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Search Results: 1 - 10 of 152105 matches for " Kevin F. Morris "
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Investigation of Chiral Molecular Micelles by NMR Spectroscopy and Molecular Dynamics Simulation  [PDF]
Kevin F. Morris, Eugene J. Billiot, Fereshteh H. Billiot, Kenny B. Lipkowitz, William M. Southerland, Yayin Fang
Open Journal of Physical Chemistry (OJPC) , 2012, DOI: 10.4236/ojpc.2012.24032
Abstract: NMR spectroscopy and Molecular Dynamics (MD) simulation analyses of the chiral molecular micelles poly-(Sodium Undecyl-(L,L)-Leucine-Valine) (poly-SULV) and poly-(Sodium Undecyl-(L,L)-Valine-Leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide headgroups. To provide experimental support for the structures from MD simulations, NOESY spectra were used to identify protons in close spatial proximity. Results from the NOESY analyses were then compared to radial distribution functions from MD simulations. In addition, the hydrodynamic radii of both molecular micelles were calculated from NMR-derived diffusion coefficients. Corresponding radii from the MD simulations were found to be in agreement with these experimental results. NMR diffusion experiments were also used to measure association constants for polar and non-polar binaphthyl analytes binding to both molecular micelles. Poly (SUVL) was found to bind the non-polar analyte enantiomers more strongly, while the more polar analyte enantiomers interacted more strongly with poly(SULV). MD simulations in turn showed that poly(SULV) had a more open structure that gave greater access for water molecules to the dipeptide headgroup region.
A Molecular Dynamics Simulation Study of Two Dipeptide Based Molecular Micelles: Effect of Amino Acid Order  [PDF]
Kevin F. Morris, Eugene J. Billiot, Fereshteh H. Billiot, Kenny B. Lipkowitz, William M. Southerland, Yayin Fang
Open Journal of Physical Chemistry (OJPC) , 2013, DOI: 10.4236/ojpc.2013.31004

Molecular dynamics (MD) simulations were used to compare the structures of the chiral molecular micelles (MM) poly-(sodium undecyl-(L,L)-leucine-valine) (poly(SULV)) and poly-(sodium undecyl-(L,L)-valine-leucine) (poly (SUVL)). Both MM contained polymerized surfactant monomers terminated by chiral dipeptide headgroups. The study was undertaken to investigate why poly(SULV) is generally a better chiral selector compared to poly(SUVL) in electrokinetic chromatography separations. When comparing poly(SULV) to poly(SUVL), poly(SULV) had the more conformational flexible dipeptide headgroup and hydrogen bond analyses revealed that the poly(SULV) headgroup conformation allowed a larger number of intramolecular hydrogen bonds to form between monomer chains. In addition, a larger number of water molecules surrounded the chiral centers of the poly(SULV) molecular micelle. Poly(SULV) was also found to have a larger solvent accessible surface area (SASA) than poly(SUVL) and fluctuations in the poly(SULV) SASA during the MD simulation allowed dynamic monomer chain motions expected to be important in chiral recognition to be identified. Finally, approximately 50% of the Na+ counterions were found in the first three solvation shells surrounding both MM, with the remainder located in the bulk. Overall the MD simulations point to both greater headgroup flexibility and solvent and analyte access to the chiral centers of the dipeptide headgroup as factors contributing to the enhanced chiral selectivity observed with poly(SULV).

Horospherical limit points of S-arithmetic groups
Dave Witte Morris,Kevin Wortman
Mathematics , 2013,
Abstract: Suppose Gamma is an S-arithmetic subgroup of a connected, semisimple algebraic group G over a global field Q (of any characteristic). It is well known that Gamma acts by isometries on a certain CAT(0) metric space X_S that is a Cartesian product of Euclidean buildings and Riemannian symmetric spaces. For a point p on the visual boundary of X_S, we show there exists a horoball based at p that is disjoint from some Gamma-orbit in X_S if and only if p lies on the boundary of a certain type of flat in X_S that we call "Q-good." This generalizes a theorem of G.Avramidi and D.W.Morris that characterizes the horospherical limit points for the action of an arithmetic group on its associated symmetric space.
