Simulations on many scales: The synapse as an example

Computer simulation methods spanning several temporal and spatial scales are reviewed, focusing on their applications on the neuromuscular synapse. Quantum mechanics treats the enzymatic catalysis of neurotransmitters on the picometer scale. Molecular dynamics reveals conformational changes of the enzyme acetylcholinesterase for nanoseconds. Brownian dynamics follow the substrate molecule in its diffusion on the microsecond level. Methods such as finite elements describe the diffusion of neurotransmitters as a changing concentration continuum in the synapse. Promising directions for future research include integration of methods on several scales, and applying these methods to the acetylcholine receptor.

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A framework for benchmarking land models

Biogeosciences ◽

10.5194/bg-9-3857-2012 ◽

2012 ◽

Vol 9 (10) ◽

pp. 3857-3874 ◽

Cited By ~ 200

Author(s):

Y. Q. Luo ◽

J. T. Randerson ◽

G. Abramowitz ◽

C. Bacour ◽

E. Blyth ◽

...

Keyword(s):

Climate Change ◽

Land Surface ◽

Research Effort ◽

Spatial Scales ◽

A Priori ◽

Model Performance ◽

Future Research ◽

Test Model ◽

Performance Skills ◽

Temporal And Spatial

Abstract. Land models, which have been developed by the modeling community in the past few decades to predict future states of ecosystems and climate, have to be critically evaluated for their performance skills of simulating ecosystem responses and feedback to climate change. Benchmarking is an emerging procedure to measure performance of models against a set of defined standards. This paper proposes a benchmarking framework for evaluation of land model performances and, meanwhile, highlights major challenges at this infant stage of benchmark analysis. The framework includes (1) targeted aspects of model performance to be evaluated, (2) a set of benchmarks as defined references to test model performance, (3) metrics to measure and compare performance skills among models so as to identify model strengths and deficiencies, and (4) model improvement. Land models are required to simulate exchange of water, energy, carbon and sometimes other trace gases between the atmosphere and land surface, and should be evaluated for their simulations of biophysical processes, biogeochemical cycles, and vegetation dynamics in response to climate change across broad temporal and spatial scales. Thus, one major challenge is to select and define a limited number of benchmarks to effectively evaluate land model performance. The second challenge is to develop metrics of measuring mismatches between models and benchmarks. The metrics may include (1) a priori thresholds of acceptable model performance and (2) a scoring system to combine data–model mismatches for various processes at different temporal and spatial scales. The benchmark analyses should identify clues of weak model performance to guide future development, thus enabling improved predictions of future states of ecosystems and climate. The near-future research effort should be on development of a set of widely acceptable benchmarks that can be used to objectively, effectively, and reliably evaluate fundamental properties of land models to improve their prediction performance skills.

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The urban harvest approach as framework and planning tool for improved water and resource cycles

Water Science & Technology ◽

10.2166/wst.2015.299 ◽

2015 ◽

Vol 72 (6) ◽

pp. 998-1006 ◽

Cited By ~ 10

Author(s):

I. Leusbrock ◽

T. A. Nanninga ◽

K. Lieberg ◽

C. M. Agudelo-Vera ◽

K. J. Keesman ◽

...

Keyword(s):

Water Cycle ◽

Spatial Scales ◽

Future Research ◽

Urban Water ◽

Water Energy Nexus ◽

Management Concepts ◽

First Results ◽

Treatment Concepts ◽

Temporal And Spatial ◽

The Impact

Water and resource availability in sufficient quantity and quality for anthropogenic needs represents one of the main challenges in the coming decades. To prepare for upcoming challenges such as increased urbanization and climate change related consequences, innovative and improved resource management concepts are indispensable. In recent years we have developed and applied the urban harvest approach (UHA). The UHA aims to model and quantify the urban water cycle on different temporal and spatial scales. This approach allowed us to quantify the impact of the implementation of water saving measures and new water treatment concepts in cities. In this paper we will introduce the UHA and its application for urban water cycles. Furthermore, we will show first results for an extension to energy cycles and highlight future research items (e.g. nutrients, water–energy–nexus).

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THE SZ4D INITIATIVE: AN EMERGING OPPORTUNITY FOR COORDINATED RESEARCH IN SUBDUCTION ZONE DEFORMATION ACROSS TEMPORAL AND SPATIAL SCALES

10.1130/abs/2019am-338373 ◽

2019 ◽

Author(s):

Harold J. Tobin ◽

◽

Alison R. Duvall

Keyword(s):

Subduction Zone ◽

Spatial Scales ◽

Temporal And Spatial ◽

Zone Deformation

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Larval Feeding: Mechanisms, Rates, and Performance in Nature

10.1093/oso/9780198786962.003.0007 ◽

2018 ◽

Keyword(s):

