417 research outputs found
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 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
Transition from vortex to wall driven turbulence production in the Taylor-Couette system with a rotating inner cylinder
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
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