Improved solution for potential flow about arbitrary axisymmetric bodies by the use of a higher-order surface source method. Part 1. Theory and results

The surface-source method of calculating potential flow is improved by refining the underlying numerical analysis. The analysis uses parabolic elements and linearly-varying source density. The result is a large increase in computing speed and accuracy. The theory is described, and the effectiveness of the modification is illustrated

An Allosteric Mechanism for Inhibiting HIV-1 Integrase with a Small Molecule

HIV-1 integrase (IN) is a validated target for developing antiretroviral inhibitors. Using affinity acetylation and mass spectrometric (MS) analysis, we previously identified a tetra-acetylated inhibitor (2E)-3-[3,4-bis(acetoxy)phenyl]-2-propenoate-N-[(2E)-3-[3,4-bis(acetyloxy)phenyl]-1-oxo-2-propenyl]-L-serine methyl ester; compound 1] that selectively modified Lys173 at the IN dimer interface. Here we extend our efforts to dissect the mechanism of inhibition and structural features that are important for the selective binding of compound 1. Using a subunit exchange assay, we found that the inhibitor strongly modulates dynamic interactions between IN subunits. Restricting such interactions does not directly interfere with IN binding to DNA substrates or cellular cofactor lens epithelium-derived growth factor, but it compromises the formation of the fully functional nucleoprotein complex. Studies comparing compound 1 with a structurally related IN inhibitor, the tetra-acetylated-chicoric acid derivative (2R,3R)-2,3-bis[[(2E)-3-[3,4-bis(acetyloxy)phenyl]-1-oxo-2-propen-1-yl]oxy]-butanedioic acid (compound 2), indicated striking mechanistic differences between these agents. The structures of the two inhibitors differ only in their central linker regions, with compounds 1 and 2 containing a single methyl ester group and two carboxylic acids, respectively. MS experiments highlighted the importance of these structural differences for selective binding of compound 1 to the IN dimer interface. Moreover, molecular modeling of compound 1 complexed to IN identified a potential inhibitor binding cavity and provided structural clues regarding a possible role of the central methyl ester group in establishing an extensive hydrogen bonding network with both interacting subunits. The proposed mechanism of action and binding site for the small-molecule inhibitor identified in the present study provide an attractive venue for developing allosteric inhibitors of HIV-1 IN

Lifelongα-tocopherol supplementation increases the median life span of C57BL/6 mice in the cold but has only minor effects on oxidative damage

The effects of dietary antioxidant supplementation on oxidative stress and life span are confused. We maintained C57BL/6 mice at 7 ± 2°C and supplemented their diet with α-tocopherol from 4 months of age. Supplementation significantly increased (p = 0.042) median life span by 15% (785 days, n = 44) relative to unsupplemented controls (682 days, n = 43) and also increased maximum life span (oldest 10%, p = 0.028). No sex or sex by treatment interaction effects were observed on life span, with treatment having no effect on resting or daily metabolic rate. Lymphocyte and hepatocyte oxidative DNA damage and hepatic lipid peroxidation were unaffected by supplementation, but hepatic oxidative DNA damage increased with age. Using a cDNA macroarray, genes associated with xenobiotic metabolism were significantly upregulated in the livers of female mice at 6 months of age (2 months supplementation). At 22 months of age (18 months supplementation) this response had largely abated, but various genes linked to the p21 signaling pathway were upregulated at this time. We suggest that α-tocopherol may initially be metabolized as a xenobiotic, potentially explaining why previous studies observe a life span extension generally when lifelong supplementation is initiated early in life. The absence of any significant effect on oxidative damage suggests that the life span extension observed was not mediated via any antioxidant properties of α-tocopherol. We propose that the life span extension observed following α-tocopherol supplementation may be mediated via upregulation of cytochrome p450 genes after 2 months of supplementation and/or upregulation of p21 signaling genes after 18 months of supplementation. However, these signaling pathways now require further investigation to establish their exact role in life span extension following α-tocopherol supplementation

Controlling the accuracy of the density matrix renormalization group method: The Dynamical Block State Selection approach

