# Recent Publications

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1. Title: Erratum: Second harmonic generation in h-BN and MoS2 monolayers: Role of electron-hole interaction

Author(s): Gruening M., Attaccalite C.

Physical Review B, 90, No. 19, pp. 199901- (November 2014)

2. Title: Graphene/MoS2 Hybrid Technology for Large-Scale Two-Dimensional Electronics

Author(s): Yu L., Lee Y., Ling X., Santos E.J.G., Shin Y.C., Lin Yuxuan, Dubey M., Kaxiras E, Kong J., Wang H., Palacios T.

Nano Letters, 14, No. 6, pp. 3055-3063 (8 May 2014)

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 high-performance 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.

3. Title: Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

Author(s): Stella L., Lorenz C.D., Kantorovich L.,

Physical Review B, 89, pp. 134303- (7 April 2014)

The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

4. Title: Second harmonic generation in h-BN and MoS2 monolayers: Role of electron-hole interaction

Author(s): Gruning M., Attaccalite C.

Physical Review B, 89, No. 8, pp. 081102- (3 February 2014)

We study second harmonic generation in h-BN and MoS2 monolayers using an ab initio approach based on many-body theory. We show that electron-hole interaction doubles the signal intensity at the excitonic resonances with respect to the contribution from independent electronic transitions. This implies that electron-hole interaction is essential to describe second harmonic generation in those materials. We argue that this finding is general for nonlinear optical properties in nanostructures and that the present methodology is the key to disclose these effects.

5. Title: Nonconservative dynamics in long atomic wires

Author(s): Cunningham B., Todorov T.N., Dundas D.

Physical Review B, 90, pp. 115430 - (24 September 2014)

The effect of nonconservative current-induced forces on the ions in a defect-free metallic nanowire is investigated using both steady-state calculations and dynamical simulations. Nonconservative forces were found to have a major influence on the ion dynamics in these systems, but their role in increasing the kinetic energy of the ions decreases with increasing system length. The results illustrate the importance of nonconservative effects in short nanowires and the scaling of these effects with system size. The dependence on bias and ion mass can be understood with the help of a simple pen and paper model. This material highlights the benefit of simple preliminary steady-state calculations in anticipating aspects of brute-force dynamical simulations, and provides rule of thumb criteria for the design of stable quantum wires.

6. Title: Epitaxial Growth of Molecular Crystals on van der Waals Substrates for High-Performance Organic Electronics

Author(s): Lee C.H., Schiros T., Santos E.J.G., Kim B., Yager K.G., Kang S.J., Lee S., Yu J., Watanabe K., Taniguchi T., Hone J., Kaxiras E., Nuckolls C., Kim P.

Advanced Materials, 26, No. 18, pp. 2812-2817 (23 January 2014)

Epitaxial van der Waals (vdW) heterostructures of organic and layered materials are demonstrated to create high-performance organic electronic devices. High-quality rubrene films with large single-crystalline domains are grown on h-BN dielectric layers via vdW epitaxy. In addition, high carrier mobility comparable to free-standing single-crystal counterparts is achieved by forming interfacial electrical contacts with graphene electrodes.

7. Title: Direct Observation of a Long-Lived Single-Atom Catalyst Chiseling Atomic Structures in Graphene

Author(s): Wang W.L., Santos E.J.G., Jiang B., Dogus Cubuk E., Ophus C., Centeno A., Pesquera A., Zurutuza A., Ciston J., Westervelt R., Kaxiras E.

Nano Letters, 14, No. 2, pp. 450-455 (21 January 2014)

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 aberration-corrected 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.

8. Title: Electron-induced hydrogen loss in uracil in a water cluster environment

Author(s): Smyth M., Kohanoff J., Fabrikant I.I.

Journal of Chemical Physics, 140, pp. 184313- (12 May 2014)

Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A′-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons.

9. Title: Current-induced forces: a simple derivation

Author(s): Todorov T.N., Dundas D., Lü J., Brandbyge M., Hedegård P.

