Geometrical frustration yields fiber formation in self-assembly

Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibers. Beyond the diversity of molecular mechanisms involved, we propose that fibers generically arise from the aggregation of irregular particles with short-range interactions. Using a minimal model of ill-fitting, sticky particles, we demonstrate robust fiber formation for a variety of particle shapes and aggregation conditions. Geometrical frustration plays a crucial role in this process, and accounts for the range of parameters in which fibers form as well as for their metastable character.Comment: 6 pages, 5 figures, 1 ancillary movie; to appear in Nature Physic

General Analysis of U-Spin Breaking in B Decays

We analyse the breaking of U-spin on a group theoretical basis. Due to the simple behaviour of the weak effective hamiltonian under U-spin and the unique structure of the breaking terms such a group theoretical analysis leads to a manageable number of parameters. Several applications are discussed, including the decays B -> J/psi K and B -> D K.Comment: 18 pages, 2 figures; Paragraph added on decays of B0 to P+P- with P=(pi,K), and several minor corrections performed. Version matches the one to appear in Phys. Rev.

Interface Simulation Distances

The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, and that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.Comment: In Proceedings GandALF 2012, arXiv:1210.202

Identification of putative steroid receptor antagonists in bottled water : combining bioassays and high-resolution mass spectrometry

Endocrine disrupting chemicals (EDCs) are man-made compounds interfering with hormone signaling and thereby adversely affecting human health. Recent reports provide evidence for the presence of EDCs in commercially available bottled water, including steroid receptor agonists and antagonists. However, since these findings are based on biological data the causative chemicals remain unidentified and, therefore, inaccessible for toxicological evaluation. Thus, the aim of this study is to assess the antiestrogenic and antiandrogenic activity of bottled water and to identify the causative steroid receptor antagonists. We evaluated the antiestrogenic and antiandrogenic activity of 18 bottled water products in reporter gene assays for human estrogen receptor alpha and androgen receptor. Using nontarget high-resolution mass spectrometry (LTQ-Orbitrap Velos), we acquired corresponding analytical data. We combined the biological and chemical information to determine the exact mass of the tentative steroid receptor antagonist. Further MS(n) experiments elucidated the molecule's structure and enabled its identification. We detected significant antiestrogenicity in 13 of 18 products. 16 samples were antiandrogenic inhibiting the androgen receptor by up to 90%. Nontarget chemical analysis revealed that out of 24520 candidates present in bottled water one was consistently correlated with the antagonistic activity. By combining experimental and in silico MS(n) data we identified this compound as di(2-ethylhexyl) fumarate (DEHF). We confirmed the identity and biological activity of DEHF and additional isomers of dioctyl fumarate and maleate using authentic standards. Since DEHF is antiestrogenic but not antiandrogenic we conclude that additional, yet unidentified EDCs must contribute to the antagonistic effect of bottled water. Applying a novel approach to combine biological and chemical analysis this is the first study to identify so far unknown EDCs in bottled water. Notably, dioctyl fumarates and maleates have been overlooked by science and regulation to date. This illustrates the need to identify novel toxicologically relevant compounds to establish a more holistic picture of the human exposome

Two-Nucleon Systems in a Finite Volume: (II) 3S1-3D1 Coupled Channels and the Deuteron

The energy spectra of two nucleons in a cubic volume provide access to the two phase shifts and one mixing angle that define the S-matrix in the 3S1-3D1 coupled channels containing the deuteron. With the aid of recently derived energy quantization conditions for such systems, and the known scattering parameters, these spectra are predicted for a range of volumes. It is found that extractions of the infinite-volume deuteron binding energy and leading scattering parameters, including the S-D mixing angle at the deuteron pole, are possible from Lattice QCD calculations of two-nucleon systems with boosts of |P| <= 2pi sqrt{3}/L in volumes with 10 fm <~ L <~ 14 fm. The viability of extracting the asymptotic D/S ratio of the deuteron wavefunction from Lattice QCD calculations is discussed.Comment: 31 pages, 17 figure

