An Arbitrary Curvilinear Coordinate Method for Particle-In-Cell Modeling

A new approach to the kinetic simulation of plasmas in complex geometries, based on the Particle-in- Cell (PIC) simulation method, is explored. In the two dimensional (2d) electrostatic version of our method, called the Arbitrary Curvilinear Coordinate PIC (ACC-PIC) method, all essential PIC operations are carried out in 2d on a uniform grid on the unit square logical domain, and mapped to a nonuniform boundary-fitted grid on the physical domain. As the resulting logical grid equations of motion are not separable, we have developed an extension of the semi-implicit Modified Leapfrog (ML) integration technique to preserve the symplectic nature of the logical grid particle mover. A generalized, curvilinear coordinate formulation of Poisson's equations to solve for the electrostatic fields on the uniform logical grid is also developed. By our formulation, we compute the plasma charge density on the logical grid based on the particles' positions on the logical domain. That is, the plasma particles are weighted to the uniform logical grid and the self-consistent mean electrostatic fields obtained from the solution of the logical grid Poisson equation are interpolated to the particle positions on the logical grid. This process eliminates the complexity associated with the weighting and interpolation processes on the nonuniform physical grid and allows us to run the PIC method on arbitrary boundary-fitted meshes.Comment: Submitted to Computational Science & Discovery December 201

Giant coherence in driven systems

We study the noise-induced currents and reliability or coherence of transport in two different classes of rocking ratchets. For this, we consider the motion of Brownian particles in the over damped limit in both adiabatic and non-adiabatic regimes subjected to unbiased temporally symmetric and asymmetric periodic driving force. In the case of a time symmetric driving, we find that even in the presence of a spatially symmetric simple sinusoidal potential, highly coherent transport occurs. These ratchet systems exhibit giant coherence of transport in the regime of parameter space where unidirectional currents in the deterministic case are observed. Outside this parameter range, i.e., when current vanishes in the deterministic regime, coherence in transport is very low. The transport coherence decreases as a function of temperature and is a non-monotonic function of the amplitude of driving. The transport becomes unreliable as we go from the adiabatic to the non-adiabatic domain of operation.Comment: 15 pages, 9 figures, replaced by the version to appear in JSTA

Symphony on strong field approximation

This paper has been prepared by the Symphony collaboration (University of Warsaw, Uniwersytet Jagiellonski, DESY/CNR and ICFO) on the occasion of the 25th anniversary of the 'simple man's models' which underlie most of the phenomena that occur when intense ultrashort laser pulses interact with matter. The phenomena in question include high-harmonic generation (HHG), above-threshold ionization (ATI), and non-sequential multielectron ionization (NSMI). 'Simple man's models' provide both an intuitive basis for understanding the numerical solutions of the time-dependent Schrodinger equation and the motivation for the powerful analytic approximations generally known as the strong field approximation (SFA). In this paper we first review the SFA in the form developed by us in the last 25 years. In this approach the SFA is a method to solve the TDSE, in which the non-perturbative interactions are described by including continuum-continuum interactions in a systematic perturbation-like theory. In this review we focus on recent applications of the SFA to HHG, ATI and NSMI from multi-electron atoms and from multi-atom molecules. The main novel part of the presented theory concerns generalizations of the SFA to: (i) time-dependent treatment of two-electron atoms, allowing for studies of an interplay between electron impact ionization and resonant excitation with subsequent ionization; (ii) time-dependent treatment in the single active electron approximation of 'large' molecules and targets which are themselves undergoing dynamics during the HHG or ATI processes. In particular, we formulate the general expressions for the case of arbitrary molecules, combining input from quantum chemistry and quantum dynamics. We formulate also theory of time-dependent separable molecular potentials to model analytically the dynamics of realistic electronic wave packets for molecules in strong laser fields. We dedicate this work to the memory of Bertrand Carre, who passed away in March 2018 at the age of 60

Open Science in Software Engineering

Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other scientific disciplines, in software engineering, we are still struggling in adapting open science to the particularities of our discipline, rendering progress in our scientific community cumbersome. In this chapter, we reflect upon the essentials in open science for software engineering including what open science is, why we should engage in it, and how we should do it. We particularly draw from our experiences made as conference chairs implementing open science initiatives and as researchers actively engaging in open science to critically discuss challenges and pitfalls, and to address more advanced topics such as how and under which conditions to share preprints, what infrastructure and licence model to cover, or how do it within the limitations of different reviewing models, such as double-blind reviewing. Our hope is to help establishing a common ground and to contribute to make open science a norm also in software engineering.Comment: Camera-Ready Version of a Chapter published in the book on Contemporary Empirical Methods in Software Engineering; fixed layout issue with side-note

