The Frenkel exciton model is a useful tool for theoretical studies of multichromophore systems. We recently showed that the exciton model could be used to coarse-grain electronic structure in ...multichromophoric systems, focusing on singly excited exciton states Acc. Chem. Res. 2014, 47, 2857−2866 . However, our previous implementation excluded charge-transfer excited states, which can play an important role in light-harvesting systems and near-infrared optoelectronic materials. Recent studies have also emphasized the significance of charge-transfer in singlet fission, which mediates the coupling between the locally excited states and the multiexcitonic states. In this work, we report on an ab initio exciton model that incorporates charge-transfer excited states and demonstrate that the model provides correct charge-transfer excitation energies and asymptotic behavior. Comparison with TDDFT and EOM-CC2 calculations shows that our exciton model is robust with respect to system size, screening parameter, and different density functionals. Inclusion of charge-transfer excited states makes the exciton model more useful for studies of singly excited states and provides a starting point for future construction of a model that also includes double-exciton states.
TeraChem was born in 2008 with the goal of providing fast on‐the‐fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as ...photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low‐cost parallel computer architecture that became more accessible for general‐purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large‐scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large‐scale nonadiabatic dynamics simulations.
This article is categorized under:
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Software > Quantum Chemistry
Structure and Mechanism > Computational Biochemistry and Biophysics
TeraChem is a quantum chemistry package designed from the ground up for graphical processing units, providing fast on‐the‐fly electronic structure calculations for workflows such as molecular dynamics, geometry optimization, and coarse‐grained fragment approaches.
Climate reanalyses provide a plethora of global atmospheric and surface parameters in a consistent
manner over multi-decadal timescales. Hence, they are widely used in many fields, and an in-depth
...evaluation of the different variables provided by reanalyses is a necessary means to provide
feedback on the quality to their users and the operational centres producing these data sets, and
to help guide their development. Recently, the European Centre for Medium-Range Weather Forecasts
(ECMWF) released the new state-of-the-art climate reanalysis ERA5, following up on its popular
predecessor ERA-Interim. Different sets of variables from ERA5 were already evaluated in a handful
of studies, but so far, the quality of land-surface energy partitioning has not been assessed.
Here, we evaluate the surface energy partitioning over land in ERA5 and concentrate on the
appraisal of the surface latent heat flux, surface sensible heat flux, and Bowen ratio against
different reference data sets and using different modelling tools. Most of our analyses point
towards a better quality of surface energy partitioning in ERA5 than in ERA-Interim, which may be
attributed to a better representation of land-surface processes in ERA5 and certainly to the
better quality of near-surface meteorological variables. One of the key shortcomings of the
reanalyses identified in our study is the overestimation of the surface latent heat flux over
land, which – although substantially lower than in ERA-Interim – still remains in ERA5. Overall,
our results indicate the high quality of the surface turbulent fluxes from ERA5 and the general
improvement upon ERA-Interim, thereby endorsing the efforts of ECMWF to improve their climate
reanalysis and to provide useful data to many scientific and operational fields.
To investigate the descend of subducted slabs we search for and analyse seismic arrivals that reflected off the surface of the slab. In order to distinguish between such arrivals and other seismic ...phases, we search for waves that reach a seismic array with a backazimuth deviating from the theoretical backazimuth of the earthquake. Source–receiver combinations are chosen in a way that their great circle paths do not intersect the slab region, hence the direct arrivals can serve as reference. We focus on the North and Northwest Pacific region by using earthquakes from Japan, the Philippines and the Hindu Kush area recorded at North American networks (e.g. USArray, Alaska and Canada). Using seismic array techniques for analysing the data and record information on slowness, backazimuth and traveltime of the observed out-of-plane arrivals we use these measurements to trace the wave back through a 1-D velocity model to its scattering/reflection location. We find a number of out-of-plane reflections. Assuming only single scattering, most out-of-plane signals have to travel as P-to-P phases and only a few as S-to-P phases, due to the length of the seismograms we processed. The located reflection points present a view of the 3-D structures within the mantle. In the upper mantle and the transition zone they correlate well with the edges of fast velocity regions in tomographic images. We also find reflection points in the mid- and lower mantle and their locations generally agree with fast velocities mapped by seismic tomography models suggesting that in the subduction regions we map, slabs enter the lower mantle. To validate our approach, we calculate and process synthetic seismograms for 3-D wave field propagation through a model containing a slab-like heterogeneity. We show, that depending on the source–receiver geometry relative to the reflection plane, it is indeed possible to observe and back-trace out-of-plane signals.
Cognitive control is proposed to rely on a rostral-to-caudal hierarchy of neural processing within the prefrontal cortex (PFC), with more rostral parts exerting control over more caudal parts. ...Anatomical and functional data suggest that this hierarchical organization of the PFC may be separated into a ventral and a dorsal component. Furthermore, recent studies indicate that the apex of the hierarchy resides within the mid-lateral rather the rostral PFC. However, investigating the hierarchical aspect of rostro-to-caudal processing requires quantification of the directed interactions between PFC regions.
Using functional near-infrared spectroscopy (fNIRS) in a sample of healthy young adults we analyzed directed interactions between rostral and caudal PFC during passive watching of nature documentaries. Directed coherence (DC) as a measure of directed interaction was computed pairwise between 38 channels evenly distributed over the lateral prefrontal convexity.
