arXiv subjects

Xin Zhou

Publications and source records attributed to Xin Zhou.

At least 415 records · Page 23Linked to original sources

arXiv2016

Expanding molecular bubble surrounding Tycho's supernova remnant (SN 1572) observed with IRAM 30 m telescope: evidence for a single-degenerate progenitor

Whether the progenitors of SNe Ia are single-degenerate or double-degenerate white dwarf (WD) systems is a highly debated topic. To address the origin of the Type Ia Tycho's supernova remnant (SNR), SN 1572, we have carried out a $^{12}$CO J=2-1 mapping and a 3-mm line survey toward the remnant using the IRAM 30 m telescope. We show that Tycho is surrounded by a clumpy molecular bubble at a local standard of rest velocity of $\sim 61$ km s$^{-1}$ which expands at a speed of $\sim 4.5$ km s$^{-1}$ and has a mass of $\sim 220$ M$_\odot$ (at the distance of 2.5 kpc). Enhanced $^{12}$CO J=2-1 line emission relative to $^{12}$CO J=1-0 emission and possible line broadenings (in velocity range $-64$ to $-60$ km s$^{-1}$) are found at the northeastern boundary of the SNR, where the shell is deformed and decelerated. These features, combined with the morphological correspondence between the expanding molecular bubble and Tycho, suggest that the SNR is associated with the bubble at the velocity range $-66$ to $-57$ km s$^{-1}$. The most plausible origin for the expanding bubble is the fast outflow (with velocity of hundreds km s$^{-1}$) driven from the vicinity of a WD as it accreted matter from a nondegenerate companion star. The SNR has been expanding in the low-density wind-blown bubble, and the shock wave has just reached the molecular cavity wall. The SNR has been expanding in the low-density wind-blown bubble, and the shock wave has just reached the molecular cavity wall. This is the first unambiguous detection of an expanding bubble driven by the progenitor of a Type-Ia SNR, which constitutes evidence for a single-degenerate progenitor for this SN Ia.

astro-ph.GA↗

arXiv2016

Manipulating Fock states of a harmonic oscillator while preserving its linearity

We present a new scheme for controlling the quantum state of a harmonic oscillator by coupling it to an anharmonic multilevel system (MLS) with first to second excited state transition frequency on-resonance with the oscillator. In this scheme that we call "ef-resonant", the spurious oscillator Kerr non-linearity inherited from the MLS is very small, while its Fock states can still be selectively addressed via an MLS transition at a frequency that depends on the number of photons. We implement this concept in a circuit-QED setup with a microwave 3D cavity (the oscillator, with frequency 6.4 GHz and quality factor QO=2E-6) embedding a frequency tunable transmon qubit (the MLS). We characterize the system spectroscopically and demonstrate selective addressing of Fock states and a Kerr non-linearity below 350 Hz. At times much longer than the transmon coherence times, a non-linear cavity response with driving power is also observed and explained.

quant-ph↗

arXiv2016

Sweeping out 3-manifold of positive Ricci curvature by short 1-cycles via estimates of min-max surfaces

We prove that given a three manifold with an arbitrary metric $(M^3, g)$ of positive Ricci curvature, there exists a sweepout of $M$ by surfaces of genus $\leq 3$ and areas bounded by $C vol(M^3, g)^{2/3}$. We use this result to construct a sweepout of $M$ by 1-cycles of length at most $C vol(M^3, g)^{1/3}$. The sweepout of surfaces is generated from a min-max minimal surface. If further assuming a positive scalar curvature lower bound, we can get a diameter upper bound for the min-max surface.

math.DG↗

arXiv2016

Existence of minimal surfaces of arbitrary large Morse index

We show that in a closed 3-manifold with a generic metric of positive Ricci curvature, there are minimal surfaces of arbitrary large Morse index, which partially confirms a conjecture by F. Marques and A. Neves. We prove this by analyzing the lamination structure of the limit of minimal surfaces with bounded Morse index.

math.DG↗

arXiv2016

Proofreading of DNA Polymerase: a new kinetic model with higher-order terminal effects

