Development and optimisation of a novel genetic algorithm for studying model protein folding

Determination of the native state of a protein from its amino acid sequence is the goal of protein folding simulations, with potential applications in gene therapy and drug design. Location of the global minimum structure for a given sequence, however, is a difficult optimisation problem. In this paper, we describe the development and application of a genetic algorithm (GA) to find the lowest-energy conformations for the 2D HP lattice bead protein model. Optimisation of the parameters of our standard GA program reveals that the GA is most successful (at finding the lowest-energy conformations) for high rates of mating and mutation and relatively high elitism. We have also introduced a number of new genetic operators: a duplicate predator—which maintains population diversity by eliminating duplicate structures; brood selection—where two parent structures undergo crossover and give rise to a brood of (not just two) offspring; and a Monte Carlo based local search algorithm—to explore the neighbourhood of all members of the population. It is shown that these operators lead to significant improvements in the success and efficiency of the GA, both compared with our standard GA and with previously published GA studies for benchmark HP sequences with up to 50 beads.     

The Sasaki Hook Is Not a [Static] Implicative Connective but Induces a Backward [in Time] Dynamic One That Assigns Causes

The Sasaki adjunction, which formally encodes the logicality that different authors tried to attach to the Sasaki hook as a ‘quantum implicative connective,’ has a fundamental dynamic nature and encodes the so-called ‘causal duality’ (Coecke et al., 2001) for the particular case of a quantum measurement with a projector as corresponding self-adjoint operator. The action of the Sasaki hook ( $a\xrightarrow{S} - $ ) for fixed antecedent a assigns to some property “the weakest cause before the measurement of actuality of that property after the measurement,” i.e., ( $a\xrightarrow{S}b$ ) is the weakest property that guarantees actuality of b after performing the measurement represented by the projector that has the ‘subspace a’ as eigenstates for eigenvalue 1, say, the measurement that ‘tests’ a. The logicality attributable to quantum systems contains a fundamentally dynamic ingredient: Causal duality actually provides a new dynamic interpretation of orthomodularity. We also reconsider the status of the Sasaki hook within ‘dynamic (operational) quantum logic,’ what leads us to the claim made in the title of this paper. The Sasaki adjunction has a physical significance in terms of causal duality. The labeled dynamic hooks (forwardly and backwardly) that encode quantum measurements, act on properties as $(a_1 \xrightarrow{{\varphi _a }}a_2 ): = (a_1 \to _L (a\xrightarrow{S}a_2 ))$ and $(a_1 \xleftarrow{{\varphi _a }}a_2 ): = ((a\xrightarrow{S}a_2 ) \to _L a_1 )$ , taking values in the ‘disjunctive extension’ $DI(L)$ of the property lattice L, where $a \in L$ is the tested property and $( - \to _L - )$ is the Heyting implication that lives on DI(L). Since these hooks $( - \xrightarrow{{\varphi _a }} - )$ and $( - \xleftarrow{{\varphi _a }} - )$ extend to DI(L)×DI(L) they constitute internal operations. The transition from either classical or constructive/intuitionistic logic to quantum logic entails besides the introduction of an additional unary connective ‘operational resolution’ (Coecke, 2002a) the shift from a binary connective implication to a ternary connective where two of the arguments refer to qualities of the system and the third, the new one, to an obtained outcome (in a measurement)     

Microcionamides A and B, bioactive peptides from the philippine sponge Clathria (Thalysias) abietina

Microcionamides A (1) and B (2) have been isolated from the Philippine marine sponge Clathria (Thalysias) abietina. These new linear peptides are cyclized via a cystine moiety and have their C-terminus blocked by a 2-phenylethylenamine group. Their total structures, including absolute stereochemistry, were determined by a combination of spectral and chemical methods. Compound 1 was shown to slowly isomerize about the C-36/C-37 double bond when stored in DMSO. Microcionamides A (1) and B (2) exhibited significant cytotoxicity against the human breast tumor cells lines MCF-7 and SKBR-3 and displayed inhibitory activity against Mycobacterium tuberculosis H(37)Ra.     