Marine Invertebrates ◽

Spatial Scales ◽

Size Spectrum ◽

Larval Feeding ◽

Natural Habitats ◽

Feeding Mechanism ◽

Temporal And Spatial ◽

And Performance ◽

Bioenergetics Models ◽

Many Particles

Larvae of many marine invertebrates must capture and ingest particulate food in order to develop to metamorphosis. These larvae use only a few physical processes to capture particles, but implement these processes using diverse morphologies and behaviors. Detailed understanding of larval feeding mechanism permits investigators to make predictions about feeding performance, including the size spectrum of particles larvae can capture and the rates at which they can capture them. In nature, larvae are immersed in complex mixtures of edible particles of varying size, density, flavor, and nutritional quality, as well as many particles that are too large to ingest. Concentrations of all of these components vary on fine temporal and spatial scales. Mechanistic models linking larval feeding mechanism to performance can be combined with data on food availability in nature and integrated into broader bioenergetics models to yield increased understanding of the biology of larvae in complex natural habitats.

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Humans and the Environment

10.1093/oso/9780199590292.001.0001 ◽

2013 ◽

Keyword(s):

Spatial Scales ◽

Empirical Studies ◽

Human Action ◽

Cultural Practice ◽

Environmental Archaeology ◽

Archaeological Data ◽

Temporal And Spatial ◽

Global And Local ◽

The Relationship ◽

The Way

The environment has always been a central concept for archaeologists and, although it has been conceived in many ways, its role in archaeological explanation has fluctuated from a mere backdrop to human action, to a primary factor in the understanding of society and social change. Archaeology also has a unique position as its base of interest places it temporally between geological and ethnographic timescales, spatially between global and local dimensions, and epistemologically between empirical studies of environmental change and more heuristic studies of cultural practice. Drawing on data from across the globe at a variety of temporal and spatial scales, this volume resituates the way in which archaeologists use and apply the concept of the environment. Each chapter critically explores the potential for archaeological data and practice to contribute to modern environmental issues, including problems of climate change and environmental degradation. Overall the volume covers four basic themes: archaeological approaches to the way in which both scientists and locals conceive of the relationship between humans and their environment, applied environmental archaeology, the archaeology of disaster, and new interdisciplinary directions.The volume will be of interest to students and established archaeologists, as well as practitioners from a range of applied disciplines.

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8-Day and Daily Maximum and Minimum Air Temperature Estimation via Machine Learning Method on a Climate Zone to Global Scale

Remote Sensing ◽

10.3390/rs13122355 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2355

Author(s):

Linglin Zeng ◽

Yuchao Hu ◽

Rui Wang ◽

Xiang Zhang ◽

Guozhang Peng ◽

...

Keyword(s):

Spatial Scale ◽

Air Temperature ◽

Spatial Scales ◽

Model Performance ◽

Global Scale ◽

Scale Model ◽

Validation Dataset ◽

Daily Maximum ◽

Climate Zone ◽

Temporal And Spatial

Air temperature (Ta) is a required input in a wide range of applications, e.g., agriculture. Land Surface Temperature (LST) products from Moderate Resolution Imaging Spectroradiometer (MODIS) are widely used to estimate Ta. Previous studies of these products in Ta estimation, however, were generally applied in small areas and with a small number of meteorological stations. This study designed both temporal and spatial experiments to estimate 8-day and daily maximum and minimum Ta (Tmax and Tmin) on three spatial scales: climate zone, continental and global scales from 2009 to 2018, using the Random Forest (RF) method based on MODIS LST products and other auxiliary data. Factors contributing to the relation between LST and Ta were determined based on physical models and equations. Temporal and spatial experiments were defined by the rules of dividing the training and validation datasets for the RF method, in which the stations selected in the training dataset were all included or not in the validation dataset. The RF model was first trained and validated on each spatial scale, respectively. On a global scale, model accuracy with a determination coefficient (R2) > 0.96 and root mean square error (RMSE) < 1.96 °C and R2 > 0.95 and RMSE < 2.55 °C was achieved for 8-day and daily Ta estimations, respectively, in both temporal and spatial experiments. Then the model was trained and cross-validated on each spatial scale. The results showed that the data size and station distribution of the study area were the main factors influencing the model performance at different spatial scales. Finally, the spatial patterns of the model performance and variable importance were analyzed. Both daytime and nighttime LST had a significant contribution in the 8-day Tmax estimation on all the three spatial scales; while their contribution in daily Tmax estimation varied over different continents or climate zones. This study was expected to improve our understanding of Ta estimation in terms of accuracy variations and influencing variables on different spatial and temporal scales. The future work mainly includes identifying underlying mechanisms of estimation errors and the uncertainty sources of Ta estimation from a local to a global scale.

