Repository of works by Caltech published authors.
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Radio and optical connected - Helou, George
With instruments of striking diversity and
precision, observational cosmologists
translate the whispers of distant galaxies
into clues to cosmic history. But the same
corner of Universe is not often probed
with more than one instrument, so we are
left to piece together that history like the
proverbial blind men examining an
elephant. When two probes do intersect,
the result is something akin to a Rosetta
Stone, where observations at various
wavelengths can be woven together to
yield a hitherto unseen picture.
C. elegans lin-45 raf gene participates in let-60 ras-stimulated vulval differentiation - Han, Min; Golden, Andy; Han, Yuming; Sternberg, Paul W.
Vulval differentiation in Caenorhabditis elegans is controlled by intercellular signalling mediated by a receptor tyrosine kinase and a ras gene product. The lin-45 gene encodes a homologue of the raf family of serine/threonine kinases and is necessary for vulval differentiation. The lin-45 raf gene product appears to act downstream of the ras protein in this pathway. A proto-oncogene-mediated signalling pathway may be a common feature of metazoan development.
Multiple intercellular signalling systems control the development of the Caenorhabditis elegans vulva - Horvitz, H. Robert; Sternberg, Paul W.
Developmental, genetic and molecular studies indicate that multiple intercellular signalling systems interact to specify the types and spatial patterns of cells generated during the formation of the vulva of the nematode Caenorhabditis elegans. Two classes of evolutionary conserved transmembrane receptors and a Ras protein function in these signalling systems. The biology of vulval development provides a framework for understanding how cell interactions control the development of animals as diverse as nematodes, insects and mammals.
Nonlinear resonances and energy transfer in finite granular chains - Lydon, Joseph; Theocharis, Georgios; Daraio, Chiara
In the present work we test experimentally and compute numerically the stability and dynamics of harmonically driven monoatomic granular chains composed of an increasing number of particles N(N=1-50). In particular, we investigate the inherent effects of dissipation and finite size on the evolution of bifurcation instabilities in the statically compressed case. The findings of the study suggest that the nonlinear bifurcation phenomena, which arise due to finite size, can be useful for efficient energy transfer away from the drive frequency in transmitted waves.
Optimizing the oxygen evolution reaction for electrochemical water oxidation by tuning solvent properties - Fortunelli, Alessandro; Goddard, William A., III; Sementa, Luca; Barcaro, Giovanni
Electrochemical water-based energy cycles provide a most promising alternative to fossil-fuel sources of energy. However, current electrocatalysts are not adequate (high overpotential, lack of selectivity toward O_2 production, catalyst degradation). We propose here mechanistic guidelines for experimental examination of modified catalysts based on the dependence of kinetic rates on the solvent dielectric constant. To illustrate the procedure we consider the fcc(111) platinum surface and show that the individual steps for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) change systematically with the polarizability of the medium. Thus changing this environmental variable can be used to tune the rate...
Crowdsourced earthquake early warning - Minson, Sarah E.; Brooks, Benjamin A.; Glennie, Craig L.; Murray, Jessica R.; Langbein, John O.; Owen, Susan E.; Heaton, Thomas H.; Iannucci, Robert A.; Hauser, Darren L.
Earthquake early warning (EEW) can reduce harm to people and infrastructure from earthquakes and tsunamis, but it has not been implemented in most high earthquake-risk regions because of prohibitive cost. Common consumer devices such as smartphones contain low-cost versions of the sensors used in EEW. Although less accurate than scientific-grade instruments, these sensors are globally ubiquitous. Through controlled tests of consumer devices, simulation of an M_w (moment magnitude) 7 earthquake on California’s Hayward fault, and real data from the M_w 9 Tohoku-oki earthquake, we demonstrate that EEW could be achieved via crowdsourcing.
Celebrating Soft Matter's 10th Anniversary: Chain configuration and rate-dependent mechanical properties in transient networks - Sing, Michelle K.; Wang, Zhen-Gang; McKinley, Gareth H.; Olsen, Bradley D.
Numerical solution of a coupled set of Smoluchowski convection-diffusion equations of associating polymers modelled as finitely extensible dumbbells enables computation of time-dependent end-to-end distributions for bridged, dangling, and looped chains in three dimensions as a function of associating end-group kinetics. Non-monotonic flow curves which can lead to flow instabilities during shear flow result at low equilibrium constant and high association rate from two complementary phenomena: a decrease in the fraction of elastically active chains with increasing shear rate and non-monotonic extension in the population of elastically active chains. Chain tumbling leads to reformation of bridges, resulting in an increased fraction...
The co-crystal of TNT/CL-20 leads to decreased sensitivity toward thermal decomposition from first principles based reactive molecular dynamics - Guo, Dezhou; An, Qi; Zybin, Sergey V.; Goddard, William A., III; Huang, Fenglei; Tang, Bin
To gain an atomistic-level understanding of the experimental observation that the cocrystal TNT/CL-20 leads to decreased sensitivity, we carried out reactive molecular dynamics (RMD) simulations using the ReaxFF reactive force field. We compared the thermal decomposition of the TNT/CL-20 cocrystal with that of pure crystals of TNT and CL-20 and with a simple physical mixture of TNT and CL-20. We find that cocrystal has a lower decomposition rate than CL-20 but higher than TNT, which is consistent with experimental observation. We find that the formation of carbon clusters arising from TNT, a carbon-rich molecule, plays an important role in the...
