1,524 research outputs found
Electron-beam-induced shift in the apparent position of a pinned vortex in a thin superconducting film
When an electron beam strikes a superconducting thin film near a pinned
vortex, it locally increases the temperature-dependent London penetration depth
and perturbs the circulating supercurrent, thereby distorting the vortex's
magnetic field toward the heated spot. This phenomenon has been used to
visualize vortices pinned in SQUIDs using low-temperature scanning electron
microscopy. In this paper I develop a quantitative theory to calculate the
displacement of the vortex-generated magnetic-flux distribution as a function
of the distance of the beam spot from the vortex core. The results are
calculated using four different models for the spatial distribution of the
thermal power deposited by the electron beam.Comment: 9 pages, 6 figures, resubmitted to PRB with referee-suggested
revisions, includes new paragraph on numerical evaluatio
Chemosensory Neurons Modulate the Response to Oomycete Recognition in Caenorhabditis elegans
Understanding how animals detect and respond to pathogen threats is central to dissecting mechanisms of host immunity. The oomycetes represent a diverse eukaryotic group infecting various hosts from nematodes to humans. We have previously shown that Caenorhabditis elegans mounts a defense response consisting of the induction of chitinase-like (chil) genes in the epidermis to combat infection by its natural oomycete pathogen Myzocytiopsis humicola. We provide here evidence that C. elegans can sense the oomycete by detecting an innocuous extract derived from animals infected with M. humicola. The oomycete recognition response (ORR) leads to changes in the cuticle and reduction in pathogen attachment, thereby increasing animal survival. We also show that TAX-2/TAX-4 function in chemosensory neurons is required for the induction of chil-27 in the epidermis in response to extract exposure. Our findings highlight that neuron-to-epidermis communication may shape responses to oomycete recognition in animal hosts
Growth of a vortex polycrystal in type II superconductors
We discuss the formation of a vortex polycrystal in type II superconductors
from the competition between pinning and elastic forces. We compute the elastic
energy of a deformed grain boundary, that is strongly non-local, and obtain the
depinning stress for weak and strong pinning. Our estimates for the grain size
dependence on the magnetic field strength are in good agreement with previous
experiments on NbMo. Finally, we discuss the effect of thermal noise on grain
growth.Comment: 4 pages, 2 figure
Local Simulation Algorithms for Coulomb Interaction
Long ranged electrostatic interactions are time consuming to calculate in
molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic
framework for simulating charged particles which modifies the dynamics so as to
allow equilibration using a local Hamiltonian. The method introduces an
auxiliary field with constrained dynamics so that the equilibrium distribution
is determined by the Coulomb interaction. We demonstrate the efficiency of the
method by simulating a simple, charged lattice gas.Comment: Last figure changed to improve demonstration of numerical efficienc
Maximum Flux Transition Paths of Conformational Change
Given two metastable states A and B of a biomolecular system, the problem is
to calculate the likely paths of the transition from A to B. Such a calculation
is more informative and more manageable if done for a reduced set of collective
variables chosen so that paths cluster in collective variable space. The
computational task becomes that of computing the "center" of such a cluster. A
good way to define the center employs the concept of a committor, whose value
at a point in collective variable space is the probability that a trajectory at
that point will reach B before A. The committor "foliates" the transition
region into a set of isocommittors. The maximum flux transition path is defined
as a path that crosses each isocommittor at a point which (locally) has the
highest crossing rate of distinct reactive trajectories. (This path is
different from that of the MaxFlux method of Huo and Straub.) It is argued that
such a path is nearer to an ideal path than others that have been proposed with
the possible exception of the finite-temperature string method path. To make
the calculation tractable, three approximations are introduced, yielding a path
that is the solution of a nonsingular two-point boundary-value problem. For
such a problem, one can construct a simple and robust algorithm. One such
algorithm and its performance is discussed.Comment: 7 figure
Dynamics of ions in the selectivity filter of the KcsA channel
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications
Elasticity-driven interaction between vortices in type-II superconductors
The contribution to the vortex lattice energy which is due to the
vortex-induced strains is calculated covering all the magnetic field range
which defines the vortex state. This contribution is compared with previously
reported ones what shows that, in the most part of the vortex state, it has
been notably underestimated until now. The reason of such underestimation is
the assumption that only the vortex cores induce strains. In contrast to what
is generally assumed, both core and non-core regions are important sources of
strains in high- superconductors.Comment: 10 pages, 1 figure, revtex
Quantitative nanoscale vortex-imaging using a cryogenic quantum magnetometer
Microscopic studies of superconductors and their vortices play a pivotal role
in our understanding of the mechanisms underlying superconductivity. Local
measurements of penetration depths or magnetic stray-fields enable access to
fundamental aspects of superconductors such as nanoscale variations of
superfluid densities or the symmetry of their order parameter. However,
experimental tools, which offer quantitative, nanoscale magnetometry and
operate over the large range of temperature and magnetic fields relevant to
address many outstanding questions in superconductivity, are still missing.
Here, we demonstrate quantitative, nanoscale magnetic imaging of Pearl vortices
in the cuprate superconductor YBCO, using a scanning quantum sensor in form of
a single Nitrogen-Vacancy (NV) electronic spin in diamond. The sensor-to-sample
distance of ~10nm we achieve allows us to observe striking deviations from the
prevalent monopole approximation in our vortex stray-field images, while we
find excellent quantitative agreement with Pearl's analytic model. Our
experiments yield a non-invasive and unambiguous determination of the system's
local London penetration depth, and are readily extended to higher temperatures
and magnetic fields. These results demonstrate the potential of quantitative
quantum sensors in benchmarking microscopic models of complex electronic
systems and open the door for further exploration of strongly correlated
electron physics using scanning NV magnetometry.Comment: Main text (5 pages, 4 figures) plus supplementary material (5 pages,
6 figures). Comments welcome. Further information under
http://www.quantum-sensing.c
Stain-free identification of tissue pathology using a generative adversarial network to infer nanomechanical signatures
Intraoperative frozen section analysis can be used to improve the accuracy of tumour margin estimation during cancer resection surgery through rapid processing and pathological assessment of excised tissue. Its applicability is limited in some cases due to the additional risks associated with prolonged surgery, largely from the time-consuming staining procedure. Our work uses a measurable property of bulk tissue to bypass the staining process: as tumour cells proliferate, they influence the surrounding extra-cellular matrix, and the resulting change in elastic modulus provides a signature of the underlying pathology. In this work we accurately localise atomic force microscopy measurements of human liver tissue samples and train a generative adversarial network to infer elastic modulus from low-resolution images of unstained tissue sections. Pathology is predicted through unsupervised clustering of parameters characterizing the distributions of inferred values, achieving 89% accuracy for all samples based on the nominal assessment (n = 28), and 95% for samples that have been validated by two independent pathologists through post hoc staining (n = 20). Our results demonstrate that this technique could increase the feasibility of intraoperative frozen section analysis for use during resection surgery and improve patient outcomes
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