Li, Ju
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Publication One-particle-thick, Solvent-free, Course-grained Model for Biological and Biomimetic Fluid Membranes(2010-07-12) Yuan, Hongyan; Huang, Changjin; Li, Ju; Lykotrafitis, George; Zhang, SulinBiological membranes are involved in numerous intriguing biophysical and biological cellular phenomena of different length scales, ranging from nanoscale raft formation, vesiculation, to microscale shape transformations. With extended length and time scales as compared to atomistic simulations, solvent-free coarse-grained membrane models have been exploited in mesoscopic membrane simulations. In this study, we present a one-particle-thick fluid membrane model, where each particle represents a cluster of lipid molecules. The model features an anisotropic interparticle pair potential with the interaction strength weighed by the relative particle orientations. With the anisotropic pair potential, particles can robustly self-assemble into fluid membranes with experimentally relevant bending rigidity. Despite its simple mathematical form, the model is highly tunable. Three potential parameters separately and effectively control diffusivity, bending rigidity, and spontaneous curvature of the model membrane. As demonstrated by selected examples, our model can naturally simulate dynamics of phase separation in multicomponent membranes and the topological change of fluid vesicles.Publication Computing the Viscosity of Supercooled Liquids(2009-06-11) Kushima, Akihiro; Lin, Xi; Li, Ju; Eapen, Jacob; Mauro, John C.; Qian, Xiafeng; Diep, Phong; Yip, SidneyWe describe an atomistic method for computing the viscosity of highly viscous liquids based on activated state kinetics. A basin-filling algorithm allowing the system to climb out of deep energy minima through a series of activation and relaxation is proposed and first benchmarked on the problem of adatom diffusion on a metal surface. It is then used to generate transition state pathway trajectories in the potential energy landscape of a binary Lennard-Jones system. Analysis of a sampled trajectory shows the system moves from one deep minimum to another by a process that involves high activation energy and the crossing of many local minima and saddle points. To use the trajectory data to compute the viscosity we derive a Markov Network model within the Green–Kubo formalism and show that it is capable of producing the temperature dependence in the low-viscosity regime described by molecular dynamics simulation, and in the high-viscosity regime (102–1012 Pa s) shown by experiments on fragile glass-forming liquids. We also derive a mean-field-like description involving a coarse-grained temperature-dependent activation barrier, and show it can account qualitatively for the fragile behavior. From the standpoint of molecular studies of transport phenomena this work provides access to long relaxation time processes beyond the reach of current molecular dynamics capabilities. In a companion paper we report a similar study of silica, a representative strong liquid. A comparison of the two systems gives insight into the fundamental difference between strong and fragile temperature variations.Publication Thermochemical and Mechanical Stabilities of the Oxide Scale of ZrB2+SiC and Oxygen Transport Mecha(2008-05-01) Li, Ju; Lenosky, Thomas J; Först, Clemens J; Yip, SidneyRefractory diboride with silicon carbide additive has a unique oxide scale microstructure with two condensed oxide phases (solid+liquid), and demonstrates oxidation resistance superior to either monolithic diboride or silicon carbide. We rationalize that this is because the silica-rich liquid phase can retreat outward to remove the high SiO gas volatility region, while still holding onto the zirconia skeleton mechanically by capillary forces, to form a "solid pillars, liquid roof" scale architecture and maintain barrier function. Basic assessment of the oxygen carriers in the borosilicate liquid in oxygen-rich condition is performed using first-principles calculations. It is estimated from entropy and mobility arguments that above a critical temperature Tc~1500°C, the dominant oxygen carriers should be network defects, such as peroxyl linkage or oxygen-deficient centers, instead of molecular O2* as in the Deal–Grove model. These network defects will lead to sublinear dependence of the oxidation rate with external oxygen partial pressure. The present work suggests that there could be significant room in improving the high-temperature oxidation resistance by refining the oxide scale microstructure as well as controlling the glass chemistry.Publication Hydrostatic compression and high-pressure elastic constants of coesite silica(2008-03-06) Ogata, Shigenobu; Kimizuka, Hajime; Li, JuUsing density-functional theory, we computed all the independent elastic constants of coesite, a high-pressure polymorph of silica, as functions of pressure up to 15 GPa. The results are in good agreement with experimental measurements under ambient conditions. Also, the predicted pressure-dependent elastic properties are consistent with x-ray data in the literature concerning lattice strains at high pressures. We find that coesite, like quartz, exhibits a gradual softening of a shear modulus B44 with increasing pressure, in contrast to the rising bulk modulus.Publication Geometric and Electronic Structure of Graphene Bilayer Edges(2010-10-09) Feng, Ji; Qi, Liang; Li, Ju; Huang, Jian YuWe present a computational investigation of free-standing graphene bilayer edge (BLE) structures, aka “fractional nanotubes.” We demonstrate that these curved carbon nanostructures possess a number of interesting properties, electronic in origin. The BLEs, quite atypical of elemental carbon, have large permanent electric dipoles of 0.87 and 1.14 debye/Å for zigzag and armchair inclinations, respectively. An unusual, weak AA interlayer coupling leads to a twinned double-cone dispersion of