Building better oscillators using nonlinear dynamics and pattern formation - Cross, M. C.; Kenig, Eyal; Allen, John-Mark A.
Frequency and time references play an essential role in modern technology and in living systems. The precision of self-sustained oscillations is limited by the effects of noise, which becomes evermore important as the sizes of the devices become smaller. In this paper, we review our recent theoretical results on using nonlinear dynamics and pattern formation to reduce the effects of noise and improve the frequency precision of oscillators, with particular reference to ongoing experiments on oscillators based on nanomechanical resonators. We discuss using resonator nonlinearity, novel oscillator architectures and the synchronization of arrays of oscillators, to improve the frequency precision.
Optofluidic ultrahigh-throughput detection of fluorescent drops - Kim, Minkyu; Pan, Ming; Gai, Ya; Pang, Shuo; Han, Chao; Yang, Changhuei; Tang, Sindy K. Y.
This paper describes an optofluidic droplet interrogation device capable of counting fluorescent drops at a throughput of 254000 drops per second. To our knowledge, this rate is the highest interrogation rate published thus far. Our device consists of 16 parallel microfluidic channels bonded directly to a filter-coated two-dimensional Complementary Metal-Oxide-Semiconductor (CMOS) sensor array. Fluorescence signals emitted from the drops are collected by the sensor that forms the bottom of the channel. The proximity of the drops to the sensor facilitates efficient collection of fluorescence emission from the drops, and overcomes the trade-off between light collection efficiency and field of view...
Photonic quasicrystal nanopatterned silicon thin film for photovoltaic applications - Ren, H.; Du, Q. G.; Ren, F.; Png, C. E.
In this paper, the authors numerically studied the optical properties of a silicon photonic quasicrystal (PQC) nanohole array for photovoltaic applications. With the same active layer thickness, the ultimate efficiency of a solar cell integrated with an optimized PQC nanohole array can be enhanced by 9.01% and 1.40% compared to that with an ordered square lattice of a nanohole array and a random nanohole array, respectively. The absorptance enhancement is mainly due to the higher-order rotational symmetry in PQC structures, which leads to the presence of additional resonant modes, the broadening of existing modes and the reduction of surface reflectance....
Numerical detection of symmetry-enriched topological phases with space-group symmetry - Wang, Ling; Essin, Andrew; Hermele, Michael; Motrunich, Olexei
Topologically ordered phases of matter, in particular so-called symmetry-enriched topological phases, can exhibit quantum number fractionalization in the presence of global symmetry. In Z_2 topologically ordered states in two dimensions, fundamental translations T_x and T_y acting on anyons can either commute or anticommute. This property, crystal momentum fractionalization, can be seen in a periodicity of the excited-state spectrum in the Brillouin zone. We present a numerical method to detect the presence of this form of symmetry enrichment given a projected entangled pair state; we study the minima of the spectrum of correlation lengths of the transfer matrix for a cylinder....
Insights into gas heating and cooling in the disc of NGC 891 from Herschel far-infrared spectroscopy - Hughes, T. M.; Foyle, K.; Schirm, M. R. P.; Parkin, T. J.; De Looze, I.; Wilson, C. D.; Bendo, G. J.; Baes, M.; Fritz, J.; Boselli, A.; Cooray, A.; Cormier, D.; Karczewski, O. Ł.; Lebouteiller, V.; Lu, N.; Madden, S. C.; Spinoglio, L.; Viaene, S.
We present Herschel PACS and SPIRE spectroscopy of the most important far-infrared cooling lines in the nearby, edge-on spiral galaxy, NGC 891: [Cii] 158 μm, [Nii] 122, 205 μm, [Oi] 63, 145 μm, and [Oiii] 88 μm. We find that the photoelectric heating efficiency of the gas, traced via the ([Cii]+[Oi]63)/FTIR ratio, varies from a mean of 3.5 × 10^(-3) in the centre up to 8 × 10^(-3) at increasing radial and vertical distances in the disc. A decrease in ([Cii]+[Oi]63)/F_(TIR) but constant ([Cii]+[Oi]63)/F_(PAH) with increasing FIR colour suggests that polycyclic aromatic hydrocarbons (PAHs) may become important for gas heating...
Crystal chemical constraints on inter-mineral Fe isotope fractionation and implications for Fe isotope disequilibrium in San Carlos mantle xenoliths - Macris, Catherine A.; Manning, Craig E.; Young, Edward D.
