DNA fragmentation by gamma radiation and electron beams using atomic force microscopy

Double-stranded pBS plasmid DNA was irradiated with gamma rays at doses ranging from 1 to 12 kGy and electron beams from 1 to 10 kGy. Fragment-size distributions were determined by direct visualization, using atomic force microscopy with nanometer-resolution operating in non-tapping mode, combined with an improved methodology. The fragment distributions from irradiation with gamma rays revealed discrete-like patterns at all doses, suggesting that these patterns are modulated by the base pair composition of the plasmid. Irradiation with electron beams, at very high dose rates, generated continuous distributions of highly shattered DNA fragments, similar to results at much lower dose rates found in the literature. Altogether, these results indicate that AFM could supplement traditional methods for high-resolution measurements of radiation damage to DNA, while providing new and relevant information.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Conference on biological applications of nuclear physics. July 12-27, 1948.

Includes bibliographies.

Essentials of biological and medical physics

Mode of access: Internet.

Time correlation function in systems with two coexisting biological species

We study a stochastic lattice model describing the dynamics of coexistence of two interacting biological species. The model comprehends the local processes of birth, death, and diffusion of individuals of each species and is grounded on interaction of the predator-prey type. The species coexistence can be of two types: With self-sustained coupled time oscillations of population densities and without oscillations. We perform numerical simulations of the model on a square lattice and analyze the temporal behavior of each species by computing the time correlation functions as well as the spectral densities. This analysis provides an appropriate characterization of the different types of coexistence. It is also used to examine linked population cycles in nature and in experiment.

A mathematical view of biological complexity

This essay is a trial on giving some mathematical ideas about the concept of biological complexity, trying to explore four different attributes considered to be essential to characterize a complex system in a biological context: decomposition, heterogeneous assembly, self-organization, and adequacy. It is a theoretical and speculative approach, opening some possibilities to further numerical and experimental work, illustrated by references to several researches that applied the concepts presented here. (C) 2008 Elsevier B.V. All rights reserved.

Assessment of the differential linear coherent scattering coefficient of biological samples

New differential linear coherent scattering coefficient, mu(CS), data for four biological tissue types (fat pork, tendon chicken, adipose and fibroglandular human breast tissues) covering a large momentum transfer interval (0.07 <= q <= 70.5 nm(-1)), resulted from combining WAXS and SAXS data, are presented in order to emphasize the need to update the default data-base by including the molecular interference and the large-scale arrangements effect. The results showed that the differential linear coherent scattering coefficient demonstrates influence of the large-scale arrangement, mainly due to collagen fibrils for tendon chicken and fibroglandular breast samples, and triacylglycerides for fat pork and adipose breast samples at low momentum transfer region. While, at high momentum transfer, the mu(CS) reflects effects of molecular interference related to water for tendon chicken and fibroglandular samples and, fatty acids for fat pork and adipose samples. (C) 2009 Elsevier B.V. All rights reserved.

Synthesis of optically complex core-shell colloidal suspensions: Pathways to multiplexed biological screening

The ability to generate enormous random libraries of DNA probes via split-and-mix synthesis on solid supports is an important biotechnological application of colloids that has not been fully utilized to date. To discriminate between colloid-based DNA probes each colloidal particle must be 'encoded' so it is distinguishable from all other particles. To this end, we have used novel particle synthesis strategies to produce large numbers of optically encoded particle suitable for DNA library synthesis. Multifluorescent particles with unique and reproducible optical signatures (i.e., fluorescence and light-scattering attributes) suitable for high-throughput flow cytometry have been produced. In the spectroscopic study presented here, we investigated the optical characteristics of multi-fluorescent particles that were synthesized by coating silica 'core' particles with up to six different fluorescent dye shells alternated with non-fluorescent silica 'spacer' shells. It was observed that the diameter of the particles increased by up to 20% as a result of the addition of twelve concentric shells and that there was a significant reduction in fluorescence emission intensities from inner shells as an increasing number of shells were deposited.

Measurement of lead concentration in biological tissues by atomic spectroscopy techniques

Dissertation for the degree of Doctor of Philosophy in Physics

Photoelectron spectroscopy of nitrogen containing molecules of biological and industrial interest

A thesis submitted for the degree of Ph. D. in Physics

Resonancia Magnética Nuclear aplicada al estudio de nuevos sistemas farmacéuticos y biológicos, complejos poliméricos y conjuntos de espines modelo. Nuclear Magnetic Resonance applied to the study of new pharmaceutical and biological systems, polymeric complexes and model spin clusters.

