# Publications

We report Time-Domain ThermoReflectance experiments measuring the Thermal Boundary Conductance (TBC) of interfaces between diamond and metal surfaces, based on samples consisting of [111]-oriented diamond substrates with hydrogen or with sp^{2} carbon surface terminations created using plasma treatments. In a concurrent theoretical study, we calculate the work of adhesion between Ni, Cu, and diamond interfaces with (111) surface orientation, with or without hydrogen termination of the diamond surface, using first-principles electronic structure calculations based on density functional theory (DFT). We find a positive correlation between the calculated work of adhesion and the measured conductance of these interfaces, suggesting that DFT could be used as a screening tool to identify metal/dielectric systems with high TBC. We also explain the negative effect of hydrogen on the thermal conductance of metal/diamond interfaces.

Thin film photovoltaic cells are increasingly important for cost-effective solar energy harvesting. Layered SnS is a promising absorber material due to its high optical absorption in the visible and good doping characteristics. We use first-principles calculations based on density functional theory to study structures of low-index surfaces of SnS using stoichiometric and oxygen-containing structural models, in order to elucidate their possible effect on the efficiency of the photovoltaic device. We find that the surface energy is minimized for the surface with orientation parallel to the layer stacking direction. Compared to stoichiometric surfaces, the oxygen-containing surfaces exhibit fewer electronic states near the band gap. This reduction of near-gap surface states by oxygen should reduce recombination losses at grain boundaries and interfaces of the SnS absorber, and should be beneficial to the efficiency of the solar cell.

The properties of two-dimensional materials, such as molybdenum disulfide, will play an important role in the design of the next generation of electronic devices. Many of those properties are determined by the dielectric constant which is one of the fundamental quantities used to characterize conductivity, refractive index, charge screening, and capacitance. We predict that the effective dielectric constant (ε) of few-layer MoS2 is tunable by an external electric field (Eext). Through first-principles electronic structure calculations, including van der Waals interactions, we show that at low fields (Eext < 0.01 V/Å) ε assumes a nearly constant value ∼4 but increases at higher fields to values that depend on the layer thickness. The thicker the structure, the stronger the modulation of ε with the electric field. Increasing of the external field perpendicular to the dichalcogenide layers beyond a critical value can drive the system to an unstable state where the layers are weakly coupled and can be easily separated. The observed dependence of ε on the external field is due to charge polarization driven by the bias. Implications on the optical properties as well as on the electronic excitations are also considered. Our results point to a promising way of understanding and controlling the screening properties of MoS_{2} through external electric fields.

The energy density of Li-ion batteries depends critically on the specific charge capacity of the constituent electrodes. Silicene, the silicon analogue to graphene, being of atomic thickness could serve as high-capacity host of Li in Li-ion secondary batteries. In this work, we employ first-principles calculations to investigate the interaction of Li with Si in model electrodes of free-standing single-layer and double-layer silicene. More specifically, we identify strong binding sites for Li, calculate the energy barriers accompanying Li diffusion, and present our findings in the context of previous theoretical work related to Liion storage in other structural forms of silicon: the bulk and nanowires. The binding energy of Li is ∼2.2 eV per Li atom and shows small variation with respect to Li content and silicene thickness (one or two layers) while the barriers for Li diffusion are relatively low, typically less than 0.6 eV. We use our theoretical findings to assess the suitability of two-dimensional silicon in the form of silicene layers for Li-ion storage.

We present an efficient method for obtaining the effective single-particle potential for electrons within density functional theory (DFT). In contrast to the independent atom model (IAM) often used to interpret microscopy experiments, our method includes the contributions from charge redistribution and exchange-correlation interactions in a realistic system. The method allows calculation of the effective potential through the widely used pseudopotential formalism instead of the costly all-electron calculations. A transferable and spin-independent core potential for each element is calculated once and for all. The nonlinear exchange-correlation interaction is treated explicitly. This scheme can be readily implemented in pseudopotential DFT codes. We demonstrate the usefulness of our method by calculating the scattering potential and simulating images of nitrogen point defects in graphene for transmission electron microscopy (TEM). The results are in good agreement with experiments.

The dielectric constant of a material is one of the fundamental features used to characterize its electrostatic properties such as capacitance, charge screening, and energy storage capability. Graphene is a material with unique behavior due to its gapless electronic structure and linear dispersion near the Fermi level, which can lead to a tunable band gap in bilayer and trilayer graphene, a superconducting-insulating transition in hybrid systems driven by electric fields, and gatecontrolled surface plasmons. All of these results suggest a strong interplay between graphene properties and external electric fields. Here we address the issue of the effective dielectric constant (*ε*) in N-layer graphene subjected to out-ofplane (*E*_{ext}^{⊥} ) and in-plane (*E*_{ext }^{∥} ) external electric fields. The value of ε has attracted interest due to contradictory reports from theoretical and experimental studies. Through extensive first-principles electronic structure calculations, including van der Waals interactions, we show that both the out-of-plane (*ε*_{⊥}) and the in-plane (*ε*_{∥}) dielectric constants depend on the value of applied field. For example, ε⊥ and ε∥ are nearly constant (∼3 and ∼1.8, respectively) at low fields (Eext < 0.01 V/Å) but increase at higher fields to values that are dependent on the system size. The increase of the external field perpendicular to the graphene layers beyond a critical value can drive the system to a unstable state where the graphene layers are decoupled and can be easily separated. The observed dependence of *ε*_{⊥} and *ε*_{∥} on the external field is due to charge polarization driven by the bias. Our results point to a promising way of understanding and controlling the screening properties of few-layer graphene through external electric fields.