the electronic states near the Dirac points. This entails a type of quantum Hall behavior markedly different from what has been observed in graphenebased materials, characterized by a magnetic field-dependent resonance in the Hall conductivity.Publication Pressure-temperature phase diagram for shapes of vesicles: A coarse-grained molecular dynamics study(2009-10-06) Liu, Ping; Li, Ju; Zhang, Yong-weiCoarse-grained molecular dynamics simulations are performed to obtain the phase diagram for shapes of a vesicle with a variation in temperature and pressure difference across the membrane. Various interesting vesicle shapes are found, in particular, a series of shape transformations are observed for a vesicle with an initial spherical shape, which changes to a prolate shape, then an oblate shape, and then a stomatocyte shape, with either increasing temperature or decreasing pressure difference across the membrane.Publication Plastic flow and failure resistance of metallic glass: Insight from in situ compression of nanopillars(2008-04-14) Shan, Z. W; Li, Ju; Cheng, Y. Q; Minor, A. M.; Syed Asif, S. A; Warren, O. L.; Ma, E.We report in situ nanocompression tests of Cu-Zr-Al metallic glass (MG) pillars in a transmission electron microscope. This technique is capable of spatially and temporally resolving the plastic flow in MGs. The observations reveal the intrinsic ability of fully glassy MGs to sustain large plastic strains, which would otherwise be preempted by catastrophic instability in macroscopic samples and conventional tests. The high ductility in volume-limited MGs and the sample size effects in suppressing the rapid failure common to MGs are analyzed by modeling the evolution of the collectivity of flow defects toward localization.Publication Quasiatomic orbitals for ab initio tight-binding analysis(2008-12-16) Li, Ju; Qian, Xiaofeng; Qi, Liang; Wang, Cai-Zhuang; Chan, Tzu-Liang; Yao, Yong-Xin; Ho, Kai-Ming; Yip, SidneyWave functions obtained from plane-wave density-functional theory (DFT) calculations using norm-conserving pseudopotential, ultrasoft pseudopotential, or projector augmented-wave method are efficiently and robustly transformed into a set of spatially localized nonorthogonal quasiatomic orbitals (QOs) with pseudoangular momentum quantum numbers. We demonstrate that these minimal-basis orbitals can exactly reproduce all the electronic structure information below an energy threshold represented in the form of environment-dependent tight-binding Hamiltonian and overlap matrices. Band structure, density of states, and the Fermi surface are calculated from this real-space tight-binding representation for various extended systems (Si, SiC, Fe, and Mo) and compared with plane-wave DFT results. The Mulliken charge and bond order analyses are performed under QO basis set, which satisfy sum rules. The present work validates the general applicability of Slater and Koster's scheme of linear combinations of atomic orbitals and points to future ab initio tight-binding parametrizations and linear-scaling DFT development.Publication Near Neutrality of an Oxygen Molecule Adsorbed on a Pt(111) Surface(2008-10-03) Qi, Liang; Qiang, Xiaofeng; Li, JuThe charge state of paramagnetic or nonmagnetic O2 adsorbed on a Pt(111) surface is analyzed using density functional theory. We find no significant charge transfer between Pt and the two adsorbed molecular precursors, suggesting these oxygen reduction reaction (ORR) intermediates are nearly neutral, and changes in magnetic moment come from self adjustment of O2 spin-orbital occupations. Our findings support a greatly simplified model of electrocatalyzed ORR, and also point to more subtle pictures of adsorbates or impurities interacting with crystal than literal integer charge transfers.Publication Calculating Phase-Coherent Quantum Transport in Nanoelectronics with ab initio Quasiatomic Orbital Basis Set(2010-11-23) Qian, Xiaofeng; Li, Ju; Yip, SidneyWe present an efficient and accurate computational approach to study phase-coherent quantum transport in molecular and nanoscale electronics. We formulate a Green’s-function method in the recently developed ab initio nonorthogonal quasiatomic orbital basis set within the Landauer-Büttiker formalism. These quasiatomic orbitals are efficiently and robustly transformed from Kohn-Sham eigenwave functions subject to the maximal atomic-orbital similarity measure. With this minimal basis set, we can easily calculate electrical conductance using Green’s-function method while keeping accuracy at the level of plane-wave density-functional theory. Our approach is validated in three studies of two-terminal electronic devices, in which projected density of states and conductance eigenchannel are employed to help understand microscopic mechanism of quantum transport. We first apply our approach to a seven-carbon atomic chain sandwiched between two finite crosssectioned Al(001) surfaces. The emergence of gaps in the conductance curve originates from the selection rule with vanishing overlap between symmetry-incompatible conductance eigenchannels in leads and conductor. In the second application, a (4,4) single-wall carbon nanotube with a substitutional silicon impurity is investigated. The complete suppression of transmission at 0.6 eV in one of the two conductance eigenchannels is attributed to the Fano antiresonance when the localized silicon impurity state couples with the continuum states of carbon nanotube. Finally, a benzene-1,4-dithiolate molecule attached to two Au(111) surfaces is considered. Combining fragment molecular orbital analysis and conductance eigenchannel analysis, we demonstrate that conductance peaks near the Fermi level result from resonant tunneling through molecular orbitals of benzene- 1,4-dithiolate molecule. In general, our conductance curves agree very well with previous results obtained using localized basis sets while slight difference is observed near the Fermi level and conductance edges.