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Collection Highlights

Simulation and Modeling Methodologies Technologies and

Applications International Conference SIMULTECH 2013
Reykjavík Iceland July 29 31 2013 Revised Selected Papers
1st Edition Mohammad S. Obaidat

Simulation and Modeling Methodologies, Technologies and

Applications: 9th International Conference, SIMULTECH 2019
Prague, Czech Republic, July 29-31, 2019, Revised Selected
Papers Mohammad S. Obaidat

Simulation and Modeling Methodologies, Technologies and

Applications: 7th International Conference, SIMULTECH 2017
Madrid, Spain, July 26–28, 2017 Revised Selected Papers
Mohammad S. Obaidat

E-Business and Telecommunications: 15th International

Joint Conference, ICETE 2018, Porto, Portugal, July 26–28,
2018, Revised Selected Papers Mohammad S. Obaidat
E Business and Telecommunications 13th International Joint
Conference ICETE 2016 Lisbon Portugal July 26 28 2016
Revised Selected Papers 1st Edition Mohammad S. Obaidat
(Eds.)

E Business and Telecommunications 16th International

Conference ICETE 2019 Prague Czech Republic July 26 28
2019 Revised Selected Papers Mohammad S. Obaidat

Sensor Networks 6th International Conference SENSORNETS

2017 Porto Portugal February 19 21 2017 and 7th
International Conference SENSORNETS 2018 Funchal Madeira
Portugal January 22 24 2018 Revised Selected Papers César
Benavente-Peces

Software Technologies Applications and Foundations STAF

2018 Collocated Workshops Toulouse France June 25 29 2018
Revised Selected Papers Manuel Mazzara

Intelligent Technologies and Applications First

International Conference INTAP 2018 Bahawalpur Pakistan
October 23 25 2018 Revised Selected Papers Imran Sarwar
Bajwa
Advances in Intelligent Systems and Computing 947

Mohammad S. Obaidat
Tuncer Ören
Floriano De Rango Editors

Simulation
and Modeling
Methodologies,
Technologies and
Applications
8th International Conference,
SIMULTECH 2018, Porto, Portugal, July
29–31, 2018, Revised Selected Papers
Advances in Intelligent Systems and Computing

Volume 947

Series Editor
Janusz Kacprzyk, Systems Research Institute, Polish Academy of Sciences,
Warsaw, Poland

Advisory Editors
Nikhil R. Pal, Indian Statistical Institute, Kolkata, India
Rafael Bello Perez, Faculty of Mathematics, Physics and Computing,
Universidad Central de Las Villas, Santa Clara, Cuba
Emilio S. Corchado, University of Salamanca, Salamanca, Spain
Hani Hagras, School of Computer Science and Electronic Engineering,
University of Essex, Colchester, UK
László T. Kóczy, Department of Automation, Széchenyi István University,
Gyor, Hungary
Vladik Kreinovich, Department of Computer Science, University of Texas
at El Paso, El Paso, TX, USA
Chin-Teng Lin, Department of Electrical Engineering, National Chiao
Tung University, Hsinchu, Taiwan
Jie Lu, Faculty of Engineering and Information Technology,
University of Technology Sydney, Sydney, NSW, Australia
Patricia Melin, Graduate Program of Computer Science, Tijuana Institute
of Technology, Tijuana, Mexico
Nadia Nedjah, Department of Electronics Engineering, University of Rio de Janeiro,
Rio de Janeiro, Brazil
Ngoc Thanh Nguyen , Faculty of Computer Science and Management,
Wrocław University of Technology, Wrocław, Poland
Jun Wang, Department of Mechanical and Automation Engineering,
The Chinese University of Hong Kong, Shatin, Hong Kong
The series “Advances in Intelligent Systems and Computing” contains publications
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Mohammad S. Obaidat Tuncer Ören
• •

Floriano De Rango
Editors

Simulation and Modeling

Methodologies, Technologies
and Applications
8th International Conference, SIMULTECH 2018,
Porto, Portugal, July 29–31, 2018,
Revised Selected Papers

123
Editors
Mohammad S. Obaidat Tuncer Ören
King Abdullah II School of Information School of Electrical Engineering
Technology and Computer Science
University of Jordan University of Ottawa
Amman, Jordan Ottawa, ON, Canada
Nazarbayev University
Astana, Kazakhstan

Floriano De Rango
University of Calabria
Rende, Cosenza, Italy

ISSN 2194-5357 ISSN 2194-5365 (electronic)

Advances in Intelligent Systems and Computing
ISBN 978-3-030-35943-0 ISBN 978-3-030-35944-7 (eBook)
https://doi.org/10.1007/978-3-030-35944-7
© Springer Nature Switzerland AG 2020
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Preface

The present book includes extended and revised versions of a set of selected papers
from the 8th International Conference on Simulation and Modeling Methodologies,
Technologies and Applications (SIMULTECH 2018), held in Porto, Portugal, in the
period July 29–31, 2018.
SIMULTECH 2018 received 83 paper submissions from 29 countries, of which
11% were included in this book. The papers were selected by the event chairs, and
their selection is based on a number of criteria that includes the reviews and
suggested comments provided by the program committee members, the session
chairs’ assessments and also the program chairs’ global view of all papers included
in the technical program. The authors of selected papers were then invited to submit
a revised and extended version of their papers having at least 30% new material.
The purpose of the 8th International Conference on Simulation and Modeling
Methodologies, Technologies and Applications (SIMULTECH 2018) was to bring
together researchers, engineers, applied mathematicians and practitioners interested
in the advances and applications in the field of system simulation. Four
simultaneous tracks were held, covering on one side domain-independent
methodologies and technologies and on the other side practical work developed
in specific application areas. The specific topics listed under each of these tracks
highlight the interest of this conference in aspects related to computing, including
conceptual modeling, agent-based modeling and simulation, interoperability,
ontologies, knowledge-based decision support, Petri nets, business process mod-
eling and simulation, among others.
The papers selected to be included in this book contribute to the understanding
of relevant trends of current research on simulation tools and platforms, formal
methods, as well as complex system modeling and simulation. The readers can find
contributions of simulation in business process analysis and risk management,
Internet of things, advanced material science and fuel cell design. Formal method
contributions include visual password systems, co-simulation of complex
subsystems, heating system application of feedback linearization for MTI systems
in a tensor framework and iterative construction of complete Lyapunov functions.

