Dusty Plasma Correlation Function Experiment

Dust particles immersed within a plasma environment, such as those in protostellar clouds, planetary rings or cometary environments, will acquire an electric charge. If the ratio of the inter-particle potential energy to the average kinetic energy is high enough the particles will form either a "liquid" structure with short-range ordering or a crystalline structure with long range ordering. Many experiments have been conducted over the past several years on such colloidal plasmas to discover the nature of the crystals formed, but more work is needed to fully understand these complex colloidal systems. Most previous experiments have employed monodisperse spheres to form Coulomb crystals. However, in nature (as well as in most plasma processing environments) the distribution of particle sizes is more randomized and disperse. This paper reports experiments which were carried out in a GEC rf reference cell modified for use as a dusty plasma system, using varying sizes of particles to determine the manner in which the correlation function depends upon the overall dust grain size distribution. (The correlation function determines the overall crystalline structure of the lattice.) Two dimensional plasma crystals were formed of assorted glass spheres with specific size distributions in an argon plasma. Using various optical techniques, the pair correlation function was determined and compared to those calculated numerically.Comment: 6 pages, Presented at COSPAR '0

Temperature mapping and thermal lensing in large-mode, high-power laser diodes

The authors use high-resolution charge-coupled device based thermoreflectance to derive two dimensional facet temperature maps of a λ = 1.55 μmλ=1.55μm InGaAsP/InPInGaAsP∕InP watt-class laser that has a large (>5×5 μm2)(>5×5μm2) fundamental optical mode. Recognizing that temperature rise in the laser will lead to refractive index increase, they use the measured temperature profiles as an input to a finite-element mode solver, predicting bias-dependent spatial mode behavior that agrees well with experimental observations. These results demonstrate the general usefulness of high-resolution thermal imaging for studying spatial mode dynamics in photonic devices.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87806/2/201110_1.pd

Coarse-grained model of entropic allostery

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators

Protein families evolve functional variation by accumulating point mutations at functionally important amino acid positions. Homologs in the LacI/GalR family of transcription regulators have evolved to bind diverse DNA sequences and allosteric regulatory molecules. In addition to playing key roles in bacterial metabolism, these proteins have been widely used as a model family for benchmarking structural and functional prediction algorithms. We have collected manually curated sequence alignments for >ﾠ3000 sequences, in vivo phenotypic and biochemical data for >ﾠ5750 LacI/GalR mutational variants, and noncovalent residue contact networks for 65 LacI/GalR homolog structures. Using this rich data resource, we compared the noncovalent residue contact networks of the LacI/GalR subfamilies to design and experimentally validate an allosteric mutant of a synthetic LacI/GalR repressor for use in biotechnology. The AlloRep database (freely available at www.AlloRep.org) is a key resource for future evolutionary studies of LacI/GalR homologs and for benchmarking computational predictions of functional change

Hemoglobin A1c improvements and better diabetes-specific quality of life among participants completing diabetes self-management programs: A nested cohort study

BACKGROUND: Numerous primary care innovations emphasize patient-centered processes of care. Within the context of these innovations, greater understanding is needed of the relationship between improvements in clinical endpoints and patient-centered outcomes. To address this gap, we evaluated the association between glycosylated hemoglobin (HbA(1c)) and diabetes-specific quality of life among patients completing diabetes self-management programs. METHODS: We conducted a retrospective cohort study nested within a randomized comparative effectiveness trial of diabetes self-management interventions in 75 diabetic patients. Multiple linear regression models were developed to examine the relationship between change in HbA(1c) from baseline to one-year follow-up and Diabetes-39 (a diabetes-specific quality of life measure) at one year. RESULTS: HbA(1c) levels improved for the overall cohort from baseline to one-year follow-up (t (74) = 3.09, p = .0029). One-year follow up HbA(1c) was correlated with worse overall quality of life (r = 0.33, p = 0.004). Improvements in HbA(1c) from baseline to one-year follow-up were associated with greater D-39 diabetes control (β = 0.23, p = .04) and D-39 sexual functioning (β = 0.25, p = .03) quality of life subscales. CONCLUSIONS: Improvements in HbA(1c) among participants completing a diabetes self-management program were associated with better diabetes-specific quality of life. Innovations in primary care that engage patients in self-management and improve clinical biomarkers, such as HbA(1c), may also be associated with better quality of life, a key outcome from the patient perspective

Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, "AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators" (Sousa et al., 2016) [1]

Submicron thermal imaging of high power slab coupled optical waveguide laser (SCOWL

ABSTRACT Nonradiative power dissipation within and near the active region of a high power single mode slab coupled optical waveguide laser is directly measured by CCD-based thermoreflectance, including its variation with device bias. By examining the high spatial resolution temperature profile at the optical output facets, we quantify heat spreading from the source in the active region both downward to the substrate and upward to the metal top contact

Engineering substrate promiscuity in halophilic alcohol dehydrogenase (HvADH2) by in silico design

An alcohol dehydrogenase from the halophilic archaeon Haloferax volcanii (HvADH2) has been engineered by rational design to broaden its substrate scope towards the conversion of a range of aromatic substrates, including flurbiprofenol, that is an intermediate of the non-steroidal anti-inflammatory drug, flurbiprofen. Wild-type HvADH2 showed minimal activity with flurbiprofenol (11.1 mU/mg). A homology model of HvADH2 was built and docking experiments with this substrate revealed that the biphenyl rings of flurbiprofenol formed strong interactions with residues F85 and F108, preventing its optimal binding in the active site. Mutations at position 85 however did not increase activity. Site directed mutagenesis at position F108 allowed the identification of three variants showing a significant (up to 2.3-fold) enhancement of activity towards flurbiprofenol, when compared to wild-type HvADH2. Interestingly, F108G variant did not show the classic inhibition in the presence of (R)-enantiomer when tested with rac-1-phenylethanol, underling its potential in racemic resolution of secondary alcohols