Expanding the Repertoire of Natural Product-Inspired Ring Pairs for Molecular Recognition of DNA

A furan amino acid, inspired by the recently discovered proximicin natural products, was incorporated into the scaffold of a DNA-binding hairpin polyamide. While unpaired oligomers of 2,4-disubstituted furan amino acids show poor DNA-binding activity, furan (Fn) carboxamides paired with N-methylpyrrole (Py) and N-methylimidazole (Im) rings demonstrate excellent stabilization of duplex DNA as well as discrimination of noncognate sequences, consistent with function as a Py mimic according to the Py/Im polyamide pairing rules

Effects of Magnetic Order on the Upper Critical Field of UPt3_3

I present a Ginzburg-Landau theory for hexagonal oscillations of the upper critical field of UPt$_3$ near $T_c$. The model is based on a $2D$ representation for the superconducting order parameter, $\vec{\eta}=(\eta_1,\eta_2)$, coupled to an in-plane AFM order parameter, $\vec{m}_s$. Hexagonal anisotropy of $H_{c2}$ arises from the weak in-plane anisotropy energy of the AFM state and the coupling of the superconducting order parameter to the staggered field. The model explains the important features of the observed hexagonal anisotropy [N. Keller, {\it et al.}, Phys. Rev. Lett. {\bf 73}, 2364 (1994).] including: (i) the small magnitude, (ii) persistence of the oscillations for $T\rightarrow T_c$, and (iii) the change in sign of the oscillations for $T> T^{*}$ and $T< T^{*}$ (the temperature at the tetracritical point). I also show that there is a low-field crossover (observable only very near $T_c$) below which the oscillations should vanish.Comment: 9 pages in a RevTex (3.0) file plus 2 postscript figures (uuencoded). Submitted to Physical Review B (December 20, 1994)

Quantization of Superflow Circulation and Magnetic Flux with a Tunable Offset

Quantization of superflow-circulation and of magnetic-flux are considered for systems, such as superfluid $^3$He-A and unconventional superconductors, having nonscalar order parameters. The circulation is shown to be the anholonomy in the parallel transport of the order parameter. For multiply-connected samples free of distributed vorticity, circulation and flux are predicted to be quantized, but generically to nonintegral values that are tunably offset from integers. This amounts to a version of Aharonov-Bohm physics. Experimental settings for testing these issues are discussed.Comment: 5 two-column pages, ReVTeX, figure available upon request (to [email protected]

BCS and generalized BCS superconductivity in relativistic quantum field theory. I. formulation

We investigate the BCS and generalized BCS theories in the relativistic quantum field theory. We select the gauge freedom as U(1), and introduce a BCS-type effective attractive interaction. After introducing the Gor'kov formalism and performing the group theoretical consideration of the mean fields, we solve the relativistic Gor'kov equation and obtain the Green's functions in analytical forms. We obtain various types of gap equations.Comment: 31 page

The Nonlinear Meissner Effect in Unconventional Superconductors

We examine the long-wavelength current response in anisotropic superconductors and show how the field-dependence of the Meissner penetration length can be used to detect the structure of the order parameter. Nodes in the excitation gap lead to a nonlinear current-velocity constitutive equation at low temperatures which is distinct for each symmetry class of the order parameter. The effective Meissner penetration length is linear in $H$ and exhibits a characteristic anisotropy for fields in the $ab$-plane that is determined by the positions of the nodes in momentum space. The nonlinear current-velocity relation also leads to an intrinsic magnetic torque for in-plane fields that are not parallel to a nodal or antinodal direction. The torque scales as $H^3$ for $T\rightarrow 0$ and has a characteristic angular dependence. We analyze the effects of thermal excitations, impurity scattering and geometry on the current response of a $d_{x^2-y^2}$ superconductor, and discuss our results in light of recent measurements of the low-temperature penetration length and in-plane magnetization of single-crystals of $YBa_2Cu_3O_{7-\delta}$ and $LuBa_2Cu_3O_{7-\delta}$.Comment: 30 pages, RevTeX file with 16 postscript figures. Submitted to Phys. Rev.

Infrared Conductivity in Layered dd-wave Superconductors

We calculate the infrared conductivity of a stack of coupled, two-dimensional superconducting planes within the Fermi liquid theory of superconductivity. We include the effects of random scattering processes and show that the presence of even a small concentration of resonant impurities, in a $d$-wave superconductor, has an important effect on both the in-plane and $c$-axis transport properties, which could serve as signatures for $d$-wave pairing.Comment: 18 pages in a RevTex (3.0) file plus 5 postscript figures (uuencoded). Replaced with minor changes as it will appear in the Physical Review B {\bf 52} issue 1 Oct. 199

Criticality and Superfluidity in liquid He-4 under Nonequilibrium Conditions

We review a striking array of recent experiments, and their theoretical interpretations, on the superfluid transition in $^4$He in the presence of a heat flux, $Q$. We define and evaluate a new set of critical point exponents. The statics and dynamics of the superfluid-normal interface are discussed, with special attention to the role of gravity. If $Q$ is in the same direction as gravity, a self-organized state can arise, in which the entire sample has a uniform reduced temperature, on either the normal or superfluid side of the transition. Finally, we review recent theory and experiment regarding the heat capacity at constant $Q$. The excitement that surrounds this field arises from the fact that advanced thermometry and the future availability of a microgravity experimental platform aboard the International Space Station will soon open to experimental exploration decades of reduced temperature that were previously inaccessible.Comment: 16 pages, 9 figures, plus harvard.sty style file for references Accepted for publication in Colloquia section of Reviews of Modern Physic

Minimal Cooling of Neutron Stars: A New Paradigm

A new classification of neutron star cooling scenarios, involving either ``minimal'' cooling or ``enhanced'' cooling is proposed. The minimal cooling scenario replaces and extends the so-called standard cooling scenario to include neutrino emission from the Cooper pair breaking and formation process. This emission dominates that due to the modified Urca process for temperatures close to the critical temperature for superfluid pairing. Minimal cooling is distinguished from enhanced cooling by the absence of neutrino emission from any direct Urca process, due either to nucleons or to exotica. Within the minimal cooling scenario, theoretical cooling models can be considered to be a four parameter family involving the equation of state of dense matter, superfluid properties of dense matter, the composition of the neutron star envelope, and the mass of the neutron star. Consequences of minimal cooling are explored through extensive variations of these parameters. Results are compared with the inferred properties of thermally-emitting neutron stars in order to ascertain if enhanced cooling occurs in any of them. All stars for which thermal emissions have been clearly detected are at least marginally consistent with the lack of enhanced cooling. The two pulsars PSR 0833-45 (Vela) and PSR 1706-44 would require enhanced cooling in case their ages and/or temperatures are on the lower side of their estimated values whereas the four stars PSR 0656+14, PSR 1055-52, Geminga, and RX J0720.4-3125 may require some source of internal heating in case their age and/or luminosity are on the upper side of their estimated values. The new upper limits on the thermal luminosity of PSR J0205+6449 and RX J0007.0+7302 are indicative of the occurrence of some enhanced neutrino emission beyond the minimal scenario.Comment: Version to appear in ApJ Supplements. Minor modifications in text and discussion of updated data with new figure

Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing

Genomic applications of DNA-binding molecules require an unbiased knowledge of their high affinity sites. We report the high-throughput analysis of pyrrole-imidazole polyamide DNA-binding specificity in a 10^(12)-member DNA sequence library using affinity purification coupled with massively parallel sequencing. We find that even within this broad context, the canonical pairing rules are remarkably predictive of polyamide DNA-binding specificity. However, this approach also allows identification of unanticipated high affinity DNA-binding sites in the reverse orientation for polyamides containing β/Im pairs. These insights allow the redesign of hairpin polyamides with different turn units capable of distinguishing 5′-WCGCGW-3′ from 5′-WGCGCW-3′. Overall, this study displays the power of high-throughput methods to aid the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinning for biological and nanotechnological applications