# Publications

2016
Montemore M, Hoyt R, Kaxiras E. Non-adiabatic effects and electronic excitations during dissociation on catalytic surfaces. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2016;252.
Montemore M, Hoyt R, Kaxiras E. Non-adiabatic energy dissipation in dissociation on catalytic surface. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2016;251.
Karakalos S, Xu Y, Kabeer FC, Chen W, Rodriguez-Reyes JCF, Tkatchenko A, Kaxiras E, Madix RJ, Friend CM. Noncovalent Bonding Controls Selectivity in Heterogeneous Catalysis: Coupling Reactions on Gold. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2016;138 (46) :15243-15250.Abstract
Enhancing the selectivity of catalytic processes has potential for substantially increasing the sustainability of chemical production. Herein, we establish relationships between reaction selectivity and molecular structure for a homologous series of key intermediates for oxidative coupling of alcohols on gold using a combination of experiment and theory. We establish a scale of binding for molecules with different alkyl structures and chain lengths and thereby demonstrate the critical nature of noncovalent van der Waals interactions in determining the selectivity by modulating the stability of key reaction intermediates bound to the surface. The binding hierarchy is the same for Au(111) and Au(110), which demonstrates a relative lack of sensitivity to the surface structure. The hierarchy of binding established in this work provides guiding principles for predicting how molecular structure affects the competition for binding sites more broadly. Besides the nature of the primary surface-molecule bonding, three additional factors that affect the stabilities of the reactive intermediates are clearly established: (1) the number of C atoms in the alkyl chain, (2) the presence of C-C bond unsaturation, and (3) the degree of branching of the alkyl group of the adsorbed molecules. We suggest that this is a fundamental principle that is generally applicable to a broad range of reactions on metal catalysts.
Tritsaris GA, Shirodkar SN, Kaxiras E, Cazeaux P, Luskin M, Plechac P, Cances E. Perturbation theory for weakly coupled two-dimensional layers. JOURNAL OF MATERIALS RESEARCH. 2016;31 (7) :959-966.Abstract
A key issue in two-dimensional structures composed of atom-thick sheets of electronic materials is the dependence of the properties of the combined system on the features of its parts. Here, we introduce a simple framework for the study of the electronic structure of layered assemblies based on perturbation theory. Within this framework, we calculate the band structure of commensurate and twisted bilayers of graphene (Gr) and hexagonal boron nitride (h-BN), and of a Gr/h-BN heterostructure, which we compare with reference full-scale density functional theory calculations. This study presents a general methodology for computationally efficient calculations of two-dimensional materials and also demonstrates that for relatively large twist in the graphene bilayer, the perturbation of electronic states near the Fermi level is negligible.
Kolesov G, Granas O, Hoyt R, Vinichenko D, Kaxiras E. Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2016;12 (2) :466-476.Abstract
We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials. Because of the short time step required for electron propagation (of order similar to 10 attoseconds), these simulations are computationally very demanding. Our methodology is based on numerical atomic-orbital-basis sets for computational efficiency. In the computational package, to which we refer as TDAP-2.0 (Time-evolving Deterministic Atom Propagator), we have implemented a number of important features and analysis tools for more accurate and efficient treatment of large, complex systems and time scales that reach into a fraction of a picosecond. We showcase the capabilities of our method using four different examples: (i) photodissociation into radicals of opposite spin, (ii) hydrogen adsorption on aluminum surfaces, (iii) optical absorption of spin-polarized organic molecule containing a metal ion, and (iv) electron transfer in a prototypical dye sensitized solar cell.
Hiebel F, Shong B, Chen W, Madix RJ, Kaxiras E, Friend CM. Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface. NATURE COMMUNICATIONS. 2016;7.Abstract
Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au-Au interactions due to bonding with the acetate. Even though the acetate is a relatively small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface.
Defo RK, Fang S, Shirodkar SN, Tritsaris GA, Dimoulas A, Kaxiras E. Strain dependence of band gaps and exciton energies in pure and mixed transition-metal dichalcogenides. PHYSICAL REVIEW B. 2016;94 (15).Abstract
