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SchNetPack: A Deep Learning Toolbox For Atomistic Systems
Schü,tt, K. T.,Kessel, P.,Gastegger, M.,Nicoli, K. A.,Tkatchenko, A.,Mü,ller, K.-R. American Chemical Society 2019 Journal of chemical theory and computation Vol.15 No.1
<P>SchNetPack is a toolbox for the development and application of deep neural networks that predict potential energy surfaces and other quantum-chemical properties of molecules and materials. It contains basic building blocks of atomistic neural networks, manages their training, and provides simple access to common benchmark datasets. This allows for an easy implementation and evaluation of new models. For now, SchNetPack includes implementations of (weighted) atom-centered symmetry functions and the deep tensor neural network SchNet, as well as ready-to-use scripts that allow one to train these models on molecule and material datasets. Based on the PyTorch deep learning framework, SchNetPack allows one to efficiently apply the neural networks to large datasets with millions of reference calculations, as well as parallelize the model across multiple GPUs. Finally, SchNetPack provides an interface to the Atomic Simulation Environment in order to make trained models easily accessible to researchers that are not yet familiar with neural networks.</P> [FIG OMISSION]</BR>
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Coordinated Molecule-Modulated Magnetic Phase with Metamagnetism in Metal-Organic Frameworks
Son, Kwanghyo,Kim, Jin Yeong,Schü,tz, Gisela,Kang, Sung Gu,Moon, Hoi Ri,Oh, Hyunchul ACS AMERICAN CHEMICAL SOCIETY 2019 Inorganic Chemistry Vol.58 No.14
<P>Most well-known metal-organic frameworks (MOFs) possessing the magnetic Ni<SUB>2</SUB>O<SUB>2</SUB>(CO<SUB>2</SUB>)<SUB>2</SUB> chains, called Ni-MOF-74, have been investigated with regard to magnetic properties at open-metal sites. We present the modulation of their magnetic phase and metamagnetism via imidazole molecule coordination.</P><P>The magnetic properties in metal−organic frameworks (MOFs), possessing Ni<SUP>II</SUP> ions in a honeycomb structure, are experimentally and theoretically investigated. The magnetically ordered state at low temperatures can be altered via imidazole molecule (IM) coordination. IM coordination influences the spin state of Ni<SUP>II</SUP> ions with orbital geometries, resulting in observed shifts in the critical temperature and field. The magnetic behavior in MOF-74-IMs reveals the coexistence of spin canting, metamagnetism, and magnetic phase transition.</P> [FIG OMISSION]</BR>
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Varea, Olga,Martin-de-Saavedra, Maria Dolores,Kopeikina, Katherine J.,Schü,rmann, Britta,Fleming, Hunter J.,Fawcett-Patel, Jessica M.,Bach, Anthony,Jang, Seil,Peles, Elior,Kim, Eunjoon,Penzes, P National Academy of Sciences 2015 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.112 No.19
<P><B>Significance</B></P><P>In this paper, we characterize, for the first time to our knowledge, synaptic phenotypes in contactin associated protein-like 2 (<I>Cntnap2</I>) knockout neurons and reveal a novel role for CNTNAP2 in the correct trafficking of AMPA-type glutamate receptors. In addition, we report that cellular phenotypes emerge late in postnatal development, suggesting a mechanism for the apparent late emergence of some <I>CNTNAP2</I>-associated disorders. Taken together, our findings may provide insight into the mechanism underlying pathogenesis of <I>CNTNAP2</I>-associated neuropsychiatric disorders.</P><P>Central glutamatergic synapses and the molecular pathways that control them are emerging as common substrates in the pathogenesis of mental disorders. Genetic variation in the contactin associated protein-like 2 (<I>CNTNAP2</I>) gene, including copy number variations, exon deletions, truncations, single nucleotide variants, and polymorphisms have been associated with intellectual disability, epilepsy, schizophrenia, language disorders, and autism. CNTNAP2, encoded by <I>Cntnap2</I>, is required for dendritic spine development and its absence causes disease-related phenotypes in mice. However, the mechanisms whereby CNTNAP2 regulates glutamatergic synapses are not known, and cellular phenotypes have not been investigated in <I>Cntnap2</I> knockout neurons. Here we show that CNTNAP2 is present in dendritic spines, as well as axons and soma. Structured illumination superresolution microscopy reveals closer proximity to excitatory, rather than inhibitory synaptic markers. CNTNAP2 does not promote the formation of synapses and cultured neurons from <I>Cntnap2</I> knockout mice do not show early defects in axon and dendrite outgrowth, suggesting that CNTNAP2 is not required at this stage. However, mature neurons from knockout mice show reduced spine density and levels of GluA1 subunits of AMPA receptors in spines. Unexpectedly, knockout neurons show large cytoplasmic aggregates of GluA1. Here we characterize, for the first time to our knowledge, synaptic phenotypes in <I>Cntnap2</I> knockout neurons and reveal a novel role for CNTNAP2 in GluA1 trafficking. Taken together, our findings provide insight into the biological roles of CNTNAP2 and into the pathogenesis of <I>CNTNAP2</I>-associated neuropsychiatric disorders.</P>
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