Luminescent Molecular Sensors for Assessment of Temperature Field in Machining

A new technique based on luminescent molecular sensors is utilized in these series of experiments for measurement of temperatures in material removal processes. 2-Dimensional machining of metals at low speeds and surface grinding configurations are used as the model experimental systems to understand the efficacy of this experimental technique. The experiments were conducted with a series of luminescent sensors and binder combinations for the temperature measurement. The luminescence of the sensor was measured through a charge-coupled device imaging camera, and intensive calibration exercises were performed on these sensors. Excellent agreement in the temperature fields measured through this new experimental approach and traditional infrared thermography is seen here. This technique offers the unique capability of allowing measurement of temperatures in the presence of a lubricant, akin to manufacturing conditions in situ. Extension of the technique to measure the temperature field at the tool-chip contact is described.

Iron(III) benzhydroxamates of dipicolylamines for photocytotoxicity in red light and cellular imaging

Benzhydroxamate (BHA) iron(III) complexes Fe(BHA)(L)ClICI (I, 2)], where L is (phenyl)dipicolylamine (phdpa in I) and (pyrenyl)dipicolylamine (pydpa in 2), were prepared and their photocytotoxicity in visible (400-700 nm) and red (600-720 nm) light was studied. Complex 1 was structurally characterized by X-ray crystallography. The complexes have high-spin iron(III) centers. Complex 2, with a pyrenyl fluorophore, was used for cellular imaging, showing both mitochondrial and nuclear localization in the fluorescence microscopic study. The complex exhibited photocytotoxicity in red light in HeLa cancer cells, giving IC50 value of 24.4(+/- 0.4) pM, but remained essentially non-toxic in the dark. The involvement of reactive oxygen species and an apoptotic nature of cell death were observed from the cellular studies. (C) 2014 Elsevier Ltd. All rights reserved.

Raman spectroscopy explores molecular structural signatures of hidden materials in depth: Universal Multiple Angle Raman Spectroscopy

Non-invasive 3D imaging in materials and medical research involves methodologies such as X-ray imaging, MRI, fluorescence and optical coherence tomography, NIR absorption imaging, etc., providing global morphological/density/absorption changes of the hidden components. However, molecular information of such buried materials has been elusive. In this article we demonstrate observation of molecular structural information of materials hidden/buried in depth using Raman scattering. Typically, Raman spectroscopic observations are made at fixed collection angles, such as, 906, 1356, and 1806, except in spatially offset Raman scattering (SORS) (only back scattering based collection of photons) and transmission techniques. Such specific collection angles restrict the observations of Raman signals either from or near the surface of the materials. Universal Multiple Angle Raman Spectroscopy (UMARS) presented here employs the principle of (a) penetration depth of photons and then diffuse propagation through non-absorbing media by multiple scattering and (b) detection of signals from all the observable angles.

Iron(III) Catecholates for Cellular Imaging and Photocytotoxicity in Red Light

Iron(III) complexes Fe(L)(L') (NO3)]-in which L is phenyl-N, N-bis(pyridin-2-yl) methyl]methanamine (1), (anthracen-9-yl)N, N-bis(pyridin-2-yl) methyl] methanamine (2), (pyreny-1-yl)-N, N-bis(pyridin- 2-yl) methyl] methanamine (3-5), and L' is catecholate (1-3), 4-tert-butyl catecholate (4), and 4-(2-aminoethyl)benzene- 1,2-diolate (5)-were synthesized and their photocytotoxic proper-ties examined. The five electron-paramagnetic complexes displayed a FeIII/ Fe-II redox couple near similar to 0.4 V versus a saturated calomel electrode (SCE) in DMF/0.1m tetrabutylammonium perchlorate (TBAP). They showed unpre-cedented photocytotoxicity in red light (600-720 nm) to give IC50-15 mm in various cell lines by means of apoptosis to generate reactive oxygen species. They were ingested in the nucleus of HeLa and HaCaT cells in 4 h, thereby interacting favorably with calf thymus (ct)-DNA and photocleaving pUC19 DNA in red light of 785 nm to form hydroxyl radicals.

