Biomedical subjects

A Vaught

Publications and source records attributed to A Vaught.

3 recordsLinked to original sources

PubMed2005

Green's function Monte Carlo method with exact imaginary-time propagation.

We present a general formulation of the Green's function Monte Carlo method in imaginary-time quantum Monte Carlo which employs exact propagators. This algorithm has no time-step errors and is obtained by minimal modifications of the time-independent Green's function Monte Carlo method. We describe how the method can be applied to the many-body Schrödinger equation, lattice Hamiltonians, and simple field theories. Our modification of the Green's function Monte Carlo algorithm is applied to the ground state of liquid 4He. We calculate the zero-temperature imaginary-time diffusion constant and relate that to the effective mass of a mass-four "impurity" atom in liquid 4He.

Journal Article↗

PubMed1993

Identification of DNA--cisplatin adducts in a blind trial of in situ scanning tunneling microscopy.

Scanning tunneling microscopy (STM) reveals nanometer scale details of hydrated DNA but the interpretation of the images is controversial because of substrate artifacts and the lack of a theory for image contrast. We demonstrate that we have overcome these problems by identifying five DNA samples by their STM images alone in a blinded trial. The samples were single-stranded and double-stranded DNA with and without covalent modification by the anti-tumor drug cisplatin. The cisplatin adducts were distinguished by substantial kinking at the drug binding site. The oligomers were 20 bases in length, which was too short to permit the kinking angle to be determined with precision. However, models with a 45 degree kink gave a better fit to the images of the duplex adducts than models with a 90 degrees kink. A variety of structures was observed for the single-stranded adducts.

Base Sequence↗

PubMed1993

Structure of hydrated oligonucleotides studied by in situ scanning tunneling microscopy.

We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrolyte under potential control, a procedure that eliminated the problem of the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecules (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base "sticky" ends). The molecules lie along symmetry directions on the reconstructed (23 x square root of 3) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stacking distances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct imaging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity that is consistent with a 36 degrees twist. The single helices appear to be more tightly twisted. A simple tunneling model of STM contrast generates good agreement between measured and calculated images.

Base Sequence↗