Italy 1989, it was the age of Commodore Amiga with its BOING demo, the bouncing ball that conquest the heart of the millions of young people living the microcomputer revolution.
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Le Forze Intermolecolari
Le forze interatomiche o intermolecolari che tengono uniti i cristalli molecolari sono di origine elettrostatica e possono essere classificate in forze a corto e lungo raggio a seconda di quanto si estende nello spazio la loro azione. Essendo funzione della distanza tra gli atomi (o molecule), queste forze sono dei campi vettoriali conservativi e sono pertanto derivabili dal gradiente di un potenziale di energia scalare, ovvero 
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L’Energia Reticolare
Con il termine energia reticolare si definisce l’energia necessaria per scomporre, alla temperatura T = 0 K, una mole di un cristallo ionico nei suoi costituenti fondamentali e portarli a distanza infinita.
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Il calcolo della costante di Madelung
In un precedente articolo è stato mostrato che il termine elettrostatico dell’energia reticolare di un cristallo contiene un fattore (A) che dipende dal tipo di reticolo cristallino. Ora esamineremo più in dettaglio come calcolare questo termine e il suo valore per un semplice sistema ionico.
L’energia potenziale totale di un cristallo ionico è uguale alla somma dei contributi di interazione elettrostatica del tipo
degli ioni (A,B) di carica 
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PERL Programming II: Applications to Bioinformatics
This article is the second part of my previous introduction to the PERL language. Here, I am going to show the use of the Perl language in simple bioinformatics applications. I will introduce by examples other aspects of this powerful language.
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Introduction to the PERL Language
PERL is an acronym for Practical Extraction and Report Language. This scripting language was initially developed by Larry Wall with the intent to extend the potentiality of the awk and sed program for text manipulation and for Unix system administration tool. It takes the best features of many other languages, such as C, sed, and awk. In addition, Perl supports both procedural and object-oriented programming. Perl is the most popular web programming language due to its capability with text manipulation and rapid development cycle. The same capabilities began a precious support to bioinformatician to data mining the rapid accumulation of a large amount of genetic information from the molecular biology research. Continue reading
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COMPUTER SIMULATIONS STUDIES OF PEPTIDES IN ORGANIC SOLVENTS AND COSOLVENTS: A SIMPLE DATABASE
SIMPEOS is a simple hypertextual database that provides a list of peptides that have been studied using molecular dynamics simulations in non-aqueous solvents. Continue reading
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The Molecular Dynamics Docking Method
Understanding the mechanisms of the molecular recognition has fundamental impacts in medicine and biotechnology. It plays an important role in discovering new drugs and in developing new biocatalyst. The theoretical study of these mechanisms has boosted the development of approximated but fast methods for screening large compound libraries and protein-protein complexes. Continue reading
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The AWK Programming Language
Awk is a powerful Unix tool. Its name derives from the surname initials of Alfred Aho, Peter Weinberger, and Brian Kernighan who originally designed it at Bell Labs in 1977. The program has a different version and implementations. A commonly used one is the gawk from the GNU (http://www.gnu.org/s/gawk/). According to the definition of one of its developer, Alfred. V. Aho: “AWK is a language for processing files of text. A file is treated as a sequence of records, and, by default, each line is a record. Each line is broken up into a sequence of fields so we can think of the first word in a line as the first field, the second word as the second field, and so on. An AWK program is a sequence of pattern-action statements. AWK reads the input a line at a time. A line is scanned for each pattern in the program, and for each pattern that matches, the associated action is executed.”
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Unix Shell Programming Notes. Part I
UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity.
Dennis Ritchie
Shell commands can be combined in script files that perform complex actions. In this first article, a concise introduction to shell programming (focusing on the csh shell) is given. In the second part, I will provide some examples of complex scripting for different applications. For other types of shells, the reader can consult comprehensive textbooks that are listed at the end of this article.
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