{{The ability to fabricate 2D device architectures with desired properties, based on stacking of weakly (van der Waals) interacting atomically thin layers, is quickly becoming reality. In order to design ever more complex devices of this type, it is crucial to know the precise strain and composition dependence of the layers' electronic and optical properties. Here, we present a theoretical study of these dependences for monolayers with compositions varying from pure MX2 to the mixed MXY, where M = Mo, W and X
S. S. Schoenholz, Cubuk ED, Sussman DM, Kaxiras E, Liu AJ. A structural approach to relaxation in glassy liquids. NATURE PHYSICS. 2016;12 (5) :469+.Abstract
In contrast with crystallization, there is no noticeable structural change at the glass transition. Characteristic features of glassy dynamics that appear below an onset temperature, T-0 (refs 1-3), are qualitatively captured by mean field theory(4-6), which assumes uniform local structure. Studies of more realistic systems have found only weak correlations between structure and dynamics(7-11). This raises the question: is structure important to glassy dynamics in three dimensions? We answer this question affirmatively, using machine learning to identify a new field, softness' which characterizes local structure and is strongly correlated with dynamics. We find that the onset of glassy dynamics at T-0 corresponds to the onset of correlations between softness (that is, structure) and dynamics. Moreover, we construct a simple model of relaxation that agrees well with our simulation results, showing that a theory of the evolution of softness in time would constitute a theory of glassy dynamics.
Cubuk ED, Schoenholz SS, Kaxiras E, Liu AJ. Structural Properties of Defects in Glassy Liquids. JOURNAL OF PHYSICAL CHEMISTRY B. 2016;120 (26) :6139-6146.Abstract
At zero temperature a disordered solid corresponds to a local minimum in the energy landscape. As the temperature is raised or the system is driven with a mechanical load, the system explores different minima via dynamical events in which particles rearrange their relative positions. We have shown recently that the dynamics of particle rearrangements are strongly correlated with a structural quantity associated with each particle, softness'', which we can identify using supervised machine learning. Particles of a given softness have a well-defined energy scale that governs local rearrangements; because of this property, softness greatly simplifies our understanding of glassy dynamics. Here we investigate the correlation of softness with other commonly used structural quantities, such as coordination number and local potential energy. We show that although softness strongly correlates with these properties, its predictive power for rearrangement dynamics is much higher. We introduce a useful metric for quantifying the quality of structural quantities as predictors of dynamics. We hope that, in the future, authors introducing new structural measures of dynamics will compare their proposals quantitatively to softness using this metric. We also show how softness correlations give insight into rearrangements. Finally, we explore the physical meaning of softness using unsupervised dimensionality reduction and reduced curve-fitting, models, and show that softness can be recast in a form that is amenable to analytical treatment.
Montemore M, Kaxiras E. Structure and reactivity of AgAu Alloys. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 2016;251.
Cao Y, Luo JY, Fatemi V, Fang S, Sanchez-Yamagishi JD, Watanabe K, Taniguchi T, Kaxiras E, Jarillo-Herrero P. Superlattice-Induced Insulating States and Valley-Protected Orbits in Twisted Bilayer Graphene. PHYSICAL REVIEW LETTERS. 2016;117 (11).Abstract
Twisted bilayer graphene (TBLG) is one of the simplest van der Waals heterostructures, yet it yields a complex electronic system with intricate interplay between moire physics and interlayer hybridization effects. We report on electronic transport measurements of high mobility small angle TBLG devices showing clear evidence for insulating states at the superlattice band edges, with thermal activation gaps several times larger than theoretically predicted. Moreover, Shubnikov-de Haas oscillations and tight binding calculations reveal that the band structure consists of two intersecting Fermi contours whose crossing points are effectively unhybridized. We attribute this to exponentially suppressed interlayer hopping amplitudes for momentum transfers larger than the moire wave vector.
