Miller Institute for Basic Research in Science

Berkeley, CA, United States

Miller Institute for Basic Research in Science

Berkeley, CA, United States
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Trevitt A.J.,Lawrence Berkeley National Laboratory | Trevitt A.J.,University of Wollongong | Goulay F.,Sandia National Laboratories | Taatjes C.A.,Sandia National Laboratories | And 3 more authors.
Journal of Physical Chemistry A | Year: 2010

Low-temperature rate coefficients are measured for the CN + benzene and CN + toluene reactions using the pulsed Laval nozzle expansion technique coupled with laser-induced fluorescence detection. The CN + benzene reaction rate coefficient at 105, 165, and 295 K is found to be relatively constant over this temperature range, (3.9-4.9) × 10 -10 cm 3 molecule -1 s -1. These rapid kinetics, along with the observed negligible temperature dependence, are consistent with a barrierless reaction entrance channel and reaction efficiencies approaching unity. The CN + toluene reaction is measured to have a rate coefficient of 1.3 × 10 -10 cm 3 molecule -1 s -1 at 105 K. At room, temperature, nonexponential decay profiles are observed for this reaction that may suggest significant back-dissociation of intermediate complexes. In separate experiments, the products of these reactions are probed at room temperature using synchrotron VUV photoionization mass spectrometry. For CN + benzene, cyanobenzene (C 6H 5CN) is the only product recorded with no detectable evidence for a C 6H 5 + HCN product channel. In the case of CN + toluene, cyanotoluene (NCC 6H 4CH 3) constitutes the only detected product. It is not possible to differentiate among the ortho, meta, and para isomers of cyanotoluene because of their similar ionization energies and the ∼40 me V photon energy resolution of the experiment. There is no significant detection of benzyl radicals (C 6H 5CH 2) that would suggest a H-abstraction or a HCN elimination channel is prominent at these conditions. As both reactions are measured to be rapid at 105 K, appearing to have barrierless entrance channels, it follows that they will proceed efficiently at the temperatures of Saturn's moon Titan (∼400 K) and are also likely to proceed at the temperature of interstellar clouds (10-20 K). © 2010 American Chemical Society.

Liu C.C.,University of California at Berkeley | Liu C.C.,Miller Institute for Basic Research in Science | Qi L.,University of California at Berkeley | Lucks J.B.,University of California at Berkeley | And 9 more authors.
Nature Methods | Year: 2012

Bacterial regulators of transcriptional elongation are versatile units for building custom genetic switches, as they control the expression of both coding and noncoding RNAs, act on multigene operons and can be predictably tethered into higher-order regulatory functions (a property called composability). Yet the less versatile bacterial regulators of translational initiation are substantially easier to engineer. To bypass this tradeoff, we have developed an adaptor that converts regulators of translational initiation into regulators of transcriptional elongation in Escherichia coli. We applied this adaptor to the construction of several transcriptional attenuators and activators, including a small molecule-triggered attenuator and a group of five mutually orthogonal riboregulators that we assembled into NOR gates of two, three or four RNA inputs. Continued application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex synthetic circuits. © 2012 Nature America, Inc. All rights reserved.

Qi L.,University of California at Berkeley | Lucks J.B.,University of California at Berkeley | Lucks J.B.,Miller Institute for Basic Research in Science | Lucks J.B.,Cornell University | And 6 more authors.
Nucleic Acids Research | Year: 2012

Non-coding RNAs (ncRNAs) are versatile regulators in cellular networks. While most trans-acting ncRNAs possess well-defined mechanisms that can regulate transcription or translation, they generally lack the ability to directly sense cellular signals. In this work, we describe a set of design principles for fusing ncRNAs to RNA aptamers to engineer allosteric RNA fusion molecules that modulate the activity of ncRNAs in a ligand-inducible way in Escherichia coli. We apply these principles to ncRNA regulators that can regulate translation (IS10 ncRNA) and transcription (pT181 ncRNA), and demonstrate that our design strategy exhibits high modularity between the aptamer ligand-sensing motif and the ncRNA target-recognition motif, which allows us to reconfigure these two motifs to engineer orthogonally acting fusion molecules that respond to different ligands and regulate different targets in the same cell. Finally, we show that the same ncRNA fused with different sensing domains results in a sensory-level NOR gate that integrates multiple input signals to perform genetic logic. These ligand-sensing ncRNA regulators provide useful tools to modulate the activity of structurally related families of ncRNAs, and building upon the growing body of RNA synthetic biology, our ability to design aptamer-ncRNA fusion molecules offers new ways to engineer ligand-sensing regulatory circuits.

