Diffusion dynamics single molecule

Abstract. Various ways of extracting information on the conformational structure, dynamics and correlations between them from single-molecule measurements of florescence resonance energy transfer are surveyed. The information obtained via those various ways is then analyzed in detail in the case of an off-lattice model of a two-stranded coiled-coil polypeptide that follows Langevin dynamics. The analysis includes a consideration of the cases of a freely diffusing and surface-immobilized polypeptide as well as the effect of different types of surface and denaturation conditions. 

Aqueous phase (2.7 mm3) was placed in the thin lower compartment of the microcell and the Dil dodecane solution (63 mm3) was added on top of the aqueous layer. Fluorescence of the interfacial Dil was observed in the range of 571-575 nm. The influence of two kinds of surfactants, sodium dodecyl sulfate (SDS) and dimyristoyl phosphatidylcholine (DMPC), on the lateral diffusion dynamics of single molecules at the interface was investigated. DMPC was dissolved in chloroform, and the solution was mixed with pure diethyl ether at a ratio of 1 19 (chloroform diethyl ether) by volume. Pure water was placed in the lower container, and the DMPC solution was subsequently (5 mm3) spread carefully on the water. After evaporation of chloroform and diethyl ether, the Dil dodecane solution was added on the DMPC layer. Since Dil has a high... 

Single-molecule fluorescence detection was subsequently demonstrated at room temperature, first by detecting the burst of light as a molecule passes through the focus of a laser beam [67,68], but each molecule could be detected only once in this way. Correlation analysis of many such bursts provides a window into a variety of dynamical effects ranging from diffusion to intersystem crossing to rotational correlation [69], and this area termed fluorescence correlation spectroscopy (FCS, ([70-72]) has been reviewed in [73]. 

Mesoporous structures are commonly characterized with diffraction, electron microscopy methods [14], and gas sorption techniques. The ensemble diffusion behavior of small molecules has been examined with pulsed-field gradient NMR spectroscopy [15] and neutron scattering [16]. Here, we are interested in techniques which give a more direct access to the real structure of the mesoporous host and to the dynamics on a single-molecule basis, and thus reveal structural and dynamic features which are not obscured by ensemble or statistical averaging as in conventional techniques. 

The third part of this text focuses on several important dynamical processes in condensed phase molecular systems. These are vibrational relaxation (Chapter 13), Chemical reactions in the barrier controlled and diffusion controlled regimes (Chapter 14), solvation dynamics in dielectric environments (Chapter 15), electron transfer in bulk (Chapter 16), and interfacial (Chapter 17) systems and spectroscopy (Chapter 18). These subjects pertain to theoretical and experimental developments of the last half century some such as single molecule spectroscopy and molecular conduction—of the last decade. 

Fluorescence correlation spectroscopy analyses the temporal fluctuations of the fluorescence intensity by means of an autocorrelation function from which translational and rotational diffusion coefficients, flow rates and rate constants of chemical processes of single molecules can be determined. For example, the dynamics of complex formation between /3-cyclodextrin as a host for guest molecules was investigated with singlemolecule sensitivity, which revealed that the formation of an encounter complex is followed by a unimolecular inclusion reaction as the rate-limiting step.263... 

---