v
vi Preface

We would like to thank all the authors for their contributions as well as to the
reviewers who have helped ensuring the quality of this publication. We also thank
the staff of INTICCC and Springer for their good efforts and cooperation.

July 2018 Mohammad S. Obaidat

Tuncer Ören
Floriano De Rango
Organization

Conference Chair
Mohammad S. Obaidat University of Jordan, Jordan, and Nazarbayev
University, Kazakhstan

Program Chairs
Tuncer Ören (Honorary) University of Ottawa, Canada
Floriano De Rango University of Calabria, Italy

Program Committee
Nael Abu-Ghazaleh University of California, Riverside, USA
Lyuba Alboul Sheffield Hallam University, UK
Mikulas Alexik University of Zilina, Slovak Republic
Carlos Argáez University of Iceland, Iceland
Gianfranco Balbo University of Torino, Italy
Isaac Barjis City University of New York, USA
Martin Benedikt Technische Universität Graz, Austria
Mohamed Bettaz Philadelphia University, Jordan
Louis Birta University of Ottawa, Canada
Wolfgang Borutzky Bonn-Rhein-Sieg University of Applied
Sciences, Germany
Christos Bouras University of Patras and CTI&P Diophantus,
Greece
António Brito INESC TEC, Faculdade de Engenharia,
Universidade do Porto, Portugal
Jesus Carretero Computer Architecture Group, University
Carlos III of Madrid, Spain
Francesco Casella Politecnico di Milano, Italy
Rodrigo Castro University of Buenos Aires, Argentina

vii
viii Organization

Srinivas Chakravarthy Kettering University, USA

Franco Cicirelli Università della Calabria, Italy
Tanja Clees Fraunhofer Institute for Algorithms and Scientific
Computing (SCAI), Germany
Flavio Correa da Silva University of Sao Paulo, Brazil
Andrea D’Ambrogio Università di Roma “Tor Vergata”, Italy
Guyh Dituba Ngoma Université du Québec en Abitibi-Témiscamingue,
Canada
Karim Djemame University of Leeds, UK
Atakan Dogan Anadolu University, Turkey
Julie Dugdale Laboratoire d’Informatique de Grenoble, France
Dirk Eisenbiegler University of Furtwangen, Germany
Sabeur Elkosantini University of Monastir, Tunisia
Georg Engel AEE - Institute for Sustainable Technologies,
Austria
Zuhal Erden Atılım University, Turkey
Denis Filatov Institute of Physics of the Earth, Russian
Academy of Sciences, Russian Federation
Jason Friedman Tel Aviv University, Israel
Marco Furini Università di Modena e Reggio Emilia, Italy
José Manuel Galán Universidad de Burgos, Spain
Petia Georgieva University of Aveiro, Portugal
Charlotte Gerritsen Vrije Universiteit Amsterdam, the Netherlands
John Goulermas University of Liverpool, UK
Alexandra Grancharova University of Chemical Technology
and Metallurgy, Bulgaria
Francisco Grimaldo Universitat de València, Spain
Mykola Gusti International Institute for Applied Systems
Analysis, Austria
Maamar Hamri Laboratoire d’Informatique et Systèmes, France
Cathal Heavey University of Limerick, Ireland
Monika Heiner Brandenburg University of Technology Cottbus,
Germany
Tsan-Sheng Hsu Institute of Information Science, Academia
Sinica, Taiwan
Xiaolin Hu Georgia State University, USA
Eric Innocenti IUT DE CORSE - University of Corsica, France
Nobuaki Ishii Kanagawa University, Japan
Mhamed Itmi INSA Rouen, France
Syed Waqar ul Qounain University of the Punjab, Pakistan
Jaffry
Emilio Jiménez Macías Universidad de La Rioja, Spain
Nina Kargapolova Institute of Computational Mathematics and
Mathematical Geophysics, Russian Federation
Peter Kemper College of William and Mary, USA
Organization ix

