Repository of works by Caltech published authors.
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Preliminary Report on the 1995 Ridgecrest Earthquake Sequence in Eastern California - Hauksson, Egill; Hutton, Kate; Kanamori, Hiroo; Jones, Lucile; Mori, James; Hough, Susan; Roquemore, Glenn
The Ridgecrest earthquake sequence began on 17 August 1995 with a M_L 5.4 earthquake. As of October 3, 1995, the Southern California Seismic Network (SCSN) had recorded over 4,500 events in the sequence, with eight events of M ≥ 4.0. These earthquakes are occurring along the eastern edge of the Indian Wells Valley along a small stretch of the thoroughgoing Eastern California Shear Zone (ECSZ). Previous large events within the ECSZ include the 1992 (M_w 7.3) Landers earthquake sequence and the 1872 (M 7.6) Owens Valley earthquake. The only large earthquake to occur near Indian Wells Valle, was the 1946...
Crystal Structure of Invasin: A Bacterial Integrin-Binding Protein - Hamburger, Zsuzsa A.; Brown, Michele S.; Isberg, Ralph R.; Bjorkman, Pamela J.
The Yersinia pseudotuberculosis invasin protein promotes bacterial entry by binding to host cell integrins with higher affinity than natural substrates such as fibronectin. The 2.3 angstrom crystal structure of the invasin extracellular region reveals five domains that form a 180 angstrom rod with structural similarities to tandem fibronectin type III domains. The integrin-binding surfaces of invasin and fibronectin include similarly located key residues, but in the context of different folds and surface shapes. The structures of invasin and fibronectin provide an example of convergent evolution, in which invasin presents an optimized surface for integrin binding, in comparison with host substrates.
Stem-Cell Homeostasis and Growth Dynamics Can Be Uncoupled in the Arabidopsis Shoot Apex - Reddy, G. Venugopala; Meyerowitz, Elliot M.
The shoot apical meristem (SAM) is a collection of stem cells that resides at the tip of each shoot and provides the cells of the shoot. It is divided into functional regions. The central zone (CZ) at the tip of the meristem is the domain of expression of the CLAVATA3 (CLV3) gene, encoding a putative ligand for a transmembrane receptor kinase, CLAVATA1, active in cells of the rib meristem (RM), located just below the CZ. We show here that CLV3 restricts its own domain of expression (the CZ) by preventing differentiation of peripheral zone cells (PZ), which surround the CZ,...
A model for MRI contrast enhancement using T_1 agents - Ahrens, E. T.; Rothbächer, U.; Jacobs, R. E.; Fraser, S. E.
Contrast in MRI relies on differences in the local environment of water and is often enhanced by using contrast agents. We present a simple model for evaluating the minimal contrast agent concentration required to produce “satisfactory” contrast enhancement in magnetic resonance images. Previous strategies have been based largely on empirical results for specific systems. The present tissue contrast model (TCM) can be applied to “conventional,” targeted, or biochemically responsive agents. The model results are formulated so that only a small number of parameters are required to analyze a given scenario. The TCM is a particularly useful tool in the development...
Two-Dimensional Photonic Band-Gap Defect Mode Laser - Painter, O.; Lee, R. K.; Scherer, A.; Yariv, A.; O'Brien, J. D.; Dapkus, P. D.; Kim, I.
A laser cavity formed from a single defect in a two-dimensional photonic crystal is demonstrated. The optical microcavity consists of a half wavelength–thick waveguide for vertical confinement and a two-dimensional photonic crystal mirror for lateral localization. A defect in the photonic crystal is introduced to trap photons inside a volume of 2.5 cubic half-wavelengths, approximately 0.03 cubic micrometers. The laser is fabricated in the indium gallium arsenic phosphide material system, and optical gain is provided by strained quantum wells designed for a peak emission wavelength of 1.55 micrometers at room temperature. Pulsed lasing action has been observed at a wavelength...
Cracks Faster than the Shear Wave Speed - Rosakis, A. J.; Samudrala, O.; Coker, D.
Classical dynamic fracture theories predict the surface wave speed to be the limiting speed for propagation of in-plane cracks in homogeneous, linear elastic materials subjected to remote loading. This report presents experimental evidence to the contrary. Intersonic shear-dominated crack growth featuring shear shock waves was observed along weak planes in a brittle polyester resin under far-field asymmetric loading. When steady-state conditions were attained, the shear cracks propagated at speeds close to √2 times the material shear wave speed. These observations have similarities to shallow earthquake events where intersonic shear rupture speeds have been surmised.
Crystal Structure of Human ZAG, a Fat-Depleting Factor Related to MHC Molecules - Sánchez, Luis M.; Chirino, Arthur J.; Bjorkman, Pamela J.
