Frequency dependent deformation of liquid crystal droplets in an external electric field

Nematic drops suspended in the isotropic phase of the same substance were subjected to alternating electrical fields of varying frequency. The system was carefully kept in the isotropic-nematic coexistance region, which was broadened due to small amounts of non-mesogenic additives. Whereas the droplets remained spherical at low (order of 10 Hz) and high frequencies (in the kHz range), at intermediate frequencies, we observed a marked flattening of the droplet in the plane perpendicular to the applied field. The deformation of the liquid crystal (LC) droplets occurred both in substances with positive and negative dielectric anisotropy. The experimental data can be quantitatively modelled with a combination of the leaky dielectric model and screening of the applied electric field due to the finite conductivity.Comment: minor change

CRBHits: From Conditional Reciprocal Best Hits toCodon Alignments and Ka/Ks in R

CRBHitsis a coding sequence (CDS) analysis pipeline inR(R Core Team, 2019). It reimple-ments the Conditional Reciprocal Best Hit (CRBH) algorithmcrb-blastand covers all necessarysteps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny.The new R package targets ecology, population and evolutionary biologists working in thefield of comparative genomics.The Reciprocal Best Hit (RBH) approach is commonly used in bioinformatics to show thattwo sequences evolved from a common ancestral gene. In other words, RBH tries to findorthologous protein sequences within and between species. These orthologous sequencescan be further analysed to evaluate protein family evolution, infer phylogenetic trees and toannotate protein function (Altenhoff et al., 2019). The initial sequence search step is classicallyperformed with the Basic Local Alignment Search Tool (blast) (Altschul et al., 1990) and dueto evolutionary constraints, in most cases protein coding sequences are compared betweentwo species. Downstream analysis use the resulting RBH to cluster sequence pairs and buildso-called orthologous groups like e.g.OrthoFinder(Emms & Kelly, 2015) and other tools.The CRBH algorithm was introduced byAubry et al.(2014) and builds upon the traditionalRBH approach to find additional orthologous sequences between two sets of sequences. Asdescribed earlier (Aubry et al., 2014;Scott, 2017), CRBH uses the sequence search results tofit an expect value (E-value) cutoff given each RBH to subsequently add sequence pairs tothe list of bona-fide orthologs given their alignment length.Unfortunately, as mentioned byScott(2017), the original implementation of CRBH (crb-blast)lag improved blast-like search algorithm to speed up the analysis. As a consequence,Scott(2017) ported CRBH to pythonshmlast, whileshmlastcannot deal with IUPAC nucleotidecode so far.CRBHitsconstitutes a new R package, which build upon previous implementations and portsCRBH into theRenvironment, which is popular among biologists.CRBHitsimprove CRBHby additional implemented filter steps (Rost, 1999) and the possibility to apply custom filtersprior E-value fitting. Further, the resulting CRBH pairs can be evaluated for the presence oftandem duplicated genes, gene order based syntenic groups and evolutionary rates

Time-resolved X-ray microscopy of nanoparticle aggregates under oscillatory shear

Of all current detection techniques with nanometer resolution, only X-ray microscopy allows imaging nanoparticles in suspension. Can it also be used to investigate structural dynamics? When studying response to mechanical stimuli, the challenge lies in applying them with precision comparable to spatial resolution. In the first shear experiments performed in an X-ray microscope, we accomplished this by inserting a piezo actuator driven shear cell into the focal plane of a scanning transmission X-ray microscope (STXM). Thus shear-induced reorganization of magnetite nanoparticle aggregates could be demonstrated in suspension. As X-ray microscopy proves suitable for studying structural change, new prospects open up in physics at small length scales.Comment: submitted to J. Synchrot. Radia

On the problem of mass-dependence of the two-point function of the real scalar free massive field on the light cone

We investigate the generally assumed inconsistency in light cone quantum field theory that the restriction of a massive, real, scalar, free field to the nullplane $\Sigma=\{x^0+x^3=0\}$ is independent of mass \cite{LKS}, but the restriction of the two-point function depends on it (see, e.g., \cite{NakYam77, Yam97}). We resolve this inconsistency by showing that the two-point function has no canonical restriction to $\Sigma$ in the sense of distribution theory. Only the so-called tame restriction of the two-point function exists which we have introduced in \cite{Ull04sub}. Furthermore, we show that this tame restriction is indeed independent of mass. Hence the inconsistency appears only by the erroneous assumption that the two-point function would have a (canonical) restriction to $\Sigma$.Comment: 10 pages, 2 figure

