Author: Danilo Roccatano

Molecular interactions and force fields

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At quite uncertain times and places,
The atoms left their heavenly path,
And by fortuitous embraces,
Engendered all that being hath.
And though they seem to cling together,
And form ‘associations’ here,
Yet, soon or late, they burst their tether,
And through the depths of space career.
James Clerk Maxwell

From ‘Molecular Evolution’, Nature, 8, 1873. In Lewis Campbell and William Garnett, The Life of James Clerk Maxwell (1882), 637.

Molecular forces are originated by the interactions of the electronic clouds of the atoms in the molecular systems. A full treatment of these interactions also accounting for the dynamics of the nuclei requires the solution of the time-dependent Schroedinger equation (the top of the modeling pyramid). This approach would provide a more accurate physical representation of the behavior of the systems in time. However, as pointed before, nowadays this approach is impracticable due to the enormous amount of computer resources need to accomplish this task even for relatively small peptides in water systems. The solution to this impasse is the application of the so-called lex parsimoniae or Ockham’s razor, a powerful approach in problem-solving to get rid of the redundant complexity. In this case, the law of parsimony suggests changing the level of scale and account of the hidden degree of freedom using an effective or mean field potential.

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PERL Programming III: Modelling DNA Thermodynamics

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After a long pause, the adventure in the PERL programming language series continues with another example of biophysics and molecular biology science application.This time, we are going to make a program to model the effect of the temperature on DNA stability in solution.

The effect of temperature DNA structure integrity plays an important role in molecular biology applications. For example, the DNA amplification method based on polymerase (the PCR method) is based on a series of temperature cycles to separate the two strand of DNA to replicate. DNA primers are used to initiate the process and the knowledge of their melting temperature (Tm) play an important role in optimizing the DNA amplification process.

The first attempts to create a model of DNA thermodynamics date back to the beginnings of 1960. Studies pionered by the groups of Zimm [1] and Tinoco [2], have shown that the relative stability of a double-stranded DNA molecule depends primarily on the nature of the nearest-neighbor bases along the sequence. This finding brought to the formulation of a simple mathematical model (called the nearest-neighbor (NN) model) to predict relative stabilities of double stranded DNA according to the nucleotide sequence [see Cantor]. Subseguently, the NN model was further improved by the contribution of several research groups. In particular, Santalucia and co-workers. proposed a set of parameters for the NN model that provides an excellent prediction of the thermodynamic properties of short DNA homo oligonucleotides and are commonly used to calculate the stability of DNA primers used for PCR applications.

In this third article on PERL programming, I will give some indication on how to implement a simple version of the NN model. To make more fancy the programming task, we are also going to provide the program with a simple Graphical user interface using PERL/Tk.

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Retro Programming Nostalgia: il Commodore Amiga e la Visualizzazione Molecolare

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Italia anno 1989, era l’era del Commodore Amiga con la sua demo di BOING, la pallina bianca e rossa che rimbalzando ha conquistato il cuore di milioni di giovani che hanno vissuto la rivoluzionaria invenzione del personal computer.

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La Spettroscopia XANES

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Questo blog contiene un estratto del capitolo introduttivo sulla spettroscopia XANES della mia tesi di laurea che discussi 25 anni fa, per cui gli argomenti non sono molto aggiornati anche se il contenuto riportato è di carattere generale. 

Spettri di assorbimento di raggi X

Fino agli inizi del 1970 c’è stata una netta distinzione tra le tecniche di spettroscopia di assorbimento e quelle di diffrazione dei raggi X. La diffrazione era tradizionalmente considerata lo strumento più importante per la determinazione della struttura atomica di un composto, mentre l’assorbimento e l’emissione di raggi X erano usati per comprenderne la struttura elettronica. Continue reading →

La Programmazione della Unix Shell

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Questo blog contiene  una breve introduzione alla programmazione della Unix shell csh/tcsh. Per altri tipi di shells, il lettore può consultare manuali dedicati a questo argomento riportati nella bibliografia alla fine di questa questo blog. Continue reading →

Il calcolo della entalpia reticolare: il ciclo di Born-Haber

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La stabilità di un reticolo cristallino, in condizioni di T e P costanti, è legata all’ energia libera di Gibbs di formazione del reticolo:

\displaystyle M^+(g) + X^-(g) \rightarrow MX(s) \ \ \ \ \ (1)

\displaystyle \Delta G^{\circ} = \Delta H^{\circ} - T \Delta S^{\circ} \ \ \ \ \ (2)

Se {\Delta G^{\circ}} risulta più negativa per la formazione della struttura {I} che per quella della struttura {II}, la transizione {II \rightarrow I} sarà spontanea e il solido avrà quella struttura.

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The calculation of the Madelung constant

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A previous article showed that the electrostatic term of the lattice energy of a crystal contains a factor (A) that depends on the type of crystalline reticulum. This article will look more in detail how to calculate this term and its value for a simple ionic system.

The total Coulomb interaction energy of a crystal is given by the sum of the single pair interaction terms:

\displaystyle V_{AB} = \frac{e^2}{4\pi\epsilon_0} \frac{Z_AZ_B}{r_{AB}} \hfill (1)

for ions with charges qA and qB and distance rAB.  The sum extends to all pairs of ions present in the solid for any crystalline structure.

The sum converges very slowly because the first neighbours give a first substantial contribution with a negative summation term. Second neighbour atoms produce a slightly weaker positive term. It then continues to infinity with terms of alternating signs by smaller and smaller values. In this way, the resulting effect will be that the attraction between cations and anions predominates and provides a favourable negative contribution to the solid’s energy.

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Introduzione alla Dinamica Molecolare

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img_20171019_174056.jpg

  • Lex. I. Corpus omne perseverare in statu suo quiescendi vel movendi uniformiter in directum, nili quatenus a viribus impressis cogitur statum illum mutare.

  • Lex. II. Muationem motus proportionalem esse vi motrici impressae, et fieri fecundum lineam rectam qua vis illa imprimitur.

  • Lex. III. Actioni contrariam semper et equalem esse reactionem: sive corporum duorum actiones in se mutuo semper esse aequales et in partes contrarias dirigi.

 

Isaac Newton.
Philosophiae Naturalis Principia Mathematica.
London, 1686.

 

Nel 1648 Isaac Newton diede alle stampe la sua prima edizione dei Principia Mathematica, uno dei più grandi capolavori scientifici di tutti i tempi.  Nelle prime pagine di questa  summa scientifica si trovano enunciate le famose tre leggi che portano il suo nome, dalle quali ha avuto inizio la fisica-matematica classica. Continue reading →

The Lignin Peroxidase

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Lignin Peroxidase (LiP), a hemoprotein isolated from the ligninolytic cultures of the white-rot fungus Phenerochaete Chrysosporium is one of the most important lignin-degrading enzymes. We have investigated the dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant in aqueous solution using MD simulations [1].

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