No / The remote robotic exploration of extraterrestrial scenarios for evidence of biological colonization in 'search for life' missions using Raman spectroscopy is critically dependent on two major factors: firstly, the Raman spectral recognition of characteristic biochemical spectral signatures in the presence of mineral matrix features; and secondly, the positive unambiguous identification of molecular biomaterials which are indicative of extinct or extant life. Both of these factors are considered here: the most important criterion is the clear definition of which biochemicals truly represent biomarkers, whose presence in the planetary geological record from an analytical astrobiological standpoint will unambiguously be indicative of life as recognized from its remote instrumental interrogation. Also discussed in this paper are chemical compounds which are associated with living systems, including biominerals, which may not in themselves be definitive signatures of life processes and origins but whose presence provides an indicator of potential life-bearing matrices.

During the past decade, many successful deterministic models of macromolecular regulatory networks have been built. Deterministic simulations of these models can show only average dynamics of the systems. However, stochastic simulations of macromolecular regulatory models can account for behaviors that are introduced by the noisy nature of the systems but not revealed by deterministic simulations. Thus, converting an existing model of value from the most common deterministic formulation to one suitable for stochastic simulation enables further investigation of the regulatory network. Although many different stochastic models can be developed and evolved from deterministic models, a direct conversion is the first step in practice. This conversion process is tedious and error-prone, especially for complex models. Thus, we seek to automate as much of the conversion process as possible. However, deterministic models often omit key information necessary for a stochastic formulation. Specifically, values in the model have to be scaled before a complete conversion, and the scaling factors are typically not given in the deterministic model. Several functionalities helping model scaling and converting are introduced and implemented in the JigCell modeling environment. Our tool makes it easier for the modeler to include complete details as well as to convert the model. Stochastic simulations are known for being computationally intensive, and thus require high performance computing facilities to be practical. With parallel computation on Virginia Tech's System X supercomputer, we are able to obtain the first stochastic simulation results for realistic cell cycle models. Stochastic simulation results for several mutants, which are thought to be biologically significant, are presented. Successful deployment of the enhanced modeling environment demonstrates the power of our techniques. / Master of Science

Este trabalho apresenta o estudo e caracterização de dois complexos moleculares, hRXRálfadeltaAB e hemocianina de Acanthoscurria gomesiana, através de técnicas estruturais e biofísicas. O uso da técnica de crio-microscopia eletrônica para o estudo da hemocianina de Acanthoscurria gomesiana, resultou em um modelo estrutural com resolução de 14 angstron- pelo métodode Fourier Shell Correlation com critério de 1/2 bit. Neste limite de resolução, já é possível observar detalhes estruturais que o mostram como sendo comptível com outros modelos de hemocianinas. Com relação ao estudo de hRXRalfadeltaAB, mostrou-se, através das técnicas de cromatografia analítica de exclusão por tamanho, eletroforese de gel de poliacrilamida e SAXS, que a proteína pode se apresentar no estado dimérico em solução, mesmo na ausência do seu ligante, 9-cis-RA. Também foi estudado a associação de hRXRalfadeltaAB a elementos responsivos: DR1, DR4, F2 e PAL. Suas constantes de dissociação foram calculadas através da técnica de espectroscopia por anisotropia de fluorescência. Os resultados obtidos mostram maior afinidade por DR1 e DR2 e indicam uma origem entrópica para o processo de associação / This work describes characterization of two biomolecular complexes: hRXR deltaAB and a hemocyanin from Acanthoscurria gomesiana using structural and biophysical techniques. Application of cryo-electron microscopy to studies of a hemocyanin from Acanthoscurria gomesiana resulted in its structural model to 14Å resolution, which was calculated by Fourier Shell Correlation with cut-off of 1/2 bit. At this resolution limit one can observe structural details of the complex which are compatible with other hemocyanin models. With respect to hRXR deltaAB, we showed using analytic size exclusion chromatography, SDS PAGE and SAXS, that the protein is dimeric in solution even at the absence of its ligand, 9-cis-RA. hRXR deltaAB binding to the responsive elements of DNA, DR1, DR4, F2 and PAL was investigated and the binding constants to these responsive elements have been determined using fluorescence anisotropy technique. Our results show higher affinity of the receptor to DR1 and DR4 and indicate entropic mechanism of DNA binding