Graphene oxide-Fe3O4 nanoparticle composite with high transverse proton relaxivity value for magnetic resonance imaging

The potential of graphene oxide-Fe3O4 nanoparticle (GO-Fe3O4) composite as an image contrast enhancing material in magnetic resonance imaging has been investigated. Proton relaxivity values were obtained in three different homogeneous dispersions of GO-Fe3O4 composites synthesized by precipitating Fe3O4 nanoparticles in three different reaction mixtures containing 0.01 g, 0.1 g, and 0.2 g of graphene oxide. A noticeable difference in proton relaxivity values was observed between the three cases. A comprehensive structural and magnetic characterization revealed discrete differences in the extent of reduction of the graphene oxide and spacing between the graphene oxide sheets in the three composites. The GO-Fe3O4 composite framework that contained graphene oxide with least extent of reduction of the carboxyl groups and largest spacing between the graphene oxide sheets provided the optimum structure for yielding a very high transverse proton relaxivity value. It was found that the GO-Fe3O4 composites possessed good biocompatibility with normal cell lines, whereas they exhibited considerable toxicity towards breast cancer cells. (C) 2015 AIP Publishing LLC.

A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis

The coupling of endocytosis and exocytosis underlies fundamental biological processes ranging from fertilization to neuronal activity and cellular polarity. However, the mechanisms governing the spatial organization of endocytosis and exocytosis require clarification. Using a quantitative imaging-based screen in budding yeast, we identified 89 mutants displaying defects in the localization of either one or both pathways. High-resolution single-vesicle tracking revealed that the endocytic and exocytic mutants she4 Delta and bud6 Delta alter post-Golgi vesicle dynamics in opposite ways. The endocytic and exocytic pathways display strong interdependence during polarity establishment while being more independent during polarity maintenance. Systems analysis identified the exocyst complex as a key network hub, rich in genetic interactions with endocytic and exocytic components. Exocyst mutants displayed altered endocytic and post-Golgi vesicle dynamics and interspersed endocytic and exocytic domains compared with control cells. These data are consistent with an important role for the exocyst in coordinating endocytosis and exocytosis.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

A Pd-8 Tetrafacial Molecular Barrel as Carrier for Water Insoluble Fluorophore

A new carbazole-based tetraimidazole ligand 1,3,6,8-tetra(1H-imidazol-1-yl)-9-methyl-9H-carbazole (L) has been synthesized. The unsymmetrical nature of L as well as the rotational freedom of imidazole donor moieties around C-N bond make it a special building unit, which upon treatment with cis-(tmeda)Pd(NO3)(2) produced an unprecedented single linkage-isomeric Pd-8 tetrafacial molecular nanobarrel (PSMBR-1) tmeda N,N,N',N'-tetramethylethane-1,2-diamine]. Unlike closed architectures, open barrel architecture of water-soluble PSMBR-1 makes it an ideal host for some water insoluble polyaromatic hydrocarbons in aqueous medium; one such inclusion complex coroneneCPSMBR-1 was characterized by X-ray diffraction study. Moreover, the potential application of PSMER-1 as carrier in aqueous medium for the transportation of water insoluble fluorophore (perylene) for live cell imaging is explored.

