Glotaran: A Java-Based Graphical User Interface for the R Package TIMP
30 Jun 2012-Journal of Statistical Software (University of California at Los Angeles)-Vol. 49, Iss: 3, pp 1-22
TL;DR: Glotaran is introduced as a Java-based graphical user interface to the R package TIMP, a problem solving environment for fitting superposition models to multi-dimensional data which features interactive and dynamic data inspection and interactive viewing of results.
Abstract: In this work the software application called Glotaran is introduced as a Java-based graphical user interface to the R package TIMP, a problem solving environment for fitting superposition models to multi-dimensional data. TIMP uses a command-line user interface for the interaction with data, the specification of models and viewing of analysis results. Instead, Glotaran provides a graphical user interface which features interactive and dynamic data inspection, easier -- assisted by the user interface -- model specification and interactive viewing of results. The interactivity component is especially helpful when working with large, multi-dimensional datasets as often result from time-resolved spectroscopy measurements, allowing the user to easily pre-select and manipulate data before analysis and to quickly zoom in to regions of interest in the analysis results. Glotaran has been developed on top of the NetBeans rich client platform and communicates with R through the Java-to-R interface Rserve. The background and the functionality of the application are described here. In addition, the design, development and implementation process of Glotaran is documented in a generic way.
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TL;DR: Direct visualization of hot-carrier migration in methylammonium lead iodide (CH3NH3PbI3) thin films by ultrafast transient absorption microscopy is reported, demonstrating three distinct transport regimes.
Abstract: The Shockley-Queisser limit for solar cell efficiency can be overcome if hot carriers can be harvested before they thermalize. Recently, carrier cooling time up to 100 picoseconds was observed in hybrid perovskites, but it is unclear whether these long-lived hot carriers can migrate long distance for efficient collection. We report direct visualization of hot-carrier migration in methylammonium lead iodide (CH3NH3PbI3) thin films by ultrafast transient absorption microscopy, demonstrating three distinct transport regimes. Quasiballistic transport was observed to correlate with excess kinetic energy, resulting in up to 230 nanometers transport distance that could overcome grain boundaries. The nonequilibrium transport persisted over tens of picoseconds and ~600 nanometers before reaching the diffusive transport limit. These results suggest potential applications of hot-carrier devices based on hybrid perovskites.
408 citations
TL;DR: It is shown that moving to the ligand allylammonium enables a narrower distribution of QW widths, creating a flattened energy landscape that leads to reduced ultrafast shallow hole trapping that originates from the most strongly confined QWs.
Abstract: Metal halide perovskites have achieved photovoltaic efficiencies exceeding 22%, but their widespread use is hindered by their instability in the presence of water and oxygen To bolster stability, researchers have developed low-dimensional perovskites wherein bulky organic ligands terminate the perovskite lattice, forming quantum wells (QWs) that are protected by the organic layers In thin films, the width of these QWs exhibits a distribution that results in a spread of bandgaps in the material arising due to varying degrees of quantum confinement across the population Means to achieve refined control over this QW width distribution, and to examine and understand its influence on photovoltaic performance, are therefore of intense interest Here we show that moving to the ligand allylammonium enables a narrower distribution of QW widths, creating a flattened energy landscape that leads to ×14 and ×19 longer diffusion lengths for electrons and holes, respectively We attribute this to reduced ultrafast
265 citations
TL;DR: A new singlet-mediated transport mechanism for triplets is revealed, which leads to an enhancement in effective triplet exciton diffusion of more than one order of magnitude on picosecond to nanosecond timescales, establishing that there are optimal energetics of singlet and tripletexciton excitons that benefit both singlet fission andexciton diffusion.
Abstract: Singlet fission presents an attractive solution to overcome the Shockley-Queisser limit by generating two triplet excitons from one singlet exciton. However, although triplet excitons are long-lived, their transport occurs through a Dexter transfer, making them slower than singlet excitons, which travel by means of a Forster mechanism. A thorough understanding of the interplay between singlet fission and exciton transport is therefore necessary to assess the potential and challenges of singlet-fission utilization. Here, we report a direct visualization of exciton transport in single tetracene crystals using transient absorption microscopy with 200 fs time resolution and 50 nm spatial precision. These measurements reveal a new singlet-mediated transport mechanism for triplets, which leads to an enhancement in effective triplet exciton diffusion of more than one order of magnitude on picosecond to nanosecond timescales. These results establish that there are optimal energetics of singlet and triplet excitons that benefit both singlet fission and exciton diffusion.
