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.

Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer.

Abstract: Proton transfer via hydronium and hydroxide ions in water is ubiquitous. It underlies acid-base chemistry, certain enzyme reactions, and even infection by the flu. Despite two centuries of investigation, the mechanism underlying why hydroxide diffuses slower than hydronium in water is still not well understood. Herein, we employ state-of-the-art density-functional-theory-based molecular dynamics-with corrections for non-local van der Waals interactions, and self-interaction in the electronic ground state-to model water and hydrated water ions. At this level of theory, we show that structural diffusion of hydronium preserves the previously recognized concerted behaviour. However, by contrast, proton transfer via hydroxide is less temporally correlated, due to a stabilized hypercoordination solvation structure that discourages proton transfer. Specifically, the latter exhibits non-planar geometry, which agrees with neutron-scattering results. Asymmetry in the temporal correlation of proton transfer leads to hydroxide diffusing slower than hydronium.

Structure and Hyperfine Parameters of E 1 ′ Centers in α -Quartz and in Vitreous SiO 2

Abstract: We report a first-principle study of the E(1) defect in alpha-quartz and of the analogous E'(gamma) defect in amorphous SiO2. Our calculation supports the attribution of both these defects to a positively charged oxygen vacancy. The ground-state configuration of these defects is characterized by a large local relaxation of the atomic network, which leads to a localization of the unpaired electron on a Si dangling bond. Using the calculated electronic spin densities, we fully characterize the hyperfine interactions with nearby Si-29. Our results explain well both the strong and the weak features that are observed in the experimental spectra.

Ab initio calculation of properties of carbon in the amorphous and liquid states

Abstract: We have carried out a detailed investigation of liquid carbon (l-C) at T\ensuremath{\simeq}5000 K, and quenched amorphous carbon (a-C) at room temperature, using a first-principles molecular-dynamics method. In this paper we report calculations performed for a fixed density corresponding to low pressures. From our results, which agree well with the limited experimental information available, we analyze the short-range order, particularly the fractions of sp, ${\mathit{sp}}^{2}$, and ${\mathit{sp}}^{3}$ sites, and the electronic properties of the two systems. In addition, we discuss new features of a-C and l-C, predicted by our calculation, and present an analysis of some models proposed in the literature to account for their electronic and bonding properties, as well as of recent controversial experiments.

Frustration effects and microscopic growth mechanisms for BN nanotubes

Abstract: Using ab initio molecular dynamics simulations, we have studied the growth mechanisms of boron-nitride (BN) nanotubes. In this experimental conditions of temperature, the behavior of single-wall BN nanotubes strongly depends on their helicity. Open-ended "zigzag" tubes close into an amorphouslike tip, preventing further growth. In the "armchair" case, the formation of squares traps the tip into a flat cap able to revert to a growing hexagonal network by incorporating incoming atoms. These findings are related to the greater stability of B-N bonds as compared to B-B or N-N bonds.

Structural, bonding, dynamical, and electronic properties of liquid silicon: An ab initio molecular-dynamics study.

Abstract: We report an extensive first-principles molecular-dynamics study of metallic liquid silicon. Our description of the local order is in excellent agreement with x-ray- and neutron-diffraction experiments. The difference in internal energy between the simulated liquid phase and the crystal agrees well with the experimental enthalpy of melting. Analysis of the valence-electronic-charge density shows persistence of some covalent bonds in the melt. These bonds give rise in the power spectrum of the system dynamics to a well-identifiable feature associated with stretching vibrations. Unlike the case in the crystal, in the liquid the covalent bonds are continuously forming and breaking in response to atomic motion. The majority of bonds are broken on average, leading to fast diffusion and to metallic behavior of the melt. The calculated electronic conductivity shows good agreement with available experimental data.

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.