Parallel biomolecular computation on surfaces with advanced finite automata

A biomolecular, programmable 3-symbol-3-state finite automaton is reported. This automaton computes autonomously with all of its components, including hardware, software, input, and output being biomolecules mixed together in solution. The hardware consisted of two enzymes: an endonuclease, BbvI, and T4 DNA ligase. The software (transition rules represented by transition molecules) and the input were double-stranded (ds) DNA oligomers. Computation was carried out by autonomous processing of the input molecules via repetitive cycles of restriction, hybridization, and ligation reactions to produce a final-state output in the form of a dsDNA molecule. The 3-symbol-3-state deterministic automaton is an extension of the 2-symbol-2-state automaton previously reported, and theoretically it can be further expanded to a 37-symbol-3-state automaton. The applicability of this design was further amplified by employing surface-anchored input molecules, using the surface plasmon resonance technology to monitor the computation steps in real time. Computation was performed by alternating the feed solutions between endonuclease and a solution containing the ligase, ATP, and appropriate transition molecules. The output detection involved final ligation with one of three soluble detection molecules. Parallel computation and stepwise detection were carried out automatically with a Biacore chip that was loaded with four different inputs.     

A Generalized Univariate Newton Method Motivated by Proximal Regularization

We devise a new generalized univariate Newton method for solving nonlinear equations, motivated by Bregman distances and proximal regularization of optimization problems. We prove quadratic convergence of the new method, a special instance of which is the classical Newton method. We illustrate the possible benefits of the new method over the classical Newton method by means of test problems involving the Lambert W function, Kullback?CLeibler distance, and a polynomial. These test problems provide insight as to which instance of the generalized method could be chosen for a given nonlinear equation. Finally, we derive a closed-form expression for the asymptotic error constant of the generalized method and make further comparisons involving this constant.     

Right Bregman nonexpansive operators in Banach spaces

We introduce and study new classes of Bregman nonexpansive operators in reflexive Banach spaces. These classes of operators are associated with the Bregman distance induced by a convex function. In particular, we characterize sunny right quasi-Bregman nonexpansive retractions, and as a consequence, we show that the fixed point set of any right quasi-Bregman nonexpansive operator is a sunny right quasi-Bregman nonexpansive retract of the ambient Banach space.     

H2S Removal from Groundwater by Chemical Free Advanced Oxidation Process Using UV-C/VUV Radiation

Sulfide species may be present in groundwater due to natural processes or due to anthropogenic activity. H₂S contamination poses odor nuisance and may also lead to adverse health effects. Advanced oxidation processes (AOPs) are considered promising treatments for hydrogen-sulfide removal from water, but conventional AOPs usually require continuous chemical dosing, as well as post-treatment, when solid catalysts are applied. Vacuum-UV (VUV) radiation can generate ·OH in situ via water photolysis, initiating chemical-free AOP. The present study investigated the applicability of VUV-based AOP for removal of H₂S both in synthetic solutions and in real groundwater, comparing combined UV-C/VUV and UV-C only radiation in a continuous-flow reactor. In deionized water, H₂S degradation was much faster under the combined radiation, dominated by indirect photolysis, and indicated the formation of sulfite intermediates that convert to sulfate at high radiation doses. Sulfide was efficiently removed from natural groundwater by the two examined lamps, with no clear preference between them. However, in anoxic conditions, common in sulfide-containing groundwater, a small advantage for the combined lamp was observed. These results demonstrate the potential of utilizing VUV-based AOP for treating H₂S contamination in groundwater as a chemical-free treatment, which can be especially attractive to remote small treatment facilities.     

Partitioning a graph into monochromatic connected subgraphs

We show that every -edge-colored graph on vertices with minimum degree at least can be partitioned into two monochromatic connected subgraphs, provided is sufficiently large. This minimum degree condition is tight and the result proves a conjecture of Bal and DeBiasio. We also make progress on another conjecture of Bal and DeBiasio on covering graphs with large minimum degree with monochromatic components of distinct colors.     

Large Monochromatic Triple Stars in Edge Colourings

Following problems posed by Gyárfás 2011, we show that for every r‐edge‐colouring of there is a monochromatic triple star of order at least , improving Ruszinkó's result 2012. An edge colouring of a graph is called a local r‐colouring if every vertex spans edges of at most r distinct colours. We prove the existence of a monochromatic triple star with at least vertices in every local r‐colouring of .     

Stratifying derived categories of cochains on certain spaces

In recent years, Benson, Iyengar and Krause have developed a theory of stratification for compactly generated triangulated categories with an action of a graded commutative Noetherian ring. Stratification implies a classification of localizing and thick subcategories in terms of subsets of the prime ideal spectrum of the given ring. In this paper two stratification results are presented: one for the derived category of a commutative ring-spectrum with polynomial homotopy and another for the derived category of cochains on certain spaces. We also give the stratification of cochains on a space a topological content.     

The property of having a k ‐regular subgraph has a sharp threshold

In this paper it is proved that in the random graph model G(n,p), the property of containing a k ‐regular subgraph, has a sharp threshold for k ≥ 3. It is also shown how to use similar methods to prove, quite easily, the (known fact of) sharpness of having a non empty k ‐core for k ≥ 3. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 42, 509–519, 2013