DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Critical exponent of the electrical conductivity in the paracoherence region of a thin film of YBa2Cu3O7?x

Critical exponent of the electrical conductivity in the paracoherence region (gamma) of the high temperature superconductor YBa2Cu3O7-x (YBCO) has been estimated for high quality thin film on ZrO2 substrate prepared by high pressure oxygen sputtering. High energy ion irradiation was carried out using 100 MeV O-16(7+) ions at liquid nitrogen to see the effects of disorder on the value of the exponent. The critical exponent from a value of about 2 to 1.62 upon irradiation. Studies were also carried film to see the effect of ageing and annealing.

Design of logical topologies for wavelength-routed optical networks

his paper studies the problem of designing a logical topology over a wavelength-routed all-optical network (AON) physical topology, The physical topology consists of the nodes and fiber links in the network, On an AON physical topology, we can set up lightpaths between pairs of nodes, where a lightpath represents a direct optical connection without any intermediate electronics, The set of lightpaths along with the nodes constitutes the logical topology, For a given network physical topology and traffic pattern (relative traffic distribution among the source-destination pairs), our objective is to design the logical topology and the routing algorithm on that topology so as to minimize the network congestion while constraining the average delay seen by a source-destination pair and the amount of processing required at the nodes (degree of the logical topology), We will see that ignoring the delay constraints can result in fairly convoluted logical topologies with very long delays, On the other hand, in all our examples, imposing it results in a minimal increase in congestion, While the number of wavelengths required to imbed the resulting logical topology on the physical all optical topology is also a constraint in general, we find that in many cases of interest this number can be quite small, We formulate the combined logical topology design and routing problem described above (ignoring the constraint on the number of available wavelengths) as a mixed integer linear programming problem which we then solve for a number of cases of a six-node network, Since this programming problem is computationally intractable for larger networks, we split it into two subproblems: logical topology design, which is computationally hard and will probably require heuristic algorithms, and routing, which can be solved by a linear program, We then compare the performance of several heuristic topology design algorithms (that do take wavelength assignment constraints into account) against that of randomly generated topologies, as well as lower bounds derived in the paper.

Brownian dynamics simulation of dense binary colloidal mixtures. I. Structural evolution and dynamics

We have carried out Brownian dynamics simulations of binary mixtures of charged colloidal suspensions of two different diameter particles with varying volume fractions phi and charged impurity concentrations n(i). For a given phi, the effective temperature is lowered in many steps by reducing n(i) to see how structure and dynamics evolve. The structural quantities studied are the partial and total pair distribution functions g(tau), the static structure factors, the time average g(<(tau)over bar>), and the Wendt-Abraham parameter. The dynamic quantity is the temporal evolution of the total meansquared displacement (MSD). All these parameters show that by lowering the effective temperature at phi = 0.2, liquid freezes into a body-centered-cubic crystal whereas at phi = 0.3, a glassy state is formed. The MSD at intermediate times shows significant subdiffusive behavior whose time span increases with a reduction in the effective temperature. The mean-squared displacements for the supercooled liquid with phi = 0.3 show staircase behavior indicating a strongly cooperative jump motion of the particles.

Motion of a charged particle in superposed Heliotron and biconical cusp fields

We have studied the behaviour of a charged particle in an axially symmetric magnetic field having a neutral point, so as to find a possibility of confining a charged particle in a thermonuclear device. In order to study the motion we have reduced a three-dimensional motion to a two-dimensional one by introducing a fictitious potential. Following Schmidt we have classified the motion, as an ‘off-axis motion’ and ‘encircling motion’ depending on the behaviour of this potential. We see that the particle performs a hybrid type of motion in the negative z-axis, i.e. at some instant it is in ‘off-axis motion’ while at another instant it is in ‘encircling motion’. We have also solved the equation of motion numerically and the graphs of the particle trajectory verify our analysis. We find that in most of the cases the particle is contained. The magnetic moment is found to be moderately adiabatic.

