Curvature and torsion in growing actin networks

Intracellular pathogens such as Listeria monocytogenes and Rickettsia rickettsii move within a host cell by polymerizing a comet-tail of actin fibers that ultimately pushes the cell forward. This dense network of cross-linked actin polymers typically exhibits a striking curvature that causes bacteria to move in gently looping paths. Theoretically, tail curvature has been linked to details of motility by considering force and torque balances from a finite number of polymerizing filaments. Here we track beads coated with a prokaryotic activator of actin polymerization in three dimensions to directly quantify the curvature and torsion of bead motility paths. We find that bead paths are more likely to have low rather than high curvature at any given time. Furthermore, path curvature changes very slowly in time, with an autocorrelation decay time of 200 seconds. Paths with a small radius of curvature, therefore, remain so for an extended period resulting in loops when confined to two dimensions. When allowed to explore a 3D space, path loops are less evident. Finally, we quantify the torsion in the bead paths and show that beads do not exhibit a significant left- or right-handed bias to their motion in 3D. These results suggest that paths of actin-propelled objects may be attributed to slow changes in curvature rather than a fixed torque

A new efficient method for determining weighted power spectra: detection of low-frequency solar p-modes by analysis of BiSON data

We present a new and highly efficient algorithm for computing a power spectrum made from evenly spaced data which combines the noise-reducing advantages of the weighted fit with the computational advantages of the Fast Fourier Transform (FFT). We apply this method to a 10-year data set of the solar p-mode oscillations obtained by the Birmingham Solar Oscillations Network (BiSON) and thereby uncover three new low-frequency modes. These are the l=2, n=5 and n=7 modes and the l=3, n=7 mode. In the case of the l=2, n=5 modes, this is believed to be the first such identification of this mode in the literature. The statistical weights needed for the method are derived from a combination of the real data and a sophisticated simulation of the instrument performance. Variations in the weights are due mainly to the differences in the noise characteristics of the various BiSON instruments, the change in those characteristics over time and the changing line-of-sight velocity between the stations and the Sun. It should be noted that a weighted data set will have a more time-dependent signal than an unweighted set and that, consequently, its frequency spectrum will be more susceptible to aliasing.Comment: 11 pages, 7 Figures, accepted for publication in MNRAS, Figure 6 had to be reduced in size to upload and so may be difficult to view on screen in .ps versio

Computer Components and Systems

Contains research objectives.U.S. Navy Bureau of Ships under Contracts NObsr 72716 and NObsr 7760

Optimum Quantum Error Recovery using Semidefinite Programming

Quantum error correction (QEC) is an essential element of physical quantum information processing systems. Most QEC efforts focus on extending classical error correction schemes to the quantum regime. The input to a noisy system is embedded in a coded subspace, and error recovery is performed via an operation designed to perfectly correct for a set of errors, presumably a large subset of the physical noise process. In this paper, we examine the choice of recovery operation. Rather than seeking perfect correction on a subset of errors, we seek a recovery operation to maximize the entanglement fidelity for a given input state and noise model. In this way, the recovery operation is optimum for the given encoding and noise process. This optimization is shown to be calculable via a semidefinite program (SDP), a well-established form of convex optimization with efficient algorithms for its solution. The error recovery operation may also be interpreted as a combining operation following a quantum spreading channel, thus providing a quantum analogy to the classical diversity combining operation.Comment: 7 pages, 3 figure

Geometric approach to Fletcher's ideal penalty function

Original article can be found at: www.springerlink.com Copyright Springer. [Originally produced as UH Technical Report 280, 1993]In this note, we derive a geometric formulation of an ideal penalty function for equality constrained problems. This differentiable penalty function requires no parameter estimation or adjustment, has numerical conditioning similar to that of the target function from which it is constructed, and also has the desirable property that the strict second-order constrained minima of the target function are precisely those strict second-order unconstrained minima of the penalty function which satisfy the constraints. Such a penalty function can be used to establish termination properties for algorithms which avoid ill-conditioned steps. Numerical values for the penalty function and its derivatives can be calculated efficiently using automatic differentiation techniques.Peer reviewe