Juš Kocijan Jozef Stefan Institute, Slovenia

Petia Koprinkova-Hristova IICT - Bulgarian Academy of Sciences, Bulgaria
Vladik Kreinovich University of Texas at El Paso, USA
Claudia Krull Otto von Guericke University Magdeburg,
Germany
Jean Le Fur IRD (Inst. Res. Development), France
Willem le Roux CSIR, South Africa
Pierre L’Ecuyer Universite de Montreal, Canada
Mike Lees University of Amsterdam, the Netherlands
Alberto Leva Politecnico di Milano, Italy
Richard Lipka University of West Bohemia, Czech Republic
Antonio Lopes University of Porto, Portugal
Maria Celia Lopes COPPE-UFRJ, Brazil
José Machado Institute of Engineering, Polytechnic of Porto,
Portugal
Maciej Malawski AGH University of Science and Technology,
Poland
Andrea Marin University of Venice, Italy
Carla Martin-Villalba UNED, Spain
Moreno Marzolla University of Bologna, Italy
Radek Matušu Tomas Bata University in Zlin, Czech Republic
Roger McHaney Kansas State University, USA
Nuno Melão Instituto Politécnico de Viseu, Escola Superior de
Tecnologia e Gestão de Viseu, Portugal
Adel Mhamdi RWTH Aachen University, Germany
Bozena Mielczarek Wroclaw University of Science Technology,
Poland
Vikram Mittal United States Military Academy, USA
Cristina Montañola Sales Universitat Politècnica de Catalunya, Spain
Roberto Montemanni IDSIA - Dalle Molle Institute for Artificial
Intelligence (USI-SUPSI), Switzerland
Jairo Montoya-Torres Universidad de La Sabana, Colombia
Bertie Müller Swansea University, UK
Ivan Mura Universidad de los Andes, Colombia
Navonil Mustafee University of Exeter, UK
Nazmun Nahar University of Jyvaskyla, Finland, and University
of Tartu, Estonia
Angela Nebot Universitat Politècnica de Catalunya, Spain
Bao Nguyen Defence R&D Canada and University of Ottawa,
Canada
Lialia Nikitina Fraunhofer Institute for Algorithms and Scientific
Computing (SCAI), Germany
James Nutaro Oak Ridge National Laboratory, USA
Mohammad Obaidat University of Jordan, Jordan, and Nazarbayev
University, Kazakhstan
x Organization

Sorin Olaru CentraleSupélec, France

Paulo Oliveira Universidade de Tras-os-Montes e Alto Douro,
Portugal
Feng Pan Liaoning Normal University, China
Victor Parque Waseda University and Egypt-Japan University
of Science and Technology (E-JUST), Japan
George Pavlidis “Athena” Research Centre, Greece
Alessandro Pellegrini Sapienza University of Rome, Italy
L. Felipe Perrone Bucknell University, USA
Alexandre Petrenko Centre de Recherche Informatique de Montreal,
Canada
Alexandr Petukhov Lobachevsky State University of Nizhni
Novgorod, Russian Federation
Régis Plateaux SUPMECA, France
Tomas Potuzak University of West Bohemia, Czech Republic
Jacinto Quintero Universidad de Los Andes, Venezuela
Mpho Raborife University of Johannesburg, South Africa
Urvashi Rathod Symbiosis Centre for Information Technology
(SCIT), India
Manuel Resinas Universidad de Sevilla, Spain
Jerzy Respondek Silesian University of Technology, Poland
M. Riazi Kuwait University, Kuwait
José Risco-Martín Universidad Complutense de Madrid, Spain
Oliver Rose Universität der Bundeswehr München
(University of the Federal Armed Forces
Munich), Germany
Rosaldo Rossetti Laboratório de Inteligência Artificial e Ciência de
Computadores, LIACC/FEUP, Portugal
Jaroslav Rozman Brno University of Technology, Czech Republic
Katarzyna Rycerz Institute of Computer Science, AGH, Krakow,
Poland
Jordi Sabater-Mir IIIA-CSIC, Spain
Paulo Salvador Instituto de Telecomunicações, DETI, University
of Aveiro, Portugal
Antonella Santone University of Molise, Italy
Jean-François Santucci SPE UMR CNRS 6134 - University of Corsica,
France
Jefrey Smith Auburn University, USA
Xiao Song Beihang University, China
Yuri Sotskov United Institute of Informatics Problems of the
National Academy of Belarus, UIIP, Minsk,
Belarus
James Spall Johns Hopkins University, USA
Giovanni Stea University of Pisa, Italy
Mu-Chun Su National Central University, Taiwan
Organization xi

Nary Subramanian The University of Texas at Tyler, USA

Peter Summons University of Newcastle, Australia
Antuela Tako Loughborough University, UK
Halina Tarasiuk Warsaw University of Technology, Poland
Constantinos Theodoropoulos The University of Manchester, UK
Mamadou Traoré University of Bordeaux, France
Klaus Troitzsch University of Koblenz-Landau, Koblenz Campus,
Germany
Zhiying Tu Harbin Institute of Technology, China
Kay Tucci Universidad de los Andes, Venezuela
Adelinde Uhrmacher University of Rostock, Germany
Alfonso Urquia Universidad Nacional de Educación a Distancia,
Spain
Durk-Jouke van der Zee University of Groningen, the Netherlands
Svetlana Bulgarian Modeling and Simulation Association
Vasileva-Boyadzhieva (BULSIM), Bulgaria
Vladimír Veselý Faculty of Information Technology, Brno
University of Technology, Czech Republic
Maria Viamonte Instituto Superior de Engenharia do Porto,
Portugal
Manuel Villen-Altamirano Universidad de Malaga, Spain
Friederike Wall Alpen-Adria-Universität Klagenfurt, Austria
Frank Werner Otto-von-Guericke-Universität Magdeburg,
Germany
Philip Wilsey Univ. of Cincinnati, USA
Kuan Yew Wong Universiti Teknologi Malaysia, Malaysia
Hui Xiao Southwestern University of Finance
and Economics, China
Yiping Yao National University of Defense Technology,
China
Gregory Zacharewicz IMT Mines Ales, France
František Zboril Faculty of Information Technology,
Czech Republic

Additional Reviewers
Gökhan Cinar Eskisehir Osmangazi University, Turkey
Tansu Filik Anadolu University, Turkey
Celal Kandemir Eskisehir Osmangazi Üniversitesi, Turkey
Francesco Mercaldo National Research Council of Italy (CNR), Italy
Ezequiel Pecker-Marcosig FIUBA, ICC, CONICET, Argentina
Lucio Santi Universidad de Buenos Aires, Argentina
Long Wang Johns Hopkins University, USA
xii Organization

Invited Speakers
Juan M. Durán University of Stuttgart, Germany
Janusz Kacprzyk Systems Research Institute, Polish Academy
of Sciences, Poland
Gabriel Wainer Carleton University, Canada
Contents

