Data processing in high-performance computing systems

The paper integrates the results of a large group of authors working in different areas that are important in the scope of big data, including but not limited to: overview of the basic solutions for the development of data centers; storage and processing; decomposition of a problem into sub-problems of lower complexity (such as applying divide and conquer algorithms); models and methods allowing broad parallelism to be realized; alternative techniques for potential acceleration; programming languages; and practical applications

13C NMR spectrum of crystalline [Rh(Acac) (CO)2]: A contribution to the discussion on [Rh(Acac) (CO)2] molecular structure in the solid state

13C MAS NMR spectrum of polycrystalline [Rh(Acac) (CO)2] (1) displays separate signals from all 7 carbon atoms: 2 doublets from CO ligand carbons along with 5 singlets from Acac carbons. GIPAW calculation of 13C shielding tensor values also revealed non-equivalence of all carbon atoms in molecule 1 in the anisotropic medium of the crystal lattice. Apparently, the C2v symmetry of molecule 1 is broken owing to the asymmetry of its contacts to the neighboring molecules. For example, the contacts O⋯HC of two CO ligands of molecule 1 to the CH group of the closest molecule in the adjacent stack are markedly different: the distances OH are 2.72 and 4.38 Å, the distances OC are 3.65 and 5.00 Å, the angles OHC are 164.9° and 126.4°

О природе изменения эффективного поверхностного заряда на кристаллах InAs при выращивании анодного оксидного слоя

Dynamics of changes in fluorine atoms distribution through grown anodic oxide layer thickness and the effective surface charge on InAs crystals under such layers has been studied. Anodic oxidation was performed in alkaline electrolyte with fluorochemical additive component in galvanostatic mode at anode current densities 0.05 or 0.5 mA·cm−2. The layers thickness in boundes 32—51 nm varied by electrodes final voltage setting in range 15—25 V. The layer thickness and refractive index was measured by ellipsometric method, and distribution of fluorine atoms through thickness — by photoelectron−spectroscopy method, combined with ion etching. At the same time, based on grown layers there were produced MIS structures, and from calculation of theirs capacitance−voltage characteristics are determined effective surface charge and surface states density, corresponding to different layer thicknesses.Main results are reduced to the facts during layers growing despite of anodizing current density comes their sealing, the profile of fluorine atoms distribution shifts towards InAs, positive effective surface charge gradually decreases from 3.6 · 1011 to 2.0 · 1011 cm−2 at surface states density in (6—7) · 1011 eV·cm−2 range for all cases. Based on comparison of these data and theoretical concepts of MIS structure charge construction, there was made a conclusion about gradual built−in charge distancing from the border with InAs in the process of growing anodic oxide layer, which explains observed effective surface charge decrease during layer thickness increasing. This results indicates that the layer growth rate exceeds the built−in charge displacement rate towards InAs.Изучена динамика изменения распределения атомов фтора по толщине выращенных слоев анодного оксида и эффективного поверхностного заряда на кристаллах InAs под такими слоями. Анодное окисление проведено в щелочном электролите с добавкой фторосодержащего компонента в гальваностатическом режиме при плотностях анодного тока 0,05 или 0,5 мА · см−2. Толщину слоев в пределах 32—51 нм варьировали, задавая конечное напряжение на электродах при выращивании в пределах значений 15—25 В. Толщина и коэффициент преломления слоев измерены методом эллипсометрии, а распределение атомов фтора по толщине — методом фотоэлектронной спектроскопии в сочетании с ионным травлением. Параллельно на основе выращенных слоев изготовлены МДП−структуры, из расчета вольт−фарадных характеристик которых определены значения эффективного поверхностного заряда и плотности поверхностных состояний, соответствующие различным толщинам слоя.Установлено, что по мере роста слоев независимо от плотности тока анодирования происходит их уплотнение. Профиль распределения атомов фтора смещается в сторону InAs, а положительный эффективный поверхностный заряд постепенно уменьшается от 3,6 · 1011 до 2,0 · 1011 см−2 при плотности поверхностных состояний в пределах (6—7) · 1011 эВ−1 · см−2 для всех случаев. На основе сопоставления полученных данных с теоретическими представлениями о зарядовом строении МДП−структуры сделан вывод о постепенном отдалении встроенного заряда от границы с InAs в процессе выращивания анодного оксидного слоя. Это объясняет наблюдаемое уменьшения эффективного поверхностного заряда с ростом толщины слоя. Полученный результат свидетельствует о том, что скорость роста слоя превышает скорость смещения встроенного заряда в сторону InAs

Calculation of the Free Energy and Cooperativity of Protein Folding

Calculation of the free energy of protein folding and delineation of its pre-organization are of foremost importance for understanding, predicting and designing biological macromolecules. Here, we introduce an energy smoothing variant of parallel tempering replica exchange Monte Carlo (REMS) that allows for efficient configurational sampling of flexible solutes under the conditions of molecular hydration. Its usage to calculate the thermal stability of a model globular protein, Trp cage TC5b, achieves excellent agreement with experimental measurements. We find that the stability of TC5b is attained through the coupled formation of local and non-local interactions. Remarkably, many of these structures persist at high temperature, concomitant with the origin of native-like configurations and mesostates in an otherwise macroscopically disordered unfolded state. Graph manifold learning reveals that the conversion of these mesostates to the native state is structurally heterogeneous, and that the cooperativity of their formation is encoded largely by the unfolded state ensemble. In all, these studies establish the extent of thermodynamic and structural pre-organization of folding of this model globular protein, and achieve the calculation of macromolecular stability ab initio, as required for ab initio structure prediction, genome annotation, and drug design