Silicon is a promising anode material for high-capacity Li-ion batteries. Recent experiments show that lithiation of crystalline silicon nanowires leads to highly anisotropic morphologies. This has been interpreted as due to anisotropy in equilibrium interface energies, but this interpretation does not capture the dynamic, nonequilibrium nature of the lithiation process. Here, we provide a comprehensive explanation of experimentally observed morphological changes, based on first-principles multiscale simulations. We identify reaction paths and associated structural transformations for Li insertion into the Si {110} and {111} surfaces and calculate the relevant energy barriers from density functional theory methods. We then perform kinetic Monte Carlo simulations for nanowires with surfaces of different orientations, which reproduce to a remarkable degree the experimentally observed profiles and the relative reaction front rates

SnS is a metal monochalcogenide suitable for use as absorber material in thin film photovoltaic cells. Its structure is an orthorhombic crystal of weakly coupled layers, each layer consisting of strongly bonded Sn-S units. We use first-principles calculations to study model single-layer, double-layer, and bulk structures of SnS in order to elucidate its electronic structure. We find that the optoelectronic properties of the material can vary significantly with respect to the number of layers and the separation between them: the calculated band gap is wider for fewer layers (2.72 eV, 1.57 eV, and 1.07 eV for single-layer, double-layer, and bulk SnS, respectively) and increases with tensile strain along the layer stacking direction (by ∼55 meV/1% strain).

We perform first-principles, density-functional-theory calculations of the electronic structure for the layered bulk materials SnS and GeS which are of interest for photovoltaic applications. Band gap corrections are computed within the *GW* approximation to the electron self-energy. The resulting quasiparticle gaps in both SnS and GeS are in excellent agreement with the majority of existing experimental measurements. In order to better understand the possible use of GeS layers as a carrier-confining barrier within a SnS-based photovoltaic device, we compute the band offsets for different orientations of a SnS/GeS heterojunction. We find the valence band offsets to be almost independent of interfacial direction while the conduction band offsets show a strong anisotropy as a result of the variation in the band gap caused by epitaxial strain along the different directions.

Using first-principles calculations within density functional theory, we investigate the electronic and chemical properties of a single-layer MoS_{2} adsorbed on Ir(111), Pd(111), or Ru(0001), three representative transition metal substrates having varying work functions but each with minimal lattice mismatch with the MoS_{2} overlayer. We find that, for each of the metal substrates, the contact nature is of Schottky-barrier type, and the dependence of the barrier height on the work function exhibits a partial Fermi-level pinning picture. Using hydrogen adsorption as a testing example, we further demonstrate that the introduction of a metal substrate can substantially alter the chemical reactivity of the adsorbed MoS_{2} layer. The enhanced binding of hydrogen, by as much as ∼0.4 eV, is attributed in part to a stronger H−S coupling enabled by the transferred charge from the substrate to the MoS_{2} overlayer, and in part to a stronger MoS_{2}-metal interface by the hydrogen adsorption. These findings may prove to be instrumental in future design of MoS_{2}-based electronics, as well as in exploring novel catalysts for hydrogen production and related chemical processes.

We consider multiphysics applications from algorithmic and architectural perspectives, where “algorithmic” includes both mathematical analysis and computational complexity, and “architectural” includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that includehydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It may be used to realistically probe dynamics of DNA strands in various environments at the μs time scale and the μm length scale.

In an electrochemical cell, crystalline silicon and lithium react at room temperature, forming an amorphous phase of lithiated silicon. The reaction front—the phase boundary between the crystalline silicon and the lithiated silicon—is atomically sharp. Evidence has accumulated recently that the velocity of the reaction front is limited by the rate of the reaction at the front, rather than by the diffusion of lithium through the amorphous phase. This paper presents a model of concurrent reaction and plasticity. We identify the driving force for the movement of the reaction front, and accommodate the reaction-induced volumetric expansion by plastic deformation of the lithiated silicon. The model is illustrated by an analytical solution of the co-evolving reaction and plasticity in a spherical particle. We derive the conditions under which the lithiation-induced stress stalls the reaction. We show that fracture is averted if the particle is small and the yield strength of lithiated silicon is low. Furthermore, we show that the model accounts for recently observed lithiated silicon of anisotropic morphologies

The rate performance of lithium-ion secondary batteries depends critically on the kinetic transport of Li within the anode material. Here we use first-principles theoretical calculations to study the diffusion of Li in the low-concentration limit, using model electrodes of crystalline and four-fold coordinated bulk amorphous silicon. We identify Li diffusion pathways that have relatively low energy barriers (<0.50 eV) in amorphous silicon and discuss how diffusion at short (∼2.5 Å), intermediate (∼10 Å), and long (>1 nm) distances depends on the atomic-scale features of the silicon host. We find that both the energy barriers for diffusion and the topology of the atomic structure control the diffusion. We estimate the diffusion rate in amorphous Si anode to be comparable to the rate in crystalline Si anodes. These findings shed light on the wide range of reported experimental results for Li diffusion in Si anodes.