Results revealed an overall predominance of rostral-to-caudal directed interactions in the PFC that further dissociated along a ventro-dorsal axis: Dorsal regions exerted stronger rostro-caudally directed interactions on dorsal than on ventral regions and vice versa. Interactions between ventral and dorsal PFC were stronger from ventral to dorsal areas than vice versa. Results further support the notion that the mid-dorsolateral PFC constitutes the apex of the prefrontal hierarchy.
Taken together these data provide novel evidence for parallel dorsal and ventral streams within the rostro-caudal hierarchical organization of the PFC. FNIRS-based analyses of directed interactions put forward a new perspective on the functional architecture of the prefrontal hierarchy and complement previous insights from functional magnetic resonance imaging.
•Near-infrared spectroscopy (NIRS) allows inference of directed functional networks.•NIRS reveals rostro-caudally directed interactions in prefrontal cortex (PFC).•Rostro-caudally directed interactions are segregated in a dorsal and ventral stream.•Rostro-caudal directed interactions peak in mid-dorsolateral PFC as apex of control.•NIRS-based analyses complement evidence from functional magnetic resonance imaging.
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell ...membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.
Towards the end of June 2021, temperature records were broken by several degrees Celsius in several cities in the Pacific Northwest areas of the US and Canada, leading to spikes in sudden deaths and ...sharp increases in emergency calls and hospital visits for heat-related illnesses. Here we present a multi-model, multi-method attribution analysis to investigate the extent to which human-induced climate change has influenced the probability and intensity of extreme heat waves in this region. Based on observations, modelling and a classical statistical approach, the occurrence of a heat wave defined as the maximum daily temperature (TXx) observed in the area 45–52∘ N, 119–123∘ W, was found to be virtually impossible without human-caused climate change. The observed temperatures were so extreme that they lay far outside the range of historical temperature observations. This makes it hard to state with confidence how rare the event was. Using a statistical analysis that assumes that the heat wave is part of the same distribution as previous heat waves in this region led to a first-order estimation of the event frequency of the order of once in 1000 years under current climate conditions. Using this assumption and combining the results from the analysis of climate models and weather observations, we found that such a heat wave event would be at least 150 times less common without human-induced climate change. Also, this heat wave was about 2 ∘C hotter than a 1-in-1000-year heat wave would have been in 1850–1900, when global mean temperatures were 1.2 ∘C cooler than today. Looking into the future, in a world with 2 ∘C of global warming (0.8 ∘C warmer than today), a 1000-year event would be another degree hotter. Our results provide a strong warning: our rapidly warming climate is bringing us into uncharted territory with significant consequences for health, well-being and livelihoods. Adaptation and mitigation are urgently needed to prepare societies for a very different future.
Despite the existing myriad of tools and models to assess
atmospheric source–receptor relationships, their uncertainties remain
largely unexplored and arguably stem from the scarcity of observations
...available for validation. Yet, Lagrangian models are increasingly used to
determine the origin of precipitation and atmospheric heat by scrutinizing the
changes in moisture and temperature along air parcel trajectories. Here, we
present a unified framework for the process-based evaluation of atmospheric
trajectories to infer source–receptor relationships of both moisture and
heat. The framework comprises three steps: (i) diagnosing precipitation,
surface evaporation, and sensible heat from the Lagrangian simulations and
identifying the accuracy and reliability of flux detection criteria; (ii) establishing source–receptor relationships through the attribution of
sources along multi-day backward trajectories; and (iii) performing a bias
correction of source–receptor relationships. Applying this framework to
simulations from the Lagrangian model FLEXPART, driven with ERA-Interim
reanalysis data, allows us to quantify the errors and uncertainties
associated with the resulting source–receptor relationships for three
cities in different climates (Beijing, Denver, and Windhoek). Our results
reveal large uncertainties inherent in the estimation of heat and
precipitation origin with Lagrangian models, but they also demonstrate that
a source and sink bias correction acts to reduce this uncertainty. The
proposed framework paves the way for a cohesive assessment of the
dependencies in source–receptor relationships.
Brain region size generally scales allometrically with brain size, but mosaic shifts in brain region size independent of brain size have been found in several lineages and may be related to the ...evolution of behavioral novelty. African weakly electric fishes (Mormyroidea) evolved a mosaically enlarged cerebellum and hindbrain, yet the relationship to their behaviorally novel electrosensory system remains unclear. We addressed this by studying South American weakly electric fishes (Gymnotiformes) and weakly electric catfishes (Synodontis spp.), which evolved varying aspects of electrosensory systems, independent of mormyroids. If the mormyroid mosaic increases are related to evolving an electrosensory system, we should find similar mosaic shifts in gymnotiforms and Synodontis. Using micro-computed tomography scans, we quantified brain region scaling for multiple electrogenic, electroreceptive, and non-electrosensing species. We found mosaic increases in cerebellum in all three electrogenic lineages relative to non-electric lineages and mosaic increases in torus semicircularis and hindbrain associated with the evolution of electrogenesis and electroreceptor type. These results show that evolving novel electrosensory systems is repeatedly and independently associated with changes in the sizes of individual major brain regions independent of brain size, suggesting that selection can impact structural brain composition to favor specific regions involved in novel behaviors.
PDF
