# Publications

2016
Montemore MM, Madix RJ, Kaxiras E. How Does Nanoporous Gold Dissociate Molecular Oxygen?. JOURNAL OF PHYSICAL CHEMISTRY C. 2016;120 (30) :16636-16640.Abstract
Nanoporous Au and other dilute AgAu alloys are highly active and selective oxidation catalysts. Their ability to dissociate O-2 is to a large extent unexplained, given that unsupported Au cannot generally dissociate O-2 while large ensembles of Ag atoms (>4) are generally necessary to lower the O-2 dissociation barrier significantly. Here, we identify a site on the surface of dilute AgAu alloys that is stable under reaction conditions and has a low O-2 dissociation barrier, in agreement with experimental measurements. Although Ag generally prefers to disperse throughout Au, the presence of adsorbed O near surface steps creates sites of high local Ag concentration, where the Ag, atoms sit in the rows next to the step Au atoms. O-2 adsorbs on the Au step atoms, but the transition state involves significant Ag-O interaction, resulting in a barrier lower than expected from the adsorption energies of either the initial or final state.
Shirodkar SN, Kaxiras E. Li intercalation at graphene/hexagonal boron nitride interfaces. PHYSICAL REVIEW B. 2016;93 (24).Abstract
Intercalation of Li in graphite and other layered structures is of interest for highly efficient energy storage devices. In this paper, we determine the extent to which Li intercalates at the different interfaces formed between graphene (G) and hexagonal boron nitride (hBN) heterostructures. We use ab initio calculations to explore in detail the position of the dispersed Li atoms, changes in the structure at the interfaces, energetic stability of the configurations, and the corresponding electronic structure with varying concentrations of the intercalant. We trace the origin of the energetic stability and maximum concentration of Li that intercalates into various layered structures to the ability of the interface to accept electrons. Our calculations indicate that Li intercalates easiest at G/G interfaces, followed by interfaces between G/hBN, whereas Li cannot intercalate in hBN/hBN interfaces. Our results provide a framework for the design of experimental setups with optimal Li intercalation and reveal the implications of intercalation on the dielectric properties of these materials and their possible application in plasmonics.
Perez D, Cubuk ED, Waterland A, Kaxiras E, Voter AF. Long-Time Dynamics through Parallel Trajectory Splicing. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2016;12 (1) :18-28.Abstract
Simulating the atomistic evolution of materials over long time scales is a longstanding challenge, especially for complex systems where the distribution of barrier heights is very heterogeneous. Such systems are difficult to investigate using conventional long-time scale techniques, and the fact that they tend to remain trapped in small regions of configuration space for extended periods of time strongly limits the physical insights gained from short simulations. We introduce a novel simulation technique, Parallel Trajectory Splicing (Par Splice), that aims at addressing this problem through the timewise parallelization of long trajectories. The computational efficiency of Par Splice stems from a speculation strategy whereby predictions of the future evolution of the system are leveraged to increase the amount of work that can be concurrently performed at any one time, hence improving the scalability of the method. ParSplice is also able to accurately account for, and potentially reuse, a substantial fraction of the computational work invested in the simulation. We validate the method on a simple Ag surface system and demonstrate substantial increases in efficiency compared to previous methods. We then demonstrate the power of ParSplice through the study of topology changes in Ag42Cu13 core shell nanoparticles.
Falcucci G, Succi S, Montessori A, Melchionna S, Prestininzi P, Barroo C, Bell DC, Biener MM, Biener J, Zugic B, et al. Mapping reactive flow patterns in monolithic nanoporous catalysts. MICROFLUIDICS AND NANOFLUIDICS. 2016;20 (7).Abstract
The development of high-efficiency porous catalyst membranes critically depends on our understanding of where the majority of the chemical conversions occur within the porous structure. This requires mapping of chemical reactions and mass transport inside the complex nanoscale architecture of porous catalyst membranes which is a multiscale problem in both the temporal and spatial domains. To address this problem, we developed a multiscale mass transport computational framework based on the lattice Boltzmann method that allows us to account for catalytic reactions at the gas-solid interface by introducing a new boundary condition. In good agreement with experiments, the simulations reveal that most catalytic reactions occur near the gas-flow facing side of the catalyst membrane if chemical reactions are fast compared to mass transport within the porous catalyst membrane.
Nourbakhsh A, Zubair A, Sajjad RN, Tavakkoli AKG, Chen W, Fang S, Ling X, Kong J, Dresselhaus MS, Kaxiras E, et al. MoS2 Field-Effect Transistor with Sub-10 nm Channel Length. NANO LETTERS. 2016;16 (12) :7798-7806.Abstract
Atomically thin molybdenum disulfide (MoS2) is an ideal semiconductor material for field-effect transistors (FETs) with sub-10 nm channel lengths. The high effective mass and large bandgap of MoS2 minimize direct source-drain tunneling, while its atomically thin body maximizes the gate modulation efficiency in ultrashort-channel transistors. However, no experimental study to date has approached the sub-10 nm scale due to the multiple challenges related to nanofabrication at this length scale and the high contact resistance traditionally observed in MoS2 transistors. Here, using the semiconducting-to-metallic phase transition of MoS2, we demonstrate sub-10 nm channel-length transistor fabrication by directed self-assembly patterning of mono- and trilayer MoS2. This is done in a 7.5 nm half-pitch periodic chain of transistors where semiconducting (2H) MoS2 channel regions are seamlessly connected to metallic-phase (1T') MoS2 access and contact regions. The resulting 7.5 nm channel-length MoS2 FET has a low off-current of 10 pA/mu m, an on/off current ratio of >10(7), and a subthreshold swing of 120 mV/dec. The experimental results presented in this work, combined with device transport modeling, reveal the remarkable potential of 2D MoS2 for future sub-10 nm technology nodes.
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.