Atomistic Modelling and Simulation of Transmission Electron

Microscopy Images: Application to Intrinsic Defects of Graphene . . . . . 1
Cyril Guedj, Léonard Jaillet, François Rousse, and Stéphane Redon
Using Simulation in Business Process Analysis and Risk
Management: The Blood Bank Case Study . . . . . . . . . . . . . . . . . . . . . . 20
Ilaria Angela Amantea, Antonio Di Leva, and Emilio Sulis
An SDN/NFV Based Approach for Mobility Management
in 5G Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
N. Omheni, F. Zarai, B. Sadoun, and M. S. Obaidat
Dockemu: An IoT Simulation Framework Based on Linux
Containers and the ns-3 Network Simulator — Application
to CoAP IoT Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Antón Román Portabales and Martín López Nores
Iterative Construction of Complete Lyapunov Functions: Analysis
of Algorithm Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Carlos Argáez, Peter Giesl, and Sigurdur Hafstein
A Pre-step Stabilization Method for Non-iterative Co-Simulation
and Effects of Interface-Jacobians Identification . . . . . . . . . . . . . . . . . . 101
Simon Genser and Martin Benedikt
A Heating Systems Application of Feedback Linearization for MTI
Systems in a Tensor Framework . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Kai Kruppa and Gerwald Lichtenberg
Syntactic Generation of Similar Pictures . . . . . . . . . . . . . . . . . . . . . . . . 153
Nuru Jingili, Sigrid Ewert, and Ian Sanders

xiii
xiv Contents

Mathematical Modeling of Alkaline Methanol Oxidation for Design

of Efficient Fuel Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Tanja Clees, Igor Nikitin, Lialia Nikitina, Sabine Pott, Ulrike Krewer,
and Theresa Haisch

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197

 Atomistic Modelling and Simulation
of Transmission Electron Microscopy Images:
Application to Intrinsic Defects of Graphene

Cyril Guedj1(&), Léonard Jaillet2, François Rousse2,

and Stéphane Redon3
1
Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France
[email protected]
2
Univ. Grenoble Alpes, Inria, CNRS,
Grenoble INP, LJK, 38000 Grenoble, France
3
OneAngstrom, Grenoble, France
[email protected]
https://www.oneangstrom.com,
https://www.minatec.org/fr/,
http://www.leti-cea.fr/cea-tech/leti,
https://www.samson-connect.net

Abstract. The characterization of advanced materials and devices in the

nanometer range requires complex tools to understand the precise links between
structure and properties. This paper demonstrates that the modelling of
graphene-based defects can be obtained efficiently for various atomic arrange-
ments using the Brenner module of the SAMSON software platform. The sig-
natures of all kinds of defects are computed in terms of energy and simulated
scanning transmission electron microscopy images. The results are in good
agreement with the majority of the available theoretical and experimental data.
This original methodology is an excellent compromise between the speed and
the precision required by the semiconductor industry and opens the possibility of
realistic in-silico research conjugated to the experimental nanocharacterization
of these promising materials. We propose a novel approach to compare the
agreement between experiment and simulation by using the projected radial
distribution function. The maximum projected Euclidian distance between the
model and the experiment is always better than 100 pm.

Keywords: Atomic modelling
Electron microscopy
STEM
Graphene

Defects
Microstructure
Image simulation
Materials
Characterization

Atomistic

1 Introduction

Digitals tools are more and more required to study, design and prototype nano-objects,
although the underlying physics is so complex that the quest for a universal tool is still
far from being over. With the increase of the computational power and the

Grenoble INP—Institute of Engineering Univ. Grenoble Alpes.

© Springer Nature Switzerland AG 2020

M. S. Obaidat et al. (Eds.): SIMULTECH 2018, AISC 947, pp. 1–19, 2020.
https://doi.org/10.1007/978-3-030-35944-7_1
2 C. Guedj et al.

improvement of the simulation methods, new possibilities are emerging. The increasing
pace of the semiconductor industry requires rapid and efficient simulation and mod-
elling strategies to analyse the results and improve the technological performances of
various nano-devices, sensors or actuators. In many systems, the optical or electronic
properties are driven by interfacial or by defect-engineered phenomena. In order to
understand the links between structure and properties, the nanocharacterization of
materials and devices must be advantageously combined with atomistic modelling
studies. The equilibrium positions of all atoms provide the necessary basis to simulate
the relevant physical properties, which are measured with increasing precision and
sensitivity. The combination of experiments conducted in parallel with simulations is
particularly relevant in the field of transmission electron microscopy (TEM), because
the correlation between the measured image and the actual arrangement of atoms is not
straightforward in general. Like most characterizations, the precise simulation of TEM
images is usually mandatory to interpret the experimental results at the atomic scale.
With developments in aberration-corrected transmission electron microscopy, it is now
possible to characterize vacancy defects in graphene [1]. This paper provides an
optimized methodology to model high resolution scanning transmission electron
microscopy (HRSTEM) experiments of graphene-based defects. For this, it uses
relaxed atomistic models obtained with the Brenner module of the Software for
Adaptative Modeling and Simulation Of Nanosystems (SAMSON) (www.samson-
connect.fr). The case of graphene-based defects is extremely interesting, because this is
a 2D material with outstanding mechanical [2–6], and electronic [7, 8] properties.
Hence, graphene belongs to a family of 2D materials which generates huge expecta-
tions in terms of possible applications [9–14]. The high mobility of graphene makes it
advantageous in the perspective of post-silicon electronics, but the defectivity remains
a recurrent critical issue. A wide variety of deviations from a perfect crystal might
occur during the processing of graphene, either due to the growth conditions or to
various sources of degradation, such as knock-on interactions, electron or ionic colli-
sions, plasma damage, chemical reactions, etc. The link between defectivity and
physical properties is critical for the device performance. Thus, defect engineering is
certainly the key of the possible industrial viability of this material. In this paper, we
study the defects in graphene in terms of structure and energy. Our methodology used
to build the systems and to simulate TEM images provides the necessary basis to
analyze graphene-based defects, in comparison with available data from the literature.

2 Methodology

2.1 State of the Art

Many methods exist to simulate hydrocarbon systems, such as molecular dynamics,
Monte Carlo and many other variants. Typically, these simulations come with ab-initio
quantum-chemistry computations. Therefore, computational studies of complex defects
are often limited by the maximum number of atoms that the first-principle methods can
handle. In all cases, these methods require an initial structural model consisting in the
description of all atoms in terms of position and chemical nature. In the case of pure
 Atomistic Modelling and Simulation of Transmission Electron Microscopy Images 3

crystals, the 3D periodicity helps in calculating all the atom positions for large systems
(i.e. more than 50 000 atoms), but in case of localised asymmetrical defects, this task is
much more tedious or even completely unfeasible in the worst cases. Hence, a com-
putational tool that is fast enough to handle physically-relevant calculations with tens
of thousands atoms is highly desirable. The SAMSON platform and its Brenner module
appear to be ideally suited to this task, since they can handle complex models and
simulate very large systems in a timescale typically less than a day, which is com-
patible with the feedback delay required by most research teams in nanomaterial
characterization. This module appears as an interactive tool for performing predictive
modelling, particularly adapted to the very sustained pace of experimentalists.

2.2 The SAMSON Software Platform

SAMSON is a user-friendly software platform for computational nanoscience devel-
oped by the NANO-D group at Inria (https://www.samson-connect.net). SAMSON has
an open architecture, and users customize their installation with SAMSON Elements,
i.e. modules for SAMSON that may contain apps, editors, builders, force fields,
optimizers, visualizations, etc. SAMSON Elements are available with a provided
Software Development Kit for further customization. At the time of writing, about fifty
SAMSON Elements are available on SAMSON Connect, for a number of application
domains, including materials science (e.g. Brenner model, graphene generator,
Universal Force Field, Crystal creator, graphene TEM image analyser, etc.) and drug
design (GROMACS force fields, AutoDock Vina, Interactive Ramachandran plots,
Normal Modes Analysis, PEPSI-SAXS, etc.). Users may mix and match SAMSON
Elements to design their own processes and workflows, and may use Python scripting
to perform modelling and simulation tasks.

2.3 Brenner Model

To simulate the structure of defects in graphene, the atomic positions are computed from
energy minimization using the well-known bond-order Brenner interatomic potential
[15–21]. This is a parametrized version of Tersoff’s potential which includes terms to
correct for the overbindings of radicals. Brenner potential is ideally suited to the inter-
active digital modelling (virtual nano-engineering) of complex hydrocarbon structures
like carbon nanotubes [22], fullerene [23], or defective single layered graphene [24]. We
detail below how the energy and forces can be described from this potential.
Energy
The Brenner interatomic potential is particular in the sense that it mostly focuses on
covalent bonds, without long-range interaction. Hence, the potential energy VB of the
bonding interactions is a sum over interacting atoms (i.e. separated by less than 0.2 nm):
X X    
VB ¼ i j[i
½V R rij  bij V A rij  ð1Þ

The details are given in the original reference [17]. Since bonds are defined
dynamically via a bond-order function evolving with the interatomic distances, this
reactive potential has the ability to describe chemical reactions.
4 C. Guedj et al.

The potential also includes angular and dihedral terms, radical energetics and the
influence of p bonds [25].
To overcome the lack of long-range interactions, a non-bonded interaction potential
term is added. It consists in a sum of pairwise potential contributions. For simplicity,
the approach of Los et al. [26] is chosen and the Van der Waals potential term is added:
r6
VNB ðrij Þ ¼ b expðc0 rÞ  2 Vshift ð2Þ
r
to adjust the precision, using b = 3224.9 eV, c0 = 35.995 nm−1, 2 ¼ 0:01396 eV and
r = 0.344 nm.
Forces
The force terms can be calculated from the gradient of the potential V. More specifi-
cally, the Force Fi applied on atom i at position xi can be written:
X   
@V @V @rji
Fi ¼  ¼ j;ði;jÞ2b dr
ð3Þ
dxi ij dxi

where rij is the distance between atoms i and j, and b is the set of all pairs of atoms
involved in the interaction:

ij g
b ¼ fi; rij\Dmax ð4Þ

with Dmax
ij being a threshold distance depending on the atom types.
Adaptive Brenner
The adaptive version of the Brenner potential has been implemented in SAMSON [25].
Its interest is that it relies on an algorithm which incrementally updates the forces and
the total potential energy. It basically consists in an incremental dynamical update of
the set of interacting atoms and all information related to one, two, three or four atoms.
Bonds are divided into 4 types: bond with a relative motion, bonds with a change in
potential, bond with a change in conjugate number, and bonds without any change in
potential. After initialization, all terms with relative motions are updated incrementally
and after a first level and second level potential update, the forces are henceforward
updated. This allows the algorithm to linearly scale with the number of updated bonds.
Therefore the computational cost is decoupled from the number of atoms in the system
and physically-based editing becomes markedly faster.
To take advantage of adaptive Brenner, an adaptive mechanism is proposed in
SAMSON to update when minimizing a system. Such an approach in Cartesian
coordinates consists in deciding for each atom if it might move or be frozen in space.
This decision is made by comparing the norm of its potential displacement with a
threshold value, either automatically deduced from the system state or by a manual
choice fixed by the user. This implementation is an extension of the internal coordi-
nates and articulated bodies simulation [27].
This efficient update mechanism allows continuous minimization of the system
energy during the edition of the system, which helps to build realistic structures in a
 Atomistic Modelling and Simulation of Transmission Electron Microscopy Images 5

very convenient manner. The user action step (creating/moving/deleting atoms) alter-
nates with the adaptative minimization steps to parallelize the structure editing and the
energy minimization.