MnFe2O4-Fe3O4 core-shell nanoparticles as a potential contrast agent for magnetic resonance imaging

In recent years, magnetic core-shell nanoparticles have received widespread attention due to their unique properties that can be used for various applications. We introduce here a magnetic core-shell nanoparticle system for potential application as a contrast agent in magnetic resonance imaging (MRI). MnFe2O4-Fe3O4 core-shell nanoparticles were synthesized by the wet-chemical synthesis method. Detailed structural and compositional charaterization confirmed the formation of a core-shell microstructure for the nanoparticles. Magnetic charaterization revealed the superparamagnetic nature of the as-synthesized core-shell nanoparticles. Average size and saturation magnetization values obtained for the as-synthesized core-shell nanoparticle were 12.5 nm and 69.34 emu g(-1) respectively. The transverse relaxivity value of the water protons obtained in the presence of the core-shell nanoparticles was 184.1 mM(-1) s(-1). To investigate the effect of the core-shell geometry towards enhancing the relaxivity value, transverse relaxivity values were also obtained in the presence of separately synthesized single phase Fe3O4 and MnFe2O4 nanoparticles. Average size and saturation magnetization values for the as-synthesized Fe3O4 nanoparticles were 12 nm and 65.8 emu g(-1) respectively. Average size and saturation magnetization values for the MnFe2O4 nanoparticles were 9 nm and 61.5 emu g(-1) respectively. The transverse relaxivity value obtained in the presence of single phase Fe3O4 and MnFe2O4 nanoparticles was 96.6 and 83.2 mM(-1) s(-1) respectively. All the nanoparticles (core-shell and single phase) were coated with chitosan by a surfactant exchange reaction before determining the relaxivity values. For similar nanoparticle sizes and saturation magnetization values, the highest value of the transverse relaxivity in the case of core-shell nanoparticles clearly illustrated that the difference in the magnetic nature of the core and shell phases in the core-shell nanoparticles creates greater magnetic inhomogeneity in the surrounding medium yielding a high value for proton relaxivity. The MnFe2O4-Fe3O4 core-shell nanoparticles exhibited extremely low toxicity towards the MCF-7 cell line. Taken together, this opens up new avenues for the use of core-shell nanoparticles in MRI.

Limited-view light sheet fluorescence microscopy for three dimensional volume imaging

We propose and demonstrate a limited-view light sheet microscopy (LV-LSM) for three dimensional (3D) volume imaging. Realizing that longer and frequent image acquisition results in significant photo-bleaching, we have taken limited angular views (18 views) of the macroscopic specimen and integrated with maximum likelihood (ML) technique for reconstructing high quality 3D volume images. Existing variants of light-sheet microscopy require both rotation and translation with a total of approximately 10-fold more views to render a 3D volume image. Comparatively, LV-LSM technique reduces data acquisition time and consequently minimizes light-exposure by many-folds. Since ML is a post-processing technique and highly parallelizable, this does not cost precious imaging time. Results show noise-free and high contrast volume images when compared to the state-of-the-art selective plane illumination microscopy. (C) 2015 AIP Publishing LLC.

Ultrafine graphene oxide-CoFe2O4 nanoparticle composite as T-1 and T-2 contrast agent for magnetic resonance imaging

Graphene oxide-CoFe2O4 nanoparticle composites were synthesized using a two step synthesis method in which graphene oxide was initially synthesized followed by precipitation of CoFe2O4 nanoparticles in a reaction mixture containing graphene oxide. Samples were extracted from the reaction mixture at different times at 80 degrees C. All the extracted samples contained CoFe2O4 nanoparticles formed over the graphene oxide. It was observed that the increase in the reflux time significantly increased the saturation magnetization value for the superparamagnetic nanoparticles in the composite. It was also noticed that the size of the nanoparticles increased with increase in the reflux time. Transverse relaxivity of the water protons increased monotonically with increase in the reflux time. Whereas, the longitudinal relaxivity value initially increased and then decreased with the reflux time. Graphene oxide-CoFe2O4 nanoparticle composites also exhibit biocompatibility towards the MCF-7 cell line.

