Large scale chromosome folding Is stable against local changes in chromatin structure

Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations, we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than 10(5) basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes. © 2016 Florescu et al

Phonon-induced electron relaxation in weakly-confined single and coupled quantum dots

We investigate charge relaxation rates due to acoustic phonons in weakly-confined quantum dot systems, including both deformation potential and piezoelectric field interactions. Single-electron excited states lifetimes are calculated for single and coupled quantum dot structures, both in homonuclear and heteronuclear devices. Piezoelectric field scattering is shown to be the dominant relaxation mechanism in many experimentally relevant situations. On the other hand, we show that appropriate structure design allows to minimize separately deformation potential and piezolectric field interactions, and may bring electron lifetimes in the range of microseconds.Comment: 20 pages (preprint format), 7 figures, submitted to Physical Review

Inversion formulas for the broken-ray Radon transform

We consider the inverse problem of the broken ray transform (sometimes also referred to as the V-line transform). Explicit image reconstruction formulas are derived and tested numerically. The obtained formulas are generalizations of the filtered backprojection formula of the conventional Radon transform. The advantages of the broken ray transform include the possibility to reconstruct the absorption and the scattering coefficients of the medium simultaneously and the possibility to utilize scattered radiation which, in the case of the conventional X-ray tomography, is typically discarded.Comment: To be submitted to Inverse Problem

XML Reconstruction View Selection in XML Databases: Complexity Analysis and Approximation Scheme

Query evaluation in an XML database requires reconstructing XML subtrees rooted at nodes found by an XML query. Since XML subtree reconstruction can be expensive, one approach to improve query response time is to use reconstruction views - materialized XML subtrees of an XML document, whose nodes are frequently accessed by XML queries. For this approach to be efficient, the principal requirement is a framework for view selection. In this work, we are the first to formalize and study the problem of XML reconstruction view selection. The input is a tree $T$, in which every node $i$ has a size $c_i$ and profit $p_i$, and the size limitation $C$. The target is to find a subset of subtrees rooted at nodes $i_1,\cdots, i_k$ respectively such that $c_{i_1}+\cdots +c_{i_k}\le C$, and $p_{i_1}+\cdots +p_{i_k}$ is maximal. Furthermore, there is no overlap between any two subtrees selected in the solution. We prove that this problem is NP-hard and present a fully polynomial-time approximation scheme (FPTAS) as a solution

Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model

We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the model successfully reproduces some of the observed properties of real systems and predictions of kinetic models. For example, sampling of the DNA sequence by the protein proceeds via a succession of 3d motion in the solvent, 1d sliding along the sequence, short hops between neighboring sites, and intersegmental transfers. Moreover, facilitated diffusion takes place in a certain range of values of the protein effective charge, that is, the combination of 1d sliding and 3d motion leads to faster DNA sampling than pure 3d motion. At last, the number of base pairs visited during a sliding event is comparable to the values deduced from single-molecule experiments. We also point out and discuss some discrepancies between the predictions of this model and some recent experimental results as well as some hypotheses and predictions of kinetic models

Behaviours, motivations and values: Validity, reliability, and utility of novice motorcyclist' self-report in road safety research

The continuing use of self-report methods demands consideration of the validity, reliability, and utility of self-report in road safety research. This thesis assesses self-report issues with respect to four key constructs in motorcycle safety research—exposure, on-road behaviours, riding motivations, and perceived value in a sample of Australian novice motorcycle riders. In Study 1 a comprehensive set of statistical analyses was performed to test the validity and reliability of various self-report measures of riding exposure. In Study 2 and Study 3 previously untested psychometric properties of stability, content validity, and predictive validity of the Motorcycle Rider Behaviour Questionnaire and the Motorcycle Rider Motivation Questionnaire in terms of police-recorded offences and crashes as well as previously assessed factor structure, internal consistency, and predictive validity in terms of self-reported crashes were examined. In Study 4 I demonstrated the utility of a contingent valuation (CV) survey in measuring, understanding, and therefore addressing the perceived value of rider training amongst novice riders. The four studies highlight that the appropriateness of self-report depends on not only the nature of the phenomenon under study but the extent to which the factors that contribute to validity and reliability are accounted for in the design of self-report measures

Coherent spin dynamics in quantum wells in quantizing magnetic field

We investigate theoretically the coherent longitudinal and transversal spin relaxation of photoexcited electrons in quantum wells in quantized magnetic fields. We find the relaxation time for typical quantum well parameters between 100 and 1000 ps. For a realistic random potential the relaxation process depends on the electron energy and g-factor, demonstrating oscillations in the spin polarization accompanying the spin relaxation. The dependence of spin relaxation on applied field, and thus on the corresponding "magnetic" length, can be used to characterize the spatial scale of disorder in quantum wells.Comment: 13 pages, 4 figure

Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars

A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches, analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scartrace, a strategy for massively parallel clonal analysis based on Cas9 induced genetic scars in the zebrafish

Microscopic derivation of the Jaynes-Cummings model with cavity losses

In this paper we provide a microscopic derivation of the master equation for the Jaynes-Cummings model with cavity losses. We single out both the differences with the phenomenological master equation used in the literature and the approximations under which the phenomenological model correctly describes the dynamics of the atom-cavity system. Some examples wherein the phenomenological and the microscopic master equations give rise to different predictions are discussed in detail.Comment: 9 pages, 3 figures New version with minor correction Accepted for publication on Physical Review