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.

Local-order metric for condensed-phase environments

Abstract: We introduce a local order metric (LOM) that measures the degree of order in the neighborhood of an atomic or molecular site in a condensed medium. The LOM maximizes the overlap between the spatial distribution of sites belonging to that neighborhood and the corresponding distribution in a suitable reference system. The LOM takes a value tending to zero for completely disordered environments and tending to one for environments that perfectly match the reference. The site-averaged LOM and its standard deviation define two scalar order parameters, $S$ and $\ensuremath{\delta}S$, that characterize with excellent resolution crystals, liquids, and amorphous materials. We show with molecular dynamics simulations that $S$, $\ensuremath{\delta}S$, and the LOM provide very insightful information in the study of structural transformations, such as those occurring when ice spontaneously nucleates from supercooled water or when a supercooled water sample becomes amorphous upon progressive cooling.

When do short-range atomistic machine-learning models fall short?

Abstract: We explore the role of long-range interactions in atomistic machine-learning models by analyzing the effects on fitting accuracy, isolated cluster properties, and bulk thermodynamic properties. Such models have become increasingly popular in molecular simulations given their ability to learn highly complex and multi-dimensional interactions within a local environment; however, many of them fundamentally lack a description of explicit long-range interactions. In order to provide a well-defined benchmark system with precisely known pairwise interactions, we chose as the reference model a flexible version of the Extended Simple Point Charge (SPC/E) water model. Our analysis shows that while local representations are sufficient for predictions of the condensed liquid phase, the short-range nature of machine-learning models falls short in representing cluster and vapor phase properties. These findings provide an improved understanding of the role of long-range interactions in machine learning models and the regimes where they are necessary.

Assessment of the Tao-Mo nonempirical semilocal density functional in applications to solids and surfaces

Abstract: Recently, Tao and Mo developed a semilocal exchange-correlation density functional. The exchange part of this functional is derived from a density-matrix expansion corrected to reproduce the fourth-order gradient expansion of the exchange energy in the slowly-varying-density limit, while the correlation part is based on the Tao-Perdew-Staroverov-Scuseria (TPSS) correlation functional, with a modification for the low-density limit. In the present paper, the Tao-Mo (TM) functional is assessed by computing various properties of solids and jellium surfaces. This includes 22 lattice constants and bulk moduli, 30 band gaps, seven cohesive energies, and jellium surface exchange and correlation energies for the density parameter ${r}_{s}$ in the range from 2 to 3 bohr. Our calculations show that the TM approximation can yield consistently high accuracy for most properties considered here, with mean absolute errors (MAEs) of 0.025 \AA{} for lattice constants, 7.0 GPa for bulk moduli, 0.08 eV/atom for cohesive energies, and $35\phantom{\rule{0.16em}{0ex}}\mathrm{erg}/\mathrm{c}{\mathrm{m}}^{2}$ for surface exchange-correlation energies. The MAE in band gaps is larger than that of TPSS, but slightly smaller than the errors of the local spin-density approximation, Perdew-Burke-Ernzerhof generalized gradient approximation, and revised TPSS. However, band gaps are still underestimated, particularly for large-gap semiconductors, compared to the Heyd-Scuseria-Ernzerhof nonlocal screened hybrid functional.

Energy-gap reduction in heavily doped silicon: Causes and consequences

Abstract: The authors review briefly the existing theoretical treatments of the various effects that contribute to the reduction of the energy gap in heavily doped Si, namely electron-electron and electron-impurity interactions and the effect of disorder in the impurity distribution. They then turn to the longstanding question why energy-gap reductions extracted from three different types of experiments have persistently produced values with substantial discrepancies, making it impossible to compare with theoretical values. First, they demonstrate that a meaningful comparison between theory and experiment can indeed be made if theoretical calculations are carried out for actual quantities that experiments measure, e.g. luminescence spectra, as recently done by Selloni and Pantelides. Then, they demonstrate that, independent of any theoretical calculations, the optical absorption spectra are fully consistent with the luminescence spectra and that the discrepancies in the energy-gap reductions extracted from the two sets of spectra are caused entirely by the curve-fitting procedures used in analyzing optical-absorption data. Finally, they show explicitly that, as already believed by many authors, energy-gap reductions extracted from electrical measurements on transistors do not correspond to true gap reductions. They identify two corrections that must be added to the values extracted from the electrical data in order to arrive at the true gap reductions and show that the resulting values are in good overall agreement with luminescence and absorption data. They, therefore, demonstrate that the observed reduction in emitter injection efficiency in bipolar transistors is not strictly due to a gap reduction, as generally believed, but to three very different effects.

Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

Abstract: We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

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.