Due to the favorable band offsets, SiC nanoparticles embedded in silica form a very interesting quantum dot (QD) system. It is possible to produce such QDs in a simple oxidation–carbonization–reoxidation process on Si wafers. This could thus enable production of Si based LED integrated into Si logic devices. However, the luminescence of these QDs, is quenched. This is attributed to defect-mediated recombination of electron–hole pairs, most probably at the SiC/SiO_{2} interface. We present tight-binding simulated annealing calculations, in order to construct models of SiC QDs in SiO_{2}, with the aim of obtaining an overview of the possible defects at the SiC/SiO_{2} interface. We identify a number of recurring interface defects which can be attributed to C or Si rich conditions or general lattice mismatch relaxation. Similar to defects have been shown to be electrically active at the SiC/SiO_{2} interface in MOS structures. We find evidence for strained Si–Si bonds, which can act as recombination centers in isolated SiC QDs. The defect classes identified in this work can serve as the basis for future, high precision simulations of their electronic structure.

The parallel implementation of MUPHY, a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries, for multiGPU platforms is presented. Performance tests show excellent results, with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration, all across the range of GPUs. The basic MUPHY scheme combines a hydrokinetic (Lattice Boltzmann) representation of the blood plasma, with a Particle Dynamics treatment of suspended biological bodies, such as red blood cells. To the best of our knowledge, this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries. This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.

A tough material commonly used in coatings is diamond-like carbon (DLC), that is, amorphous carbon with content in four-fold coordinated C higher than ∼70%, and its composites with metal inclusions. This study aims to offer useful guidelines for the design and development of metal-containing DLC coatings for solar collectors, where the efficiency of the collector depends critically on the performance of the absorber coating. We use first-principles calculations based on density functional theory to study the structural, electronic, optical, and elastic properties of DLC and its composites with Ag and Cu inclusions at 1.5% and 3.0% atomic concentration, to evaluate their suitability for solar thermal energy harvesting. We find that with increasing metal concentration optical absorption is significantly enhanced while at the same time, the composite retains good mechanical strength: DLC with 70–80% content in four-fold coordinated C and small metal concentrations (<3 at. %) will show high absorption in the visible (absorption coefficients higher than 10^{5} cm^{−1}) and good mechanical strength (bulk and Young's modulus higher than 300 and 500 GPa, respectively).

The current understanding of epigenetic signaling assigns a central role to post-translational modifications that occur in the histone tails. In this context, it has been proposed that methylation of K9 and phosphorylation of S10 in the tail of histone H3 represent a binary switch that controls its reversible association to heterochromatin protein 1 (HP1). To test this hypothesis, we performed a comprehensive molecular dynamics study in which we analyzed a crystallographically defined complex that involves the HP1 chromodomain and an H3 tail peptide. Microsecond-long simulations show that the binding of the trimethylated K9 H3 peptide in the aromatic cage of HP1 is only slightly affected by S10 phosphorylation, because the modified K9 and S10 do not interact directly with one another. Instead, the phosphate group of S10 seems to form a persistent intramolecular salt bridge with R8, an interaction that can provoke a major structural change and alter the hydrogen-bonding regime in the H3-HP1 complex. These observations suggest that interactions between adjacent methyl-lysine and phosphoserine side chains do not by themselves provide a binary switch in the H3-HP1 system, but arginine-phosphoserine interactions, which occur in both histones and nonhistone proteins in the context of a conserved RKS motif, are likely to serve a key regulatory function.

We study the embrittlement of Ni due to the presence of S impurities, considering their effect in the bulk and at grain boundaries (GBs). For bulk Ni, we employ Rice’s theory based on generalized-stacking-fault energetics and the unstable stacking energy criterion. We use first-principles density-functionaltheory calculations to determine the ductility parameter D = γs/γus, the ratio of the surface energy γs to the unstable stacking energy γus, for bulk Ni with substitutional S impurities. Similar arguments based on Rice’s theory for the mechanical properties of GBs are invoked. We study the 5(012) GB with interstitial S impurities, in which case D is defined as the ratio of the work of separation Ws and the unstable stacking energy γus, to model the competition between grain decohesion and shear-induced plastic deformation due to grain boundary sliding (GBS). The presence of S impurities is found to increase the value of D by ∼40% in bulk Ni, but reduces it by over 80% for the GB. These results support earlier suggestions that embrittlement of Ni by S impurities is related to their effect on GBs. We further calculate relevant tensile and shear stresses to study the expected fracture mode and find that intergranular crack propagation accommodated by GBS is inhibited in the system considered here.