The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in 1970s' and the basic idea was widely accepted by later models. However, all these models did not systematically and rigorously investigate the dominant factor on DNAP fidelity, i.e, the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.

q-bio.SC↗

arXiv2016

An Outer Arm in the Second Galactic Quadrant: Structure

The lack of arm tracers, especially the remote tracers, is one of the most difficult problems preventing us from studying the structure of the Milky Way. Fortunately, with its high-sensitivity CO survey, the Milky Way Imaging Scroll Painting (MWISP) project offers such an opportunity. Since completing about one-third of its mission, an area of l=[100,150] deg, b=[-3,5] deg has nearly been covered. The Outer arm of the Milky Way first clearly revealed its shape in the second galactic quadrant in the form of molecular gas --- this is the first time that the Outer arm has been reported in such a large-scale mapping of molecular gas. Using the 115 GHz 12CO(1-0) data of MWISP at the LSR velocity ~= [-100,-60] km s^-1 and in the area mentioned above, we have detected 481 molecular clouds in total, and among them 332 (about 69\%) are newly detected and 457 probably belong to the Outer arm. The total mass of the detected Outer arm clouds is ~ 3.1*10^6 M_sun. Assuming that the spiral arm is a logarithmic spiral, the pitch angle is fitted as ~ 13.1 deg. Besides combining both the CO data from MWISP and the 21 cm HI data from the Canadian Galactic Plane Survey (CGPS), the gas distribution, warp, and thickness of the Outer arm are also studied.

astro-ph.GA↗

arXiv2016

PT Symmetry Breaking and Nonlinear Optical Isolation in Coupled Microcavities

We perform a theoretical study of nonlinear optical isolator devices based on coupled microcavities with gain and loss. Using coupled-mode theory, we derive a correspondence between the boundary of asymptotic stability in the nonlinear regime, where gain saturation is present, and the PT-breaking transition in the underlying linear system. For zero detuning and weak input intensity, the onset of optical isolation can be rigorously derived, and corresponds precisely to the PT transition point. When the couplings to the external ports are unequal, the isolation ratio exhibits an abrupt jump at the transition point, determined by the ratio of the couplings. This could be exploited to realize an actively controlled nonlinear optical isolator, in which strong optical isolation can be switched on or off using tiny variations in the inter-resonator separation.

physics.optics↗

arXiv2015

Equilibrium sampling by re-weighting non-equilibrium simulation trajectories

With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy barriers. The applied non-equilibrium process in simulations could enhance the transitions among these conformational regions, and the associated non-equilibrium effects can be removed by employing the Jarzynski equality (JE), then the global equilibrium distribution can be reproduced. However, the original JE requires the initial distribution of the non-equilibrium process is equilibrium, which largely limits the application of the non-equilibrium method in equilibrium sampling. By extending the previous method, the reweighted ensemble dynamics (RED), which re-weights many equilibrium simulation trajectories from arbitrary initial distribution to reproduce the global equilibrium, to non-equilibrium simulations, we present a method, named as re-weighted non-equilibrium ensemble dynamics (RNED), to generalize the JE in the non-equilibrium trajectories started from an arbitrary initial distribution, thus provide an efficient method to reproduce the equilibrium distribution based on multiple independent (short) non-equilibrium trajectories. We have illustrated the validity of the RNED in a one-dimensional toy model and in a Lennard-Jones system to detect the liquid-solid phase coexistence.

cond-mat.soft↗

arXiv2015

Jarzynski matrix equality: calculating free energy difference by non-equilibrium simulations with an arbitrary initial distribution

The Jarzynski equality (JE), which relates works of non-equilibrium trajectories to the free energy difference of the initial and final states of the non-equilibrium process, provides an efficient way to calculate free energies of systems in simulations and experiments. However, wider applications of the JE are limited by the requirement that the initial distribution of non-equilibrium trajectories must be equilibrium. Here we extend the JE to a matrix form, the Jarzynski matrix equality (JME), which transforms the free energies of metastable conformational regions in the initial system to that of final one. Therefore, we can calculate the free energies from non-equilibrium trajectories which started from an arbitrary initial distribution. We demonstrate the application of the JME in toy models, Lennard-Jones fluids, and polymer chain models, show its good efficiency in calculation of free energy with a satisfactory accuracy. The JME extends applications of the non-equilibrium method in estimate of free energy in complex system where the initial global equilibrium is difficult to reach.

