Snails as intermediate hosts for parasitic infections: host-parasite relationships and intervention strategies

A fundamental prerequisite in the fight against medically and veterinary important parasites transmitted by intermediate host snails is a good knowledge of their life cycles, host specificity and geographical distribution. With scientists around the world collecting material from the wild and generating vast amounts of sequencing data, there is a huge opportunity to expand our knowledge of host-parasite relationships from the comfort of an office chair. With these motivations in mind, a bioinformatics tool was developed that has proven to be time efficient and accurate for the rapid identification of hidden parasites in publicly available datasets. Several dozen hidden parasite infections were discovered from the 2150 gastropod datasets tested, and some of these relationships have not yet been described. With our better understanding and the rapid progress in development of molecular and genetic methods, new avenues are opening for the control and eradication of diseases caused by vector-borne parasites. To study crucial parasite-snail interactions and eventually try to interfere with the infection, it is desirable to edit the host genome. Thus, in the framework of this work, preliminary experiments for the development of the CRISPR/Cas9 protocol in Biomphalaria glabrata, the intermediate host of the dangerous blood fluke Schistosoma mansoni, were also performed. The most significant findings in this case are the proof-of-concept of cultivation of B. glabrata embryos in glass capillaries using natural egg fluid and the demonstration that dilution of this fluid or complete replacement by other culture media are not suitable for successful cultivation. I also show that the Diaphanous gene, which has been used in the past to optimize CRISPR/Cas9 in another snail model, is not suitable for our model. The ultimate goal of the development of this molecular-genetic toolbox is the eradication of schistosomiasis by replacing susceptible populations in nature with resistant populations using gene drive technology. Although disrupted by COVID-19 pandemic, this work’s contribution to progress in the fight against helminthic parasitic infections is considerable

Relativistic Real-Time Methods

Recent advances in laser technology enable to follow electronic motion at its natural time-scale with ultrafast pulses, leading the way towards atto- and femtosecond spectroscopic experiments of unprecedented resolution. Understanding of these laser-driven processes, which almost inevitably involve non-linear light-matter interactions and non-equilibrium electron dynamics, is challenging and requires a common effort of theory and experiment. Real-time electronic structure methods provide the most straightforward way to simulate experiments and to gain insights into non-equilibrium electronic processes. In this Chapter, we summarize the fundamental theory underlying the relativistic particle-field interaction Hamiltonian as well as equation-of-motion for exact-state wave function in terms of the one- and two-electron reduced density matrix. Further, we discuss the relativistic real-time electron dynamics mean-field methods with an emphasis on Density-Functional Theory and Gaussian basis, starting from the four-component (Dirac) picture and continue to the two-component (Pauli) picture, where we introduce various flavours of modern exact two-component (X2C) Hamiltonians for real-time electron dynamics. We also overview several numerical techniques for real-time propagation and signal processing in quantum electron dynamics. We close this Chapter by listing selected applications of real-time electron dynamics to frequency-resolved and time-resolved spectroscopies

X-ray absorption resonances near L2,3-edges from real-time propagation of the Dirac–Kohn–Sham density matrix

Published version. Source at http://doi.org/10.1039/c5cp03712c.The solution of the Liouville–von Neumann equation in the relativistic Dirac–Kohn–Sham density matrix formalism is presented and used to calculate X-ray absorption cross sections. Both dynamical relaxation effects and spin–orbit corrections are included, as demonstrated by calculations of the X-ray absorption of SF6 near the sulfur L2,3-edges. We also propose an analysis facilitating the interpretation of spectral transitions from real-time simulations, and a selective perturbation that eliminates nonphysical excitations that are artifacts of the finite basis representation

Cost-Efficient High-Resolution Linear Absorption Spectra Through Extrapolating the Dipole Moment from Real-Time Time-Dependent Electronic-Structure Theory

