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>

On procedures for reliability assessment of mechanical systems and structures

G. I. Schuëller 국제구조공학회 2007 Structural Engineering and Mechanics, An Int'l Jou Vol.25 No.3

In this paper a brief overview of methods to assess the reliability of mechanical systems and structures is presented. A selection of computational procedures, stochastic structural dynamics, stochastic fatigue crack growth and reliability based optimization are discussed. It is shown that reliability based methods may form the basis for a rational decision making.

Structural and Molecular Genetic Insight into a Widespread Sulfur Oxidation Pathway

Christiane Dahl,Andrea Schu1te,Yvonne Stockdreher,Connie Hong,Frauke Grimm,Johannes Sander,Rosalind Kim,Kim, Sung-Hou,Shin, Dong Hae 이화여자대학교 약학연구소 2009 藥學硏究論文集 Vol.- No.19

Many environmentally important photo- and chemolithoautotrophic bacteria accumulate globules of polymeric, water-insoluble sulfur as a transient product during oxidation of reduced sulfur compounds. Oxidation of this sulfur requires the concerted action of Dsr proteins. However, individual functions and interplay of these proteins are largely unclear. We proved with a ΔdsrE mutant experiment that the cytoplasmic α₂β₂γ₂-structured protein DsrEFH is absolutely essential for the oxidation of sulfur stored in the intracellular sulfur globules of the purple sulfur bacterial model organism Allochromatium vinosum. The ability to degrade stored sulfur was fully regained upon complementation with dsrEFH in trans. The crystal structure of DsrEFH was determined at 2.5 ? resolution to assist functional assignment in detail. In conjunction with phylogenetic analyses, two different types of putative active sites were identified in DsrE and DsrH and shown to be characteristic for sulfur-oxidizing bacteria. Conserved Cys78 of A. vinosum DsrE corresponds to the active cysteines of Escherichia coli YchN and TusD. TusBCD and the protein TusE are parts of sulfur relay system involved in thiouridine biosynthesis. DsrEFH interacts with DsrC, a TusE homologue encoded in the same operon. The conserved penultimate cysteine residue in the carboxy-terminus of DsrC is essential for the interaction. Here, we show that Cys78 of DsrE is strictly required for interaction with DsrC while Cys20 in the putative active site of DsrH is dispensable for that reaction. In summary, our findings point at the occurrence of sulfur transfer reactions during sulfur oxidation via the Dsr proteins.

The effects of uncertainties in structural analysis

M. F. Pellissetti,G. I. Schuëller 국제구조공학회 2007 Structural Engineering and Mechanics, An Int'l Jou Vol.25 No.3

Model-based predictions of structural behavior are negatively affected by uncertainties of various type and in various stages of the structural analysis. The present paper focusses on dynamic analysis and addresses the effects of uncertainties concerning material and geometric parameters, mainly in the context of modal analysis of large-scale structures. Given the large number of uncertain parameters arising in this case, highly scalable simulation-based methods are adopted, which can deal with possibly thousands of uncertain parameters. In order to solve the reliability problem, i.e., the estimation of very small exceedance probabilities, an advanced simulation method called Line Sampling is used. In combination with an efficient algorithm for the estimation of the most important uncertain parameters, the method provides good estimates of the failure probability and enables one to quantify the error in the estimate. Another aspect here considered is the uncertainty quantification for closely-spaced eigenfrequencies. The solution here adopted represents each eigenfrequency as a weighted superposition of the full set of eigenfrequencies. In a case study performed with the FE model of a satellite it is shown that the effects of uncertain parameters can be very different in magnitude, depending on the considered response quantity. In particular, the uncertainty in the quantities of interest (eigenfrequencies) turns out to be mainly caused by very few of the uncertain parameters, which results in sharp estimates of the failure probabilities at low computational cost.

논총(論叢) : 평화선(平和線)과 어업보존수역(漁業保存水域)에 관(關)한 국제법상(國際法上)의 고찰(考察)

김수만 ( Schu Man Kim ) 국방대학교 안보문제연구소 1965 국방연구 Vol.17 No.-

제3차(第3次) 해양법회의(海洋法會議)와 해양국제법(海洋國際法)의 신동향(新動向)

김수만 ( Schu Man Kim ) 국방대학교 안보문제연구소 1976 국방연구 Vol.19 No.1

The First U.N. Conference on the Law of the Sea in 1938 Concluded four multilateral conventions dealing with (a) Territorial Sea and the Contiguous Zone; (b) High Sea; (c) Continental Shelf; (d) Fishing and Conservation of the Living Resources of the High Sea. This Conference, as well as the second one in 1960, failed to reach agreement on the breadth of the territorial sea, the precise outer boundary of the continental Shelf, and many other issues. As a result of three major developments during past 15 years, namley growing tendency by many countries to extend unilaterally their claims over 200 nautical miles from the shore. The problem has increased international relation over the degradation of the marine environment, and mankind`s increasing ability to exploit both living and mineral resources of the oceans and seabeds. Before the third U.N. Conference on the Law of the Sea, the groundwork for the Conference was laid at a series of six preparatory meetings from 1971 to 1973 of the U.N. Committee on the Peaceful Uses of the Seabed and Ocean Floor Beyond the Limits of National Jurisdiction, so called the U.N. Seabed Committee. The third U.N. Conference on the Law of the Sea began in New York City with the first session December 3-14, 1973. The second, substantive conference session took place in Caracas, June 20-August 29, 1974, the third session in Geneva, March 17-May 9, 1975, and the fourth session is taken place twice in New York City, March 15 this year and is going on yet. Just as we have mentioned above, the groundwork of the conference was prepared for three years by the U.N. Seabed Committee and it`s sessions have been hold several times for a long time, but in spite of all these efforts, have not yet reached any agreement to adopt an international convention dealing with all matters relating to the law of the sea. Now, we need to know the reasons that an agreement has not reached yet. Indeed, Seeking of each national interests is the real obstacle to achieve an agreement. The national interests on the law of Sea involve the economical resources and military interests. The former is living and mineral resources, the latter is free transit or unimpeded transit of the warship and submarine through and overs traits used for international navigation. On the transit of the warship and submarine in. international straits, on group of States insists free transit of the Warship and submarine, and the another claims innocent passage. In my paper, I have studied principally the results of agreement on the living and mineral resources of the sea and two the opposit groups, insisting of free transit and maintaining innocent passage in the international straits among the representatives of all nations.