Heller EJ, Yang Y, Kocia L, Chen W, Fang S, Borunda M, Kaxiras E. Theory of Graphene Raman Scattering. ACS NANO. 2016;10 (2) :2803-2818.Abstract
Raman scattering plays a key role in unraveling the quantum dynamics of graphene, perhaps the most promising material of recent times. It is crucial to correctly interpret the meaning of the spectra. It is therefore very surprising that the widely accepted understanding of Raman scattering, i.e., Kramers Heisenberg Dirac theory, has never been applied to graphene. Doing so here, a remarkable mechanism we term''transition sliding'' is uncovered, explaining the uncommon brightness of overtones in graphene. Graphene's dispersive and fixed Raman bands, missing bands, defect density and laser frequency dependence of band intensities, widths of overtone bands, Stokes, anti -Stokes anomalies, and other known properties emerge simply and directly.
2015
Fang S, Defo RK, Shirodkar SN, Lieu S, Tritsaris GA, Kaxiras E. Ab initio tight-binding Hamiltonian for transition metal dichalcogenides. PHYSICAL REVIEW B. 2015;92 (20).Abstract
We present an accurate ab initio tight-binding Hamiltonian for the transition metal dichalcogenides, MoS2, MoSe2, WS2, WSe2, with a minimal basis (the d orbitals for the metal atoms and p orbitals for the chalcogen atoms) based on a transformation of theKohn-Sham density functional theory Hamiltonian to a basis of maximally localized Wannier functions. The truncated tight-binding Hamiltonian, with only on-site, first, and partial second neighbor interactions, including spin-orbit coupling, provides a simple physical picture and the symmetry of the main band-structure features. Interlayer interactions between adjacent layers are modeled by transferable hopping terms between the chalcogen p orbitals. The full-range tight-binding Hamiltonian can be reduced to hybrid-orbital k . p effective Hamiltonians near the band extrema that capture important low-energy excitations. These ab initio Hamiltonians can serve as the starting point for applications to interacting many-body physics including optical transitions and Berry curvature of bands, of which we give some examples.
Kolesov G, Vinichenko D, Tritsaris GA, Friend CM, Kaxiras E. Anatomy of the Photochemical Reaction: Excited-State Dynamics Reveals the C-H Acidity Mechanism of Methoxy Photo-oxidation on Titania. JOURNAL OF PHYSICAL CHEMISTRY LETTERS. 2015;6 (9) :1624-1627.Abstract
Light-driven chemical reactions on semiconductor surfaces have potential for addressing energy and pollution needs through efficient chemical synthesis; however, little is known about the time evolution of excited states that determine reaction pathways. Here, we study the photo-oxidation of methoxy (CH3O) derived from methanol on the rutile TiO2(110) surface using ab initio simulations to create a molecular movie of the process. The movie sequence reveals a wealth of information on the reaction intermediates, time scales, and energetics. The reaction is broken in three stages, described by Lewis structures directly derived from the hole'' wave functions that lead to the concept of `photoinduced C-H acidity''. The insights gained from this work can be generalized to a set of simple rules that can predict the efficiency of photo-oxidation reactions in reactant-catalyst pairs.
Cubuk ED, S. S. Schoenholz, Rieser JM, Malone BD, Rottler J, Durian DJ, Kaxiras E, Liu AJ. Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods. PHYSICAL REVIEW LETTERS. 2015;114 (10).Abstract
We use machine-learning methods on local structure to identify flow defects-or particles susceptible to rearrangement-in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.
Huang D, Song C-L, Webb TA, Fang S, Chang C-Z, Moodera JS, Kaxiras E, Hoffman JE. Revealing the Empty-State Electronic Structure of Single-Unit-Cell FeSe/SrTiO3. PHYSICAL REVIEW LETTERS. 2015;115 (1).Abstract
We use scanning tunneling spectroscopy to investigate the filled and empty electronic states of superconducting single-unit-cell FeSe deposited on SrTiO3(001). We map the momentum-space band structure by combining quasiparticle interference imaging with decay length spectroscopy. In addition to quantifying the filled-state bands, we discover a Gamma-centered electron pocket 75 meV above the Fermi energy. Our density functional theory calculations show the orbital nature of empty states at Gamma and explain how the Se height is a key tuning parameter of their energies, with broad implications for electronic properties.
Huang D, Song C-L, Webb TA, Fang S, Chang C-Z, Moodera JS, Kaxiras E, Hoffman JE. Revealing the Empty-State Electronic Structure of Single-Unit-Cell FeSe /SrTiO3. Physical Review Letters. 2015;115 :017002.Abstract

