Research

Retro Programming Nostalgia: quando l’Amiga 500 calcolava le cariche atomiche

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Un programma in GFA BASIC, il metodo di Gasteiger–Marsili e un ricordo della mia tesi di laurea in Chimica.

All’epoca della ricerca per il mio progetto di laurea in chimica, ero ancora un entusiasta possessore dell’Amiga 500. Il kernel del Linux OS era stato appena ufficialmente rilasciato nella versione 0.01 da Linus Torvalds, e la distribuzione Slackware sarebbe stata rilasciata nel luglio del 1993. Come descritto nel mio articolo sulla mia tesi di laurea, all’epoca l’Apple Macintosh per scrivere la tesi e il mainframe IBM 3090 per i calcoli. Il mio primo PC lo acquistai durante il mio dottorato di ricerca con l’idea di installarlo con Linux in dual boot con MS Windows. All’epoca conoscevo bene il BASIC disponibile sui vari microcomputer che ho avuto (vedi i miei articoli sul retrocomputing) e l’Amiga Basic del mio Amiga 500 che acquistai durante i miei primi anni universitari. Quando iniziai la mia tesi di laurea, cominciai a imparare a programmare in FORTRAN 77, linguaggio usato per scrivere i codici per le simulazioni di dinamica molecolare. Continui limitatamente ad usare anche il mio Amiga 500 per la grafica e la programmazione.

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Rediscovering Halometry with Raspberry Pi and Laser Diffraction

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One of the aspects of experimental science that I find most fascinating is the rediscovery of historical scientific instruments and techniques that have gradually disappeared from modern laboratories. In my latest Instructable project, I explored the reconstruction of a remarkable optical device once used in hematology during the early twentieth century: the halometer.

Before the advent of automated blood analyzers and digital microscopy, researchers investigated ingenious indirect methods for estimating the average size of red blood cells. One of these methods relied on diffraction phenomena produced when coherent light passed through thin blood smears. The resulting circular halos could be related to the average diameter of erythrocytes, providing a rapid—although approximate—diagnostic technique for conditions such as pernicious anemia.

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Easter 2026: The Patterns on Coturnix Egg

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Last year, after a series of unsuccessful attempts and acquiring three incubators across two countries, my youngest son’s unwavering determination finally paid off.  From a batch of twelve mixed quail eggs, seven hatched successfully, marking the start of our new venture into farm animal husbandry.  Currently, we’ve settled for manageable pets like a Siberian hamster, an aquarium, and pond fish, plus several rounds of stick insects, mantises, and spiders, along with their grasshopper and locust food supplies.  However, quail care is more demanding. While our sons’ happiness is undoubtedly the most important reward, the delicious eggs produced by our farm breeding activity are equally rewarding for the whole family.  It’s particularly satisfying collecting every evening the two expected eggs from the punctual quail hens and admiring their different sizes and pigmentation like beautiful little gems.

If you’re still reading, you’ve probably guessed the main topics of my traditional Easter blog: quail eggs and their shapes and patterns.

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The Smoluchowski Diffusion Equation

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The Smoluchowski diffusion equation describes the time evolution of the probability density function (PDF) of a particle undergoing overdamped Brownian motion in a potential energy landscape. It is a central equation in statistical mechanics, soft matter physics, and chemical physics.

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Bringing FRET and Molecular Dynamics Together to Understand Flexible Peptides

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Important structural components of proteins, like linker loops and intrinsically disordered regions, are highly flexible and constantly change shape in solution. These flexible protein regions — especially those containing glycine- and serine-rich segments — do not behave like neatly folded proteins. They fluctuate, breathe, and explore broad conformational landscapes. These motions can often be central to biological function. But capturing them consistently, both structurally and dynamically, remains challenging. To understand the physics of this flexibility, we often turn to short model peptides that isolate the essential ingredients of chain dynamics. In an earlier work, we explored glycine- and serine-rich octapeptides using molecular dynamics (MD) simulations in combination with concepts from FRET (Förster Resonance Energy Transfer) spectroscopy. The goal was to understand how flexible chains fluctuate and how these fluctuations are reflected in experimentally measurable distances.