We have applied the momentum space version of the Density Matrix Renormalization Group method ($k$-DMRG) in quantum chemistry in order to study the accuracy of the algorithm in the new context. We have shown numerically that it is possible to determine the desired accuracy of the method in advance of the calculations by dynamically controlling the truncation error and the number of block states using a novel protocol which we dubbed Dynamical Block State Selection (DBSS). The relationship between the real error and truncation error has been studied as a function of the number of orbitals and the fraction of filled orbitals. We have calculated the ground state of the molecules CH$_2$, H$_2$O, and F$_2$ as well as the first excited state of CH$_2$. Our largest calculations were carried out with 57 orbitals, the largest number of block states was 1500--2000, and the largest dimensions of the Hilbert space of the superblock configuration was 800.000--1.200.000.Comment: 12 page

Blood Substitutes in Cardiac Surgery

A safe, inexpensive, noninfectious substitute for red blood cells has long been sought. Despite tremendous advances in blood banking, the logistics of collecting, transporting, and storing human red blood cells contin ues to create infection and shortage problems. The two basic types of blood substitutes currently under devel opment are hemoglobin based and fluorocarbon based. Although they each transport oxygen differently, the basic advantages and limitations are the same. Blood substitute advantages include the unique capacity for room temperature storage, noninfectivity, adequate supply, and low toxicity. Restrictions include limited dosing in the acute period, limited intravascular half-life and, for the fluorocarbons, a requirement for a high PaO2. In addition, there remain questions about the relationship of nitric oxide metabolism to hypertension in hemoglobin solutions. Early clinical and laboratory trials have shown that both types of solutions are effective oxygen-delivery agents, with acceptable side- effect profiles. Clinical trials are currently underway to determine the safety and efficacy of these solutions in patients undergoing cardiopulmonary bypass.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68576/2/10.1177_108925329800200403.pd

Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Vortex precession in Bose-Einstein condensates: observations with filled and empty cores

We have observed and characterized the dynamics of singly quantized vortices in dilute-gas Bose-Einstein condensates. Our condensates are produced in a superposition of two internal states of 87Rb, with one state supporting a vortex and the other filling the vortex core. Subsequently, the state filling the core can be partially or completely removed, reducing the radius of the core by as much as a factor of 13, all the way down to its bare value. The corresponding superfluid rotation rates, evaluated at the core radius, vary by a factor of 150, but the precession frequency of the vortex core about the condensate axis changes by only a factor of two.Comment: 4 pages, 3 figure

Quantitative nanoscale vortex-imaging using a cryogenic quantum magnetometer

Microscopic studies of superconductors and their vortices play a pivotal role in our understanding of the mechanisms underlying superconductivity. Local measurements of penetration depths or magnetic stray-fields enable access to fundamental aspects of superconductors such as nanoscale variations of superfluid densities or the symmetry of their order parameter. However, experimental tools, which offer quantitative, nanoscale magnetometry and operate over the large range of temperature and magnetic fields relevant to address many outstanding questions in superconductivity, are still missing. Here, we demonstrate quantitative, nanoscale magnetic imaging of Pearl vortices in the cuprate superconductor YBCO, using a scanning quantum sensor in form of a single Nitrogen-Vacancy (NV) electronic spin in diamond. The sensor-to-sample distance of ~10nm we achieve allows us to observe striking deviations from the prevalent monopole approximation in our vortex stray-field images, while we find excellent quantitative agreement with Pearl's analytic model. Our experiments yield a non-invasive and unambiguous determination of the system's local London penetration depth, and are readily extended to higher temperatures and magnetic fields. These results demonstrate the potential of quantitative quantum sensors in benchmarking microscopic models of complex electronic systems and open the door for further exploration of strongly correlated electron physics using scanning NV magnetometry.Comment: Main text (5 pages, 4 figures) plus supplementary material (5 pages, 6 figures). Comments welcome. Further information under http://www.quantum-sensing.c

Self-Similar Interpolation in Quantum Mechanics

An approach is developed for constructing simple analytical formulae accurately approximating solutions to eigenvalue problems of quantum mechanics. This approach is based on self-similar approximation theory. In order to derive interpolation formulae valid in the whole range of parameters of considered physical quantities, the self-similar renormalization procedure is complimented here by boundary conditions which define control functions guaranteeing correct asymptotic behaviour in the vicinity of boundary points. To emphasize the generality of the approach, it is illustrated by different problems that are typical for quantum mechanics, such as anharmonic oscillators, double-well potentials, and quasiresonance models with quasistationary states. In addition, the nonlinear Schr\"odinger equation is considered, for which both eigenvalues and wave functions are constructed.Comment: 1 file, 30 pages, RevTex, no figure