200 citations
TL;DR: Performance of individuals with ADHD on social cognition lies intermediate between ASD and healthy controls, however, developmental trajectories of social cognition probably differ between ADHD and ASD as social cognitive deficits in ADHD might be improving with age in most individuals.
Abstract: Background Impairment in social cognition is an established finding in autism spectrum disorders (ASD). Emerging evidence suggests that attention-deficit/hyperactivity disorder (ADHD) might be also associated with deficits in theory of mind (ToM) and emotion recognition. However, there are inconsistent findings, and it has been debatable whether such deficits persist beyond childhood and how similar social cognitive deficits are in ADHD v. ASD. Method We conducted a meta-analysis of social cognition, including emotion recognition and ToM, studies in ADHD compared with healthy controls and ASD. The current meta-analysis involved 44 studies comparing ADHD (n = 1999) with healthy controls (n = 1725) and 17 studies comparing ADHD (n = 772) with ASD (n = 710). Results Facial and vocal emotion recognition (d = 0.40–0.44) and ToM (d = 0.43) abilities were significantly impaired in ADHD. The most robust facial emotion recognition deficits were evident in anger and fear. Social cognitive deficits were either very subtle (emotion recognition) or non-significant (ToM) in adults with ADHD. Deficits in social cognition, especially ToM, were significantly more pronounced in ASD compared with ADHD. General cognitive impairment has contributed to social cognitive deficits in ADHD. Conclusions Performance of individuals with ADHD on social cognition lies intermediate between ASD and healthy controls. However, developmental trajectories of social cognition probably differ between ADHD and ASD as social cognitive deficits in ADHD might be improving with age in most individuals. There is a need for studies investigating a potential subtype of ADHD with persistent social cognitive deficits and exploring longitudinal changes in social cognition during development.
187 citations
TL;DR: TA spectroscopy reveals an electron-transfer cascade that correlates with a near-doubling in photocatalytic activity from 2050 to 3810 μmol h-1 g-1 when the authors infuse a suspension of bulk g-C3N4 with 10% mass loading of chemically exfoliated carbon nitride.
Abstract: Solar hydrogen generation from water represents a compelling component of a future sustainable energy portfolio. Recently, chemically robust heptazine-based polymers known as graphitic carbon nitrides (g-C3N4) have emerged as promising photocatalysts for hydrogen evolution using visible light while withstanding harsh chemical environments. However, since g-C3N4 electron-transfer dynamics are poorly understood, rational design rules for improving activity remain unclear. Here, we use visible and near-infrared femtosecond transient absorption (TA) spectroscopy to reveal an electron-transfer cascade that correlates with a near-doubling in photocatalytic activity from 2050 to 3810 μmol h–1 g–1 when we infuse a suspension of bulk g-C3N4 with 10% mass loading of chemically exfoliated carbon nitride. TA spectroscopy indicates that exfoliated carbon nitride quenches photogenerated electrons on g-C3N4 at rates approaching the molecular diffusion limit. The TA signal for photogenerated electrons on g-C3N4 decays wi...
172 citations
References
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Journal Article•
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.
272,030 citations
"Glotaran: A Java-Based Graphical Us..." refers methods in this paper
...Glotaran aims to lower the barrier to access the advanced analysis and modeling capabilities of TIMP by eliminating the need to learn R syntax (R Development Core Team 2012) or specific TIMP code, while at the same time maintaining compatibility between models written in TIMP and models designed in Glotaran....
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...…to lower the barrier to access the advanced analysis and modeling capabilities of TIMP by eliminating the need to learn R syntax (R Development Core Team 2012) or specific TIMP code, while at the same time maintaining compatibility between models written in TIMP and models designed in Glotaran....
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Book•
01 Aug 1988
TL;DR: This book offers a balanced presentation of the theoretical, practical, and computational aspects of nonlinear regression and provides background material on linear regression, including the geometrical development for linear and nonlinear least squares.
Abstract: Wiley-Interscience Paperback Series The Wiley-Interscience Paperback Series consists of selected books that have been made more accessible to consumers in an effort to increase global appeal and general circulation. With these new unabridged softcover volumes, Wiley hopes to extend the lives of these works by making them available to future generations of statisticians, mathematicians, and scientists. "The authors have put together an extraordinary presentation of concepts and methods concerning the use and analysis of nonlinear regression models ...highly recommend[ed] ...for anyone needing to use and/or understand issues concerning the analysis of nonlinear regression models." -Technometrics "[This book] provides a good balance of relevant theory and application with many examples ...[and it] provides the most balanced approach to theory and application appropriate for a first course in nonlinear regression modeling for graduate statistics students." -Mathematical Reviews "[This book] joins a distinguished list of publications with a reputation for balancing technical rigor with readability, and theory with application. [It] upholds tradition ...[and is] a worthwhile reference for the marketing researcher with a serious interest in linear models. " -Journal of Marketing Research This book offers a balanced presentation of the theoretical, practical, and computational aspects of nonlinear regression and provides background material on linear regression, including the geometrical development for linear and nonlinear least squares. The authors employ real data sets throughout, and their extensive use of geometric constructs and continuing examples makes the progression of ideas appear very natural. The book also includes pseudocode for computing algorithms.
3,202 citations
"Glotaran: A Java-Based Graphical Us..." refers background or methods in this paper
...Thus Equation 1 can be represented mathematically: Ψ(λ, t) = ncomp∑ l=1 cl,λ(t, θ)ǫl(λ) (3) Now that a model for the concentration of each component has been defined, the unknown parameters θ and the conditionally linear parameters ǫl(λ) can be estimated by means of variable projection (Golub and LeVeque 1979; Bates and Watts 1988; Mullen and Van Stokkum 2009)....
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...…θ)ǫl(λ) (3) Now that a model for the concentration of each component has been defined, the unknown parameters θ and the conditionally linear parameters ǫl(λ) can be estimated by means of variable projection (Golub and LeVeque 1979; Bates and Watts 1988; Mullen and Van Stokkum 2009)....
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...They are often described as compartmental models (Godfrey 1983; Bates and Watts 1988)....
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...Now that a model for the concentration of each component has been defined, the unknown parameters θ and the conditionally linear parameters l(λ) can be estimated by means of variable projection (Golub and LeVeque 1979; Bates and Watts 1988; Mullen and Van Stokkum 2009)....
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TL;DR: The methodology for global and target analysis of time-resolved spectra is reviewed and the combination of a model for the kinetics and for the spectra of the components results in a more powerful spectrotemporal model.
1,388 citations
"Glotaran: A Java-Based Graphical Us..." refers methods in this paper
...The singular value decomposition (SVD) is a matrix factorization technique which can be used to explore the number of spectrally and temporally independent components in the data matrix (Golub and Van Loan 1996), which is an important aspect of defining an initial model....
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...Glotaran stands for global and target analysis, the method by which these measurements can effectively be modeled and analyzed as described by Van Stokkum, Larsen, and Van Grondelle (2004)....
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...Development on Glotaran started at the physics department of the VU University Amsterdam as a GUI for the R package TIMP as reported by Snellenburg, Van Stokkum, and Mullen (2008)....
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...TIMP was introduced as an R package for modeling multi-way spectroscopic measurements by Mullen and Van Stokkum (2007)....
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...Thus Equation 1 can be represented mathematically: Ψ(λ, t) = ncomp∑ l=1 cl,λ(t, θ)ǫl(λ) (3) Now that a model for the concentration of each component has been defined, the unknown parameters θ and the conditionally linear parameters ǫl(λ) can be estimated by means of variable projection (Golub and LeVeque 1979; Bates and Watts 1988; Mullen and Van Stokkum 2009)....
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