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E. Werner

Publications and source records attributed to E. Werner.

At least 19 recordsLinked to original sources

Improving traffic sign recognition by active search

We describe an iterative active-learning algorithm to recognise rare traffic signs. A standard ResNet is trained on a training set containing only a single sample of the rare class. We demonstrate that by sorting the samples of a large, unlabeled set by the estimated probability of belonging to the rare class, we can efficiently identify samples from the rare class. This works despite the fact that this estimated probability is usually quite low. A reliable active-learning loop is obtained by labeling these candidate samples, including them in the training set, and iterating the procedure. Further, we show that we get similar results starting from a single synthetic sample. Our results are important as they indicate a straightforward way of improving traffic-sign recognition for automated driving systems. In addition, they show that we can make use of the information hidden in low confidence outputs, which is usually ignored.

cs.LG

Distribution of label spacings for genome mapping in nanochannels

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.

physics.bio-ph

Hairpins in the conformations of a confined polymer

If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.

physics.bio-ph

One-parameter scaling theory for DNA extension in a nanochannel

Experiments measuring DNA extension in nanochannels are at odds with even the most basic predictions of current scaling arguments for the conformations of confined semiflexible polymers such as DNA. We show that a theory based on a weakly self-avoiding, one-dimensional "telegraph" process collapses experimental data and simulation results onto a single master curve throughout the experimentally relevant region of parameter space and explains the mechanisms at play.

physics.bio-ph

Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.

q-bio.BM

Finite-size corrections for confined polymers in the extended de Gennes regime

Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favourably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear $λ$-DNA confined to nanochannels at the high ionic strengths used in many experiments.

cond-mat.soft

Extension of nano-confined DNA: quantitative comparison between experiment and theory

The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose we performed new experiments, measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic buffer strength. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths the agreement is less good. We discuss possible reasons. Our approach allows, in principle, to measure the Kuhn length and effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

physics.bio-ph

The Relation between Solar Eruption Topologies and Observed Flare Features I: Flare Ribbons

In this paper we present a topological magnetic field investigation of seven two-ribbon flares in sigmoidal active regions observed with Hinode, STEREO, and SDO. We first derive the 3D coronal magnetic field structure of all regions using marginally unstable 3D coronal magnetic field models created with the flux rope insertion method. The unstable models have been shown to be a good model of the flaring magnetic field configurations. Regions are selected based on their pre-flare configurations along with the appearance and observational coverage of flare ribbons, and the model is constrained using pre-flare features observed in extreme ultraviolet and X-ray passbands. We perform a topology analysis of the models by computing the squashing factor, Q, in order to determine the locations of prominent quasi-separatrix layers (QSLs). QSLs from these maps are compared to flare ribbons at their full extents. We show that in all cases the straight segments of the two J-shaped ribbons are matched very well by the flux-rope-related QSLs, and the matches to the hooked segments are less consistent but still good for most cases. In addition, we show that these QSLs overlay ridges in the electric current density maps. This study is the largest sample of regions with QSLs derived from 3D coronal magnetic field models, and it shows that the magnetofrictional modeling technique that we employ gives a very good representation of flaring regions, with the power to predict flare ribbon locations in the event of a flare following the time of the model.

astro-ph.SR

A model for melting of confined DNA

When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.

physics.bio-ph

Scaling regimes of a semi-flexible polymer in a rectangular channel

We derive scaling relations for the extension statistics and the confinement free energy for a semi-flexible polymer confined to a channel with a rectangular cross-section. Our motivation are recent numerical results [Gupta {\em et al.}, JCP {\bf 140} (2014) 214901] indicating that extensional fluctuations are quite different in rectangular channels compared to square channels. Our results are of direct relevance for interpreting current experiments on DNA molecules confined to nano-channels, as many experiments are performed for rectangular channels with large aspect ratios while theoretical and simulation results are usually obtained for square channels.

