passing for Rome. The Colleggio Romano was a school established by founder of the Society of Jesus St. Ignatius of Loyola in 1551. It is located in the Piazza del Collegio Romano in the Pigna District. P.A. Secchi was the director of the astronomic observatory of the school. The Monte Mario Observatory was constructed in 1934, at Villa Mellini. This moved the prime meridian for Rome there. It was used as the reference meridian for Italy’s geographic maps until 1960.

The geographic coordinates of the cathedral of Alatri given by Google Maps are 41.7248° N, 13.3443° E. Therefore, Sacchi approximated the longitude to the one of the Collegio Romano (41.8988° N, 12.4807° E) that he could accurately calculate. According to Google Earth, the sundial’s position is 41°43′ 35.86″ N, 13° 20′ 33.86″ E. Therefore, the prime meridian is used to calculate the real-time of the sundial.

Figure 2: Position of the Piazza Santa Maria Maggiore and of the cathedral of Alatri (bottom complex). Source Google Earth.

The length of the shadow cast by the sundial varies with the Sun’s altitude, and it also changes during the year as the Earth moves along an orbit that is inclined by ~23.4° concerning the ecliptic plane (the position of the Sun’s equator). The length defines a particular position for the Earth in its orbit, as the solstices and equinoxes are the dates in between. The length of the shadow is marked on the solar clock with seven declination arcs. The latter ones go from left to right, delimited by the Zodiac signs and solstices, and equinoctial dates. Using the Zodiac sign is a convenient way to divide into 12 sectors of 30° the ecliptic longitude along the Earth’s orbit. This leads to 7 arcs, five crossed twice by the Sun (when its declination is increasing and decreasing), plus two for solstices (extreme declinations). As Sun’s altitude varies between +/- 23° 26′, it is also possible to draw arcs every 5° of declination, with the equinoctial line (March 21st and September 22nd) in the middle which corresponds to 0° of declination (Sun on the equator).

Description of the Components of the Sundial

The Secchi’s sundial in Alatri consists of several key components that contribute to its functionality and accuracy in measuring time. These components include the gnomon, the dial plate, the hour lines, and the declination arcs. The dial plate serves as the surface upon which the shadow of the gnomon falls. It is typically a flat, horizontal surface with markings or engravings that denote the hours of the day. In the case of this sundial, the dial plate features hour lines and declination arcs that aid in reading the time and understanding the position of the Sun.

By combining the gnomon, the dial plate with hour lines, and the declination arcs, the Secchi’s sundial allows for the accurate measurement of time-based on the position and length of the shadow cast by the gnomon. Observers can align the shadow with the hour lines to determine the time of day. At the same time, the declination arcs provide insights into the Sun’s position along the ecliptic throughout the year.

It is worth noting that the accuracy of the sundial’s measurements can be influenced by factors such as the precise alignment of the gnomon, the dial plate’s orientation, and the location’s latitude. However, the design of the Secchi’s sundial, with its North-South alignment and inclusion of declination arcs, enhances its accuracy and usefulness as a time-measuring device in Alatri.

Molekulare Maschinen: Die Coronavirus SARS-CoV-2 Bedrohung, Teil I.

Was Freunde mit und für uns tun, ist auch ein Erlebtes; denn es stärkt und fördert unsere Persönlichkeit. Was Feinde gegen uns unternehmen, erleben wir nicht, wir erfahren’s nur, lehnen’s ab und schützen uns dagegen wie gegen Frost, Sturm, Regen und Schloßenwetter oder sonst äußere Übel, die zu erwarten sind.

Johann Wolfgang von Goethe (1749-1832), Maximen und Reflexionen. Aphorismen und Aufzeichnungen.

Ein Virus ist Leben in der einfachsten Form. Es ist die minimalistische Reduktion eines Organismus auf seine wesentlichen Funktionselemente. Noch pragmatischer ist ein Virus ein Behälter mit genetischem Code mit einem effizienten molekularen Mechanismus, der es ihm ermöglicht, in eine Wirtszelle eines Organismus einzudringen, der sich selbstständig reproduzieren kann. Als molekulare Maschine kann ein Virus der Form und der zerstörerischen Kraft des Todessterns in der Star-Wars-Saga ähneln. Daher ist es eine Art molekulare Maschine, die wir absolut nicht in uns haben wollen!

