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.

beta -phase of Pb on Ge(111): The competing roles of electronic bonding and thermal fluctuations.

Abstract: We have studied the low temperature phases of Pb/Ge(111) at Pb coverages Θ=1/3, 1, and 4/3 using ab initio molecular dynamics. Stable phases are found to occur at Θ=1/3 and 4/3. For the low-coverage (Θ=1/3) α phase, we confirm the model of Pb atoms adsorbed at T4 sites of the Ge(111) substrate. For the high coverage (Θ=4/3) β phase and very low temperature, we determine a structure characterized by the presence of covalently bonded Pb chains parallel to 〈11¯0〉 substrate directions. At room temperature, fluctuations are found to disrupt long-range Pb chains and restore the threefold symmetry of the ideal Ge(111) surface. The calculated structure factors and local density of states agree well with x-ray diffraction and STM data.

Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics.

Abstract: A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car–Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine’s energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

Molecular and solid-state (8-hydroxy-quinoline)aluminum interaction with magnesium: A first-principles study

Abstract: The interaction between Mg and (8-hydroxyquinoline)aluminum, Alq3, is investigated via ab initio molecular dynamics based on density-functional theory. We model the Alq3 thin film both with a single Alq3 molecule in vacuo (as is usually done in the literature) and with an Alq3 crystalline structure. Comparing the results from these two models, we show that bulk calculations provide a better description of the chemical processes involved, allowing the Mg atom to react with two neighboring Alq3 molecules, as was alluded to in a previous publication [S. Meloni, A. Palma, A. Kahn, J. Schwartz, and R. Car, J. Am. Chem. Soc. 125, 7808 (2003)]. Moreover, core-level shift calculations are in good agreement with experimental measurements only when using the solid phase approach. We also propose a different interpretation of the Al(2p) experimental core level presented in a previous work [C. Shen, A. Kahn, and J. Schwartz, J. Appl. Phys. 89, 449 (2001)].

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.