European Journal of Physics, 35, No. 6, pp. 065004- (02 September 2014)

We revisit the problem of forces on atoms under current in nanoscale conductors. We derive and discuss the five principal kinds of force under steady-state conditions from a simple standpoint that—with the help of background literature—should be accessible to physics undergraduates. The discussion aims at combining methodology with an emphasis on the underlying physics through examples. We discuss and compare two forces present only under current—the non-conservative electron wind force and a Lorentz-like velocity-dependent force. It is shown that in metallic nanowires both display significant features at the wire surface, making it a candidate for the nucleation of current-driven structural transformations and failure. Finally we discuss the problem of force noise and the limitations of Ehrenfest dynamics

10. Title: One-pot two-step mechanochemical synthesis: ligand and complex preparation without isolating intermediates.

Author(s): Ferguson M., Giri N., Huang X., Apperley D., James S.L.

Green Chemistry, 16, pp. 1374-1382 (2014)

Although the use of ball milling to induce reactions between solids (mechanochemical synthesis) can provide lower-waste routes to chemical products by avoiding solvent during the reaction, there are further potential advantages in using one-pot multistep syntheses to avoid the use of bulk solvents for the purification of intermediates. We report here two-step syntheses involving formation of salen-type ligands from diamines and hydroxyaldehydes followed directly by reactions with metal salts to provide the corresponding metal complexes. Five salen-type ligands 2,2’-[1,2-ethanediylbis[(E)-nitrilomethylidyne]]bis-phenol,‘salenH2’,1; 2,2’-[(±)-1,2-cyclohexanediylbis-[(E)-nitrilomethylidyne]]bis-phenol,2 ;2,2’-[1,2-phenylene-bis(nitrilomethylidyne)]-bis-phenol, ‘salphenH2’ 3; 2-[[(2-aminophenyl)imino]methyl]-phenol, 4; 2,2’-[(±)-1,2-cyclohexanediylbis[(E)-nitrilomethylidyne]]-bis[4,6-bis(1,1-dimethylethyl)]-phenol, ‘Jacobsen ligand’,5) were found to form readily in a shaker-type ball mill at 0.5 to 3 g scale from their corresponding diamine and aldehyde precursors. Although in some cases both starting materials were liquids, ball milling was still necessary to drive those reactions to completion because precipitation of the product and or intermediates rapidly gave in thick pastes which could not be stirred conventionally. The only ligand which required the addition of solvent was the Jacobsen ligand 5 which required 1.75 mol equivalents of methanol to go to completion. Ligands 1–5 were thus obtained directly in 30–60 minutes in their hydrated forms, due to the presence of water by-product, as free-flowing yellow powders which could be dried by heating to give analytically pure products. The one-armed salphen ligand 4 could also be obtained selectively by changing the reaction stoichiometry to 1 : 1. SalenH2 1 was explored for the one-pot two-step synthesis of metal complexes. In particular, after in situ formation of the ligand by ball milling, metal salts (ZnO, Ni(OAc)2·4H2O or Cu(OAc)2·H2O) were added directly to the jar and milling continued for a further 30 minutes. Small amounts of methanol (0.4–1.1 mol equivalents) were needed for these reactions to run to completion. The corresponding metal complexes [M(salen)] (M = Zn,6; Ni,7;or Cu,8) were thus obtained quantitatively after 30 minutes in hydrated form, and could be heated briefly to give analytically pure dehydrated products. The all-at-once ‘tandem’ synthesis of [Zn(salen)] 6 was also explored by milling ZnO, ethylene diamine and salicylaldehyde together in the appropriate mole ratio for 60 minutes. This approach also gave the target complex selectively with no solvent needing to be added. Overall, these syntheses were found to be highly efficient in terms of time and the in avoidance of bulk solvent both during the reaction and for the isolation of intermediates. The work demonstrates the applicability of mechanochemical synthesis to one-pot multi-step strategies.

11. Title: Second harmonic generation in h-BN and MoS2 monolayers: Role of electron-hole interaction

Author(s): Gruening M., Attaccalite C.