A determination of the Cabibbo-Kobayashi-Maskawa parameter |V us| using KL decays

We present a determination of the Cabibbo-Kobayashi-Maskawa parameter |V(us)| based on new measurements of the six largest K(L) branching fractions and semileptonic form factors by the KTeV (E832) experiment at Fermilab. We find |V(us)|=0.2252+/-0.0008(KTeV)+/-0.0021(ext), where the errors are from KTeV measurements and from external sources. We also use the measured branching fractions to determine the CP violation parameter |eta(+-)|=(2.228+/-0.005(KTeV)+/-0.009(ext))x10(-3).     

Measurements of the Decay KL-->e+ e- mu+ mu-

The KTeV experiment at Fermilab has isolated a total of 132 events from the rare decay K(L)-->e+ e- mu+ mu-, with an estimated background of 0.8 events. The branching ratio of this mode is determined to be [2.69+/-0.24(stat)+/-0.12(syst)]x10(-9), with a radiative cutoff of M(2)(ee mu mu)/M(2)(K)>0.95. The first measurement using this mode of the parameter alpha from the D'Ambrosio-Isidori-Portolès (DIP) model of the K(L)gamma*gamma* vertex yields a result of -1.59+/-0.37, consistent with values obtained from other decay modes. Because of the limited statistics, no sensitivity is found to the DIP parameter beta. We use this decay mode to set limits on CP and lepton violation.     

Rheological studies of concentrated guar gum

Polymers and surfactants are essential ingredients of the printing paste. Polysaccharides are used commercially to thicken, suspend or stabilise aqueous systems. Also they are used to produce gels and to act as flocculates, binders, lubricants, to serve as modifiers of film properties, and have a function as adjusters of rheological parameters. Surfactants, on the other hand, perform numerous functions acting as dispersants, wetting agents, emulsifiers and antifoaming agents. The rheological properties of polysaccharide thickeners (guar gums with different substitution levels and different producers) at different concentrations and temperatures and, second, the effects produced by the addition of nonionic surfactants (polyoxyethylene stearyl alcohols with different numbers of EO groups) have been studied under linear and nonlinear shear conditions. Experimental data have been correlated with the different models: flow curves with the Cross, Carreau and Meter-Bird model, and mechanical spectra with the generalized Maxwell model and Friedrich-Braun model. The surface tensions of aqueous systems containing polysaccharide and/or surfactants have been determined over extended concentration ranges in order to detect the CMC conditions and to provide a better understanding about the polysaccharide-surfactant interactions.     

Stereoselective synthesis of beta-(chloro)vinylsilanes using a regio- and (E)-stereoselective bis-stannylation of unsymmetrically substituted butadiynes: application to the synthesis of a masked triyne

[reaction: see text] A highly regio- and stereoselective bis-stannylation of unsymmetrically substituted butadiyne 3 provides bis-stannane 4. Selective lithiation of the internal tin residue effects a 1,4-retro-Brook rearrangement to afford vinylsilane 5. This was elaborated into the novel diethynylethene 1, which also functions as a masked triyne.     

Analysis of acrylamide in food by isotope-dilution liquid chromatography coupled with electrospray ionization tandem mass spectrometry

A confirmatory method for the determination of low levels of acrylamide in different food products is presented. The method entails extraction of acrylamide with water, precipitation of matrix constituents with acetonitrile, and two clean-up steps consecutively over Isolute Multimode and cation-exchange cartridges. The final extract is analyzed by liquid chromatography (LC) coupled to positive electrospray ionization tandem mass spectrometry employing [13C3]-acrylamide as internal standard. For the chromatographic step, a LC column based on a polymethacrylate gel is employed which shows good retention of acrylamide under isocratic flow conditions (k' = 1.2). Mass spectral acquisition is done by selected reaction monitoring, choosing the characteristic transitions m/z 72-->55, 72-->54 and 72-->27. In-house validation data for breakfast cereals and crackers show good precision of the method, with intra- and interassay variation below 10%. The limits of detection for crackers and breakfast cereals, respectively are estimated at 15 and 20 microg/kg, and recoveries of fortified samples ranged between 58 and 76%. Furthermore, the method is applicable to a number of different food products, including biscuits, crisp bread, wafers, confectionery cocoa liquor, and nuts. Finally, the good results obtained in several small-scale interlaboratory tests provided additional confidence in the performance of the method.