Anomalous phase transitions in soft colloid-polymer binary mixtures

We have shown earlier [1] that these PGNPs resemble star polymers or spherical brushes in terms of their morphology in the melt. However, these particles show dynamics in melt which is quite different from other soft colloidal particles. Since most of the work on soft colloidal particles have been performed in solutions we have now explored the phase behavior of the PGNPs in good solvent using microscopic structural and dynamical measurements on binary mixtures of homopolymers and soft colloids consisting of polymer grafted nanoparticles. We observe anomalous structural and dynamical phase transitions of these binary mixtures, including appearance of spontaneous orientational alignment and logarithmic structural relaxations, as a function of added homopolymers of different molecular weights. Our experiments points to the possibility of exploiting the phase space in density and homopolymer size, of such hybrid systems, to create new materials with unique properties.

Physical understanding of pore formation on supported lipid bilayer by bacterial toxins

Pore forming toxins are being classified in the protein community based on their ability of forming pores in living cell membranes. Some initial study has apparently pointed out the crystallographic pathway rather can be viewed as a structural as well as morphological changes of proteins in terms of self assembly before and during the pore formation process in surfactant medium. Being a water soluble compound, it changes its conformation and originates some pre-pore complex, which later partially goes inside the cell membrane causing a pore. The physical mechanism for this whole process is still unknown. In this study we have tried to understand these types of biological processes from physical point of view by using supported lipid bilayer as a model system.

Fractal dimension method for delamination detection in composite beams

A new delaminated composite beam element is formulated for Timoshenko as well as Euler-Bernoulli beam models. Shape functions are derived from Timoshenko functions; this provides a unified formulation for slender to moderately deep beam analyses. The element is simple and easy to implement, results are on par with those from free mode delamination models. Katz fractal dimension method is applied on the mode shapes obtained from finite element models, to detect the delamination in the beam. The effect of finite element size on fractal dimension method of delamination detection is quantified.

PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function to drug discovery and protein engineering. Here, we describe an algorithm for the comparison of three-dimensional ligand-binding sites in protein structures. A previously described algorithm, PocketMatch (version 1.0) is optimised, expanded, and MPI-enabled for parallel execution. PocketMatch (version 2.0) rapidly quantifies binding-site similarity based on structural descriptors such as residue nature and interatomic distances. Atomic-scale alignments may also be obtained from amino acid residue pairings generated. It allows an end-user to compute database-wide, all-to-all comparisons in a matter of hours. The use of our algorithm on a sample dataset, performance-analysis, and annotated source code is also included.

Metallic Nanoparticles Arranged in a Helical Geometry: Route Towards Strong and Broadband Chiro-optical Response

Recent advances in nanotechnology have paved ways to various techniques for designing and fabricating novel nanostructures incorporating noble metal nanoparticles, for a wide range of applications. The interaction of light with metal nanoparticles (NPs) can generate strongly localized electromagnetic fields (Localized Surface Plasmon Resonance, LSPR) at certain wavelengths of the incident beam. In assemblies or structures where the nanoparticles are placed in close proximity, the plasmons of individual metallic NPs can be strongly coupled to each other via Coulomb interactions. By arranging the metallic NPs in a chiral (e.g. helical) geometry, it is possible to induce collective excitations, which lead to differential optical response of the structures to right-and left circularly polarized light (e.g. Circular Dichroism - CD). Earlier reports in this field include novel techniques of synthesizing metallic nanoparticles on biological helical templates made from DNA, proteins etc. In the present work, we have developed new ways of fabricating chiral complexes made of metallic NPs, which demonstrate a very strong chiro-optical response in the visible region of the electromagnetic spectrum. Using DDA (Discrete Dipole Approximation) simulations, we theoretically studied the conditions responsible for large and broadband chiro-optical response. This system may be used for various applications, for example those related to polarization control of visible light, sensing of proteins and other chiral bio-molecules, and many more.

Electronic band Structure and Photoemission Spectra of Graphene on Silicon Substrate

Synergizing graphene on silicon based nanostructures is pivotal in advancing nano-electronic device technology. A combination of molecular dynamics and density functional theory has been used to predict the electronic energy band structure and photo-emission spectrum for graphene-Si system with silicon as a substrate for graphene. The equilibrium geometry of the system after energy minimization is obtained from molecular dynamics simulations. For the stable geometry obtained, density functional theory calculations are employed to determine the energy band structure and dielectric constant of the system. Further the work function of the system which is a direct consequence of photoemission spectrum is calculated from the energy band structure using random phase approximations.