2.4 Simulation of Microscopy Images

Once the structure is fully relaxed, it is possible to compute the corresponding high-
resolution scanning transmission microscopy image by using the QSTEM software
[28]. This program allows accurate image simulations including fully dynamic calcu-
lations. QSTEM computes the true 3D potential distribution and numerically integrates
every slice of the potential map. This enables a thickness reduction without limitations
in the multislice calculation. In addition, it is possible to explore a wide range of
experimental setups in order to evaluate the best conditions to observe the defects. Here
the images are simulated using a typical voltage of 80 kV, a C3 spherical aberration of
0.001 mm, a Cc chromatic aberration of 1 mm, an energy spread of 0.16 eV and a
convergence angle of 20 mrad, which are reasonable values to compare with high-
resolution scanning transmission electron microscopy (HRSTEM) experiments from an
aberration-corrected microscope. The detectors collection angle are chosen between 50
mrad and 200 mrad for realistic high-angle annular dark field (HAADF) conditions. In
this conditions of Z-contrast imaging, the contrast scales with the atomic number with a
power-law dependence [29]. In addition, the HRTEM images are also calculated with
QSTEM using a voltage of 80 kV, all aberration coefficients equals to zero except for
the chromatic aberration of 1 mm, a spherical aberration of 5 µm and a vibration of
3 nm in all directions. In these conditions, the HRTEM contrasts are usually compa-
rable to HRSTEM, and the superimposition of the atomic model to the (S)TEM image
provides an efficient method of validation. To outlines the most striking features and
compare the relative positions, we have used suitable look-up tables (LUT) to colorize
the experimental TEM and the simulated STEM images.

2.5 Quantitative Comparison Between Experiment and Simulation

The difference between the model and the reality is required to evaluate the trueness and
the precision of the simulations. This point is usually far from trivial. In our case, the
TEM image is compared to the simulated one, but many sources of errors and drifts
usually bias the experimental results. Graphene can be damaged via knock-on damage,
where atoms are displaced by the impacts of the imaging electron beam, therefore low-
dose and low-energy (< 80 keV) conditions are required. Other radiation damage such as
ionization [30] may also create and modify the defects during the observation, therefore
the TEM sample is usually affected by dynamical changes during the measurement. In
addition, the electrical parameters of the microscope are also subjected to possible drifts,
therefore images have to be acquired only within a small time window. A permanent
compromise between resolution and sample damage has to be obtained [31–33].
In addition, all kinds of instabilities including electrostatic, magnetic and electro-
magnetic noise [34] or instabilities caused by the sample stage can lead to image
blurring in case of long exposure times. Hence, obtaining a good image of a graphene
defect with atomic resolution is a real challenge [35].
6 C. Guedj et al.

The simulation process may be also affected by errors. HAADF-HRSTEM images

can match simulations quantitatively to within few percent [36, 37], therefore the
current understanding of image formation should be adequate when the model correctly
accounts for the contributions of thermal diffuse scattering which dominates the Z-
contrast.
However, quantitative comparisons in HRTEM may be prone to a large (100–
400%) discrepancy between theory and experiment, (Stobbs factor) [38–44]. This
factor may be impacted by the superficial amorphous layer resulting from the sample
preparation process. Many parameters are used to model the optical properties of the
microscope lens, and the precision and accuracies of these parameters strongly affect
the confidence of the fit. A quantitative approach therefore relies on both a precise
determination of the experimental parameters of the sample and the microscope, and a
reliable measure for the degree of similarity between the simulations and the experi-
mental image.
To take into account the large variations of experimental parameters used for
microscopy in the literature, we propose here to obtain a quantitative comparison
between experiment and simulation by using the projected radial distribution function
(p-RDF) of the HRTEM or the HRSTEM image transformed into atomic positions via
proper image simulation. The radial distribution function RDF (or pair correlation
function) is classically defined in statistical mechanics by the probability to find one
atom at a given distance from a reference atom. To evaluate this function, it is nec-
essary to compute the distribution of distances between all particle pairs around a
reference atom. The RDF is very sensitive to local ordering effects at the atomic scale,
for instance in graphene [45]. Here, in a way similar to astrophysics, we define the
projected RDF, labelled p-RDF by the distribution of interatomic distances projected
on the observation plan. For TEM experiments, the observation plan is obviously the
sample orientation plan, perpendicular to the electron beam. The projected distances
between spots in a HR(S)TEM image can be measured, they constitute an observable
linked to the real atomic positions, after TEM image simulations. Hence, the experi-
mental results can be quantitatively compared with the simulations using the p-RDF.

3 Results and Discussion

3.1 Introducing Remarks

In the following, we illustrate the cases of typical defects induced by electron-beam
damage during TEM observation. The probability to observe these defects is relatively
high, for instance when the electron beam energy is set up above the threshold for
knock-on damage in sp2-bonded carbon structures (i.e. >100 keV) [46, 47]. These
defects could also be obtained by other interactions, such as ionic or mechanical or by
plasma damage. Here we focus the analysis on simple topological defects, vacancies
and adatom, but the same conclusion applies to all defects we have studied so far
(dislocations, novel phases, extended defects, etc.), based on available published data.
In the following figures, colorization of experimental images is obtained with the
Fiji software [48]. The various atomistic models correspond to flake system of 1308
 Atomistic Modelling and Simulation of Transmission Electron Microscopy Images 7

atoms with flat borders, built in SAMSON and optimized thanks to the Brenner
module. The clear advantage of the Brenner approach compared to ab-initio is a *4
orders of magnitude improvement in terms of simulation speed. Moreover, as we will
see, the precision achieved is sufficient to match the experimental results and we
obtained similar findings for all the graphene-based defects we found in literature,
without apparent limitation, and even for systems with tens of thousands of atoms. In
the following, all experimental data already published are used with permissions.

3.2 Stone-Wales Defect

Graphene has the ability to form nonhexagonal rings, and the simplest example is the
Stone-Wales (SW) defect [49] in which four hexagons are transformed into two pen-
tagons and two heptagons [SW(55-77) defect] by an in-plane 90° rotation of two
carbon atoms with respect to the midpoint of the C-C bond (Fig. 1).

Fig. 1. Left: atomistic ball and stick model of the unstable flat SW(55-77) defect in graphene.
Black balls represent carbon atoms. Right: Corresponding HRSTEM-HAADF simulated image.

In pure graphene, the C-C bond distance is 0.142 nm according to Pauling [50], which
is the exact value provided by our code. The simulation also matches very well previous
experimental results [51–53] and the corresponding ab-initio simulations [54, 55].
The planar configuration is unstable and may relax in the 3D sinelike or cosinelike
configuration. In our case, the minimum energy configuration of 6 eV is obtained for
the sinelike configuration (Fig. 2), in reasonable agreement with the configuration and
the energy of 5.82 ± 0.03 eV obtained by quantum Monte Carlo [55] and the value of
5.9 eV obtained by DFT-LDA [56].
An absolute comparison with the exact and precise value of the formation energy is
difficult, because of the significant dispersion of formation energies published in the
literature, depending on the DFT options or the size of the supercell [54, 55, 57–59].
Meanwhile, the buckling height value of 0.156 nm is very close to the value of
0.161 nm obtained by DFT for the biggest cell (11  11) of Ma et al. [55].
The SW defects are not simple planar defects but rather involve 3D displacements
(Fig. 3).
The Fig. 4 shows that a reasonable agreement is obtained between the experimental
and simulated p-RDF but many factors may influence these results. Experimentally, the
8 C. Guedj et al.

Fig. 2. Atomistic model of the lowest energy configuration SW(55-77) sinelike defect in
graphene, with bond distances, superimposed with the experimental HRTEM image of Kotakoski
[52, 53]. Colorization has been added to help the interpretation.

Fig. 3. Sideview of the SW(55-77) sinelike defect in orthographic projection.

HRTEM image may suffer from optical aberration, sample drift, contamination and
damage, especially with the very fragile defects of graphene. The presence of surface
oxycarboneous species or hydrogen at the surface may slighty modify the images
during these difficult measurements. The microscope parameters are usually prone to
various sources of instabilities, therefore a direct comparison between experiment and
simulation is not straightforward, nevertheless a reasonable agreement is obtained.
A first major peak around 142 pm is observed in both the experimental and sim-
ulated p-RDF, which corresponds to the carbon atoms in first nearest neighbour (C1nn)
configuration. The peak is very sharp in the simulation, because the positions are frozen
around the equilibrium configuration. In the HRTEM experiment, a significant devi-
ation from the ideal positions is observed, because of all sources of blurring and noise.
The maximum deviation between experiment and simulation is around ±40 pm, as can
be verified at looking the experimental broadening of the C1nn peak. Hence, in this
case, a fairly good quantitative agreement between experiment and simulation is
obtained, with a maximum relative deviation of atomic positions less than 40 pm.
 Atomistic Modelling and Simulation of Transmission Electron Microscopy Images 9

Fig. 4. Comparison between the p-RDF deduced from the HRTEM image of Kotakoski [52, 53]
and from the atomistic simulations using the Brenner potential (bottom).

3.3 Monovacancy (V1 Defects)

V1 (5-9)
The removal of one carbon atom from the graphene network results in the formation of
a single vacancy, which has been studied both theoretically and experimentally [52–55,
60, 61].
Our simulated model matches extremely well the experimental HRTEM images
published in the literature (Figs. 5, 6 and 7). We obtained a formation energy of
5.45 eV, which is less than the range of [7.6, 7.9] eV obtained by DFT [59]. The
symmetric monovacancy (s-MV) is known to exhibit a Jahn Teller distortion, and may
reconstruct into a closed five- and nine-membered pair of rings. The reconstructed
monovacancy (r-MV) arrangement lowers the energy of the symmetrical vacancy
structure in agreement with ab-initio calculations [62].

Fig. 5. Let: atomistic model of the V1 (5-9) defect superimposed to the colorized experimental
HRTEM image [52, 53]. Right: simulated HRSTEM-HAADF image.
10 C. Guedj et al.

Another comparison with HRTEM experiment (Fig. 6) shows that the best
agreement between experiment and simulation is obtained for the reconstructed model
r-MV, in expected agreement with our lowest computed energy. Hence, our method-
ology provides a convenient and realistic approach to model the HRTEM images at the
atomic scale for this case.
We found similar findings for all the cases we have studied, without any exception.
In general, the precise comparison with experiment must include the possible extrinsic
contamination by oxycarboneous species, by hydrogen or by water for instance to be
fully significant, therefore a significant comparison should take all these possible
effects into account.
Once again, the quantitative comparison between experiment and simulation is
verified via the p-RDF, and an overall good agreement is obtained. The maximum
deviation in the atomic positions corresponds to a broadening of the C1nn peak less than
*30 pm (Fig. 8).

