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11. CMT3D - Software

Author(s):
Sawade, Lucas
Abstract:
Software packages to invert for Global Centroid Moment Tensors (GCMT). The software is written in Python and fully modular. Especially the forward modelling method can easily be changed. The software was written with the goal in mind to use the global, seismic forward-modelling software SPECFEM3D_GLOBE to compute three-dimensional, heterogeneous Green's functions for the inversion of the moment tensor.
Type:
Software
Issue Date:
20 December 2021

12. Princeton Open Ventilation Monitor

Author(s):
Bourrianne, Philippe; Chidzik, Stanley; Cohen, Daniel; Elmer, Peter; Hallowell, Thomas; Kilbaugh, Todd J.; Lange, David; Leifer, Andrew M.; Marlow, Daniel R.; Meyers, Peter D.; Normand, Edna; Nunes, Janine; Oh, Myungchul; Page, Lyman; Periera, Talmo; Pivarski, Jim; Schreiner, Henry; Stone, Howard A.; Tank, David W.; Thiberge, Stephan; Tully, Christopher
Abstract:
The detailed information on the design and construction of the Princeton Open Ventilation Monitor device and software are contained in this data repository. This information consists of the electrical design files, mechanical design files, bill of materials, human subject recording and analysis code, and a copy of the code repository for operating the patient monitors and central station.
Type:
Dataset, Software, and Image
Issue Date:
22 November 2021

14. Chiral Tetramer Molecular Model

Author(s):
Petsev, Nikolai D.; Stillinger, Frank H.; Debenedetti, Pablo G.
Abstract:
Source code for our energy-conserving reformulation of the 4-site molecular model for chiral phenomena originally introduced by Latinwo et al. [F. Latinwo, F. H. Stillinger, and P. G. Debenedetti, Molecular Model for Chirality Phenomena, J. Chem. Phys. 145, 154503 (2016)]. The reformulation includes an additional 8-body force that arises from an explicit configuration-dependent term in the potential energy function, resulting in a coarse-grained energy-conserving force field for molecular dynamics simulations of chirality phenomena. In this model, the coarse-grained interaction energy between two tetramers depends on their respective chiralities, and is controlled by a parameter λ, where favors local configurations involving tetramers of opposite chirality, and gives energetic preference to configurations involving tetramers of the same chirality. The source code is for use with the LAMMPS simulation package.
Type:
Software
Issue Date:
3 August 2021

15. The Attention Schema Theory in an Artificial Neural Network Agent: Controlling Visuospatial Attention Using a Descriptive Model of Attention

Author(s):
Wilterson, Andrew; Graziano, Michael
Abstract:
In the attention schema theory, the brain constructs a model of attention, the attention schema, to aid in the endogenous control of attention. Growing behavioral evidence appears to support this proposal. However, a central question remains: does a controller of attention actually benefit by having access to an attention schema? We constructed an artificial, deep Q-learning, neural network agent that was trained to control a simple form of visuospatial attention, tracking a stimulus with its attention spotlight in order to solve a catch task. The agent was tested with and without access to an attention schema. In both conditions, the agent received sufficient information such that it should, theoretically, be able to learn the task. We found that with an attention schema present, the agent learned to control its attention spotlight and learned the catch task to a high degree of performance. Once the agent learned, if the attention schema was disabled, the agent could no longer perform effectively. If the attention schema was removed before learning began, the agent was drastically impaired at learning. The results show how the presence of even a simple attention schema provides a profound benefit to a controller of attention. We interpret these results as supporting the central argument of AST: the brain evolved an attention schema because of its practical benefit in the endogenous control of attention.
Type:
Dataset and Software
Issue Date:
2021

16. Regional hydroclimatic variability due to contemporary deforestation in southern Amazonia and associated boundary layer characteristics

Author(s):
Khanna, Jaya; Medvigy, David; Fisch, Gilberto; Neves, Theomar Trindade de Araújo Tiburtino
Abstract:
Amazonian deforestation causes systematic changes in regional dry season precipitation. Some of these changes at contemporary large scales (a few hundreds of kilometers) of deforestation have been associated with a ‘dynamical mesoscale circulation’, induced by the replacement of rough forest with smooth pasture. In terms of decadal averages, this dynamical mechanism yields increased precipitation in downwind regions and decreased precipitation in upwind regions of deforested areas. Daily, seasonal, and interannual variations in this phenomenon may exist, but have not yet been identified or explained. This study uses observations and numerical simulations to develop relationships between the dynamical mechanism and the local- and continental-scale atmospheric conditions across a range of time scales. It is found that the strength of the dynamical mechanism is primarily controlled by the regional-scale thermal and dynamical conditions of the boundary layer, and not by the continental- and global-scale atmospheric state. Lifting condensation level and wind speed within the boundary layer have large and positive correlations with the strength of the dynamical mechanism. The strength of these relationships depends on time scale and is strongest over the seasonal cycle. Overall, the dynamical mechanism is found to be strongest during times when the atmosphere is relatively stable. Hence, for contemporary large scales of deforestation this phenomenon is found to be the prevalent convective triggering mechanism during the dry and parts of transition seasons (especially during the dry-to-wet transition), significantly affecting the hydroclimate during this period.
Type:
Dataset and Software
Issue Date:
2018

17. Data for Nature Climate Change article 'Regional dry-season climate changes due to three decades of Amazonian deforestation'

Author(s):
Khanna, Jaya; Medvigy, David; Fueglistaler, Stephan; Walko, Robert
Abstract:
More than 20% Amazon rainforest has been cleared in the past three decades triggering important hydroclimatic changes. Small-scale (~few kilometers) deforestation in the 1980s has caused thermally-triggered atmospheric circulations that increase regional cloudiness and precipitation frequency. However, these circulations are predicted to diminish as deforestation increases. Here we use multi-decadal satellite records and numerical model simulations to show a regime shift in the regional hydroclimate accompanying increasing deforestation in Rondônia, Brazil. Compared to the 1980s, present-day deforested areas in downwind western Rondônia are found to be wetter than upwind eastern deforested areas during the local dry season. The resultant precipitation change in the two regions is approximately ±25% of the deforested area mean. Meso-resolution simulations robustly reproduce this transition when forced with increasing deforestation alone, showing a negligible role of large-scale climate variability. Furthermore, deforestation-induced surface roughness reduction is found to play an essential role in the present-day dry season hydroclimate. Our study illustrates the strong scale-sensitivity of the climatic response to Amazonian deforestation and suggests that deforestation is sufficiently advanced to have caused a shift from a thermally- to a dynamically-driven hydroclimatic regime.
Type:
Dataset and Software
Issue Date:
2017

19. Attentional Modulation of Brain Responses to Primary Appetitive and Aversive Stimuli

Author(s):
Cara L. Buck; Jonathan D. Cohen; Field, Brent; Daniel Kahneman; Samuel M. McClure; Leigh E. Nystrom
Abstract:
Studies of subjective well-being have conventionally relied upon self-report, which directs subjects’ attention to their emotional experiences. This method presumes that attention itself does not influence emotional processes, which could bias sampling. We tested whether attention influences experienced utility (the moment-by-moment experience of pleasure) by using functional magnetic resonance imaging (fMRI) to measure the activity of brain systems thought to represent hedonic value while manipulating attentional load. Subjects received appetitive or aversive solutions orally while alternatively executing a low or high attentional load task. Brain regions associated with hedonic processing, including the ventral striatum, showed a response to both juice and quinine. This response decreased during the high-load task relative to the low-load task. Thus, attentional allocation may influence experienced utility by modulating (either directly or indirectly) the activity of brain mechanisms thought to represent hedonic value.
Type:
Dataset, Software, and text
Issue Date:
11 February 2015

20. Dataset for JGR Article (DOI: 10.1002/2014JD022278)

Abstract:
This dataset contains all the data, model and MATLAB codes used to generate the figures and data reported in the article (DOI: 10.1002/2014JD022278). The data was generated during September 2013 and February 2014 using the Ocean-Land-Atmosphere Model also provided with this package. The data was generated using the computational resources supported by the PICSciE OIT High Performance Computing Center and Visualization Laboratory at Princeton University. The dataset contains a pdf Readme file which explains in detail how the data can be used. Users are recommended to go through this file before using the data.
Type:
Dataset, Image, Software, and text
Issue Date:
19 November 2014