Controlling patterns of geospatial phenomena

Modeling spatially distributed phenomena in terms of its controlling factors is a recurring problem in geoscience. Most efforts concentrate on predicting the value of response variable in terms of controlling variables either through a physical model or a regression model. However, many geospatial systems comprises complex, nonlinear, and spatially non-uniform relationships, making it difficult to even formulate a viable model. This paper focuses on spatial partitioning of controlling variables that are attributed to a particular range of a response variable. Thus, the presented method surveys spatially distributed relationships between predictors and response. The method is based on association analysis technique of identifying emerging patterns, which are extended in order to be applied more effectively to geospatial data sets. The outcome of the method is a list of spatial footprints, each characterized by a unique “controlling pattern”—a list of specific values of predictors that locally correlate with a specified value of response variable. Mapping the controlling footprints reveals geographic regionalization of relationship between predictors and response. The data mining underpinnings of the method are given and its application to a real world problem is demonstrated using an expository example focusing on determining variety of environmental associations of high vegetation density across the continental United States.     

Michell cantilevers constructed within a half strip. Tabulation of selected benchmark results

The paper delivers the benchmark results for the Michell cantilevers constructed within a half strip, for selected values of the σ _T /σ _C ratio, σ _T , σ _C being the admissible stresses in tension and compression, respectively.     

TSV constraints related to temperature excursion, pressure during molding, materials used and handling loads

The current paper focuses on several mechanical aspects of a waferlevel packaging approach using a direct face-to-face Chip-to-Wafer (C2W) bonding of a MEMS device on an ASIC substrate wafer. Requirements of minimized inherent stress from packaging and good decoupling from forces applied in manufacturing and application are discussed with particular attention to the presence of through-silicon vias (TSV) in the substrate wafer. The paper deals with FEM analysis of temperature excursion, pressure during molding, materials used and handling load influence on mechanical stress within the TSV system and on wafer level, which can be large enough to disintegrate the system.     

XtalOpt version r7: An open-source evolutionary algorithm for crystal structure prediction

A new version of XtalOpt, a user-friendly GPL-licensed evolutionary algorithm for crystal structure prediction, is available for download from the CPC library or the XtalOpt website, http://xtalopt.openmolecules.net. The new version now supports four external geometry optimization codes (VASP, GULP, PWSCF, and CASTEP), as well as three queuing systems: PBS, SGE, SLURM, and “Local”. The local queuing system allows the geometry optimizations to be performed on the user?s workstation if an external computational cluster is unavailable. Support for the Windows operating system has been added, and a Windows installer is provided. Numerous bugfixes and feature enhancements have been made in the new release as well.

New version program summary

Program title:XtalOptCatalogue identifier: AEGX_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v2_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 125 383No. of bytes in distributed program, including test data, etc.: 11 607 415Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: Linux, MS WindowsClassification: 7.7External routines: Qt [2], Open Babel [3], Avogadro [4], and one of: VASP [5], PWSCF [6], GULP [7], CASTEP [8]Catalogue identifier of previous version: AEGX_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 372Does the new version supersede the previous version?: YesNature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum of a crystalline structure on its potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available for use and collaboration under the GNU Public License. See the original publication on XtalOpt?s implementation [11] for more information on the method.Reasons for new version: Since XtalOpt?s initial release in June 2010, support for additional optimizers, queuing systems, and an operating system has been added. XtalOpt can now use VASP, GULP, PWSCF, or CASTEP to perform local geometry optimizations. The queue submission code has been rewritten, and now supports running any of the above codes on ssh-accessible computer clusters that use the Portable Batch System (PBS), Sun Grid Engine (SGE), or SLURM queuing systems for managing the optimization jobs. Alternatively, geometry optimizations may be performed on the user?s workstation using the new internal “Local” queuing system if high performance computing resources are unavailable. XtalOpt has been built and tested on the Microsoft Windows operating system (XP or later) in addition to Linux, and a Windows installer is provided. The installer includes a development version of Avogadro that contains expanded crystallography support [12] that is not available in the mainline Avogadro releases. Other notable new developments include:

• • 

  LIBSSH [10] is distributed with the XtalOpt sources and used for communication with the remote clusters, eliminating the previous requirement to set up public-key authentication;

• • 

  Plotting enthalpy (or energy) vs. structure number in the plot tab will trace out the history of the most stable structure as the search progresses A read-only mode has been added to allow inspection of previous searches through the user interface without connecting to a cluster or submitting new jobs;

• • 

  The tutorial [13] has been rewritten to reflect the changes to the interface and the newly supported codes. Expanded sections on optimizations schemes and save/resume have been added;

• • 

  The included version of SPGLIB has been updated. An option has been added to set the Cartesian tolerance of the space group detection. A new option has been added to the Progress table?s right-click menu that copies the selected structure?s POSCAR formatted representation to the clipboard;

• • 

  Numerous other small bugfixes/enhancements.

Summary of revisions: See “Reasons for new version” above.Running time: User dependent. The program runs until stopped by the user.References:

•  [1] 

  http://www.gnu.org/licenses/gpl.html.

•  [2] 

  http://www.trolltech.com/.

•  [3] 

  http://openbabel.org/.

•  [4] 

  http://avogadro.openmolecules.net.

•  [5] 

  http://cms.mpi.univie.ac.at/vasp.

•  [6] 

  http://www.quantum-espresso.org.

•  [7] 

  https://www.ivec.org/gulp.

•  [8] 

  http://www.castep.org.