Accepted manuscript, submitted to Journal of Chemical Theory and Computation: https://pubs.acs.org/action/doSearch?AllField=Journal+of+Chemical+Theory+and+Computation.We present a novel function fitting method for approximating the propagation of the time-dependent electric dipole moment from real-time electronic structure calculations. Real-time calculations of the electronic absorption spectrum require discrete Fourier transforms of the electric dipole moment. The spectral resolution is determined by the total propagation time, i.e. the trajectory length of the dipole moment, causing a high computational cost. Our developed method uses function fitting on shorter trajectories of the dipole moment, achieving arbitrary spectral resolution through extrapolation. Numerical testing shows that the fitting method can reproduce high-resolution spectra using short dipole trajectories. The method converges with as little as 100 a.u. dipole trajectories for some systems, though the difficulty converging increases with the spectral density. We also introduce an error estimate of the fit, reliably assessing its convergence and hence the quality of the approximated spectrum

Exact two-component TDDFT with simple two-electron picture-change corrections: X-ray absorption spectra near L- and M-edges of four-component quality at two-component cost

X-ray absorption spectroscopy (XAS) has gained popularity in recent years as it probes matter with high spatial and elemental sensitivities. However, the theoretical modeling of XAS is a challenging task since XAS spectra feature a fine structure due to scalar (SC) and spin-orbit (SO) relativistic effects, in particular near L and M absorption edges. While full four-component (4c) calculations of XAS are nowadays feasible, there is still interest in developing approximate relativistic methods that enable XAS calculations at the two-component (2c) level while maintaining the accuracy of the parent 4c approach. In this article we present theoretical and numerical insights into two simple yet accurate 2c approaches based on an (extended) atomic mean-field exact two-component Hamiltonian framework, (e)amfX2C, for the calculation of XAS using linear eigenvalue and damped response time-dependent density functional theory (TDDFT). In contrast to the commonly used one-electron X2C (1eX2C) Hamiltonian, both amfX2C and eamfX2C account for the SC and SO two-electron and exchange-correlation picture-change (PC) effects that arise from the X2C transformation. As we demonstrate on L- and M-edge XAS spectra of transition metal and actinide compounds, the absence of PC corrections in the 1eX2C approximation results in a substantial overestimation of SO splittings, whereas (e)amfX2C Hamiltonians reproduce all essential spectral features such as shape, position, and SO splitting of the 4c references in excellent agreement, while offering significant computational savings. Therefore, the (e)amfX2C PC correction models presented here constitute reliable relativistic 2c quantum-chemical approaches for modeling XAS. © 2023 The Authors. Published by American Chemical Society.2/0135/21; NN4654K; Ministerstvo Školství, Mládeže a Tělovýchovy, MŠMT: RP/CPS/2022/007; Agentúra na Podporu Výskumu a Vývoja, APVV: APVV-19-0516, APVV-21-0497; Norges Forskningsråd: 262695, 314814, 315822; Horizon 2020: 945478, SASPRO

Relativistic Real-Time Methods

Recent advances in laser technology enable to follow electronic motion at its natural time-scale with ultrafast pulses, leading the way towards atto- and femtosecond spectroscopic experiments of unprecedented resolution. Understanding of these laser-driven processes, which almost inevitably involve non-linear light-matter interactions and non-equilibrium electron dynamics, is challenging and requires a common effort of theory and experiment. Real-time electronic structure methods provide the most straightforward way to simulate experiments and to gain insights into non-equilibrium electronic processes. In this Chapter, we summarize the fundamental theory underlying the relativistic particle–field interaction Hamiltonian as well as equation-of-motion for exact-state wave function in terms of the one- and two-electron reduced density matrix. Further, we discuss the relativistic real-time electron dynamics mean-field methods with an emphasis on Density-Functional Theory and Gaussian basis, starting from the four-component (Dirac) picture and continue to the two-component (Pauli) picture, where we introduce various flavours of modern exact two-component (X2C) Hamiltonians for real-time electron dynamics. We also overview several numerical techniques for real-time propagation and signal processing in quantum electron dynamics. We close this Chapter by listing selected applications of real-time electron dynamics to frequency-resolved and time-resolved spectroscopies

Relativistic four-component linear damped response TDDFT for electronic absorption and circular dichroism calculations

