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Yujun Zheng

Publications and source records attributed to Yujun Zheng.

12 recordsLinked to original sources
PubMed2006

Single molecule photon counting statistics for quantum mechanical chromophore dynamics.

We extend the generating function technique for calculation of single molecule photon emission statistics (Zheng, Y.; Brown, F. L. H. Phys. Rev. Lett. 2003, 90, 238305) to systems governed by multi-level quantum dynamics. This opens up the possibility to study phenomena that are outside the realm of purely stochastic and mixed quantum-stochastic models. In particular, the present methodology allows for calculation of photon statistics that are spectrally resolved and subject to quantum coherence. Several model calculations illustrate the generality of the technique and highlight quantitative and qualitative differences between quantum mechanical models and related stochastic approximations when they arise. Calculations suggest that studying photon statistics as a function of photon frequency has the potential to reveal more about system dynamics than the usual broadband detection schemes.

Color↗
PubMed2005

Synthesis and evaluation of a potent and selective cell-permeable p300 histone acetyltransferase inhibitor.

This paper describes the first potent and selective p300 histone acetyltransferase (HAT) inhibitor which is effective in live cells. This compound 7 is a coenzyme A analogue conjugated to a cell permeabilizing oligoArg peptide via disulfide linkage. This compound was shown to block cellular histone acetylation and transcription using a p300-sensitive reporter. It should thus be broadly useful for dissecting the role of p300 HAT activity in physiologic and disease states.

Journal Article↗
PubMed2005

Fluorescence analysis of a dynamic loop in the PCAF/GCN5 histone acetyltransferase.

PCAF and GCN5 are histone acetyltransferase (HAT) paralogs which play roles in the remodeling of chromatin in health and disease. Previously, a conformationally flexible loop in the catalytic domain had been observed in the X-ray structures of GCN5 in different liganded states. Here, the conformation and dynamics of this PCAF/GCN5 alpha5-beta6 loop was investigated in solution using tryptophan fluorescence. A mutant human PCAF HAT domain (PCAF(Wloop)) was created in which the natural tryptophan (Trp-514) remote from the alpha5-beta6 loop was replaced with tyrosine and a glutamate within the loop (Glu-641) was substituted with tryptophan. This PCAF(Wloop) protein exhibited catalytic parameters within 3-fold of those of the wild-type PCAF catalytic domain, suggesting that the loop mutation was not deleterious for HAT activity. While saturating CoASH induced a 30% quenching of Trp fluorescence in PCAF(Wloop), binding of the high-affinity bisubstrate analogue H3-CoA-20 led to a 2-fold fluorescence increase. These different effects correlate with the different alpha5-beta6 loop conformations seen previously in X-ray structures. On the basis of stopped-flow fluorescence studies, binding of H3-CoA-20 to PCAF(Wloop) proceeds via a rapid association step followed by a slower conformational change involving loop movement. Time-resolved fluorescence measurements support a model in which the alpha5-beta6 loop in the H3-CoA-20-PCAF(Wloop) complex exists in a narrower ensemble of conformations compared to free PCAF(Wloop). The relevance of loop dynamics to PCAF/GCN5 catalysis and substrate specificity are discussed.

Animals↗
PubMed2005

Quantum transition state theory for the full three-dimensional H+H2 reaction.

A recently developed quantum transition state theory (QTST) [E. Pollak and J. L. Liao, J. Chem. Phys. 108, 2733 (1998)] for calculating thermal rate constants of chemical reactions is applied to the full three-dimensional hydrogen exchange reaction. Results are compared with other numerical results, for temperatures ranging from T=300 K to T=1500 K. The QTST rate is almost exact at high temperature and is 20% greater than the exact rate at T=300 K, where there is extensive tunneling.

Journal Article↗
PubMed2004

Single molecule photon emission statistics in the slow modulation limit.

A framework for calculating photon emission statistics for single chromophores perturbed by slow environmental fluctuations is introduced. When internal chromophore dynamics are significantly faster than time scales for environmental modulation it becomes possible to invoke a type of adiabatic approximation, allowing for straightforward calculation of photon counting moments including explicitly quantum effects. Unlike previous exact treatments, the present methodology involves calculation of dynamics reflecting only the modulation characteristics of the environment and quantum dynamics of an isolated chromophore separately, i.e., the complicated intermingling of chromophore quantum dynamics and the environmental modulation are suppressed via the adiabatic approximation. This leads to significant conceptual and computational simplifications. Within its regime of applicability, the present approximation reproduces exact calculations quantitatively. We demonstrate this accuracy explicitly for the case of a two-level chromophore modulated by a number of different stochastic models.