The origin of variations in iron isotope compositions of mantle minerals is uncertain, and predictions of equilibrium inter-mineral iron isotope fractionation conflict. This hinders interpretation of the petrologic and geochemical implications of Fe isotope data from mantle lithologies. To address this, we present a revised ionic model for predicting equilibrium iron isotope fractionation between mantle minerals and use it to interpret measured inter-mineral iron isotopic fractionation from five distinct mantle xenolith lithologies from San Carlos, Arizona. The samples represent a broad range of modal abundances and include lherzolite, harzburgite, dunite, clinopyroxenite, and websterite. The xenoliths exhibit Fe-isotopic variation between minerals...
Gravitational lensing by spinning black holes in astrophysics, and in the movie Interstellar - James, Oliver; von Tunzelmann, Eugénie; Franklin, Paul; Thorne, Kip S.
Interstellar is the first Hollywood movie to attempt depicting a black hole as it would actually be seen by somebody nearby. For this, our team at Double Negative Visual Effects, in collaboration with physicist Kip Thorne, developed a code called Double Negative Gravitational Renderer (DNGR) to solve the equations for ray-bundle (light-beam) propagation through the curved spacetime of a spinning (Kerr) black hole, and to render IMAX-quality, rapidly changing images. Our ray-bundle techniques were crucial for achieving IMAX-quality smoothness without flickering; and they differ from physicists' image-generation techniques (which generally rely on individual light rays rather than ray bundles), and...
Combined ^(40)Ar/^(39)Ar and (U–Th)/He geochronological constraints on long-term landscape evolution of the Second Paraná Plateau and its ruiniform surface features, Paraná, Brazil - Riffel, Silvana B.; Vasconcelos, Paulo M.; Carmo, Isabela O.; Farley, Kenneth A.
Regional correlation of dated weathered land surfaces provides the necessary constraints to test long-term continental landscape evolution models, but major challenges remain in properly dating these surfaces. The geomorphological province of Second Paraná Plateau, Paraná State, Brazil, is a high elevation (ca. 800 m) land surface characterized by widely distributed deep saprolites and scattered lateritic profiles (e.g., Vila Velha and Serra das Almas). Prolonged exposure to weathering and erosion has promoted the pseudo-karstic and ruiniform features that are characteristic of this landscape. In this study, ^(40)Ar/^(39)Ar laser incremental heating geochronology on 22 grains of supergene Mn oxyhydroxides from lateritic profiles...
Unified Structural Representation of the southern California crust and upper mantle - Shaw, John H.; Plesch, Andreas; Tape, Carl; Suess, M. Peter; Jordan, Thomas H.; Ely, Geoffrey; Hauksson, Egill; Tromp, Jeroen; Tanimoto, Toshiro; Graves, Robert; Olsen, Kim; Nicholson, Craig; Maechling, Philip J.; Rivero, Carlos; Lovely, Peter; Brankman, Charles M.; Munster, Jason
We present a new, 3D description of crust and upper mantle velocity structure in southern California implemented as a Unified Structural Representation (USR). The USR is comprised of detailed basin velocity descriptions that are based on tens of thousands of direct velocity (Vp, Vs) measurements and incorporates the locations and displacement of major fault zones that influence basin structure. These basin descriptions were used to developed tomographic models of crust and upper mantle velocity and density structure, which were subsequently iterated and improved using 3D waveform adjoint tomography. A geotechnical layer (GTL) based on Vs30 measurements and consistent with the...
Nearly extremal apparent horizons in simulations of merging black holes - Lovelace, Geoffrey; Scheel, Mark A.; Owen, Robert; Giesler, Matthew; Katebi, Reza; Szilágyi, Béla; Chu, Tony; Demos, Nicholas; Hemberger, Daniel A.; Kidder, Lawrence E.; Pfeiffer, Harald P.; Afshari, Nousha
The spin angular momentum S of an isolated Kerr black hole is bounded by the surface area A of its apparent horizon: 8πS ≤ A, with equality for extremal black holes. In this paper, we explore the extremality of individual and common apparent horizons for merging, rapidly spinning binary black holes. We consider simulations of merging black holes with equal masses M and initial spin angular momenta aligned with the orbital angular momentum, including new simulations with spin magnitudes up to S/M^2 = 0.994. We measure the area and (using approximate Killing vectors) the spin on the individual and common...
Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation - Strobel, Scott A.; Dervan, Peter B.
Physical mapping of chromosomes would be facilitated by methods of breaking large DNA into manageable fragments, or cutting uniquely at genetic markers of interest. Key issues in the design of sequence-specific DNA cleaving reagents are the specificity of binding, the generalizability of the recognition motif, and the cleavage yield. Oligonucleotide-directed triple helix formation is a generalizable motif for specific binding to sequences longer than 12 base pairs within DNA of high complexity. Studies with plasmid DNA show that triple helix formation can limit the operational specificity of restriction enzymes to endonu-clease recognition sequences that overlap oligonucleotide-binding sites. Triple helix formation,...
Gene Ontology Consortium: going forward - Blake, J. A.; Chan, J.; Kishore, R.; Sternberg, P. W.; Van Auken, K.; Müller, H. M.; Done, J.; Li, Y.
The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we...