Quantitative characterization of short-range orthorhombic fluctuations in FeSe through pair distribution function analysis

Neutron and x-ray total scattering measurements have been performed on powder samples of the iron chalcogenide superconductor FeSe. Using pair distribution function (PDF) analysis of the total scattering data to investigate short-range atomic correlations, we establish the existence of an instantaneous, local orthorhombic structural distortion attributable to nematic fluctuations that persists well into the high-temperature tetragonal phase, at least up to 300 K and likely to significantly higher temperatures. This short-range orthorhombic distortion is correlated over a length scale of about 1 nm at 300 K and grows to several nm as the temperature is lowered toward the long-range structural transition temperature. In the low-temperature nematic state, the local instantaneous structure exhibits an enhanced orthorhombic distortion relative to the average structure with a typical relaxation length of 3 nm. The quantitative characterization of these orthorhombic fluctuations sheds light on nematicity in this canonical iron-based superconductor

Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression.

Retinoblastoma is an aggressive childhood cancer of the developing retina that initiates by biallelic RB1 gene inactivation. Tumor progression in retinoblastoma is driven by epigenetics, as retinoblastoma genomes are stable, but the mechanism(s) that drive these epigenetic changes remain unknown. Lymphoid-specific helicase (HELLS) protein is an epigenetic modifier directly regulated by the RB/E2F pathway. In this study, we used novel genetically engineered mouse models to investigate the role of HELLS during retinal development and tumorigenesis. Our results indicate that Hells-null retinal progenitor cells divide, undergo cell-fate specification, and give rise to fully laminated retinae with minor bipolar cells defects, but normal retinal function. Despite the apparent nonessential role of HELLS in retinal development, failure to transcriptionally repress Hells during retinal terminal differentiation due to retinoblastoma (RB) family loss significantly contributes to retinal tumorigenesis. Loss of HELLS drastically reduced ectopic division of differentiating cells in Rb1/p107-null retinae, significantly decreased the incidence of retinoblastoma, delayed tumor progression, and increased overall survival. Despite its role in heterochromatin formation, we found no evidence that Hells loss directly affected chromatin accessibility in the retina but functioned as transcriptional co-activator of E2F3, decreasing expression of cell cycle genes. We propose that HELLS is a critical downstream mediator of E2F-dependent ectopic proliferation in RB-null retinae. Together with the nontoxic effect of HELLS loss in the developing retina, our results suggest that HELLS and its downstream pathways could serve as potential therapeutic targets for retinoblastoma

The Individual and Collective Effects of Exact Exchange and Dispersion Interactions on the Ab Initio Structure of Liquid Water

In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local vdW/dispersion interactions, via a fully self-consistent density-dependent dispersion correction, and approximate nuclear quantum effects (aNQE), via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx, vdW, and aNQE as resulting from a large-scale AIMD simulation of (H$_2$O)$_{128}$ at the PBE0+vdW level of theory, significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, $S_{\rm OO}(Q)$, and corresponding oxygen-oxygen radial distribution function, $g_{\rm OO}(r)$, that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment as demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of the PBE0 hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions

Atemporal diagrams for quantum circuits

A system of diagrams is introduced that allows the representation of various elements of a quantum circuit, including measurements, in a form which makes no reference to time (hence ``atemporal''). It can be used to relate quantum dynamical properties to those of entangled states (map-state duality), and suggests useful analogies, such as the inverse of an entangled ket. Diagrams clarify the role of channel kets, transition operators, dynamical operators (matrices), and Kraus rank for noisy quantum channels. Positive (semidefinite) operators are represented by diagrams with a symmetry that aids in understanding their connection with completely positive maps. The diagrams are used to analyze standard teleportation and dense coding, and for a careful study of unambiguous (conclusive) teleportation. A simple diagrammatic argument shows that a Kraus rank of 3 is impossible for a one-qubit channel modeled using a one-qubit environment in a mixed state.Comment: Minor changes in references. Latex 32 pages, 13 figures in text using PSTrick

Deterministic and Unambiguous Dense Coding

Optimal dense coding using a partially-entangled pure state of Schmidt rank $\bar D$ and a noiseless quantum channel of dimension $D$ is studied both in the deterministic case where at most $L_d$ messages can be transmitted with perfect fidelity, and in the unambiguous case where when the protocol succeeds (probability $\tau_x$) Bob knows for sure that Alice sent message $x$, and when it fails (probability $1-\tau_x$) he knows it has failed. Alice is allowed any single-shot (one use) encoding procedure, and Bob any single-shot measurement. For $\bar D\leq D$ a bound is obtained for $L_d$ in terms of the largest Schmidt coefficient of the entangled state, and is compared with published results by Mozes et al. For $\bar D > D$ it is shown that $L_d$ is strictly less than $D^2$ unless $\bar D$ is an integer multiple of $D$, in which case uniform (maximal) entanglement is not needed to achieve the optimal protocol. The unambiguous case is studied for $\bar D \leq D$, assuming $\tau_x>0$ for a set of $\bar D D$ messages, and a bound is obtained for the average \lgl1/\tau\rgl. A bound on the average \lgl\tau\rgl requires an additional assumption of encoding by isometries (unitaries when $\bar D=D$) that are orthogonal for different messages. Both bounds are saturated when $\tau_x$ is a constant independent of $x$, by a protocol based on one-shot entanglement concentration. For $\bar D > D$ it is shown that (at least) $D^2$ messages can be sent unambiguously. Whether unitary (isometric) encoding suffices for optimal protocols remains a major unanswered question, both for our work and for previous studies of dense coding using partially-entangled states, including noisy (mixed) states.Comment: Short new section VII added. Latex 23 pages, 1 PSTricks figure in tex