cond-mat.soft

Confined polymers in the extended de Gennes regime

We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means of computer simulations. The exact solution predicts precisely how the conformational fluctuations depend upon the channel width and upon the microscopic parameters characterising the physical properties of the polymer.

cond-mat.soft

Monomer distributions and intra-chain collisions of a polymer confined to a channel

We study the conformations of a self-avoiding polymer confined to a channel by computing the cross-sectional distributions of the positions of its monomers. By means of Monte-Carlo simulations for a self-avoiding, freely-jointed chain we determine how the cross-sectional distribution for a given monomer depends on its location in the polymer, and how strongly this distribution is affected by self avoidance. To this end we analyze how the frequency of intra-chain collisions between monomers depends on their spatial position in the channel and on their location within the polymer. We show that most collisions occur between closely neighboring monomers. As a consequence the collision probability depends only weakly on the spatial position of the monomers. Our results explain why the effect of self-avoidance on the monomer distributions is weaker than predicted by mean-field theory. We discuss the relevance of our results for studies of DNA conformations in nanofluidic channels.

cond-mat.soft

Orientational correlations in confined DNA

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.

cond-mat.soft

Functional affine-isoperimetry and an inverse logarithmic Sobolev inequality

We give a functional version of the affine isoperimetric inequality for log-concave functions which may be interpreted as an inverse form of a logarithmic Sobolev inequality inequality for entropy. A linearization of this inequality gives an inverse inequality to the Poincar'e inequality for the Gaussian measure.

math.FA

The fine-tuning problem revisited in the light of the Taylor-Lagrange renormalization scheme

We re-analyse the perturbative radiative corrections to the Higgs mass within the Standard Model in the light of the Taylor-Lagrange renormalization scheme. This scheme naturally leads to completely finite corrections, depending on an arbitrary dimensionless scale. This formulation avoids very large individual corrections to the Higgs mass. In other words, it is a confirmation that the so-called fine-tuning problem in the Standard Model is just an artefact of the regularization scheme and should not lead to any physical interpretation in terms of the energy scale at which new physics should show up, nor to the appearance of a new symmetry. We analyse the characteristic physical scales relevant for the description of these radiative corrections.

hep-th

Taylor-Lagrange renormalization scheme, Pauli-Villars subtraction, and light-front dynamics

We show how the recently proposed Taylor-Lagrange renormalization scheme can lead to extensions of singular distributions which are reminiscent of the Pauli-Villars subtraction. However, at variance with the Pauli-Villars regularization scheme, no infinite mass limit is performed in this scheme. As an illustration of this mechanism, we consider the calculation of the self-energy in second order perturbation theory in the Yukawa model, within the covariant formulation of light-front dynamics. We show in particular how rotational invariance is preserved in this scheme.

hep-th

Clustering of exponentially separating trajectories

It might be expected that trajectories for a dynamical system which has no negative Lyapunov exponent (implying exponential growth of small separations will not cluster together. However, clustering can occur such that the density $ρ(Δx)$ of trajectories within distance $Δx$ of a reference trajectory has a power-law divergence, so that $ρ(Δx)\sim Δx^{-β}$ when $Δx$ is sufficiently small, for some $0<β<1$. We demonstrate this effect using a random map in one dimension. We find no evidence for this effect in the chaotic logistic map, and argue that the effect is harder to observe in deterministic maps.

nlin.CD

Taylor-Lagrange renormalization scheme. Application to light-front dynamics

The recently proposed renormalization scheme based on the definition of field operators as operator valued distributions acting on specific test functions is shown to be very convenient in explicit calculations of physical observables within the framework of light-front dynamics. We first recall the main properties of this procedure based on identities relating the test functions to their Taylor remainder of any order expressed in terms of Lagrange's formulae, hence the name given to this scheme. We thus show how it naturally applies to the calculation of state vectors of physical systems in the covariant formulation of light-front dynamics. As an example, we consider the case of the Yukawa model in the simple two-body Fock state truncation.

hep-th