A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown

Comment on ``Relativistic cluster dynamics of nucleons and mesons. II. Formalism and examples''

In a recent paper [Phys.\ Rev.\ C{\bf 49}, 2142 (1994)], Haberzettl presented cluster N-body equations for arbitrarily large systems of nucleons and mesons. Application to the three-nucleon system is claimed to yield a new kind of three-nucleon force. We demonstrate that these three-nucleon equations contain double counting.Comment: 6 pages in Revtex 3.0, 6 Postscript figures. Accepted for publication in Phys. Rev.

Qualification model spacecraft tests for DEMP, SGEMP, and ESD effects

The development of a satellite design demonstration test program is described. The test approach is comprehensive in that it includes the effects from electrostatic discharge (ESD), system generated electromagnetic pulse (SGEMP), as well as dispersed electromagnetic pulses (DEMP). The comprehensive test concept is based on the similarity of the satellite's response to several environments

Integrated Vertical Bloch Line (VBL) memory

Vertical Bloch Line (VBL) Memory is a recently conceived, integrated, solid state, block access, VLSI memory which offers the potential of 1 Gbit/sq cm areal storage density, data rates of hundreds of megabits/sec, and submillisecond average access time simultaneously at relatively low mass, volume, and power values when compared to alternative technologies. VBLs are micromagnetic structures within magnetic domain walls which can be manipulated using magnetic fields from integrated conductors. The presence or absence of BVL pairs are used to store binary information. At present, efforts are being directed at developing a single chip memory using 25 Mbit/sq cm technology in magnetic garnet material which integrates, at a single operating point, the writing, storage, reading, and amplification functions needed in a memory. The current design architecture, functional elements, and supercomputer simulation results are described which are used to assist the design process

Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.

The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 - 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 - 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes

Centrifuge modeling of one-step outflow tests for unsaturated parameter estimations

International audienceCentrifuge modeling of one-step outflow tests were carried out using a 2-m radius geotechnical centrifuge, and the cumulative outflow and transient pore pressure were measured during the tests at multiple gravity levels. Based on the scaling law of centrifuge modeling, the measurements generally showed reasonable agreement with prototype data calculated from forward simulations with input parameters determined from standard laboratory tests. The parameter optimizations were examined for three different combinations of input data sets using the test measurements. Within the gravity level examined in this study up to 40 g, the optimized unsaturated parameters compared well when accurate pore pressure measurements were included along with cumulative outflow as input data. The centrifuge modeling technique with its capability to implement variety of instrumentations under well controlled initial and boundary conditions, shortens testing time and can provide significant information for the parameter estimation procedure

Three-Nucleon Force and the Δ\Delta-Mechanism for Pion Production and Pion Absorption

The description of the three-nucleon system in terms of nucleon and $\Delta$ degrees of freedom is extended to allow for explicit pion production (absorption) from single dynamic $\Delta$ de-excitation (excitation) processes. This mechanism yields an energy dependent effective three-body hamiltonean. The Faddeev equations for the trinucleon bound state are solved with a force model that has already been tested in the two-nucleon system above pion-production threshold. The binding energy and other bound state properties are calculated. The contribution to the effective three-nucleon force arising from the pionic degrees of freedom is evaluated. The validity of previous coupled-channel calculations with explicit but stable $\Delta$ isobar components in the wavefunction is studied.Comment: 23 pages in Revtex 3.0, 9 figures (not included, available as postscript files upon request), CEBAF-TH-93-0