# Publications

2016
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.

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 :108001.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.

2014
Wang WL, Santos EJG, Jiang B, Cubuk ED, Ophus C, Centeno A, Pesquera A, Zurutuza A, Ciston J, Westervelt R, et al. Direct Observation of a Long-Lived Single-Atom Catalyst Chiseling Atomic Structures in Graphene. NanoLetters. 2014;14 :450-455.Abstract

Fabricating stable functional devices at the atomic scale is an ultimate goal of nanotechnology. In biological processes, such high-precision operations are accomplished by enzymes. A counterpart molecular catalyst that binds to a solid-state substrate would be highly desirable. Here, we report the direct observation of single Si adatoms catalyzing the dissociation of carbon atoms from graphene in an aberrationcorrected high-resolution transmission electron microscope (HRTEM). The single Si atom provides a catalytic wedge for energetic electrons to chisel off the graphene lattice, atom by atom, while the Si atom itself is not consumed. The products of the chiseling process are atomic-scale features including graphene pores and clean edges. Our experimental observations and first-principles calculations demonstrated the dynamics, stability, and selectivity of such a single-atom chisel, which opens up the possibility of fabricating certain stable molecular devices by precise modification of materials at the atomic scale.

Tritsaris GA, Vinichenko D, Kolesov G, Friend CM, Kaxiras E. Dynamics of the Photogenerated Hole at the Rutile TiO2(110)/Water Interface: A Nonadiabatic Simulation Study. Journal of Physical Chemistry C . 2014;118 :27393-27401.Abstract

Hydrogen production in photoelectrochemical cells constitutes an important avenue toward carbon-free fuel. The most convenient process for hydrogen production is the splitting of water molecules, which necessitates a catalytic
reaction involving a semiconductor. Here, we introduce a framework for the study of photocatalyzed reactions on semiconductor surfaces based on time-dependent density functional theory that explicitly accounts for the evolution of electronically excited states. Within this framework, we investigate the possibility of hole-mediated splitting of molecularly adsorbed water on a representative metal oxide surface the rutile TiO2(110). We find that oxidative dehydrogenation of water is possible in synergy with thermal effects at temperatures between 60 and 100 K only when defects like Ti interstitials are present in the subsurface region. This study presents a general computational strategy for describing photoexcited semiconductor/adsorbate interfaces and also demonstrates that the occurrence of water dissociation on the rutile TiO2(110) surface depends sensitively on the local atomic environment and external parameters such as temperature.

Malone BD, Gali A, Kaxiras E. First principles study of point defects in SnS. Physical Chemistry Chemical Physics. 2014;16 :26176-26183.Abstract

Photovoltaic cells based on SnS as the absorber layer show promise for efficient solar devices containing non-toxic materials that are abundant enough for large scale production. The efficiency of SnS cells has been increasing steadily, but various loss mechanisms in the device, related to the presence of defects in the material, have so far limited it far below its maximal theoretical value. In this work we perform first principles, density-functional-theory calculations to examine the behavior and nature of both intrinsic and extrinsic defects in the SnS absorber layer. We focus on the elements known to exist in the environment of SnS-based photovoltaic devices during growth. In what concerns intrinsic defects, our calculations support the current understanding of the role of the Sn vacancy (VSn) acceptor defect, namely that it is responsible for the p-type conductivity in SnS. We also present calculations for extrinsic defects and make extensive comparison to experimental expectations. Our detailed treatment of electrostatic correction terms for charged defects provides theoretical predictions on both the highfrequency and low-frequency dielectric tensors of SnS.

Yu L, Lee Y-H, Ling X, Santos EJG, Shin YC, Lin Y, Dubey M, Kaxiras E, Kong J, Wang H, et al. Graphene/MoS2 Hybrid Technology for Large-Scale Two-Dimensional Electronics. NanoLetters. 2014;14 :30553063.Abstract

Two-dimensional (2D) materials have generated great interest in the past few years as a new toolbox for electronics. This family of materials includes, among others, metallic graphene, semiconducting transition metal dichalcogenides (such as MoS2), and insulating boron nitride. These materials and their heterostructures offer excellent mechanical flexibility, optical transparency, and favorable transport properties for realizing electronic, sensing, and optical systems on arbitrary surfaces. In this paper, we demonstrate a novel technology for constructing large-scale electronic systems based on graphene/molybdenum disulfide (MoS2) heterostructures grown by chemical vapor deposition. We have fabricated highperformance devices and circuits based on this heterostructure, where MoS2 is used as the transistor channel and graphene as contact electrodes and circuit interconnects. We provide a systematic comparison of the graphene/MoS2 heterojunction contact to more traditional MoS2-metal junctions, as well as a theoretical investigation, using density functional theory, of the origin of the Schottky barrier height. The tunability of the graphene work function with electrostatic doping significantly improves the ohmic contact to MoS2. These high-performance large-scale devices and circuits based on this 2D heterostructure pave the way for practical flexible transparent electronics.