Feasibility of Protein a for the Oriented Immobilization of Immunoglobulin on Silicon Surface for a Biosensor with Imaging Ellipsometry

The feasibility of using protein A to immobilize antibody on silicon surface for a biosensor with imaging ellipsometry was presented in this study. The amount of human IgG bound with anti-IgG immobilized by the protein A on silicon surface was much more than that bound with anti-IgG immobilized by physical adsorption. The result indicated that the protein A could be used to immobilize antibody molecules in a highly oriented manner and maintain antibody molecular functional configuration on the silicon surface. High reproducibility of the amount of antibody immobilization and homogenous antibody adsorption layer on surfaces could be obtained by this immobilization method. Imaging ellipsometry has been proven to be a fast and reliable detection method and sensitive enough to detect small changes in a molecular monolayer level. The combination of imaging ellipsometry and surface modification with protein A has the potential to be further developed into an efficient immunoassay protein chip.

Visualization of molecule interaction between antigen and antibody - One of ellipsometric imaging applications

It is to investigate molecule interactions between antigen and antibody with ellipsometric imaging technique and demonstrate some features and possibilities offered by applications of the technique. Molecule interaction is an important interest for molecule biologist and immunologist. They have used some established methods such as immufluorcence, radioimmunoassay and surface plasma resonance, etc, to study the molecule interaction. At the same time, experimentalists hope to use some updated technique with more direct visual results. Ellipsometric imaging is non-destructive and exhibits a high sensitivity to phase transitions with thin layers. It is capable of imaging local variations in the optical properties such as thickness due to the presence of different surface concentration of molecule or different deposited molecules. If a molecular mono-layer (such as antigen) with bio-activity were deposited on a surface to form a sensing surface and then incubated in a solution with other molecules (such as antibody), a variation of the layer thickness when the molecules on the sensing surface reacted with the others in the solution could be observed with ellipsometric imaging. Every point on the surface was measured at the same time with a high sensitivity to distinguish the variation between mono-layer and molecular complexes. Ellipsometric imaging is based on conventional ellipsometry with charge coupled device (CCD) as detector and images are caught with computer with image processing technique. It has advantages of high sensitivity to thickness variation (resolution in the order of angstrom), big field of view (in square centimeter), high sampling speed (a picture taken within one second), and high lateral resolution (in the order of micrometer). Here it has just shown one application in study of antigen-antibody interaction, and it is possible to observe molecule interaction process with an in-situ technique.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Lurking in ULIRGs: Molecular Gas in local Merging Galaxies

Mergers and interacting galaxies are pivotal to the evolution of galaxies in the universe. They are the sites of prodigious star formation and key to understanding the starburst processes: the physical and chemical properties and the dynamics of the molecular gas. ULIRGs or Ultraluminous Infrared Galaxies are a result of many of these mergers. They host extreme starbursts, AGNs, and mergers. They are the perfect laboratory to probe the connection between starbursts, black hole accretion and mergers and to further our understanding of star formation and merging.

NGC 6240 and Arp 220 can be considered the founding members of this very active class of objects. They are in different stages of merging and hence are excellent case studies to further our understanding about the merging process. We have imaged the dense star-forming regions of these galaxies at sub-arcsec resolution with CARMA C and B Configurations (2" and 0.5 - 0.8"). Multi-band imaging allows excitation analysis of HCN, HCO⁺, HNC, and CS along with CO transitions to constrain the properties of the gas. Our dataset is unique in that we have observed these lines at similar resolutions and high sensitivity which can be used to derive line ratios of faint high excitation lines.

Arp 220 has not had confirmed X-ray AGN detections for either nuclei. However, our observations indicate HCN/HNC ratios consistent with the chemistry of X-ray Dominated Regions (XDRs) -- a likely symptom of AGN. We calculated the molecular Hydrogen densities using each of the molecular species and conclude that assuming abundances of HNC and HCO⁺ similar to those in galactic sources are incorrect in the case of ULIRGs. The physical conditions in the dense molecular gas in ULIRGs alter these abundances. The derived H2 volume densities are ~ 5 x 10⁴ cm^-3 in both Arp 220 nuclei and ~ 10⁴ cm^-3 in NGC 6240.