We have developed a new DNA microarray-based technology, termed protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding site sequence specificities of the yeast transcription factors Abf1, Rap1, and Mig1. Comparison of these proteins' in vitro binding sites versus their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1, and Mig1 bound to 107, 90, and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames (ORFs). Comparative sequence analysis indicates that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and thus are likely to be functional in vivo binding sites that potentially are utilized in a conditionspecific manner. Similar PBM experiments will likely be useful in identifying novel cis regulatory elements and transcriptional regulatory networks in various genomes.The interactions between transcription factors (TFs) and their DNA binding sites are an integral part of transcriptional regulatory networks. They control the coordinated expression of thousands of genes during normal growth and in response to external stimuli. Significant progress has been made recently in the accumulation and analysis of mRNA transcript Correspondence should be addressed to M.L.B.

We propose a general strategy to develop accurate Force Fields (FF) for metallic systems derived from ab initio quantum mechanical (QM) calculations; we illustrate this approach for tantalum. As input data to the FF we use the linearized augmented plane wave method (LAPW) with the generalized gradient approximation (GGA) to calculate: (i) the zero temperature equation of state (EOS) of Ta for bcc, fcc, and hcp crystal structures for pressures up to ∼ 500 GPa. (ii) Elastic constants. (iii) We use a mixed-basis pseudopotential code to calculate volume relaxed vacancy formation energy also as a function of pressure. In developing the Ta FF we also use previous QM calculations of: (iv) the equation of state for the A15 structure.(v) the surface energy bcc (100). (vi) energetics for shear twinning of the bcc crystal. We find that with appropriate parameters an embedded atom model force field (denoted as qEAM FF) is able to reproduce all this QM data. Thus, the same FF describes with good accuracy the bcc, fcc, hcp and A15 phases of Ta for pressures from ∼ −10 GPa to ∼ 500 GPa, while also describing the vacancy, surface energy, and shear transformations. The ability of this single FF to describe such a range of systems with a variety of coordinations suggests that it would be accurate for describing defects such as dislocations, grain boundaries, etc. We illustrate the use of the qEAM FF with molecular dynamics to calculate such finite temperature properties as the melting curve up to 300 GPa; we obtain a zero pressure melting temperature of T melt = 3150 ± 50 K in good agreement with experiment (3213 − 3287 K). We also report on the thermal expansion of Ta in a wide temperature range; our calculated thermal expansivity agrees well with experimental data.

Using a first principles based, magnetic tight-binding total energy model, the magnetization energy and moments are computed for various ordered spin configurations in the high pressure polymorphs of iron (fcc, or γ-Fe, and hcp, or ǫ-Fe), as well ferromagnetic bcc iron (α-Fe). For hcp, a non-collinear, antiferromagnetic, spin configuration that minimizes unfavorable ferromagnetic nearest neighbor ordering is the lowest energy state and is more stable than non-magnetic ǫ iron up to about 75 GPa. Accounting for non-collinear magnetism yields better agreement with the experimental equation of state, in contrast to the non-magnetic equation of state, which is in poor agreement with experiment below 50 GPa.

Using a mixed basis pseudopotential method, total energy calculations were performed to obtain the enthalpy of vacancy formation in Ta as a function of pressure, which is important for understanding the effects of pressure on mechanical properties. The vacancy formation enthalpy is found to increase from 2.95 eV at ambient pressures to 12.86 eV at 300 GPa, and the vacancy formation volume decreases from being 53±5% of the bulk volume per atom at ambient pressure to 20 ±2% at 300 GPa, for a 54-atom supercell. We also show that there is a strong correspondence between the vacancy formation enthalpy and the melting temperature in Ta.

We study the dynamical exponents d w and d s for a particle diffusing in a disordered medium (modeled by a percolation cluster), from the regime of extreme disorder (i.e., when the percolation cluster is a fractal at p = p c ) to the Lorentz gas regime when the cluster has weak disorder at p > p c and the leading behavior is standard diffusion. A new technique of relating the velocity autocorrelation function and the return to the starting point probability to the asymptotic spectral properties of the hopping transition probability matrix of the diffusing particle is used, and the latter is numerically analyzed using the Arnoldi-Saad algorithm. We also present evidence for a new scaling relation for the second largest eigenvalue in terms of the size of the cluster, | ln λ max | ∼ S −dw/d f , which provides a very efficient and accurate method of extracting the spectral dimension d s where d s = 2d f /d w . 05.40.+j, 05.50.+q, 64.60.Fr Typeset using REVT E X

Using simple scaling arguments, we calculate the external field required to propagate a domain wall from the soft to the hard phase in a composite media. In the absence of the external field the domain-wall energy is lower in the soft phase, resulting in an energy barrier between the hard and soft phases. It is shown that as the external field increases the domain-wall energy in the soft phase also increases, and there is a corresponding wall energy reduction in the hard phase, resulting in the lowering of the energy barrier. The switching field is obtained as the field, which equalizes the domain-wall energies in both phases, reduces the wall barrier to zero, and leads to wall propagation and reversal. The calculation allows identification of field dependent anisotropies and wall widths of the two phases, which become equal at the reversal field. The reversal field is found to linearly depend upon the intrinsic anisotropy difference and inversely on the sum of magnetization of the two phases. Moreover, the reversal field is found to be independent of the volume of the two phases. An attempt at exhaustive comparison with experiments is made.

In the paper we consider the problem of uniqueness of derivatives of meromorphic functions when they share two or three sets and obtained five results which will improve all the existing results.

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