Two-Baryon Systems with Twisted Boundary Conditions

We explore the use of twisted boundary conditions in extracting the nucleon mass and the binding energy of two-baryon systems, such as the deuteron, from Lattice QCD calculations. Averaging the results of calculations performed with periodic and anti-periodic boundary conditions imposed upon the light-quark fields, or other pair-wise averages, improves the volume dependence of the deuteron binding energy from ~exp(-kappa*L)/L to ~exp(-sqrt(2)kappa*L)/L. However, a twist angle of pi/2 in each of the spatial directions improves the volume dependence from ~exp(-kappa*L)/L to ~exp(-2kappa*L)/L. Twist averaging the binding energy with a random sampling of twist angles improves the volume dependence from ~exp^(-kappa*L)/L to ~exp(-2kappa*L)/L, but with a standard deviation of ~exp(-kappa*L)/L, introducing a signal-to-noise issue in modest lattice volumes. Using the experimentally determined phase shifts and mixing angles, we determine the expected energies of the deuteron states over a range of cubic lattice volumes for a selection of twisted boundary conditions.Comment: 20 pages, 3 figure

Deep redshift topological lensing: strategies for the T^3 candidate

The 3-torus (T^3) FLRW model better fits the nearly zero large-scale auto-correlation of the WMAP CMB sky maps than the infinite flat model. The T^3 model's WMAP parameters imply approximately equal-redshift topological lensing at z \sim 6. We investigate observational strategies for rejecting the T^3 solution or providing candidate topologically lensed galaxy pairs. T^3 holonomies are applied to (i) existing z \sim 6 observations and (ii) simulated observations, creating multiply connected catalogues. Corresponding simply connected catalogues are generated. Each catalogue is analysed using a successive filter method and collecting matched quadruples. Quadruple statistics between the multiply and simply connected catalogues are compared. The expected rejection of the hypothesis, or detection of candidate topologically lensed galaxies, is possible at a significance of 5% for a pair of T^3 axis-centred northern and southern surveys if photometric redshift accuracy is \sigma(\zphot) < 0.01 for a pair of nearly complete 100 deg^2 surveys with a total of > 500 galaxies over 4.3 < z < 6.6, or for a pair of 196 deg^2 surveys with > 400 galaxies and \sigma(\zphot) < 0.02 over 4<z<7. Dropping the maximum time interval in a pair from \Delta t =1 Gyr/h to \Delta t =0.1 Gyr/h yields a requirement of \sigma(\zphot) < 0.005 or \sigma(\zphot) < 0.01, respectively. Millions of z \sim 6 galaxies will be observed over fields of these sizes during the coming decades, implying much stronger constraints. The question is not if the hypothesis will be rejected or confirmed, it is when.Comment: 13 pages, 9 figures, 5 tables, MNRAS, accepte

Dissection of a Bug Dataset: Anatomy of 395 Patches from Defects4J

Well-designed and publicly available datasets of bugs are an invaluable asset to advance research fields such as fault localization and program repair as they allow directly and fairly comparison between competing techniques and also the replication of experiments. These datasets need to be deeply understood by researchers: the answer for questions like "which bugs can my technique handle?" and "for which bugs is my technique effective?" depends on the comprehension of properties related to bugs and their patches. However, such properties are usually not included in the datasets, and there is still no widely adopted methodology for characterizing bugs and patches. In this work, we deeply study 395 patches of the Defects4J dataset. Quantitative properties (patch size and spreading) were automatically extracted, whereas qualitative ones (repair actions and patterns) were manually extracted using a thematic analysis-based approach. We found that 1) the median size of Defects4J patches is four lines, and almost 30% of the patches contain only addition of lines; 2) 92% of the patches change only one file, and 38% has no spreading at all; 3) the top-3 most applied repair actions are addition of method calls, conditionals, and assignments, occurring in 77% of the patches; and 4) nine repair patterns were found for 95% of the patches, where the most prevalent, appearing in 43% of the patches, is on conditional blocks. These results are useful for researchers to perform advanced analysis on their techniques' results based on Defects4J. Moreover, our set of properties can be used to characterize and compare different bug datasets.Comment: Accepted for SANER'18 (25th edition of IEEE International Conference on Software Analysis, Evolution and Reengineering), Campobasso, Ital