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Principal Component Analysis: Key to Analyzing Biomolecular Dynamics

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I have recently written, for WIREs Computational Molecular Science, a review article on the use of Principal Component Analysis (PCA) in the study of dynamical systems, with a particular focus on molecular dynamics (MD) simulations of biomolecules [1]. The aim of this work is to provide a clear and practical overview of how PCA has become a central tool for extracting meaningful collective motions from high-dimensional simulation data, and how modern methodological extensions continue to expand its capabilities.

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RaPenduLa: Una Video piattaforma Fai-Da-Te Per Studiare Oscillazioni Meccaniche

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AGGIORNAMENTO 2: Un primo articolo sulla Rapendula è stato pubblicato l’8 gennaio 2026 [1] sul The European Journal of Physics .

AGGIORNAMENTO1: Nel maggio 2025, il progetto ha ottenuto riconoscimento vincendo il 1° premio nel concorso Instructables All Things Pi. Un grande grazie al team di Instructables!

Qualche giorno fa ho pubblicato un nuovo progetto educativo sul mio sito Instructables. Il dispositivo, che ho battezzato RaPenduLa (dalle iniziali in inglese di RaspPi Pendulum Laboratory), è stato ribattezzato in italiano CAMPO (Computer Analisi Moto Pendolare Oscillante) grazie a un suggerimento di ChatGPT. Ma, come direbbe Shakespeare, ‘What’s in a name? That which we call a rose by any other name would smell as sweet’: il cuore del progetto è infatti una piattaforma video per lo studio delle oscillazioni meccaniche. Utilizzando un Raspberry Pi Zero W2 dotato di modulo fotocamera, il sistema registra ad alta velocità il movimento dei pendoli. Poi, con un’analisi video basata su Python e OpenCV, RaPenduLa è in grado di tracciare il percorso preciso della punta del pendolo, visualizzandone il comportamento oscillatorio in 2D.

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Easter 2025: Exploring Egg-Shaped Billiards

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It has become a recurrent habit for me to write a blog on the shape of eggs to wish you a Happy Easter. Not repeating oneself and finding a new interesting topic is a brainstorming exercise of lateral thinking and a systematic search in literature to find an interesting connection. This year, I wanted to explore an idea that has been lurching in my mind for some time for other reasons: billiards.

I used to play snooker from time to time with some old friends. I am a far cry from being even an amateur in the billiard games, but I had a lot of fun verifying the laws of mechanics on a green table. I soon discovered that studying the dynamics of bouncing collision of an ideal cue ball in billiards of different shapes keeps brilliant mathematicians and physicists engaged in recreational academic studies and important theoretical implications.

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RaPenduLa: A DIY Video Platform for Exploring Mechanical Oscillations

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UPDATE2: On 8 January 2026, a paper on Rapendula was published in the European Journal of Physics [1].

UPDATE 1: In May 2025, the project achieved recognition by winning first prize in the Instructables contest “All Things Pi.” A big thank you to the Instructables teams!

I have recently published another educational project on my Instructables website. I called the device RaPenduLa for the RaspPi Pendulum Laboratory, and it is a video platform for studying mechanical oscillations. It uses a Raspberry Pi Zero W2 equipped with a camera module to record the motion of pendulums at high speed. The interesting part happens through video analysis: using Python and the fantastic OpenCV library, RaPenduLa can track the precise path of a pendulum’s tip and help visualize its oscillatory behavior in two dimensions.

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A Virtual Microscope for Nanoscience

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I am pleased to announce the publication of the second edition of my book chapter: “A Short Introduction to the Molecular Dynamics Simulation of Nanomaterials” [1] in Micro and Nanomanufacturing, Volume II, edited by W. Ahmed and M. J. Jackson, Springer, 2025. This new edition reflects both the rapid evolution of molecular dynamics (MD) simulations over the past decade and their growing role in nanoscience.

Molecular dynamics simulations have become a cornerstone of modern nanoscience. They allow us to observe matter at the atomic scale, following the motion of thousands—or millions—of atoms in time, effectively turning the computer into a virtual microscope. From nanoparticles and nanotubes to polymers, membranes, and bio–nano interfaces, MD simulations provide insights that are often inaccessible to experiments alone. They help us understand:

  • Structural organization at the nanoscale
  • Dynamic processes such as adsorption, diffusion, and self-assembly
  • Thermodynamic and mechanical properties relevant to material design

This chapter is written with the explicit goal of making these ideas accessible, without sacrificing physical rigor.

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