Keyes DE, McInnes LC, Woodward C, Gropp W, Myra E, et al. Multiphysics Simulations: Challenges and Opportunities. International Journal of High Performance Computing Applications. 2013;27 (1) :4-83.Abstract

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.

Hsu CW, Fyta M, Lakatos G, Melchionna S, Kaxiras E. Ab initio determination of coarse-grained interactions in double-stranded DNA. Journal of Chemical Physics. 2012;137 :105102.Abstract

We derive the coarse-grained interactions between DNA nucleotides from 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.

Zhao K, Pharr M, Wan Q, Wang WL, Kaxiras E, Vlassak JJ, Suo Z. Concurrent Reaction and Plasticity during Initial Lithiation of Crystalline Silicon in Lithium-Ion Batteries. Journal of the Electrochemical Society. 2012;159 (3) :A238-A243.Abstract

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

Tritsaris GA, Zhao K, Okeke OU, Kaxiras E. Diffusion of Lithium in Bulk Amorphous Silicon: A Theoretical Study. Journal of Physical Chemistry C. 2012;116 :22212-22216.Abstract

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.

Voros M, Gali A, Kaxiras E, Frauenheim T, Knaup JM. Identification of defects at the interface between 3C-SiC quantum dots and a SiO2 embedding matrix. Physica Status Solidi. 2012;B 249 (2) :360-367.Abstract

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/SiO2 interface. We present tight-binding simulated annealing calculations, in order to construct models of SiC QDs in SiO2, with the aim of obtaining an overview of the possible defects at the SiC/SiO2 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/SiO2 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.

Bisson M, Bernaschi M, Melchionna S, Succi S, Kaxiras E. Multiscale Hemodynamics Using GPU Clusters. Communications in Computer Physics. 2012;11 (1) :48-64.Abstract

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.

Tritsaris GA, Mathioudakis C, Kelires PC, Kaxiras E. Optical and elastic properties of diamond-like carbon with metallic inclusions: A theoretical study. Journal of Applied Physics. 2012;112 :103503.Abstract

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 105 cm−1) and good mechanical strength (bulk and Young's modulus higher than 300 and 500 GPa, respectively).

Papamokos GV, Tziatzos G, Papageorgiou DG, Georgatos SD, Politou AS, Kaxiras E. Structural Role of RKS Motifs in Chromatin Interactions: A Molecular Dynamics Study of HP1 Bound to a Variably Modified Histone Tail. Biophysical Journal. 2012;102 :1926-1933.Abstract

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.

Schusteritsch G, Kaxiras E. Sulfur-induced embrittlement of nickel: a first-principles study. Modeling and Simulation in Materials Science and Engineering. 2012;20 :065007.Abstract

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.

Wang WL, Bhandari S, Yi W, Bell DC, Westervelt R, Kaxiras E. Direct Imaging of Atomic-Scale Ripples in Few-Layer Graphene. NanoLetters. 2012;12 :2278-2282.Abstract

Graphene has been touted as the prototypical two-dimensional solid of extraordinary stability and strength. However, its very existence relies on out-of-plane ripples as predicted by theory and confirmed by experiments. Evidence of the intrinsic ripples has been reported in the form of broadened diffraction spots in reciprocal space, in which all spatial information is lost. Here we show direct real-space images of the ripples in a few-layer graphene (FLG) membrane resolved at the atomic scale using monochromated aberrationcorrected transmission electron microscopy (TEM). The thickness of FLG amplifies the weak local effects of the ripples, resulting in spatially varying TEM contrast that is unique up to inversion symmetry. We compare the characteristic TEM contrast with simulated images based on accurate first-principles calculations of the scattering potential. Our results characterize the ripples in real space and suggest that such features are likely common in ultrathin materials, even in the nanometer-thickness range.

