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This book is a unique reference work in the area of atomic-scale simulation of glasses. For the first time, a highly selected panel of about 20 researchers provides, in a single book, their views, methodologies and applications on the use of molecular dynamics as a tool to describe glassy materials. The book covers a wide range of systems covering "traditional" network glasses, such as chalcogenides and oxides, as well as glasses for applications in the area of phase change materials. The novelty of this work is the interplay between molecular dynamics methods (both at the classical and first-principles level) and the structure of materials for which, quite often, direct experimental structural information is rather scarce or absent. The book features specific examples of how quite subtle features of the structure of glasses can be unraveled by relying on the predictive power of molecular dynamics, used in connection with a realistic description of forces.



Chapter 1. The Atomic-Scale Structure of Network Glass-Forming Materials

A prerequisite for understanding the physico-chemical properties of network glass-forming materials is knowledge about their atomic-scale structure. The desired information is not, however, easy to obtain because structural disorder in a liquid or glass leads to complexity. It is therefore important to design experiments to give site-specific information on the structure of a given material in order to test the validity of different molecular dynamics models. In turn, once a molecular dynamics scheme contains the correct theoretical ingredients, it can be used both to enrich the information obtained from experiment and to predict the composition and temperature/pressure dependence of a material’s properties, a first step in using the principles of rational design to prepare glasses with novel functional properties. In this chapter the symbiotic relationship between experiment and simulation is explored by focussing on the structures of liquid and glassy ZnCl\(_2\) and GeSe\(_2\), and on the structure of glassy GeO\(_2\) under pressure. Issues to be addressed include extended range ordering on a nanometre scale, the formation of homopolar (like-atom) bonds, and the density-driven mechanisms of network collapse.
Philip S. Salmon, Anita Zeidler

Chapter 2. First-Principles Molecular Dynamics Methods: An Overview

This chapter proposes an overview of computational approaches used nowadays in the field of first-principles simulations to model amorphous and liquid materials. The scope is to bring to the attention of the readership advances and (still existing) limitations in the description of the interactions among atoms which, starting in general from an ordered crystallographic structure, undergo significant modifications in the underlying electronic structure for the disordered phases. These subtle details are difficult to capture by resorting on classical model potentials and call for an accurate description of the quantum mechanical description of the intimate constituent of a glassy compound. The heavy computational workload associated can be nowadays overcome in virtue of the increasing computing power of last-generation high performance computers. Also of paramount importance are advances in algorithms and methods capable of providing the required speed-up in terms of both performances and accuracy.
Mauro Boero, Assil Bouzid, Sebastien Le Roux, Burak Ozdamar, Carlo Massobrio

Chapter 3. Metadynamics Simulations of Nucleation

This chapter offers an overview of recent applications of the metadynamics method to the study of nucleation and related phenomena. In the first section, the classical nucleation theory and the metadynamics method are introduced. The second section is devoted to applications, including computational studies of the surface tension, which affects the size and energy of criticial nuclei, and investigation of crystal nucleation from the amorphous and supercooled liquid state.
Ider Ronneberger, Riccardo Mazzarello

Chapter 4. Challenges in Modeling Mixed Ionic-Covalent Glass Formers

Archetypical glass formers such as SiO\(_{2}\), GeO\(_{2}\) and B\(_{2}\)O\(_{3}\) pose an especial challenge for atomistic level modeling due to the mixed ionic-covalent bonding and the highly polarizable oxygen ion. Though significant improvements have been made in the past few decades in developing potential models for such systems, mostly based on pair-wise potentials, with or without taking into account of three-body or many-body effects, there is still much room for further advancement in the development of reliable, effective, and transferable potential models for mixed ionic-covalent glass formers.
Liping Huang, John Kieffer

Chapter 5. Computational Modeling of Silicate Glasses: A Quantitative Structure-Property Relationship Perspective

This article reviews the present state of Quantitative Structure-Property Relationships (QSPR) in glass design and gives an outlook into future developments. First an overview is given of the statistical methodology, with particular emphasis to the integration of QSPR with molecular dynamics simulations to derive informative structural descriptors. Then, the potentiality of this approach as a tool for interpretative and predictive purposes is highlighted by a number of recent inspiring applications.
Alfonso Pedone, Maria Cristina Menziani

