Short conformational change

The classical microscopic description of molecular processes leads to a mathematical model in terms of Hamiltonian differential equations. In principle, the discretization of such systems permits a simulation of the dynamics. However, as will be worked out below in Section 2, both forward and backward numerical analysis restrict such simulations to only short time spans and to comparatively small discretization steps. Fortunately, most questions of chemical relevance just require the computation of averages of physical observables, of stable conformations or of conformational changes. The computation of averages is usually performed on a statistical physics basis. In the subsequent Section 3 we advocate a new computational approach on the basis of the mathematical theory of dynamical systems we directly solve a... 

Figure 9. Proposed cyclic mechanism for ATP synthesis by complex V involving all three catalytic sites of F,. In this scheme only the a and p subunits of F, are shown these are connected by a short stalk to F, in the inner membrane. Proton translocation through Fq driven by the proton motive force (AP) causes sequential conformational changes in each of the p-subunits and ATP synthesis as described in the text hexagons, high-affinity sites semicircles, low affinity sites parallelepipeds, intermediate-affinity sites (with no movement of F,).

The recent interest in substituted silane polymers has resulted in a number of theoretical (15-19) and spectroscopic (19-21) studies. Most of the theoretical studies have assumed an all-trans planar zig-zag backbone conformation for computational simplicity. However, early PES studies of a number of short chain silicon catenates strongly suggested that the electronic properties may also depend on the conformation of the silicon backbone (22). This was recently confirmed by spectroscopic studies of poly(di-n-hexylsilane) in the solid state (23-26). Complementary studies in solution have suggested that conformational changes in the polysilane backbone may also be responsible for the unusual thermochromic behavior of many derivatives (27,28). In order to avoid the additional complexities associated with this thermochromism and possible aggregation effects at low temperatures, we have limited this report to polymer solutions at room temperature. 

The time window available for FRET is dictated by the lifetime of the donor. Is there an optimal lifetime If very short , it is more difficult to measure in FLIM. If it is very long , the levels of fluorescence are low ( /-limited , [1]). In addition, the lifetime is a relevant parameter when one is interested in dynamics, either of binding, conformational change, or diffusion (translational, rotational). These processes influence FRET via the parameters K2 andrDA (Table 12.1). Long lifetimes are useful in luminescence RET (LRET) and can help to reduce background and increase signal-to-noise ratios. 

Other chemical changes can be much faster than the RNA conformational changes illustrated here. Photodissociation of sodium iodide (Nal) in the gas phase occurs on the time scale of a few picoseconds (10-12 seconds). To measure this phenomenon, Nal molecules are irradiated by a sub-picosecond ultraviolet pulse of radiation, and the subsequent events are clocked by another short light pulse that detects the newborn... 

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