Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as “K”. We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics

Enhancing the Stretchability of Two-Dimensional Materials through Kirigami: A Molecular Dynamics Study on Tungsten Disulfide

In recent years, the 'kirigami' technique has gained significant attention for creating meta-structures and meta-materials with exceptional characteristics, such as unprecedented stretchability. These properties, not typically inherent in the original materials or structures, present new opportunities for applications in stretchable electronics and photovoltaics. However, despite its scientific and practical significance, the application of kirigami patterning on a monolayer of tungsten disulfide (WS2), a van der Waals material with exceptional mechanical, electronic, and optical properties, has remained unexplored. This study utilizes molecular dynamics (MD) simulations to investigate the mechanical properties of monolayer WS2 with rectangular kirigami cuts. We find that, under tensile loading, the WS2 based kirigami structure exhibits a notable increase in tensile strain and a decrease in strength, thus demonstrating the effectiveness of the kirigami cutting technique in enhancing the stretchability of monolayer WS2. Additionally, increasing the overlap ratio enhances the stretchability of the structure, allowing for tailored high strength or high strain requirements. Furthermore, our observations reveal that increasing the density of cuts and reducing the length-to-width ratio of the kirigami nanosheet further improve the fracture strain, thereby enhancing the overall stretchability of the proposed kirigami patterned structure of WS2.Comment: 19 pages, 5 figure

Saving the Greater Adjutant Stork by Changing Perceptions and Linking to Assamese Traditions in India

https://ojs.ethnobiology.org/index.php/ebl/article/view/1648https://ojs.ethnobiology.org/index.php/ebl/article/view/164

Bayesian Evidence and Model Selection

In this paper we review the concepts of Bayesian evidence and Bayes factors, also known as log odds ratios, and their application to model selection. The theory is presented along with a discussion of analytic, approximate and numerical techniques. Specific attention is paid to the Laplace approximation, variational Bayes, importance sampling, thermodynamic integration, and nested sampling and its recent variants. Analogies to statistical physics, from which many of these techniques originate, are discussed in order to provide readers with deeper insights that may lead to new techniques. The utility of Bayesian model testing in the domain sciences is demonstrated by presenting four specific practical examples considered within the context of signal processing in the areas of signal detection, sensor characterization, scientific model selection and molecular force characterization.Comment: Arxiv version consists of 58 pages and 9 figures. Features theory, numerical methods and four application

Detection, occurrence, and fate of emerging contaminants in agricultural environments (2019)

A review of 82 papers published in 2018 is presented. The topics ranged from detailed descriptions of analytical methods, to fate and occurrence studies, to ecological effects and sampling techniques for a wide variety of emerging contaminants likely to occur in agricultural environments. New methods and studies on veterinary pharmaceuticals, microplastics, and engineered nanomaterials in agricultural environments continue to expand our knowledge base on the occurrence and potential impacts of these compounds. This review is divided into the following sections: Introduction, Analytical Methods, Fate and Occurrence, Pharmaceutical Metabolites, Anthelmintics, Microplastics, and Engineered Nanomaterials

High spatial resolution imaging of methane and other trace gases with the airborne Hyperspectral Thermal Emission Spectrometer (HyTES)

Currently large uncertainties exist associated with the attribution and quantification of fugitive emissions of criteria pollutants and greenhouse gases such as methane across large regions and key economic sectors. In this study, data from the airborne Hyperspectral Thermal Emission Spectrometer (HyTES) have been used to develop robust and reliable techniques for the detection and wide-area mapping of emission plumes of methane and other atmospheric trace gas species over challenging and diverse environmental conditions with high spatial resolution that permits direct attribution to sources. HyTES is a pushbroom imaging spectrometer with high spectral resolution (256 bands from 7.5 to 12 µm), wide swath (1–2 km), and high spatial resolution (∼ 2 m at 1 km altitude) that incorporates new thermal infrared (TIR) remote sensing technologies. In this study we introduce a hybrid clutter matched filter (CMF) and plume dilation algorithm applied to HyTES observations to efficiently detect and characterize the spatial structures of individual plumes of CH_4, H_2S, NH_3, NO_2, and SO_2 emitters. The sensitivity and field of regard of HyTES allows rapid and frequent airborne surveys of large areas including facilities not readily accessible from the surface. The HyTES CMF algorithm produces plume intensity images of methane and other gases from strong emission sources. The combination of high spatial resolution and multi-species imaging capability provides source attribution in complex environments. The CMF-based detection of strong emission sources over large areas is a fast and powerful tool needed to focus on more computationally intensive retrieval algorithms to quantify emissions with error estimates, and is useful for expediting mitigation efforts and addressing critical science questions

