Dynamics of a driven probe molecule in a liquid monolayer

We study dynamics of a probe molecule, driven by an external constant force in a liquid monolayer on top of solid surface. In terms of a microscopic, mean-field-type approach, we calculate the terminal velocity of the probe molecule. This allows us to establish the analog of the Stokes formula, in which the friction coefficient is interpreted in terms of the microscopic parameters characterizing the system. We also determine the distribution of the monolayer particles as seen from the stationary moving probe molecule and estimate the self-diffusion coefficient for diffusion in a liquid monolayer.Comment: Latex, 7 pages, 1 figur

A photoactivatable small molecule probe for the in vivo capture of polyketide intermediates

A photolabile carba(dethia) malonyl N‐acetylcysteamine derivative was devised and prepared for the trapping of biosynthetic polyketide intermediates following light activation. From the lasalocid A polyketide assembly in a mutant strain of the soil bacterium S. lasaliensis, a previously undetected cyclised intermediate was identified and characterised, providing a new outlook on the timing of substrate processing

An experimental study of molecular surface interactions at velocities up to and exceeding space probe escape velocities Final report

Momentum accomodation coefficients obtained from low velocity molecule-surface interactions, for space probe drag calculation

Ultrafast spectroscopy of single molecules

We present a single-molecule study on femtosecond dynamics in multichromophoric systems, combining fs pump-probe, emission-spectra and fluorescence-lifetime analysis. At the single molecule level a wide range of exciton delocalisation lengths and energy redistribution times is revealed. Next, two color pump-probe experiments are presented as a step to addressing ultrafast energy transfer in individual complexes

Influence of correlations on molecular recognition

The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models. A general two-stage approach is utilised where an ensemble of probe molecules is designed first and the recognition ability of the probe ensemble is related to the free energy of association with both the target molecule and a different rival molecule in a second step. The influence of correlation effects are investigated using numerical Monte Carlo techniques and mean field methods. Correlations lead to different optimum characteristic lengths of the hydrophobic and polar patches for the mutual design of the two biomolecules on the one hand and their recognition ability in the presence of other molecules on the other hand.Comment: 15 pages, 5 figure

Two-probe theory of scanning tunneling microscopy of single molecules: Zn(II)-etioporphyrin on alumina

We explore theoretically the scanning tunneling microscopy of single molecules on substrates using a framework of two local probes. This framework is appropriate for studying electron flow in tip/molecule/substrate systems where a thin insulating layer between the molecule and a conducting substrate transmits electrons non-uniformly and thus confines electron transmission between the molecule and substrate laterally to a nanoscale region significantly smaller in size than the molecule. The tip-molecule coupling and molecule-substrate coupling are treated on the same footing, as local probes to the molecule, with electron flow modelled using the Lippmann-Schwinger Green function scattering technique. STM images are simulated for various positions of the stationary (substrate) probe below a Zn(II)-etioporphyrin I molecule. We find that these images have a strong dependence on the substrate probe position, indicating that electron flow can depend strongly on both tip position and the location of the dominant molecule-substrate coupling. Differences in the STM images are explained in terms of the molecular orbitals that mediate electron flow in each case. Recent experimental results, showing STM topographs of Zn(II)-etioporphyrin I on alumina/NiAl(110) to be strongly dependent on which individual molecule on the substrate is being probed, are explained using this model. A further experimental test of the model is also proposed.Comment: Physical Review B, in pres

Single-molecule interfacial electron transfer dynamics manipulated by external electric current

Interfacial electron transfer (IET) dynamics in 1,1'-dioctadecyl-3, 3, 3', 3'-tetramethylindodicarbocyanine (DiD) dye molecules / indium tin oxide (ITO) film system have been probed at the ensemble and single-molecule level by recording the change of fluorescence emission intensity. By comparing the difference of the external electric current (EEC) dependence of lifetime and intensity for enambles and single molecules, it is shown that the single-molecule probe can effcienly demonstrate the IET dynamics. The backward electron transfer and electron transfer of ground state induce the single molecules fluorescence quenching when an EEC is applied to ITO film.Comment: 6 pages, 6 figure

Effect of Disorder on Ultrafast Exciton Dynamics Probed by Single Molecule Spectroscopy

We present a single-molecule study unraveling the effect of static disorder on the vibrational-assisted ultrafast exciton dynamics in multichromophoric systems. For every single complex, we probe the initial exciton relaxation process by an ultrafast pump-probe approach and the coupling to vibrational modes by emission spectra, while fluorescence lifetime analysis measures the amount of static disorder. Exploiting the wide range of disorder found from complex to complex, we demonstrate that static disorder accelerates the dephasing and energy relaxation rate of the exciton