Acoustic voice characteristics with and without wearing a facemask

Facemasks are essential for healthcare workers but characteristics of the voice whilst wearing this personal protective equipment are not well understood. In the present study, we compared acoustic voice measures in recordings of sixteen adults producing standardised vocal tasks with and without wearing either a surgical mask or a KN95 mask. Data were analysed for mean spectral levels at 0–1 kHz and 1–8 kHz regions, an energy ratio between 0–1 and 1–8 kHz (LH1000), harmonics-to-noise ratio (HNR), smoothed cepstral peak prominence (CPPS), and vocal intensity. In connected speech there was significant attenuation of mean spectral level at 1–8 kHz region and there was no significant change in this measure at 0–1 kHz. Mean spectral levels of vowel did not change significantly in mask-wearing conditions. LH1000 for connected speech significantly increased whilst wearing either a surgical mask or KN95 mask but no significant change in this measure was found for vowel. HNR was higher in the mask-wearing conditions than the no-mask condition. CPPS and vocal intensity did not change in mask-wearing conditions. These findings implied an attenuation effects of wearing these types of masks on the voice spectra with surgical mask showing less impact than the KN95

Juvenile survival and movements of two threatened oceanic sharks in the North Atlantic Ocean inferred from tag-recovery data

Understanding population dynamics, movements, and fishing mortality is critical to establish effective shark conservation measures across international boundaries in the ocean. There are few survival and dispersal estimates of juveniles of oceanic shark species in the North Atlantic despite it being one of the most fished regions in the world. Here we provide estimates of dispersal, survival, and proportion of fishing mortality in the North Atlantic for two threatened oceanic sharks: the blue shark (Prionace glauca) and the shortfin mako shark (Isurus oxyrinchus). Our results are based on multi-event models applied to tag-recovery data of 700 blue sharks and 132 shortfin makos tagged over a decade. A total of 60 blue sharks (8.57% of tagged) and 30 makos (22.73%) were recovered by the longline fishery between 2009 and 2017. Tag-reporting rate (percentage of returned information when a tagged shark was caught) was estimated to be high (0.794 ± 0.232 SE). Mean annual survival, as predicted from the models, was higher for blue shark (0.835 ± 0.040 SE) than for shortfin mako (0.618 ± 0.189 SE). Models predicted that fishing caused more than a half of total mortality in the study area for both species (0.576 ± 0.209), and more than a third of tagged individuals dispersed from the study area permanently (0.359 ± 0.073). Our findings, focused mainly on juveniles from oceanic areas, contribute to a better understanding of shark population dynamics in the North Atlantic and highlight the need for further conservation measures for both blue shark and shortfin mako, such as implementing efficient bycatch mitigation measures and static/dynamic time–area closures in the open ocea

A mixed-mode shell-model theory for nuclear structure studies

We introduce a shell-model theory that combines traditional spherical states, which yield a diagonal representation of the usual single-particle interaction, with collective configurations that track deformations, and test the validity of this mixed-mode, oblique basis shell-model scheme on $^{24}$Mg. The correct binding energy (within 2% of the full-space result) as well as low-energy configurations that have greater than 90% overlap with full-space results are obtained in a space that spans less than 10% of the full space. The results suggest that a mixed-mode shell-model theory may be useful in situations where competing degrees of freedom dominate the dynamics and full-space calculations are not feasible.Comment: 20 pages, 8 figures, revtex 12p

The energy dependence of flow in Ni induced collisions from 400 to 1970A MeV

We study the energy dependence of collective (hydrodynamic-like) nuclear matter flow in 400-1970 A MeV Ni+Au and 1000-1970 A MeV Ni+Cu reactions. The flow increases with energy, reaches a maximum, and then gradually decreases at higher energies. A way of comparing the energy dependence of flow values for different projectile-target mass combinations is introduced, which demonstrates a common scaling behaviour among flow values from different systems.Comment: 12 pages, 3 figures. Submitted to Physical Review Letter