Randles A, Kaxiras E. Parallel in time approximation of the lattice Boltzmann method for laminar flows. Journal of Computational Physics. 2014;270 :577-586.Abstract

Fluid dynamics simulations using grid-based methods, such as the lattice Boltzmann equation, can benefit from parallel-in-space computation. However, for a fixed-size simulation of this type, the efficiency of larger processor counts will saturate when the number of grid points per core becomes too small. To overcome this fundamental strong scaling limit in space-parallel approaches, we present a novel time-parallel version of the lattice Boltzmann method using the parareal algorithm. This method is based on a predictor–corrector scheme combined with mesh refinement to enable the simulation of larger number of time steps. We present results of up to a 32× increase in speed for a model system consisting of a cylinder with conditions for laminar flow. The parallel gain obtainable is predicted with strong accuracy, providing a quantitative understanding of the potential impact of this method.

Zhang G, Li X, Wu G, Wang J, Culcer D, Kaxiras E, Zhang Z. Quantum phase transitions and topological proximity effects in graphene nanoribbon heterostructures. Nanoscale. 2014;6 :3259-3267.Abstract

Topological insulators are bulk insulators that possess robust chiral conducting states along their interfaces with normal insulators. A tremendous research effort has recently been devoted to topological insulatorbased heterostructures, in which conventional proximity effects give rise to a series of exotic physical phenomena. Here we establish the potential existence of topological proximity effects at the interface between a topological insulator and a normal insulator, using graphene-based heterostructures as prototypical systems. Unlike conventional proximity effects in topological insulator based heterostructures, which refer to various phase transitions associated with the symmetry breaking of specific local order parameters, topological proximity effects describe the rich variety of quantum phase transitions associated with the global properties of the system measured by the location of the topological edge states. Specifically, we show that the location of the topological edge states exhibits a versatile tunability as a function of the interface orientation, the strength of the interface tunnel coupling between a topological graphene nanoribbon and a normal graphene nanoribbon, the spin–orbit coupling strength in the normal graphene nanoribbon, and the width of the system. For zigzag and bearded graphene nanoribbons, the topological edge states can be tuned to be either at the interface or outer edge of the normal ribbon. For armchair graphene nanoribbons, the potential location of the topological edge state can be further shifted to the edge of or within the normal ribbon, to the interface, or diving into the topological graphene nanoribbon. We further show that the topological phase diagram established for the prototypical graphene heterostructures can also explain the intriguing quantum phase transition reported recently in other topological-insulator heterostructures. We also discuss potential experimental realizations of the predicted topological proximity effects, which may pave the way for integrating the salient functionality of topological insulators and graphene in future device applications.

Randles A, Kaxiras E. A Spatio-Temporal Coupling Method to Reduce the Time-to-Solution of Cardiovascular Simulations. 2014 IEEE 28th International Parallel & Distributed Processing Symposium. 2014 :593-602.Abstract

We present a new parallel-in-time method designed to reduce the overall time-to- solution of a patientspecific cardiovascular flow simulation. Using a modified parareal algorithm, our approach extends strong scalability beyond spatial parallelism with fully controllable accuracy and no decrease in stability. We discuss the coupling of spatial and temporal domain decompositions used in our implementation, and showcase the use of the method on a study of blood flow through the aorta. We observe an additional 40% reduction in overall wall clock time with no significant loss of accuracy, in agreement with a predictive performance model.

Cheng J, Wang WL, Mosallaei H, Kaxiras E. Surface Plasmon Engineering in Graphene Functionalized with Organic Molecules: A Multiscale Theoretical Investigation. NanoLetters. 2014;14 :50-56.Abstract

Graphene was recently shown to support deep subwavelength surface plasmons at terahertz frequencies characterized by low energy loss and strong field localization, both highly desirable. The properties of graphene can be locally tuned by applying an external gate voltage or by the adsorption of organic molecules that lead to doping through charge transfer. Local tuning of the electronic features of graphene opens the possibility to realize any desired gradient index profile and thus brings large flexibility to control and manipulate the propagation of surface plasmons. Here, we explore this possibility created by functionalizing graphene with organic molecules. We employ a multiscale theoretical approach that combines firstprinciples electronic structure calculations and finite-difference time-domain simulations coupled by surface conductivity. We show that by patterning two types of organic molecules on graphene, a plasmonic metasurface can be realized with any gradient effective refractive index profile to manipulate surface plasmon beams as desired. The special properties of such devices based on functionalized graphene are compared to the similar metamaterials based on metallic films on top of a gradient index dielectric substrate. Using this idea, we design and analyze an ultrathin broadband THz plasmonic lens as proof-of-concept, while more sophisticated index profiles can also be realized and various plasmonic applications are readily accessible.