Quantum diffusion in polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate quantum diffusion of an electron in a model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with fluctuation of the parameters due to the impact of colored noise. The randomness is introduced by fluctuations of distance between two consecutive bases along the stacked base pairs. We demonstrate that in the model the decay time of the correlation can control the spread of the electronic wavepacket. Furthermore it is shown that in a motional narrowing regime the averaging over fluctuation causes ballistic propagation of the wavepacket, and in the adiabatic regime the electronic states are affected by localization.     

Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.     

Multidimensional LC-LC and LC-CE for high-resolution separations of biological molecules

In multidimensional separations, two or more independent separation methods are coupled in an effort to resolve complex mixtures. The displacement mechanisms of each method should be orthogonal, such that little correlation exists between the retention of compounds in each dimension. When multiple orthogonal separation methods are coupled such that all sample components are subjected to complete analysis on all dimensions, the method is considered comprehensive. The primary advantage of comprehensive multidimensional separations over their one-dimensional counterparts is the potential for dramatically enhanced resolution. High resolving power can be achieved because the peak capacity of a comprehensive multidimensional separation is roughly equal to the product of the individual peak capacities of each dimension. In this review, the theory and instrumentation of two-dimensional liquid chromatography (LC-LC) and liquid chromatography-capillary electrophoresis (LC-CE) separations are discussed. Some applications of these techniques to the separation of biological molecules are highlighted. Future directions for the development of multidimensional separations are also considered.     

Connecting cluster dynamics and protein folding

The relaxation dynamics of clusters can be interpreted in terms of the topographies of their potential surfaces. Systems with short-range potentials have sawtooth-like potential surfaces with small drops in energy from one local minimum to the next and few-body motions as the clusters move from one minimum to another; such systems readily take on amorphous structures. These are called “glass-formers". Systems with long-range forces have potentials whose topographies are like rough staircases, with some large drops in energy from one minimum to the next; their well-to-well passages involve very collective motions and such systems are excellent structure-seekers. They find their way to well-ordered, highly selective structures under almost all circumstances. These characteristics generalize to describe the potential surfaces and folding behavior of polypeptides and proteins. The forces are effective long-range forces due to the polymer chain. Staircase topographies emerge both from direct sampling of potential surfaces and from the inversion of the kinetics generated by a much more aaabstract topological model, from which folding pathways can be inferred. Received 4 December 2000     

Overlap distribution in random and designed heteropolymers

We study the overlap between low-energy states in lattice models of heteropolymers with contact interactions. The overlap distribution gives information on the degree of correlation in the energy landscape. Designed sequences have rather correlated energy landscapes, which favor fast folding kinetics. Chains with random interactions have much less correlated energy landscapes. It is indeed believed that the mean-field theory for this model coincides with the Random Energy Model, whose different low-energy states are completely unrelated. This picture has been supported by numerical studies of maximally compact configurations. Without applying this constraint, we find that the overlap distribution is indeed bimodal as expected, but it has a broad peak at large overlap, indicating a non-vanishing width for the valleys of low-energy states. This feature probably plays an important role in the kinetics of the model. It is not evident that the range of such correlations shrinks to zero for large systems. The range of the correlations seems to be influenced by the number of contacts per residue in the ground state: the smaller this quantity, the larger the correlations. Received 16 August 2000     

Michrochip chromatography using an open‐tubular microchannel and a ternary water–ACN–ethyl acetate mixture carrier solution

A capillary chromatography system has been developed using a ternary mixed‐solvents solution, i.e. water–hydrophilic/hydrophobic organic solvent mixture as a carrier solution. Here, we tried to carry out the chromatographic system on a microchip incorporating the open‐tubular microchannels. A model analyte solution of isoluminol isothiocyanate (ILITC) and ILITC‐labeled biomolecule was injected to the double T‐junction part on the microchip. The analyte solution was delivered in the separation microchannel (40 μm deep, 100 μm wide, and 22 cm long) with the ternary water–ACN–ethyl acetate mixture carrier solution (3:8:4 volume ratio, the organic solvent rich or 15:3:2 volume ratio, the water‐rich). The analyte, free‐ILITC and labeled BSA mixture, was separated through the microchannel, where the carrier solvents were radially distributed in the separation channel generating inner and outer phases. The outer phase acts as a pseudo‐stationary phase under laminar flow conditions in the system. The ILITC and the labeled BSA were eluted and detected with chemiluminescence reaction.     