cond-mat.soft↗

arXiv2015

Plasmonic Crystal Cavity on Single-Mode Optical Fiber End Facet for Label-Free Biosensing

All surface plasmon resonance (SPR) devices on single-mode optical fibers' (SMF) end facets, as reported up to date, are limited by severely broad and shallow resonance spectra. The consequent poor performance when they are used as refractive index sensors, together with the challenge of nanofabrication on fiber end facets, has prohibited the development of such devices for label-free biosensing. Meanwhile, the planewave coupled, multimode fiber and fiber sidewall SPR counterparts are extensively employed for label-free biosensing. In this paper, we report the design, fabrication and characterization of a plasmonic crystal cavity on a SMF end facet, which shows high performance label-free sensing capability that comes from a steep cavity resonance near the plasmonic bandedge. The experimental figure-of-merit is 68 RIU^-1, which is over twenty times improvement to previous reports. The refractive index detection limit is 3.5*10^-6 RIU at 1 s integration time. We also describe a novel glue-and-strip process to transfer gold nano structures onto fiber end facets.

physics.optics↗

arXiv2015

On The Existence of Min-Max Minimal Surface of Genus $g\geq 2$

In this paper, we build up a min-max theory for minimal surfaces using sweepouts of surfaces of genus $g\geq 2$. We develop a direct variational methods similar to the proof of the famous Plateau problem by J. Douglas and T. Rado. As a result, we show that the min-max value for the area functional can be achieved by a bubble tree limit consisting of branched genus-$g$ minimal surfaces with nodes, and possibly finitely many branched minimal spheres. We also prove a Colding-Minicozzi type strong convergence theorem similar to the classical mountain pass lemma. Our results extend the min-max theory developed by Colding-Minicozzi and the author to all genera.

math.DG↗

arXiv2015

Entropy of closed surfaces and min-max theory

Entropy is a natural geometric quantity measuring the complexity of a surface embedded in $\mathbb{R}^3$. For dynamical reasons relating to mean curvature flow, Colding-Ilmanen-Minicozzi-White conjectured that the entropy of any closed surface is at least that of the self-shrinking two-sphere. We prove this conjecture for all closed embedded $2$-spheres. Assuming a conjectural Morse index bound (announced recently by Marques-Neves), we can improve the result to apply to all closed embedded surfaces that are not tori. Our results can be thought of as the parabolic analog to the Willmore conjecture and our argument is analogous in many ways to that of Marques-Neves on the Willmore problem. The main tool is the min-max theory applied to the Gaussian area functional in $\mathbb{R}^3$ which we also establish. To any closed surface in $\mathbb{R}^3$ we associate a four parameter canonical family of surfaces and run a min-max procedure. The key step is ruling out the min-max sequence approaching a self-shrinking plane, and we accomplish this with a degree argument. To establish the min-max theory for $\mathbb{R}^3$ with Gaussian weight, the crucial ingredient is a tightening map that decreases the mass of non-stationary varifolds (with respect to the Gaussian metric of $\mathbb{R}^3$) in a continuous manner.

math.DG↗

arXiv2015

Residual Weighted Learning for Estimating Individualized Treatment Rules

Personalized medicine has received increasing attention among statisticians, computer scientists, and clinical practitioners. A major component of personalized medicine is the estimation of individualized treatment rules (ITRs). Recently, Zhao et al. (2012) proposed outcome weighted learning (OWL) to construct ITRs that directly optimize the clinical outcome. Although OWL opens the door to introducing machine learning techniques to optimal treatment regimes, it still has some problems in performance. In this article, we propose a general framework, called Residual Weighted Learning (RWL), to improve finite sample performance. Unlike OWL which weights misclassification errors by clinical outcomes, RWL weights these errors by residuals of the outcome from a regression fit on clinical covariates excluding treatment assignment. We utilize the smoothed ramp loss function in RWL, and provide a difference of convex (d.c.) algorithm to solve the corresponding non-convex optimization problem. By estimating residuals with linear models or generalized linear models, RWL can effectively deal with different types of outcomes, such as continuous, binary and count outcomes. We also propose variable selection methods for linear and nonlinear rules, respectively, to further improve the performance. We show that the resulting estimator of the treatment rule is consistent. We further obtain a rate of convergence for the difference between the expected outcome using the estimated ITR and that of the optimal treatment rule. The performance of the proposed RWL methods is illustrated in simulation studies and in an analysis of cystic fibrosis clinical trial data.

