Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage), to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least) two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the J-factor for looping

Optimized Boundary Conditions and Data Assimilation with Application to the M-2 Tide in the Yellow Sea

An optimization approach is derived for assimilating tidal height information along the open boundaries of a numerical model. The approach is then extended so that similar data along transects inside a model domain can also be optimally assimilated. To test the application of such an optimized methodology, M-2 tidal simulations were conducted with a numerical ocean model of the Yellow Sea, an area with a strong tidal influence. The use of the optimized open boundary conditions and internal data assimilation leads to a significant improvement of the predictive skill of the model. Average errors can be reduced by up to 75% when compared to nonoptimized boundary conditions

Influence of oxygen ordering kinetics on Raman and optical response in YBa_2Cu_3O_{6.4}

Kinetics of the optical and Raman response in YBa_2Cu_3O_{6.4} were studied during room temperature annealing following heat treatment. The superconducting T_c, dc resistivity, and low-energy optical conductivity recover slowly, implying a long relaxation time for the carrier density. Short relaxation times are observed for the B_{1g} Raman scattering -- magnetic, continuum, and phonon -- and the charge transfer band. Monte Carlo simulations suggest that these two relaxation rates are related to two length scales corresponding to local oxygen ordering (fast) and long chain and twin formation (slow).Comment: REVTeX, 3 pages + 4 PostScript (compressed) figure

Reply to Comment on:"Nonmonotonic d_{x^2-y^2} Superconducting Order Parameter in Nd_{2-x}Ce_xCuO_4"

We confirm that all the results of scanning SQUID, tunneling, ARPES, penetration depth and Raman experiments are consistent with a nonmonotonic d_{x^2-y^2} superconducting order parameter proposed in Phys. Rev. Lett., 88, 107002 (2002).Comment: Reply to Comment by F. Venturini, R. Hackl, and U. Michelucci cond-mat/020541

Constant effective mass across the phase diagram of high-Tc_{c} cuprates

We investigate the hole dynamics in two prototypical high temperature superconducting systems: La$_{2-x}$Sr$_{x}$CuO$_{4}$ and YBa$_{2}$Cu$_{3}$O$_{y}$ using a combination of DC transport and infrared spectroscopy. By exploring the effective spectral weight obtained with optics in conjunction with DC Hall results we find that the transition to the Mott insulating state in these systems is of the "vanishing carrier number" type since we observe no substantial enhancement of the mass as one proceeds to undoped phases. Further, the effective mass remains constant across the entire underdoped regime of the phase diagram. We discuss the implications of these results for the understanding of both transport phenomena and pairing mechanism in high-T$_{c}$ systems.Comment: 5 pages, 2 figure

Is there an integrative center in the vertebrate brain-stem? A robotic evaluation of a model of the reticular formation viewed as an action selection device

Neurobehavioral data from intact, decerebrate, and neonatal rats, suggests that the reticular formation provides a brainstem substrate for action selection in the vertebrate central nervous system. In this article, Kilmer, McCulloch and Blum’s (1969, 1997) landmark reticular formation model is described and re-evaluated, both in simulation and, for the first time, as a mobile robot controller. Particular model configurations are found to provide effective action selection mechanisms in a robot survival task using either simulated or physical robots. The model’s competence is dependent on the organization of afferents from model sensory systems, and a genetic algorithm search identified a class of afferent configurations which have long survival times. The results support our proposal that the reticular formation evolved to provide effective arbitration between innate behaviors and, with the forebrain basal ganglia, may constitute the integrative, ’centrencephalic’ core of vertebrate brain architecture. Additionally, the results demonstrate that the Kilmer et al. model provides an alternative form of robot controller to those usually considered in the adaptive behavior literature

Crystal structure and high-field magnetism of La2CuO4

Neutron diffraction was used to determine the crystal structure and magnetic ordering pattern of a La2CuO4 single crystal, with and without applied magnetic field. A previously unreported, subtle monoclinic distortion of the crystal structure away from the orthorhombic space group Bmab was detected. The distortion is also present in lightly Sr-doped crystals. A refinement of the crystal structure shows that the deviation from orthorhombic symmetry is predominantly determined by displacements of the apical oxygen atoms. An in-plane magnetic field is observed to drive a continuous reorientation of the copper spins from the orthorhombic b-axis to the c-axis, directly confirming predictions based on prior magnetoresistance and Raman scattering experiments. A spin-flop transition induced by a c-axis oriented field previously reported for non-stoichiometric La2CuO4 is also observed, but the transition field (11.5 T) is significantly larger than that in the previous work

Raman Response in Doped Antiferromagnets

The resonant part of the $B_{1g}$ electronic Raman scattering response is calculated within the $t-J$ model on a planar lattice as a function of temperature and hole doping, using a finite-temperature diagonalization method for small systems. Results, directly applicable to experiments on cuprates, reveal on doping a very pronounced increase of the width of the two-magnon Raman peak, accompanied by a decrease of the total intensity. At the same time the peak position does not shift substantially in the underdoped regime.Comment: 11 pages revtex, 3 postscript figures. Minor corrections and changes from previous version, to be published in Phys. Rev.