A Perspective View

Encouraging progress has been made recently, and we are now in an era of active application of molecular dynamics simulation to study the folding process. Because of the vital importance of water in protein folding and in the cell, the explicit repre- 

We extrapolate from two simulations, the 10 ps simulation on bovine pancreatic trypsin inhibitor (BPTI) reported over twenty years ago [61] and the recent 1 gs simulation on the villin headpiece subdomain. [9] Each of these was a state-of-the-art simulation, using the best algorithms and the most powerful hardware available at the time. 

The computational power, P, of a molecular dynamics simulation is proportional to the length of the time period being simulated (t, measured in seconds) and to the rth power of the number of heavy (nonhydrogen) atoms, n. The value of r depends on how one calculates the interatomic interactions. There are about n2/2 pairwise interactions, so r=2 if all interactions are included in the calculation. At the other extreme, a common approach is to use a finite cutoff distance, in which case there 

An exact determination of the relative values of P for the BPTI and villin simulations is not possible, because some algorithmic developments reduce computational costs (particularly methods that allow one to increase the size of the time step and to efficiently treat long-range interactions), while others increase the costs (e.g., more detailed force fields and appropriate boundary conditions). But we can place reasonable bounds on the historical growth rate of P by using r=l and r=2 as lower and upper limits on the costs of calculating interatomic interactions. 

As in all computer applications for the past few decades, P has been growing exponentially with time. It is a straightforward calculation to show that in the 21 years between the BPTI simulation (t = KTns n 600) and the villin headpiece simulation (t = KT6 s n 12 000), P has been increasing by a factor of 10 every 3-4 years. A simple extrapolation would thus predict that a simulation covering the replication cyde of an intact E. coli with a volume of about 1 p3 (t 1000 s n=3x 1010) could be expected some time in the second half of the next century if computational power continued to grow exponentially at historical rates. 

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Figure B3.2.7. A perspective view of the cetineite (Na Se). The height of the figure is tluee lattice constants c. The shaded tube is included only as a guide to the eye. (From [88].)...

Figure 5.1-5 shows a perspective view of one loop of the system. Note that in this system, kinematic constraints in the form of pipe supports, anchors, and hangers are minimal. Only the pumps are laterally braced by the suppressors. The pumps in this system are supported by hangers from above. 

Sawhorse structure (Section 3.6) A manner of representing stereochemistry that uses a stick drawing and gives a perspective view of the conformation around a single bond. 

All aspects of interferogram and experimental data acquisition and optical test rig control are provided by a computer program that also performs film thickness evaluation. It is believed that the film thickness resolution of the colorimetric interferometry measurement technique is about 1 nm. The lateral resolution of a microscope imaging system used is 1.2 /u,m. Figure 10 shows a perspective view of the measurement system configuration. This is an even conventional optical test rig equipped with a microscope imaging system and a control unit. 

Fig. 3. A perspective view of the structure of Cl3SiRh(H)(Cl)(PPh3)2. (There is a close o-H/Rh contact.)...

A perspective view of 12 is shown in Figure 6.2. X-ray structure analysis8 on the fluoran shows that the xanthene moiety is slightly bent... 

Keith H, Telliard WA (1979) Priority pollutants I. A perspective view. Environ Sci Technol 13 416-423... 

In this paper, first we will briefly describe the Pt[P(i-Pr 3"ca al zed W9S reacti°n (4). Recently we have studied RhHLg (L=PRj)-catalyzed wgs reaction in much more details. In comparison with the PtLj reaction, a perspective view of RhHLj (here we confine I PO-Pr) )-catalyzed wgs reaction will be given below. 

In Fig. 18, flow path lines are shown in a perspective view of the 3D WS. By displaying the path lines in a perspective view, the 3D structure of the field, and of the path lines, becomes more apparent. To create a better view of the flow field, some particles were removed. For Fig. 18, the particles were released in the bottom plane of the geometry, and the flow paths are calculated from the release point. From the path line plot, we see that the diverging flow around the particle-wall contact points is part of a larger undulating flow through the pores in the near-wall bed structure. Another flow feature is the wake flow behind the middle particle in the bottom near-wall layer. It can also be seen that the fluid is transported radially toward the wall in this wake flow. 

Figure 1.14 Crystal structure of sodium chloride, NaCl (a) a perspective view of one unit cell and (h) projection down [010], the b axis.

Figure 3.18 Cadmium iodide, Cdl2, structure (a) perspective view of the structure as layers of Cdlg octahedra (b) one layer of the structure, with the lower I- anion (A) layer and the middle Cd2+ (c) layer shown complete and just three anions of the upper (B) layer indicated. The vector b represents the Burgers vector of one of three unit dislocations and bl and b2 represent the Burgers vectors of the two equivalent partial dislocations. The unit cell dimensions are a, b, and c.