High spatial resolution imaging of methane and other trace gases with the airborne Hyperspectral Thermal Emission Spectrometer (HyTES)

Currently large uncertainties exist associated with the attribution and quantification of fugitive emissions of criteria pollutants and greenhouse gases such as methane across large regions and key economic sectors. In this study, data from the airborne Hyperspectral Thermal Emission Spectrometer (HyTES) have been used to develop robust and reliable techniques for the detection and wide-area mapping of emission plumes of methane and other atmospheric trace gas species over challenging and diverse environmental conditions with high spatial resolution that permits direct attribution to sources. HyTES is a pushbroom imaging spectrometer with high spectral resolution (256 bands from 7.5 to 12 µm), wide swath (1–2 km), and high spatial resolution (∼ 2 m at 1 km altitude) that incorporates new thermal infrared (TIR) remote sensing technologies. In this study we introduce a hybrid clutter matched filter (CMF) and plume dilation algorithm applied to HyTES observations to efficiently detect and characterize the spatial structures of individual plumes of CH4, H2S, NH3, NO2, and SO2 emitters. The sensitivity and field of regard of HyTES allows rapid and frequent airborne surveys of large areas including facilities not readily accessible from the surface. The HyTES CMF algorithm produces plume intensity images of methane and other gases from strong emission sources. The combination of high spatial resolution and multi-species imaging capability provides source attribution in complex environments. The CMF-based detection of strong emission sources over large areas is a fast and powerful tool needed to focus on more computationally intensive retrieval algorithms to quantify emissions with error estimates, and is useful for expediting mitigation efforts and addressing critical science questions

Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis

<p>Abstract</p> <p>Background</p> <p>In the yeast <it>Saccharomyces cerevisiae</it>, interactions between galactose, Gal3p, Gal80p, and Gal4p determine the transcriptional status of the genes required for the galactose utilization. Increase in the cellular galactose concentration causes the galactose molecules to bind onto Gal3p which, via Gal80p, activates Gal4p, which induces the GAL3 and GAL80 gene transcription. Recently, a linear time-invariant multi-input multi-output (MIMO) model of this GAL regulatory network has been proposed; the inputs being galactose and Gal4p, and the outputs being the active Gal4p and galactose utilization. Unfortunately, this model assumes the cell culture to be homogeneous, although it is not so in practice. We overcome this drawback by including more biochemical reactions, and derive a quadratic ordinary differential equation (ODE) based model.</p> <p>Results</p> <p>We show that the model, referred to above, does not exhibit bistability. We establish sufficiency conditions for the domain of attraction of an equilibrium point of our ODE model for the special case of full-state feedback controller. We observe that the GAL regulatory system of <it>Kluyveromyces lactis </it>exhibits an aberration of monotone nonlinearity and apply the Rantzer multipliers to establish a class of stabilizing controllers for this system.</p> <p>Conclusion</p> <p>Feedback in a GAL regulatory system can be used to enhance the cellular memory. We show that the system can be modeled as a quadratic nonlinear system for which the effect of feedback on the domain of attraction of the equilibrium point can be characterized using <it>linear matrix inequality </it>(LMI) conditions that are easily implementable in software. The benefit of this result is that a mathematically sound approach to the synthesis of full-state and partial-state feedback controllers to regulate the cellular memory is now possible, irrespective of the number of state-variables or parameters of interest.</p

Performance of a North American Field Population and a Laboratory Colony of the Potato Tuberworm, Phthorimaea operculella, on Foliage of Resistant and Susceptible Potato Clones

Foliar resistance of two potato clones was tested against a Columbia Basin field population (CBFP) and a Colorado laboratory colony (COLC) of the potato tuberworm, Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae). The first clone was a cross of a cultivated potato, Solanum tuberosum L. (Solanales: Solanaceae), and a wild potato, Solanum berthaultii Hawkes (Q 174-2); the second clone was cv. Allegany, S. tuberosum L.. In no-choice assays, defoliation by P. operculella larvae of COLC and CBFP did not differ on Allegany and Q174-2. Larval weight and production of COLC and CBFP colonies were similarly reduced on Q174-2 compared to cv. Allegany, although larval weights and production of the CBFP population were slightly less affected by the host. Larval production by the COLC on Allegany was greater than that on Q174-2, while that of the CBFP on Allegany and Q174-2 did not differ. However, production of P. operculella larvae by the CBFP on Q174-2 during no-choice assays was greater than that in choice tests, indicating reduced host preference. Most of the larvae recovered from either host were fourth instars, followed by third instars. Although the levels of resistance expressed by Q174-2 potato clone to the two P. operculella populations differed in magnitude, nearly all of P. operculella performance criteria measured in this study were adversely affected by Q174-2 foliage compared to the commercial potato cultivar, cv. Allegany