Chapter 6. Recrystallization of Silicon by Classical Molecular Dynamics

Recrystallization of amorphous silicon is studied by classical molecular dynamics. First, a simulation scheme is developed to systematically determine the amorphous on crystal (a/c) silicon motion and compare it to established measurements by Olson and Roth [1]. As a result, it is shown that MD simulations using Tersoff [2] potential are adapted to simulate solid phase epitaxy, although a temperature shift to high values should be accounted for, while simulations using Stillinger-Weber [3] allows to study liquid phase epitaxy. In a second part, the simulation approach is applied to the case of a nanostructure [4] where classical recipes fail to achieve complete recrystallization. MD simulations are shown to be in agreement with experimental observations. The analysis of the structural evolution with time provide a support to understand the origin of the defects.
Evelyne Lampin

Chapter 7. Challenges in Molecular Dynamics Simulations of Multicomponent Oxide Glasses

Despite tremendous progresses made in the past few decades in molecular dynamics simulations of glass and related materials, there exist a number of challenges in MD simulations of multicomponent glasses. This chapter summarizes the progresses in this field and present the challenges that include the reliable and transferable empirical potentials, cooling rate, system size and concentration effect on the simulated glass structures, and the validating structures of multicomponent oxide systems. Several practical examples on multicomponent and technologically important glass systems using classical MD simulations are also given to highlight the capabilities and challenges.
Jincheng Du

Chapter 8. Structural Insight into Transition Metal Oxide Containing Glasses by Molecular Dynamic Simulations

In the last years, glass research focused particular attention on transition metal oxide containing systems for semi-conductive applications, for instance glasses for solid-state devices and secondary batteries. In glass matrices, transition metal ions show multiple oxidation states that lead to peculiar structures and to highly complex systems, which produce interesting optical, electrical and magnetic properties. Computational methods have been largely employed as complementary tool to experimental techniques, in order to improve the knowledge on the materials and their performances. In this work, Molecular Dynamic (MD) simulations have been performed on a series of alkali vanado-phosphate glasses in order to gain deep comprehension of the glass structure. The short and medium range order of the \(\mathrm{V}^{4+}\) and the \(\mathrm{V}^{5+}\) sites in terms of coordination, pair distribution function, V–O–V linkages, bridging and non-bridging oxygen distributions were calculated and discussed. Finally, the comparison between MD and experimental results shows a very good agreement allowing the validation of the computational model and highlights the correlations between the structure and the conduction mechanism in these glasses. This allows enriching the know-how on these glass systems that result still ambiguous until now.
Monia Montorsi, Giulia Broglia, Consuelo Mugoni

Chapter 9. Modelling Networks in Varying Dimensions

Simulation methods and results for two key (related) network-forming systems (SiO\(_2\) and C) are described and reviewed. The application of relatively simple potential models, in which the interaction energies are expressed as functions of atom positions and momenta, are described. The properties of these two key target systems are studied over a range of dimensionalities. Pressure-driven structural changes in glassy SiO\(_2\) are described and a simple ring-closure model developed to map the changes. The phase diagrams (liquid/crystal melting curves) are mapped in both 3- and 2-dimensions for carbon and key structural changes on phase change are studied. A liquid to amorphous phase transformation is identified for carbon in three dimensions and investigated. The two dimensional carbon phase diagram is used to develop methods for generating amorphous structures of two dimensional carbon (amorphous graphene, a-G) and the structures of the materials produced are investigated as a function of the generation conditions. The a-G structures are used as a basis for generating bilayers of SiO\(_2\) and are also folded to form amorphous carbon nanotube (a-CNT) structures.
Mark Wilson

Chapter 10. Rationalizing the Biodegradation of Glasses for Biomedical Applications Through Classical and Ab-initio Simulations

The gradual dissolution of a glass in a living host determines the rate at which processes leading to tissue regeneration can occur, which is of crucial importance for the success of biomedical implants and scaffolds for tissue engineering based on the glass. In-situ radiotherapy applications are also affected—in an opposite way—by the rate at which the glass vector used to deliver radioisotopes will degrade in the bloodstream. This chapter illustrates how a combination of classical and ab-initio simulations techniques, mainly centred on Molecular Dynamics, can shed new light into structural and dynamical features that control the biodegradation of these materials.
Antonio Tilocca

Chapter 11. Topological Constraints, Rigidity Transitions, and Anomalies in Molecular Networks

