Signatures of the self-modulation instability of relativistic proton bunches in the AWAKE experiment

We investigate numerically the detection of the self-modulation instability in a virtual detector located downstream from the plasma in the context of AWAKE. We show that the density structures, appearing in the temporally resolving virtual detector, map the transverse beam phase space distribution at the plasma exit. As a result, the proton bunch radius that appears to grow along the bunch in the detector results from the divergence increase along the bunch, related with the spatial growth of the self-modulated wakefields. In addition, asymmetric bunch structures in the detector are a result of asymmetries of the bunch divergence, and do not necessarily reflect asymmetric beam density distributions in the plasma.Comment: Accepted for publication in NIM-A for the proceedings of the 3rd European Advanced Accelerator Workshop. 5 pages, 2 figure

Conditions for the onset of the current filamentation instability in the laboratory

Current Filamentation Instability (CFI) is capable of generating strong magnetic fields relevant to explain radiation processes in astrophysical objects and lead to the onset of particle acceleration in collisionless shocks. Probing such extreme scenarios in the laboratory is still an open challenge. In this work, we investigate the possibility of using neutral $e^{-}$ $e^{+}$ beams to explore the CFI with realistic parameters, by performing 2D particle-in-cell simulations. We show that CFI can occur unless the rate at which the beam expands due to finite beam emittance is larger than the CFI growth rate and as long as the role of competing electrostatic two-stream instability (TSI) is negligible. We also show that the longitudinal energy spread, typical of plasma based accelerated electron-positron fireball beams, plays a minor role in the growth of CFI in these scenarios

Electron trapping and acceleration by the plasma wakefield of a self-modulating proton beam

It is shown that co-linear injection of electrons or positrons into the wakefield of the self-modulating particle beam is possible and ensures high energy gain. The witness beam must co-propagate with the tail part of the driver, since the plasma wave phase velocity there can exceed the light velocity, which is necessary for efficient acceleration. If the witness beam is many wakefield periods long, then the trapped charge is limited by beam loading effects. The initial trapping is better for positrons, but at the acceleration stage a considerable fraction of positrons is lost from the wave. For efficient trapping of electrons, the plasma boundary must be sharp, with the density transition region shorter than several centimeters. Positrons are not susceptible to the initial plasma density gradient.Comment: 9 pages, 9 figures, 1 table, 44 reference

Space-efficient merging of succinct de Bruijn graphs

We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB 2014]. Our algorithm has the same asymptotic cost of the state of the art tool for the same problem presented by Muggli et al. [bioRxiv 2017, Bioinformatics 2019], but it uses less than half of its working space. A novel important feature of our algorithm, not found in any of the existing tools, is that it can compute the Variable Order succinct representation of the union graph within the same asymptotic time/space bounds.Comment: Accepted to SPIRE'1

Disentangled long-read de Bruijn graphs via optical maps

Peer reviewe

Fast and accurate correction of optical mapping data via spaced seeds

Motivation: Optical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes. The challenge faced in error correction is in determining pairs of Rmaps that originate from the same region of the same genome. Results: We create an efficient method for determining pairs of Rmaps that contain significant overlaps between them. Our method relies on the novel and nontrivial adaption and application of spaced seeds in the context of optical mapping, which allows for spurious and deleted cut sites to be accounted for. We apply our method to detecting and correcting these errors. The resulting error correction method, referred to as Elmeri, improves upon the results of state-of-the-art correction methods but in a fraction of the time. More specifically, cOMet required 9.9 CPU days to error correct Rmap data generated from the human genome, whereas Elmeri required less than 15 CPU hours and improved the quality of the Rmaps by more than four times compared to cOMet.Peer reviewe