Эффективность алгоритмов классической молекулярной динамики на суперкомпьютерном аппаратном обеспечении
The intercalation of H2O, CO2, and other fluid species in expandable clay minerals (smectites) may play a significant role in controlling the behavior of these species in geological C-sequestration and enhanced petroleum production and has been the subject of intensive study in recent years. This paper reports the results of a computational study of the effects of the properties of the charge balancing, exchangeable cations on H2O and CO2 intercalation in the smectite mineral, hectorite, in equilibrium with an H2O-saturated supercritical CO2 fluid under reservoir conditions using Grand Canonical Molecular Dynamics (GCMD) methods. The results show that the intercalation behavior is greatly different with cations with relatively low hydration energies and high affinities for CO2 (here Cs+) than with cations with higher hydration energies (here Ca2+). With Cs+, CO2 intercalation occurs in a 1-layer structure and does not require H2O intercalation, whereas with Ca2+ the presence of a sub-monolayer of H2O is required for CO2 intercalation. The computational results provide detailed structural, dynamical and energetic insight into the differences in intercalation behavior and are in excellent agreement with in situ experimental XRD, IR, quartz crystal microbalance, and NMR results for smectite materials obtained under reservoir conditions.
This paper reviews atomistic force field parameterizations for molecular simulations of cementitious minerals, such as tricalcium silicate (C3S), portlandite (CH), tobermorites (model C-S-H). Computational techniques applied to these materials include classical molecular simulations, density functional theory and energy minimization. Such simulations hold promise to capture the nanoscale mechanisms operating in cementitious materials and guide in performance optimization. Many force fields have been developed, such as Born–Mayer–Huggins, InterfaceFF (IFF), ClayFF, CSH-FF, CementFF, GULP, ReaxFF, and UFF. The benefits and limitations of these approaches are discussed and a database is introduced, accessible via a web-link (http://cemff.epfl.ch). The database provides information on the different force fields, energy expressions, and model validations using systematic comparisons of computed data with benchmarks from experiment and from ab-initio calculations. The cemff database aims at helping researchers to evaluate and choose suitable potentials for specific systems. New force fields can be added to the database.
Receptor tyrosine kinases form an important class of membrane proteins that regulate cell life cycle and metabolism. Among wide variety of receptors, they have simple structure with single alpha-helix crossing the membrane. This transmembrane domain is functionalm as dimeric state conformation defines active/inactive state of the receptor. The lipid environment can modulate functioning of such proteins, but the exact details are not well described yet. In addition to specific interactions with certain types of lipids, cholesterol and gangliosides, there are non-specific ones, since physico-chemical parameters are dependent on local lipid composition around protein molecule. However, there are opposite hypotheses about what is the driving force of heterogeneities formation in the membrane: lipid molecules themselves or membrane proteins embedded in the bilayer. To answer the question on mutual influence of proteins and their lipid environment, we used atomistic computer modeling: molecular dynamics simulations followed by a detailed analysis of intermolecular contacts to identify key amino acid residues that determine protein-lipid interactions. It was shown that the number of protein-lipid contacts depends on the conformation of the dimeric state, and their distribution over the monolayers is asymmetric. The results of the work will help in understanding the mechanism of signal transduction by receptor tyrosine kinases and finding ways to influence their activity.
The purpose of this manual is to consolidate the theoretical knowledge in areas of "computer microarchitecture", "CPU", "CISC-to-RISC pipelines". In this manual describes the features of the organization of the work of contemporary superscalar processors, the Intel architecture when running native commands. At the end of the laboratory work the student must have an understanding of the cycle and phases of operation of the processor core for execution of the command, the micro-operations and the number of them for different phases of the command. The student should be able to explain the graphs and tables the results of modeling for their version of the task and answer the questions placed at the end of this study guide.
A model for organizing cargo transportation between two node stations connected by a railway line which contains a certain number of intermediate stations is considered. The movement of cargo is in one direction. Such a situation may occur, for example, if one of the node stations is located in a region which produce raw material for manufacturing industry located in another region, and there is another node station. The organization of freight traﬃc is performed by means of a number of technologies. These technologies determine the rules for taking on cargo at the initial node station, the rules of interaction between neighboring stations, as well as the rule of distribution of cargo to the ﬁnal node stations. The process of cargo transportation is followed by the set rule of control. For such a model, one must determine possible modes of cargo transportation and describe their properties. This model is described by a ﬁnite-dimensional system of diﬀerential equations with nonlocal linear restrictions. The class of the solution satisfying nonlocal linear restrictions is extremely narrow. It results in the need for the “correct” extension of solutions of a system of diﬀerential equations to a class of quasi-solutions having the distinctive feature of gaps in a countable number of points. It was possible numerically using the Runge–Kutta method of the fourth order to build these quasi-solutions and determine their rate of growth. Let us note that in the technical plan the main complexity consisted in obtaining quasi-solutions satisfying the nonlocal linear restrictions. Furthermore, we investigated the dependence of quasi-solutions and, in particular, sizes of gaps (jumps) of solutions on a number of parameters of the model characterizing a rule of control, technologies for transportation of cargo and intensity of giving of cargo on a node station.
Generalized error-locating codes are discussed. An algorithm for calculation of the upper bound of the probability of erroneous decoding for known code parameters and the input error probability is given. Based on this algorithm, an algorithm for selection of the code parameters for a specified design and input and output error probabilities is constructed. The lower bound of the probability of erroneous decoding is given. Examples of the dependence of the probability of erroneous decoding on the input error probability are given and the behavior of the obtained curves is explained.
Event logs collected by modern information and technical systems usually contain enough data for automated process models discovery. A variety of algorithms was developed for process models discovery, conformance checking, log to model alignment, comparison of process models, etc., nevertheless a quick analysis of ad-hoc selected parts of a journal still have not get a full-fledged implementation. This paper describes an ROLAP-based method of multidimensional event logs storage for process mining. The result of the analysis of the journal is visualized as directed graph representing the union of all possible event sequences, ranked by their occurrence probability. Our implementation allows the analyst to discover process models for sublogs defined by ad-hoc selection of criteria and value of occurrence probability
Let G be a semisimple algebraic group whose decomposition into the product of simple components does not contain simple groups of type A, and P⊆G be a parabolic subgroup. Extending the results of Popov , we enumerate all triples (G, P, n) such that (a) there exists an open G-orbit on the multiple flag variety G/P × G/P × . . . × G/P (n factors), (b) the number of G-orbits on the multiple flag variety is finite.
I give the explicit formula for the (set-theoretical) system of Resultants of m+1 homogeneous polynomials in n+1 variables