Biomedical subjects

Chen-Xu Wu

Publications and source records attributed to Chen-Xu Wu.

6 recordsLinked to original sources

PubMed2006

Facilitated diffusion of DNA-binding proteins: Simulation of large systems.

The recently introduced method of excess collisions to estimate reaction times of protein-DNA systems in the presence of facilitated diffusion ("sliding") requires a cell of full system size. This bottleneck is avoided with a modification, by which a set of empirical parameters is calibrated using numerical simulations of a small test system. Once this is done, reaction times for systems of arbitrary dimensions are derived by extrapolation. It is shown that at physiological sliding lengths a test system of the order of 100 nm radius suffices to extract accurate reaction times for realistic cell dimensions. The achieved speedup, when compared to explicit simulations of the reaction process, is increasing in third order of the extrapolated radius of the cell.

Algorithms↗

PubMed2006

Phase separation of a binary two-dimensional core-softened fluid.

Using molecular dynamics simulations, we study the phase separation in a binary two-dimensional core-softened fluid with different size ratios and concentrations. The correlation functions for both components are analyzed to show the dependence of the configurational structure of the binary fluid on size ratio and concentration. A phase separation diagram is obtained and the structural features of the phase separation are further investigated using the direct imaging method.

Journal Article↗

PubMed2006

Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions.

In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size.

Binding Sites↗

PubMed2006

Facilitated diffusion of DNA-binding proteins.

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.

DNA↗

PubMed2004

Abnormal IR effects of Pt nanostructured surfaces upon CO chemisorption due to interaction and electron-hole damping.

The abnormal IR effects (AIREs) characterized by a positive-going peak of platinum (Pt) nanostructured surface generated in a square-wave potential treatment upon CO molecule chemisorption was observed and analyzed with a consideration of the interparticle interaction and electron-hole damping between nanoislands and CO molecules. A theoretical simulation shows that the islanded nanostructured Pt surfaces, which gives rise to interparticle interaction, coupling with electron-hole mechanism, may contribute to the origins of positive-going peak (AIREs) observed by in situ Fourier transformation IR (FTIR) experiments.

Journal Article↗

PubMed2002

Weak boundary anchoring, twisted nematic effect, and homeotropic to twisted-planar transition.

Expansion analysis shows that in second order, the weak boundary coupling of nematic liquid crystals should be depicted by two anchoring coefficients and an orthonormal vector triplet. Using this binomial anchoring energy, we have derived the analytical expression of the threshold and saturation properties of the twisted nematic effect and the homeotropic to twisted-planar transition. Our results prove clearly that these two quite different transitions are reverse effects of each other.

Journal Article↗