In this chapter, we present the first connection between realistic atomic scale simulations and topological constraint theory which has been introduced in the context of rigidity transitions of network glasses. Such rigid constraints can be computed rather simply by changing composition at low temperature but their estimates as a function of temperature or pressure remains challenging. We introduce and describe a method based on the calculation of standard deviations of relevant neighbor or partial bond-angle distributions which allows to estimate with confidence atomic stretching and bending topological constraints. The counting is illustrated from several archetypal liquids and glasses, including oxides and chalcogenides (SiO\(_2\), Ge\(_x\)Se\(_{1-x}\),...). These results permit connecting the role of mechanical constraints in disordered systems to elucidating some of its most intruiging features (adaptation), with calculated anomalies in structural and dynamic properties.
M. Micoulaut, M. Bauchy, H. Flores-Ruiz

Chapter 12. First-Principles Modeling of Binary Chalcogenides: Recent Accomplishments and New Achievements

This contribution is focussed on a set of first-principles molecular dynamics results obtained over the past fifteen years for disordered chalcogenides. In the first part, we sketch and review the historical premises underlying research efforts devoted to the understanding of structural properties in liquid and glassy Ge\(_x\)Se\(_{1-x}\) systems. We stress the importance of selecting well performing exchange-correlation functionals (within density functional theory) to achieve a correct description of short and intermediate range order. In the second part, we provide a specific, comparative example of structural analysis for chalcogenide GeX\(_4\) systems differing by the chemical identity of the X atom. We are able to demonstrate that the correct account of differences between the coordination environments of the two corresponding glasses requires system sizes substantially larger than \(\sim \)100 atoms. Finally, the role played by the pressure in altering the structural properties of glassy GeSe\(_2\) is invoked, in light of recent studies devoted to a density-driven structural transformation occurring in this system.
Assil Bouzid, Sébastien Le Roux, Guido Ori, Christine Tugène, Mauro Boero, Carlo Massobrio

Chapter 13. Molecular Modeling of Glassy Surfaces

Progress in computational materials science has allowed the development of realistic models for a wide range of materials including both crystalline and glassy solids. In recent years, with the growing interest in nanoparticles and porous materials, more attention has been devoted to the design of realistic models of glassy surfaces and finely divided materials. The structural disorder in glassy surfaces, however, poses a major challenge which consists of describing such surfaces using computer simulations. In this paper, we show how atomic-scale simulations can be used to develop and investigate the properties of glassy surfaces. We illustrate how both first principles calculations and classical molecular mechanics can be used to follow the trajectory at finite temperature of these systems, and obtain statistical thermodynamic averages to compare against available experiments. Both glassy oxide (silica) and non-oxide (chalcogenide) surfaces are considered.
Guido Ori, Carlo Massobrio, Assil Bouzid, B. Coasne

Chapter 14. Rings in Network Glasses: The $$\mathrm{B_2O_3}$$ B 2 O 3 Case

There has been a considerable debate, in particular since the emergence of atomistic simulations , about the structure of glassy \(\mathrm{B_2O_3}\) , a prototypical network-forming system based on trigonal units. Some intermediate-range order in the form of threefold rings, present in the glass but not in the crystalline phases, has remained so far very difficult to reproduce in atomistic simulations. After a brief summary of the evidences accumulated regarding the boroxol rings , a review of the numerical studies of liquid and glassy \(\mathrm{B_2O_3}\) is provided. The reasons for the failure of the quench-from-the-melt techniques are stressed and a methodology, based on first-principles calculations of experimental observables (diffraction, NMR, Raman, IR, heat capacity) from various glassy models is devised to provide incontrovertible answers to the debate. This allows assessing not only the content of boroxol rings but also the sensitivity of each observable to this quantity. The presence of threefold rings in the glass is then showed to have ramifications for the understanding of the crystalline and liquid phases. This includes the prediction of yet unknown \(\mathrm{B_2O_3}\) polymorphs structurally close to the glass, the understanding of the so-called crystallisation anomaly and the evidencing of structural transitions in the liquid . Finally, the discussion is extended to parent systems such as \(\mathrm{B_2S_3}\).
Guillaume Ferlat

Chapter 15. Functional Properties of Phase Change Materials from Atomistic Simulations