Zhao J.,Fudan University | Zhao J.,University of California at Berkeley | Zhao J.,Miller Institute for Basic Research in Science | Rotundu C.R.,Lawrence Berkeley National Laboratory | And 8 more authors.
Physical Review Letters | Year: 2013

Magnetic correlations in isovalently doped Ba(Fe1-xRu x)2As2 (x=0.25, Tc=14.5 K; x=0.35, Tc=20 K) are studied by elastic and inelastic neutron scattering techniques. A relatively large superconducting spin gap accompanied by a weak resonance mode is observed in the superconducting state in both samples. In the normal state, the magnetic excitation intensity is dramatically reduced with increasing Ru doping toward the optimally doped regime. Our results favor that the weakening of the electron-electron correlations by Ru doping is responsible for the dampening of the resonance mode, as well as the suppression of the normal state antiferromagnetic correlations near the optimally doped regime in this system. © 2013 American Physical Society.

Haber L.H.,Lawrence Berkeley National Laboratory | Haber L.H.,Columbia University | Doughty B.,Lawrence Berkeley National Laboratory | Leone S.R.,Lawrence Berkeley National Laboratory | Leone S.R.,Miller Institute for Basic Research in Science
Molecular Physics | Year: 2010

Time-resolved anisotropy parameters and cross-section ratios of the positive and negative sidebands from two-colour two-photon above threshold ionization of helium atoms are measured using photoelectron velocity map imaging with the selected 19th high-order harmonic at 29.1 eV in an 810 nm perturbative dressing field. The intensities of both the sidebands and the single-photon ionization depletion follow a Gaussian correlation function where the photoelectron angular distributions and cross-section ratios of the sidebands do not change as a function of the temporal delay between the extreme ultraviolet and infrared pulses. The experimental results are compared with theoretical predictions using the soft-photon approximation, showing poor agreement, and analytical expressions are derived using second-order perturbation theory to determine the relative magnitudes of the resulting S and D partial waves of the above threshold ionization features. © 2010 Taylor & Francis.

Doughty B.,Lawrence Berkeley National Laboratory | Haber L.H.,Lawrence Berkeley National Laboratory | Haber L.H.,Columbia University | Hackett C.,Lawrence Berkeley National Laboratory | And 2 more authors.
Journal of Chemical Physics | Year: 2011

Photoelectron angular distributions (PADs) are obtained for a pair of 4s14p66p1 (a singlet and a triplet) autoionizing states in atomic krypton. A high-order harmonic pulse is used to excite the pair of states and a time-delayed 801 nm ionization pulse probes the PADs to the final 4s14p6 continuum with femtosecond time resolution. The ejected electrons are detected with velocity map imaging to retrieve the time-resolved photoelectron spectrum and PADs. The PAD for the triplet state is inherently separable by virtue of its longer autoionization lifetime. Measuring the total signal over time allows for the PADs to be extracted for both the singlet state and the triplet state. Anisotropy parameters for the triplet state are measured to be β2 = 0.55 ± 0.17 and β4 = -0.01 ± 0.10, while the singlet state yields β2 = 2.19 ± 0.18 and β4 = 1.84 ± 0.14. For the singlet state, the ratio of radial transition dipole matrix elements, X, of outgoing S to D partial waves and total phase shift difference between these waves, Δ , are determined to be X = 0.56± 0.08 andΔ = 2.19 ± 0.11 rad. The continuum quantum defect difference between the S and D electron partial waves is determined to be -0.15± 0.03 for the singlet state. Based on previous analyses, the triplet state is expected to have anisotropy parameters independent of electron kinetic energy and equal to β2 5/7 and β4 -12/7. Deviations from the predicted values are thought to be a result of state mixing by spin-orbit and configuration interactions in the intermediate and final states; theoretical calculations are required to quantify these effects. © 2011 American Institute of Physics.