Zn-α_2-glycoprotein (ZAG) is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain β_2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions.
Transcriptional Activation of APETALA1 by LEAFY - Wagner, Doris; Sablowski, Robert W. M.; Meyerowitz, Elliot M.
Plants produce new appendages reiteratively from groups of stem cells called shoot apical meristems. LEAFY (LFY) and APETALA1 (AP1) are pivotal for the switch to the reproductive phase, where instead of leaves the shoot apical meristem produces flowers. Use of steroid-inducible activation of LFY demonstrated that early expression of AP1 is a result of transcriptional induction by LFY. This AP1 induction is independent of protein synthesis and occurs specifically in the tissues and at the developmental stage in which floral fate is assumed. Later expression of AP1 appears to be only indirectly affected by LFY.
Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein - Tezcan, F. Akif; Kaiser, Jens T.; Mustafi, Debarshi; Walton, Mika Y.; Howard, James B.; Rees, Douglas C.
Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron...
Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor - Floriano, Wely B.; Vaidehi, Nagarajan; Goddard, William A., III; Singer, Michael S.; Shepherd, Gordon M.
The prevailing paradigm for G protein-coupled receptors is that each receptor is narrowly tuned to its ligand and closely related agonists. An outstanding problem is whether this paradigm applies to olfactory receptor (ORs), which is the largest gene family in the genome, in which each of 1,000 different G protein-coupled receptors is believed to interact with a range of different odor molecules from the many thousands that comprise “odor space.” Insights into how these interactions occur are essential for understanding the sense of smell. Key questions are: (i) Is there a binding pocket? (ii) Which amino acid residues in the...
Large libraries reveal diverse solutions to an RNA recognition problem - Barrick, Jeffrey E.; Takahashi, Terry T.; Ren, Jinsong; Xia, Tianbing; Roberts, Richard W.
RNA loops that adopt a characteristic GNRA “tetraloop” fold are common in natural RNAs. Here, we have used in vitro selection by means of mRNA-peptide fusions to select peptides that bind an example of this RNA loop motif. Starting with the RNA recognition domain from the λ N protein, we have constructed libraries containing 150, 1,600, and 9 trillion different peptide sequences as mRNA-peptide fusions and isolated those capable of high-affinity RNA binding. These selections have resulted in more than 80 different peptides that bind the same RNA loop. The highest affinity peptides exhibit low nanomolar dissociation constants as well...
Electron Tunneling Through Organic Molecules in Frozen Glasses - Wenger, Oliver S.; Leigh, Brian S.; Villahermosa, Randy M.; Gray, Harry B.; Winkler, Jay R.
Reaction rates extracted from measurements of donor luminescence quenching by randomly dispersed electron acceptors reveal an exponential decay constant of 1.23 per angstrom for electron tunneling through a frozen toluene glass (with a barrier to tunneling of 1.4 electron volts). The decay constant is 1.62 per angstrom (the barrier, 2.6 electron volts) in a frozen 2-methyl-tetrahydrofuran glass. Comparison to decay constants for tunneling across covalently linked xylyl (0.76 per angstrom) and alkyl (1.0 per angstrom) bridges leads to the conclusion that tunneling between solvent molecules separated by ∼2 angstroms (van der Waals contact) is 20 to 50 times slower than...
Protein deamidation - Robinson, Noah E.
A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically relevant phenomenon in a remarkably large percentage of proteins.
Nonharmonic phonons in α-iron at high temperatures - Mauger, L.; Lucas, M. S.; Muñoz, J. A.; Tracy, S. J.; Kresch, M.; Xiao, Yuming; Chow, Paul; Fultz, B.
Phonon densities of states (DOS) of bcc α−^(57)Fe were measured from room temperature through the 1044 K Curie transition and the 1185 K fcc γ-Fe phase transition using nuclear resonant inelastic x-ray scattering. At higher temperatures all phonons shift to lower energies (soften) with thermal expansion, but the low transverse modes soften especially rapidly above 700 K, showing strongly nonharmonic behavior that persists through the magnetic transition. Interatomic force constants for the bcc phase were obtained by iteratively fitting a Born–von Kármán model to the experimental phonon spectra using a genetic algorithm optimization. The second-nearest-neighbor fitted axial force constants weakened...
Peroxone chemistry: Formation of H_2O_3 and ring-(HO_2)(HO_3) from O_3/H_2O_2 - Xu, Xin; Goddard, William A., III
The recent observation [Wentworth, P., Jones, L. H., Wentworth, A. D., Zhu, X. Y., Larsen, N. A., Wilson, I. A., Xu, X., Goddard, W. A., Janda, K. D., Eschenmoser, A. & Lerner, R. A. (2001) Science 293, 1806–1811] that antibodies form H_2O_2 from ^1O_2 plus H_2O was explained in terms of the formation of the H_2O_3 species that in the antibody reacts with a second H_2O_3 to form H_2O_2. There have been few reports of the chemistry for forming H_2O_3, but recently Engdahl and Nelander [Engdahl, A. & Nelander, B. (2002) Science 295, 482–483] reported that photolysis of the ozone–hydrogen...