Electrothermally tunable MEMS filters

MEMS resonators have potential application in the area of frequency selective devices (e.g., gyroscopes, mass sensors, etc.). In this paper, design of electro thermally tunable resonators is presented. SOIMUMPs process is used to fabricate resonators with springs (beams) and a central mass. When voltage is applied, due to joule heating, temperature of the conducting beams goes up. This results in increase of electrical resistance due to mobility degradation. Due to increase in the temperature, springs start softening and therefore the fundamental frequency decreases. So for a given structure, one can modify the original fundamental frequency by changing the applied voltage. Coupled thermal effects result in non-uniform heating. It is observed from measurements and simulations that some parts of the beam become very hot and therefore soften more. Consequently, at higher voltages, the structure (equivalent to a single resonator) behaves like coupled resonators and exhibits peak splitting. In this mode, the given resonator can be used as a band rejection filter. This process is reversible and repeatable. For the designed structure, it is experimentally shown that by varying the voltage from 1 to 16V, the resonant frequency could be changed by 28%.

Detection of Target DNA using Photo-Reactive Protoporphyrin Moeity on a Nanocomposite Substrate

Detection of pathogens from infected biological samples through conventional process involves cell lysis and purification. The main objective of this work is to minimize the time and sample loss, as well as to increase the efficiency of detection of biomolecules. Electrical lysis of medical sample is performed in a closed microfluidic channel in a single integrated platform where the downstream analysis of the sample is possible. The device functions involve, in a sequence, flow of lysate from lysis chamber passed through a thermal denaturation counter where dsDNA is denatured to ssDNA, which is controlled by heater unit. A functionalized binding chamber of ssDNA is prepared by using ZnO nanorods as the matrix and functionalized with bifunctional carboxylic acid, 16-(2-pyridyldithiol) hexadecanoic acid (PDHA) which is further attached to a linker molecule 1-ethyl-3-(3-dimethylaminopropyl) (EDC). Linker moeity is then covalently bound to photoreactive protoporphyrin (PPP) molecule. The photolabile molecule protoporphyrin interacts with -NH2 labeled single stranded DNA (ssDNA) which thus acts as a probe to detect complimentary ssDNA from target organisms. Thereafter the bound DNA with protoporphyrin is exposed to an LED of particular wavelength for a definite period of time and DNA was eluted and analyzed. UV/Vis spectroscopic analysis at 260/280 nm wavelength confirms the purity and peak at 260 nm is reconfirmed for the elution of target DNA. Quantitative and qualitative data obtained from the current experiments show highly selective detection of biomolecule such as DNA which have large number of future applications in Point-of-Care devices.

Design and synthesis of new low band gap organic semiconductors for photovoltaic applications

Donor-acceptor (D-A) conjugated polymers have attracted a good deal of attention in recent years. In D-A systems, the introduction of electron withdrawing groups reduces E-g by lowering the LUMO levels whereas, the introduction of electron donating groups reduces E-g by raising the HOMO levels. Also, conjugated polymers with desired HOMO and LUMO energy levels could be obtained by the proper selection of donor and acceptor units. Because of this reason, D-A conjugated polymers are emerging as promising materials particularly for polymer light emitting diodes (PLEDs) and polymer solar cells (PSCs). We report the design and synthesis of four new narrow band gap donor-acceptor (D-A) conjugated polymers, PTCNN, PTCNF, PTCNV and PTCNO, containing electron donating 3,4-didodecyloxythiophene and electron accepting cyanovinylene units. The effects of further addition of electron donating and electron withdrawing groups to the repeating unit of a D-A conjugated polymer (PTCNN) on its optical and electrochemical properties are discussed. The studies revealed that the nature of D and A units as well as the extent of alternate D-A structure influences the optical and the electrochemical properties of the polymers. All the polymers are thermally stable up to a temperature of 300 degrees C under nitrogen atmosphere. The electrochemical studies revealed that the polymers possess low-lying HOMO energy levels and low-lying LUMO energy levels. In the UV-Vis absorption study, the polymer films displayed broad absorption in the wavelength region of 400-700 nm. The polymers exhibited low optical band gaps in the range 1.70 - 1.77 eV.

