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Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Aims: This study aimed to develop a random amplified polymorphic DNA (RAPD)‐based sequence characterized amplified region (SCAR) marker for species‐specific detection of Phytophthora nicotianae, a global plant pathogen. Another objective was to develop a multiplex PCR assay for simultaneous detection of P. nicotianae and huanglongbing‐causing bacterium, Candidatus Liberibacter asiaticus (CaLas) in citrus roots using the developed SCAR marker and a previously published 16SrDNA‐based CaLas‐specific primer set. Methods and Results: The RAPD primer, OPA4, amplified a specific fragment of c. 400 bp only in P. nicotianae isolates. The fragment was eluted, purified, cloned and sequenced. One set of SCAR primers (SCAR4F/SCAR4R1), developed from the sequence information of the fragment, was found specific to P. nicotianae and produced an amplicon of 330 bp size, and was found non‐specific to the five Phytophthora species (P. citrophthora, P. palmivora, P. lacustris, P. boehmeriae and P. insolita) and five other pathogens (Mycosphaerella citri, Alternaria alternata, Septobasidium pseudopedicillatum, Phytopythium vexans and Colletotrichum gloeosporioides) isolated from the citrus agroecosystem. The sensitivity of the primer pair was 5 pg µl−1 of mycelial DNA. Furthermore, the specific SCAR primers coupled with a previously reported CaLas‐specific primer set were used effectively in developing a multiplex PCR assay to detect P. nicotianae and CaLas simultaneously in root tissues of citrus plants. Conclusions: A rapid method using a RAPD‐based SCAR marker for the detection of P. nicotianae was developed. Furthermore, a multiplex PCR assay was established for simultaneous detection of P. nicotianae and CaLas in citrus roots. Significance and Impact of the Study: A RAPD‐SCAR marker‐based detection system and the one‐step multiplex PCR method developed in this study can be applied to index citrus trees infected (individually or conjointly) with P. nicotianae and CaLas. The present technique developed would also be useful in monitoring disease epidemiology and phytosanitary surveillance. [ABSTRACT FROM AUTHOR]

Most animal cell types are classified as non-excitable because they do not generate action potentials observed in excitable cells, such as neurons and muscle cells. Thus, resolving voltage signals in non-excitable cells demands sensors with exceptionally high voltage sensitivity. In this study, the ultrabright, ultrasensitive, and calibratable genetically encoded voltage sensor rEstus is developed using structure-guided engineering. rEstus is most sensitive in the resting voltage range of non-excitable cells and offers a 3.6-fold improvement in brightness change for fast voltage spikes over its precursor ASAP3. Using rEstus, it is uncovered that the membrane voltage in several non-excitable cell lines (A375, HEK293T, MCF7) undergoes spontaneous endogenous alterations on a second to millisecond timescale. Correlation analysis of these optically recorded voltage alterations provides a direct, real-time readout of electrical cell-cell coupling, showing that visually connected A375 and HEK293T cells are also largely electrically connected, while MCF7 cells are only weakly coupled. The presented work provides enhanced tools and methods for non-invasive voltage imaging in living cells and demonstrates that spontaneous endogenous membrane voltage alterations are not limited to excitable cells but also occur in a variety of non-excitable cell types., (© 2024 The Authors. Advanced Science published by Wiley‐VCH GmbH.)

Tensor algebra operations such as contractions in computational chemistry consume a significant fraction of the computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. TAMM decouples the specification of the computation from the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM, whereas high-performance computing developers can direct their attention to various optimizations on the underlying constructs, such as efficient data distribution, optimized scheduling algorithms, and efficient use of intra-node resources (e.g., graphics processing units). The modular structure of TAMM allows it to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to the sustainable development of scalable ground- and excited-state electronic structure methods. We present case studies highlighting the ease of use, including the performance and productivity gains compared to other frameworks., (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

The breakup pathway of the Rayleigh fission process observed in the past experiments carried out using high-speed imaging of a charged drop levitated in an AC quadrupole trap has shown to exhibit several cycles of shape and center-of-mass oscillations followed by asymmetric breakup by ejecting a jet in the upward direction (i.e., opposite to the direction of gravity). We recently attempted to explain this using boundary integral simulations in the Stokes flow limit, wherein the position of the droplet and the polarity of the end cap electrodes were assigned using physical arguments, and the center-of-mass motion was not estimated consistently invoking quasi-static conditions. In this work, we explain the experimental observation of upward breakup of charged droplets in a quadrupolar field, using numerical calculations based on the boundary element method considering inviscid droplets levitated electrodynamically using quadrupole electric fields. The center-of-mass motion and the end cap are consistently calculated in the numerical scheme. The simulations show that the gravity-induced downward shift in the equilibrium position of the drop in the trap causes significant, large-amplitude shape oscillations superimposed over the center-of-mass oscillations of the drop. An important observation here is that the shape oscillations due to the applied quadrupole fields result in sufficient deformations that act as triggers for the onset of the instability below the Rayleigh limit, thereby admitting a subcritical instability. The center-of-mass oscillations of the droplet within the trap, which follow the applied frequency, are out of phase with the applied AC signal. Thus the combined effect of shape deformations and dynamic position of the drop leads to an asymmetric breakup such that the Rayleigh fission occurs upward via the ejection of a jet at the north pole of the deformed drop., (© 2022. The Author(s), under exclusive licence to EDP Sciences, SIF and Springer-Verlag GmbH Germany, part of Springer Nature.)

