Proteins are not always rigid structures. Many of their most important parts — linkers, loops, and disordered regions — are highly flexible, constantly changing shape in solution. To understand how these regions behave, scientists often study short model peptides that capture the essential physics of flexibility. In a new article [1], I have explored the behavior of glycine- and serine-rich octapeptides using molecular dynamics simulations combined with concepts from FRET (Förster Resonance Energy Transfer) spectroscopy (see also my previous post).
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Easter 2024: Dinosaur Eggs, Kinder Surprise, Drug Capsules, Jumping Beans Toy and Retro programming
Oh my God. Do you know what this is? This is a dinosaur egg. The dinosaurs are breeding.
Dr. Alan Grant, Jurassic Park movie (1993)
We are again approaching Easter time and, as tradition, I would like to celebrate with an article dedicated to the most perfect thing in nature: the egg. I came across interesting books about the discovery of dinosaur eggs last year. Dinosaurs are the ancestors of birds and modern reptiles, so we will take a little detour from the traditional Easter egg, and with the spirit of equal opportunity justice, we will look at the shape of these.
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El cálculo de la constante de Madelung
To all the Spanish-speaking readers, this is an AI-assisted translation experiment using WordPress. Please bear with me as my knowledge of the Spanish language is limited, so I cannot detect possible incorrect translations of the original test in Italiano. If you appreciate my efforts, please let me know. If you notice any errors in the translation, please send me a message to correct them. You can find my original versions in English, Italian, and German language of this text by clicking the links.
Estimados lectores de habla hispana, este es un experimento de traducción asistida por IA utilizando WordPress. Les pido paciencia ya que mi conocimiento del idioma español es limitado, por lo que no puedo detectar posibles traducciones incorrectas del texto original en italiano. Si aprecian mis esfuerzos, por favor háganmelo saber. Si notan algún error en la traducción, por favor envíenme un mensaje para corregirlo. Pueden encontrar las versiones originales en inglés, italiano y alemán de este texto haciendo clic en los enlaces.
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Methods of Calculating Atomic Charges based on Electronegativity. Part I.
The electronegativity of a chemical element measures the tendency of an atom to attract electrons around it. This definition was formalized for the first time, in a semi-empirical form, by the chemist Linus Pauling in the early 1930s, but it had already been proposed in the late 1800s by the Swedish chemist Berzelius. In molecules, this tendency determines the molecular electronic distribution and therefore influences molecular properties such as the distribution of partial charges and chemical reactivity. Pauling provided an electronegativity scale by comparing bond dissociation energies of pairs of atoms (A, B) using the equation
With $E_{AB}$, $E_{AA}$, and $E_{BB}$ being the dissociation energies of the molecules AB, AA, and BB, respectively.
A few years later, in 1934, Mulliken proposed an expanded definition of electronegativity based on spectroscopically measurable atomic properties such as ionization potential (I) and electron affinity (E):
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I Metodi di Calcolo delle Cariche Atomiche basati sull’Elettronegatività. Parte I.
L’elettronegatività di un elemento chimico misura la tendenza di un atomo ad attrarre intorno a sé elettroni. Questa definizione fu formalizzata per la prima volta, in foma semi-empirica, dal chimico Linus Pauling all’inizio del 1930 ma era già stata proposta nella seconda metà dell’1800 dal chimico svedese Berzelius. Nelle molecole, questa tendenza determina la distribuzione elettronica molecolare e quindi influenza le proprietà molecolari quali per esempio, la distribuzione delle cariche parziali e la reattività chimica. Pauling ha fornito una scala di elettronegatività confrontando le energie di dissociazione di legame di coppie di atomi (A, B) usando la relazione
con 
Qualche anno dopo, nel 1934, Mulliken propose una definizione estesa di elettronegatività basata su proprietà atomiche misurabili spettroscopicamente, quali il potenziale di ionizzazione (I) e l’affinità elettronica (E):
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Retro Programming Nostalgia V: Phase Plane of Autonomous Planar System of DE
What is the origin of the urge, the fascination that drives physicists, mathematicians, and presumably other scientists as well? Psychoanalysis suggests that it is sexual curiosity. You start by asking where little babies come from, one thing leads to another, and you find yourself preparing nitroglycerine or solving differential equations. This explanation is somewhat irritating, and therefore probably basically correct. David Ruelle, in Chance and Chaos
Here I am again for a new appointment with the Italian version of the column “Retro Programming Nostalgia“, my very own adventure in computer archaeology, rediscovering old programs written some time ago on microcomputers that have made their mark on an era.
This time, in my old floppy disks for the glorious Amiga 500, I found a program in Amiga Basic that I wrote during the early years of my university studies, when I was taking the course on differential equations II. Specifically, I was very fascinated by autonomous systems of differential equations due to their numerous applications in mathematical modeling of physical, chemical, and biological systems, as well as their importance in the theory of chaos. As in the series articles, I want to release an adapted version for the QB64 BASIC meta-compiler, but before presenting the program, I want to briefly explain what an autonomous system of differential equations is.
