A New FronTIR in Targeted Protein Degradation and Plant Development

Three papers, two in a recent issue of Nature and one in the July issue of Developmental Cell, identify a family of F box proteins as the long-sought receptors for the plant growth hormone auxin. The new studies reveal that auxin, a small molecule, regulates F box proteins, which are involved in ubiquitin-mediated protein degradation. This finding has profound implications for understanding plant physiology and development and for defining new modes of regulation of SCF ubiquitin ligase complexes

Quantum Separability and Entanglement Detection via Entanglement-Witness Search and Global Optimization

We focus on determining the separability of an unknown bipartite quantum state $\rho$ by invoking a sufficiently large subset of all possible entanglement witnesses given the expected value of each element of a set of mutually orthogonal observables. We review the concept of an entanglement witness from the geometrical point of view and use this geometry to show that the set of separable states is not a polytope and to characterize the class of entanglement witnesses (observables) that detect entangled states on opposite sides of the set of separable states. All this serves to motivate a classical algorithm which, given the expected values of a subset of an orthogonal basis of observables of an otherwise unknown quantum state, searches for an entanglement witness in the span of the subset of observables. The idea of such an algorithm, which is an efficient reduction of the quantum separability problem to a global optimization problem, was introduced in PRA 70 060303(R), where it was shown to be an improvement on the naive approach for the quantum separability problem (exhaustive search for a decomposition of the given state into a convex combination of separable states). The last section of the paper discusses in more generality such algorithms, which, in our case, assume a subroutine that computes the global maximum of a real function of several variables. Despite this, we anticipate that such algorithms will perform sufficiently well on small instances that they will render a feasible test for separability in some cases of interest (e.g. in 3-by-3 dimensional systems)

Column generation for airline problems

Issued as Progress report, and Final project report, Project no. E-24-66

Submodular Maximization Meets Streaming: Matchings, Matroids, and More

We study the problem of finding a maximum matching in a graph given by an input stream listing its edges in some arbitrary order, where the quantity to be maximized is given by a monotone submodular function on subsets of edges. This problem, which we call maximum submodular-function matching (MSM), is a natural generalization of maximum weight matching (MWM), which is in turn a generalization of maximum cardinality matching (MCM). We give two incomparable algorithms for this problem with space usage falling in the semi-streaming range---they store only $O(n)$ edges, using $O(n\log n)$ working memory---that achieve approximation ratios of $7.75$ in a single pass and $(3+\epsilon)$ in $O(\epsilon^{-3})$ passes respectively. The operations of these algorithms mimic those of Zelke's and McGregor's respective algorithms for MWM; the novelty lies in the analysis for the MSM setting. In fact we identify a general framework for MWM algorithms that allows this kind of adaptation to the broader setting of MSM. In the sequel, we give generalizations of these results where the maximization is over "independent sets" in a very general sense. This generalization captures hypermatchings in hypergraphs as well as independence in the intersection of multiple matroids.Comment: 18 page

Mixed state discrimination using optimal control

We present theory and experiment for the task of discriminating two nonorthogonal states, given multiple copies. We implement several local measurement schemes, on both pure states and states mixed by depolarizing noise. We find that schemes which are optimal (or have optimal scaling) without noise perform worse with noise than simply repeating the optimal single-copy measurement. Applying optimal control theory, we derive the globally optimal local measurement strategy, which outperforms all other local schemes, and experimentally implement it for various levels of noise.Comment: Corrected ref 1 date; 4 pages & 4 figures + 2 pages & 3 figures supplementary materia

Complexity of Strong Implementability

We consider the question of implementability of a social choice function in a classical setting where the preferences of finitely many selfish individuals with private information have to be aggregated towards a social choice. This is one of the central questions in mechanism design. If the concept of weak implementation is considered, the Revelation Principle states that one can restrict attention to truthful implementations and direct revelation mechanisms, which implies that implementability of a social choice function is easy to check. For the concept of strong implementation, however, the Revelation Principle becomes invalid, and the complexity of deciding whether a given social choice function is strongly implementable has been open so far. In this paper, we show by using methods from polyhedral theory that strong implementability of a social choice function can be decided in polynomial space and that each of the payments needed for strong implementation can always be chosen to be of polynomial encoding length. Moreover, we show that strong implementability of a social choice function involving only a single selfish individual can be decided in polynomial time via linear programming

An oil pipeline design problem

Copyright @ 2003 INFORMSWe consider a given set of offshore platforms and onshore wells producing known (or estimated) amounts of oil to be connected to a port. Connections may take place directly between platforms, well sites, and the port, or may go through connection points at given locations. The configuration of the network and sizes of pipes used must be chosen to minimize construction costs. This problem is expressed as a mixed-integer program, and solved both heuristically by Tabu Search and Variable Neighborhood Search methods and exactly by a branch-and-bound method. Two new types of valid inequalities are introduced. Tests are made with data from the South Gabon oil field and randomly generated problems.The work of the first author was supported by NSERC grant #OGP205041. The work of the second author was supported by FCAR (Fonds pour la Formation des Chercheurs et l’Aide à la Recherche) grant #95-ER-1048, and NSERC grant #GP0105574

Stochastic make-to-stock inventory deployment problem: an endosymbiotic psychoclonal algorithm based approach

Integrated steel manufacturers (ISMs) have no specific product, they just produce finished product from the ore. This enhances the uncertainty prevailing in the ISM regarding the nature of the finished product and significant demand by customers. At present low cost mini-mills are giving firm competition to ISMs in terms of cost, and this has compelled the ISM industry to target customers who want exotic products and faster reliable deliveries. To meet this objective, ISMs are exploring the option of satisfying part of their demand by converting strategically placed products, this helps in increasing the variability of product produced by the ISM in a short lead time. In this paper the authors have proposed a new hybrid evolutionary algorithm named endosymbiotic-psychoclonal (ESPC) to decide what and how much to stock as a semi-product in inventory. In the proposed theory, the ability of previously proposed psychoclonal algorithms to exploit the search space has been increased by making antibodies and antigen more co-operative interacting species. The efficacy of the proposed algorithm has been tested on randomly generated datasets and the results compared with other evolutionary algorithms such as genetic algorithms (GA) and simulated annealing (SA). The comparison of ESPC with GA and SA proves the superiority of the proposed algorithm both in terms of quality of the solution obtained and convergence time required to reach the optimal/near optimal value of the solution