The breakup pathway of Rayleigh fission of a charged drop is unequivocally demonstrated by continuous, high-speed imaging of a drop levitated in an AC quadrupole trap. The experimental observations consistently exhibited asymmetric, subcritical Rayleigh breakup with an upward (i.e., opposite to the direction of gravity) ejection of a jet from the levitated drop. These experiments supported by numerical calculations show that the gravity induced downward shift of the equilibrium position of the drop in the trap causes significant, large amplitude shape oscillations superimposed over the center-of-mass oscillations. The shape oscillations result in sufficient deformations to act as triggers for the onset of instability below the Rayleigh limit (a subcritical instability). The concurrently occurring, center-of-mass oscillations, which are out of phase with the applied voltage, are shown to lead to an asymmetric breakup such that the Rayleigh fission occurs upwards via the ejection of a jet at the pole of the deformed drop. As an important application, it follows by inference that the nanodrop generation in electrospray devices will occur, more as a rule rather than as an exception, via asymmetric, subcritical Rayleigh fission events of microdrops due to inherent directionality provided by the external electric fields.

The experimental demonstration of Rayleigh instability that results in the breakup of a charged droplet, levitated in a quadrupole trap, has been investigated in the literature, but only scarcely. We report here the asymmetric breakup of a charged drop, levitated in a loose trap, wherein the droplet is stabilized at an off-center location in the trap. This aspect of levitation leads to an asymmetric breakup of the charged drop, predominantly in a direction opposite to that of gravity. In the present work, we report the evidence of successive events of the deformation and breakup of a charged drop and its subsequent relaxation after jet ejection using high-speed imaging at a couple of hundred thousand frames per second. Several relevant aspects of this phenomenon such as the effect of the electrodynamic (ED) trap parameters in terms of the applied potential as well as physical parameters such as the size of the drop, gravity, and conductivity on the characteristics of droplet breakup are explored. A clear effect of the trap strength on the deformation (both symmetric and asymmetric) is observed. Moreover, the cone angle at the pole undergoing asymmetric breakup is almost independent of the applied field investigated in the experiments. All of the experimental observations are compared with numerical simulations carried out using the boundary element method (BEM) in the Stokes flow limit. The BEM simulations are also extended to other experimentally achievable parameters. It is observed that the breakup in our study is mostly field-influenced and not field-induced. A plausible theory for the observations is reported, and a sensitive role of the sign of the charge on the droplet and the sign of the end-cap potential, as well as the off-center location of the droplet in the trap, is elucidated.

It has been demonstrated in laboratory systems that U(VI) can be reduced to immobile U(IV) by bacteria in natural environments. The ultimate efficacy of bioreduction at the field scale, however, is often challenging to quantify and depends on site characteristics. In this work, uranium bioreduction rates at the field scale are quantified, for the first time, using an integrated approach. The approach combines field data, inverse and forward hydrological and reactive transport modeling, and quantification of reduction rates at different spatial scales. The approach is used to explore the impact of local scale (tens of centimeters) parameters and processes on field scale (tens of meters) system responses to biostimulation treatments and the controls of physicochemical heterogeneity on bioreduction rates. Using the biostimulation experiments at the Department of Energy Old Rifle site, our results show that the spatial distribution of hydraulic conductivity and solid phase mineral (Fe(III)) play a critical role in determining the field-scale bioreduction rates. Due to the dependence on Fe-reducing bacteria, field-scale U(VI) bioreduction rates were found to be largely controlled by the abundance of Fe(III) minerals at the vicinity of the injection wells and by the presence of preferential flow paths connecting injection wells to down gradient Fe(III) abundant areas.

In recent years several types of sensors and measurement techniques have been developed for measuring the moisture content, water saturation, or the volumetric water content of landfilled wastes. In this work, we review several of the most promising techniques. The basic principles behind each technique are discussed and field applications of the techniques are presented, including cost estimates. For several sensors, previously unpublished data are given. Neutron probes, electrical resistivity (impedance) sensors, time domain reflectometry (TDR) sensors, and the partitioning gas tracer technique (PGTT) were field tested with results compared to gravimetric measurements or estimates of the volumetric water content or moisture content. Neutron probes were not able to accurately measure the volumetric water content, but could track changes in moisture conditions. Electrical resistivity and TDR sensors tended to provide biased estimates, with instrument-determined moisture contents larger than independent estimates. While the PGTT resulted in relatively accurate measurements, electrical resistivity and TDR sensors provide more rapid results and are better suited for tracking infiltration fronts. Fiber optic sensors and electrical resistivity tomography hold promise for measuring water distributions in situ, particularly during infiltration events, but have not been tested with independent measurements to quantify their accuracy. Additional work is recommended to advance the development of some of these instruments and to acquire an improved understanding of liquid movement in landfills by application of the most promising techniques in the field.