We use scanning tunneling spectroscopy to investigate the filled and empty electronic states of superconducting single-unit-cell FeSe deposited on SrTiO3(001). We map the momentum-space band structure by combining quasiparticle interference imaging with decay length spectroscopy. In addition to quantifying the filled-state bands, we discover a Γ-centered electron pocket 75 meV above the Fermi energy. Our density functional theory calculations show the orbital nature of empty states at Γ and explain how the Se height is a key tuning parameter of their energies, with broad implications for electronic properties.

Ostadhossein A, Cubuk ED, Tritsaris GA, Kaxiras E, Zhang S, van Duin ACT. Stress effects on the initial lithiation of crystalline silicon nanowires: reactive molecular dynamics simulations using ReaxFF. Physical Chemistry Chemical Physics. 2015;17 :3832-3840.Abstract

Silicon (Si) has been recognized as a promising anode material for the next-generation high-capacity lithium (Li)-ion batteries because of its high theoretical energy density. Recent in situ transmission electron microscopy (TEM) revealed that the electrochemical lithiation of crystalline Si nanowires
(c-SiNWs) proceeds by the migration of the interface between the lithiated Si (LixSi) shell and the pristine unlithiated core, accompanied by solid-state amorphization. The underlying atomic mechanisms of Li insertion into c-Si remain poorly understood. Herein, we perform molecular dynamics (MD) simulations using the reactive force field (ReaxFF) to characterize the lithiation process of c-SiNWs. Our calculations show that ReaxFF can accurately reproduce the energy barriers of Li migration from DFT calculations in
both crystalline (c-Si) and amorphous Si (a-Si). The ReaxFF-based MD simulations reveal that Li insertion into interlayer spacing between two adjacent (111) planes results in the peeling-off of the (111) facets and subsequent amorphization, in agreement with experimental observations. We find that breaking of the Si–Si bonds between (111)-bilayers requires a rather high local Li concentration, which explains the atomically sharp amorphous–crystalline interface (ACI). Our stress analysis shows that lithiation induces compressive stress at the ACI layer, causing retardation or even the stagnation of the reaction front, also in good agreement with TEM observations. Lithiation at high temperatures (e.g. 1200 K) shows that Li insertion into c-SiNW results in an amorphous to crystalline phase transformation at Li : Si composition
of B4.2 : 1. Our modeling results provide a comprehensive picture of the effects of reaction and diffusion-induced stress on the interfacial dynamics and mechanical degradation of SiNW anodes under chemo-mechanical lithiation.

Kolesov G, Vinichenko D, Tritsaris GA, Friend CM, Kaxiras E. Anatomy of the Photochemical Reaction: Excited-State Dynamics Reveals the C−H Acidity Mechanism of Methoxy Photo-oxidation on Titania. Journal of Physical Chemistry Letters. 2015;6 :1624-1627.Abstract

Light-driven chemical reactions on semiconductor surfaces have potential for
addressing energy and pollution needs through efficient chemical synthesis; however, little is known about the time evolution of excited states that determine reaction pathways. Here, we study the photo-oxidation of methoxy (CH3O) derived from methanol on the rutile TiO2(110) surface using ab initio simulations to create a molecular movie of the process. The movie sequence reveals a wealth of information on the reaction intermediates, time scales, and energetics. The reaction is broken in three stages, described by Lewis structures directly derived from the “hole” wave functions that lead to the concept of “photoinduced C−H acidity”. The insights gained from this work can be generalized to a set of simple rules that can predict the efficiency of photo-oxidation reactions in reactant−catalyst pairs.

Chen W, Cui P, Zhu W, Kaxiras E, Gao Y, Zhang Z. Atomistic mechanisms for bilayer growth of graphene on metal substrates. Physical Review B. 2015;91 :045408.Abstract

Epitaxial growth on metal substrates has been shown to be the most powerful approach in producing large-scale high-quality monolayer graphene, yet it remains a major challenge to realize uniform bilayer graphene growth. Here we carry out a comparative study of the atomistic mechanisms for bilayer graphene growth on the (111) surfaces of Cu and Ni, using multiscale approaches combining first-principles calculations and rate-equation analysis. We first show that the relatively weak graphene-Cu interaction enhances the lateral diffusion and effective nucleation of C atoms underneath the graphene island, thereby making it more feasible to grow bilayer graphene on Cu. In contrast, the stronger graphene-Ni interaction suppresses the lateral mobility and dimerization of C atoms underneath the graphene, making it unlikely to achieve controlled growth of bilayer graphene on Ni. We then determine the critical graphene size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse “Ehrlich-Schwoebel barrier” effect, becoming smaller
for faster C migration from the Cu surface to the graphene-Cu interface sites across the graphene edge. These findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene.