Sequence-dependent parameters

Using the Jensen-Shannon divergence, JS, as a measure of complexity for the generated sequences, one can obtain an interesting result (see Fig. lib). The most important feature is that the JS value is a nonmonotonous function of epp, whereas Shannon s entropy, Shannon s index, and many other sequence-dependent parameters change always gradually [70]. 

Delineation of conformational preferences of individual residues under various conditions, which can be considered the original goal of the host-guest technique, seems to be of subordinate importance in the light of these findings. However, this approach in addition opens the door to systematic studies on sequence-dependent parameters and stereochemical factors influencing secondary structure formation. 

The key question we want to answer is what are the intrinsic sequence dependent factors tliat not only detennine tire folding rates but also tire stability of tire native state It turns out tliat many of tire global aspects of tire folding kinetics of proteins can be understood in tenns of tire equilibrium transition temperatures. In particular, we will show tliat tire key factor tliat governs tire foldability of sequences is tire single parameter... 

We now introduce the concept of the control parameter X (see Section III. A). In the present scheme the discrete time sequence Xk Q transition probability Wt(C C) now depends explicitly on time through the value of an external time-dependent parameter X. The parameter Xk may indicate any sort of externally controlled variable that determines the state of the system, for instance, the value of the external magnetic field applied on a magnetic system, the value of the mechanical force applied to the ends of a molecule, the position of a piston containing a gas, or the concentrations of ATP and ADP in a molecular reaction coupled to hydrolysis (see Fig. 3). The time variation of the control parameter, X = - Xk)/At, is... 

D. Mathews, J. Sabina, M. Zucker, and H. Turner. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol, 288 911-940, 1999. 

A 128-unit flexible-chain heteropolymer with a HP composition fixed at 1 1 was simulated for the condition when hydrophobic H monomers strongly attract each other, thus stabilizing a dense globular core, whereas the attraction energy epp between hydrophilic P monomers was considered as a parameter (the interaction between H and P monomers is given by hp = V hh pp). For this model system, various conformation-dependent and sequence-dependent properties, including information-theoretic-based quantities, can be calculated. 

Even in the absence of relaxation, Hartmann-Hahn transfer depends on a large number of parameters pulse sequence parameters (multiple-pulse sequence, irradiation frequency, average rf power, etc.) and spin system parameters (size of the spin system, chemical shifts, /-coupling constants). For most multiple-pulse sequences, these parameters may be destilled into effective coupling tensors, which completely determine the transfer of polarization and coherence in the spin system. This provides a general classification scheme for homo- and heteronuclear Hartmann-Hahn experiments and allows one to characterize the transfer properties of related... 

Figure 6 below, shows the normalized distributions for the values obtained from the simulations for AA/TT, AT and TA steps, for the six bps parameters. In all cases, the distributions belonging to TA steps are wider than those of the other steps, and we interpret that as a reflection of the greater flexibility of this step. Except for tilt, all these parameters are important for understanding sequence specific binding to TATA boxes [89,100,101,109], because TBP forces the conformation of DNA into regions of conformational space that are not well sampled by free DNA in the simulations or in the available free DNA structures contained in the NDB. It is also obvious from these plots that slide, rise and roll have a marked sequence dependence [110]. 

Brukner, I., Sanchez, R., Suck, D. Pongor, S. (1995). Sequence-dependent bending propensity of DNA as revealed by DNase I parameters for trinucleotides. EMBO J. 14, 1812-1818. 

In synthetic polymers, the interpretation is necessarily more difficult The form of Equation 4 and Equation 5 requires that the kinetics of formation and decay of complexes are modelled adequately by rate-constants and that they take place in a homogeneous medium. If, as in synthetic polymers, the population of excimer trap sites, may occur through energy migration or rotational diffusion, a rate-constant may not be an adequate representation of the process, some time-dependent parameter being required (see below.) Heterogeneity may also play an important role. Thus in earlier work the fluorescence decay of excimer-forming polymers was modelled adequately by a scheme based upon simple excimer kinetics to which had been added terms to account for the occurrence in co-polymers of monomer sites which, by their isolation, could not form excimers (4-10). For polymers which contain isotactic and syndiotactic sequences, or rather, are made up of meso and racemic triads (14), the kinetics may be similarly a superimposition of simple schemes appropriate for the different sequences. 

In Eq. (3.1), a = iMcjJl, and the other barred quantities are the usual time-dependent parameters. The formation of the coherent state (3.1) by nonresonant optical impulsive excitation [30] and the dependence of the initial values of the parameters on pulse sequence and molecular orientation are discussed in Appendix A. 

In Fig. 5, a spectrum is plotted, which exhibits the oscillatory features of the symmetric stretch motion of Naa in its electronically excited B-state, indicating the well-known oscillation time of 320 fe. The pump-probe spectnun was obtained with transform-limited pulses of 80 fs duration at a center wavelength of 620 nm. Then the experiment was repeated by changing one experimental parameter only the duration of the pump pulse. This was accomplished — as indicated in Fig. 11 — by passing the pump beam across a set of two parallel gratings. The assembly creates a linear frequency chirp. Its duration and spectral sequence depends only on the incidence angle... 

Several generalizations of the ATC rule have been developed in order to take into account release dates as well as sequence dependent setup times. These generalizations require the initial computation of a number of factors. These factors, together with the particular machine environment, can then be used to determine a number of the parameters (see Lee et al. 1997). 

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