Photoelectron spectra of anionic sodium clusters from time-dependent density-functional theory in real-time

We calculate the excitation energies of small neutral sodium clusters in the framework of time-dependent density-functional theory. In the presented calculations, we extract these energies from the power spectra of the dipole and quadrupole signals that result from a real-time and real-space propagation. For comparison with measured photoelectron spectra, we use the ionic configurations of the corresponding single-charged anions. Our calculations clearly improve on earlier results for photoelectron spectra obtained from static Kohn-Sham eigenvalues

Physical signatures of discontinuities of the time-dependent exchange-correlation potential

The exact exchange-correlation (XC) potential in time-dependent density-functional theory (TDDFT) is known to develop steps and discontinuities upon change of the particle number in spatially confined regions or isolated subsystems. We demonstrate that the self-interaction corrected adiabatic local-density approximation for the XC potential has this property, using the example of electron loss of a model quantum well system. We then study the influence of the XC potential discontinuity in a real-time simulation of a dissociation process of an asymmetric double quantum well system, and show that it dramatically affects the population of the resulting isolated single quantum wells. This indicates the importance of a proper account of the discontinuities in TDDFT descriptions of ionization, dissociation or charge transfer processes.Comment: 17 pages, 6 figure

Excitations and benchmark ensemble density functional theory for two electrons

A new method for extracting ensemble Kohn-Sham potentials from accurate excited state densities is applied to a variety of two electron systems, exploring the behavior of exact ensemble density functional theory. The issue of separating the Hartree energy and the choice of degenerate eigenstates is explored. A new approximation, spin eigenstate Hartree-exchange (SEHX), is derived. Exact conditions that are proven include the signs of the correlation energy components, the virial theorem for both exchange and correlation, and the asymptotic behavior of the potential for small weights of the excited states. Many energy components are given as a function of the weights for two electrons in a one-dimensional flat box, in a box with a large barrier to create charge transfer excitations, in a three-dimensional harmonic well (Hooke's atom), and for the He atom singlet-triplet ensemble, singlet-triplet-singlet ensemble, and triplet bi-ensemble.Comment: 15 pages, supplemental material pd

Non-adiabatic electron dynamics in time-dependent density-functional theory

Time-dependent density-functional theory (TDDFT) treats dynamical exchange and correlation (xc) via a single-particle potential, Vxc(r,t), defined as a nonlocal functional of the density n(r',t'). The popular adiabatic local-density approximation (ALDA) for Vxc(r,t) uses only densities at the same space-time point (r,t). To go beyond the ALDA, two local approximations have been proposed based on quantum hydrodynamics and elasticity theory: (a) using the current as basic variable (C-TDDFT) [G. Vignale, C. A. Ullrich, and S. Conti, Phys. Rev. Lett. 79, 4878 (1997)], (b) working in a co-moving Lagrangian reference frame (L-TDDFT) [I. V. Tokatly, Phys. Rev. B 71, 165105 (2005)]. This paper illustrates, compares, and analyzes both non-adiabatic theories for simple time-dependent model densities in the linear and nonlinear regime, for a broad range of time and frequency scales. C- and L-TDDFT are identical in certain limits, but in general exhibit qualitative and quantitative differences in their respective treatment of elastic and dissipative electron dynamics. In situations where the electronic density rapidly undergoes large deformations, it is found that non-adiabatic effects can become significant, causing the ALDA to break down.Comment: 15 pages, 15 figure

Molecular effects in the ionization of N2_2, O2_2 and F2_2 by intense laser fields

In this paper we study the response in time of N$_2$, O$_2$ and F$_2$ to laser pulses having a wavelength of 390nm. We find single ionization suppression in O$_2$ and its absence in F$_2$, in accordance with experimental results at $\lambda = 800$nm. Within our framework of time-dependent density functional theory we are able to explain deviations from the predictions of Intense-Field Many-Body $S$-Matrix Theory (IMST). We confirm the connection of ionization suppression with destructive interference of outgoing electron waves from the ionized electron orbital. However, the prediction of ionization suppression, justified within the IMST approach through the symmetry of the highest occupied molecular orbital (HOMO), is not reliable since it turns out that, e.g. in the case of F$_2$, the electronic response to the laser pulse is rather complicated and does not lead to dominant depletion of the HOMO. Therefore, the symmetry of the HOMO is not sufficient to predict ionization suppression. However, at least for F$_2$, the symmetry of the dominantly ionized orbital is consistent with the non-suppression of ionization.Comment: 19 pages, 5 figure