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Are We Doing ‘Systems’ Research? An Assessment of Methods for Climate Change Adaptation to Hydrohazards in a Complex World

Sustainability ◽

10.3390/su11041163 ◽

2019 ◽

Vol 11 (4) ◽

pp. 1163 ◽

Cited By ~ 4

Author(s):

Melissa Bedinger ◽

Lindsay Beevers ◽

Lila Collet ◽

Annie Visser

Keyword(s):

Climate Change ◽

Human Nature ◽

Climate Change Adaptation ◽

Time Scales ◽

Spatial Scales ◽

Local Context ◽

Multiple Time Scales ◽

Future Research ◽

Multiple Time ◽

Systems Research

Climate change is a product of the Anthropocene, and the human–nature system in which we live. Effective climate change adaptation requires that we acknowledge this complexity. Theoretical literature on sustainability transitions has highlighted this and called for deeper acknowledgment of systems complexity in our research practices. Are we heeding these calls for ‘systems’ research? We used hydrohazards (floods and droughts) as an example research area to explore this question. We first distilled existing challenges for complex human–nature systems into six central concepts: Uncertainty, multiple spatial scales, multiple time scales, multimethod approaches, human–nature dimensions, and interactions. We then performed a systematic assessment of 737 articles to examine patterns in what methods are used and how these cover the complexity concepts. In general, results showed that many papers do not reference any of the complexity concepts, and no existing approach addresses all six. We used the detailed results to guide advancement from theoretical calls for action to specific next steps. Future research priorities include the development of methods for consideration of multiple hazards; for the study of interactions, particularly in linking the short- to medium-term time scales; to reduce data-intensivity; and to better integrate bottom–up and top–down approaches in a way that connects local context with higher-level decision-making. Overall this paper serves to build a shared conceptualisation of human–nature system complexity, map current practice, and navigate a complexity-smart trajectory for future research.

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Sequential modelling of the Earth’s core magnetic field

Earth Planets and Space ◽

10.1186/s40623-020-01230-1 ◽

2020 ◽

Vol 72 (1) ◽

Cited By ~ 3

Author(s):

Guillaume Ropp ◽

Vincent Lesur ◽

Julien Baerenzung ◽

Matthias Holschneider

Keyword(s):

Magnetic Field ◽

Prior Information ◽

Spatial Scales ◽

Model Parameters ◽

International Geomagnetic Reference Field ◽

The Earth ◽

Temporal And Spatial ◽

Different Sources ◽

Original Approach ◽

Modelling Approach

Abstract We describe a new, original approach to the modelling of the Earth’s magnetic field. The overall objective of this study is to reliably render fast variations of the core field and its secular variation. This method combines a sequential modelling approach, a Kalman filter, and a correlation-based modelling step. Sources that most significantly contribute to the field measured at the surface of the Earth are modelled. Their separation is based on strong prior information on their spatial and temporal behaviours. We obtain a time series of model distributions which display behaviours similar to those of recent models based on more classic approaches, particularly at large temporal and spatial scales. Interesting new features and periodicities are visible in our models at smaller time and spatial scales. An important aspect of our method is to yield reliable error bars for all model parameters. These errors, however, are only as reliable as the description of the different sources and the prior information used are realistic. Finally, we used a slightly different version of our method to produce candidate models for the thirteenth edition of the International Geomagnetic Reference Field.

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Dissecting the turbulent weather driven by mechanical AGN feedback

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/staa2747 ◽

2020 ◽

Vol 498 (4) ◽

pp. 4983-5002

Author(s):

D Wittor ◽

M Gaspari

Keyword(s):

Feedback Loop ◽

Spatial Scales ◽

Self Regulation ◽

Cosmic Time ◽

Massive Galaxies ◽

Temporal And Spatial ◽

Lagrangian Tracers ◽

Field Unit ◽

Integral Field ◽

Gaseous Halo

ABSTRACT Turbulence in the intracluster, intragroup, and circumgalactic medium plays a crucial role in the self-regulated feeding and feedback loop of central supermassive black holes. We dissect the 3D turbulent ‘weather’ in a high-resolution Eulerian simulation of active galactic nucleus (AGN) feedback, shown to be consistent with multiple multiwavelength observables of massive galaxies. We carry out post-processing simulations of Lagrangian tracers to track the evolution of enstrophy, a proxy of turbulence, and its related sinks and sources. This allows us to isolate in depth the physical processes that determine the evolution of turbulence during the recurring strong and weak AGN feedback events, which repeat self-similarly over the Gyr evolution. We find that the evolution of enstrophy/turbulence in the gaseous halo is highly dynamic and variable over small temporal and spatial scales, similar to the chaotic weather processes on Earth. We observe major correlations between the enstrophy amplification and recurrent AGN activity, especially via its kinetic power. While advective and baroclinc motions are always subdominant, stretching motions are the key sources of the amplification of enstrophy, in particular along the jet/cocoon, while rarefactions decrease it throughout the bulk of the volume. This natural self-regulation is able to preserve, as ensemble, the typically observed subsonic turbulence during cosmic time, superposed by recurrent spikes via impulsive anisotropic AGN features (wide outflows, bubbles, cocoon shocks). This study facilitates the preparation and interpretation of the thermo-kinematical observations enabled by new revolutionary X-ray integral field unit telescopes, such as XRISM and Athena.

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