Andrew M. Rappe

Bio: Andrew M. Rappe is an academic researcher from University of Pennsylvania. The author has contributed to research in topics: Ferroelectricity & Density functional theory. The author has an hindex of 82, co-authored 425 publications receiving 23836 citations. Previous affiliations of Andrew M. Rappe include University of California, Berkeley & Drexel University.

Dirac semimetal in three dimensions.

Abstract: We show that the pseudorelativistic physics of graphene near the Fermi level can be extended to three dimensional (3D) materials. Unlike in phase transitions from inversion symmetric topological to normal insulators, we show that particular space groups also allow 3D Dirac points as symmetry protected degeneracies. We provide criteria necessary to identify these groups and, as an example, present ab initio calculations of β-cristobalite BiO(2) which exhibits three Dirac points at the Fermi level. We find that β-cristobalite BiO(2) is metastable, so it can be physically realized as a 3D analog to graphene.

Perovskite oxides for visible-light-absorbing ferroelectric and photovoltaic materials

Abstract: Most known ferroelectric photovoltaic materials have very wide electronic bandgaps (that is, they absorb only high-energy photons) but here a family of perovskite oxides is described that have tunable bandgaps, allowing their use across the whole visible-light spectrum. The spontaneous electrical polarization that characterizes a ferroelectric material is attractive for solar-cell applications as the positive and negative charges generated by light absorption have a natural tendency to separate, making them easier to harvest efficiently. Unfortunately most known ferroelectrics have wide electronic bandgaps — that is they absorb only higher energy photons that make up a small fraction of the solar spectrum. Ilya Grinberg and colleagues now show that a classic ferroelectric can be chemically engineered to tune the bandgap over a broad range, achieving strong absorption and photocurrent generation across the solar spectrum. Ferroelectrics have recently attracted attention as a candidate class of materials for use in photovoltaic devices, and for the coupling of light absorption with other functional properties1,2,3,4,5,6,7. In these materials, the strong inversion symmetry breaking that is due to spontaneous electric polarization promotes the desirable separation of photo-excited carriers and allows voltages higher than the bandgap, which may enable efficiencies beyond the maximum possible in a conventional p–n junction solar cell2,6,8,9,10. Ferroelectric oxides are also stable in a wide range of mechanical, chemical and thermal conditions and can be fabricated using low-cost methods such as sol–gel thin-film deposition and sputtering3,5. Recent work3,5,11 has shown how a decrease in ferroelectric layer thickness and judicious engineering of domain structures and ferroelectric–electrode interfaces can greatly increase the current harvested from ferroelectric absorber materials, increasing the power conversion efficiency from about 10−4 to about 0.5 per cent. Further improvements in photovoltaic efficiency have been inhibited by the wide bandgaps (2.7–4 electronvolts) of ferroelectric oxides, which allow the use of only 8–20 per cent of the solar spectrum. Here we describe a family of single-phase solid oxide solutions made from low-cost and non-toxic elements using conventional solid-state methods: [KNbO3]1 − x[BaNi1/2Nb1/2O3 − δ]x (KBNNO). These oxides exhibit both ferroelectricity and a wide variation of direct bandgaps in the range 1.1–3.8 electronvolts. In particular, the x = 0.1 composition is polar at room temperature, has a direct bandgap of 1.39 electronvolts and has a photocurrent density approximately 50 times larger than that of the classic ferroelectric (Pb,La)(Zr,Ti)O3 material. The ability of KBNNO to absorb three to six times more solar energy than the current ferroelectric materials suggests a route to viable ferroelectric semiconductor-based cells for solar energy conversion and other applications.

Donor and acceptor modes in photonic band structure.

Abstract: Three-dimensionally periodic dielectric structures, photonic crystals, possessing a forbidden gap for electromagnetic wave propagation, a photonic band gap, are now known. If the perfect 3D periodicity is broken by a local defect, local electromagnetic modes can occur within the forbidden band gap. Addition of extra dielectric material locally, inside the photonic crystal, produces ``donor'' modes. Conversely, local removal of dielectric material from the crystal produces ``acceptor'' modes. It is now possible to make high-Q electromagnetic cavities of \ensuremath{\sim}1 cubic wavelength, for short wavelengths at which metallic cavities are useless. These new dielectric cavities can cover the range from mm waves to UV wavelengths.

Dirac Semimetal in Three Dimensions

Abstract: We show that the pseudorelativistic physics of graphene near the Fermi level can be extended to three dimensional (3D) materials. Unlike in phase transitions from inversion symmetric topological to normal insulators, we show that particular space groups also allow 3D Dirac points as symmetry protected degeneracies. We provide criteria necessary to identify these groups and, as an example, present ab initio calculations of β-cristobalite BiO(2) which exhibits three Dirac points at the Fermi level. We find that β-cristobalite BiO(2) is metastable, so it can be physically realized as a 3D analog to graphene.

Dirac Line Nodes in Inversion-Symmetric Crystals.

Abstract: We propose and characterize a new Z2 class of topological semimetals with a vanishing spin-orbit interaction. The proposed topological semimetals are characterized by the presence of bulk one-dimensional (1D) Dirac line nodes (DLNs) and two-dimensional (2D) nearly flat surface states, protected by inversion and time-reversal symmetries. We develop the Z2 invariants dictating the presence of DLNs based on parity eigenvalues at the parity-invariant points in reciprocal space. Moreover, using first-principles calculations, we predict DLNs to occur in Cu_{3}N near the Fermi energy by doping nonmagnetic transition metal atoms, such as Zn and Pd, with the 2D surface states emerging in the projected interior of the DLNs. This Letter includes a brief discussion of the effects of spin-orbit interactions and symmetry breaking as well as comments on experimental implications.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

Abstract: QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

The SIESTA method for ab initio order-N materials simulation

Abstract: We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.