Self-assembling DNA-caged particles: nanoblocks for hierarchical self-assembly

DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted particles. In this article we theoretically study the self-assembly of DNA-caged particles. These nanoblocks combine DNA grafted particles with more complicated purely DNA based constructs. Geometrically the nanoblock is a sphere (DNA grafted particle) inscribed inside a polyhedron (DNA cage). The faces of the DNA cage are open, and the edges are made from double stranded DNA. The cage vertices are modified DNA junctions. We calculate the equilibriuim yield of self-assembled, tetrahedrally caged particles, and discuss their stability with respect to alternative structures. The experimental feasability of the method is discussed. To conclude we indicate the usefulness of DNA-caged particles as nanoblocks in a hierarchical self-assembly strategy.Comment: v2: 21 pages, 8 figures; revised discussion in Sec. 2, replaced 2 figures, added new reference

Binary pattern tile set synthesis is NP-hard

In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-PATS). The $k$-PATS problem is that of designing a tile assembly system with the smallest number of tile types which will self-assemble an input pattern of $k$ colors. Of both theoretical and practical significance, $k$-PATS has been studied in a series of papers which have shown $k$-PATS to be NP-hard for $k = 60$, $k = 29$, and then $k = 11$. In this paper, we close the fundamental conjecture that 2-PATS is NP-hard, concluding this line of study. While most of our proof relies on standard mathematical proof techniques, one crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof of the four color theorem by Appel and Haken (simplified later by Robertson, Sanders, Seymour, and Thomas) or the recent important advance on the Erd\H{o}s discrepancy problem by Konev and Lisitsa using computer programs. We utilize a massively parallel algorithm and thus turn an otherwise intractable portion of our proof into a program which requires approximately a year of computation time, bringing the use of computer-assisted proofs to a new scale. We fully detail the algorithm employed by our code, and make the code freely available online

SuperB: a linear high-luminosity B Factory

This paper is based on the outcome of the activity that has taken place during the recent workshop on "SuperB in Italy" held in Frascati on November 11-12, 2005. The workshop was opened by a theoretical introduction of Marco Ciuchini and was structured in two working groups. One focused on the machine and the other on the detector and experimental issues. The present status on CP is mainly based on the results achieved by BaBar and Belle. Estabilishment of the indirect CP violation in B sector in 2001 and of the direct CP violation in 2004 thanks to the success of PEP-II and KEKB e+e- asymmetric B Factories operating at the center of mass energy corresponding to the mass of the Y(4s). With the two B Factories taking data, the Unitarity Triangle is now beginning to be overconstrained by improving the measurements of the sides and now also of the angles alpha, and gamma. We are also in presence of the very intriguing results about the measurements of sin(2 beta) in the time dependent analysis of decay channels via penguin loops, where b --> s sbar s and b --> s dbar d. Tau physics, in particular LFV search, as well as charm and ISR physics are important parts of the scientific program of a SuperB Factory. The physics case together with possible scenarios for the high luminosity SuperB Factory based on the concepts of the Linear Collider and the related experimental issues are discussed.Comment: 22 pages, 22 figures, INFN Roadmap Repor

Status of the Super-B factory Design

The SuperB international team continues to optimize the design of an electron-positron collider, which will allow the enhanced study of the origins of flavor physics. The project combines the best features of a linear collider (high single-collision luminosity) and a storage-ring collider (high repetition rate), bringing together all accelerator physics aspects to make a very high luminosity of 10$^{36}$ cm$^{-2}$ sec$^{-1}$. This asymmetric-energy collider with a polarized electron beam will produce hundreds of millions of B-mesons at the $\Upsilon$(4S) resonance. The present design is based on extremely low emittance beams colliding at a large Piwinski angle to allow very low $\beta_y^\star$ without the need for ultra short bunches. Use of crab-waist sextupoles will enhance the luminosity, suppressing dangerous resonances and allowing for a higher beam-beam parameter. The project has flexible beam parameters, improved dynamic aperture, and spin-rotators in the Low Energy Ring for longitudinal polarization of the electron beam at the Interaction Point. Optimized for best colliding-beam performance, the facility may also provide high-brightness photon beams for synchrotron radiation applications

Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in <i>C. elegans</i>

Parkinson's disease (PD), the second most prevalent neurodegenerative disease after Alzheimer's disease, is linked to the gradual loss of dopaminergic neurons in the substantia nigra. Disease loci causing hereditary forms of PD are known, but most cases are attributable to a combination of genetic and environmental risk factors. Increased incidence of PD is associated with rural living and pesticide exposure, and dopaminergic neurodegeneration can be triggered by neurotoxins such as 6-hydroxydopamine (6-OHDA). In C. elegans, this drug is taken up by the presynaptic dopamine reuptake transporter (DAT-1) and causes selective death of the eight dopaminergic neurons of the adult hermaphrodite. Using a forward genetic approach to find genes that protect against 6-OHDA-mediated neurodegeneration, we identified tsp-17, which encodes a member of the tetraspanin family of membrane proteins. We show that TSP-17 is expressed in dopaminergic neurons and provide genetic, pharmacological and biochemical evidence that it inhibits DAT-1, thus leading to increased 6-OHDA uptake in tsp-17 loss-of-function mutants. TSP-17 also protects against toxicity conferred by excessive intracellular dopamine. We provide genetic and biochemical evidence that TSP-17 acts partly via the DOP-2 dopamine receptor to negatively regulate DAT-1. tsp-17 mutants also have subtle behavioral phenotypes, some of which are conferred by aberrant dopamine signaling. Incubating mutant worms in liquid medium leads to swimming-induced paralysis. In the L1 larval stage, this phenotype is linked to lethality and cannot be rescued by a dop-3 null mutant. In contrast, mild paralysis occurring in the L4 larval stage is suppressed by dop-3, suggesting defects in dopaminergic signaling. In summary, we show that TSP-17 protects against neurodegeneration and has a role in modulating behaviors linked to dopamine signaling

Elasticity of entangled polymer loops: Olympic gels

In this note we present a scaling theory for the elasticity of olympic gels, i.e., gels where the elasticity is a consequence of topology only. It is shown that two deformation regimes exist. The first is the non affine deformation regime where the free energy scales linear with the deformation. In the large (affine) deformation regime the free energy is shown to scale as $F \propto \lambda^{5/2}$ where $\lambda$ is the deformation ratio. Thus a highly non Hookian stress - strain relation is predicted.Comment: latex, no figures, accepted in PRE Rapid Communicatio

Iron Deficiency and the Well-being of Older Adults: Early Results From a Randomized Nutrition Intervention

Iron deficiency is widespread throughout the developing world. We provide new evidence on the effect of iron deficiency on economic and social prosperity of older adults drawing on data from a random assignment treatment-control design intervention. The Work and Iron Status Evaluation is an on-going study following over 17,000 individuals in Central Java, Indonesia. Half the respondents receive a treatment of 120 mg of iron every week for a year; the controls receive a placebo. Compliance is monitored carefully. Results from the first six months of the intervention are presented for adults age 30 through 70 years. Males who were iron deficient prior to the intervention and who are assigned to the treatment are better off in terms of physical health, psycho-social health and economic success. These men are more likely to be working, sleep less, lose less work time to illness, are more energetic, more able to conduct physically arduous activities and their psycho-social health is better. There is evidence that economic productivity of these males also increased. Among iron-deficient males assigned to the treatment who were also self-employed prior to the baseline, hourly earnings rose substantially and so they earned more on a monthly basis. Benefits for women are in the same direction but the effects are more muted. The results provide unambiguous evidence in support of the hypothesis that health has a causal effect on economic prosperity of males during middle and older ages

Observation of the Dynamic Beta Effect at CESR with CLEO

Using the silicon strip detector of the CLEO experiment operating at the Cornell Electron-positron Storage Ring (CESR), we have observed that the horizontal size of the luminous region decreases in the presence of the beam-beam interaction from what is expected without the beam-beam interaction. The dependence on the bunch current agrees with the prediction of the dynamic beta effect. This is the first direct observation of the effect.Comment: 9 page uuencoded postscript file, postscritp file also available through http://w4.lns.cornell.edu/public/CLNS, submitted to Phys. Rev.

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined