Biomedical subjects

B J Garrison

Publications and source records attributed to B J Garrison.

5 recordsLinked to original sources

PubMed2006

Understanding gold-thiolate cluster emission from self-assembled monolayers upon kiloelectronvolt ion bombardment.

This article focuses on the emission of organometallic clusters upon kiloelectronvolt ion bombardment of self-assembled monolayers. It is particularly relevant for the elucidation of the physical processes underlying secondary ion mass spectrometry (SIMS). The experimental system, an overlayer of octanethiols on gold, was modeled by classical molecular dynamics, using a hydrocarbon potential involving bonding and nonbonding interactions (AIREBO). To validate the model, the calculated mass and energy distributions of sputtered atoms and molecules were compared to experimental data. Our key finding concerns the emission mechanism of large clusters of the form MxAuy up to M6Au5 (where M is the thiolate molecule), which were not observed under sub-kiloelectronvolt projectile bombardment. Statistically, they are predominantly formed in high-yield events, where many atoms, fragments, and (supra)molecular species are desorbed from the surface. From the microscopic viewpoint, these high-yield events mostly stem from the confinement of the projectile and recoil atom energies in a finite microvolume of the sample surface. As a result of the high local energy density, molecular aggregates desorb from an overheated liquidlike region surrounding the impact point of the projectile.

Computer Simulation↗

PubMed2006

Sputtering of water ice induced by C60 bombardment: onset of plume formation.

The interaction of a 5 keV C(60) projectile with amorphous water ice is studied using molecular dynamics computer simulations. The energetic C(60) molecule causes large-scale collisional events in the subsurface region, involving more than 10(4) water molecules in a time of less than 3 ps. The energy deposited in the sample is sufficiently large to turn the ice into a superheated and superdense gas. The gas is expelled into the vacuum, leading to the formation of a flow that manifests itself in the angular and velocity distributions of emitted water molecules.

Journal Article↗

PubMed2000

Molecular dynamics simulation of the laser disintegration of aerosol particles.

The mechanisms of disintegration of submicrometer particles irradiated by short laser pulses are studied by a molecular dynamics simulation technique. Simulations at different laser fluences are performed for particles with homogeneous composition and particles with transparent inclusions. Spatially nonuniform deposition of laser energy is found to play a major role in defining the character and the extent of disintegration. The processes that contribute to the disintegration include overheating and explosive decomposition of the illuminated side of the particle, spallation of the backside of large particles, and disruption of the transparent inclusion caused by the relaxation of the laser-induced pressure. The observed mechanisms are related to the nature of the disintegration products and implications of the simulation results for aerosol time-of-flight mass spectrometry are discussed. Application of multiple laser pulses is predicted to be advantageous for efficient mass spectrometry sampling of aerosols with a large size to laser penetration depth ratio.

Aerosols↗

PubMed2000

Molecule liftoff from surfaces.

Molecular dynamics simulations have been used to model the kiloelectronvolt particle bombardment of organic layers on metal substrates such as occurs in the analytical techniques of secondary ion mass spectrometry and fast atom bombardment mass spectrometry. Vignettes of insights gained from the simulations along with comparisons to experimental data are presented in this Account. Topics include intact molecular ejection vs fragmentation, prediction of reaction pathways, influence of the substrate, and quantitative predictions of energy and angular distributions.

Mass Spectrometry↗

PubMed1997

Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate.

Poisson-Boltzmann calculations were used to determine the pKa of protein functional groups in the unliganded dihydrofolate reductase enzyme, and the pKa of protein and ligand groups in methotrexate-enzyme complexes. The results reported here are in conflict with two fundamental tenets of dihydrofolate reductase inhibition by methotrexate: (1) Asp27 is not expected to be protonated near pH 6.5 in the apoenzyme as previously proposed based on fitting of empirical equations to binding data, and (2) the calculated pKa for the pteridine N1 of the inhibitor while bound to the protein is significantly lower than that estimated for this group from interpretation of NMR data (>10). In fact, the electrostatic calculations and complementary quantum chemical calculations indicate that Asp27 is likely protonated when methotrexate is bound, resulting in a neutral dipole-dipole interaction rather than a salt-bridge between the enzyme and the inhibitor. Reasons for this discrepancy with the experimental data are discussed. Furthermore, His45 and Glu17 in the Escherichia coli enzyme are proposed to be in part responsible for the pH dependence of the conformational degeneracy in the inhibitor-enzyme complex.

4-Aminobenzoic Acid↗