Wie der große Goethe sagt, ist der Feind Teil unserer Erfahrung und wir müssen ihn jagen und uns tatsächlich vor anderen möglichen Feinden schützen. Dieser epische Naturkrieg veranlasste mich, diesen Blog zu starten, in dem ich mitteilen werde, was ich über diese gefährliche molekulare Maschine lerne.

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Le Macchine Molecolari: La minaccia del Coronavirus SARS-CoV-2. Parte I

Difficilmente è vinto colui che sa conoscere le forze sue e quelle del nemico.

Nicollò Machiavelli in Dell’arte della guerra (1519-1520)

Un virus è la vita nella forma più semplice. È la riduzione minimalista di un organismo ai suoi elementi essenziali di funzionalità. Più pragmaticamente, un virus è un contenitore di codice genetico dotato di un efficiente meccanismo molecolare che gli consente d’invadere una cellula ospite di un organismo capace di riprodursi autonomamente. Come macchina molecolare, un virus può assomigliare nella forma e potere distruttivo, alla Morte Nera della saga di Star Wars. Pertanto, è un tipo di macchina molecolare che non vogliamo assolutamente avere dentro di noi!

La diffusione del coronavirus SARS-CoV-2 (COVID-19) ha prodotto una nuova pandemia, ovvero una infezione causata da un agente patogeno che colpisce l’intera popolazione di una specie vivente, in questo caso quella umana. Questa situazione di emergenza globale è il risultato di una competizione naturale tra specie viventi che ci rammenta di essere ancora un tassello nell’ecosistema di Gaia. Tuttavia, anche se sia sempre arduo da credere visto lo stato in cui abbiamo ridotto il nostro pianeta, siamo la forma di vita più intelligente nell’universo conosciuto. Quindi sarebbe abbastanza imbarazzante essere sconfitti da un nemico invisibile.

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Retro programming nostalgia IV: L’Equilibrio e la Titolazione Acido/Base (Parte I)

La motivazione per questo articolo nasce dal mio interesse per il retro-computing connesso, da una parte, alla rivalutazione delle mie esplorazioni giovanili del calcolo scientifico in linguaggio BASIC e dall’altra, alla popolarità che, negli ultimi anni, stanno avendo nel settore amatoriale e della didattica i microcomputer su scheda singola  (single-board computer, quali, per esempio  il Raspberry Pi).  Questi piccoli computer hanno una potenza considerevolmente maggiore a un costo decisamente inferiore dei microcalcolatori degli anni 80. Questo ha reso possibile l’emulazione su questi calcolatori dei sistemi operativi di mitici modelli di home computer della Commodore e i modelli MSX.

Pertanto sta prendendo piede anche un rinnovato interesse nel linguaggio di programmazione BASIC. Questo interesse nel retro-computing riflette la nostalgia nelle grandi emozioni che negli anni 70-80 lo sviluppo della tecnologia informatica consumistica ha portato alla mia generazione. Ricordo che rimasi folgorato dalla creatività nell’uso e nella programmazione di questi microcomputer al punto che ha ridiretto i miei interessi scientifici e la mia carriera accademica. 

Ho raccontato in altri articoli delle mie prime avventure di programmazione con  home computer della Commodore e i sistemi MSX alla fine degli anni ’80 e inizi degli anni ’90 e delle mie riscoperte di archeologia informatica. Tra i reperti ho rinvenuto un piccolo programma che ho usato per studiare le titolazioni acido/base sviluppato in MSX BASIC. Pertanto ho colto l’occasione per scrivere delle note sull’equilibrio acido base  e la titolazione e quindi fornire una versione restaurata e migliorate del mio programma, a gli studenti appassionati di programmazione  che sono  alle prese con questo importante concetto della chimica analitica.

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Easter 2020: Modelling Natural Shapes: (Easter) Eggs

One year ago, I wrote an article about the modelling of the egg shapes, promising at one point to come back on the topics. A next step in studying eggs shapes is to look to real one or a copy of it. A happy occasion for experimenting with the model using three-dimensional graphics and 3d Printing! That is a natural indeed step: take half of the symmetric curve representing the egg shape

y=T(1+x)^{\frac{\lambda}{1+\lambda}}(1-x)^{\frac{1}{1+\lambda}},

where T and \lambda are two parameters, and rotate it around the central axis

\begin{aligned} x'&=&x\\ y' &=&y*cos(\theta) \\ z' &=& y*sin(\theta) \end{aligned}

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Nanoparticles in Biology and Medicine

I am very pleased to announce that the second edition of the book Nanoparticles in Biology and Medicine edited by Enrico Ferrari, Mikhail Soloviev is now out.

