A simple variational approach to the quantum Frenkel-Kontorova model

We present a simple and complete variational approach to the one-dimensional quantum Frenkel-Kontorova model. Dirac's time-dependent variational principle is adopted together with a Hatree-type many-body trial wavefunction for the atoms. The single-particle state is assumed to have the Jackiw-Kerman form. We obtain an effective classical Hamiltonian for the system which is simple enough for a complete numerical solution for the static ground state of the model. Numerical results show that our simple approach captures the essence of the quantum effects first observed in quantum Monte Carlo studies.Comment: 12 pages, 2 figure

Computational repurposing of oncology drugs through off‐target drug binding interactions from pharmacological databases

PurposeSystematic repurposing of approved medicines for another indication may accelerate drug development in oncology. We present a strategy combining biomarker testing with drug repurposing to identify new treatments for patients with advanced cancer.MethodsTumours were sequenced with the Illumina TruSight Oncology 500 (TSO-500) platform or the FoundationOne CDx panel. Mutations were screened by two medical oncologists and pathogenic mutations were categorised referencing literature. Variants of unknown significance were classified as potentially pathogenic using plausible mechanisms and computational prediction of pathogenicity. Gain of function (GOF) mutations were evaluated through repurposing databases Probe Miner (PM), Broad Institute Drug Repurposing Hub (Broad Institute DRH) and TOPOGRAPH. GOF mutations were repurposing events if identified in PM, not indexed in TOPOGRAPH and excluding mutations with a known Food and Drug Administration (FDA)-approved biomarker. The computational repurposing approach was validated by evaluating its ability to identify FDA-approved biomarkers. The total repurposable genome was identified by evaluating all possible gene-FDA drug-approved combinations in the PM dataset.ResultsThe computational repurposing approach was accurate at identifying FDA therapies with known biomarkers (94%). Using next-generation sequencing molecular reports (n = 94), a meaningful percentage of patients (14%) could have an off-label therapeutic identified. The frequency of theoretical drug repurposing events in The Cancer Genome Atlas pan-cancer dataset was 73% of the samples in the cohort.ConclusionA computational drug repurposing approach may assist in identifying novel repurposing events in cancer patients with no access to standard therapies. Further validation is needed to confirm a precision oncology approach using drug repurposing. Repurposing identified Food and Drug Administration-approved drug-biomarker combinations with high sensitivity and specificity. In a real-world dataset, repurposing identified novel drug-biomarker combinations in patients who were ineligible for standard therapies or biomarker-matched trials. Preliminary functional validation was demonstrated for two drug-biomarker combinations. Using The Cancer Genome Atlas data, the potential scope of repurposing was identified. imag

Controlling Cherenkov angles with resonance transition radiation

Cherenkov radiation provides a valuable way to identify high energy particles in a wide momentum range, through the relation between the particle velocity and the Cherenkov angle. However, since the Cherenkov angle depends only on material's permittivity, the material unavoidably sets a fundamental limit to the momentum coverage and sensitivity of Cherenkov detectors. For example, Ring Imaging Cherenkov detectors must employ materials transparent to the frequency of interest as well as possessing permittivities close to unity to identify particles in the multi GeV range, and thus are often limited to large gas chambers. It would be extremely important albeit challenging to lift this fundamental limit and control Cherenkov angles as preferred. Here we propose a new mechanism that uses constructive interference of resonance transition radiation from photonic crystals to generate both forward and backward Cherenkov radiation. This mechanism can control Cherenkov angles in a flexible way with high sensitivity to any desired range of velocities. Photonic crystals thus overcome the severe material limit for Cherenkov detectors, enabling the use of transparent materials with arbitrary values of permittivity, and provide a promising option suited for identification of particles at high energy with enhanced sensitivity.Comment: There are 16 pages and 4 figures for the manuscript. Supplementary information with 18 pages and 5 figures, appended at the end of the file with the manuscript. Source files in Word format converted to PDF. Submitted to Nature Physic

A framework for automated enrichment of functionally significant inverted repeats in whole genomes

<p>Abstract</p> <p>Background</p> <p>RNA transcripts from genomic sequences showing dyad symmetry typically adopt hairpin-like, cloverleaf, or similar structures that act as recognition sites for proteins. Such structures often are the precursors of non-coding RNA (ncRNA) sequences like microRNA (miRNA) and small-interfering RNA (siRNA) that have recently garnered more functional significance than in the past. Genomic DNA contains hundreds of thousands of such inverted repeats (IRs) with varying degrees of symmetry. But by collecting statistically significant information from a known set of ncRNA, we can sort these IRs into those that are likely to be functional.</p> <p>Results</p> <p>A novel method was developed to scan genomic DNA for partially symmetric inverted repeats and the resulting set was further refined to match miRNA precursors (pre-miRNA) with respect to their density of symmetry, statistical probability of the symmetry, length of stems in the predicted hairpin secondary structure, and the GC content of the stems. This method was applied on the <it>Arabidopsis thaliana</it> genome and validated against the set of 190 known Arabidopsis pre-miRNA in the miRBase database. A preliminary scan for IRs identified 186 of the known pre-miRNA but with 714700 pre-miRNA candidates. This large number of IRs was further refined to 483908 candidates with 183 pre-miRNA identified and further still to 165371 candidates with 171 pre-miRNA identified (i.e. with 90% of the known pre-miRNA retained).</p> <p>Conclusions</p> <p>165371 candidates for potentially functional miRNA is still too large a set to warrant wet lab analyses, such as northern blotting, on all of them. Hence additional filters are needed to further refine the number of candidates while still retaining most of the known miRNA. These include detection of promoters and terminators, homology analyses, location of candidate relative to coding regions, and better secondary structure prediction algorithms. The software developed is designed to easily accommodate such additional filters with a minimal experience in Perl.</p

