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

Single photons on demand from 3D photonic band-gap structures

We describe a practical implementation of a (semi-deterministic) photon gun based on stimulated Raman adiabatic passage pumping and the strong enhancement of the photonic density of states in a photonic band-gap material. We show that this device allows {\em deterministic} and {\em unidirectional} production of single photons with a high repetition rate of the order of 100kHz. We also discuss specific 3D photonic microstructure architectures in which our model can be realized and the feasibility of implementing such a device using ${Er}^{3+}$ ions that produce single photons at the telecommunication wavelength of $1.55 \mu$m.Comment: 4 pages, 4 EPS figure

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

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

Self-optimization of optical confinement in ultraviolet photonic crystal slab laser

We studied numerically and experimentally the effects of structural disorder on the performance of ultraviolet photonic crystal slab lasers. Optical gain selectively amplifies the high-quality modes of the passive system. For these modes, the in-plane and out-of-plane leakage rates may be automatically balanced in the presence of disorder. The spontaneous optimization of in-plane and out-of-plane confinement of light in a photonic crystal slab may lead to a reduction of the lasing threshold.Comment: 5 pages, 5 figure

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

Role of Fragment Higher Static Deformations in the Cold Binary Fission of 252^{252}Cf

We study the binary cold fission of $^{252}$Cf in the frame of a cluster model where the fragments are born to their respective ground states and interact via a double-folded potential with deformation effects taken into account up to multipolarity $\lambda=4$. The preformation factors were neglected. In the case when the fragments are assumed to be spherical or with ground state quadrupole deformation, the $Q$-value principle dictates the occurence of a narrow region around the double magic $^{132}$Sn, like in the case of cluster radioactivity. When the hexadecupole deformation is turned on, an entire mass-region of cold fission in the range 138 - 156 for the heavy fragment arise, in agreement with the experimental observations. This fact suggests that in the above mentioned mass-region, contrary to the usual cluster radioactivity where the daughter nucleus is always a neutron/proton (or both) closed shell or nearly closed shell spherical nucleus, the clusterization mechanism seems to be strongly influenced by the hexadecupole deformations rather than the $Q$-value.Comment: 10 pages, 12 figure

Single photons on demand from tunable 3D photonic band-gap structures

In this article we propose to build a (semi-)deterministic photon gun by modifying the spontaneous decay in a photonic band-gap material. We show that such a device allows for deterministic and unidirectional single-photon emission with a repetition rate of the order of 100 kHz. We describe a specific realization of the 1D band-gap model by means of a 3D photonic-crystal heterostructure and the feasability of implementing such a device using Er3+ ions that produce single photons at the telecommunication wavelength of 1.55,m, important for many applications

Exploiting the quantum Zeno effect to beat photon loss in linear optical quantum information processors

We devise a new technique to enhance transmission of quantum information through linear optical quantum information processors. The idea is based on applying the Quantum Zeno effect to the process of photon absorption. By frequently monitoring the presence of the photon through a QND (quantum non-demolition) measurement the absorption is suppressed. Quantum information is encoded in the polarization degrees of freedom and is therefore not affected by the measurement. Some implementations of the QND measurement are proposed.Comment: 4 pages, 1 figur