Facilitated movement of inertial Brownian motors driven by a load under an asymmetric potential

Based on recent work [L. Machura, M. Kostur, P. Talkner, J. Luczka, and P. Hanggi, Phys. Rev. Lett. 98, 040601 (2007)], we extend the study of inertial Brownian motors to the case of an asymmetric potential. It is found that some transport phenomena appear in the presence of an asymmetric potential. Within tailored parameter regimes, there exists two optimal values of the load at which the mean velocity takes its maximum, which means that a load can facilitate the transport in the two parameter regimes. In addition, the phenomenon of multiple current reversals can be observed when the load is increased.Comment: 7 pages, 3 figure

Nonsequential Double Ionization with Polarization-gated Pulses

We investigate laser-induced nonsequential double ionization by a polarization-gated laser pulse, constructed employing two counter-rotating circularly polarized few cycle pulses with a time delay $T_{d}$. We address the problem within a classical framework, and mimic the behavior of the quantum-mechanical electronic wave packet by means of an ensemble of classical electron trajectories. These trajectories are initially weighted with the quasi-static tunneling rate, and with suitably chosen distributions for the momentum components parallel and perpendicular to the laser-field polarization, in the temporal region for which it is nearly linearly polarized. We show that, if the time delay $T_{d}$ is of the order of the pulse length, the electron-momentum distributions, as functions of the parallel momentum components, are highly asymmetric and dependent on the carrier-envelope (CE) phase. As this delay is decreased, this asymmetry gradually vanishes. We explain this behavior in terms of the available phase space, the quasi-static tunneling rate and the recollision rate for the first electron, for different sets of trajectories. Our results show that polarization-gating technique may provide an efficient way to study the NSDI dynamics in the single-cycle limit, without employing few-cycle pulses.Comment: 17 pages, 6 figure

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

Since the read lengths of high throughput sequencing (HTS) technologies are short, de novo assembly which plays significant roles in many applications remains a great challenge. Most of the state-of-the-art approaches base on de Bruijn graph strategy and overlap-layout strategy. However, these approaches which depend on k-mers or read overlaps do not fully utilize information of paired-end and single-end reads when resolving branches. Since they treat all single-end reads with overlapped length larger than a fix threshold equally, they fail to use the more confident long overlapped reads for assembling and mix up with the relative short overlapped reads. Moreover, these approaches have not been special designed for handling tandem repeats (repeats occur adjacently in the genome) and they usually break down the contigs near the tandem repeats. We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds using paired-end reads and different read overlap size ranging from Omax to Omin to resolve the gaps and branches. By constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. When the correct extension cannot be determined, PERGA will try to extend the contig by all feasible extensions and determine the correct extension by using look-ahead approach. Many difficult-resolved branches are due to tandem repeats which are close in the genome. PERGA detects such different copies of the repeats to resolve the branches to make the extension much longer and more accurate. We evaluated PERGA on both Illumina real and simulated datasets ranging from small bacterial genomes to large human chromosome, and it constructed longer and more accurate contigs and scaffolds than other state-of-the-art assemblers. PERGA can be freely downloaded at https://github.com/hitbio/PERGA.published_or_final_versio

Persistence, extinction and spatio-temporal synchronization of SIRS cellular automata models

Spatially explicit models have been widely used in today's mathematical ecology and epidemiology to study persistence and extinction of populations as well as their spatial patterns. Here we extend the earlier work--static dispersal between neighbouring individuals to mobility of individuals as well as multi-patches environment. As is commonly found, the basic reproductive ratio is maximized for the evolutionary stable strategy (ESS) on diseases' persistence in mean-field theory. This has important implications, as it implies that for a wide range of parameters that infection rate will tend maximum. This is opposite with present results obtained in spatial explicit models that infection rate is limited by upper bound. We observe the emergence of trade-offs of extinction and persistence on the parameters of the infection period and infection rate and show the extinction time having a linear relationship with respect to system size. We further find that the higher mobility can pronouncedly promote the persistence of spread of epidemics, i.e., the phase transition occurs from extinction domain to persistence domain, and the spirals' wavelength increases as the mobility increasing and ultimately, it will saturate at a certain value. Furthermore, for multi-patches case, we find that the lower coupling strength leads to anti-phase oscillation of infected fraction, while higher coupling strength corresponds to in-phase oscillation.Comment: 12page

