Molecular computations

Oxford Center for Molecular Sciences United Kingdom 

Life is computation. Every single living cell reads information from a memory, rewrites it, receives data input (information about the state of its environment), processes the data and acts according to the results of all this computation. Globally, the zillions of cells populating the biosphere certainly perform more computation steps per unit of time than all man made computers put together. 

While the genetic role of nucleic acids has been known for several decades, the roles of proteins for molecular computation in the cell is only just beginning to be explored. Signal transduction even if it is only to do with yes or no signals, is a complex business, which only very slowly yields to massive research efforts. Even more so, the more complex logical connections and quantitative interdependencies in the cell have eluded research so far. A brief overview on nature s reservoir of 

Non-Standard Computation. T. GramQ, S. Bomholdt, M. GroB, M. Mitchell, T. Pellizzari Copyright 1998 WILEY-VCH Verlag GmbH, Weinheim ISBN 3-527-29427-9 

While we seem to know more about the computational aspects of DNA than of those of proteins in the cell, this situation is reversed in the application of biomolecules in artificial computing systems. Although some light harvesting proteins such as bacteriorhodopsin (bR) have been used in attempts to create molecular (computer) memories since the early 1970s, the notion of DNA-based computing only came up in 1994. This paradox may partly be explained by the fact that relatively small populations of bR molecules can be manipulated and read by laser light which has been available for several decades, whereas the methods to deal with small amounts of DNA have only been developed very recently. Computational applications of both DNA and proteins in artificial systems will be discussed in detail in Sect. 2.2 

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Texas Center for Advanced Molecular Computation, University of Houston, Houston, TX 77204-5502, USA... 

One way to model a solid is to use software designed for gas-phase molecular computations. A large enough piece of the solid can be modeled so that the region in the center for practical purposes describes the region at the center of an inhnite crystal. This is called a cluster calculation. 

In addition to various analytic or semi-analytic methods, which are based on the theory of the liquid state and which are not the subject of this chapter, almost the entire toolbox of molecular computer simulation methods has been applied to the theoretical study of aqueous interfaces. They have usually been adapted and modified from schemes developed in a different context. 

Rothschild W. G. Vibrational resonance energy transfer and dephasing in liquid nitrogen near its boiling point molecular computations, J. Chem. Phys. 65, 2958-61 (1976). 

The dissemination of computers, and the diffusion of complex computational packages, has given origin to another type of members of group 111, the "molecular computers". 

Abstract A review is provided on the contribution of modern surface-science studies to the understanding of the kinetics of DeNOx catalytic processes. A brief overview of the knowledge available on the adsorption of the nitrogen oxide reactants, with specific emphasis on NO, is provided first. A presentation of the measurements of NO, reduction kinetics carried out on well-characterized model system and on their implications on practical catalytic processes follows. Focus is placed on isothermal measurements using either molecular beams or atmospheric pressure environments. That discussion is then complemented with a review of the published research on the identification of the key reaction intermediates and on the determination of the nature of the active sites under realistic conditions. The link between surface-science studies and molecular computational modeling such as DFT calculations, and, more generally, the relevance of the studies performed under ultra-high vacuum to more realistic conditions, is also discussed. 

Uchiyama S, McClean GD, Iwai K et al (2005) Membrane media create small nanospaces for molecular computation. J Am Chem Soc 127 8920-8921... 

L.M. Adlernan, Molecular computation of solutions to combinatorial problems. Science 266, 1021-1024 (1994). 

Molecular complexity, scales of, 24 31 Molecular computers, 27 61-62 24 60 Molecular design, computer-aided, 26 999 Molecular diffusion, 20 751. See also Diffusion... 

Rotational suspension separation encapsulation process, 16 450 Rotational viscometers, 21 731-737 computers in, 21 732 operation of, 21 736 Rotations, of molecules cause of color, 7 326t, 328 Rotavirus vaccine, 25 496 Rotaxanes, 17 61, 24 31, 33, 51 as molecular computers, 24 60 Rotenone (Chem-Fish Synergized,... 

Molecular and supramolecular devices incorporated into ultra-micro-circuits represent potential hardware components of eventual systems that might qualify as molecular computers, whose highly integrated architecture and operation would not be of the von Neumann type. On the biological side, the fabrication of components for sensory and motor protheses could be considered. All these entities may result from the self-assembly of suitably instructed subunits so that computing via self-assembly may be envisaged. 

M. Conrad, Molecular computing the lock-key paradigm. Computer, 11,11-20 (1992). 

F. T. Hong, The bacteriorhodopsin model membrane system as a prototype molecular computing element, BioSystems, 19, 223-236 (1986). 

The purpose of this section is to present a short overview, with relevant examples, of some aspects of molecular computations. In-depth treatments can be found in textbooks such as that by Levine, and in the overview by Irikura and Frurip. ... 

This is a burgeoning area of research and it is now obvious that this type of work holds out the potential for molecular computers and neural networks using photon mode input (see also Chapter 5, section 5.7). ... 

Nanowires can also be deposited from a flowing liquid causing them to lie in the same direction and forming arrays. Changing the direction of flow allows an overlay of a second layer, and such arrays can be used for various electronic devices such as transistors and diodes. The thrust of this type of research is aimed at miniaturization, and ultimately with producing a molecular computer. 

We have developed ultrahigh-precision coherent control based on this WPI, in which we have succeeded in visualizing and controlling the ultrafast evolution of a WP interference in a molecule with precisions on the picometer spatial and attosec-ond (as) temporal scales [37-39], This is the cutting edge of coherent control. We have utilized this ultrahigh-precision coherent control to develop a molecular computer that executes ultrafast Fourier transform with molecular wave functions in 145 fs [40,41], More recently, we have extended the target of our coherent control to wave functions delocalized in a bulk solid [42,43], In this account, we will describe these developments of our experimental toolbox and the outlook toward the coherent control around the quantum-classical boundary. 

Here we describe the development of the coherent-control toolbox with gas-phase iodine molecules [37 1, 48]. The gas-phase molecules are isolated from each other, so that they have long coherence lifetime, serving as an ideal platform to observe and control quantum coherence. First, we describe our experiments to observe and control the temporal evolution of the WP interference. Second, the eigenstate picture of the WP interference is presented. Finally, we demonstrate the application of WPI to ultrafast molecular computing. 

As a first step of MEIP, we have utilized our ultrahigh-precision WPI to develop an ultrafast molecular computer in which the amplitudes and phases of the iodine... 

In order to begin to understand and appreciate how a protein may interact with a surface, it is important to be able to see the protein in three dimensions. This usually requires the use of models which, in the case of proteins, are terribly cumbersome and expensive. In many institutions molecular models have been replaced by three-dimensional molecular computer graphics. There are some 70 major molecular graphics installations throughout the world which have the capabilities of imaging large macro-molecular structures in three dimensions. 

The adsorption of protein from single component solutions is qualitatively understood, although a quantitative understanding and models or theories with predictive character are not yet available. If the structure and solution properties of the protein are known and if the solid-buffer interface properties are known, then by careful examination of the surface of the protein (ideally via molecular computer graphics), we can indeed predict what orientation of the protein is preferred on that particular surface. 

TOMOCOMD-CARDD topological molecular computer design-computer aided rational drug design... 

In order to carry out sophisticated computation the molecular computers of tomorrow will need not just basic elements such as switches, memory and connectors but also more sophisticated components, particularly logic gates. A logic gate is an element of a computer that gives a particular output for a... 

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