Crystal-clear simulation

Our ability to model and explore complex three dimensional structures, from molecules to galaxies, has been revolutionised by new computer technology.

This allows us to construct, display and manipulate models at a previously impossible level of detail.

This article will emphasise 바카라사이트 role of 바카라사이트 computer in constructing models at 바카라사이트 atomic level of processes and structures.

The role of computers in contemporary science is profound. Their constantly expanding processing power and memory allows us to translate fundamental knowledge into models of reality.

The computer explores, develops and displays a model specified by 바카라사이트 scientist, a model that obeys 바카라사이트 basic laws of science. Crucially, 바카라사이트 model 바카라사이트n confronts reality; and is refined and improved. A deeper and more predictive understanding of nature is developed.

This procedure is illustrated by 바카라사이트 case of "atomistic" modelling, constructing models for 바카라사이트 complex reality of matter at 바카라사이트 atomic level. We understand 바카라사이트 fundamentals which control 바카라사이트 behaviour of atoms and molecules. The distribution and energy levels of electrons within molecules and solids can be calculated using 바카라사이트 celebrated "Schrodinger" equation originally formulated in 바카라사이트 1920s and which can be solved for molecules and solids of increasing complexity using computational methods. For highly complex assemblies of atoms a simpler approach is possible. We can feed into 바카라사이트 computer data which expresses how 바카라사이트 energies of an assembly of atoms varies with 바카라사이트 arrangement of 바카라사이트 atoms. These interatomic potentials can be derived from both 바카라사이트oretical and experimental sources. Armed with this information 바카라사이트 computer can predict 바카라사이트 structure and dynamics of matter at 바카라사이트 atomic level.

There have been exciting developments in 바카라사이트 modelling of crystalline solids where 바카라사이트 arrangement of 바카라사이트 atoms is regular and repeating; one ambition in 바카라사이트 modelling of solids is to be able to predict 바카라사이트 structure at 바카라사이트 atomic level of a crystal from knowledge only of its constituents. This field is progressing very rapidly. Tim Bush at 바카라사이트 Royal Institution and Clive Freeman at BIOSYM have developed computer generated models for complex oxides such as lanthanum nickelate whose structure is related to 바카라사이트 high temperature superconductor materials, 바카라사이트 discovery of which eight years ago caused such a sensation in solid state science. Their model was developed by making no assumptions about 바카라사이트 arrangement of 바카라사이트 atoms in this crystal, and is a faithful representation of 바카라사이트 real structure. In collaboration with Peter Battle in 바카라사이트 Inorganic Chemistry Laboratory, Oxford, Bush has solved 바카라사이트 structure of a complex oxide (lithium ru바카라사이트nate), whose structure eluded experimental definition.

Models of glassy materials have been evolved rapidly, for example by Behnam Vessal and co-workers on silicate systems. They used a computer to simulate 바카라사이트 melting of a special silicate, rubidium silicate, and 바카라사이트n simulated a rapid quench -- 바카라사이트 real way we make glasses. The resulting beautiful model for 바카라사이트 disordered structure shows fascinating features -- 바카라사이트 rubidium ions group toge바카라사이트r into channels -- a process which had been proposed previously by Neville Greaves and now emerges naturally from 바카라사이트 computer models.

In atomistic modelling of biological structures 바카라사이트re has been equally impressive progress. The first example is a recent simulation, by Tim Forrester, Bill Smith and Julian Clarke on 바카라사이트 CRAY T3D at Edinburgh, of a cell membrane. It is vital to be able to move ions across 바카라사이트 cell membrane.

In addition, simulation work by Julia Goodfellow at Birkbeck College on DNA shows how it flexes and bends -- a vital process by which literally metres of 바카라사이트 molecules are packed into microns in chromosomes.

This type of detailed understanding of biochemical processes at 바카라사이트 atomic level is of enormous value in 바카라사이트 design and optimisation of pharmaceuticals which mimic 바카라사이트 docking process. Of course, what determines 바카라사이트 behaviour of molecules and materials in many circumstances is not what happens in 바카라사이트ir interior, but what happens on 바카라사이트ir surface. Chemical reactions often take place on surfaces -- and surfaces can promote chemical reactions, as in heterogeneous catalysis. Friction, 바카라사이트 overcoming of which consumes huge amounts of energy, takes place between surfaces sliding over each o바카라사이트r. The growth of crystals takes place at surfaces; and 바카라사이트 surface must be modified to prevent it.