Lubricants play an integral role in the operation of several technologies and in biology also, ranging from moving parts in machinery to the biolubrication of artificial joints. We have found that a colloidal dispersion consisting of easily synthesized highly spherical and uniform graphitic carbon particles results in a very efficient water based "green" and environmentally sustainable lubricant with very low friction coefficients and excellent surface wear protection. These particles use a rolling mechanism similar to nano --or microscale ball bearing under confinement. The effect of particle size on lubrication will be introduced and discussed. Additionally, carbon from sugars and carbohydrates, considered as "green precursors" because of their abundance in nature, have been favored for their low environmental impact and cost when compared to traditional oil based lubricants. The second part of my dissertation presents the fabrication and design of a novel bidirectional membrane device to assist child delivery in resource-limited settings. Approximately one third of pregnancies are delivered by one out of three possible operative methods: vacuum extraction, forceps operation, or caesarean section. Using these traditional devices or alternative methods, the risk of injuring to the mother and the fetus is elevated tremendously in the wake of poor training. Here, I present a polymer-based membrane, which will provide ultra-low friction thus facilitating child delivery but also have the ability to provide high friction when needed for child extraction. Specifically, the friction properties between polydimethylsiloxane (PDMS) and a borosilicate surface were studied using different lubricating media. The dynamics of the anisotropic surface morphology will be discussed and applied to this novel membranous device.

The interactions of biomolecules and cells at solid-liquid interfaces play a pivotal role in a range of biomedical applications and have hence been studied in detail. An improved understanding of these interactions results in the ability to manipulate biomolecules and concurrently cells spatially and temporally at surfaces with high precision. Spatial control can be achieved using patterned surface chemistries whilst temporal control is achieved by switchable surfaces. The combination of these two surface properties offers unprecedented control over the behaviour of biomolecules and cells at the solid-liquid interface. This is particularly relevant for cell microarray applications, where a range of biological processes must be duly controlled in order to maximise the efficiency and throughput of these devices. Of particular interest are transfected cell microarrays (TCMs), which significantly widen the scope of microarray genomic analysis by enabling the high-throughput analysis of gene function within living cells Initially, this thesis focuses on the spatially controlled, electro-stimulated adsorption and desorption of DNA. Surface modification of a silicon chip with an allylamine plasma polymer (ALAPP) layer resulted in a surface that supported DNA adsorption and sustained cell attachment. Subsequent high density grafting of poly(ethylene glycol) (PEG) formed a layer resistant to biomolecule adsorption and cell attachment. PEG grafted surfaces also showed significantly reduced attachment of DNA with an equilibrium binding constant of 23 ml/mg as compared with 1600 ml/mg for ALAPP modified surfaces. Moreover, both hydrophobic and electrostatic interactions were shown to contribute to the binding of DNA to ALAPP. Spatial control over the surface chemistry was achieved using excimer laser ablation of the PEG coating which enabled the production of patterns of re-exposed ALAPP with high resolution. Preferential electro-stimulated adsorption of DNA to the ALAPP regions and subsequent desorption by the application of a negative bias was observed. Furthermore, this approach was investigated for TCM applications. Cell culture experiments demonstrated efficient and controlled transfection of cells. Electro-stimulated desorption of DNA was shown to yield enhanced solid phase transfection efficiencies with values of up to 30%. The ability to spatially control DNA adsorption combined with the ability to control the binding and release of DNA by application of a controlled voltage enables an advanced level of control over DNA bioactivity on solid substrates and lends itself to biochip applications. As an alternative approach to surface patterning, the fabrication and characterisation of chemical patterns using a technique that can be readily integrated with methods currently used for the formation of microarrays is also presented. Here, phenylazide modified polymers were printed onto low fouling ALAPP-PEG modified surfaces. UV irradiation of these polymer arrays resulted in the crosslinking of the polymer spots and their covalent attachment to the surface. Cell attachment was shown to follow the patterned surface chemistry. Due to the use of a microarray contact printer it was easily possible to deposit DNA on top of the polymer microarray spots. A transfected cell microarray was generated in this way, demonstrating the ability to limit cell attachment to specific regions and the suitability of this approach for high density cell assays. In order to allow for the high-throughput characterisation of the resultant polymer microarrays, surface plasmon resonance imaging was utilised to study the adsorption and desorption of bovine serum albumin, collagen and fibronectin. This analysis enabled insights into the underlying mechanisms of cell attachment to the polymers studied. For the system analysed here, electrostatic interactions were shown to dominate cellular behaviour.

