Month: September 2020

A Practical Introduction to the C Language for Computational Chemistry. Part 2

/ Danilo Roccatano / Leave a comment

In the first part of this introduction to C language, we have learnt the basic of the C language by writing simple programs for the calculation of the non-bonded interaction between two particles at variable distances. Some solutions to the first part exercises are reported in the appendix of this article.

In this second tutorial, we will learn how to use arrays data types and how to load them with a set of data read from a file. We will also use these data to perform numerical calculations and write results in output files.

Arrays and Pointers Datatypes

The program that calculate the energy of interaction between two particle doe not take in account the actual position in space of the two particle but only their distance. If we want to study the dynamics of a system composed by multiple atoms in a tridimensional space, it is way more convenient to represent the and calculate their interactions by using the coordinates directly to evaluate the distances.

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The Dandelion (Taraxacum Officinalis) and OpenCV

/ Danilo Roccatano / Leave a comment

The dandelion’s pallid tube
Astonishes the grass,
And winter instantly becomes
An Infinite Alas —

The tube uplifts a signal Bud
And then a shouting Flower, —
The Proclamation of the Suns
That septulture is o’er.

– Emily Dickinson

The yellow flowers and the delicate and beautiful inflorescence of Dandelion catch the attention of both romantic and curious souls. The aerial consistency of the fine silk decorated seeds that glance to the sunlight as crystalline material became the favorite subject of the inspired photographers and the toy of amused children. Besides the grace of its forms, other interesting and the curious secret is hidden in its phloem fluids. In fact, if you cut one of the stems of the plant, a milky, sticky liquid will flow out of the wound resection. This latex is going to polymerize at 30-35 oC in a few minutes in a yellow-brown quite solid mass. Around the year 1982, I have annotated this observation but I could not find in my later notes further follow-ups study on the topics. It was a casual observation but I didn’t know at that time that this latex is indeed very useful. A variety of the Taraxacum (Taraxacum koksaghyz, Russian Dandelion) was used in Russian and American to produce a replacement of the natural rubber from Brazil during WWII that was in shortage because of the war. Nowadays, many studies are in progress to exploit the lattice of Taraxacum and also Taraxacum brevicorniculatumas a convenient replacement of the rubber plant lattice. A recent study has shown the presence of rubber particles in the lattice of these plants in 32% proportion composed prevalently by poly(cis-1,4-isoprene) at >95% of purity (www.biomedcentral.com/1471-2091/11/11). The brownish lattice condensate that, as I reported in my note, forms after exposing for several minutes the latex to the air, is caused by the presence of the polyphenol oxidase (PPO) enzyme that produces the fast coagulation of the latex by catalyzing the oxidation of polyphenols. Genetic engineer the plant, it is possible to reduce the amount of PPO in the latex making economically competitive the use of this resource for the production of latex.

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