•  [9] 

  http://spglib.sourceforge.net.

• [10] 

  http://www.libssh.org.

• [11] 

  D. Lonie, E. Zurek, Comp. Phys. Comm. 182 (2011) 372–387, doi:10.1016/j.cpc.2010.07.048.

• [12] 

  http://davidlonie.blogspot.com/2011/03/new-avogadro-crystallography-extension.html.

• [13] 

  http://xtalopt.openmolecules.net/globalsearch/docs/tut-xo.html.

     

XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

The implementation and testing of XtalOpt, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XtalOpt are optimized using a novel benchmarking scheme. XtalOpt is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface.

Program summary

Program title:XtalOptCatalogue identifier: AEGX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 36 849No. of bytes in distributed program, including test data, etc.: 1 149 399Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: LinuxClassification: 7.7External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7].Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available to the scientific community for use and collaboration under the GNU Public License.Running time: User dependent. The program runs until stopped by the user.References:

• [1] 

  http://www.gnu.org/licenses/gpl.html.

• [2] 

  http://www.trolltech.com/.

• [3] 

  http://openbabel.org/.

• [4] 

  http://avogadro.openmolecules.net.

• [5] 

  http://cms.mpi.univie.ac.at/vasp.

• [6] 

  http://www.quantum-espresso.org.

• [7] 

  https://www.ivec.org/gulp.

• [8] 

  http://spglib.sourceforge.net.

     

Reducing Protocol Analysis with XOR to the XOR-Free Case in the Horn Theory Based Approach

In the Horn theory based approach for cryptographic protocol analysis, cryptographic protocols and (Dolev?CYao) intruders are modeled by Horn theories and security analysis boils down to solving the derivation problem for Horn theories. This approach and the tools based on this approach, including ProVerif, have been very successful in the automatic analysis of cryptographic protocols. However, dealing with the algebraic properties of operators, such as the exclusive OR (XOR), which are frequently used in cryptographic protocols has been problematic. In particular, ProVerif cannot deal with XOR. In this paper, we show how to reduce the derivation problem for Horn theories with XOR to the XOR-free case. Our reduction works for an expressive class of Horn theories. A large class of intruder capabilities and protocols that employ the XOR operator can be modeled by these theories. Our reduction allows us to carry out protocol analysis using tools, such as ProVerif, that cannot deal with XOR, but are very efficient in the XOR-free case. We implemented our reduction and, in combination with ProVerif, used it for the fully automatic analysis of several protocols that employ the XOR operator. Among others, our analysis revealed a new attack on an IBM security module.     

Leftist Grammars and the Chomsky Hierarchy

Leftist grammars are characterized in terms of rules of the form a → ba and cd → d, without distinction between terminals and nonterminals. They were introduced by Motwani et al. [13], where the accessibility problem for some general protection system was related to these grammars. This protection system was originally proposed in [4] and [15] in the context of Java virtual worlds. The accessibility problem is formulated in the form "Can object p gain (illegal) access to object q by a series of legal moves (as prescribed by the policy)?" The membership problem for leftist grammar is decidable [13], which implies decidability of the accessibility problem for the appropriate protection system. We study relationships between language classes defined by various types of leftist grammars and classes of the Chomsky hierarchy. We show that general leftist grammars can define languages which arenot context free, answering in the negative a question from [13]. Moreover, we study some restricted variants of leftist grammars and relate them to regular, deterministic context-free, and context-free languages.     

4′-Methylflavanone Glycosides Obtained Using Biotransformation in the Entomopathogenic Filamentous Fungi Cultures as Potential Anticarcinogenic,Antimicrobial, and Hepatoprotective Agents

Flavonoid compounds exhibit numerous biological activities and significantly impact human health. The presence of methyl or glucosyl moieties attached to the flavonoid core remarkably modifies their physicochemical properties and improves intestinal absorption. Combined chemical and biotechnological methods can be applied to obtain such derivatives. In the presented study, 4′-methylflavanone was synthesized and biotransformed in the cultures of three strains of entomopathogenic filamentous fungi, i.e., Isaria fumosorosea KCH J2, Beauveria bassiana KCH J1.5, and Isaria farinosa KCH J2.1. The microbial transformation products in the culture of I. fumosorosea KCH J2, flavanone 4′-methylene-O-β-D-(4″-O-methyl)-glucopyranoside, 2-phenyl-(4′-hydroxymethyl)-4-hydroxychromane, and flavanone 4′-carboxylic acid were obtained. Biotransformation of 4′-methylflavanone in the culture of B. bassiana KCH J1.5 resulted in the formation of one main product, i.e., flavanone 4′-methylene-O-β-D-(4″-O-methyl)-glucopyranoside. In the case of I. farinosa KCH J2.6 as a biocatalyst, three products, i.e., flavanone 4′-methylene-O-β-D-(4″-O-methyl)-glucopyranoside, flavanone 4′-carboxylic acid, and 4′-hydroxymethylflavanone 4-O-β-D-(4″-O-methyl)-glucopyranoside were obtained. The Swiss-ADME online simulations confirmed the increase in water solubility of 4′-methylflavanone glycosides and analyses performed using the Way2Drug Pass Online prediction tool indicated that flavanone 4′-methylene-O-β-D-(4″-O-methyl)-glucopyranoside and 4′-hydroxymethylflavanone 4-O-β-D-(4″-O-methyl)-glucopyranoside, which had not been previously reported in the literature, are promising anticarcinogenic, antimicrobial, and hepatoprotective agents.