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Retro Programming Nostalgia V: Sistemi Autonomi di Equazioni differenziali
“Qual è l’origine del desiderio, della fascinazione che spinge i fisici, i matematici e presumibilmente anche altri scienziati? La psicoanalisi suggerisce che si tratti di curiosità sessuale. Si comincia chiedendosi da dove vengano i bambini piccoli, una cosa porta all’altra e ci si ritrova a preparare il nitroglicerina o a risolvere equazioni differenziali. Questa spiegazione è un po’ irritante, e quindi probabilmente fondamentalmente corretta.” – David Ruelle, in “Chance and Chaos”
Eccomi di nuovo per un nuovo appuntamento con la versione in italiano della Rubrica “Retro Programming Nostalgia “, la mia personalissima avventura d’ archeologia informatica alla riscoperta di vecchi programmi scritti qualche tempo fa su microcomputers che hanno segnato un’epoca.
Questa volta, nei miei vecchi dischetti per il glorioso Amiga 500, ho trovato un programma in Amiga Basic che scrissi durante i primi anni dei miei studi universitari, quando studiavo nel corso di matematica II, i sistemi d’equazioni differenziali. In particolare, ero molto affascinato dai sistemi di equazioni differenziali autonomi per via delle molteplici applicazioni nella modellazione matematica di sistemi fisici, chimici e biologici, e per la loro importanza nella teoria del caos. Come negli articoli della serie, voglio rilasciare una versione riadattata per il meta compilatore QB64 BASIC, ma prima di presentare il programma, voglio brevemente spiegare cosa sia un sistema autonomo di equazioni differenziali.
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Madelung定数の計算
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以前の記事で、結晶の格子エネルギーにおける静電エネルギー項の計算について説明しました。この記事では、この項を計算する方法について詳しく説明し、また単純なイオン系におけるこの項の値を提供します。
晶体の総クーロン相互作用エネルギーは、個々の相互作用項の合計として与えられます。
固体の結晶構造では、電荷qAとqBを持つイオン対の間の距離rABによって生じるクーロン相互作用力で構成されます。この和は、固体中のすべてのイオン対にわたって計算されます。
最初の近傍は負の重要な寄与を提供するため、この和は非常に遅く収束します。2番目の近傍原子はわずかに弱い正の項を生成します。このプロセスは無限遠まで続き、交互の符号でますます小さい値を通じて行われます。このようにして、陽イオンと陰イオンの間の引力が主導し、固体のエネルギーに有益な負の寄与を提供します。
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Madelung常数的计算
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在之前的一篇文章中展示了晶体晶格能的静电项包含了一个因子（A），该因子取决于晶体的晶格类型。本文将详细介绍如何计算这一项，并给出一个简单离子系统中该项的值。
晶体的总库仑相互作用能由各个单对相互作用项的总和给出：
固体晶体结构中，它是由具有电荷qA和qB的离子对之间距离为rAB的库伦相互作用力组成。这个求和范围扩展到固体中所有的离子对。
由于第一个邻居提供了一个带有负和的重要贡献，所以这个和式收敛得很慢。第二个邻居原子产生稍弱的正面项。这一过程将持续到无穷远，通过越来越小的数值以交替的符号进行。这样一来，阳离子和阴离子之间的吸引力占主导地位，为固体的能量提供了有利的负面贡献。
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The shell of a snail and its 3D Digitization with the Structure-from-Motion algorithm
To grass, or leaf, or fruit, or wall,
The snail sticks close, nor fears to fall,
As if he grew there, house and all
Together.
Within that house secure he hides,
When danger imminent betides
Of storm, or other harm besides
Of weather.
Give but his horns the slightest touch,
His self-collecting power is such,
He shrinks into his house, with much
Displeasure.
Where’er he dwells, he dwells alone,
Except himself has chattels none,
Well satisfied to be his own
Whole treasure.
Thus, hermit-like, his life he leads,
Nor partner of his banquet needs,
And if he meets one, only feeds
The faster.
Who seeks him must be worse than blind,
(He and his house are so combin’d)
If, finding it, he fails to find
Its master.The Snail by William Cowper (1731-1800)
Introduzione
The beautiful poetry of Cowper expresses the pleasant charm that this small inhabitant of our gardens instills. I have always been fascinated by this gastropod, to the point that it was one of my favorite invertebrates for my amateur naturalistic observations. Furthermore, I still recall with pleasure and nostalgia the collection of those called ‘ciammaruchelle‘ in the Ciociaro dialect, which are small snails. These were gathered by the handful in the wheat fields after the harvest. It was one of the various culinary traditions that involved my entire family every year and were carried out with constant devotion. The collection was organized with careful timing, locations, and weather conditions to increase the likelihood of success. Usually, we would return home with a rich and tasty haul, but not without difficulties, as the little snails would climb onto the thistle plants (Cynara cardunculus L., 1753) where they would hide among the thorns to protect themselves from predators. Unfortunately for them, the predator Homo Sapiens Sapiens Frusinenses, equipped with keen eyesight and great tenacity, did not easily give up its prey!
The collected species was a variety of the snail Eobania vermiculata, commonly known as “rigatella,” which is very common in Mediterranean regions. The snails were gathered in woven baskets and, once back home, they were enclosed in circular cages with fine mesh walls for several days to purge their intestines. They were then cooked for a few hours in a tomato base spiced with mint (Clinopodium nepeta), following an ancient recipe. The dish was consumed with fresh or, even better, baked bread to make it crispy. It was a vibrant celebration of scents, flavors, and colors, with the sound of slurping as they tried to empty the succulent contents of their shells. A delicate feast of aromas and flavors: the scent of tomato infused with snail meat and mint, combined with the red color of the snails’ shells adorned with white-brown stripes.
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