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Register a new userProposal for probing energy transfer pathway by single-molecule pump-dump experiment
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The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex has long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.
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Motivated by recent experiments on photon statistics from individual dye pairs planted on biomolecules and coupled by fluorescence resonance energy transfer (FRET), we show here that the FRET dynamics can be modelled by Gaussian random processes with colored noise. Using Monte-Carlo numerical simulations, the photon intensity correlations from the FRET pairs are calculated, and are turned out to be very close to those observed in experiment. The proposed stochastic description of FRET is consistent with existing theories for microscopic dynamics of the biomolecule that carries the FRET coupled dye pairs.
Homodyne X-ray diffraction signals produced by classical light and classical detectors are given by the modulus square of the charge density in momentum space $left|sigma(mathbf{q})right|^{2}$, missing its phase which is required in order to invert the signal to real space. We show that quantum detection of the radiation field yields a linear diffraction pattern that reveals $sigma(mathbf{q})$ itself, including the phase. We further show that repeated diffraction measurements with variable delays constitute a novel multidimensional measure of spontaneous charge-density fluctuations. Classical diffraction, in contrast, only reveals a subclass of even-order correlation functions. Simulations of two dimensional signals obtained by two diffraction events are presented for the amino acid cysteine.
Glycans play a central role as mediators in most biological processes, but their structures are complicated by isomerism. Epimers and anomers, regioisomers, and branched sequences contribute to a structural variability that dwarfs those of nucleic acids and proteins, challenging even the most sophisticated analytical tools, such as NMR and mass spectrometry. Here, we introduce an electron tunneling technique that is label-free and can identify carbohydrates at the single-molecule level, offering significant benefits over existing technology. It is capable of analyzing sub-picomole quantities of sample, counting the number of individual molecules in each subset in a population of coexisting isomers, and is quantitative over more than four orders of magnitude of concentration. It resolves epimers not well separated by ion-mobility and can be implemented on a silicon chip. It also provides a readout mechanism for direct single-molecule sequencing of linear oligosaccharides.
Anisotropy is a fundamental property of particle interactions. It occupies a central role in cold and ultra-cold molecular processes, where long range forces have been found to significantly depend on orientation in ultra-cold polar molecule collisions. Recent experiments have demonstrated the emergence of quantum phenomena such as scattering resonances in the cold collisions regime due to quantization of the intermolecular degrees of freedom. Although these states have been shown to be sensitive to interaction details, the effect of anisotropy on quantum resonances has eluded experimental observation so far. Here, we directly measure the anisotropy in atom-molecule interactions via quantum resonances by changing the quantum state of the internal molecular rotor. We observe that a quantum scattering resonance at a collision energy of $k_B$ x 270 mK appears in the Penning ionization of molecular hydrogen with metastable helium only if the molecule is rotationally excited. We use state of the art ab initio and multichannel quantum molecular dynamics calculations to show that the anisotropy contributes to the effective interaction only for $H_2$ molecules in the first excited rotational state, whereas rotationally ground state $H_2$ interacts purely isotropically with metastable helium. Control over the quantum state of the internal molecular rotation allows us to switch the anisotropy on or off and thus disentangle the isotropic and anisotropic parts of the interaction. These quantum phenomena provide a challenging benchmark for even the most advanced theoretical descriptions, highlighting the advantage of using cold collisions to advance the microscopic understanding of particle interactions.
We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.
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