El presente proyecto plantea utilizar integralmente la técnica de Resonancia Magnética Nuclear en sólidos como un medio experimental que permite entender fenómenos de la física fundamental, como así también realizar aplicaciones de interés en el campo de la química, los desarrollos farmacéuticos y la biología. Novedosas técnicas experimentales serán empleadas, en conjunción con otras más tradicionales, en la caracterización de nuevas estructuras poliméricas acomplejadas a metales, membranas biológicas y compuestos de interés farmacéutico en vías de desarrollo, los cuales presentan el fenómeno de polimorfismo . Esto se llevará a cabo complementando los resultados de RMN en sólidos con técnicas tanto espectroscópicas como analíticas (Infrarrojo, Difracción de Rayos X, Calorimetría, RMN en solución) y trabajo interdisciplinario. Paralelamente al desarrollo de estos temas, profundizaremos mediante investigación básica, en la compresión de la dinámica cuántica y el surgimiento de la irreversibilidad en sistemas de espines nucleares. Observaremos en particular la generación, evolución y control de las coherencias cuánticas múltiples en sistemas cuánticos abiertos, lo cual nos da información sobre tamaño de clusters de espines. Esto permitirá la correcta implementación de secuencias de pulsos sofisticadas, como así también desarrollar nuevos métodos de medición aplicados a la caracterización estructural y a la dinámica molecular de sólidos complejos. Debemos resaltar que este proyecto está conectado con aspectos tanto básicos como aplicados de la RMN en sólidos como técnica experimental, la cual se desarrolla en el país únicamente en FaMAF-UNC. Se nutre además de trabajo multidisciplinario promoviendo la colaboración con investigadores y becarios de distintas áreas (física, química, farmacia, biología) provenientes de distintos puntos del país. Finalmente podemos afirmar que este plan impulsa la aplicación de la física básica proyectada a diferentes áreas del conocimiento, en el ámbito de la provincia de Córdoba. The aim of the present proyect is to use Nuclear Magnetic Resonance (NMR) as a complete techique that allows the understanding of fundamental physics phenomena and, at the same time, it leads to important applications in the fields of chemistry, pharmaceutical developments and biology. New experiments will be used together with traditional ones, in the characterization of new metal-polymer complexes, biological membranes and pharmaceutical compounds, some of them presenting polymorfism. NMR experiments will be complemented with diverse spectroscopic and analytical techniques: Infrared, X ray Diffraction, Thermal Analysis, solution NMR, as well as multidisciplinary investigation. Additionally, the present proyect plans to study in depth several aspects of quantum dynamics phenomena and decoherence in nuclear spin systems. The present proyect is connected with basic and applied aspects of the solid state NMR technique, developed in our country, only at FaMAF-UNC. It is is composed by multidisciplinary work and it promotes the collaboration with researchers and students coming from different fields (physics, chemistry, pharmaceutical developments, biology) and different points of our country.

Geometry and physics of catenanes applied to the study of DNA replication.

The concept of ideal geometric configurations was recently applied to the classification and characterization of various knots. Different knots in their ideal form (i.e., the one requiring the shortest length of a constant-diameter tube to form a given knot) were shown to have an overall compactness proportional to the time-averaged compactness of thermally agitated knotted polymers forming corresponding knots. This was useful for predicting the relative speed of electrophoretic migration of different DNA knots. Here we characterize the ideal geometric configurations of catenanes (called links by mathematicians), i.e., closed curves in space that are topologically linked to each other. We demonstrate that the ideal configurations of different catenanes show interrelations very similar to those observed in the ideal configurations of knots. By analyzing literature data on electrophoretic separations of the torus-type of DNA catenanes with increasing complexity, we observed that their electrophoretic migration is roughly proportional to the overall compactness of ideal representations of the corresponding catenanes. This correlation does not apply, however, to electrophoretic migration of certain replication intermediates, believed up to now to represent the simplest torus-type catenanes. We propose, therefore, that freshly replicated circular DNA molecules, in addition to forming regular catenanes, may also form hemicatenanes.

New Radicals and new applications of Dynamic Nuclear Polarization of biological systems

Dynamic Nuclear Polarization (DNP) is an emerging technique that could revolutionize the NMR study of small molecules at very low concentrations by the increase in sensitivity that results from transfer of polarization between electronic and nuclear spins. Although the underlying physics has been known for a long time, in the last few years there has been a lot of excitement on the chemistry and biology NMR community caused by the demonstration that the highly polarized nuclei that are prepared in solid state at very low temperatures (1-2 K) could be rapidly transferred to liquid samples at room temperature and studied in solution by conventional NMR techniques. In favorable cases several order of magnitude increases in sensitivity have been achieved. The technique is now mature enough that a commercial instrument is available. The efficiency of DNP depends on two crucial aspects: i) the efficiency of the nuclear polarization process and ii) the efficiency of the transfer from the initial solid state to the fluid state in which NMR is measured. The preferred areas of application (iii) will be dictated by situations in which the low concentration of the sample or its intrinsic low receptivity are the limiting factors .

physics of the Web

Science is search for the laws of underlying phenomena of the nature. Engineering constructs the nature as we wish. Interestingly the huge engineering infrastructure like world wide web has grown in such a complex structure such that we need to see the fundamental science behind the structure and behaviour of these networks. This talk covers the science behind the complex networks like web, biological, social etc. The talk aim to discuss the basic theories that govern the static as well as the dynamics of such interesting networks

Time-multiplexed Laguerre-Gaussian holographic optical tweezers for biological applications

A ferroelectric liquid crystal spatial light modulator is used to generate up to 24 independently controllable traps in a holographic optical tweezers system using time-multiplexed Fresnel zone plates. For use in biological applications, helical zone plates are used to generate Laguerre-Gaussian laser modes. The high speed switching of the ferroelectric device together with recent advances in computer technology enable fast, smooth movement of traps that can be independently controlled in real time. This is demonstrated by the trapping and manipulation of yeast cells and fungal spores. (c) 2006 Optical Society of America.