This fully updated volume presents a wide range of methods for synthesis, surface modification, characterization and application of nano-sized materials (nanoparticles) in the life science and medical fields, with a focus on drug delivery and diagnostics. Beginning with a section on the synthesis of nanoparticles and their applications, the book continues with detailed chapters on nanoparticle derivatization, bio-interface, and nanotoxicity, as well as nanoparticle characterization and advanced methods development. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Nanoparticles in Biology and Medicine: Methods and Protocols, Second Edition serves as an ideal guide for scientists at all levels of expertise to a wide range of biomedical and pharmaceutical applications including functional protein studies, drug delivery, immunochemistry, imaging, and more.

I have contributed with a chapter (14) titled The Molecular Dynamics Simulation of Peptides on Gold Nanosurfaces.

In this chapter a short tutorial on the preparation of molecular dynamics (MD) simulations for a peptide in solution at the interface of an uncoated gold nanosurface is given. Specifically, the step-by-step procedure will give guidance to set up the simulation of a 16 amino acid long antimicrobial peptide on a gold layer using the program Gromacs for Molecular Dynamics simulations.

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

Questo è il secondo articolo di questa serie dedicata alla soluzione numerica delle equazioni differenziali. La serie prende spunto dagli eventi che hanno portato l’uomo sulla Luna.

Nel luglio del 2019, quando ho iniziato a scrivere questo articolo, ricorreva il 50esimo anniversario della missione Apollo 11 (Neil A. Armstrong, Edwin A. Aldrin and Michael Collins) in cui gli astronauti Armstrong, Aldrin hanno posato il piede sulla superficie lunare. Un evento epocale nella storia umana che segna anche l’inizio della esplorazione spaziale. Dopo 50 anni, la NASA come altre agenzia spaziali e compagnie private, si stanno preparando per tornare sulla Luna per creare avamposti per l’esplorazione umana di pianeti più distanti come per esempio Marte. Questo anniversario mi portò ad interessarmi per raccogleire idee per la mia attività d’insegnamento e per curiosità personale, alle tecniche d’integrazione numerica delle equazioni differenziali usate per effettuare i calcoli delle traiettorie dal sistema di guida delle astronavi Apollo e dai calcolatori che hanno assistito l’impresa dalla Terra. In questo articolo semi divulgativo riassumo le informazione che ho raccolto leggendo (in maniera incompleta) la documentazione della NASA e quella ottenuta leggendo dei libri sull’argomento. Come mio solito presenterò anche dei semplici programmi che implementano questo algoritmi.

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Molecular Machines: the Coronavirus SARS-CoV-2 Menace. Part 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 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 cells of another host organism. As a molecular machine, a virus can resemble in shape and destructive power the Death Star spaceship of the Star War saga. Therefore, it is a molecular machine that we do not definitively want to have within us!

The spread of the coronavirus SARS-CoV-2 has produced a new pandemic, i.e. an infection caused by a pathogen that affects the entire population of a living species, in this case the human one. This global emergency situation is the result of a natural competition between living species that reminds us that we are still a small brick of the Gaia ecosystem. However, although it is always difficult to believe given the state in which we have reduced our planet, we are the most intelligent life form in the known universe. So it would be quite embarrassing to be defeated by an invisible enemy.

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Examples of the Particle in a Box Model Applications

In a previous article, I have shown a simple derivation of the properties of a quantum particle confined in a one-dimensional box. Although the model is straightforward with unrealistic assumptions, such as the infinite walls, it produced qualitative results that paved the way for the development of quantum chemistry. There are several example practical applications in chemistry and nanoscience where the particle in a box model can be applied or serves as a conceptual foundation.

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Physical Chemistry. 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 the Nobel Prize in Physics just seven years later, his breakthrough discovery). He discovered that a quantum system’s state composed of particles (such as electrons and nucleons) could 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 is the solution of a wave equation: 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 molecules. 

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