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We present the generate-and-select hierarchy for tertiary protein structure prediction. The foundation of this hierarchy is the Restrained Generic Protein (RGP) Direct Monte Carlo method. The RGP method is a highly efficient off-lattice residue buildup procedure that can quickly generate the complete set of topologies that satisfy a very small number of(More)
We report on the applicability of combining surface-enhanced Raman scattering (SERS) with coherent anti-Stokes Raman scattering for high-sensitivity detection of biological molecules. We found that this combination of techniques provides more than 3 orders of signal enhancement compared with SERS and permits monitoring of biological molecules such as(More)
To obtain a coding system for multiplex detection, we have developed a method to synthesize a new type of nanomaterial called composite organic-inorganic nanoparticles (COINs). The method allows the incorporation of a broad range of organic compounds into COINs to produce surface enhanced Raman scattering (SERS)-like spectra that are richer in variety than(More)
Composite organic-inorganic nanoparticles (COINs) are novel optical labels for detection of biomolecules. We have previously developed methods to encapsulate COINs and to functionalize them with antibodies. Here we report the first steps toward application of COINs to the detection of proteins in human tissues. Two analytes, PSA and CK18, are detected(More)
BACKGROUND Detection of single cell epitopes has been a mainstay of immunophenotyping for over three decades, primarily using fluorescence techniques for quantitation. Fluorescence has broad overlapping spectra, limiting multiplexing abilities. METHODOLOGY/PRINCIPAL FINDINGS To expand upon current detection systems, we developed a novel method for(More)
Raman nanoparticle probes are an emerging new class of optical labels for interrogation of physiological and pathological processes in bioassays, cells, and tissues. Although their unique emission signatures are ideal for multiplexing, the full potential of these probes has not been realized because conventional analysis methods are inadequate. We report a(More)
Achieving high signal amplification in surface-enhanced Raman scattering (SERS) is important for reaching single molecule level sensitivity and has been the focus of intense research efforts. We introduce a novel chemical enhancer, lithium chloride, that provides an additional order of magnitude increase in SERS relative to previously reported enhancement(More)
Surface-enhanced Raman scattering (SERS) nanoparticles are emerging as a new approach for optical detection of biomolecules. In a model assay in formalin-fixed paraffin-embedded (FFPE) prostate tissue sections, we detect prostate-specific antigen (PSA) using antibody (Ab) conjugated to composite organic-inorganic nanoparticles (COINs), and we use identical(More)
Posttranslational modification (PTM) of proteins is likely to be the most common mechanism of altering the expression of genetic information. It is essential to characterize PTMs to establish a complete understanding of the activities of proteins. Here, we present a sensitive detection method using surface-enhanced Raman spectroscopy (SERS) that can detect(More)
The project reported in this chapter is based on the combination, interrelationships and synergies of four pedagogical approaches to improve student engagement with learning. These approaches are mobile learning; constructivist learning, with contemporary emphasis in the form of connectivism; situated learning of skills in purpose-built workrooms and(More)