Atoms visualizing

Figure 5.4. Atomic visualization of NEMCA during ethylene C2H

Y.l. Comparison of the Pauli deformation for two hydrogen atoms and for two helium atoms, (a) Two hydrogen atoms. Visualization of p — p calculated in the plane containing the nuclei (the net result is zero). One of the protons is located at the... 

Atoms visualized as spheres have diameters of around 1-3 X 10 ° m (100-300 pm). By way of comparison, a small marble has a diameter of around 1 cm (1 X 10 m), which is about 100 000 000 times that of a typical atom. 

C. Bigg, Evident atoms visuality in Jean Perrin s Brownian motion research. Stud. Hist. Phil. Sci. 

C. Bigg, Evident atoms visuality in Jean Perrin s Brownian motion research. Stud. Hist. Phil. Sci. 39(3), 312-322 (2008). doi 10.1016/j.shpsa.2008.06.003... 

Fig. Y.l. Coin)arison of the Pauli deformation for two hydrogen atoms and for two helium atoms, (a) Two hydrogen atoms. Visualization of p — calculated in the plane containing the nuclei (the net result is zero). One of the protons is located at the origin, and the other has the coordinates (0, /f, 0), with / = 1.4 a.u. (the distance close to the equilibrium). For this distance, the overly integral (see Appendix R available at booksite.elsevier.com/978-0-444-59436-5, p. el37) 5 = (1 + / + )exp —R) amounts to 0.752943. As we can see, the electronic density has flown from the nuclei to the bond, (b) Two helium atoms. The only difference with respect to (a) is that two electrons have been added. But the visualization of p — p( reveals a completely different pattern. This time, the electronic density has been removed from the bond region and increased in the region of the nuclei.

G.V.Akulov, V.I.Bogdashkin, V.A.Moskalev, V.L.Nikolaev, A.V.Tzimbalist, V.V.Shashov, V.G.Shestakov - Mobile betatron installation on energy of 25 MeV for radiative visualization of dynamic processes and flaw detection in field conditions. Atomic science and technique problems. Electrophysical equipment. -1987,v.23,p. 19-21. 

While field ion microscopy has provided an effective means to visualize surface atoms and adsorbates, field emission is the preferred technique for measurement of the energetic properties of the surface. The effect of an applied field on the rate of electron emission was described by Fowler and Nordheim [65] and is shown schematically in Fig. Vlll 5. In the absence of a field, a barrier corresponding to the thermionic work function, prevents electrons from escaping from the Fermi level. An applied field, reduces this barrier to 4> - F, where the potential V decreases linearly with distance according to V = xF. Quantum-mechanical tunneling is now possible through this finite barrier, and the solufion for an electron in a finite potential box gives... 

These electronic energies dependence on the positions of the atomic centres cause them to be referred to as electronic energy surfaces such as that depicted below in figure B3.T1 for a diatomic molecule. For nonlinear polyatomic molecules having atoms, the energy surfaces depend on 3N - 6 internal coordinates and thus can be very difficult to visualize. In figure B3.T2, a slice tln-oiigh such a surface is shown as a fimction of two of the 3N - 6 internal coordinates. 

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

The space filling model developed by Corey, Pauling, and Koltun is also known as the CPK model, or scale model [197], It shows the relative volume (size) of different elements or of different parts of a molecule (Figure 2-123d). The model is based on spheres that represent the "electron cloud . These atomic spheres can be determined from the van der Waals radii (see Section 2.10.1), which indicate the most stable distance between two atoms (non-bonded nuclei). Since the spheres are all drawn to the same scale, the relative size of the overlapping electron clouds of the atoms becomes evident. The connectivities between atoms, the bonds, are not visualized because they are located beneath the atom spheres and are not visible in a non-transparent display (see Section 2.10). In contrast to other models, the CPK model makes it possible to visualize a first impression of the extent of a molecule. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

Some of the other features of this program are the ability to compute transition states, coordinate driving, conformation searches, combinatorial tools, and built-in visualization. The builder includes atoms and fragments for organics, inorganics, peptides, nucleotides, chelates, high-coordination geometries, and... 

Wave functions can be visualized as the total electron density, orbital densities, electrostatic potential, atomic densities, or the Laplacian of the electron density. The program computes the data from the basis functions and molecular orbital coefficients. Thus, it does not need a large amount of disk space to store data, but the computation can be time-consuming. Molden can also compute electrostatic charges from the wave function. Several visualization modes are available, including contour plots, three-dimensional isosurfaces, and data slices. 

The First Reactor. When word about the discovery of fission in Germany reached the United States, researchers thereafter found that (/) the principal uranium isotope involved was uranium-235 (2) slow neutrons were very effective in causing fission (J) several fast neutrons were released and (4) a large energy release occurred. The possibiUty of an atom bomb of enormous destmctive power was visualized. 

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