Differential systems associated with tableaux over Lie algebras

We give an account of the construction of exterior differential systems based on the notion of tableaux over Lie algebras as developed in [Comm. Anal. Geom 14 (2006), 475-496; math.DG/0412169]. The definition of a tableau over a Lie algebra is revisited and extended in the light of the formalism of the Spencer cohomology; the question of involutiveness for the associated systems and their prolongations is addressed; examples are discussed.Comment: 16 pages; to appear in: "Symmetries and Overdetermined Systems of Partial Differential Equations" (M. Eastwood and W. Miller, Jr., eds.), IMA Volumes in Mathematics and Its Applications, Springer-Verlag, New Yor

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories

Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, the majority of these methods’ implementations are either not published, rely on proprietary software, or do not provide documented interfaces, which has precluded their mainstream adoption in the field. In this work we present cameo, a platform-independent software that enables <i>in silico</i> design of cell factories and targets both experienced modelers as well as users new to the field. It is written in Python and implements state-of-the-art methods for enumerating and prioritizing knockout, knock-in, overexpression, and down-regulation strategies and combinations thereof. Cameo is an open source software project and is freely available under the Apache License 2.0. A dedicated Web site including documentation, examples, and installation instructions can be found at http://cameo.bio. Users can also give cameo a try at http://try.cameo.bio

Chemical kinetic performance losses for a hydrogen laser thermal thruster

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77288/1/AIAA-25927-132.pd

Mode-Locking in Driven Disordered Systems as a Boundary-Value Problem

We study mode-locking in disordered media as a boundary-value problem. Focusing on the simplest class of mode-locking models which consists of a single driven overdamped degree-of-freedom, we develop an analytical method to obtain the shape of the Arnol'd tongues in the regime of low ac-driving amplitude or high ac-driving frequency. The method is exact for a scalloped pinning potential and easily adapted to other pinning potentials. It is complementary to the analysis based on the well-known Shapiro's argument that holds in the perturbative regime of large driving amplitudes or low driving frequency, where the effect of pinning is weak.Comment: 6 pages, 7 figures, RevTeX, Submitte

Effective interaction between helical bio-molecules

The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than $6\AA$ it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog

Chiral three-nucleon forces and bound excited states in neutron-rich oxygen isotopes

We study the spectra of neutron-rich oxygen isotopes based on chiral two- and three-nucleon interactions. First, we benchmark our many-body approach by comparing ground-state energies to coupled-cluster results for the same two-nucleon interaction, with overall good agreement. We then calculate bound excited states in 21,22,23O, focusing on the role of three-nucleon forces, in the standard sd shell and an extended sdf7/2p3/2 valence space. Chiral three-nucleon forces provide important one- and two-body contributions between valence neutrons. We find that both these contributions and an extended valence space are necessary to reproduce key signatures of novel shell evolution, such as the N = 14 magic number and the low-lying states in 21O and 23O, which are too compressed with two-nucleon interactions only. For the extended space calculations, this presents first work based on nuclear forces without adjustments. Future work is needed and open questions are discussed.Comment: 6 pages, 4 figures, published versio

A spinor approach to Walker geometry

A four-dimensional Walker geometry is a four-dimensional manifold M with a neutral metric g and a parallel distribution of totally null two-planes. This distribution has a natural characterization as a projective spinor field subject to a certain constraint. Spinors therefore provide a natural tool for studying Walker geometry, which we exploit to draw together several themes in recent explicit studies of Walker geometry and in other work of Dunajski (2002) and Plebanski (1975) in which Walker geometry is implicit. In addition to studying local Walker geometry, we address a global question raised by the use of spinors.Comment: 41 pages. Typos which persisted into published version corrected, notably at (2.15