Zhao K, Tritsaris GA, Pharr M, Wang WL, Okeke O, Suo Z, Vlassak JJ, Kaxiras E. Reactive Flow in Silicon Electrodes Assisted by the Insertion of Lithium. NanoLetters. 2012;12 :4397-4403.Abstract

In the search for high-energy density materials for Li-ion batteries, silicon has emerged as a promising candidate for anodes due to its ability to absorb a large number of Li atoms. Lithiation of Si leads to large deformation and concurrent changes in its mechanical properties, from a brittle material in its pure form to a material that can sustain large inelastic deformation in the lithiated form. These remarkable changes in behavior pose a challenge to theoretical treatment of the material properties. Here, we provide a detailed picture of the origin of changes in the mechanical properties, based on first-principles calculations of the atomic-scale structural and electronic properties in a model amorphous silicon (a-Si) structure. We regard the reactive flow of lithiated silicon as a nonequilibrium process consisting of concurrent Li insertion driven by unbalanced chemical potential and flow driven by deviatoric stress. The reaction enables the material to flow at a lower level of stress. Our theoretical model is in excellent quantitative agreement with experimental measurements of lithiation-induced stress on a Si thin film.

Ren J, Meng S, Kaxiras E. Theoretical Investigation of the C60/Copper Phthalocyanine Organic Photovoltaic Heterojunction. Nano Research. 2012;5 :248-257.Abstract

Molecular heterojunctions, such as the one based on copper phthalocyanine (CuPc) and carbon fullerene (C60) molecules, are commonly employed in organic photovoltaic cells as electron donor–acceptor pairs. We have investigated the different atomic structures and electronic and optical properties of the C60/CuPc heterojunction through first-principles calculations based on density functional theory (DFT) and time-dependent DFT. In general, configurations with the CuPc molecule “lying down” on C60 are energetically more favorable than configurations with the CuPc molecule “standing up”. The lying-down configurations also facilitate charge transfer between the two molecules, due to the stronger interaction and the larger overlap between electronic wavefunctions at the interface. The energetically preferred structure consists of CuPc placed so that the Cu atom is above a bridge site of C60, with one N–Cu–N bond of CuPc being parallel to a C–C bond of C60. We also considered the structure of a periodic CuPc monolayer deposited on the (001) surface of a face-centered cubic (fcc) crystal of C60 molecules with the lying-down orientation and on the (111) surface with the standing-up configuration. We find that the first arrangement can lead to larger open circuit voltage due to an enhanced electronic interaction between CuPc and C60 molecules. 

Mao Y, Wang WL, Wei D, Kaxiras E, Sodroski JG. Graphene Structures at an ExtremeDegree of Buckling. ACSNano. 2011;5 :1395.
Ren J, Meng S, Wang Y-L, Ma X-C, Xue Q-K, Kaxiras E. Properties of copper (fluoro-)phthalocyanine layers depositedon epitaxial graphene. J. Chem. Phys. 2011;134 :194706.
Baker TA, Xu B, Jensen SC, andEfthimios Kaxiras CMF. Role of defects in propene adsorption and reaction on a partiallyO-covered Au(111) surface. Catal. Sci. Technol. 2011;1 :1166.
Haubrich J, Kaxiras E, Friend CM. The Role of Surface and Subsurface Point Defects for Chemical ModelStudies on TiO2: A First-Principles Theoretical Study of FormaldehydeBonding on Rutile TiO2(110). Chem. Eur. J. 2011;17 :4496.
Li H, Knaup JM, Kaxiras E, Vlassak JJ. Stiffening of organosilicate glasses by organic cross-linking. Acta Mater. 2011;59 :44.
Lin M-W, Ling C, Agapito LA, Kioussis N, Zhang Y, Cheng MM-C, Wang WL, Kaxiras E, Zhixian Zhou1. Approaching the intrinsic band gap in suspended high-mobility graphene nanoribbons. PHYSICAL REVIEW B. 2011;84 :125411.
Meng S, Kaxiras E, Nazeeruddin MK, Gratzel M. Design of Dye Acceptors for Photovoltaics from First-PrinciplesCalculations. J. Phys. Chem. C. 2011;115 :9276.
Heiss M, Conesa-Boj S, Ren J, Tseng H-H, Gali A, Rudolph A, Uccelli E, Peiro F, Morante JR, Schuh D, et al. Direct correlation of crystal structure and optical properties in wurtzite/zinc-blendeGaAs nanowire heterostructures. PHYSICAL REVIEW B. 2011;83 :045303.