540 research outputs found
Geometry of open strings ending on backreacting D3-branes
We investigate open string theory on backreacting D3-branes using a spacetime
approach. We study in detail the half-BPS supergravity solutions describing
open strings ending on D3-branes, in the near horizon of the D3-branes. We
recover quantitatively several non-trivial features of open string physics
including the appearance of D3-brane spikes, the polarization of fundamental
strings into D5-branes, and the Hanany-Witten effect. Finally we detail the
computation of the gravitational potential between two open strings, and
contrast it with the holographic computation of Wilson lines. We argue that the
D-brane backreaction has a large influence on the low-energy gravity, which may
lead to experimental tests for string theory brane-world scenarios.Comment: 64 pages, 20 figure
Geometry-controlled kinetics
It has long been appreciated that transport properties can control reaction
kinetics. This effect can be characterized by the time it takes a diffusing
molecule to reach a target -- the first-passage time (FPT). Although essential
to quantify the kinetics of reactions on all time scales, determining the FPT
distribution was deemed so far intractable. Here, we calculate analytically
this FPT distribution and show that transport processes as various as regular
diffusion, anomalous diffusion, diffusion in disordered media and in fractals
fall into the same universality classes. Beyond this theoretical aspect, this
result changes the views on standard reaction kinetics. More precisely, we
argue that geometry can become a key parameter so far ignored in this context,
and introduce the concept of "geometry-controlled kinetics". These findings
could help understand the crucial role of spatial organization of genes in
transcription kinetics, and more generally the impact of geometry on
diffusion-limited reactions.Comment: Submitted versio
Tibial coverage, meniscus position, size and damage in knees discordant for joint space narrowing - data from the Osteoarthritis Initiative.
INTRODUCTION: Meniscal extrusion is thought to be associated with less meniscus coverage of the tibial surface, but the association of radiographic disease stage with quantitative measures of tibial plateau coverage is unknown. We therefore compared quantitative and semi-quantitative measures of meniscus position and morphology in individuals with bilateral painful knees discordant on medial joint space narrowing (mJSN). METHODS: A sample of 60 participants from the first half (2,678 cases) of the Osteoarthritis Initiative cohort fulfilled the inclusion criteria: bilateral frequent pain, Osteoarthritis Research Society International (OARSI) mJSN grades 1-3 in one, no-JSN in the contra-lateral (CL), and no lateral JSN in either knee (43 unilateral mJSN1; 17 mJSN2/3; 22 men, 38 women, body mass index (BMI) 31.3 + 3.9 kg/m(2)). Segmentation and three-dimensional quantitative analysis of the tibial plateau and meniscus, and semi-quantitative evaluation of meniscus damage (magnetic resonance imaging (MRI) osteoarthritis knee score = MOAKS) was performed using coronal 3T MR images (MPR DESSwe and intermediate-weighted turbo spin echo (IW-TSE) images). CL knees were compared using paired t-tests (between-knee, within-person design). RESULTS: Medial tibial plateau coverage was 36 + 9% in mJSN1 vs 45 + 8% in CL no-JSN knees, and was 31 + 9% in mJSN2/3 vs 46 + 6% in no-JSN knees (both P < 0.001). mJSN knees showed greater meniscus extrusion and damage (MOAKS), but no significant difference in meniscus volume. No significant differences in lateral tibial coverage, lateral meniscus morphology or position were observed. CONCLUSIONS: Knees with medial JSN showed substantially less medial tibial plateau coverage by the meniscus. We suggest that the less meniscal coverage, i.e., less mechanical protection may be a reason for greater rates of cartilage loss observed in JSN knees. Copyright 2012 Osteoarthritis Research Society International. All rights reserved
Relationship between knee pain and the presence, location, size and phenotype of femorotibial denuded areas of subchondral bone as visualized by MRI
Objective: Conflicting associations between imaging biomarkers and pain in knee osteoarthritis (OA) have been reported. A relation between pain and denuded areas of subchondral bone (dABs) has been suggested and this study explores this relationship further by relating the presence, phenotype, location and size of dABs to different measures of knee pain. Methods: 633 right knees from the Osteoarthritis Initiative (OAI) (250 men, age 61.7 +/- 9.6 yrs, BMI 29.4 +/- 4.7 kg/m(2)) were included. Manual segmentation of the femorotibial cartilage plates was performed on 3 T coronal fast low angle shot with water excitation (FLASHwe) images. dABs were defined as areas where the subchondral bone was uncovered by cartilage. The following measures of pain were used: weightbearing-, non-weightbearing-, moderate-to-severe-, infrequent- and frequent knee pain. Results: Using pain measures from subjects without dABs as a reference, those with at least one dAB had a 1.64-fold higher prevalence ratio [PR, 95% confidence interval (CI) 1.24-2.18] to have frequent and 1.45-fold higher for moderate-to-severe knee pain (95% CI 1.13-1.85). Subjects with dABs in central subregions had a 1.53-fold increased prevalence of having weightbearing pain (95% Cl 1.20-1.97), especially when the central subregion was moderately (>10%) denuded (PR 1.81, 95% CI 135-2.42). Individuals with cartilage-loss-type dABs had a slightly higher prevalence (PR 1.13, 95% CI 1.00-1.27) of having frequent knee pain compared to individuals with intra-chondral-osteophyte-type dABs. Conclusion: This study supports a positive relation between femorotibial dABs and knee pain, especially when the dABs are located centrally (i.e., in weightbearing regions) or when the respective central subregion is moderately denuded. (C) 2013 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved
Kinetics of active surface-mediated diffusion in spherically symmetric domains
We present an exact calculation of the mean first-passage time to a target on
the surface of a 2D or 3D spherical domain, for a molecule alternating phases
of surface diffusion on the domain boundary and phases of bulk diffusion. We
generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a
biased diffusion in a general annulus with an arbitrary number of regularly
spaced targets on a partially reflecting surface. The presented approach is
based on an integral equation which can be solved analytically. Numerically
validated approximation schemes, which provide more tractable expressions of
the mean first-passage time are also proposed. In the framework of this minimal
model of surface-mediated reactions, we show analytically that the mean
reaction time can be minimized as a function of the desorption rate from the
surface.Comment: Published online in J. Stat. Phy
Persistent Cell Motion in the Absence of External Signals: A Search Strategy for Eukaryotic Cells
Eukaryotic cells are large enough to detect signals and then orient to them
by differentiating the signal strength across the length and breadth of the
cell. Amoebae, fibroblasts, neutrophils and growth cones all behave in this
way. Little is known however about cell motion and searching behavior in the
absence of a signal. Is individual cell motion best characterized as a random
walk? Do individual cells have a search strategy when they are beyond the range
of the signal they would otherwise move toward? Here we ask if single,
isolated, Dictyostelium and Polysphondylium amoebae bias their motion in the
absence of external cues. We placed single well-isolated Dictyostelium and
Polysphondylium cells on a nutrient-free agar surface and followed them at 10
sec intervals for ~10 hr, then analyzed their motion with respect to velocity,
turning angle, persistence length, and persistence time, comparing the results
to the expectation for a variety of different types of random motion. We find
that amoeboid behavior is well described by a special kind of random motion:
Amoebae show a long persistence time (~10 min) beyond which they start to lose
their direction; they move forward in a zig-zag manner; and they make turns
every 1-2 min on average. They bias their motion by remembering the last turn
and turning away from it. Interpreting the motion as consisting of runs and
turns, the duration of a run and the amplitude of a turn are both found to be
exponentially distributed. We show that this behavior greatly improves their
chances of finding a target relative to performing a random walk. We believe
that other eukaryotic cells may employ a strategy similar to Dictyostelium when
seeking conditions or signal sources not yet within range of their detection
system.Comment: 15 pages, 11 figures, accepted for publication in PLOS On
A liquid xenon ionization chamber in an all-fluoropolymer vessel
A novel technique has been developed to build vessels for liquid xenon
ionization detectors entirely out of ultra-clean fluoropolymer. We describe the
advantages in terms of low radioactivity contamination, provide some details of
the construction techniques, and show the energy resolution achieved with a
prototype all-fluoropolymer ionization detector.Comment: 12 pages, 9 figure
Residence Time Statistics for Normal and Fractional Diffusion in a Force Field
We investigate statistics of occupation times for an over-damped Brownian
particle in an external force field. A backward Fokker-Planck equation
introduced by
Majumdar and Comtet describing the distribution of occupation times is
solved. The solution gives a general relation between occupation time
statistics and probability currents which are found from solutions of the
corresponding problem of first passage time. This general relationship between
occupation times and first passage times, is valid for normal Markovian
diffusion and for non-Markovian sub-diffusion, the latter modeled using the
fractional Fokker-Planck equation. For binding potential fields we find in the
long time limit ergodic behavior for normal diffusion, while for the fractional
framework weak ergodicity breaking is found, in agreement with previous results
of Bel and Barkai on the continuous time random walk on a lattice. For
non-binding potential rich physical behaviors are obtained, and classification
of occupation time statistics is made possible according to whether or not the
underlying random walk is recurrent and the averaged first return time to the
origin is finite. Our work establishes a link between fractional calculus and
ergodicity breaking.Comment: 12 page
Classes of fast and specific search mechanisms for proteins on DNA
Problems of search and recognition appear over different scales in biological
systems. In this review we focus on the challenges posed by interactions
between proteins, in particular transcription factors, and DNA and possible
mechanisms which allow for a fast and selective target location. Initially we
argue that DNA-binding proteins can be classified, broadly, into three distinct
classes which we illustrate using experimental data. Each class calls for a
different search process and we discuss the possible application of different
search mechanisms proposed over the years to each class. The main thrust of
this review is a new mechanism which is based on barrier discrimination. We
introduce the model and analyze in detail its consequences. It is shown that
this mechanism applies to all classes of transcription factors and can lead to
a fast and specific search. Moreover, it is shown that the mechanism has
interesting transient features which allow for stability at the target despite
rapid binding and unbinding of the transcription factor from the target.Comment: 65 pages, 23 figure
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