Geometric entanglement from matrix product state representations

An efficient scheme to compute the geometric entanglement per lattice site for quantum many-body systems on a periodic finite-size chain is proposed in the context of a tensor network algorithm based on the matrix product state representations. It is systematically tested for three prototypical critical quantum spin chains, which belong to the same Ising universality class. The simulation results lend strong support to the previous claim [Q.-Q. Shi, R. Or\'{u}s, J. O. Fj{\ae}restad, and H.-Q. Zhou, New J. Phys \textbf{12}, 025008 (2010); J.-M. St\'{e}phan, G. Misguich, and F. Alet, Phys. Rev. B \textbf{82}, 180406R (2010)] that the leading finite-size correction to the geometric entanglement per lattice site is universal, with its remarkable connection to the celebrated Affleck-Ludwig boundary entropy corresponding to a conformally invariant boundary condition.Comment: 4+ pages, 3 figure

Quality evaluation for measurements of wind field and turbulent fluxes from a UAV-based eddy covariance system

Instrumentation packages for eddy covariance (EC) measurements have been developed for unoccupied aerial vehicles (UAVs) to measure the turbulent fluxes of latent heat (LE), sensible heat (H), and CO2 (Fc) in the atmospheric boundary layer. This study aims to evaluate the performance of this UAV-based EC system. First, the measurement precision (1σ) of georeferenced wind was estimated to be 0.07 m s−1. Then, the effect of the calibration parameter and aerodynamic characteristics of the UAV on wind measurement was examined by conducting a set of calibration flights. The results showed that the calibration improved the quality of the measured wind field, and the influence of upwash and the leverage effect can be ignored in wind measurement by the UAV. Third, for the measurements of turbulent fluxes, the error caused by instrumental noise was estimated to be 0.03 µmolm-2s-1 for Fc, 0.02 W m−2 for H, and 0.08 W m−2 for LE. Fourth, data from the standard operational flights were used to assess the influence of resonance on the measurements and to test the sensitivity of the measurement under the variation (±30 %) in the calibration parameters around their optimum value. The results showed that the effect of resonance mainly affected the measurement of CO2 (∼5 %). The pitch offset angle (εθ) significantly affected the measurement of vertical wind (∼30 %) and turbulent fluxes (∼15 %). The heading offset angle (εψ) mainly affected the measurement of horizontal wind (∼15 %), and other calibration parameters had no significant effect on the measurements. The results lend confidence to the use of the UAV-based EC system and suggest future improvements for the optimization of the next-generation system.</p

Spatiotemporal complexity of a ratio-dependent predator-prey system

In this paper, we investigate the emergence of a ratio-dependent predator-prey system with Michaelis-Menten-type functional response and reaction-diffusion. We derive the conditions for Hopf, Turing and Wave bifurcation on a spatial domain. Furthermore, we present a theoretical analysis of evolutionary processes that involves organisms distribution and their interaction of spatially distributed population with local diffusion. The results of numerical simulations reveal that the typical dynamics of population density variation is the formation of isolated groups, i.e., stripelike or spotted or coexistence of both. Our study shows that the spatially extended model has not only more complex dynamic patterns in the space, but also chaos and spiral waves. It may help us better understand the dynamics of an aquatic community in a real marine environment.Comment: 6pages, revtex

Resonance and frequency-locking phenomena in spatially extended phytoplankton-zooplankton system with additive noise and periodic forces

