Exhaustive enumeration unveils clustering and freezing in random 3-SAT

We study geometrical properties of the complete set of solutions of the random 3-satisfiability problem. We show that even for moderate system sizes the number of clusters corresponds surprisingly well with the theoretic asymptotic prediction. We locate the freezing transition in the space of solutions which has been conjectured to be relevant in explaining the onset of computational hardness in random constraint satisfaction problems.Comment: 4 pages, 3 figure

The Phase Diagram of 1-in-3 Satisfiability Problem

We study the typical case properties of the 1-in-3 satisfiability problem, the boolean satisfaction problem where a clause is satisfied by exactly one literal, in an enlarged random ensemble parametrized by average connectivity and probability of negation of a variable in a clause. Random 1-in-3 Satisfiability and Exact 3-Cover are special cases of this ensemble. We interpolate between these cases from a region where satisfiability can be typically decided for all connectivities in polynomial time to a region where deciding satisfiability is hard, in some interval of connectivities. We derive several rigorous results in the first region, and develop the one-step--replica-symmetry-breaking cavity analysis in the second one. We discuss the prediction for the transition between the almost surely satisfiable and the almost surely unsatisfiable phase, and other structural properties of the phase diagram, in light of cavity method results.Comment: 30 pages, 12 figure

Low-temperature UV photoluminescence of ion beam synthesized Si nanoclusters embedded in Si

Ultraviolet (UV) photoluminescence (PL) data taken on a double Au implanted Si matrix are reported. This has been studied over a wide temperature range of 28-220 K. At low temperature, the spectrum shows four peaks corresponding to a zero-phonon line (ZP

No spin glass phase in ferromagnetic random-field random-temperature scalar Ginzburg-Landau model

Krzakala, Ricci-Tersenghi and Zdeborova have shown recently that the random field Ising model with non-negative interactions and arbitrary external magnetic field on an arbitrary lattice does not have a static spin glass phase. In this paper we generalize the proof to a soft scalar spin version of the Ising model: the Ginzburg-Landau model with random magnetic field and random temperature-parameter. We do so by proving that the spin glass susceptibility cannot diverge unless the ferromagnetic susceptibility does.Comment: 9 page

Shape Shifting Leads to Small-Molecule Allosteric Drug Discovery

SummaryEnzymes that regulate their activity by modulating an equilibrium of alternate, nonadditive, functionally distinct oligomeric assemblies (morpheeins) constitute a recently described mode of allostery. The oligomeric equilibrium for porphobilinogen synthase (PBGS) consists of high-activity octamers, low-activity hexamers, and two dimer conformations. A phylogenetically diverse allosteric site specific to hexamers is proposed as an inhibitor binding site. Inhibitor binding is predicted to draw the oligomeric equilibrium toward the low-activity hexamer. In silico docking enriched a selection from a small-molecule library for compounds predicted to bind to this allosteric site. In vitro testing of selected compounds identified one compound whose inhibition mechanism is species-specific conversion of PBGS octamers to hexamers. We propose that this strategy for inhibitor discovery can be applied to other proteins that use the morpheein model for allosteric regulation

Absolute instruments and perfect imaging in geometrical optics

We investigate imaging by spherically symmetric absolute instruments that provide perfect imaging in the sense of geometrical optics. We derive a number of properties of such devices, present a general method for designing them and use this method to propose several new absolute instruments, in particular a lens providing a stigmatic image of an optically homogeneous region and having a moderate refractive index range.Comment: 20 pages, 9 image

Site-specific C-terminal and internal loop labeling of proteins using sortase-mediated reactions

Methods for site-specific modification of proteins should be quantitative and versatile with respect to the nature and size of the biological or chemical targets involved. They should require minimal modification of the target, and the underlying reactions should be completed in a reasonable amount of time under physiological conditions. Sortase-mediated transpeptidation reactions meet these criteria and are compatible with other labeling methods. Here we describe the expression and purification conditions for two sortase A enzymes that have different recognition sequences. We also provide a protocol that allows the functionalization of any given protein at its C terminus, or, for select proteins, at an internal site. The target protein is engineered with a sortase-recognition motif (LPXTG) at the place where modification is desired. Upon recognition, sortase cleaves the protein between the threonine and glycine residues, facilitating the attachment of an exogenously added oligoglycine peptide modified with the functional group of choice (e.g., fluorophore, biotin, protein or lipid). Expression and purification of sortase takes ∼3 d, and sortase-mediated reactions take only a few minutes, but reaction times can be extended to increase yields.National Institutes of Health (U.S.) (Grant RO1 AI08787

Longitudinal associations between specific types of emotional reactivity and psychological, physical health, and school adjustment

Using a multimethod, multiinformant longitudinal design, we examined associations between specific forms of positive and negative emotional reactivity at age 5, children’s effortful control (EC), emotion regulation, and social skills at age 7, and adolescent functioning across psychological, academic, and physical health domains at ages 15/16 (N = 383). We examined how distinct components of childhood emotional reactivity directly and indirectly predict domain-specific forms of adolescent adjustment, thereby identifying developmental pathways between specific types of emotional reactivity and adjustment above and beyond the propensity to express other forms of emotional reactivity. Age 5 high-intensity positivity was associated with lower age 7 EC and more adolescent risk-taking; age 5 low-intensity positivity was associated with better age 7 EC and adolescent cardiovascular health, providing evidence for the heterogeneity of positive emotional reactivity. Indirect effects indicated that children’s age 7 social skills partially explain several associations between age 5 fear and anger reactivity and adolescent adjustment. Moreover, age 5 anger reactivity, low-, and high-intensity positivity were associated with adolescent adjustment via age 7 EC. The findings from this interdisciplinary, long-term longitudinal study have significant implications for prevention and intervention work aiming to understand the role of emotional reactivity in the etiology of adjustment and psychopathology

Probabilistic Reconstruction in Compressed Sensing: Algorithms, Phase Diagrams, and Threshold Achieving Matrices

Compressed sensing is a signal processing method that acquires data directly in a compressed form. This allows one to make less measurements than what was considered necessary to record a signal, enabling faster or more precise measurement protocols in a wide range of applications. Using an interdisciplinary approach, we have recently proposed in [arXiv:1109.4424] a strategy that allows compressed sensing to be performed at acquisition rates approaching to the theoretical optimal limits. In this paper, we give a more thorough presentation of our approach, and introduce many new results. We present the probabilistic approach to reconstruction and discuss its optimality and robustness. We detail the derivation of the message passing algorithm for reconstruction and expectation max- imization learning of signal-model parameters. We further develop the asymptotic analysis of the corresponding phase diagrams with and without measurement noise, for different distribution of signals, and discuss the best possible reconstruction performances regardless of the algorithm. We also present new efficient seeding matrices, test them on synthetic data and analyze their performance asymptotically.Comment: 42 pages, 37 figures, 3 appendixe