Chromatin, Non-Coding RNAs, and the Expression of HIV
Jessica N. Groen,Kevin V. Morris
Viruses , 2013, DOI: 10.3390/v5071633
Abstract: HIV is a chronic viral infection affecting an estimated 34 million people worldwide. Current therapies employ the use of a cocktail of antiretroviral medications to reduce the spread and effects of HIV, however complete eradication from an individual currently remains unattainable. Viral latency and regulation of gene expression is a key consideration when developing effective treatments. While our understanding of these processes remains incomplete new developments suggest that non-coding RNA (ncRNA) mediated regulation may provide an avenue to controlling both viral expression and latency. Here we discuss the importance of known regulatory mechanisms and suggest directions for further study, in particular the use ncRNAs in controlling HIV expression.
Microstructure and rheology of finite inertia neutrally buoyant suspensions
Hamed Haddadi,Jeffrey F. Morris
Physics , 2014, DOI: 10.1017/jfm.2014.238
Abstract: The microstructure and rheological properties of suspensions of neutrally buoyant hard spherical particles in Newtonian fluid under conditions of finite inertia are studied using the lattice-Boltzmann method (LBM), which is based on a discrete Boltzmann model for the fluid and Newtonian dynamics for the particles. The suspensions are subjected to simple-shear flow and the properties are studied as a function of Reynolds number and volume fraction, $\phi$. The inertia is characterized by the particle-scale shear flow Reynolds number $Re = \frac{\rho \dot{\gamma}a^{2}}{\mu}$, where $a$ is the particle radius, $\dot{\gamma}$ is the shear rate and $\rho$ and $\mu$ are the density and viscosity of the fluid, respectively. The influences of inertia and of the volume fraction are studied for $0.005\leqslant Re \leqslant 5$ and $0.1\leqslant \phi \leqslant 0.35$. The flow-induced microstructure is studied using the pair distribution function $g(\boldsymbol{r})$. Different stress mechanisms, including those due to surface tractions (stresslet), acceleration, and the Reynolds stress due to velocity fluctuations are computed and their influence on the first and second normal stress differences, the particle pressure and the viscosity of the suspensions are detailed. The probability density functions of particle force and torque are also presented.
Starburst Clusters in Galactic Nuclei
Donald F. Figer,Mark Morris
Physics , 2000,
Abstract: Galactic nuclei often harbor a disproportionately large amount of star formation activity with respect to their surrounding disks. Not coincidentally, the density of molecular material in galactic nuclei is often also much greater than that in disks (Table 1 in Kennicutt 1998). The interplay between rich populations of young stars and dense molecular environments is evident in our own Galactic center, which hosts over 10% of Galactic star formation activity within only $<$0.1% of the volume of the Galactic disk. Data obtained with the VLA and HST reveal a variety of star forming sites in the Galactic Center, including a substantial population of stars that are formed in very dense and massive clusters, while other stars are formed in somewhat sparsely populated associations of massive stars. Indeed, three of the stellar clusters are the most massive and densest in the Galaxy. In this paper, we discuss the Galactic center environment and its compact young star clusters, and compare them to their counterparts in star forming galactic nuclei, concluding that dense molecular environments and large velocity dispersions combine to alter star formation activity in both cases, particularly as regards massive young clusters.
Active microrheology of colloidal suspensions: simulation and microstructural theory
Ehssan Nazockdast,Jeffrey F. Morris
Physics , 2015,
Abstract: Accelerated Stokesian Dynamics (ASD) simulation and a microstructural theory are applied to study structure and the viscosity of hard-sphere Brownian suspensions in active microrheology (MR).We consider moderate to dense suspensions, from near to far from equilibrium conditions.The theory explicitly considers many-body hydrodynamic interactions (HIs) in active MR, and is compared with ASD.Two conditions of moving the probe with constant force (CF) and constant velocity (CV) are considered.The structure is quantified using the probability distribution of colloidal particles around the probe, g(r), which is computed as a solution to the pair Smoluchowski equation (SE) for 0.2<\phi<0.50, and a range of Peclet numbers (Pe), describing the ratio of external force on the probe to thermal forces.Results of ASD and theory demonstrate that a wake zone depleted of bath particles behind the moving probe forms at large Pe, while a boundary-layer accumulation develops upstream.The wake length saturates at Pe>>1 for CF while it continuously grows in CV.This contrast in behavior is related to the dispersion in the motion of the probe under CF conditions, while CV motion has no dispersion.This effect is incorporated in the theory as a force-induced hydrodynamic diffusion flux in the pair SE. We also demonstrate that, despite this difference of structure in CF and CV, g(r) near the probe is set by Pe, for both CF and CV resulting in similar values for their viscosity.Using the theory, the structural anisotropy and Brownian viscosity near equilibrium are shown to be quantitatively similar in both CF and CV motions, which is in contrast with the dilute theory which predict distortions and Brownian viscosities twice as large in CV, relative to CF.This difference arises due to the many-body interactions associated with the equilibrium structure in the moderate to dense regime.