Fast iterative solution of reaction-diffusion control problems arising from chemical processes

PDE-constrained optimization problems, and the development of preconditioned iterative methods for the efficient solution of the arising matrix system, is a field of numerical analysis that has recently been attracting much attention. In this paper, we analyze and develop preconditioners for matrix systems that arise from the optimal control of reaction-diffusion equations, which themselves result from chemical processes. Important aspects in our solvers are saddle point theory, mass matrix representation and effective Schur complement approximation, as well as the outer (Newton) iteration to take account of the nonlinearity of the underlying PDEs

Structured Near-Optimal Channel-Adapted Quantum Error Correction

We present a class of numerical algorithms which adapt a quantum error correction scheme to a channel model. Given an encoding and a channel model, it was previously shown that the quantum operation that maximizes the average entanglement fidelity may be calculated by a semidefinite program (SDP), which is a convex optimization. While optimal, this recovery operation is computationally difficult for long codes. Furthermore, the optimal recovery operation has no structure beyond the completely positive trace preserving (CPTP) constraint. We derive methods to generate structured channel-adapted error recovery operations. Specifically, each recovery operation begins with a projective error syndrome measurement. The algorithms to compute the structured recovery operations are more scalable than the SDP and yield recovery operations with an intuitive physical form. Using Lagrange duality, we derive performance bounds to certify near-optimality.Comment: 18 pages, 13 figures Update: typos corrected in Appendi

A multi-object spectral imaging instrument

We have developed a snapshot spectral imaging system which fits onto the side camera port of a commercial inverted microscope. The system provides spectra, in real time, from multiple points randomly selected on the microscope image. Light from the selected points in the sample is directed from the side port imaging arm using a digital micromirror device to a spectrometer arm based on a dispersing prism and CCD camera. A multi-line laser source is used to calibrate the pixel positions on the CCD for wavelength. A CMOS camera on the front port of the microscope allows the full image of the sample to be displayed and can also be used for particle tracking, providing spectra of multiple particles moving in the sample. We demonstrate the system by recording the spectra of multiple fluorescent beads in aqueous solution and from multiple points along a microscope sample channel containing a mixture of red and blue dye

Are short-term variations in solar oscillation frequencies the signature of a second solar dynamo?

In addition to the well-known 11-year solar cycle, the Sun's magnetic activity also shows significant variation on shorter time scales, e.g. between one and two years. We observe a quasi-biennial (2-year) signal in the solar p-mode oscillation frequencies, which are sensitive probes of the solar interior. The signal is visible in Sun-as-a-star data observed by different instruments and here we describe the results obtained using BiSON, GOLF, and VIRGO data. Our results imply that the 2-year signal is susceptible to the influence of the main 11-year solar cycle. However, the source of the signal appears to be separate from that of the 11-year cycle. We speculate as to whether it might be the signature of a second dynamo, located in the region of near-surface rotational shear.Comment: 6 pages, 2 figures, proceedings for SOHO-24/GONG 2010 conference, to be published in JPC

An Ontology Engineering Approach to User Profiling for Virtual Tours of Museums and Galleries

This paper describes a study of the development of a hierarchical ontology for producing and maintaining personalized profiles to improve the experience of visitors to virtual art galleries and museums. The paper begins by describing some of the features of virtual exhibitions and offers examples of virtual tours that the reader may wish to examine in more detail. The paper then discusses the ontology engineering (OE) approach and domain modelling languages (e.g. KACTUS, SENSUS and METHONTOLOGY). It then follows a basic OE approach to define classes for a cultural heritage virtual tour and to produce a Visitor Profile Ontology that is hierarchical and has static and dynamic elements. It concludes by suggesting ways in which the ontology may be automated to provide a richer, more immersive personalized visitor experience