Fluorescence Fluctuation Spectroscopy Enables Quantitative Imaging of Single mRNAs in Living Cells

AbstractImaging mRNA with single-molecule sensitivity in live cells has become an indispensable tool for quantitatively studying RNA biology. The MS2 system has been extensively used due to its unique simplicity and sensitivity. However, the levels of the coat protein needed for consistent labeling of mRNAs limits the sensitivity and quantitation of this technology. Here, we applied fluorescence fluctuation spectroscopy to quantitatively characterize and enhance the MS2 system. Surprisingly, we found that a high fluorescence background resulted from inefficient dimerization of fluorescent protein (FP)-labeled MS2 coat protein (MCP). To mitigate this problem, we used a single-chain tandem dimer of MCP (tdMCP) that significantly increased the uniformity and sensitivity of mRNA labeling. Furthermore, we characterized the PP7 coat protein and the binding to its respective RNA stem loop. We conclude that the PP7 system performs better for RNA labeling. Finally, we used these improvements to study endogenous β-actin mRNA, which has 24xMS2 binding sites inserted into the 3′ untranslated region. The tdMCP-FP allowed uniform RNA labeling and provided quantitative measurements of endogenous mRNA concentration and diffusion. This work provides a foundation for quantitative spectroscopy and imaging of single mRNAs directly in live cells

Gradual Enhancement of Stripe-Type Antiferromagnetism in Spin Ladder Material BaFe2_2S3_3 Under Pressure

We report pressure-dependent neutron diffraction and muon spin relaxation/rotation measurements combined with first-principles calculations to investigate the structural, magnetic, and electronic properties of BaFe$_2$S$_3$ under pressure. The experimental results reveal a gradual enhancement of the stripe-type ordering temperature with increasing pressure up to 2.6 GPa and no observable change in the size of the ordered moment. The ab initio calculations suggest that the magnetism is highly sensitive to the Fe-S bond lengths and angles, clarifying discrepancies with previously published results. In contrast to our experimental observations, the calculations predict a monotonic reduction of the ordered moment with pressure. We suggest that the robustness of the stripe-type antiferromagnetism is due to strong electron correlations not fully considered in the calculations

Glow-Discharge Enhanced Permeation of Oxygen Through Silver

The permeation of oxygen through Ag0.05Zr over the temperature range of 300-650°C under glow-discharge conditions has been studied and compared to the permeation of thermally dissociated molecular oxygen. A low-energy dc glow-discharge in O2 has been employed which produced approximately 10% atoms. The permeation rate during the glow discharge was found to be much higher (a factor of ∼10) than without the glow discharge. The small fraction of oxygen atoms generated appears to dominate the permeation because of much higher solution probabilities. Below 500°C, the activation energy for the permeation with glow discharge was found to be 15.5 kcal/mol compared to 22.0 kcal/mol without glow discharge (molecular oxygen). Above 500°C, the enhanced permeation with glow discharge gradually diminishes with increasing temperature and approaches that observed without the glow discharge at high temperature; the reason for this is primarily because of the thermal instability of the supersaturated high-pressure interface where atoms recombine and desorb back into the gas phase

Efficient Energy Transfer in Light-Harvesting Systems, II: Quantum-Classical Comparison, Flux Network, and Robustness Analysis

Following the calculation of optimal energy transfer in thermal environment in our first paper (Wu et al., New J. Phys., 2010, 12, 105012), full quantum dynamics and leading-order `classical' hopping kinetics are compared in the seven-site Fenna-Matthews-Olson (FMO) protein complex. The difference between these two dynamic descriptions is due to higher-order quantum corrections. Two thermal bath models, classical white noise (the Haken-Strobl-Reineker model) and quantum Debye model, are considered. In the seven-site FMO model, we observe that higher-order corrections lead to negligible changes in the trapping time or in energy transfer efficiency around the optimal and physiological conditions (2% in the HSR model and 0.1% in the quantum Debye model for the initial site at BChl 1). However, using the concept of integrated flux, we can identify significant differences in branching probabilities of the energy transfer network between hopping kinetics and quantum dynamics (26% in the HSR model and 32% in the quantum Debye model for the initial site at BChl 1). This observation indicates that the quantum coherence can significantly change the distribution of energy transfer pathways in the flux network with the efficiency nearly the same. The quantum-classical comparison of the average trapping time with the removal of the bottleneck site, BChl 4, demonstrates the robustness of the efficient energy transfer by the mechanism of multi-site quantum coherence. To reconcile with the latest eight-site FMO model, the quantum-classical comparison with the flux network analysis is summarized in the appendix. The eight-site FMO model yields similar trapping time and network structure as the seven-site FMO model but leads to a more disperse distribution of energy transfer pathways.Comment: submitted to Journal of Chemical Physic