A DFT study of electron or hole localization in a peptide containing asparagin

The mechanisms of protein degradation induced by ionisation are of great interest for radiobiology, improvement of mass spectroscopy and industrial processes such as radio sterilisation. Sequences containing asparagin are very sensitive especially if surrounded by glycine. Very few techniques allow a satisfying understanding of the processes induced by creation of an anionic or cationic site in a peptide. We used the methods of quantum chemistry (DFT/B3LYP with 6-31G^* basis set) to characterise the geometry modifications induced in the cations or in the anions derived from peptide Gly Asn Gly. The cationic sites are localised mostly close to the first peptidic bond and induce a lengthening of the Ca-C(O) bond. Conversely the anionic sites are localised on a carbonyl function. Implications are discussed considering the radiolytic products and the proposed mechanisms. Received 21 January 2002 Published online 13 September 2002     

Strengths and weaknesses of in-tube solid-phase microextraction: A scoping review

In-tube solid-phase microextraction (in-tube SPME or IT-SPME) is a sample preparation technique which has demonstrated over time its ability to couple with liquid chromatography (LC), as well as its advantages as a miniaturized technique. However, the in-tube SPME perspectives in the forthcoming years depend on solutions that can be brought to the environmental, industrial, food and biomedical analysis. The purpose of this scoping review is to examine the strengths and weaknesses of this technique during the period 2009 to 2015 in order to identify research gaps that should be addressed in the future, as well as the tendencies that are meant to strengthen the technique.     

Biomolecules as promising ligands in the synthesis of metal nanoclusters: Sensing,bioimaging and catalytic applications

The use of metal nanoclusters as sensing probes has recently attracted considerable interest from researchers. In particular, metallic nanoclusters (e.g., Au, Ag, Cu, Pt) have been noticed a wide range of applications in the field of fluorescence sensing and bioimaging. The stabilization of metal nanoclusters with organic molecules, proteins, and amino acids enhances their optical properties and analytical applications. In this review, synthetic routes for the fabrication of metal nanoclusters are summarized. This review also describes the metal nanoclusters properties including aggregation-induced emission, optical absorption, non-linear optical, and chiral properties. We discussed the analytical applications of metal nanoclusters for sensing of wide variety of analytes including drugs, biomolecules, biomarkers. Further, the catalytic applications of metal nanoclusters are also briefly summarized. Finally, we summarize the challenges and future perspectives of metal nanoclusters in analytical chemistry.     

Biosorption: a new rise for elemental solid phase extraction methods

Biosorption is a term that usually describes the removal of heavy metals from an aqueous solution through their passive binding to a biomass. Bacteria, yeast, algae and fungi are microorganisms that have been immobilized and employed as sorbents in biosorption processes. The binding characteristics of microorganisms are attributed to functional groups on the surface providing some features to the biosorption process like selectivity, specificity and easy release. These characteristics turn the biosorption into an ideal process to be introduced in solid phase extraction systems for analytical approaches. This review encompasses the research carried out since 2000, focused on the employment of biosorption processes as an analytical tool to improve instrumental analysis. Since aminoacids and peptides as synthetic analogues of natural metallothioneins, proteins present in the cell wall of microorganisms, have been also immobilized on solid supports (controlled pore glass, carbon nanotubes, silica gel polyurethane foam, etc.) and introduced into solid phase extraction systems; a survey attending this issue will be developed as well in this review.