Zhao J.,University of California at Berkeley | Zhao J.,Miller Institute for Basic Research in Science | Cao H.,Oak Ridge National Laboratory | Bourret-Courchesne E.,Lawrence Berkeley National Laboratory | And 3 more authors.
Physical Review Letters | Year: 2012

The recently discovered K-Fe-Se high-temperature superconductor has caused heated debate regarding the nature of its parent compound. Transport, angle-resolved photoemission spectroscopy, and STM measurements have suggested that its parent compound could be insulating, semiconducting, or even metallic. Because the magnetic ground states associated with these different phases have not yet been identified and the relationship between magnetism and superconductivity is not fully understood, the real parent compound of this system remains elusive. Here, we report neutron-diffraction experiments that reveal a semiconducting antiferromagnetic (AFM) phase with rhombus iron vacancy order. The magnetic order of the semiconducting phase is the same as the stripe AFM order of the iron pnictide parent compounds. Moreover, while the √5×√5 block AFM phase coexists with superconductivity, the stripe AFM order is suppressed by it. This leads us to conjecture that the new semiconducting magnetic ordered phase is the true parent phase of this superconductor. © 2012 American Physical Society.

Shekhawat A.,Lawrence Berkeley National Laboratory | Shekhawat A.,University of California at Berkeley | Shekhawat A.,Miller Institute for Basic Research in Science | Ritchie R.O.,Lawrence Berkeley National Laboratory | Ritchie R.O.,University of California at Berkeley
Nature Communications | Year: 2016

Pristine monocrystalline graphene is claimed to be the strongest material known with remarkable mechanical and electrical properties. However, graphene made with scalable fabrication techniques is polycrystalline and contains inherent nanoscale line and point defects - grain boundaries and grain-boundary triple junctions - that lead to significant statistical fluctuations in toughness and strength. These fluctuations become particularly pronounced for nanocrystalline graphene where the density of defects is high. Here we use large-scale simulation and continuum modelling to show that the statistical variation in toughness and strength can be understood with 'weakest-link' statistics. We develop the first statistical theory of toughness in polycrystalline graphene, and elucidate the nanoscale origins of the grain-size dependence of its strength and toughness. Our results should lead to more reliable graphene device design, and provide a framework to interpret experimental results in a broad class of two-dimensional materials. © 2016, NPG. All rights reserved.

Liu C.C.,University of California at Berkeley | Liu C.C.,Miller Institute for Basic Research in Science | Qi L.,University of California at Berkeley | Yanofsky C.,Stanford University | And 2 more authors.
Nature Biotechnology | Year: 2011

Small-molecule regulation of gene expression is intrinsic to cellular function and indispensable to the construction of new biological sensing, control and expression systems. However, there are currently only a handful of strategies for engineering such regulatory components and fewer still that can give rise to an arbitrarily large set of inducible systems whose members respond to different small molecules, display uniformity and modularity in their mechanisms of regulation, and combine to actuate universal logics. Here we present an approach for small-molecule regulation of transcription based on the combination of cis-regulatory leader-peptide elements with genetically encoded unnatural amino acids (amino acids that have been artificially added to the genetic code). In our system, any genetically encoded unnatural amino acid (UAA) can be used as a small-molecule attenuator or activator of gene transcription, and the logics intrinsic to the network defined by expanded genetic codes can be actuated. © 2011 Nature America, Inc. All rights reserved.

Ophus C.,Lawrence Berkeley National Laboratory | Shekhawat A.,Miller Institute for Basic Research in Science | Shekhawat A.,Lawrence Berkeley National Laboratory | Rasool H.,Lawrence Berkeley National Laboratory | And 3 more authors.
Physical Review B - Condensed Matter and Materials Physics | Year: 2015

We have characterized the structure of 176 different single-layer graphene grain boundaries grown with chemical vapor deposition using >1000 experimental high-resolution transmission electron microscopy images using a semiautomated structure processing routine. We introduce an algorithm for generating grain boundary structures for a class of hexagonal two-dimensional materials and use this algorithm and molecular dynamics to simulate the structure of >79000 linear graphene grain boundaries covering 4122 unique orientations distributed over the entire parameter space. The dislocation content and structural properties are extracted from all experimental and simulated boundaries, and various trends are explored. We find excellent agreement between the simulated and experimentally observed grain boundaries. Our analysis demonstrates the power of a statistically significant number of measurements as opposed to a small number of observations in atomic science. © 2015 American Physical Society.

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