In this paper, we present a spatial version of phytoplankton-zooplankton model that includes some important factors such as external periodic forces, noise, and diffusion processes. The spatially extended phytoplankton-zooplankton system is from the original study by Scheffer [M Scheffer, Fish and nutrients interplay determines algal biomass: a minimal model, Oikos \textbf{62} (1991) 271-282]. Our results show that the spatially extended system exhibit a resonant patterns and frequency-locking phenomena. The system also shows that the noise and the external periodic forces play a constructive role in the Scheffer's model: first, the noise can enhance the oscillation of phytoplankton species' density and format a large clusters in the space when the noise intensity is within certain interval. Second, the external periodic forces can induce 4:1 and 1:1 frequency-locking and spatially homogeneous oscillation phenomena to appear. Finally, the resonant patterns are observed in the system when the spatial noises and external periodic forces are both turned on. Moreover, we found that the 4:1 frequency-locking transform into 1:1 frequency-locking when the noise intensity increased. In addition to elucidating our results outside the domain of Turing instability, we provide further analysis of Turing linear stability with the help of the numerical calculation by using the Maple software. Significantly, oscillations are enhanced in the system when the noise term presents. These results indicate that the oceanic plankton bloom may partly due to interplay between the stochastic factors and external forces instead of deterministic factors. These results also may help us to understand the effects arising from undeniable subject to random fluctuations in oceanic plankton bloom.Comment: Some typos errors are proof, and some strong relate references are adde

H11-induced immunoprotection is predominantly linked to N-glycan moieties during Haemonchus contortus infection

Nematodes are one of the largest groups of animals on the planet. Many of them are major pathogens of humans, animals and plants, and cause destructive diseases and socioeconomic losses worldwide. Despite their adverse impacts on human health and agriculture, nematodes can be challenging to control, because anthelmintic treatments do not prevent re-infection, and excessive treatment has led to widespread drug resistance in nematode populations. Indeed, many nematode species of livestock animals have become resistant to almost all classes of anthelmintics used. Most efforts to develop commercial anti-nematode vaccines (native or recombinant) for use in animals and humans have not succeeded, although one effective (dead) vaccine (Barbervax) has been developed to protect animals against one of the most pathogenic parasites of livestock animals – Haemonchus contortus (the barber’s pole worm). This vaccine contains native molecules, called H11 and H-Gal-GP, derived from the intestine of this blood-feeding worm. In its native form, H11 alone consistently induces high levels (75-95%) of immunoprotection in animals against disease (haemonchosis), but recombinant forms thereof do not. Here, to test the hypothesis that post-translational modification (glycosylation) of H11 plays a crucial role in achieving such high immunoprotection, we explored the N-glycoproteome and N-glycome of H11 using the high-resolution mass spectrometry and assessed the roles of N-glycosylation in protective immunity against H. contortus. Our results showed conclusively that N-glycan moieties on H11 are the dominant immunogens, which induce high IgG serum antibody levels in immunised animals, and that anti-H11 IgG antibodies can confer specific, passive immunity in naïve animals. This work provides the first detailed account of the relevance and role of protein glycosylation in protective immunity against a parasitic nematode, with important implications for the design of vaccines against metazoan parasites.Peer Reviewe

Quantum Thermodynamic Cycles and quantum heat engines

In order to describe quantum heat engines, here we systematically study isothermal and isochoric processes for quantum thermodynamic cycles. Based on these results the quantum versions of both the Carnot heat engine and the Otto heat engine are defined without ambiguities. We also study the properties of quantum Carnot and Otto heat engines in comparison with their classical counterparts. Relations and mappings between these two quantum heat engines are also investigated by considering their respective quantum thermodynamic processes. In addition, we discuss the role of Maxwell's demon in quantum thermodynamic cycles. We find that there is no violation of the second law, even in the existence of such a demon, when the demon is included correctly as part of the working substance of the heat engine.Comment: 17 pages, 9 figures, 4 table