Computer Simulation↗
PubMed2004

Single molecule photon emission statistics for non-Markovian blinking models.

The statistics of photon emission from a single molecule under continuous wave excitation are considered. In particular, we study stochastic model systems where photon emission rates evolve in time with non-Markovian dynamics. Our calculations are based on the recently introduced generalized optical Bloch equation (GBE) formalism, but with numerical complications beyond those seen in previous Markovian stochastic models. A spectral representation is introduced to facilitate the numerical solution of the GBE equations for these more challenging cases.

Journal Article↗
PubMed2003

Single-molecule photon counting statistics via generalized optical Bloch equations.

We derive the generating function for single molecule photon emission events within the context of the stochastically modulated optical Bloch equations. Statistical properties of single molecule photon counting experiments are deduced from a set of coupled differential equations only slightly more complicated than the Bloch equations themselves. This formulation allows for the study of photon bunching and antibunching within a single theoretical framework and provides a description of these behaviors that emphasizes the connection with single molecule experiments. Application is made to the spectroscopy of a chromophore coupled to a single two level system.

Journal Article↗
PubMed2003

Peptidyl fluorescent chemosensors for the detection of divalent copper.

Fluorescent organic chemosensors for the detection of divalent copper with high selectivity and sensitivity are the subject of intense research in the recent years. Structurally, ionophore and fluorophore are two essential parts determining the resultant performance of the chemosensor. While much work has been focused on designing highly selective ligands, little attention has been paid to the possible influence of ionophore-fluorophore interaction on their properties in metal ion binding. We studied here fluorescent chemosensors based on the Gly-His peptidyl motif and found that the functionality of the chemosensors was greatly influenced by the spatial alignment of the fluorophore in the molecules. In Gly-His-Lys(Dns) (1), the dansyl group is on a side branch and does not interact with copper, while in Dpr(Dns)-His-Lys (2), the dansyl group is also on a side branch but the close placement allows it to directly participate in the binding with copper ions. Therefore, although dansyl can signal the binding event in both molecules, the mechanisms involved are quite different, and this difference resulted in different sensing performance, e.g., the selectivity. Even more strikingly, the dansyl group in Dns-Gly-His-Gly (3) exhibited a profound effect on the molecular complexation. The binding constant decreased, and binding mode was affected since only 1:1 binding was observed while in side-branch-labeled ligands, a 2:1 binding may also be involved. In contrast to those side-chain-labeled ligands, molecule 3 is extremely simple in structure and possesses superior detecting qualities such as selectivity, molecular sensitivity, and applicability in a wide range of pH.

Biosensing Techniques↗
PubMed2003

Development of fluorescent film sensors for the detection of divalent copper.

Monolayers of several peptide lipids at air-water and air-solid interfaces were prepared using Langmuir and Langmuir-Blodgett (LB) film techniques, and tested as fluorescent sensors for copper ions in aqueous phase. In one method, both the ionophore and the fluorophore were in the same molecule (lipid A), so intramolecular interaction was responsible for the fluorescence quenching of monolayers of this lipid. In the other method, ionophore and fluorophore were located on two different molecules (lipids B and C) so the intramolecular coupling does not exist; instead the fluorescence quenching was realized by a through-space interaction mechanism. Several experimental techniques, including pi-A isotherm, epifluorescence microscopy, and absorption and emission spectroscopies were used to study the different characteristics of copper ion effect on the properties of the lipid monolayers. Additionally, the fluorescence quenching properties of the Langmuir monolayers were found to be transferred to the one-layer LB films. On LB films, the fluorescence response presented a clear selectivity for copper ions in comparison with several other transition metal ions. Further, an excellent reversibility was observed: the fluorescence was switched OFF by immersing the solid substrate in copper ion solution and ON by washing with HCl solution. The intermolecular approach used here seems to be a very flexible and general method to design surface-oriented fluorescent sensors to meet different analytic purposes.

Cations, Divalent↗
PubMed2002

ZL-DHP lignin model compound at the air-water interface.

In this paper we present our surface chemistry studies of enzymatically polymerized, poly-coniferyl alcohol lignin model compound (dehydrogenate polymer a.k.a. ZL-DHP) at the air-water interface. Using the CHCl(3)/MeOH (5:1 v/v) spreading solvent, we found an average molecular area of ZL-DHP of approximately 1200 A(2). The monolayer expresses a high compressibility with a collapsed area of 500 A(2) and collapsed surface pressure of 28 mN m(-1). In the range of applied surface pressures, ZL-DHP polymer have no phase changes, as shown by the very high linearity (R=0.994) of absorbance vs. surface pressure cure. There was no symmetry transitions observed as shown by absence of shifts of absorption peak maximums.

Air↗