First-principles simulations of the initial phase of self-aggregation of a cyanine dye: structure and optical spectra

Using first-principles simulations, we investigated the initial steps of the self-aggregation of the dye pseudoisocyanine (PIC) in water. First, we performed molecular dynamics (MD) simulations of the self-aggregation process, in which pile-of-coins oligomers ranging from dimers to stacks of about 20 molecules formed. The oligomer structures were found to be very flexible, with the dimers entering a weakly coupled state and then returning to a stable π-π stacked conformation on a nanosecond time scale. The structural information from the MD simulations was combined with quantum chemical calculations to generate a time-dependent Frenkel exciton Hamiltonian for monomers, dimers, and trimers, which included vibronic coupling. This Hamiltonian, in turn, was used to calculate the absorption spectra for these systems. The simulated dimer spectrum compared well to experiment, validating the face-to-face stacked dimer arrangement found in our MD simulations. Comparison of the simulated trimer spectrum to experiment suggested that oligomers larger than the dimer cannot be abundant at the onset of J-aggregation. Finally, the conformation of the PIC J-aggregate was investigated by testing the stability of several possible conformations in our MD simulations; none of the tested structures was found to be stable

Self-assembly, structure, and optical properties of molecular aggregates

Dit proefschrift bevat een theoretisch onderzoek naar moleculaire aggregaten die, onder de juiste omstandigheden, spontaan gevormd worden door synthetische kleurstofmoleculen wanneer deze in een vloeistof zijn opgelost. In de aggregaten zijn de kleurstofmoleculen op een geordende manier gestapeld tot bijvoorbeeld een ring- of een cilindervorm. Door de nabijheid van de kleurstofmoleculen verschilt de interactie van de aggregaten met licht fundamenteel van de interactie tussen individuele kleurstofmoleculen en licht. Dit maakt de aggregaten interessant en bovendien mogelijk toepasbaar in nieuwe technologieën, bijvoorbeeld in nieuwe types organische zonnecellen. Met behulp van computersimulaties hebben we de spontane aggregatie, de vorm en interne structuur, en de optische eigenschappen van de aggregaten onderzocht. Eerst hebben we de spontane vorming van een aggregaat op de computer nagebootst. Zo verkregen we informatie over de vorm van het aggregaten en de manier waarop de kleurstofmoleculen in het aggregaat op elkaar gestapeld zijn. Deze informatie is vaak nog niet bekend omdat de aggregaten zo klein zijn dat je ze lastig met een (elektronen-)microscoop kunt zien. De zo verkregen informatie over de structuur van het aggregaat hebben we vervolgens gebruikt om de optische eigenschappen uit te rekenen. Onze berekeningen geven een dieper begrip van de speciale optische eigenschappen van aggregaten van kleurstofmoleculen

Novel magnetic excitations beyond the single- and double-magnons

Conventional wisdom suggests that one photon that carries one unit of angular momentum can change the spin angular momentum of a magnetic system with one unit (delta Ms = +-1) at most. This would imply that a two-photon scattering process can manipulate the spin angular momentum of the magnetic system with a maximum of two units. Here we examine the fundamental limit of the photon-driven transport of angular momentum by studying the magnon spectrum of {\alpha}-Fe2O3 using resonant inelastic x-ray scattering. We discovered a cascade of higher-rank magnons carrying double, triple, quadruple, and quintuple the spin angular momentum of a single-magnon. Guided by theoretical calculations, we reveal how a two-photons scattering process can create exotic higher-rank magnons and the relevance of these quasiparticles for magnon-based applications.Comment: Work presented as an invited talk by Hebatalla Elnaggar at the IXS conference 2021 https://www.bnl.gov/rixsrexs2021

Atomic and itinerant effects at the transition metal x-ray absorption K-pre-edge exemplified in the case of V2_2O3_3

X-ray absorption spectroscopy is a well established tool for obtaining information about orbital and spin degrees of freedom in transition metal- and rare earth-compounds. For this purpose usually the dipole transitions of the L- (2p to 3d) and M- (3d to 4f) edges are employed, whereas higher order transitions such as quadrupolar 1s to 3d in the K-edge are rarely studied in that respect. This is due to the fact that usually such quadrupolar transitions are overshadowed by dipole allowed 1s to 4p transitions and, hence, are visible only as minor features in the pre-edge region. Nonetheless, these features carry a lot of valuable information, similar to the dipole L-edge transition, which is not accessible in experiments under pressure due to the absorption of the diamond anvil pressurecell. We recently performed a theoretical and experimental analysis of such a situation for the metal insulator transition of (V(1-x)Crx)2O3. Since the importance of the orbital degrees of freedom in this transition is widely accepted, a thorough understanding of quadrupole transitions of the vanadium K-pre-edge provides crucial information about the underlying physics. Moreover, the lack of inversion symetry at the vanadium site leads to onsite mixing of vanadium 3d- and 4p- states and related quantum mechanical interferences between dipole and quadrupole transitions. Here we present a theoretical analysis of experimental high resolution x-ray absorption spectroscopy at the V pre-K edge measured in partial fluorescence yield mode for single crystals. We carried out density functional as well as configuration interaction calculations in order to capture effects coming from both, itinerant and atomic limits

Report Topsector Potato India and Ethiopia 2015/16

The Agricultural Counsellor of the Netherlands Embassy in Delhi initiated a BOCI project ‘Overview of the potato chain in India’ in early 2011. In September 2012 this initiative has been adopted by the Dutch and Indian stakeholders and the Pubic Private Partnership (PPS) was established to facilitate the intensification of collaboration between Dutch and Indian stakeholders of the potato chain. A team of Wageningen UR researchers was commissioned to carry out this project. In 2011, the team collected information from reports, personal files, internet and some Dutch companies and reported the information in “An overview of the potato sector in India and prospects of Indo & Dutch cooperation”. The team also participated in the Netherlands Trade mission to India (5 & 11 June 2011) and visited the Central Potato Research Institute at Shimla. Furthermore jointly with the Agricultural Counsellor we organized a potato seminar to present our findings on 5 October 2011 in Delhi. Major potato stakeholders both from India and from the Netherlands attended the seminar; total number of participants was about 60 persons. In 2012, 2013, 2014, 2015 and 2016 the team carried out different tasks such as presenting information on various subjects of the Dutch and Indian potato chain to exchange knowledge. In addition, several identified subjects were investigated. All actions and activities aimed to facilitate collaboration between Dutch and Indian stakeholders. Visits to different locations of India accompanied by Dutch stakeholders, meetings with experts of the Indian potato production chain both stakeholders and researchers, and topics such as skin curing and chemical haulm killing, reduce storage losses and the establishment of the Centres of Excellence (CoE) in Punjab (Jalandhar) and Uttar Pradesh, and the Centre of Potato Expertise (COPE) at Ludhiana (Punjab) were successfully accomplished

Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred