Relevant Scales Research Articles

Physics-Based Protein Networks Might Recover Effectful Mutations─a Case Study on Cathepsin G.

Molecular dynamics simulations have been remarkably effective for observing and analyzing structures and dynamics of proteins, with longer trajectories being computed every day. Still, often, relevant time scales are not observed. Adequately analyzing the generated trajectories can highlight the interesting areas within a protein such as mutation sites or allosteric hotspots, which might foreshadow dynamics untouched by the simulations. We employ a physics-based protein network and propose that such a network can adequately analyze the protein dynamics. The analysis is conducted on simulations of cathepsin G and neutrophil elastase, which are remarkably similar but with different specificities. However, a single mutation in cathepsin G recovers the specificity of neutrophil elastase. The physics-based network built on the interactions between residues instead of the distances can pinpoint the active triad in the proteins studied. Overall, the network seems to capture the structural behavior better than purely distance-based networks.

A preliminary comparison of the clinical efficacy of repetitive transcranial magnetic stimulation with facial feature point localization and navigated localization in the treatment of depression

ObjectiveTo compare the clinical efficacy of repetitive transcranial magnetic stimulation (rTMS) under facial feature point localization (FFP) localization versus neuro-navigated localization for depression. Methods42 depressed patients were randomly assigned to two groups, received 10 Hz rTMS twice daily for 10 consecutive days. Relevant symptom scale assessments were conducted by professionals at baseline, after 10 sessions, and at the end of treatment. The confidence interval was calculated at a 95 % confidence level. The significant level was set at p < 0.05. ResultsThe absolute change in HAMD total score from baseline to the end of therapy did not differ significantly between the groups. The generalized estimating equation showed the main effect of time was significant, which showed improvement of depressive symptoms in patients throughout treatment. Upon completion of the treatment, FFP group showed a response rate of 64.7 % and a remission rate of 29.4 %, whereas the navigated group exhibited a response rate of 61.1 % and a remission rate of 44.4 %. There was no serious adverse events occurred during the treatment process. Throughout the study, no intervention was made on the normal medication treatment, and some patients had concomitant antidepressants and benzodiazepines. ConclusionThere was no significant difference in clinical efficacy between FFP localization and navigation localization in the small-sample study. However, due to the limited sample size and lack of rigorous non-inferiority testing, the superiority of one over the other remains uncertain, necessitating rigorous experimental design to validate the efficacy difference between the two localization methods.

On identifying dynamic length scales in crystal plasticity

Materials are often heterogeneous at various length scales, with variations in grain structure, defects, and composition which has a strong influence on the emergent macroscopic plastic behavior. In particular, heterogeneities lead to fluctuations in the plastic response in the form of jerky flow and ubiquitous strain bursts. One of the crucial aspects of plasticity modeling is scale bridging: In order to deliver physically correct crystal plasticity models, one needs to determine relevant microstructural length scales. In this paper we advance the idea that continuum descriptions of dislocation mediated plasticity cannot neglect dynamic correlations related to the avalanche behavior. We present an extensive weakest link analysis of crystal plasticity by means of three-dimensional discrete dislocation dynamics simulations with and without spherical precipitates. We investigate strain bursts and related length scales and conclude that while sufficiently strong obstacles to dislocation motion tend to confine the dislocation avalanches within well-defined sub-volumes, in pure dislocation systems the avalanches may span the system, implying that the dynamic length scale is, in fact, the size of the entire sample. Consequences of this finding on continuum modeling are thoroughly discussed.

Strong evidence for universality in homogeneous compressible turbulence

Quantifying the degree of universality in compressible turbulence is challenging due to the existence of different modes and their complex interactions. For a restricted family of flows, Donzis and John [Phys. Rev. Fluids 5, 084609 (2020)] showed that universal behavior is indeed observed in compressible turbulence if the ratio of dilatational to solenoidal root mean square (rms) velocities (δ=u′d/u′s) is incorporated as a scaling parameter along with the traditional turbulent Mach number (Mt=u′/〈c〉, where u′ is the rms velocity and 〈c〉 is the mean speed of sound). In this paper, we argue for the generality of those results by analyzing a wide range of compressible turbulent flows spanning a variety of flow configurations and setups to assess the degree of universal behavior. These include, among others, reacting flows, flows with solenoidal, thermal, and dilatational forcing, and flows with mean shear and bulk viscosity. We also performed new direct numerical simulations, which include turbulence in situations where vibrational modes of constitutive molecules are not in thermal equilibrium. Collectively, we offer the largest comparison across studies in the literature to date. We find that despite the wide range of forcing conditions and physical processes, universality holds across all these turbulent flows to a very satisfactory degree when both δ and Mt are considered as intrinsic compressibility parameters. The statistics investigated here—single-point statistics up to order four—are chosen such that they represent different ranges across the spectrum of dynamically relevant turbulence scales. We discuss the applicability of the purposed universal behavior for other key statistics in these turbulent flows, including two-point statistics and inhomogeneity effects, and the perspective it opens for modeling them.

Vertical Distribution of Rocky Intertidal Organisms Shifts With Sea-Level Variability on the Northeast Pacific Coast.

Disentangling the effects of cyclical variability in environmental forcing and long-term climate change on natural communities is a major challenge for ecologists, managers, and policy makers across ecosystems. Here we examined whether the vertical distribution of rocky intertidal taxa has shifted with sea-level variability occurring at multiple temporal scales and/or long-term anthropogenic sea-level rise (SLR). Because of the distinct zonation characteristic of intertidal communities, any shift in tidal dynamics or average sea level is expected to have large impacts on community structure and function. We found that across the Northeast Pacific Coast (NPC), sea level exhibits cyclical seasonal variability, tidal amplitude exhibits ecologically significant variability coherent with the 18.6-year periodicity of lunar declination, and long-term sea-level rise is occurring. Intertidal taxa largely do not exhibit significant vertical distribution shifts coherent with short-term (monthly to annual) sea-level variability but do exhibit taxa-specific vertical distribution shifts coherent with cyclical changes in lunar declination and long-term SLR at decadal timescales. Finally, our results show that responses to cyclical celestial mechanics and SLR vary among taxa, primarily according to their vertical distribution. Long-term SLR is occurring on ecologically relevant scales, but the confounding effects of cyclical celestial mechanics make interpreting shifts in zonation or community structure challenging. Such cyclical dynamics alternatingly amplify and dampen long-term SLR impacts and may modify the impacts of other global change related stressors, such as extreme heat waves and swell events, on intertidal organisms living at the edge of their physiological tolerances. As a result, intertidal communities will likely experience cyclical periods of environmental stress and concomitant nonlinear shifts in structure and function as long-term climate change continues. Our results demonstrate that consistent, large-scale monitoring of marine ecosystems is critical for understanding natural variability in communities and documenting long-term change.

The Effect of Conflict Management Strategies on Job Satisfaction: A Study in the Accounting Sector

The aim of this study is to examine the effect of conflict management on job satisfaction for the accounting sectorand to examine the effect between the conflict management strategies used by employees and their job satisfaction. Also, demographic characteristics are to contribute to the related literature by examining the effect of job satisfaction, conflict management, and conflict management strategies. In this study, survey research method and relational screening model were used. Then, e-survey was applied to 451 accounting professionals through convenience sampling among approximately 200.000 accounting sector employees operating in Turkey and 403 questionnaires were analysed. The factor loadings of the scales were examined, followed by reliability and normal distribution analyses of the relevant scales and then parametric tests were performed. Pearson correlation analysis and regression analysis were performed to examine the relationship between constructive, adaptive, coercive, avoidant and compromising subscales of job satisfaction scale and conflict management strategy scale. According to the results, conflict management has a positive effect on job satisfaction. Also, constructive, accommodative, compromise, avoidant and coercive conflict management strategies were also found to have a positive effect on job satisfaction. When demographic characteristics were analysed, it was found that there was no significant difference between gender, marital status, age, education level variables and job satisfaction, conflict management, adaptive, constructive, coercive, avoidant and accommodative conflict management strategies. It was observed that there was a significant difference between the professional experience variable and compatible conflict management strategy, also between the occupation variable and coercive conflict management strategy.

Multiphase flow modelling of gas migration from a hypothetical integrity-compromised petroleum well in the peace region of North-eastern British Columbia, Canada

Well-integrity failure occurs in a small subset of petroleum wells, resulting in release of fugitive gas into intersected geologic formations. Released fugitive gas from geoenergy systems is a growing environmental concern that can contaminate groundwater aquifers and emit greenhouse gases (GHGs) to atmosphere. Currently, the roles of well-cement quality and properties of intersected geologic formations on the environmental outcomes of well-integrity failure is poorly understood. To advance understanding, we numerically modelled a hypothetical fugitive methane release from a petroleum well intersecting the Sunset Paleovalley aquifer system in Northeast British Columbia, Canada. We simulate a 10-year release and migration of fugitive gas into a two dimensional, two-phase, two-component advective flow field with the subsurface properties informed by field and laboratory data. We evaluate the effects of cement quality, gas release depth, and geologic heterogeneity on fugitive-gas containment or emission by defining and/or evaluating three key numbers: a) emission-retention ratio (ERR), b) well integrity index (WII), and c) fugitive gas mobility ratio (MR) over relevant spatiotemporal scales. We show that ERR and WII capture the bifurcated impacts of fugitive gas from petroleum wells, including groundwater contamination and atmospheric emissions. A WII close to one reduces vertical fugitive-gas migration along the well bore, fosters lateral migration into intersected geologic materials and significantly limits GHG emissions to atmosphere. MR and ERR values show fugitive-gas migration and fate are primarily controlled by the casing annulus cement quality, particularly when fugitive gas is released at shallow depths. We conclude that the quality of petroleum-well cement is among the parameters controlling the migration pathways, impacts, and fate of fugitive-gas release.

Introductory Tutorials for Simulating Protein Dynamics with GROMACS.

Atomistic molecular dynamics (MD) simulations have become an indispensable tool for investigating the structure, dynamics, and energetics of biomolecules. Continual optimization of software algorithms and hardware has enabled investigators to access biologically relevant time scales in feasible amounts of computing time. Given the widespread use and utility of MD simulations, there is considerable interest in learning essential skills in performing them. Here, we present a set of introductory tutorials for performing MD simulations of proteins in the popular, open-source GROMACS package. Three exercises are detailed, including simulating a single protein, setting up a protein complex, and performing umbrella sampling simulations to model the unfolding of a short polypeptide. Essential features and input settings are illustrated throughout. The purpose of these tutorials is to provide new users with a general understanding of foundational workflows, from which they can design their own simulations.

Quantitative matching of forensic evidence fragments using fracture surface topography and statistical learning

The complex jagged trajectory of fractured surfaces of two pieces of forensic evidence is used to recognize a “match” by using comparative microscopy and tactile pattern analysis. The material intrinsic properties and microstructures, as well as the exposure history of external forces on a fragment of forensic evidence have the premise of uniqueness at a relevant microscopic length scale (about 2–3 grains for cleavage fracture), wherein the statistics of the fracture surface become non-self-affine. We utilize these unique features to quantitatively describe the microscopic aspects of fracture surfaces for forensic comparisons, employing spectral analysis of the topography mapped by three-dimensional microscopy. Multivariate statistical learning tools are used to classify articles and result in near-perfect identification of a “match” and “non-match” among candidate forensic specimens. The framework has the potential for forensic application across a broad range of fractured materials and toolmarks, of diverse texture and mechanical properties.

Self-chemophoresis in the thin diffuse interface approximation

Self-chemophoresis is an appealing and quite successful interpretation of the motility exhibited by certain chemically active colloidal particles suspended in a solution of their ‘fuel’: the particle has a phoretic response to self-generated, rather than externally imposed, inhomogeneities in the chemical composition of the solution. The postulated mechanism of chemophoresis is the interaction of the particle (via an adsorption potential) with the chemical inhomogeneities in the surrounding medium. When the range of this interaction is much smaller than any other relevant scale in the system, the (translational and rotational) phoretic velocities can be described in terms of a phoretic coefficient and a slip fluid velocity at the surface of the particle. Using the case of a spherical particle as a simple and physically insightful example, here we exploit an integral representation of the rigid-body motion to critically re-examine this framework. The systematic analysis highlights two steps in the approximation: first the thin–layer approximation (very large particle size), and subsequently a lubrication approximation (slow variation of the adsorption potential along the tangential direction). We also discuss how these approximations could be relaxed and the effect of this on the particle's motion.

High-resolution urban climate simulations for heat and health applications in Philadelphia

Stakeholders need high-resolution urban climate information for city planning and adaptation to climate risks. Climate models have too coarse a spatial resolution to properly represent cities at the relevant scale, and downscaled products often fail to account for urban effects. We propose here a methodological framework for producing high-resolution urban databases that are used to drive the SURFEX-TEB land surface and urban canopy models. A historical simulation is carried out over the period 1991–2020, based on a reanalysis of the city of Philadelphia (Pennsylvania, USA). The simulation is compared with observations outside and inside the city, as well as with a field campaign. The results show good agreement between the model and observations, with average summer biases of only −1 °C and + 0.8 °C for daily minimum and maximum temperatures outside the city, and almost none inside. The simulation is used to calculate the maximum daily heat index (HIX) and to study emergency heat alerts. The HIX is slightly overestimated and, consequently, the model simulates too many heat events if not bias corrected. Overall, HIX conditions at Philadelphia International Airport are found to be suitable proxies for city-wide summer conditions, and therefore are appropriate to use for emergency heat declarations.

Multiferroicity in plastically deformed SrTiO3

Quantum materials have a fascinating tendency to manifest novel and unexpected electronic states upon proper manipulation. Ideally, such manipulation should induce strong and irreversible changes and lead to new relevant length scales. Plastic deformation introduces large numbers of dislocations into a material, which can organize into extended structures and give rise to qualitatively new physics as a result of the huge localized strains. However, this approach is largely unexplored in the context of quantum materials, which are traditionally grown to be as pristine and clean as possible. Here we show that plastic deformation induces robust magnetism in the quantum paraelectric SrTiO3, a property that is completely absent in the pristine material. We combine scanning magnetic measurements and near-field optical microscopy to find that the magnetic order is localized along dislocation walls and coexists with ferroelectric order along the walls. The magnetic signals can be switched on and off via external stress and altered by external electric fields, which demonstrates that plastically deformed SrTiO3 is a quantum multiferroic. These results establish plastic deformation as a versatile knob for the manipulation of the electronic properties of quantum materials.

Low-income consumers’ informal and formal financial service experiences: perceptions of access, inclusion, and social dependence

Purpose Low-income consumers’ perceptions of access and inclusion in financial services, remain underresearched. To fill this gap, the purpose of this study, is to investigate elements of low-income consumers’ informal and formal financial service experiences, from their personal experience. Design/methodology/approach Mixed methods using data collected from low-income consumers in Latin America, reveal a spectrum of consumer perceptions making up access, inclusion and social dependence within financial service experiences. Scales, grounded in the consumer experience, are developed, validated and used to test a model of consumers’ service inclusivity perceptions. Findings Service costs, information and documentation difficulty, convenience and social dynamics influence low-income consumers’ perceptions of financial service inclusivity. Research limitations/implications Analysis reveals differentiation in the impact of aspects of low-income consumers’ experiences between formal and informal financial services. Working directly with this unique population exposes the nuance of their financial service experiences. Practical implications This research provides a more holistic perspective on low-income consumers’ financial service experience and provides contextually relevant scales with robust psychometric properties. Services marketers can use this research to inform design and evaluation of financial service offerings for low-income consumers. Originality/value This research contributes to study of the wellbeing of low-income consumers by providing understanding of their financial service experiences from their point-of-view and providing contextually-relevant, empirically validated tools for future inquiry.

PSInet: a new global water potential network.

Given the pressing challenges posed by climate change, it is crucial to develop a deeper understanding of the impacts of escalating drought and heat stress on terrestrial ecosystems and the vital services they offer. Soil and plant water potential play a pivotal role in governing the dynamics of water within ecosystems and exert direct control over plant function and mortality risk during periods of ecological stress. However, existing observations of water potential suffer from significant limitations, including their sporadic and discontinuous nature, inconsistent representation of relevant spatio-temporal scales and numerous methodological challenges. These limitations hinder the comprehensive and synthetic research needed to enhance our conceptual understanding and predictive models of plant function and survival under limited moisture availability. In this article, we present PSInet (PSI-for the Greek letter Ψ used to denote water potential), a novel collaborative network of researchers and data, designed to bridge the current critical information gap in water potential data. The primary objectives of PSInet are as follows. (i) Establishing the first openly accessible global database for time series of plant and soil water potential measurements, while providing important linkages with other relevant observation networks. (ii) Fostering an inclusive and diverse collaborative environment for all scientists studying water potential in various stages of their careers. (iii) Standardizing methodologies, processing and interpretation of water potential data through the engagement of a global community of scientists, facilitated by the dissemination of standardized protocols, best practices and early career training opportunities. (iv) Facilitating the use of the PSInet database for synthesizing knowledge and addressing prominent gaps in our understanding of plants' physiological responses to various environmental stressors. The PSInet initiative is integral to meeting the fundamental research challenge of discerning which plant species will thrive and which will be vulnerable in a world undergoing rapid warming and increasing aridification.

Thermochemical recycling of polystyrene waste by pyrolysis using a pilot-scale auger reactor: Process demonstration in a relevant environment

This study presents the pyrolysis of polystyrene waste using a single-auger pyrolysis reactor at an industrially relevant scale, i.e. within the fifth technology readiness level (TRL-5). In order to gain a better understanding of the influence of the main variables involved in this technology, a thorough experimental campaign was performed with PS feed rates of 6 and 9 kg/h, covering a temperature range of 450–600 °C. These variables influence not only the distribution of the products, but also the presence of compounds that may affect the suitability of the pyro-oil for re-polymerisation processes. In this sense, gas chromatography (GC), gas chromatography coupled to mass spectrometry (GC/MS) and simulated distillation (SimDist) of the resulting pyro-oils provided valuable insights into styrene purification. The data collected confirms the strength of the auger reactor for thermochemical recycling of polystyrene waste, and contributes to the future development of the plastics circularity on an industrial scale.

Multi-phase-field modeling of the dissolution behavior of stoichiometric particles on experimentally relevant length scales

The dissolution of stoichiometric particles within a melt plays a crucial role in various material processes. This study presents a comprehensive phase-field model to analyze the dissolution behavior of these stoichiometric particles under experimental conditions. Our approach addresses the classical phase-field challenges related to modeling stoichiometric compounds and scaling to experimentally relevant lengths in a multi-phase, multi-component context. To overcome the difficulties posed by stoichiometric compounds, we rederive the classical phase-field evolution equations for a multi-phase system, adopting a composition-independent free energy expression for the stoichiometric compound. Additionally, we extend Feyen’s high driving force model [Feyen and Moelans, Acta Materialia, 256 (2023)] to multi-component systems, allowing us to perform quantitative simulations for technologically relevant material systems at experimental length scales within a reasonable computing time. The model’s precision in capturing diffusion-controlled transformations, including dissolution, growth, and the Gibbs–Thomson effect, is validated against analytical solutions for a hypothetical system. The quantitative nature of the model is validated by applying it to the dissolution of Al2O3 particles in CaO–Al2O3–SiO2 slags. We break new ground by conducting three-dimensional simulations for a system size of 875μm×875μm×875μm, directly comparable to confocal scanning laser microscopy experiments, where previous models were limited to two-dimensional simulations and a system size of 2μm×2μm. This validation underscores the model’s proficiency to quantitatively describe the diffusion-controlled dissolution of Al2O3 at the experimentally relevant length scales.

A study on the scale dependence of mixing indices for Eulerian multiphase models

AbstractMixing can vary based on the scale at which the system is observed, and a mixing index that can capture the features at different length scales is desirable. In this article, we analyze the scale dependence of the mixing indices developed for Eulerian multiphase models. Relevant length scales are distinguished by filtering solid fraction fields. The scale‐dependence study is first done on manufactured fields of solid fraction to assess the performance of the mixing indices. The study is extended to a two‐dimensional CFD simulation of the segregation of a bidisperse gas–solid mixture. The local mixing index performs well in capturing the spatial variation of mixing at different scales. The scale dependence of two global mixing indices is considered in the study, where the state of mixing is defined based on statistical measures. We demonstrate that the choice of measures influences the sensitivity of mixing indices to mixing at different scales.

Cross-cultural validation of the genetic counseling outcome scale in Korea.

The Genetic Counseling Outcome Scale (GCOS-24) was developed to measure patient-reported outcomes to evaluate the effectiveness of genetic counseling and testing services. In the current study, the Korean version of GCOS (K-GCOS) was developed to reflect the sociocultural characteristics of Korea, and its clinical applicability was assessed. Overall, 231 Koreans, including patients with genetic diseases and their family members, participated and completed the K-GCOS, Hospital Anxiety and Depression Scale (HADS), Multidimensional Health Locus of Control (MHLC) scale, and Satisfaction with Life Scale (SWLS). Validity was examined by assessing the correlations between K-GCOS scores and other relevant scale scores. Reliability was confirmed using Cronbach's alpha and test-retest scores, measured over 2 weeks. We performed exploratory factor analysis of the five structures of GCOS-24. For K-GCOS, four-factor structures were identified: "cognitive-behavioral control," "uncertainty about control," "hope," and "emotional regulation." Four original GCOS-24 items were removed because of low factor loadings and small inter-item correlations. K-GCOS-20 scores were positively correlated with SWLS (r = 0.456) and MHLC-internal (r = 0.213) scores but negatively correlated with HADS (anxiety r = -0.428, depression r = -0.469) and MHLC-internal (r = -0.278) scores. These findings demonstrate that K-GCOS-20 is a reliable and valid tool for evaluating genetic counseling services in Korea.

Landscape-scale predictions of future grassland conversion to cropland or development.

Grassland conservation planning often focuses on high-risk landscapes, but many grassland conversion models are not designed to optimize conservation planning because they lack multidimensional risk assessments and are misaligned with ecological and conservation delivery scales. To aid grassland conservation planning, we developed landscape-scale models at relevant scales that predict future (2021-2031) total and proportional loss of unprotected grassland to cropland or development. We developed models for 20 ecoregions across the contiguous United States by relating past conversion (2011-2021) to a suite of covariates in random forest regression models and applying the models to contemporary covariates to predict future loss. Overall, grassland loss models performed well, and explanatory power varied spatially across ecoregions (total loss model: weighted group mean R2=0.89 [range: 0.83-0.96], root mean squared error [RMSE]=9.29ha [range: 2.83-22.77ha]; proportional loss model: weighted group mean R2=0.74 [range: 0.64-0.87], RMSE=0.03 [range: 0.02-0.06]). Amount of crop in the landscape and distance to cities, ethanol plants, and concentrated animal feeding operations had high variable importance in both models. Total grass loss was greater when there were moderate amounts of grass, crop, or development (∼50%) in the landscape. Proportional grass loss was greater when there was less grass (∼<30%) and more crop or development (∼>50%). Some variables had a large effect on only a subset of ecoregions, for example, grass loss was greater when ∼>70% of the landscape was enrolled in the Conservation Reserve Program. Our methods provide a simple and flexible approach for developing risk layers well suited for conservation that can be extended globally. Our conversion models can support conservation planning by enabling prioritization as a function of risk that can be further optimized by incorporating biological value and cost.

Critical surface adsorption of confined binary liquids with locally conserved mass and composition

Close to a solid surface, the properties of a fluid deviate significantly from their bulk values. In this context, we study the surface adsorption profiles of a symmetric binary liquid confined to a slit pore by means of molecular dynamics simulations; the latter naturally entails that mass and concentration are locally conserved. Near a bulk consolute point, where the liquid exhibits a demixing transition with the local concentration as the order parameter, we determine the order parameter profiles and characterise the relevant critical scaling behaviour, in the regime of strong surface attraction, for a range of pore widths and temperatures. The obtained order parameter profiles decay monotonically near the surfaces, also in the presence of a pronounced layering in the number density. Overall, our results agree qualitatively with recent theoretical predictions from a mesoscopic field-theoretical approach for the canonical ensemble.