Challenges in imaging and predictive modeling of rhizosphere processes

Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes

Potential energy landscape-based extended van der Waals equation

The inherent structures ({\it IS}) are the local minima of the potential energy surface or landscape, $U({\bf r})$, of an {\it N} atom system. Stillinger has given an exact {\it IS} formulation of thermodynamics. Here the implications for the equation of state are investigated. It is shown that the van der Waals ({\it vdW}) equation, with density-dependent $a$ and $b$ coefficients, holds on the high-temperature plateau of the averaged {\it IS} energy. However, an additional ``landscape'' contribution to the pressure is found at lower $T$. The resulting extended {\it vdW} equation, unlike the original, is capable of yielding a water-like density anomaly, flat isotherms in the coexistence region {\it vs} {\it vdW} loops, and several other desirable features. The plateau energy, the width of the distribution of {\it IS}, and the ``top of the landscape'' temperature are simulated over a broad reduced density range, $2.0 \ge \rho \ge 0.20$, in the Lennard-Jones fluid. Fits to the data yield an explicit equation of state, which is argued to be useful at high density; it nevertheless reproduces the known values of $a$ and $b$ at the critical point

The Potential Energy Landscape and Mechanisms of Diffusion in Liquids

The mechanism of diffusion in supercooled liquids is investigated from the potential energy landscape point of view, with emphasis on the crossover from high- to low-T dynamics. Molecular dynamics simulations with a time dependent mapping to the associated local mininum or inherent structure (IS) are performed on unit-density Lennard-Jones (LJ). New dynamical quantities introduced include r2_{is}(t), the mean-square displacement (MSD) within a basin of attraction of an IS, R2(t), the MSD of the IS itself, and g_{loc}(t) the mean waiting time in a cooperative region. At intermediate T, r2_{is}(t) posesses an interval of linear t-dependence allowing calculation of an intrabasin diffusion constant D_{is}. Near T_{c} diffusion is intrabasin dominated with D = D_{is}. Below T_{c} the local waiting time tau_{loc} exceeds the time, tau_{pl}, needed for the system to explore the basin, indicating the action of barriers. The distinction between motion among the IS below T_{c} and saddle, or border dynamics above T_{c} is discussed.Comment: submitted to pr

Development and Characterisation of a Gas System and its Associated Slow-Control System for an ATLAS Small-Strip Thin Gap Chamber Testing Facility

A quality assurance and performance qualification laboratory was built at McGill University for the Canadian-made small-strip Thin Gap Chamber (sTGC) muon detectors produced for the 2019-2020 ATLAS experiment muon spectrometer upgrade. The facility uses cosmic rays as a muon source to ionise the quenching gas mixture of pentane and carbon dioxide flowing through the sTGC detector. A gas system was developed and characterised for this purpose, with a simple and efficient gas condenser design utilizing a Peltier thermoelectric cooler (TEC). The gas system was tested to provide the desired 45 vol% pentane concentration. For continuous operations, a state-machine system was implemented with alerting and remote monitoring features to run all cosmic-ray data-acquisition associated slow-control systems, such as high/low voltage, gas system and environmental monitoring, in a safe and continuous mode, even in the absence of an operator.Comment: 23 pages, LaTeX, 14 figures, 4 tables, proof corrections for Journal of Instrumentation (JINST), including corrected Fig. 8b

The dynamical structure factor in topologically disordered systems

A computation of the dynamical structure factor of topologically disordered systems, where the disorder can be described in terms of euclidean random matrices, is presented. Among others, structural glasses and supercooled liquids belong to that class of systems. The computation describes their relevant spectral features in the region of the high frequency sound. The analytical results are tested with numerical simulations and are found to be in very good agreement with them. Our results may explain the findings of inelastic X-ray scattering experiments in various glassy systems.Comment: Version to be published in J. Chem. Phy

Analytic computation of the Instantaneous Normal Modes spectrum in low density liquids

We analytically compute the spectrum of the Hessian of the Hamiltonian for a system of N particles interacting via a purely repulsive potential in one dimension. Our approach is valid in the low density regime, where we compute the exact spectrum also in the localized sector. We finally perform a numerical analysis of the localization properties of the eigenfunctions.Comment: 4 RevTeX pages, 4 EPS figures. Revised version to appear on Phys. Rev. Let

Recent Deformation in the Bottom Sediments of Western and Southeastern Lake Ontario and its Association with Major Structures and Seismicity