Physical Review B (Rapid), 89, pp. 081102- (2014)

We study second-harmonic generation in h-BN and MoS$_2$ monolayers using a novel \emph{ab initio} approach based on Many-body theory. We show that electron-hole interaction doubles the signal intensity at the excitonic resonances with respect to the contribution from independent electronic transitions. This implies that electron-hole interaction is essential to describe second-harmonic generation in those materials. We argue that this finding is general for nonlinear optical properties in nanostructures and that the present methodology is the key to disclose these effects.

12. Title: Universal tight binding model for chemical reactions in solution and at surfaces. III. Stoichiometric and reduced surfaces of titania and the adsorption of water

Author(s): Lozovoi A.Y., Pashov D.L., Sheppard T.J., Kohanoff J.J., Paxton A.T.

Journal of Chemical Physics, 141, pp. 044505- (2014)

We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster.

13. Title: Universal tight binding model for chemical reactions in solution and at surfaces. II. Water

Author(s): Lozovoi A.Y., Pashov D.L., Sheppard T.J., Kohanoff J.J., Paxton A.T.

Journal of Chemical Physics, 141, pp. 044504- (2014)

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice—leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

14. Title: Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

Author(s): Lozovoi A.Y., Pashov D.L., Sheppard T.J., Kohanoff J.J., Paxton A.T.

Journal of Chemical Physics, 141, pp. 044503- (2014)

As is now well established, a first order expansion of the Hohenberg–Kohn total energy density functional about a trial input density, namely, the Harris–Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

15. Title: Irradiation of Water Ice by C+ Ions in the Cosmic Environment

Author(s): McBride E.J., Millar T.J., Kohanoff J.J.

Journal of PPhysical Chemistry A, 118, No. 34, pp. 6991-6998 (2014)

We present a first-principles MD (FPMD) study of the interaction of low-energy, positively charged carbon (C+) projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon ion at an initial energy of 11 and 1.7 eV with a 30-molecule cluster have been investigated. Simulations indicate that the neutral isoformyl radical, COH•, and carbon monoxide, CO, are the dominant products of these reactions. All of these reactions are accompanied by the transfer of a proton from the reacting water molecule to the ice, where it forms a hydronium ion. We find that COH• is formed either via a direct, “knock-out”, mechanism following the impact of the C+ projectile upon a water molecule or by creation of a COH2+ intermediate. The direct mechanism is more prominent at higher energies. CO is generally produced following the dissociation of COH•. More frequent production of the formyl radical, HCO•, is observed here than in gas-phase calculations. A less commonly occurring product is the dihydroxymethyl, CH(OH)2•, radical. Although a minor result, its existence gives an indication of the increasing chemical complexity that is possible in such heterogeneous environments.

16. Title: Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study

Author(s): Gu B., Smyth M., Kohanoff J.

Physical Chemistry Chemical Physics, 16, pp. 24350-24358 (2014)

17. Title: Graphene/MoS2 Schottky diodes and their integration for metal base transistors

Author(s): Barreiro A., Seol J., Lee C., Meric I., Santos E., Wang L., Kaxiras E., Hone J., Shepard K., Guo J., Kim P.

APS March Meeting 2014, abstract #Q37.008 (2014)

In this contribution we present an experimental and theoretical investigation of graphene/MoS2 Schottky diodes and MoS2/graphene/MoS2 metal base transistors. We observe that the Schottky barrier height can be modulated by the chemical potential of the graphene and MoS2 layers with the back gate and tuned in the range of 0-450 meV. To extract further information regarding the quality of the graphene/MoS2 interfaces and the conduction mechanism across them, we analyze the ideality factor as a function of temperature and find it can vary from n =3 at 270 K to n =12.9 at 100 K. We attribute this strong temperature dependence to a spatial variation of the Schottky barrier, caused by 2D electrostatic effects. Moreover, we have fabricated MoS2/graphene/MoS2 metal base transistors that work as a permeable base transistors.