Richard J. Saykally

Bio: Richard J. Saykally is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Spectroscopy & Absorption spectroscopy. The author has an hindex of 94, co-authored 457 publications receiving 40997 citations. Previous affiliations of Richard J. Saykally include University of California & Lawrence Berkeley National Laboratory.

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. II. (H2O)2

Abstract: Terahertz laser VRT spectra of the water dimer consisting of 731 transitions measured with an average precision of 2 MHz and involving four (D2O)2 intermolecular vibrations (one previously published) have been measured between 65 and 104 cm−1. The precisely determined energy level patterns differ both qualitatively and quantitatively from the predictions of several dimer potentials tested, and reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by standard normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. Particularly, the 83 cm−1 (acceptor wag) and 90 cm−1 (D2O)2 (acceptor twist) vibrations interact through a Coriolis perturbation. These spectra provide the basis for our recent determination of the water pair potential. The corresponding data set for (H2O)2 is presented in an accompanying paper.

Infrared Cavity Ringdown Spectroscopy of the Water Cluster Bending Vibrations

Abstract: We report the first measurement of water monomer bending vibrations in gaseous (H2O)n clusters. Infrared cavity ringdown spectroscopy reveals discrete and sequentially blue-shifted bands near 6 μm for n = 2−4 and unresolved broad features for n > 4, supporting both theoretical predictions and solid-state spectroscopy results. These measurements provide a measure of the monomer distortion that accompanies sequential hydrogen bond formation, which will be valuable for the construction of potential energy surfaces for describing water.

Simulated infrared emission spectra of highly excited polyatomic molecules: a detailed model of the PAH-UIR hypothesis.

Abstract: A detailed description of the polycyclic aromatic hydrocarbon (PAH)/unidentified infrared band (UIR) mechanism is presented in which experimental spectral bandshape functions are used to simulate IR emission spectra for individual molecules. These spectra are additively superimposed to produce a conglomerate spectrum representative of a family of PAH molecules. Ab initio vibrational frequencies and intensities for nine PAHs (neutral and cationic) as large as ovalene are used in conjunction with measured bandshape and temperature-dependent redshift data to simulate the UIR bands. The calculated spectra of cations provide a closer match to the UIRs than do those of the neutrals. However, the PAH cations used in the simulations fail to reproduce the details of the UIR emission spectra. The discrepancies are potentially alleviated if both larger PAHs and a greater number of PAHs were included in the simulation.

Infrared cavity ringdown spectroscopy of methanol clusters: Single donor hydrogen bonding

Abstract: Infrared cavity ringdown laser absorption spectroscopy has been used to study the O–H stretching vibrations of jet-cooled methanol clusters in direct absorption. Rovibrational bands for (CH3OH)2, (CH3OH)3, and (CH3OH)4 have been measured. Both bonded and free O–H stretches were measured for the dimer, indicating that its structure is linear. Five bands were assigned to the methanol trimer, indicating the presence of a second cyclic isomer in the molecular beam. A detailed study of the free O–H stretching region shows that methanol clusters larger than dimer must exist in cyclic ring configurations. In order to facilitate spectral assignment, harmonic frequencies and infrared intensities were calculated for the methanol monomer, dimer, and trimer with second order Mo/ller–Plesset perturbation theory. Using the theoretical infrared intensities and measured vibrational band absorptions, absolute cluster concentrations were calculated. Results agree with previous experimental and theoretical work.

Investigation of volatile liquid surfaces by synchrotron x-ray spectroscopy of liquid microjets

Abstract: Soft x-ray absorption spectroscopy is a powerful probe of surface electronic and geometric structure in metals, semiconductors, and thin films. Because these techniques generally require ultrahigh vacuum, corresponding studies of volatile liquid surfaces have hitherto been precluded. We describe the design and implementation of an x-ray experiment based on the use of liquid microjets, permitting the study of volatile liquid surfaces under quasi-equilibrium conditions by synchrotron-based spectroscopy. The liquid microjet temperatures are also characterized by Raman spectroscopy, which connects our structural studies with those conducted on liquid samples under equilibrium conditions. In recent experiments, we have observed and quantified the intermolecular surface relaxation of liquid water and methanol and have identified a large population of “acceptor-only” molecules at the liquid water interface.

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.

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。

The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment

Abstract: The optical properties of metal nanoparticles have long been of interest in physical chemistry, starting with Faraday's investigations of colloidal gold in the middle 1800s. More recently, new lithographic techniques as well as improvements to classical wet chemistry methods have made it possible to synthesize noble metal nanoparticles with a wide range of sizes, shapes, and dielectric environments. In this feature article, we describe recent progress in the theory of nanoparticle optical properties, particularly methods for solving Maxwell's equations for light scattering from particles of arbitrary shape in a complex environment. Included is a description of the qualitative features of dipole and quadrupole plasmon resonances for spherical particles; a discussion of analytical and numerical methods for calculating extinction and scattering cross-sections, local fields, and other optical properties for nonspherical particles; and a survey of applications to problems of recent interest involving triangula...

Dye-Sensitized Solar Cells

Abstract: Dye-sensitized solar cells (DSCs) offer the possibilities to design solar cells with a large flexibility in shape, color, and transparency. DSC research groups have been established around the worl ...

Quantum Dot Bioconjugates for Ultrasensitive Nonisotopic Detection

Abstract: Highly luminescent semiconductor quantum dots (zinc sulfide-capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection. In comparison with organic dyes such as rhodamine, this class of luminescent labels is 20 times as bright, 100 times as stable against photobleaching, and one-third as wide in spectral linewidth. These nanometer-sized conjugates are water-soluble and biocompatible. Quantum dots that were labeled with the protein transferrin underwent receptor-mediated endocytosis in cultured HeLa cells, and those dots that were labeled with immunomolecules recognized specific antibodies or antigens.