Geophysical surveys, undertaken in the Toronto-Burlington corridor of western Lake Ontario and in the Rochester Basin of southeastern Lake Ontario, revealed the presence of features affecting the young lake-bottom sediments. In the western part of the lake, they include inferred pop-ups in bedrock, and plumose structures, dark linear patterns, and linear belts of circular to elliptical signatures in the modern mud. In southeastern Lake Ontario the glacial and post-glacial sediments display vertical separations of on the order of 10-15 m. Pop-ups are tectonically-induced structures. The features in the modern mud commonly parallel the orientation of P-stresses measured in Paleozoic rocks nearby and, along with the pop-ups, are spatially related to an aeromagnetic lineament. Furthermore, all of these features occur within a seismically active belt. The vertical displacements of the layered glacial and post-glacial sediments, within the Rochester Basin, are located along the southern margin of the postulated WSW extension of the seismically active St. Lawrence rift system and are interpreted to be due to faulting. The geologically young age of the sediments affected by the various deformational features, along with the characteristics of the features themselves, suggest that the lake-bottom sediments surveyed in this study may have recorded the effects of neotectonic processes.Des levés géophysiques effectués dans le corridor Toronto-Burlington, dans l'ouest du lac Ontario, a révélé la présence d'éléments qui altèrent les jeunes sédiments lacustres du fond. Dans la partie ouest du lac, dans la roche en place, il s'agit de structures de soulèvement (pop-ups) et, dans les boues récentes, de structures plumeuses, de réseaux de traits sombres et de zones linéaires de tracés circulaires à elliptiques. Dans la partie sud-est du lac Ontario, il y a dans les sédiments glaciaires et postglaciaires des rejets verticaux de l'ordre de 10 à 15 m. Les structures de soulèvement sont d'origine tectonique. Les formes dans les boues récentes, généralement parallèles à l'orientation des contraintes de compression mesurées dans les roches paléozoïques voisines, sont spatialement reliés, comme les structures de soulèvement, à un linéament aéromagnétique. De plus, toutes ces formes se trouvent dans une zone sismique active. Les rejets verticaux dans les sédiments glaciaires et postglaciaires stratifiés, à l'intérieur du basssin de Rochester, sont localisés le long de la bordure sud du prolongement présumé WSW du système actif du rift du Saint-Laurent et sont probablement attribuables à la formation de failles. La jeunesse des sédiments altérés par les déformations et les caractéristiques des déformations mêmes laissent croire que ces sédiments ont probablement enregistré les effets de processus néotectoniques.Geophysikalische Vermessungen, die im Toronto Burlington-Korridor des westlichen Ontariosees und im Rochester-Becken des sùdôstlichen Ontariosees durchgefùhrt wurden, deckten die Anwesenheit von Elementen auf, welche auf die jungen Seegrundsedimente einwirken. Im westlichen Teil des Sees bestehen sie aus Hebungen im anste-henden Gestein und im modernen Schlamm aus federartigen Strukturen, dunklen linearen Mustern und linearen Gùrteln mit kreisformigen bis ellipsenfôrmigen Umrissen. Im sùdôstlichen Ontariosee gibt es in den glazialen und postglazialen Sedimenten verti-kale Verwùrfe der GrôRenordnung von 10-15 m. Die Hebungen sind tektonischen Ursprungs. Die Formen im modernen Schlamm liegen im allgemeinen paralell zu der Orientierung der in den benachbarten palàozoischen Felsen gemessenen P-Stresse und sind zusammen mit den Hebungen ràumlich mit einem aeromagnetischen Lineament verbunden. AuRerdem treten aile dièse Formen innerhalb eines seismisch aktiven Gùrtels auf. Die vertikalen Verstellungen der geschichteten glazialen und postglazialen Sedimente innerhalb des Rochester-Beckens werden entlang des sùdlichen Rands der angenommenen WSW-Verlàngerung des seismisch aktiven Sankt-Lorenz-Spaltensystems lokalisiert. Das geologisch relativ junge Alter der durch die verschiedenen Verformungen Iàf3t vermu-ten, daB die in dieser Studie gemessenen Seegrundsedimente moglicherweise die Wirkungen neotektonischer Prozesse aufgezeichnet haben

Mode-coupling theory for multiple-time correlation functions of tagged particle densities and dynamical filters designed for glassy systems

The theoretical framework for higher-order correlation functions involving multiple times and multiple points in a classical, many-body system developed by Van Zon and Schofield [Phys. Rev. E 65, 011106 (2002)] is extended here to include tagged particle densities. Such densities have found an intriguing application as proposed measures of dynamical heterogeneities in structural glasses. The theoretical formalism is based upon projection operator techniques which are used to isolate the slow time evolution of dynamical variables by expanding the slowly-evolving component of arbitrary variables in an infinite basis composed of the products of slow variables of the system. The resulting formally exact mode-coupling expressions for multiple-point and multiple-time correlation functions are made tractable by applying the so-called N-ordering method. This theory is used to derive for moderate densities the leading mode coupling expressions for indicators of relaxation type and domain relaxation, which use dynamical filters that lead to multiple-time correlations of a tagged particle density. The mode coupling expressions for higher order correlation functions are also succesfully tested against simulations of a hard sphere fluid at relatively low density.Comment: 15 pages, 2 figure

Stigma as a fundamental hindrance to the United States opioid overdose crisis response.

Alexander Tsai and co-authors discuss the role of stigma in responses to the US opioid crisis

Mean-atom-trajectory model for the velocity autocorrelation function of monatomic liquids

We present a model for the motion of an average atom in a liquid or supercooled liquid state and apply it to calculations of the velocity autocorrelation function $Z(t)$ and diffusion coefficient $D$. The model trajectory consists of oscillations at a distribution of frequencies characteristic of the normal modes of a single potential valley, interspersed with position- and velocity-conserving transits to similar adjacent valleys. The resulting predictions for $Z(t)$ and $D$ agree remarkably well with MD simulations of Na at up to almost three times its melting temperature. Two independent processes in the model relax velocity autocorrelations: (a) dephasing due to the presence of many frequency components, which operates at all temperatures but which produces no diffusion, and (b) the transit process, which increases with increasing temperature and which produces diffusion. Because the model provides a single-atom trajectory in real space and time, including transits, it may be used to calculate all single-atom correlation functions.Comment: LaTeX, 8 figs. This is an updated version of cond-mat/0002057 and cond-mat/0002058 combined Minor changes made to coincide with published versio