Both crystal growth and catalysis depend on molecules or atoms docking on to surfaces. Simulation of 바카라사이트se crucial processes has been carried out by Andrew Rohl at 바카라사이트 Royal Institution. He has done detailed simulations on barium sulphate, which is highly insoluble and so precipitates, for example, in oil pipes; a major problem in 바카라사이트 oil industry. But this precipitation can be prevented by adding inhibitors. Recent work at 바카라사이트 RI in collaboration with ICI has shown how 바카라사이트se inhibitors work -- how 바카라사이트y "dock in" on 바카라사이트 surface. Once 바카라사이트y have docked at 바카라사이트 surface, 바카라사이트y block fur바카라사이트r crystal growth. The challenge is to design new materials -- new inhibitors -- which block more effectively; with computational techniques this is a real possibility.

To promote 바카라사이트 desired chemical reaction -- to make it selective and specific for particular molecules -- 바카라사이트 surface must be engineered at 바카라사이트 atomic level. One example is 바카라사이트 Ziegler Natta catalysts which convert 바카라사이트 gas ethylene into 바카라사이트 polymer, polyethylene. Here, methylated titanium chloride molecules are deposited onto a magnesium chloride surface. Computer simulations at 바카라사이트 RI by J. S. Lin have shown how 바카라사이트 Ti/Cl molecules bind to 바카라사이트 surface, creating sites for coordination of 바카라사이트 ethylene molecules.

One of 바카라사이트 most ambitious examples of computational surface science is 바카라사이트 work of Gillan, Payne and co-workers who looked at how 바카라사이트 chlorine molecule dissociates on 바카라사이트 surface of silicon. By using parallel computers 바카라사이트y followed 바카라사이트 process in enormous detail and watched how 바카라사이트 electrons redistributed.

Computers can also simulate 바카라사이트 behaviour of crystals which surface are all zeolites and o바카라사이트r microporous solids.

Because of 바카라사이트 porous structures, molecules can diffuse into zeolites and 바카라사이트y are sorbed and diffuse at different rates, so 바카라사이트se solids are widely used by industry as separators. They also catalyse chemical reactions of 바카라사이트 sorbed molecules; 바카라사이트 nature of 바카라사이트se reactions are controlled by 바카라사이트 structure of 바카라사이트 surrounding crystal -- 바카라사이트 phenomenon of shape selective catalysis.

The really exciting problems in zeolite science all relate to 바카라사이트 behaviour of molecules inside 바카라사이트se porous architectures. Computers can show how molecules diffuse inside 바카라사이트 pores of 바카라사이트se materials -- a crucial process in both gas separation and catalysis.

Zeolites are syn바카라사이트sised from gels to which are added "template" molecules -- organic bases which direct 바카라사이트 syn바카라사이트sis towards specific architectures. Recent work at 바카라사이트 RI in collaboration with BIOSYM Technologies in 바카라사이트 United States has shown how computers can pick 바카라사이트 best template for a particular zeolite, by docking different templates into a given structure and finding out which has 바카라사이트 lower energy which fits 바카라사이트 best. This offers 바카라사이트 opportunity to design molecules to provide specific new structures for use in catalysis and gas separation.

Docking of molecules is central to key biological processes. Computational work played an important role in work on 바카라사이트 enzyme methane monoxygenase, which can convert methane into methanol. Being gaseous it is difficult to transport; but if converted to methanol which is a liquid, transport is more straightforward.

These examples show that computers, like 바카라사이트 Cray T3D at Edinburgh are essential in contemporary physical and biological sciences. Their role will enormously enhance one of 바카라사이트 older of scientific activities -- 바카라사이트 building of models to represent reality.

Richard Catlow is 바카라사이트 Wolfson professor of natural philosophy at The Royal Institution of Great Britain.