Roberto Car

Bio: Roberto Car is an academic researcher from Princeton University. The author has contributed to research in topics: Density functional theory & Ab initio. The author has an hindex of 99, co-authored 389 publications receiving 76681 citations. Previous affiliations of Roberto Car include International School for Advanced Studies & University of Geneva.

Nitrogen incorporation at Si(001)-SiO2 interfaces: Relation between N 1s core-level shifts and microscopic structure

Abstract: Using a first-principles approach, we study the incorporation of nitrogen at the Si(001)-SiO2 interface by calculating N Is core-level shifts for several relaxed interface models. The unusually large shift with oxide thickness of the principal peak in photoemission spectra is explained in terms of a single first-neighbor configuration in which the N atom Is always bonded to three Si atoms, both in the interfacial region and further in the oxide. Core-hole relaxation and second nearest neighbor effects concur in yielding larger binding energies in the oxide than at the interface. The calculations do not support the occurrence of N-O bonds at nitrided Si(001)-SiO2 interfaces.

Dynamical charge tensors and infrared spectrum of amorphous sio2

Abstract: Using a model structure consisting of a network of corner sharing tetrahedra, we calculate the infrared spectrum of amorphous SiO2 within a first-principles approach and find good agreement with experiment both for the positions and the intensities of the main peaks. In addition to the vibrational properties, this required the dynamical charge tensors, which were obtained applying the recent quantum polarization theory. The relative intensities in the spectrum depend sensitively on the charge tensors and their anisotropic components are crucial to obtain good agreement with experiment. We find that the Born charges can be correlated to the local structural properties.

First principles study of adsorbed cun (n=1-4) microclusters on mgo(100): structural and electronic properties

Abstract: We present a density functional study of the structural and electronic properties of small Cun (n=1,4) aggregates on defect-free MgO(100). The calculations employ a slab geometry with periodic boundary conditions, supercells with up to 76 atoms, and include full relaxation of the surface layer and of all adsorbed atoms. The preferred adsorption site for a single Cu adatom is on top of an oxygen atom. The adsorption energy and Cu–O distance are ES−A=0.99 eV and dS−A=2.04 A using the Perdew–Wang gradient corrected exchange correlation functional. The saddle point for surface diffusion is at the “hollow” site, with a diffusion barrier of around 0.45 eV. For the adsorbed copper dimer, two geometries, one parallel and one perpendicular to the surface, are very close in energy. For the adsorbed Cu3, a linear configuration is preferred to the triangular geometry. As for the tetramer, the most stable adsorbed geometry for Cu4 is a rhombus. The adsorption energy per Cu atom decreases with increasing the size of th...

A comparison of methods for the calculation of NMR chemical shifts

Abstract: A theory (MPL) to compute the NMR chemical shifts in condensed matter systems using periodic boundary conditions was presented by F. Mauri, B. Pfrommer, and S. G. Louie [Phys. Rev. Lett. 77, 5300 (1996)]. The MPL method has been implemented so far within a pseudopotential formulation in which the wave functions are expanded in plane waves. In this paper, we compare analytically the MPL approach within the density functional theory to existing methods for the calculation of the chemical shifts such as GIAO (gauge-including atomic orbitals), CSGT (continuous set of gauge transformations), and IGAIM (individual gauges for atoms in molecules). To this end we apply the MPL approach to molecules since the latter methods are conceived only for finite systems. We show theoretically the equivalence between a variant of the CSGT and the MPL method applied to finite systems. Moreover, we analyze numerically the efficiency of the different methods when atomic orbital basis sets are employed, by comparing the basis-se...

Boron-mediated growth of long helicity-selected carbon nanotubes

Abstract: We investigate the growth of B-doped carbon nanotubes combining experimental and theoretical techniques. Electron microscopy observations and electron diffraction patterns reveal that B doping considerably increases the length of carbon tubes and leads to a remarkable preferred zigzag chirality. These findings are corroborated by first-principles static add dynamical simulations which indicate that, in the zigzag geometry, B atoms act as a surfactant during growth, preventing tube closure. This mechanism does not extend to armchair tubes, suggesting a helicity selection during growth.

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。

Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium.

Abstract: We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.