Biomedical subjects

Predrag S Krstić

Publications and source records attributed to Predrag S Krstić.

3 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

First-principles transversal DNA conductance deconstructed.

First-principles calculation of the transverse conductance across DNA fragments placed between gold nanoelectrodes reveals that such conductance describes electron tunneling that depends critically on geometrical rather than electronic-structure properties. By factoring the first-principles result into two simple and approximately independent tunneling factors, we show that the conductances of the A, C, G, and T fragments differ only because of their sizes: the larger is the DNA base, the smaller its distance to the electrode, and the larger its conductance. Because the geometrical factors are difficult to control in an experiment, the direct-current measurements across DNA with gold contact electrodes may not be a convenient approach to DNA sequencing.

Computer Simulation↗

PubMed2005

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Journal Article↗