# Publications by Year: 2015

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.