More Like this

1. Computational characterization of charge transport resiliency in molecular solids

   https://doi.org/10.1039/D1ME00163A  

   Pokuri, Balaji Sesha; Ryno, Sean M.; Noruzi, Ramin; Risko, Chad; Ganapathysubramanian, Baskar (June 2022, Molecular Systems Design & Engineering)

   Molecular systems are analyzedviathe construction of a molecular graph and quantifying the resiliency for charge transport through metrics for graph centrality, in the context of charge pathways between the source and drain electrodes. 

   more » « less
2. One dimensional temperature measurements by resonantly ionized photoemission thermometry of molecular nitrogen

   https://doi.org/10.1364/OPTCON.503546  

   McCord, Walker; Clarks, Aleksander; Zhang, Zhili (October 2023, Optics Continuum)

   This paper presents an extensive parameter study of a non-intrusive and non-seeded laser diagnostic method for measuring one dimensional (1D) rotational temperature of molecular nitrogen (N₂) at 165 - 450 K. Compared to previous efforts using molecular oxygen, here resonantly ionized and photoelectron induced fluorescence of molecular nitrogen for thermometry (N₂RIPT) was demonstrated. The RIPT signal is generated by directly probing various rotational levels within the rovibrational absorption band of N₂, corresponding to the 3-photon transition of N₂(X¹Σ_g⁺,v=0→b¹Π_u,v^′=6) near 285 nm, without involving collisional effects of molecular oxygen and nitrogen. The photoionized N₂produces strong first negative band of N₂⁺(B²Σ_u⁺−X²Σ_g⁺) near 390 nm, 420 nm, and 425 nm. Boltzmann analyses of various discrete fluorescence emission lines yield rotational temperatures of molecular nitrogen. By empirically choosing multiple rotational levels within the absorption band, non-scanning thermometry can be accurately achieved for molecular nitrogen. It is demonstrated that the N₂RIPT technique can measure 1D temperature profile up to ∼5 cm in length within a pure N₂environment. Multiple wavelengths are thoroughly analyzed and listed that are accurate for RIPT for various temperature ranges. 

   more » « less
3. ClassicalGSG : Prediction of log P using classical molecular force fields and geometric scattering for graphs

   https://doi.org/10.1002/jcc.26519  

   Donyapour, Nazanin; Hirn, Matthew; Dickson, Alex (March 2021, Journal of Computational Chemistry)

   Abstract This work examines methods for predicting the partition coefficient (logP) for a dataset of small molecules. Here, we use atomic attributes such as radius and partial charge, which are typically used as force field parameters in classical molecular dynamics simulations. These atomic attributes are transformed into index‐invariant molecular features using a recently developed method called geometric scattering for graphs (GSG). We call this approach “ClassicalGSG” and examine its performance under a broad range of conditions and hyperparameters. We train ClassicalGSG logPpredictors with neural networks using 10,722 molecules from the OpenChem dataset and apply them to predict the logPvalues from four independent test sets. The ClassicalGSG method's performance is compared to a baseline model that employs graph convolutional networks. Our results show that the best prediction accuracies are obtained using atomic attributes generated with the CHARMM generalized force field and 2D molecular structures. 

   more » « less
4. The Phyllotis xanthopygus complex (Rodentia, Cricetidae) in central Andes, systematics and description of a new species

   https://doi.org/10.1111/zsc.12510  

   Jayat, J. Pablo; Teta, Pablo; Ojeda, Agustina A.; Steppan, Scott J.; Osland, Jared M.; Ortiz, Pablo E.; Novillo, Agustina; Lanzone, Cecilia; Ojeda, Ricardo A. (August 2021, Zoologica Scripta)

   Abstract PhyllotisWaterhouse 1837 is one of the most studied genera of South American cricetid rodents. As currently understood, it includes 20 small to medium‐sized species of predominantly rocky habitats. Among them, populations of the yellow‐rumped leaf‐eared mouse, traditionally referred toP. xanthopygus(Waterhouse 1837), are the most widely distributed, extending from central Peru to southern Chile and Argentina. Based mostly on molecular evidence, previous studies suggested thatP. xanthopygusconstitutes a species complex, being characterized by geographically structured and genetically divergent clades. In this work, we compare the molecular phylogenetic hypothesis for populations distributed on the eastern slopes of the central Andes with morphometric evidence using univariate and multivariate analyses. Quantitative morphological and molecular evidence suggests that at least four nearly cryptic species of theP. xanthopyguscomplex occur from southern Bolivia to west‐central Argentina. Three of these taxa have available names; one of them,P. caprinus, is currently recognized to the species level; the other two, the clades ofP. x. posticalis‐P. x. rupestrisandP. vaccarum, are both recognized as subspecies ofP. xanthopygus. The remaining taxon represents a new species distributed in the west‐central Andes of Argentina. We discuss our morphological results in the light of other sources of evidence (e.g. qualitative and quantitative state characters, genetic and phylogenetic studies, and cytogenetic data) and name the new species asP. pehuenche, honouring the original native people that historically inhabited west‐central Andes of Argentina. 

   more » « less
5. PDRs4All: IX. Sulfur elemental abundance in the Orion Bar

   https://doi.org/10.1051/0004-6361/202449229  

   Fuente, Asunción; Roueff, Evelyne; Le_Petit, Franck; Le_Bourlot, Jacques; Bron, Emeric; Wolfire, Mark G; Babb, James F; Yan, Pei-Gen; Onaka, Takashi; Black, John H; et al (July 2024, Astronomy & Astrophysics)

   Context.One of the main problems in astrochemistry is determining the amount of sulfur in volatiles and refractories in the interstellar medium. The detection of the main sulfur reservoirs (icy H₂S and atomic gas) has been challenging, and estimates are based on the reliability of models to account for the abundances of species containing less than 1% of the total sulfur. The high sensitivity of theJames WebbSpace Telescope provides an unprecedented opportunity to estimate the sulfur abundance through the observation of the [SI] 25.249 µm line. Aims.Our aim is to determine the amount of sulfur in the ionized and warm molecular phases toward the Orion Bar as a template to investigate sulfur depletion in the transition between the ionized gas and the molecular cloud in HII regions. Methods.We used the [S III] 18.7 µm, [S IV] 10.5 µm, and [S l] 25.249 µm lines to estimate the amount of sulfur in the ionized and molecular gas along the Orion Bar. For the theoretical part, we used an upgraded version of the Meudon photodissociation region (PDR) code to model the observations. New inelastic collision rates of neutral atomic sulfur with ortho-and para- molecular hydrogen were calculated to predict the line intensities. Results.The [S III] 18.7 µm and [S IV] 10.5 µm lines are detected over the imaged region with a shallow increase (by a factor of 4) toward the HII region. This suggests that their emissions are partially coming from the Orion Veil. We estimate a moderate sulfur depletion, by a factor of ~2, in the ionized gas. The corrugated interface between the molecular and atomic phases gives rise to several edge-on dissociation fronts we refer to as DF1, DF2, and DF3. The [S l] 25.249 µm line is only detected toward DF2 and DF3, the dissociation fronts located farthest from the HII region. This is the first ever detection of the [S l] 25.249 µm line in a PDR. The detailed modeling of DF3 using the Meudon PDR code shows that the emission of the [S l] 25.249 µm line is coming from warm (>40 K) molecular gas located atA_V~1–5 mag from the ionization front. Moreover, the intensity of the [S l] 25.249 µm line is only accounted for if we assume the presence of undepleted sulfur. Conclusions.Our data show that sulfur remains undepleted along the ionic, atomic, and molecular gas in the Orion Bar. This is consistent with recent findings that suggest that sulfur depletion is low in massive star-forming regions because of the interaction of the UV photons coming from the newly formed stars with the interstellar matter. 

   more » « less