Loop folding

Figure 23. Aquaporin, water-channel protein, (a) End-on view of the pore from extracellular surface, (b) side-view of the pore-canal, (c) six membrane spanning helices of the aquaporin monomer. The asparagine-proline-alanine (NPA) motifs in the second and fifth loops fold in to produce the water channel.

The gather and scatter phases in the above are not directly vec-torisable on the CRAY, but may be quasi-vectorised by means of loop folding techniques in the Scalar hardware. Hie timing for... 

The folded structure of the ATP-binding region from one of these RNAs was determined by nuclear magnetic resonance (Section 4.5.1) methods (Figure 7.25). As expected, this 40-nucleotide molecule is composed of two Watson-Crick base-paired helical regions separated by an 11-nucleotide loop. This loop folds back on itself in an intricate way to form a deep pocket into which the adenine ring can fit. Thus, a structure was generated, or evolved, that was capable of a specific interaction. 

CHAPTER 36, FIGURE 7 A group of structurally similar protein inhibitors of the serine proteinases known as SERPINS (SERine Proteinase INhibitors). The structure shown is human antithrombin. The reference SERPIN, a j-proteinase inhibitor or a. -antitrypsin contains -30% a helix (9 helices) and 40% sheet (5 3 sheets). Other members of the SERPIN family contain both additional helices and p sheets. The reactive center loop of antithrombin, residues 378-396, contains the reactive site residues Arg and Ser . Upon reaction with the target proteinase or after cleavage by the target proteinase (a reaction that inactivates the inhibitor without inactivating the proteinase), the reactive center loop folds between the S3 and S5 sheets. 

Iwata and coworkers ° ° also investigated enzyme adsorption to copolymer single crystals, and reported that PHA depolymerase adsorbed randomly on the surfaces of single crystals. However, the concentrations of adsorbed enzjune on the surface of copolymer single crystals are lower than that for P(3HB) homopolymer single crystals. PHA depolymerase molecules cannot bind tighdy to the irregular surface of copolymer crystals since the copolymer chains with second monomer units have loose loop folds. 

Figure 9 Distribution graphs of multiplier resources before (left) and after loop folding.

Figure 10 Flow graph of DHRC example after loop folding.

P. Pochmiiller and M. Glesner. Force directed loop folding. ITG-Fachbericht 122, VDE-Verlag, pages 135-146, Nov 1992. 

Performs loop folding, overlapping the execution of successive loop iterations. 

CATHEDRALL-II overview, scheduling, EXU assignment, loop folding, and a fifth-order filter for a PCM telephony application. 

Performs loop folding, overlapping the execution of successive loop iterations. Then uses list scheduling, with priorily to... 

Extensions to the basic algorithm handle pipelined functional units, a pipelined data path, and loop folding. 

The concept of loop folding is very similar to that of function pipelining. The only difference is that in loop folding, there exists data dependencies across loop iterations, while in function pipelining, there is no data dependency between instances. 

Thus, the latency of a pipelined data path can be arbitrarily small, provided that the resources are unlimited. In the loop folding case, the latency (or loop length[15]) depends on not only the resources available but also the structure of the DFG. 

We have tested THEDA using a number of well-known benchmarks. Here, we show the results of the fifth order elliptic filter[10]. It contains 26 additions and 8 multiplications. A multiplication takes 2 cycles while an addition takes 1 cycle to complete. The critical path length is 17 cycles and it can be reduced to 16 cycles by loop folding. TABLE II shows the results obtained by this system. Fig. 5(a) shows the schedule of 17 control steps by Pipeline List Scheduling[7] and Fig. 5(b) shows the allocation result. 

For large problems, the zone scheduling is applied. The pipeline list scheduling can be used in functional pipelining and loop folding. 

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