Photonic Hydrogel Beads for Controlled Release of Risedronate

pH-sensitive photonic composite hydrogel beads composed of sodium alginate and risedronate sodium (SA/RIS) was prepared crosslinked by Ca2+ owing to the ionic gelation of SA. The structure and surface morphology of the composite hydrogel beads were characterized by SEM. pH-sensitivity of these composite hydrogels beads and the release behaviors of drug from them were investigated. The results showed that the composite hydrogel beads had good pH-sensitivity. The drug loading and encapsulation efficiency were 27.7% and 92% for RIS, respectively. The cumulative release ratios of RIS from the composite hydrogel beads were 2.47% in pH 2.1 solution and 83 % in pH 6.8 solutions within 24 h, respectively. However, the cumulative release ratio of RIS in pH 7.4 solution reached 91% within 7 h. It is proposed that the novel photonic SA/RIS composite hydrogel bead could possess the potential of an increased intestinal absorption and fewer adverse effects of RIS. The pH and salt response of photonic hydrogel bead, as well as the encapsulation of macromolecules, are promising for applications in biomedicine and biotechnology.

Born-ratio type data normalization improves quantitation in photoacoustic tomography

In this report, we present a Born-ratio type of data normalization for reconstruction of initial acoustic pressure distribution in photoacoustic tomography (PAT). The normalized Born-ratio type of data is obtained as a ratio of photoacoustic pressure obtained with tissue sample in a coupling medium to the one obtained using purely coupling medium. It is shown that this type of data normalization improves the quantitation (intrinsic contrast) of the reconstructed images in comparison to the traditional techniques (unnormalized) that are currently available in PAT. Studies are carried out using various tissue samples. The robustness of the proposed method is studied at various noise levels added to the collected data. The improvement in quantitation can enable accurate estimation of pathophysiological parameter (optical absorption coefficient, a) of tissue sample under investigation leading to better sensitivity in PAT.

Intense Acoustic Burst Ultrasound Modulated Optical Tomography for Elasticity Mapping of Soft Biological Tissue Mimicking Phantom: A Laser Speckle Contrast Analysis Study

This report addresses the assessment of variation in elastic property of soft biological tissues non-invasively using laser speckle contrast measurement. The experimental as well as the numerical (Monte-Carlo simulation) studies are carried out. In this an intense acoustic burst of ultrasound (an acoustic pulse with high power within standard safety limits), instead of continuous wave, is employed to induce large modulation of the tissue materials in the ultrasound insonified region of interest (ROI) and it results to enhance the strength of the ultrasound modulated optical signal in ultrasound modulated optical tomography (UMOT) system. The intensity fluctuation of speckle patterns formed by interference of light scattered (while traversing through tissue medium) is characterized by the motion of scattering sites. The displacement of scattering particles is inversely related to the elastic property of the tissue. We study the feasibility of laser speckle contrast analysis (LSCA) technique to reconstruct a map of the elastic property of a soft tissue-mimicking phantom. We employ source synchronized parallel speckle detection scheme to (experimentally) measure the speckle contrast from the light traversing through ultrasound (US) insonified tissue-mimicking phantom. The measured relative image contrast (the ratio of the difference of the maximum and the minimum values to the maximum value) for intense acoustic burst is 86.44 % in comparison to 67.28 % for continuous wave excitation of ultrasound. We also present 1-D and 2-D image of speckle contrast which is the representative of elastic property distribution.

3-D GPU Based Real Time Diffuse Optical Tomographic System

3-Dimensional Diffuse Optical Tomographic (3-D DOT) image reconstruction algorithm is computationally complex and requires excessive matrix computations and thus hampers reconstruction in real time. In this paper, we present near real time 3D DOT image reconstruction that is based on Broyden approach for updating Jacobian matrix. The Broyden method simplifies the algorithm by avoiding re-computation of the Jacobian matrix in each iteration. We have developed CPU and heterogeneous CPU/GPU code for 3D DOT image reconstruction in C and MatLab programming platform. We have used Compute Unified Device Architecture (CUDA) programming framework and CUDA linear algebra library (CULA) to utilize the massively parallel computational power of GPUs (NVIDIA Tesla K20c). The computation time achieved for C program based implementation for a CPU/GPU system for 3 planes measurement and FEM mesh size of 19172 tetrahedral elements is 806 milliseconds for an iteration.