Amplitude Analysis of the Decays η′→π+π−π0\eta^\prime \rightarrow \pi^+\pi^-\pi^0 and η′→π0π0π0\eta^\prime \rightarrow \pi^0\pi^0\pi^0

Based on a sample of $1.31 \times 10^9$ $J/\psi$ events collected with the BESIII detector, an amplitude analysis of the isospin-violating decays $\eta^\prime \rightarrow \pi^+\pi^-\pi^0$ and $\eta^\prime \rightarrow \pi^0\pi^0\pi^0$ is performed. A significant $P$-wave contribution from $\eta^\prime \rightarrow \rho^{\pm} \pi^{\mp}$ is observed for the first time in $\eta^\prime \rightarrow \pi^+\pi^-\pi^0$. The branching fraction is determined to be ${\mathcal B}(\eta^\prime \rightarrow \rho^{\pm}\pi^{\mp})=(7.44\pm0.60\pm1.26\pm1.84)\times 10^{-4}$, where the first uncertainty is statistical, the second systematic, and the third model dependent. In addition to the nonresonant $S$-wave component, there is a significant $\sigma$ meson component. The branching fractions of the combined $S$-wave components are determined to be ${\mathcal B}(\eta^\prime \rightarrow \pi^+\pi^-\pi^0)_S=(37.63\pm0.77\pm2.22\pm4.48)\times 10^{-4}$ and ${\mathcal B}(\eta^\prime \rightarrow \pi^0\pi^0\pi^0)=(35.22\pm0.82\pm2.54)\times 10^{-4}$, respectively. The latter one is consistent with previous BESIII measurements.Comment: 7 pages, 3 figure

Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure

Galaxy Occupation Statistics of Dark Matter Haloes: Observational Results

We study the occupation statistics of galaxies in dark matter haloes using galaxy groups identified from the 2-degree Field Galaxy Redshift Survey with the halo-based group finder of Yang et al. The occupation distribution is considered separately for early and late type galaxies, as well as in terms of central and satellite galaxies. The mean luminosity of the central galaxies scales with halo mass approximately as $L_c\propto M^{2/3}$ for haloes with masses M<10^{13}h^{-1}\msun, and as $L_c\propto M^{1/4}$ for more massive haloes. The characteristic mass of 10^{13} h^{-1} \Msun is consistent with the mass scale where galaxy formation models suggest a transition from efficient to inefficient cooling. Another characteristic halo mass scale, M\sim 10^{11} h^{-1}\msun, which cannot be probed directly by our groups, is inferred from the conditional luminosity function (CLF) that matches the observed galaxy luminosity function and clustering. For a halo of given mass, the distribution of $L_c$ is rather narrow. The satellite galaxies are found to follow a Poissonian number distribution. The central galaxies in low-mass haloes are mostly late type galaxies, while those in massive haloes are almost all early types. We also measure the CLF of galaxies in haloes of given mass. Over the mass range that can be reliably probed with the present data (13.3 \lta {\rm log}[M/(h^{-1}\Msun)] \lta 14.7), the CLF is reasonably well fit by a Schechter function. Contrary to recent claims based on semi-analytical models of galaxy formation, the presence of central galaxies does not show up as a strong peak at the bright end of the CLF. (Abridged)Comment: 17 pages, 11 figures, revised version. Two figures added. A few small changes. Main conclusions remain unchange

Critical Review of Theoretical Models for Anomalous Effects (Cold Fusion) in Deuterated Metals

We briefly summarize the reported anomalous effects in deuterated metals at ambient temperature, commonly known as "Cold Fusion" (CF), with an emphasis on important experiments as well as the theoretical basis for the opposition to interpreting them as cold fusion. Then we critically examine more than 25 theoretical models for CF, including unusual nuclear and exotic chemical hypotheses. We conclude that they do not explain the data.Comment: 51 pages, 4 Figure

Internal kinematics of groups of galaxies in the Sloan Digital Sky Survey data release 7

We present measurements of the velocity dispersion profile (VDP) for galaxy groups in the final data release of the Sloan Digital Sky Survey (SDSS). For groups of given mass we estimate the redshift-space cross-correlation function (CCF) with respect to a reference galaxy sample, xi(r_p, pi), the projected CCF, w_p(r_p), and the real-space CCF, xi(r). The VDP is then extracted from the redshift distortion in xi(r_p, pi), by comparing xi(r_p, pi) with xi(r). We find that the velocity dispersion (VD) within virial radius (R_200) shows a roughly flat profile, with a slight increase at radii below ~0.3 R_200 for high mass systems. The average VD within the virial radius, sigma_v, is a strongly increasing function of central galaxy mass. We apply the same methodology to N-body simulations with the concordance Lambda cold dark matter cosmology but different values of the density fluctuation parameter sigma_8, and we compare the results to the SDSS results. We show that the sigma_v-M_* relation from the data provides stringent constraints on both sigma_8 and sigma_ms, the dispersion in log M_* of central galaxies at fixed halo mass. Our best-fitting model suggests sigma_8 = 0.86 +/- 0.03 and sigma_ms = 0.16 +/- 0.03. The slightly higher value of sigma_8 compared to the WMAP7 result might be due to a smaller matter density parameter assumed in our simulations. Our VD measurements also provide a direct measure of the dark matter halo mass for central galaxies of different luminosities and masses, in good agreement with the results obtained by Mandelbaum et al. (2006) from stacking the gravitational lensing signals of the SDSS galaxies.Comment: 17 pages, 10 figures, 1 table, accepted for publication in ApJ, text slightly changed, abstract substantially shortened, two new panels added to Figs. 2 and 3 showing w_p and VDP as functions of r_p/R_200 instead of r_