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.

Canonical Statistical Averages of Coupled Quantum-Classical Systems

Abstract: We study the thermal-equilibrium distribution generated by a Nose-Hoover thermostat coupled to a mixed quantum-classical system, whose time evolution is taken to be either Ehrenfest (E), or Car-Parrinello (CP) type. It is found that neither E or CP dynamics lead to the correct averages for the quantum subsystem. A new classical modified CP dynamics is introduced which mimics the level quantization and yield the correct quantum averages after a suitable reweighting of the trajectories. We support our theoretical formulation with numerical simulations on a simple model system.

Momentum distribution, vibrational dynamics, and the potential of mean force in ice

Abstract: By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasiharmonic context, anharmonicity in the ground-state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.

Quantization of the dipole moment and of the end charges in push-pull polymers.

Abstract: A theorem for end-charge quantization in quasi-one-dimensional stereoregular chains is formulated and proved. It is a direct analog of the well-known theorem for surface charges in physics. The theorem states the following: (1) Regardless of the end groups, in stereoregular oligomers with a centrosymmetric bulk, the end charges can only be a multiple of 1∕2 and the longitudinal dipole moment per monomer p can only be a multiple of 1∕2 times the unit length a in the limit of long chains. (2) In oligomers with a noncentrosymmetric bulk, the end charges can assume any value set by the nature of the bulk. Nonetheless, by modifying the end groups, one can only change the end charge by an integer and the dipole moment p by an integer multiple of the unit length a. (3) When the entire bulk part of the system is modified, the end charges may change in an arbitrary way; however, if upon such a modification the system remains centrosymmetric, the end charges can only change by multiples of 1∕2 as a direct consequen...

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.