The gas phase reaction of singlet dioxygen with water: A water-catalyzed mechanism - Xu, Xin; Muller, Richard P.; Goddard, William A., III
Stimulated by the recent surprising results from Wentworth et al. [Wentworth, A. D., Jones, L. H., Wentworth, P., Janda, K. D. & Lerner, R. A. (2000) Proc. Natl. Acad. Sci. USA 97, 10930–10935] that Abs efficiently catalyze the conversion of molecular singlet oxygen (^1O_2) plus water to hydrogen peroxide (HOOH), we used quantum chemical methods (B3LYP density functional theory) to delineate the most plausible mechanisms for the observed efficient conversion of water to HOOH. We find two reasonable pathways. In Pathway I, (i) H_2O catalyzes the reaction of ^1O_2 with a second water to form HOOOH; (ii) two HOOOH form...
Electrolytic actuators: Alternative, high-performance, material-based devices - Cameron, Colin G.; Freund, Michael S.
The emerging field of materials-based actuation continues to be the focus of considerable research because of its inherent scalability and its promise to drive micromechanical devices that cannot be realized with conventional mechanical actuator strategies. The electrolytic phase transformation actuator offers a new broad-spectrum solution to the problem of direct conversion of electrical to mechanical energy. Strains of 136,000% and unoptimized work cycle efficiencies near 50% are demonstrated in a prototype device. Conceivably capable of generating stress beyond 200 MPa, this new approach promises performance orders of magnitude beyond other novel actuation strategies.
Laser Guide Star Adaptive Optics Imaging Polarimetry of Herbig Ae/Be Stars - Perrin, Marshall D.; Graham, James R.; Kalas, Paul; Lloyd, James P.; Max, Claire E.; Gavel, Donald T.; Pennington, Deanna M.; Gates, Elinor L.
We have used laser guide star adaptive optics and a near-infrared dual-channel imaging polarimeter to observe light scattered in the circumstellar environment of Herbig Ae/Be stars on scales of 100 to 300 astronomical units. We revealed a strongly polarized, biconical nebula 10 arc seconds (6000 astronomical units) in diameter around the star LkHα 198 and also observed a polarized jet-like feature associated with the deeply embedded source LkHα 198-IR. The star LkHα 233 presents a narrow, unpolarized dark lane consistent with an optically thick circumstellar disk blocking our direct view of the star. These data show that the lower-mass T...
Phosphatized Polar Lobe-Forming Embryos from the Precambrian of Southwest China - Chen, Jun-Yuan; Bottjer, David J.; Davidson, Eric H.; Dornbos, Stephen Q.; Gao, Xiang; Yang, Yong-Hua; Li, Chia-Wei; Li, Gang; Wang, Xiu-Qiang; Xian, Ding-Chang; Wu, Hung-Jen; Hwu, Yeu-Kuang; Tafforeau, Paul
In developing embryos of some extant spiralian animals, polar lobe formation is one of the symmetry-breaking mechanisms for segregation of maternal cytoplasmic substances to certain blastomeres and not others. Polar lobe formation leads to unique early cleavage morphologies that include trilobed, J-shaped, and five-lobed structures. Fossil embryos similar to modern lobeforming embryos are recognized from the Precambrian Doushantuo Formation phosphates, Weng'an, Guizhou Province, China. These embryos are abundant and form a developmental sequence comparable to different developing stages observed in lobe-forming embryos of extant spiralians. These data imply that lobe formation is an evolutionarily ancient process of embryonic specification.
The ATLAS^(3D) project – XXVII. Cold gas and the colours and ages of early-type galaxies - Young, Lisa M.; Scott, Nicholas; Serra, Paolo; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Cappellari, Michele; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; McDermid, Richard M.; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Weijmans, Anne-Marie
We present a study of the cold gas contents of the ATLAS^(3D) early-type galaxies, in the context of their optical colours, near-ultraviolet colours and Hβ absorption line strengths. Early-type (elliptical and lenticular) galaxies are not as gas poor as previously thought, and at least 40 per cent of local early-type galaxies are now known to contain molecular and/or atomic gas. This cold gas offers the opportunity to study recent galaxy evolution through the processes of cold gas acquisition, consumption (star formation) and removal. Molecular and atomic gas detection rates range from 10 to 34 per cent in red sequence early-type...