Elimination of the numerical Cerenkov instability for spectral EM-PIC codes

When using an electromagnetic particle-in-cell (EM-PIC) code to simulate a relativistically drifting plasma, a violent numerical instability known as the numerical Cerenkov instability (NCI) occurs. The NCI is due to the unphysical coupling of electromagnetic waves on a grid to wave-particle resonances, including aliased resonances, i.e., $\omega + 2\pi\mu/\Delta t=(k_1+ 2\pi\nu_1/\Delta x_1)v_0$, where $\mu$ and $\nu_1$ refer to the time and space aliases and the plasma is drifting relativistically at velocity $v_0$ in the $\hat{1}$-direction. Recent studies have shown that an EM-PIC code which uses a spectral field solver and a low pass filter can eliminate the fastest growing modes of the NCI. Based on these studies a new spectral PIC code for studying laser wakefield acceleration (LWFA) in the Lorentz boosted frame was developed. However, we show that for parameters of relevance for LWFA simulations in the boosted frame, a relativistically drifting plasma is susceptible to a host of additional unstable modes with lower growth rates, and that these modes appear when the fastest growing unstable modes are filtered out. We show that these modes are most easily identified as the coupling between modes which are purely transverse (EM) and purely longitudinal (Langmuir) in the rest frame of the plasma for specific time and space aliases. We rewrite the dispersion relation of the drifting plasma for a general field solver and obtain analytic expressions for the location and growth rate for each unstable mode, i.e, for each time and space aliased resonances. We show for the spectral solver that when the fastest growing mode is eliminated a new mode at the fundamental resonance ($\mu=\nu_1=0$) can be seen. (Please check the whole abstract in the paper).Comment: 36 pages, 12 figure

Mitigation of numerical Cerenkov radiation and instability using a hybrid finite difference-FFT Maxwell solver and a local charge conserving current deposit

A hybrid Maxwell solver for fully relativistic and electromagnetic (EM) particle-in-cell (PIC) codes is described. In this solver, the EM fields are solved in $k$ space by performing an FFT in one direction, while using finite difference operators in the other direction(s). This solver eliminates the numerical Cerenkov radiation for particles moving in the preferred direction. Moreover, the numerical Cerenkov instability (NCI) induced by the relativistically drifting plasma and beam can be eliminated using this hybrid solver by applying strategies that are similar to those recently developed for pure FFT solvers. A current correction is applied for the charge conserving current deposit to correctly account for the EM calculation in hybrid Yee-FFT solver. A theoretical analysis of the dispersion properties in vacuum and in a drifting plasma for the hybrid solver is presented, and compared with PIC simulations with good agreement obtained. This hybrid solver is applied to both 2D and 3D Cartesian and quasi-3D (in which the fields and current are decomposed into azimuthal harmonics) geometries. Illustrative results for laser wakefield accelerator simulation in a Lorentz boosted frame using the hybrid solver in the 2D Cartesian geometry are presented, and compared against results from 2D UPIC-EMMA simulation which uses a pure spectral Maxwell solver, and from OSIRIS 2D lab frame simulation using the standard Yee solver. Very good agreement is obtained which demonstrates the feasibility of using the hybrid solver for high fidelity simulation of relativistically drifting plasma with no evidence of the numerical Cerenkov instability

A Novel Iron Transporter SPD_1590 in Streptococcus pneumoniae Contributing to Bacterial Virulence Properties

Streptococcus pneumoniae, a Gram-positive human pathogen, has evolved three main transporters for iron acquisition from the host: PiaABC, PiuABC, and PitABC. Our previous study had shown that the mRNA and protein levels of SPD_1590 are significantly upregulated in the ΔpiuA/ΔpiaA/ΔpitA triple mutant, suggesting that SPD_1590 might be a novel iron transporter in S. pneumoniae. In the present study, using spd1590-knockout, -complemented, and -overexpressing strains and the purified SPD_1590 protein, we show that SPD_1590 can bind hemin, probably supplementing the function of PiuABC, to provide the iron necessary for the bacterium. Furthermore, the results of iTRAQ quantitative proteomics and cell-infection studies demonstrate that, similarly to other metal-ion uptake proteins, SPD_1590 is important for bacterial virulence properties. Overall, these results provide a better understanding of the biology of this clinically important bacterium

Extremely powerful and frequency-tunable terahertz pulses from a table-top laser-plasma wiggler

The production of broadband, terawatt terahertz (THz) pulses has been demonstrated by irradiating relativistic lasers on solid targets. However, the generation of extremely powerful, narrow-band, and frequency-Tunable THz pulses remains a challenge. Here, we present a novel approach for such THz pulses, in which a plasma wiggler is elaborated by a tabletop laser and a near-critical density plasma. In such a wiggler, the laser-Accelerated electrons emit THz radiations with a period closely related to the plasma thickness. Theoretical model and numerical simulations predict a THz pulse with a laser-THz energy conversion over 2.0%, an ultra-strong field exceeding 80 GV/m, a divergence angle approximately 20?, and a center-frequency tunable from 4.4 to 1.5 THz, can be generated from a laser of 430 mJ. Furthermore, we demonstrate that this method can work across a wide range of laser and plasma parameters, offering potential for future applications with extremely powerful THz pulse. © 2023 Authors. All rights reserved.11Nsciescopu

The water lily genome and the early evolution of flowering plants

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1–3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.Supplementary Tables: This file contains Supplementary Tables 1-21.National Natural Science Foundation of China, the open funds of the State Key Laboratory of Crop Genetics and Germplasm Enhancement (ZW201909) and State Key Laboratory of Tree Genetics and Breeding, the Fujian provincial government in China, the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement and the Special Research Fund of Ghent University.http://www.nature.com/naturecommunicationsam2021BiochemistryGeneticsMicrobiology and Plant Patholog