Partial coherence in the core/halo picture of Bose-Einstein n-particle correlations

We study the influence of a possible coherent component in the boson source on the two-, three- and $n$-particle correlation functions in a generalized core/halo type of boson-emitting source. In particular, a simple formula is presented for the strengh of the $n$-particle correlation functions for such systems. Graph rules are obtained to evaluate the correlation functions of arbitrary high order. The importance of experimental determination of the 4-th and 5-th order Bose-Einstein correlation function is emphasized.Comment: 15 pages, Latex, 3 EPS files, 1 tabl

Clustered bottlenecks in mRNA translation and protein synthesis

We construct an algorithm that generates large, band-diagonal transition matrices for a totally asymmetric exclusion process (TASEP) with local hopping rate inhomogeneities. The matrices are diagonalized numerically to find steady-state currents of TASEPs with local variations in hopping rate. The results are then used to investigate clustering of slow codons along mRNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size, beyond $\approx 3-4$, does not significantly reduce ribosome current. Our results are verified by extensive Monte-Carlo simulations and provide a biologically-motivated explanation for the experimentally-observed clustering of low-usage codons

Towards a model for protein production rates

In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two ``bottlenecks'' (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel ``edge'' effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions.Comment: 8 pages, 8 figure

Reconstruction on trees and spin glass transition

Consider an information source generating a symbol at the root of a tree network whose links correspond to noisy communication channels, and broadcasting it through the network. We study the problem of reconstructing the transmitted symbol from the information received at the leaves. In the large system limit, reconstruction is possible when the channel noise is smaller than a threshold. We show that this threshold coincides with the dynamical (replica symmetry breaking) glass transition for an associated statistical physics problem. Motivated by this correspondence, we derive a variational principle which implies new rigorous bounds on the reconstruction threshold. Finally, we apply a standard numerical procedure used in statistical physics, to predict the reconstruction thresholds in various channels. In particular, we prove a bound on the reconstruction problem for the antiferromagnetic ``Potts'' channels, which implies, in the noiseless limit, new results on random proper colorings of infinite regular trees. This relation to the reconstruction problem also offers interesting perspective for putting on a clean mathematical basis the theory of glasses on random graphs.Comment: 34 pages, 16 eps figure

Disorder-induced magnetic memory: Experiments and theories

Beautiful theories of magnetic hysteresis based on random microscopic disorder have been developed over the past ten years. Our goal was to directly compare these theories with precise experiments. We first developed and then applied coherent x-ray speckle metrology to a series of thin multilayer perpendicular magnetic materials. To directly observe the effects of disorder, we deliberately introduced increasing degrees of disorder into our films. We used coherent x-rays to generate highly speckled magnetic scattering patterns. The apparently random arrangement of the speckles is due to the exact configuration of the magnetic domains in the sample. In effect, each speckle pattern acts as a unique fingerprint for the magnetic domain configuration. Small changes in the domain structure change the speckles, and comparison of the different speckle patterns provides a quantitative determination of how much the domain structure has changed. How is the magnetic domain configuration at one point on the major hysteresis loop related to the configurations at the same point on the loop during subsequent cycles? The microscopic return-point memory(RPM) is partial and imperfect in the disordered samples, and completely absent when the disorder was not present. We found the complementary-point memory(CPM) is also partial and imperfect in the disordered samples and completely absent when the disorder was not present. We found that the RPM is always a little larger than the CPM. We also studied the correlations between the domains within a single ascending or descending loop. We developed new theoretical models that do fit our experiments.Comment: 26 pages, 25 figures, Accepted by Physical Review B 01/25/0

Ultra-large bandwidth hollow-core guiding in all-silica Bragg fibers with nano-supports

We demonstrate a new class of hollow-core Bragg fibers that are composed of concentric cylindrical silica rings separated by nanoscale support bridges. We theoretically predict and experimentally observe hollow-core confinement over an octave frequency range. The bandwidth of bandgap guiding in this new class of Bragg fibers exceeds that of other hollow-core fibers reported in the literature. With only three rings of silica cladding layers, these Bragg fibers achieve propagation loss of the order of 1 dB/m.Comment: 9 pages including 5 figure