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>

Synaptic abnormalities and cytoplasmic glutamate receptor aggregates in contactin associated protein-like 2<i>/Caspr2</i> knockout neurons

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>

Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases

Jurmeister, Philipp,Bockmayr, Michael,Seegerer, Philipp,Bockmayr, Teresa,Treue, Denise,Montavon, Gré,goire,Vollbrecht, Claudia,Arnold, Alexander,Teichmann, Daniel,Bressem, Keno,Schu¨ller, Ulrich American Association for the Advancement of Scienc 2019 Science translational medicine Vol.11 No.509

<P>Head and neck squamous cell carcinoma (HNSC) patients are at risk of suffering from both pulmonary metastases or a second squamous cell carcinoma of the lung (LUSC). Differentiating pulmonary metastases from primary lung cancers is of high clinical importance, but not possible in most cases with current diagnostics. To address this, we performed DNA methylation profiling of primary tumors and trained three different machine learning methods to distinguish metastatic HNSC from primary LUSC. We developed an artificial neural network that correctly classified 96.4% of the cases in a validation cohort of 279 patients with HNSC and LUSC as well as normal lung controls, outperforming support vector machines (95.7%) and random forests (87.8%). Prediction accuracies of more than 99% were achieved for 92.1% (neural network), 90% (support vector machine), and 43% (random forest) of these cases by applying thresholds to the resulting probability scores and excluding samples with low confidence. As independent clinical validation of the approach, we analyzed a series of 51 patients with a history of HNSC and a second lung tumor, demonstrating the correct classifications based on clinicopathological properties. In summary, our approach may facilitate the reliable diagnostic differentiation of pulmonary metastases of HNSC from primary LUSC to guide therapeutic decisions.</P>

The influence of foreign vs. North American emissions on surface ozone in the US

Reidmiller, D. R.,Fiore, A. M.,Jaffe, D. A.,Bergmann, D.,Cuvelier, C.,Dentener, F. J.,Duncan, B. N.,Folberth, G.,Gauss, M.,Gong, S.,Hess, P.,Jonson, J. E.,Keating, T.,Lupu, A.,Marmer, E.,Park, R.,Schu Copernicus GmbH 2009 Atmospheric Chemistry and Physics Vol.9 No.14

<P>Abstract. As part of the Hemispheric Transport of Air Pollution (HTAP; http:// www.htap.org) project, we analyze results from 15 global and 1 hemispheric chemical transport models and compare these to Clean Air Status and Trends Network (CASTNet) observations in the United States (US) for 2001. Using the policy-relevant maximum daily 8-h average ozone (MDA8 O3) statistic, the multi-model ensemble represents the observations well (mean r2=0.57, ensemble bias = +4.1 ppbv for all US regions and all seasons) despite a wide range in the individual model results. Correlations are strongest in the northeastern US during spring and fall (r2=0.68); and weakest in the midwestern US in summer (r2=0.46). However, large positive mean biases exist during summer for all eastern US regions, ranging from 10-20 ppbv, and a smaller negative bias is present in the western US during spring (~3 ppbv). In nearly all other regions and seasons, the biases of the model ensemble simulations are ≤5 ppbv. Sensitivity simulations in which anthropogenic O3-precursor emissions (NOx + NMVOC + CO + aerosols) were decreased by 20% in four source regions: East Asia (EA), South Asia (SA), Europe (EU) and North America (NA) show that the greatest response of MDA8 O3 to the summed foreign emissions reductions occurs during spring in the West (0.9 ppbv reduction due to 20% emissions reductions from EA + SA + EU). East Asia is the largest contributor to MDA8 O3 at all ranges of the O3 distribution for most regions (typically ~0.45 ppbv) followed closely by Europe. The exception is in the northeastern US where emissions reductions in EU had a slightly greater influence than EA emissions, particularly in the middle of the MDA8 O3 distribution (response of ~0.35 ppbv between 35-55 ppbv). EA and EU influences are both far greater (about 4x) than that from SA in all regions and seasons. In all regions and seasons O3-precursor emissions reductions of 20% in the NA source region decrease MDA8 O3 the most - by a factor of 2 to nearly 10 relative to foreign emissions reductions. The O3 response to anthropogenic NA emissions is greatest in the eastern US during summer at the high end of the O3 distribution (5-6 ppbv for 20% reductions). While the impact of foreign emissions on surface O3 in the US is not negligible - and is of increasing concern given the recent growth in Asian emissions - domestic emissions reductions remain a far more effective means of decreasing MDA8 O3 values, particularly those above 75 ppb (the current US standard). </P>