The solution of large-scale least-squares problems on supercomputers

We discuss methods for solving medium to large-scale sparse least-squares problems on supercomputers, illustrating our remarks by experiments on the CRAY-2 supercomputer at Harwell. The method we are primarily concerned with is an augmented system approach which has the merit of both robustness and accuracy, in addition to a kernel operation that is just the solution of a symmetric indefinite system. We consider extensions to handle weighted and constrained problems, and include experiments on systems similar to those arising in the Karmarkar algorithm for linear programming. We indicate how recent improvements to the kernel software could greatly improve the performance of the least-squares code.This paper is based on an invited talk by the author at a Workshop on Supercomputers and Large-Scale Optimization held at the Minnesota Supercomputing Center on 16th to 18th May, 1988.     

A <Emphasis Type="Italic">Z</Emphasis>-monitor to calibrate Higgs production via vector boson fusion with rapidity gaps at the LHC

We study central Z-boson production accompanied by rapidity gaps on either side as a way to gauge Higgs weak boson fusion production at the LHC. We analyse the possible backgrounds for the -decay mode and show that these can be substantially reduced. Special attention is paid to the evaluation of the gap survival factor, which is the major source of theoretical uncertainty in the rate of H, Z and W central production events with rapidity gaps. Received: 1 August 2002 / Revised version: 27 September 2002 / Published online: 31 October 2002     

Hadronic antenna patterns to distinguish production mechanisms for large-E T jets

Hadronic antenna patterns provide a tool able to diagnose different patterns of colour flow in large-E _T jet events. They reflect the underlying short-distance dynamics, and are sensitive to colour coherence and interference between the initial- and final-state partons. We discuss how hadronic antenna patterns may be used on large-E _T events from the Fermilab Tevatron or the CERN LHC to distinguish between conventional QCD and new physics production mechanisms such as a possible Z′ boson or compositeness.     

Construction of a New Class of Tetracycline Lead Structures with Potent Antibacterial Activity through Biosynthetic Engineering

Antimicrobial resistance and the shortage of novel antibiotics have led to an urgent need for new antibacterial drug leads. Several existing natural product scaffolds (including chelocardins) have not been developed because their suboptimal pharmacological properties could not be addressed at the time. It is demonstrated here that reviving such compounds through the application of biosynthetic engineering can deliver novel drug candidates. Through a rational approach, the carboxamido moiety of tetracyclines (an important structural feature for their bioactivity) was introduced into the chelocardins, which are atypical tetracyclines with an unknown mode of action. A broad‐spectrum antibiotic lead was generated with significantly improved activity, including against all Gram‐negative pathogens of the ESKAPE panel. Since the lead structure is also amenable to further chemical modification, it is a platform for further development through medicinal chemistry and genetic engineering.     

Extended formulations in mixed integer conic quadratic programming

In this paper we consider the use of extended formulations in LP-based algorithms for mixed integer conic quadratic programming (MICQP). Extended formulations have been used by Vielma et al. (INFORMS J Comput 20: 438–450, 2008) and Hijazi et al. (Comput Optim Appl 52: 537–558, 2012) to construct algorithms for MICQP that can provide a significant computational advantage. The first approach is based on an extended or lifted polyhedral relaxation of the Lorentz cone by Ben-Tal and Nemirovski (Math Oper Res 26(2): 193–205 2001) that is extremely economical, but whose approximation quality cannot be iteratively improved. The second is based on a lifted polyhedral relaxation of the euclidean ball that can be constructed using techniques introduced by Tawarmalani and Sahinidis (Math Programm 103(2): 225–249, 2005). This relaxation is less economical, but its approximation quality can be iteratively improved. Unfortunately, while the approach of Vielma, Ahmed and Nemhauser is applicable for general MICQP problems, the approach of Hijazi, Bonami and Ouorou can only be used for MICQP problems with convex quadratic constraints. In this paper we show how a homogenization procedure can be combined with the technique by Tawarmalani and Sahinidis to adapt the extended formulation used by Hijazi, Bonami and Ouorou to a class of conic mixed integer programming problems that include general MICQP problems. We then compare the effectiveness of this new extended formulation against traditional and extended formulation-based algorithms for MICQP. We find that this new formulation can be used to improve various LP-based algorithms. In particular, the formulation provides an easy-to-implement procedure that, in our benchmarks, significantly improved the performance of commercial MICQP solvers.     

Compound prioritization methods increase rates of chemical probe discovery in model organisms

Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided.     

Facile charge-displacement at silicon gives spaced-out reaction

Adsorbates on metals, but not previously on semiconductors, have been observed to display long-range repulsive interactions. On metals, due to efficient dissipation, the repulsions are weak, typically on the order of 5 meV at 10 ?. On the 7×7 reconstruction of the Si(111) surface, charge transport through the surface has been demonstrated by others using charge injection by STM tips. Here we show that for both physisorbed brominated molecules, and for chemisorbed Br-atoms, induced charge-transfer in the Si(111)-7×7 surface can lead to a strong repulsive interaction between adsorbates, calculated as 200 meV at 13.4 ?. This large repulsive interaction must be channeled through the surface since it causes widely spaced "one-per-corner-hole" patterns of physisorption (three cases--directly observed here) and subsequent chemisorption (four cases observed). The patterns were observed by ultrahigh vacuum scanning tunneling microscopy for four different brominated hydrocarbon adsorbates; 1,2-dibromoethane, 1-bromopropane, 1-bromopentane, and bromobenzene, deposited individually on the surface. In every case, adsorbates were overwhelmingly more likely to be found singly than multiply adjacent to a corner-hole, constituting a distinctive pattern having a probability p = 7 × 10(-5) compared to a random distribution.     

Mechanism of the Pechmann reaction: a theoretical study

One of the most widespread synthetic routes to coumarins is the condensation of esters and phenols via the Pechmann reaction. Despite the industrial and technological importance of the reaction, its mechanism is still poorly understood. We have explored several possible reaction paths by DFT calculations at the M05-2X/6-31+G* level. Amphoteric groups and the solvent have a crucial role in the frequent proton-transfer steps of the mechanisms; therefore, we have employed a mixed solvent model, where we combined the implicit PCM model together with an explicit water molecule placed at the actual proton transfer region. The Gibbs free-energy profiles of the possible routes suggest that three parallel channels (featuring water elimination, trans-esterification, and electrophilic attack) operate simultaneously. Enolic routes have prohibitively high activation barriers rendering these paths untenable. The calculated profiles indicate that in each feasible route the first elementary step has the highest activation energy. Reaction intermediates identified on the free-energy profiles can explain several experimental observations.