We present a detailed theory, implementation, and a benchmark study of a linear damped response time-dependent density functional theory (TDDFT) based on the relativistic four-component (4c) Dirac–Kohn–Sham formalism using the restricted kinetic balance condition for the small-component basis and a noncollinear exchange–correlation kernel. The damped response equations are solved by means of a multifrequency iterative subspace solver utilizing decomposition of the equations according to Hermitian and time-reversal symmetry. This partitioning leads to robust convergence, and the detailed algorithm of the solver for relativistic multicomponent wavefunctions is also presented. The solutions are then used to calculate the linear electric- and magnetic-dipole responses of molecular systems to an electric perturbation, leading to frequency-dependent dipole polarizabilities, electronic absorption, circular dichroism (ECD), and optical rotatory dispersion (ORD) spectra. The methodology has been implemented in the relativistic spectroscopy DFT program ReSpect, and its performance was assessed on a model series of dimethylchalcogeniranes, C4H8X (X = O, S, Se, Te, Po, Lv), and on larger transition metal complexes that had been studied experimentally, [M(phen)3]3+ (M = Fe, Ru, Os). These are the first 4c damped linear response TDDFT calculations of ECD and ORD presented in the literature

Exact Two-Component TDDFT with Simple Two-Electron Picture-Change Corrections: X-ray Absorption Spectra Near L- and M-Edges of Four-Component Quality at Two-Component Cost

X-ray absorption spectroscopy (XAS) has gained popularity in recent years as it probes matter with high spatial and elemental sensitivities. However, the theoretical modeling of XAS is a challenging task since XAS spectra feature a fine structure due to scalar (SC) and spin–orbit (SO) relativistic effects, in particular near L and M absorption edges. While full four-component (4c) calculations of XAS are nowadays feasible, there is still interest in developing approximate relativistic methods that enable XAS calculations at the two-component (2c) level while maintaining the accuracy of the parent 4c approach. In this article we present theoretical and numerical insights into two simple yet accurate 2c approaches based on an (extended) atomic mean-field exact two-component Hamiltonian framework, (e)amfX2C, for the calculation of XAS using linear eigenvalue and damped response time-dependent density functional theory (TDDFT). In contrast to the commonly used one-electron X2C (1eX2C) Hamiltonian, both amfX2C and eamfX2C account for the SC and SO two-electron and exchange–correlation picture-change (PC) effects that arise from the X2C transformation. As we demonstrate on L- and M-edge XAS spectra of transition metal and actinide compounds, the absence of PC corrections in the 1eX2C approximation results in a substantial overestimation of SO splittings, whereas (e)amfX2C Hamiltonians reproduce all essential spectral features such as shape, position, and SO splitting of the 4c references in excellent agreement, while offering significant computational savings. Therefore, the (e)amfX2C PC correction models presented here constitute reliable relativistic 2c quantum-chemical approaches for modeling XAS

Software emulator of nuclear pulse generation with different pulse shapes and pile-up

WOS: 000377399700011The optimal detection of output signals from nuclear counting devices represents one of the key physical factors that govern accuracy and experimental reproducibility. In this context, the fine calibration of the detector under diverse experimental scenarios, although time costly, is necessary. However this process can be rendered easier with the use of systems that work in lieu of emulators. In this report we describe an innovative programmable pulse generator device capable to emulate the scintillation detector signals, in a way to mimic the detector performances under a variety of experimental conditions. The emulator generates a defined number of pulses, with a given shape and amplitude in the form of a sampled detector signal. The emulator output is then used off-line by a spectrometric system in order to set up its optimal performance. Three types of pulse shapes are produced by our device, with the possibility to add noise and pulse pile-up effects into the signal. The efficiency of the pulse detection, pile-up rejection and/or correction, together with the dead-time of the system, are therein analyzed through the use of some specific algorithms for pulse processing, and the results obtained validate the beneficial use of emulators for the accurate calibration process of spectrometric systems. (C) 2016 Elsevier B.V. All rights reserved.internal IGA grant of Palacky University [IGA_PrF_2016_022]; Operational Program Education for Competitiveness - European Social Fund of Ministry of Education, Youth and Sports of the Czech Republic [CZ.1.07/2.2.00/28.0168]; Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [1059B211404723]Authors thank to internal IGA grant of Palacky University (IGA_PrF_2016_022) and the support by the Operational Program Education for Competitiveness - European Social Fund (project CZ.1.07/2.2.00/28.0168) of the Ministry of Education, Youth and Sports of the Czech Republic. This work was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) under project No. 1059B211404723. Authors thank to Helena Sedlackova and Giorgio Zoppellaro for their help