Figure 2.31. Schematic representation of the P/T equilibria in a simple two-component system (forming continuous solid and liquid solutions). In (a) a perspective view of the P-T-X diagram is shown in (b) its projection on the P/T plane. Notice the two single-component systems represented, for instance, for the component B by the three lines SB/G (sublimation line of B representing the gas/so lid equilibrium), SB/LB (melting equilibrium of B) and the boiling line LB/G. The solid solution is indicated by a. Notice in (a) the isobaric and isothermal sections of the diagrams (compare with Fig. 2.1).

A perspective view of the graphical symbols used in the International Tables (Hahn 2002) for the different axes is shown, (t is the shortest translation vector in the direction of the axes). The projection (along these axes) on the base plane of the equivalent points is also shown notice that the same projection is obtained in all the cases illustrated. The coordinates of all the equivalent points in the different sets are listed. Notice that the x, y, z coordinates are fractional coordinates they indicate the positions along the corresponding directions as fractions of the constants a, b and c (in these examples c = t). 

Figure 4.36. The body centred tetragonal structure of Ti5Te4. (a) perspective view of three superimposed unit cells. A Ti5Te4 chain passing through the centres of the cells is outlined. Inside see the clusters Ti6Te8. In every unit cluster, the Ti6 octahedron and the Te8 cube are shown.

A perspective view of this structure and a projection of the unit cell are shown in Fig. 4.36. Notice the chain structure resulting from the condensation of Ti6Te8 clusters. Similar groups (such as Mo6S8) are found, as building units, in several compounds. 

The hP3-A B2 type is presented as another example of the use of characteristic projections. A perspective view of the unit cell and the section sequence along the c axis of the cell are depicted in Fig. 7.5. Convenient representative projections in this case may be those on two perpendicular planes, that is on plane (001) and (110). The projection on the plane (001) of a portion (nine cells) of the structure is shown with the trace of the conventional hexagonal cells and the rectangular trace of the equivalent ortho-hexagonal cell (see the 3.6.1.3). The projection on a diagonal vertical plane (110), is also shown. 

The characteristic sections of a few adjacent cells of NaCl are shown in Fig. 7.21. A perspective view of the cell is shown in Fig. 3.33. 

Figure 7.53. tP6-Ti02 rutile. The sequence of characteristic sections of the structure and a perspective view of the unit cell are shown. Notice the Ti atom surrounded hy 6 O forming an (irregular) octahedron. 

Fig. 10. Molecular and electronic structure of cation 74. (a) Perspective view on the cation 74. (b) Coordination sphere of the Pb atom, selected interatomic distances (pm) and angles (deg) Pb-(center CC, C7), 281.7 Pb-(center C6 CT), 280.7 Pbl-C2, 227(2) Pbl-C2 221.1(15) Pbl-C8, 231.0(19) C6-C7, 133(2) CC-CT 132(2) (center C6, C7)-Pb-(center C6, C7 163.6. (c) Contour plots of the Laplacian distribution [V p(r)] in the plane containing the atoms Pb, C6 and C7. Solid and dotted lines designate regions of local charge concentration and depletion, respectively. The bond paths are indicated by the solid back lines, bond critical points are marked with a black square. (Reprinted with permission from Ref. 53. Copyright 2003, Wiely-VCH.)...

A perspective view of one of the molecules isolated, (NPAz2)2(NSOAz), is shown in Fig. 40 the chosen model belongs to SOAz (I). In this Fig., obtained using the program Ortep of Johnson the numbering of the atoms is indicated, and is identical for both structures SOAz (I) and SOAz (II) (molecules A and B). 

Fig. 12. Structure of 4-nitro-l,2-benzenediamine [18]crown-6 complex 22) a a perspective view, b as viewed almost perpendicular to the plane of the crown, hydrogen bonds marked with dotted lines...

Figure 8 A perspective view of the [Zr(S2C6H4)3]2 anion. The complex is located on a crystallographic twofold axis...

Figure 17 A perspective view of [VOCl2(Me3N)2]. The bond lengths are in A. The angles in the equatorial plane are...

Figure 36 A perspective view of the molecular structure of [VO(2-methyl-8-quinolinolato)2] with some internuclear...

A perspective view of an [MXJL chain showing the proposed structure of the Cr11—Cr pair. The corners of the octahedra are occupied by halide ions.1080... 

Keither, L. H. Telliard, W.A. (1979). Priority pollutants. I. A perspective view. Environmental Science and Technology, 13, 416-23-... 

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