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.     

ELECTROCHEMICAL MACHINING OF CURVILINEAR SURFACES

In this work a theoretical analysis of the ECM process of curvilinear surfaces has been presented. The purpose of this analysis is to predict the shape evolution of the machined object using: a shaping surface of small thickness (flat issue) and a blade of hydrodynamic machine (quasi-three dimensional issue). ECM modeling involves prediction of the machined surface shape evolution and distribution of physical-chemical parameters inside the interelectrode gap. The problem has been solved with the use of an equation of the electrolyte and hydrogen mixture (liquid and gas) flat flow inside the interelectrode gap. After introducing simplifying assumptions for the flow, void fraction distribution and the gap thickness, the equations were solved partly analytically, partly numerically. The obtained solutions for assigned parameters of the machining process are presented graphically in the form of distributions of: static pressure, the mixture flow rate, temperature, void fraction and evolution of the machined surface shape evolution.     

Generalized model of vibro-isolation systems with seated human body for single-axis transmission of vibration

A generalized model of vibration isolation systems with a human body in a seated position is developed. The system dynamics is modeled for a single-axis transmission of vibration, that is, longitudinal x, lateral y and vertical z, to limit whole-body vibration exposure. The developed model can be successfully employed to describe the propagation of vibration waves from the source to a vibrating object. The proposed mathematical model can be widely used to protect a human body against vibration.     

From Cyclo[18]carbon to the Novel Nanostructures—Theoretical Predictions

In this paper, we present a number of novel pure-carbon structures generated from cyclo[18]carbon. Due to the very high reactivity of cyclo[18]carbon, it is possible to link these molecules together to form bigger molecular systems. In our studies, we generated new structures containing 18, 36 and 72 carbon atoms. They are of different shapes including ribbons, sheets and tubes. All these new structures were obtained in virtual reactions driven by external forces. For every reaction, the energy requirement was evaluated exactly when the corresponding transition state was found or it was estimated through our new approach. A small HOMO–LUMO gap in these nanostructures indicates easy excitations and the multiple bonds network indicates their high reactivity. Both of these factors suggest that some potential applications of the new nanostructures are as components of therapeutically active carbon quantum dots, terminal fragments of graphene or carbon nanotubes obtained after fracture or growing in situ in catalytic reactions leading to the formation of carbonaceous materials.     

Neutrophil Count as Atrioventricular Block (AVB) Predictor following Pediatric Heart Surgery

Neutrophils play a significant role in immune and inflammatory reactions. The preoperative inflammatory activation may have a detrimental effect on postoperative outcomes. The aim of the study was to investigate the relation between preoperative hematological indices on postoperative complications’ risk in pediatric cardiac congenital surgery. The retrospective single center analysis included 93 pediatric patients (48 (65%) males and 45 (35%) females), mean age of 7 (3–30) months referred for cardiac surgery in cardiopulmonary bypass due to functional single ventricle disease (26 procedures), shunts lesions (40 procedures) and cyanotic disease (27 procedures). Among simple hematological indices, the receiver-operating-characteristic curve showed that a neutrophil count below 2.59 K/uL was found as an optimal cut-off point for predicting postoperative atrioventricular block following pediatric cardiac surgery (AUC = 0.845, p < 0.0001) yielding a sensitivity of 100% and a specificity of 65.62%. Preoperative values of neutrophil count below 2.59 K/uL in whole blood analysis can be regarded as a predictive factor (AUC = 0.845, p < 0.0001) for postoperative atrioventricular block in pediatric cardiac surgery.     

Nontoxic and Naturally Occurring Active Compounds as Potential Inhibitors of Biological Targets in Liriomyza trifolii

In recent years, novel strategies to control insects have been based on protease inhibitors (PIs). In this regard, molecular docking and molecular dynamics simulations have been extensively used to investigate insect gut proteases and the interactions of PIs for the development of resistance against insects. We, herein, report an in silico study of (disodium 5′-inosinate and petunidin 3-glucoside), (calcium 5′-guanylate and chlorogenic acid), chlorogenic acid alone, (kaempferol-3,7-di-O-glucoside with hyperoside and delphinidin 3-glucoside), and (myricetin 3′-glucoside and hyperoside) as potential inhibitors of acetylcholinesterase receptors, actin, α-tubulin, arginine kinase, and histone receptor III subtypes, respectively. The study demonstrated that the inhibitors are capable of forming stable complexes with the corresponding proteins while also showing great potential for inhibitory activity in the proposed protein-inhibitor combinations.