Effect of screening of intermicellar interactions on the linear and nonlinear rheology of a viscoelastic gel

We report our studies of the linear and nonlinear rheology of aqueous solutions of the surfactant cetyl trimethylammonium tosylate (CTAT) with varying amounts of sodium chloride (NaCl). The CTAT concentration is fixed at 42 mM, and the salt concentration is varied between 0 and 120 mM. On increasing the salt (NaCl) concentration, we see three distinct regimes in the zero-shear viscosity and the high-frequency plateau modulus data. In regime 1, the zero-shear viscosity shows a weak increase with salt concentration due to enhanced micellar growth. The decrease in the zero-shear viscosities with salt concentration in regimes II and III can be explained in terms of intermicellar branching. The most intriguing feature of our data, however, is the anomalous behavior of the high-frequency plateau modulus in regime II (0.12 less than or equal to [NaCl]/[CTAT] less than or equal to 1.42). In this regime, the plateau modulus increases with an increase in NaCl concentration. This is highly interesting, since the correlation length of concentration fluctuations and hence the plateau modulus G(0) are not expected to change appreciably in the semidilute regime. We propose to explain the changes in regime II in terms of a possible unbinding of the organic counterions (tosylate) from the CTA(+) surfaces on the addition of NaCl. In the nonlinear flow curves of the samples with high salt content, significant deviations from the predictions of the Giesekus model for entangled micelles are observed.

Infrared Photodetectors Based on Reduced Graphene Oxide and Graphene Nanoribbons

The use of reduced graphene oxide (RGO) and graphene nanoribbons (GNRs) as infrared photodetectors is explored, based on recent results dealing with solar cells, light-emitting devices, photodetectors, and ultrafast lasers. IR detection is demonstrated by both RGO and GNRs (see image) in terms of the time-resolved photocurrent and photoresponse. The responsivity of the detectors and their functioning are presented.

An Overview of Homogenization

Homogenization of partial differential equations is relatively a new area and has tremendous applications in various branches of engineering sciences like: material science,porous media, study of vibrations of thin structures, composite materials to name a few. Though the material scientists and others had reasonable idea about the homogenization process, it was lacking a good mathematical theory till early seventies. The first proper mathematical procedure was developed in the seventies and later in the last 30 years or so it has flourished in various ways both application wise and mathematically. This is not a full survey article and on the other hand we will not be concentrating on a specialized problem. Indeed, we do indicate certain specialized problems of our interest without much details and that is not the main theme of the article. I plan to give an introductory presentation with the aim of catering to a wider audience. We go through few examples to understand homogenization procedure in a general perspective together with applications. We also present various mathematical techniques available and if possible some details about some of the techniques. A possible definition of homogenization would be that it is a process of understanding a heterogeneous (in-homogeneous) media, where the heterogeneties are at the microscopic level, like in composite materials, by a homogeneous media. In other words, one would like to obtain a homogeneous description of a highly oscillating in-homogeneous media. We also present other generalizations to non linear problems, porous media and so on. Finally, we will like to see a closely related issue of optimal bounds which itself is an independent area of research.

Minimal Triangulations of Manifolds

Finding vertex-minimal triangulations of closed manifolds is a very difficult problem. Except for spheres and two series of manifolds, vertex-minimal triangulations are known for only few manifolds of dimension more than 2 (see the table given at the end of Section 5). In this article, we present a brief survey on the works done in last 30 years on the following:(i) Finding the minimal number of vertices required to triangulate a given pl manifold. (ii) Given positive integers n and d, construction of n-vertex triangulations of different d-dimensional pl manifolds. (iii) Classifications of all the triangulations of a given pl manifold with same number of vertices.In Section 1, we have given all the definitions which are required for the remaining part of this article. A reader can start from Section 2 and come back to Section 1 as and when required. In Section 2, we have presented a very brief history of triangulations of manifolds. In Section 3,we have presented examples of several vertex-minimal triangulations. In Section 4, we have presented some interesting results on triangulations of manifolds. In particular, we have stated the Lower Bound Theorem and the Upper Bound Theorem. In Section 5, we have stated several results on minimal triangulations without proofs. Proofs are available in the references mentioned there. We have also presented some open problems/conjectures in Sections 3 and 5.

