Linked circles

The resolvases act on supercoiled cointegrated DNA molecules that contain two directly repeated res sites to produce two singly linked circles (which are still supercoiled) each containing one res site as shown in Fig. 27-32. The two res (resolution) sites within the transposons are aligned, the open circle of DNA shown at the upper left being folded as shown in the lower part of the drawing. The DNA substrate is not knotted. However, after recombination it is catentated and will require action of a topoisomerase to separate... 

Let us start by examining the connectivity of the AOs intervening in the reaction. They are numbered as indicated in 34. In 35, overlapping AOs are represented as linked circles. As shown in 36, this system may be considered as resulting from the union of two alternant radicals (drawn in bold lines). Union of their nonbonding MO gives two null, one favorable and three unfavorable interactions. The thermal reaction is thus not favorable. 

Figure 10.32 An auxetic network. The bonds (drawn as lines) between elements of the stmcture are of fixed length, but the links (circles) are flexible, (a) Initial state, (b) Configuration under an applied force, F the material expands both parallel and perpendicular to the direction of the force...

The dark circles represent 0-linked carbohydrate and the dark squares represent /V-1inked carbohydrate. Both types of carbohydrate are added after... 

Fig. 2. A representation of the cellulose chain ia solution, projected against three two-dimensional surfaces. The circles represent the oxygen atoms that link the iadividual glucose residues, and the lines take the place of the sugar residues. This result of a modeling study (39) iadicated a molecule somewhat more...

Vibrating grizzlies. These are simply bar grizzlies mounted on eccentrics so that the entire assembly is given a back-and-forth movement or a positive circle throw. These are made by companies such as AUis-Chalmers, Hewitt Robins, Nordberg, Link-Belt, Simphcity, and Tyler. 

As we mentioned above, however, linearly inseparable problems such as the XOR-problem can be solved by adding one or more hidden layers to the perceptron. Figure 10.9, for example, shows a solution to the XOR-problem using a perceptron that has one hidden layer added to it. The numbers appearing by the links are the values of the synaptic weights. The numbers inside the circles (which represent the hidden and output neurons) are the required thresholds r. Notice that the hidden neuron takes no direct input but acts as just another input to the output neuron. Notice also that since the hidden neuron s threshold is set at r = 1.5, it does not fire unless both inputs are equal to 1. Table 10.3 summarizes the perceptron s output. 

Figure 1. The crystal structure of Zr2(0H)2(SO4)3(H2O)4> reprinted with permission from Ref. 5, copyright 1966, American Chemical Society. Zirconium atoms are shown as solid circles, oxygen atoms as open circles. The Pu compound is isomorphous, Zr being replaced by Pu. la shows the manner in which the bridging sulfates link Pu atoms to form layers, lb shows the manner in which layers are linked through the double hydroxide bridges.

Fig. 8.—Packing arrangement of four symmetry-related 2-fold helices of mannan II (6). (a) Stereo view of two unit cells approximately normal to flic frc-plane. The two chains in the back (open bonds) and the two in the front (filled bonds) are linked successively by 6-0H-- 0-6 bonds. The front and back chains, both at left and right, are further connected by 0-2 -1V -0-2 bridges, (h) Projection of the unit cell along the c-axis the a-axis is down the page. This highlights the two sets of interchain hydrogen bonds between antiparallel chains, distinguished by filled and open bonds. The crossed circles are water molecules at special positions.

Fig. 9. — Antiparallel packing arrangement of the 3-fold helices of (1— 4)-(3-D-xylan (7). (a) Stereo view of two unit cells roughly normal to the helix axis and along the short diagonal of the ab-plane. The two helices, distinguished by filled and open bonds, are connected via water (crossed circles) bridges. Cellulose type 3-0H-0-5 hydrogen bonds stabilize each helix, (b) A view of the unit cell projected along the r-axis highlights that the closeness of the water molecules to the helix axis enables them to link adjacent helices.

Fig. 28.—Antiparallel packing arrangement of 4-fold helices of sodium hyaluronate (26). (a) Stereo view of a unit cell approximately normal to the hc-plane. The two comer chains in the front (filled bonds) are linked directly by hydrogen bonds. The chain at the center (open bonds) interacts with die comer chains via sodium ions (crosses circles) and hydrogen bonds.

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

FlC. 32.—Antiparallel packing arrangement of the 2-fold helices of calcium chondroitin 4-sulfate (35). (a) Stereo view of two unit cells approximately normal to the he-plane. The two comer chains, drawn in filled bonds are hydrogen bonded to the antiparallel center chain (open bonds). Calcium ions (crossed circles), associating with sulfate and carboxylate groups and water molecules link adjacent antiparallel chains, which ate also directly hydrogen bonded. 

Fig. 3.4 Polyamide-DNA binding motifs with equilibrium association constants K,). Hairpin amino-substitution at the a-position of the y-turn residue leads to enhanced binding affinity (10-fold) without loss of specificity, and with higher orientational selectivity and offers potential for further substitution. Cycle Cyclic polyamides show higher affinity than analogous hairpin molecules with the same number of cationic groups and eliminate all possibility of extended 1 1 binding. H-pin and U-pin compared to their non-linked analogs, H-pins and U-pins exhibit higher binding affinity. The black and open circles represent Im and Py rings, respectively diamonds repre-...

Fig. 8.1 Biosynthesis of peptidoglycan. The large circles represent A -acetylglucosamine orN-acetylmuramic acid to the latter is linked initially a pentapeptide chain comprising L-alanine, D-glutamic acid and meso-diaminopiraelic acid (small circles) terminating in two D-alanine residues (small, darker circles). The lipid molecule is undecaprenyl phosphate. In the initial (cytoplasm) stage where inhibition by the antibiotic D-cycloserine is shown, two molecules of Dalanine (small circles) are converted by an isomerase to the D-forms (small, darker circles), alter which a ligase joins the two D-alanines together to produce a D-alanyl-D-alanine dipeptide.

Fig. 8.1 Hypothetical two-dimensional model of human P-glycoprotein. Small circles amino acid residues large circles ATP sites squiggly lines N-linked glycosylation sites (modified from [15]).

Fig. 15 (a) Scheme of the interface of a two Hg-drops electrochemical junction incorporating covalently linked Ru(II)-based redox sites yellow circles), (b) I—V curves obtained by keeping one electrode potential fixed at —0.02 V and sweeping the potential applied at the second electrode, (c) Representation of the operating self-exchange mechanism red circles represent the Ru(III) oxidation state. All potentials are measured against an Ag/AgCl reference electrode... 

Figure 2. Interconversion coordinate used in generic group exchange reactions. In this case a Sjq2 model is described. The donor and acceptor in the scheme above would correspond for instance to an halide ion Y- entering from the right in the APC and the leaving group is the halide ion Y-. The central carbon is shetched by the dark circle. The distance R is determined by the SPi-1, and the quantum states to the left and the right of the plane formed by the 3-substituents linked to the C-atom being different, they cannot physically be reached by an adiabatic process as implied in the BO-scheme if quantum mechanics must prevail (two different quantum states cannot be linked adiabatically ).

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