Direct Numerical Simulation of turbulent Taylor-Couette flow

The direct numerical simulation (DNS) of the Taylor--Couette flow in the fully turbulent regime is described. The numerical method extends the work by Quadrio & Luchini (Eur. J. Mech. B / Fluids, v.21, pp.413--427, 2002), and is based on a parallel computer code which uses mixed spatial discretization (spectral schemes in the homogeneous directions, and fourth-order, compact explicit finite-difference schemes in the radial direction). A DNS is carried out to simulate for the first time the turbulent Taylor--Couette flow in the turbulent regime. Statistical quantities are computed to complement the existing experimental information, with a view to compare it to planar, pressure-driven turbulent flow at the same value of the Reynolds number. The main source for differences in flow statistics between plane and curved-wall flows is attributed to the presence of large-scale rotating structures generated by curvature effects.Comment: To appear in European Journal of Mechanics B / Fluid

Applying Laser Doppler Anemometry inside a Taylor-Couette geometry - Using a ray-tracer to correct for curvature effects

In the present work it will be shown how the curvature of the outer cylinder affects Laser Doppler anemometry measurements inside a Taylor-Couette apparatus. The measurement position and the measured velocity are altered by curved surfaces. Conventional methods for curvature correction are not applicable to our setup, and it will be shown how a ray-tracer can be used to solve this complication. By using a ray-tracer the focal position can be calculated, and the velocity can be corrected. The results of the ray-tracer are verified by measuring an a priori known velocity field, and after applying refractive corrections good agreement with theoretical predictions are found. The methods described in this paper are applied to measure the azimuthal velocity profiles in high Reynolds number Taylor-Couette flow for the case of outer cylinder rotation

Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal Dali alignments for the very first time

Angular momentum transport and turbulence in laboratory models of Keplerian flows

We present angular momentum transport (torque) measurements in two recent experimental studies of the turbulent flow between independently rotating cylinders. In addition to these studies, we reanalyze prior torque measurements to expand the range of control parameters for the experimental Taylor-Couette flows. We find that the torque may be described as a product of functions that depend only on the Reynolds number, which describes the turbulent driving intensity, and the rotation number, which characterizes the effects of global rotation. For a given Reynolds number, the global angular momentum transport for Keplerian-like flow profiles is approximately 14% of the maximum achievable transport rate. We estimate that this level of transport would produce an accretion rate of $\dot{M}/\dot{M_0} \sim 10^{-3}$ in astrophysical disks. We argue that this level of transport from hydrodynamics alone could be significant.Comment: 17 pages, 7 figures, 2 tables, submitted to Astronomy & Astrophysics (2011

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Hydrodynamic turbulence cannot transport angular momentum effectively in astrophysical disks

The most efficient energy sources known in the Universe are accretion disks. Those around black holes convert 5 -- 40 per cent of rest-mass energy to radiation. Like water circling a drain, inflowing mass must lose angular momentum, presumably by vigorous turbulence in disks, which are essentially inviscid. The origin of the turbulence is unclear. Hot disks of electrically conducting plasma can become turbulent by way of the linear magnetorotational instability. Cool disks, such as the planet-forming disks of protostars, may be too poorly ionized for the magnetorotational instability to occur, hence essentially unmagnetized and linearly stable. Nonlinear hydrodynamic instability often occurs in linearly stable flows (for example, pipe flows) at sufficiently large Reynolds numbers. Although planet-forming disks have extreme Reynolds numbers, Keplerian rotation enhances their linear hydrodynamic stability, so the question of whether they can be turbulent and thereby transport angular momentum effectively is controversial. Here we report a laboratory experiment, demonstrating that non-magnetic quasi-Keplerian flows at Reynolds numbers up to millions are essentially steady. Scaled to accretion disks, rates of angular momentum transport lie far below astrophysical requirements. By ruling out purely hydrodynamic turbulence, our results indirectly support the magnetorotational instability as the likely cause of turbulence, even in cool disks.Comment: 12 pages and 4 figures. To be published in Nature on November 16, 2006, available at http://www.nature.com/nature/journal/v444/n7117/abs/nature05323.htm

Wall roughness induces asymptotic ultimate turbulence

Turbulence is omnipresent in Nature and technology, governing the transport of heat, mass, and momentum on multiple scales. For real-world applications of wall-bounded turbulence, the underlying surfaces are virtually always rough; yet characterizing and understanding the effects of wall roughness for turbulence remains a challenge, especially for rotating and thermally driven turbulence. By combining extensive experiments and numerical simulations, here, taking as example the paradigmatic Taylor-Couette system (the closed flow between two independently rotating coaxial cylinders), we show how wall roughness greatly enhances the overall transport properties and the corresponding scaling exponents. If only one of the walls is rough, we reveal that the bulk velocity is slaved to the rough side, due to the much stronger coupling to that wall by the detaching flow structures. If both walls are rough, the viscosity dependence is thoroughly eliminated in the boundary layers and we thus achieve asymptotic ultimate turbulence, i.e. the upper limit of transport, whose existence had been predicted by Robert Kraichnan in 1962 (Phys. Fluids {\bf 5}, 1374 (1962)) and in which the scalings laws can be extrapolated to arbitrarily large Reynolds numbers

Biogenetically-Inspired Total Synthesis of Epidithiodiketopiperazines and Related Alkaloids

Natural products chemistry has historically been the prime arena for the discovery of new chemical transformations and the fountain of insights into key biological processes. It remains a fervent incubator of progress in the fields of chemistry and biology and an exchange mediating the flow of ideas between these allied fields of science. It is with this ethos that our group has taken an interest in and pursued the synthesis of a complex family of natural products termed the dimeric epipolythiodiketopiperazine (ETP) alkaloids. We present here an Account of the highly complex target molecules to which we pegged our ambitions, our systematic and relentless efforts toward those goals, the chemistry we developed in their pursuit, and the insight we have gained for their translational potential as potent anticancer molecules.National Institute of General Medical Sciences (U.S.) (Grant GM089732)Amgen Inc

Targeting of B and T lymphocyte associated (BTLA) prevents graft-versus-host disease without global immunosuppression

One-time treatment with an antibody against BTLA provides long-term protection against graft-versus-host disease without affecting effector T cell responses to tumors or pathogens