Biomedical subjects

Xiongce Zhao

Publications and source records attributed to Xiongce Zhao.

5 recordsLinked to original sources

PubMed2006

Characterization of the tunneling conductance across DNA bases.

Characterization of the electrical properties of the DNA bases (adenine, cytosine, guanine, and thymine), in addition to building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotidelike molecules of the DNA bases, placed in a 1.5 nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the density-functional theory exchange-correlation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.

Computer Simulation↗

PubMed2006

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study.

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.

Journal Article↗

PubMed2006

Molecular dynamics study of carbon nanotube oscillators revisited.

We performed molecular dynamics simulation of double walled carbon nanotube (DWCNT) oscillators under constant energy and constant temperatures with various commensurations and nanotube lengths. We clarify and resolve questions and differences raised by previous simulation results of similar systems. At constant energy, sustained oscillation is available for a wide range of initial temperatures. But low initial temperature is advantageous for DWCNTs to sustain oscillation under constant energy. We observed sustained oscillation at constant energy for both commensurate and incommensurate DWCNTs. On the other hand, under constant temperatures, both high and low temperatures are disadvantageous to sustain DWCNT oscillations. At constant low temperature, neither commensurate nor incommensurate DWCNTs can maintain oscillation. At appropriate constant temperatures, the oscillatory behavior of incommensurate nanotubes is much more sustained than that of commensurate tubes. The oscillatory frequency of DWCNTs depends significantly on the length of tubes. The initial oscillatory frequency is inversely proportional to the DWCNT lengths. The oscillation frequency of DWCNTs is insensitive to the initial temperatures at constant energy, but slightly dependent on the temperature at constant temperatures.

Journal Article↗

PubMed2005

C60 binds to and deforms nucleotides.

Atomistic molecular dynamics simulations are performed for up to 20 ns to monitor the formation and the stability of complexes composed of single- or double-strand DNA molecules and C60 in aqueous solution. Despite the hydrophobic nature of C60, our results show that fullerenes strongly bind to nucleotides. The binding energies are in the range -27 to -42 kcal/mol; by contrast, the binding energy of two fullerenes in aqueous solution is only -7.5 kcal/mol. We observe the displacement of water molecules from the region between the nucleotides and the fullerenes and we attribute the large favorable interaction energies to hydrophobic interactions. The features of the DNA-C60 complexes depend on the nature of the nucleotides: C60 binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C60 binds to single-strand DNA and deforms the nucleotides significantly. Unexpectedly, when the double-strand DNA is in the A-form, fullerenes penetrate into the double helix from the end, form stable hybrids, and frustrate the hydrogen bonds between end-group basepairs in the nucleotide. When the DNA molecule is damaged (specifically, a gap was created by removing a piece of the nucleotide from one helix), fullerenes can stably occupy the damaged site. We speculate that this strong association may negatively impact the self-repairing process of the double-strand DNA. Our results clearly indicate that the association between C60 and DNA is stronger and more favorable than that between two C60 molecules in water. Therefore, our simulation results suggest that C60 molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.

Binding Sites↗

PubMed2004

Surface tension of quantum fluids from molecular simulations.

We present the first molecular simulations of the vapor-liquid surface tension of quantum liquids. The path integral formalism of Feynman was used to account for the quantum mechanical behavior of both the liquid and the vapor. A replica-data parallel algorithm was implemented to achieve good parallel performance of the simulation code on at least 32 processors. We have computed the surface tension and the vapor-liquid phase diagram of pure hydrogen over the temperature range 18-30 K and pure deuterium from 19 to 34 K. The simulation results for surface tension and vapor-liquid orthobaric densities are in very good agreement with experimental data. We have computed the interfacial properties of hydrogen-deuterium mixtures over the entire concentration range at 20.4 and 24 K. The calculated equilibrium compositions of the mixtures are in excellent agreement with experimental data. The computed mixture surface tension shows negative deviations from ideal solution behavior, in agreement with experimental data and predictions from Prigogine's theory. The magnitude of the deviations at 20.4 K are substantially larger from simulations and from theory than from experiments. We conclude that the experimentally measured mixture surface tension values are systematically too high. Analysis of the concentration profiles in the interfacial region shows that the nonideal behavior can be described entirely by segregation of H(2) to the interface, indicating that H(2) acts as a surfactant in H(2)-D(2) mixtures.

Journal Article↗