stat.ME↗

arXiv2015

On the free boundary min-max geodesics

Given a Riemannian manifold and a closed submanifold, we find a geodesic segment with free boundary on the given submanifold. This is a corollary of the min-max theory which we develop in this article for the free boundary variational problem. In particular, we develop a modified Birkhoff curve shortening process to achieve a strong "Colding-Minicozzi" type min-max approximation result.

math.DG↗

arXiv2015

Reweighted ensemble dynamics simulations: theory, improvement, and application

Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provides schemes on selection of basis functions, determination of free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enable to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.

cond-mat.stat-mech↗

arXiv2015

Optimization of coarse-grained models: matching probability density in conformational space

Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium values of sufficient physical quantities of its AA model, which requires to match the equilibrium probability density of the CG model to that of the AA model in conformational space. The present work proposes for constructing effective CG models a novel methodology that aims at minimizing the distance between CG model and AA model. The distance is defined as a functional of conformational probability densities in CG and AA models and further expanded by ensemble averages of a set of sufficient and independent basis functions. An orthogonalization strategy is adopted to get the independent basis functions from sufficiently preselected interesting physical quantities of the system. Two variational methods are developed to optimize parameters of effective CG force field by minimizing the functional of probability densities, are then generalized so that the CG model also reproduce the pressure of AA model. The general CG framework is verified in constructing one-site CG water from TIP3P water model.

cond-mat.stat-mech↗

arXiv2015

The Metal-enriched Thermal Composite Supernova Remnant Kesteven 41 (G337.8-0.1) in a Molecular Environment

The physical nature of thermal composite supernova remnants (SNRs) remains controversial. We have revisited the archival XMM-Newton and Chandra data of the thermal composite SNR Kesteven 41 (Kes 41 or G337.8-0.1) and performed a millimeter observation toward this source in the $^{12}$CO, $^{13}$CO, and C$^{18}$O lines. The X-ray emission, mainly concentrated toward the southwestern part of the SNR, is characterized by distinct S and Ar He-like lines in the spectra. The X-ray spectra can be fitted with an absorbed nonequilibrium ionization collisional plasma model at a temperature of 1.3-2.6 keV and an ionization timescale of 0.1-1.2$\times$10$^{12}$ cm$^{-3}$ s. The metal species S and Ar are overabundant, with 1.2-2.7 and 1.3-3.8 solar abundances, respectively, which strongly indicate the presence of a substantial ejecta component in the X-ray-emitting plasma of this SNR. Kes 41 is found to be associated with a giant molecular cloud (MC) at a systemic local standard of rest velocity of -50 km s$^{-1}$ and confined in a cavity delineated by a northern molecular shell, a western concave MC that features a discernible shell, and an HI cloud seen toward the southeast of the SNR. The birth of the SNR in a preexisting molecular cavity implies a mass of $\gtrsim$18 M$_{\odot}$ for the progenitor if it was not in a binary system. Thermal conduction and cloudlet evaporation seem to be feasible mechanisms to interpret the X-ray thermal composite morphology, and the scenario of gas reheating by the shock reflected from the cavity wall is quantitatively consistent with the observations. An updated list of thermal composite SNRs is also presented in this paper.

astro-ph.HE↗

arXiv2015

Asymptotic Weights of Syzygies of Toric Varieties

The purpose of the paper is to give a sharp asymptotic description of the weights that appear in the syzygies of a toric variety. We prove that as the positivity of the embedding increases, in any strand of syzygies, torus weights after normalization stabilize to the same fixed shape that we explicitly specify.

math.AG↗