Fig. 6. Atomistic model of the V1 (5-9) defect superimposed to the experimental HRTEM
image published by Robertson [63]. Left: r-MV (also labelled C2v). Right: s-MV.

Fig. 7. Atomistic model of the V1 (5-9) defect r-MV superimposed to the experimental HRTEM
defect image entitled “SALVE-III-project-HRTEM-graphene-vacance-foreign-atoms-defects-
zoom.png” obtained by the SALVE III project [64].
 Atomistic Modelling and Simulation of Transmission Electron Microscopy Images 11

Fig. 8. Comparison between the p-RDF deduced from the experimental image of the SALVE III
project (top) and from the Brenner atomistic simulations (bottom).

Fig. 9. Left: atomistic model of the V1 (5-5) defect superimposed to the simulated HRSTEM
image. Right: model superimposed to the experimental HRSTEM image [65].

V1 (5-5)
The V1 (5-5) state (Fig. 6) may be considered as intermediary between the V1 (5-9) r-
MV and s-MV [58]. Our calculations predicts a formation energy of 5.01 eV, which
means that such defect should be observable in principle. The simulated HRSTEM-
HAADF of Fig. 9 is so close to the image of pure graphene that it might not be
identified in most cases, except perhaps in ultra-low doses quantitative experiments to
minimize the knock-on energy provided by the incident electrons and at very low
temperatures to freeze the thermal motion.
In the supplementary movie provided by Lehtinen [65], a pattern similar to the V1
(5-5) is possibly obtained, just prior to the formation of a more extended defect.
Although the contrasts are very rapidly changing, the V1 (5-5) is presumably a reactive
seed for more complex defect growth. This type of defect has been observed experi-
mentally with the central 4-fold atom being substituted by silicon [66].
The quantitative comparison between experiment and simulation is provided with
the p-RDF (Fig. 10), and a good agreement is obtained. The maximum deviation in the
atomic positions corresponds to a broadening of the C1nn peak inferior to *40 pm.
12 C. Guedj et al.

Fig. 10. Comparison between the p-RDF of V1 (5-5) deduced from the experimental image
(top) and from the Brenner atomistic simulations (bottom).

3.4 Divacancy (V2 Defects)

V2 (5-8-5)
When two individual diffusing mono-vacancies meet they will coalesce into a nearest-
neighbour divacancy defect (equivalent to removing a carbon dimer from the lattice).
This process results in the formation of the stable pentagon–octagon–pentagon (5-8-5)
structure, which has been widely observed in high-resolution transmission electron
microscopy (HRTEM) images [52, 53, 63, 65, 67]. Our calculation provides a for-
mation energy of 7.29 eV, not far from 7.59 eV by DT-LDA [68] and 7.52 eV by
Tight Binding [69, 70].
The comparison with experiment (Fig. 11) is once again very positive, with a
nearly perfect match with published experimental TEM results. The V2 (5-8-5) defects
may mutate into the V2 (555-777) and V2 (5555-6-7777) states due to electron beam
irradiation for instance, and these transitions were observed by HRTEM [52, 53, 71].

Fig. 11. Left: atomistic model of the V2 (5-8-5) defect superimposed to the colorized
experimental HRTEM image [52, 53]. Right: simulated HRSTEM-HAADF image.
 Atomistic Modelling and Simulation of Transmission Electron Microscopy Images 13

The quantitative comparison between experiment and simulation is quantified via

the p-RDF (Fig. 12), and a good agreement is obtained. The maximum deviation in the
atomic positions corresponds to a broadening of the C1nn peak inferior to *40 pm.

Fig. 12. Comparison between the p-RDF of the V2 (5-8-5) defect deduced from the
experimental image (top) and from the Brenner atomistic simulations (bottom).

Case V2 (555-777)
The structure of the V2 (555-777) divacancy is displayed in Fig. 13, showing an
excellent agreement between experiment and simulation (Fig. 14).

Fig. 13. Left: atomistic model of the V2 (555-777) defect superimposed to the colorized
experimental HRTEM image [52, 53]. Right: simulated HRSTEM-HAADF image.

Fig. 14. Comparison between the p-RDF of the V2 (555-777) defect deduced from the
experimental image (top) and from the Brenner atomistic simulations (bottom).
14 C. Guedj et al.

The calculated formation energy is 7.14 eV, in reasonable agreement with the value
of 7.41 eV obtained by DFT-PBE/DNP [72]. Hence the V2 (555-777) state should be
more stable than the V2 (5-8-5), in agreement with all DFT results published [59].

3.5 Carbon Adatom

Fig. 15. Left: atomistic model of the 1C adatom defect superimposed to the colorized
experimental HRTEM image extracted from the supplementary movie 6 provided in [65]. Right:
corresponding simulated HRSTEM-HAADF image.

The healing (self-repair) of various graphene defects by migration of adatoms has been
observed by HRTEM [71, 73]. The result of our calculation is displayed in Fig. 19.
DFT studies usually gives three stable positions of the adatom on graphene [74]. The
bridge position is predicted to be the most stable and was observed by HRTEM [75]
and by HRSTEM [76]. We obtain a formation energy of 2.69 eV, therefore such defect
should form easily during processing of a graphene-based nanodevice. The DFT
method provides a value of the order of 1.5–2 eV for the binding energy of the carbon
adatom [77, 78] (Figs. 15 and 16).

Fig. 16. Comparison between the p-RDF of the 1C adatom defect deduced from the
experimental image (top) and from the Brenner atomistic simulations (bottom).

The perpendicular distance of the adatom to the graphite surface is *0.222 nm,
not too far from the value of 0.187 nm previously obtained by ab-initio calculations for
50 atoms [78]. In our case, we find that the 5th nearest neighbours around the carbon
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