Reliability and validity of a single item measure of quality of life scale for adult patients with cystic fibrosis
Abebaw M Yohannes, Mary Dodd, Julie Morris, Kevin Webb
Health and Quality of Life Outcomes , 2011, DOI: 10.1186/1477-7525-9-105
Abstract: 121 (men = 66, women = 55) adult cystic fibrosis patients self-completed the CF-QOL, the Hospital Anxiety Depression Scale, and the single item global quality of life scale at the out patient clinic. 33 (17 women) completed the repeat questionnaires at home within two weeks. Socio-demographic characteristic and lung function data were extracted from the recent medical notes.Mean (SD) age was 29.6 (8.9) years and mean (SD) forced expiratory volume in 1 second was 2.20 (0.94) litres. The test-retest reproducibility using the intra-class correlation coefficient (ICC) for the CF-QOL was 0.83, 95% confidence interval 0.68 to 0.91. The single item global quality of life ICC score was 0.78, 95% confidence interval 0.59 to 0.88. Concurrent validity of the single-item global quality of life was examined in relation to all items of the CF-QOL, frequent episodes of readmission, anxiety and depression (all, p < 0.01) were moderately correlated.The study provides preliminary evidence that the single-item quality of life scale is acceptable, valid and repeatable for adult patients with cystic fibrosis. It is a promising tool that can be easily incorporated into a routine clinical practice to assess patients' quality of life.There are disease-specific validated health related quality of life (HRQOL) scales [1,2] that measure dimensions of health, not otherwise assessed by conventional lung function tests in order to determine the severity of the disease for adult patients with cystic fibrosis (CF). HRQOL scales are regarded as relevant endpoints to measure the efficacy of clinical drug trials and the benefits of rehabilitation for adult CF patients [3,4]. They also provide additional information that is specific to an individual and not captured, for example, by lung function tests or other endpoints.HRQOL scales provide the overall impact of the disease and to gain further insight from the patients' perspective. The most commonly used disease-specific HRQOL scales for patients wi
Bias, Randomization, and Ovarian Proteomic Data: A Reply to
Keith A. Baggerly, Kevin R. Coombes, and Jeffrey S. Morris
Cancer Informatics , 2005,
Abstract: : Proteomic patterns derived from mass spectrometry have recently been put forth as potential biomarkers for the early diagnosis of cancer. This approach has generated much excitement, particularly as initial results reported on SELDI profiling of serum suggested that near perfect sensitivity and specificity could be achieved in diagnosing ovarian cancer. However, more recent reports have suggested that much of the observed structure could be due to the presence of experimental bias. A rebuttal to the findings of bias, subtitled “Producers and Consumers”, lists several objections. In this paper, we attempt to address these objections. While we continue to find evidence of experimental bias, we emphasize that the problems found are associated with experimental design and processing, and can be avoided in future studies.
An explicit counterexample to the Lagarias-Wang finiteness conjecture
Kevin G. Hare,Ian D. Morris,Nikita Sidorov,Jacques Theys
Mathematics , 2010,
Abstract: The joint spectral radius of a finite set of real $d \times d$ matrices is defined to be the maximum possible exponential rate of growth of long products of matrices drawn from that set. A set of matrices is said to have the \emph{finiteness property} if there exists a periodic product which achieves this maximal rate of growth. J.C. Lagarias and Y. Wang conjectured in 1995 that every finite set of real $d \times d$ matrices satisfies the finiteness property. However, T. Bousch and J. Mairesse proved in 2002 that counterexamples to the finiteness conjecture exist, showing in particular that there exists a family of pairs of $2 \times 2$ matrices which contains a counterexample. Similar results were subsequently given by V.D. Blondel, J. Theys and A.A. Vladimirov and by V.S. Kozyakin, but no explicit counterexample to the finiteness conjecture has so far been given. The purpose of this paper is to resolve this issue by giving the first completely explicit description of a counterexample to the Lagarias-Wang finiteness conjecture. Namely, for the set \[ \mathsf{A}_{\alpha_*}:= \{({cc}1&1\\0&1), \alpha_*({cc}1&0\\1&1)\}\] we give an explicit value of \alpha_* \simeq 0.749326546330367557943961948091344672091327370236064317358024...] such that $\mathsf{A}_{\alpha_*}$ does not satisfy the finiteness property.
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