Binning

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Bin M, Gaidis M C, Zmuidzinas J and Phillips T G 1997 Quasi-optioal SIS mixers with normal tuning struotures IEEE Trans. Appl. Supercond. 7 3584-8... 

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

The only density estimators discussed in the protein literature are histogram estimates. However, these are nonsmooth and thus not suitable for global optimization techniques that combine local and global search. Moreover, histogram estimates have, even for an optimally chosen bin size, the extremely poor accuracy of only, for a sample of size n. The theo-... 

One therefore needs a smooth density estimation techniques that is more reliable than the histogram estimates. The automatic estimation poses additional problems in that the traditional statistical techniques for estimating densities usually require the interactive selection of some smoothing parameter (such as the bin size). Some publicly available density estimators are available, but these tended to oversmooth the densities. So we tried a number of ideas based on numerical differentiation of the empirical cdf to devise a better density estimator. 

Th c eigen value of ih is Sch riidiri gcr equation. the electron ie energy deperi ds parametrically, as sh own, on the coord in ales of th e nuclei (assumed to he fixed for the purposes of calcti lali ri g each Heie.lK), bin variable in general), I h e electronic energy, combined with y, (K,K) is the total energy of Single Point semi-em pirical calculation s. 

Coni pile th e ch ern. nil file Lo a n ew Lypenile.bin file as described in the previon s paragraph. 

The fiinctioiial form for electrostatic in teraction s m AMBER is identical with that shown in equation (2fi) on page 179. You normally use a dielectric scaling of D=1 with AMBER com bin ed with a constant functional form when solvent molecules are explicitly... 

The dBASEIV (ordBASEIIT) form of th e parameter sets come in ld( /filcs analogous to the Tt,v( files. Th ese dbf files are bin ary files, so yon can t read them directly. They arenot retpiired for the product and are provided only as an option. In most situations where there is no exten sive use of database operation s on parameter sets, the text form is probably more convenient to use. Many spreadsheet programs, including Microsoft Excel, are also capable of reading files. 

I ll c COM LracLcd Gaussian fiiricLiori s arc a liri car com bin atiori ofthc prim iti VC Gaii ssiari fun cliuti s. Th alls. 

Figure 7.13 reprinted with permission from Jorgensen W L, R C Binning Jr and B Bigot. Structures md Properties of Organic Liquids u-Butane and 1,2-Dichloroethane and Their Conformational Equilibria. The Journal of the American Chemical Society 103 4393-4399. 1981 American Chemical Society. 

C Binning Jr and B Bigot 1931. Structures and Properties of Organic Liquids n-Butane and 1,2-... 

A major potential drawback with cluster analysis and dissimilarity-based methods f selecting diverse compounds is that there is no easy way to quantify how completel one has filled the available chemical space or to identify whether there are any hole This is a key advantage of the partition-based approaches (also known, as cell-bas( methods). A number of axes are defined, each corresponding to a descriptor or son combination of descriptors. Each axis is divided into a number of bins. If there are axes and each is divided into b bins then the number of cells in the multidimension space so created is ... 

Compile the chem.rul file to a new typerule.bin file as described in the previous paragraph. 

Any one bin can be electronically distinguished from the next one, and therefore the bins can be used like the tick of a standard clock. Each bin serves as one tick, which lasts for only 0.3 nsec. By counting the ticks and knowing into which bin the ion pulse has gone, the time taken for the ion to arrive at the detector can be measured to an accuracy of 0.3 nsec, which is the basis for measuring very short ion arrival times after the ions have traveled along the TOE analyzer tube. Each ion arrival pulse (event) is extracted from its time bin and stored in an associated computer memory location. 

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