Photocatalytic degradation of dimethoate using LbL fabricated TiO2/polymer hybrid films

Degradation of dimethoate under UV irradiation using TiO2/polymer films prepared by the layer-by-layer (LbL) method was investigated. The thin films were fabricated on glass slides and the surface morphology and roughness of the thin films were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM) and atomic force microscopy (AFM). The effect of lamp intensity, catalyst loading in the layers, number of bilayers, pH and initial dimethoate concentration on the degradation of dimethoate was systematically studied. The degradation was monitored using high performance liquid chromatography (HPLC) analysis and total organic carbon (TOC) measurements as a function of irradiation time, to see the change in concentration of dimethoate and mineralization, respectively. Complete degradation of dimethoate was achieved under TiO2 optimum loading of 4 g/L at an UV irradiation time of 180 min. Increase in the lamp intensity, catalyst loading and number of bilayers increased the rate of degradation. At a pH of 4.62, complete degradation of dimethoate was observed. The degradation efficiency decreased with increase in initial dimethoate concentration. The degradation byproducts were analyzed and confirmed by gas chromatography-mass spectra (GC-MS). Toxicity of the irradiated samples was measured using the luminescence of bacteria Vibrio fischeri after 30 min of incubation and the results showed more toxicity than the parent compound. Catalyst reusability studies revealed that the fabricated thin films could be repeatedly used for up to ten times without affecting the photocatalytic activity of the films. The findings of the present study are very useful for the treatment of wastewaters contaminated with pesticides. (C) 2011 Elsevier B.V. All rights reserved.

Coupled Wavenumbers in an Infinite Flexible Fluid-Filled Circular Cylindrical Shell: Comparison between Different Shell Theories

Analytical expressions are found for the wavenumbers in an infinite flexible in vacuo I fluid-filled circular cylindrical shell based on different shell-theories using asymptotic methods. Donnell-Mushtari theory (the simplest shell theory) and four higher order theories, namely Love-Timoshenko, Goldenveizer-Novozhilov, Flugge and Kennard-simplified are considered. Initially, in vacuo and fluid-coupled wavenumber expressions are presented using the Donnell-Mushtari theory. Subsequently, the wavenumbers using the higher order theories are presented as perturbations on the Donnell-Mushtari wavenumbers. Similarly, expressions for the resonance frequencies in a finite shell are also presented, using each shell theory. The basic differences between the theories being what they are, the analytical expressions obtained from the five theories allow one to see how these differences propagate into the asymptotic expansions. Also, they help to quantify the difference between the theories for a wide range of parameter values such as the frequency range, circumferential order, thickness ratio of the shell, etc.

Structural characterization of backbone-expanded helices in hybrid peptides: (αγ) n and (αβ) n sequences with unconstrained β and γ homologues of L-Val

Learning your αβγ's: The diversity of hydrogen-bonding patterns in backbone-expanded hybrid helices is shown by crystal-structure determination of several oligomeric peptides (see scheme; C=gray; H=white; O=red; N=blue). C 12 helices were observed in the αγ peptide series for n=2-8. In comparison, the αα peptide and αβ peptide sequences show C 10 and mixed C 14/C 15 helices, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SuSeFLAV: A program for calculating supersymmetric spectra and lepton flavour violation

The program SuSeFLAV is introduced for computing supersymmetric mass spectra with flavour violation in various supersymmetric breaking scenarios with/without see-saw mechanism. A short user guide summarizing the compilation, executables and the input files is provided.

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.