S. Ramos-Bernal

Characterization of Selective Antibacterial Peptides by Polarity Index

In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups.

A simple model of the thermal prebiotic oligomerization of amino acids.

We construct a probabilistic model with the aid of the Markov chain formalism to describe and give a physico-chemical justification to an oligomerization process of a set of amino acids under certain prebiotic conditions. Such chemical process shows a remarkable bias in the polymer products that our model can explain. Some predictions and limitations are also discussed.

Prebiotic thermal polymerization of crystals of amino acids via the diketopiperazine reaction

In this work, we continue our studies on the thermal prebiotic oligomerization of amino acids. The next step is to consider all four types of electromagnetic interactions that our model may admit. In addition, only the polymerization of amino acids via the formation of diketopiperazine, which arises from the cyclodehydration of two amino acids, will be considered. By assuming that only one residue group of two will predominate in the diketopiperazine molecule, it is possible to reduce the three-body problem to a simpler situation with the two objects that we have already solved.

Biased polymers in the origin of life

We delve into the study of a Markov chain formalism applied to the thermal prebiotic oligomerization of amino acids. We find for the case of only two types of electromagnetic interactions, that the steady state attainment by the Markov chain is a built in mechanism limiting the expected variability in sequences in a population of polymers. Such result may be of importance as it makes more accessible the replication of a minimal chemical machinery compatible with life.

A Thermoluminescence Study of Bio-Organic Compounds Adsorbed in a Clay Mineral

Clay minerals have been implicated as a probable active surface for pre-biological chemical reactions occurring during the early evolution of the Earth. In this context, it is very important to explain the role of these surfaces and how much a solid is involved in the chemical transformation that is taking place at its surface. The aim of this work is to present experimental results from the ultraviolet spectroscopy and thermoluminescence behavior of samples of adenine and poly A, nucleic acid components, adsorbed in a clay mineral (Na-montmorillonite) and irradiated with gamma rays. The results obtained show that both compounds are adsorbed readily in the clay. The TL response of the samples showed that there are differences depending on whether the adsorbate is present, and it is pH dependent. In the system under study, the recovery of adenine from the adenine-clay system was much higher than in a homogeneous phase, in which the survival of the adsorbed molecule versus doses was low. A decrease in the TL signal is observed probably because adenine interfere with the recombination of the electrons with the hole trapped and reduce the presence of sites that induce luminescence emission to the aluminum-hole centers. This is of particular interest because there are modes of energy transfer across interfaces that do not exist in homogeneous phases.

Radiolysis of carboxylic acids adsorbed in clay minerals

Abstract This research is aimed at studing the effect of ionizing radiation in an heterogeneous system formed by a carboxylic acid adsorbed in a clay mineral. The study is focussed to discriminate if the presence of a solid surface alters the formation and distribution of radiolytic products in relation to the radiolysis of the carboxylic acid without the surface (clay). The results showed that the radiolysis of the system clay-acid goes along a defined path rather than showing various pathways of decomposition as in the case of simple aqueous solutions. The main pathway was the decarboxylation of the target compound rather than condensation/dimerization reactions.

Calcium carbonate as a possible dosimeter for high irradiation doses

The aim of this work is to analyze the interactions of 5MeV electron beam radiation and a 290MeV/u Carbon beam with calcium carbonate (powder) at 298K and at different irradiation doses, for the potential use of calcium carbonate as a high-dose dosimeter. The irradiation doses with the electron beam were from 0.015 to 9MGy, and with Carbon beam from 1.5kGy to 8kGy. High-energy radiation induces the formation of free radicals in solid calcium carbonate that can be detected and measured by electron paramagnetic resonance (EPR). An increase of the EPR response for some of the free radicals produced in the sample was observed as a function of the irradiation dose. These measurements are reproducible; the preparation of the sample is simple and inexpensive; and the signal is stable for several months. The response curves show that the dosimeter tends to saturate at 10MGy. Based on these properties, we propose this chemical compound as a high-dose dosimeter, mainly for electron irradiation.

Adsorption of HCN onto sodium montmorillonite dependent on the pH as a component to chemical evolution

The aim of this work is to study the behaviour of hydrogen cyanide (HCN) adsorbed onto mineral surfaces (sodium montmorillonite, a clay mineral) in different pH environments as a possible prebiotic process for complexation of organics. Our experimental results show that specific sites on the surface of the clay increased the concentration of HCN molecules dependent on the pH values. Moreover, this adsorption can occur through physical and chemical interactions enhanced by the channel structure of the sodium montmorillonite. The three-dimensional channelling structure of the clay accumulates the organics, hindering the releasing (desorption) of the organic molecules. A molecular model developed here also confirms the role of the pH as a regulating factor in the adsorption of HCN onto the inorganic surfaces and the possibility for further reactions forming more complex molecules, as an abiotic mechanism important in prebiotic chemical evolution processes. Received 12 February 2014, accepted 27 March 2014, first published online 12 May 2014

On the reproducibility of the glow curve of single crystal and commercial LiF

Abstract Heterogeneous interstitial nucleation was observed as a result of the exposure to high dose rate and repeated irradiations of single crystals of LiF doped with Mg and Ti. A comparison under the same conditions with the irradiation of commercial LiF dosimeters was done. The temperature region for which the observations were made applies to the region where V K centers are mobile. Therefore, the recombination of some defects produced by gamma radiation are primarily actual for the behavior around room temperature. Glow curves were obtained from irradiated LiF. The main disadvantages found are almost the same as those presented for commercial LiF. Also, in both cases we found differences in the thermoluminiscence response after storage was observed. The study was also focused to answering the question of how many times a dosimeter can be re-used after a severe irradiation.

Radiation heterogeneous processes of14C-acetic acid adsorbed in Na-Montmorillonite

This research addresses itself to the study of the mechanism of the acetic acid decarboxylation in Na-Montmorillonite exposed to ionizing radiation. The results obtained indicated that the decarboxylation reaction is enhanced several times by the irradiation. This behavior is probably due to an oxidation reaction at the edges of the clay. Also it is by energy transfer from the clay to adsorbed molecules by an interaction of non-equilibrium charge carriers with the adsorbed molecules.