5,220 research outputs found
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 . 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 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
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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
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