Chalcogenide alloys are materials of interest for optical recording and electronic nonvolatile memories. These applications rest on an ensemble of functional properties: a fast and reversible transformation between the amorphous and the crystalline phase upon heating and a strong optical and electronic contrast between the two phases that allow discriminating the two states of the memory. We discuss the insights gained from atomistic simulations based on Density Functional Theory on the functional properties of the prototypical phase change compounds Ge\(_2\)Sb\(_2\)Te\(_5\) and GeTe. We review the results on the structural and bonding properties of the crystalline and amorphous phases, the origin of the optical and electronic contrast between the two phases and the source of the fast crystallization of the supercooled liquid. The results on the crystallization kinetics obtained from large scale simulations with interatomic potentials based on Neural Network methods are also discussed.
Sebastiano Caravati, Gabriele C. Sosso, Marco Bernasconi

Chapter 16. Ab Initio Molecular-Dynamics Simulations of Doped Phase-Change Materials

The physical behaviour and device performance of phase-change, non-volatile memory materials can often be improved by the incorporation of small amounts of dopant atoms. In certain cases, new functionality can also be introduced, for example a contrast in magnetic properties between amorphous and crystalline phases of the host phase-change material when certain transition-metal dopants are included. This Chapter reviews some of the experimental data relating to doped phase-change materials and, in particular, a survey is given of the role played by molecular-dynamics simulations in understanding the atomistic mechanisms involved in the doping process. In addition, some examples are given of the in silico discovery of new phase-change compositions resulting from ab initio molecular-dynamics (AIMD) simulations.
J. M. Skelton, T. H. Lee, S. R. Elliott

Chapter 17. The Prototype Phase Change Material $${\mathrm{Ge}_2}{\mathrm{Sb}_2}{\mathrm{Te}_5}$$ Ge 2 Sb 2 Te 5 : Amorphous Structure and Crystallization

The widespread use of phase change materials in storage media is based on the extremely rapid and reversible switching between the amorphous and crystalline phases of some families of semiconducting alloys. Detailed information about the structure of the amorphous phase and the mechanism of crystallization are essential for the development of new storage media, and we study both aspects here using density functional/molecular dynamics simulations of \({\mathrm{Ge}_2}{\mathrm{Sb}_2}{\mathrm{Te}_5}\), the prototype phase change material of the Ge/Sb/Te semiconductor family.
Jaakko Akola, Janne Kalikka, Robert O. Jones

Chapter 18. Amorphous Phase Change Materials: Structure, Stability and Relation with Their Crystalline Phase

Phase Change Materials should be stable enough in their amorphous phase to achieve a durable data retention, however they should also be bad glass formers to be able to recrystallise at high speed. To understand these contradicting properties, we construct models of amorphous Ge–Sb–Te systems using Ab Initio Molecular Dynamics and analyse the structures in relation with the relevant crystalline state. We show that structural patterns that are precursors of the crystalline phase exist in the amorphous state and we identify the signature of the various types of local atomic orders in the X-ray absorption spectra that we compute using Density Functional Theory. We first analyse the mechanical properties of the amorphous phase in the framework of the Maxwell rigidity theory, showing that all efficient Phase Change Materials deviate from the perfect glass and are mechanically stressed-rigid. Additionally, we show that the stability of Phase Change Materials is related to the density of low frequency vibrational modes (Boson peak). We describe how an adequate doping can result in an increased stability of the amorphous phase while keeping intact the phase change ability of the material.
Jean-Yves Raty, Céline Otjacques, Rengin Peköz, Vincenzo Lordi, Christophe Bichara

Chapter 19. Transition Metals in Phase-Change Memory Materials: Impact upon Crystallization

We employed plane wave density functional molecular dynamics to simulate the crystallization of Ge\(_{2}\)Sb\(_{2}\)Te\(_{5}\) materials alloyed with \({\sim }{2}\,\%\) transition metals (Cu, Ag, and Au) and studied the resulting structural modifications. Despite having very different chemistry, we show that under many circumstances, transition metals join the crystalline structure essentially substitutionally. Bader charge analysis revealed similar positive atomic charges for Cu and Ag whereas negative charge for Au was observed. The optical contrast is preserved in Ag or Au doped Ge\(_{2}\)Sb\(_{2}\)Te\(_{5}\), but not in Cu doped Ge\(_{2}\)Sb\(_{2}\)Te\(_{5}\). The estimation of the crystallization time for the transition metal doped Ge\(_{2}\)Sb\(_{2}\)Te\(_{5}\)  showed large variation which were attributed to the presence of different fractions of wrong bonds in the alloys.
Binay Prasai, D. A. Drabold


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