Nanotechnology is a term used to describe nanometer scaled systems. This thesis presents various nanomaterials and systems for the investigation of biologically relevant analytes in general, and in particular for their detection, decontamination, or destruction. The validation of short peptide fragments as models for protein aggregation is initially discussed through applying spectroscopic and microscopic techniques to Langmuir monolayer surface chemistry. Following this validation, the use of nanogold as a photoablative material for the destruction of aggregated protein is investigated. Subsequently, the versatility of nanotechnology is shown by investigating a different form of nanogold; namely, gold quantum dots and the interesting phenomenon that arise when dealing with materials on a nanoscale. Experiments involving a complex between these gold quantum dots and an antibody are performed for the detection of an immunoglobulin in solution. The power of this analytical technique is highlighted by the capability of detecting the analyte at nanomolar concentrations. Finally, a limitation-the multiple synthetic steps necessary for imparting biological activity-- of quantum dots is addressed: a single step reaction is studied that allows for direct stabilization and conjugation of quantum dots with proteins and enzymes. As a representative application of the above mentioned procedure, the detection and decontamination of an organophosphorus compound is explored. In general, methods for overcoming limitations of nanoparticles and nanocrystals are discussed.

It is often a challenge to atomically determine the structure of large macromolecular assemblies, even if successfully crystallized, due to their weak diffraction of X-rays. Refinement algorithms that work with low-resolution diffraction data are necessary for researchers to obtain a picture of the structure from limited experimental information. Relationship between the structure and function of proteins implies that a refinement approach delivering accurate structures could considerably facilitate further research on their function and other related applications such as drug design. Here a refinement algorithm called the Deformable Complex Network is presented. Computation results revealed that, significant improvement was observed over the conventional refinement and DEN refinement, across a wide range of test systems from the Protein Data Bank, indicated by multiple criteria, including the free R value, the Ramachandran Statistics, the GDT (<1Å) score, TM-score as well as associated electron density map.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 140-158).

Electrostatics interaction plays a very important role in almost all biomolecular systems. The Poisson-Boltzmann equation is widely used to treat this electrostatic effect in an ionic solution. In this work, a simple mixed discrete-continuum model is considered and boundary element method is used to solve for the solution. / Singapore-MIT Alliance (SMA)

xiv, 171 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. / Biological molecular motors, which use chemical energy from ATP hydrolysis to generate mechanical force, are involved in a variety of important mechanical processes in eukaryotic cells, such as intracellular transport, cell division and muscle contraction. These motors, which produce motion on the nanoscale, operate in the presence of substantial thermal noise. In this dissertation, two approaches are used to model the physics of nanoscale motors: (1) A theoretically established type of Brownian motor called the "flashing ratchet" is studied. This motor transports diffusive particles in a preferred direction. (2) A coarse-grained mechanical model for the biological molecular motor myosin-V is developed, and used to study the role of Brownian diffusion, and the interaction between chemical and mechanical degrees of freedom, in the transport mechanism of this motor. In chapter III, Brownian dynamics simulations and analytical calculations demonstrate that the average velocity of rigid chains of particles in a flashing ratchet reverses direction in response to changing the size of the chain or the temperature of the heat bath. Recent studies have introduced policies for "closed-loop" control of a flashing ratchet, in which the system is controlled based on information about its internal state (such as the positional distribution of particles). In chapter IV, the effect of time delay on the implementation of closed-loop control of a flashing ratchet is investigated. For a large ensemble, a well-chosen delay time improves the ratchet performance (increasing the velocity) by synchronizing into a quasi-stable mode that takes advantage of the semi-deterministic nature of the time development of average quantities for a large ensemble. I n chapter V, a coarse-grained mechanical model is presented for the transport mechanism of myosin-V, which walks along intracellular filaments. The model is well constrained by experimental data on the mechanical properties of myosin V and on the kinetic cycle. An experimentally motivated model for the intramolecular coordination of the motor's steps is proposed and tested. / Adviser: Heiner Linke