Biomedical subjects

Angela Violi

Publications and source records attributed to Angela Violi.

7 recordsLinked to original sources

PubMed2006

Radical-molecule reactions for aromatic growth: a case study for cyclopentadienyl and acenaphthylene.

Polycyclic aromatic hydrocarbon growth from acenaphthylene and cyclopentadienyl was investigated by using the B3LYP/6-31G(d,p) and BH&HLYP/6-31G(d,p) levels of theory as well as transition state theory. The reaction pathways of cyclopentadienyl bearing hydrocarbons are different from those without these moieties and cannot be adequately accounted for by the existing acetylene addition and aryl-aryl addition mechanisms. The reaction mechanisms identified in this paper lead to the formation of fluoranthene, aceanthrylene, and acephenanthrylene. Rate constants of the radical-molecule addition and subsequent intramolecular addition steps predict that the 1,2 double bond in acenaphthylene is much more reactive than the 3,4 and 4,5 double bonds. Fluoranthene is the most abundant product produced at high temperatures and the yield of acephenanthrylene is bigger than that of aceanthrylene. The computational results are discussed in light of pyrolysis experiments on CPD-indene and CPD-acenaphthylene mixtures conducted by Prof. Mulholland's research group reported in a previous work.

Acenaphthenes↗

PubMed2006

Combustion-generated nanoparticles produced in a benzene flame: a multiscale approach.

This paper details the multiscale methodology developed to analyze the formation of nanoparticles in a manner that makes it possible to follow the evolution of the structures in a chemically specific way. The atomistic model for particle inception code that combines the strengths of kinetic Monte Carlo and molecular dynamics is used to study the chemical and physical properties of nanoparticles generated in a premixed fuel-rich benzene flame, providing atomistic scale structures (bonds, bond angles, dihedral angles) as soot precursors evolve into a three-dimensional structure. Morphology, density, porosity, and other physical properties are computed. Two heights corresponding to two different times in the benzene flame, experimentally studied by Bittner and Howard [Proc. Combust. Inst. 18, 1105 (1981)], were chosen to examine the influence of different environments on structural properties of the particles formed.

Journal Article↗

PubMed2006

Formation of naphthalene, indene, and benzene from cyclopentadiene pyrolysis: a DFT study.

Four new reaction pathways for polycyclic aromatic hydrocarbon growth from cyclopentadiene pyrolysis are proposed and investigated using the B3LYP/6-31G(d,p) level of theory. These pathways allow for the production of indene, naphthalene, and benzene through intramolecular addition, C-H beta-scission, and C-C beta-scission reaction mechanisms, respectively. Results show that the intramolecular addition channel is favored at low temperatures, and the C-H beta-scission channel and the newly identified C-C beta-scission pathway become significant when the temperature increases. These results are in qualitative agreement with the experimental results previously obtained by this research group indicating that the main product at low temperature is indene, while benzene and naphthalene production dominate at the high-temperature end.

Algorithms↗

PubMed2006

Insights into the effect of combustion-generated carbon nanoparticles on biological membranes: a computer simulation study.

Classical molecular dynamics simulations of atomistic models of combustion-generated carbon nanoparticles and lipid bilayers have been performed to explore their possible structural, dynamical, and thermodynamic effects on biological membranes. The DREIDING generic force field is used for the carbonaceous nanoparticles of different morphologies, as produced from combustion sources, and the united atom model was employed for the dimyristoylphosphatidylcholine (DMPC) bilayer. It is observed that particle shape and structure have significant effects on solvation, mobility, adsorption, and permeation behavior of the particles. While combustion-generated carbon nanoparticles with an aspect ratio close to unity prefer to stay near the membrane center, precursors with other shapes mostly reside within the hydrocarbon tail region of the membrane. Carbon nanoparticles are not trapped in a local region even inside the membranes but move freely with a speed depending on their molecular weight. The adsorption of the particles on the surface of the biological membrane is comparable to thermal fluctuations because the weak segregation effect by water molecules is the main driving force to the adsorption behavior. The bigger the precursors are, the stronger they are bound to the membrane surface. The presence of combustion-generated nanoparticles inside the membrane perturbs local lipid density by pushing the neighboring lipid molecules away from the nanoparticles. This, coupled with thermal fluctuations, can induce an instantaneous membrane pore to allow water protrusion. From the umbrella sampling method, the potential of mean force for the permeation of carbona nanoparticles into the bilayer was also obtained. Surprisingly, elongated particles have a free energy barrier an order of magnitude smaller compared with more round ones. In addition, the round carbon nanoparticles showed strong hysteresis due to the local trapping of water molecules. Although the carbon soot precursors studied in this work are not the well-known carbon nanoparticles such as fullerenes or carbon nanotubes, the qualitative features of this study may be applicable to them as well.

Carbon↗

PubMed2005

Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation.

A recently developed multiscale coarse-graining procedure [Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469] is extended to derive coarse-grained models for nanoparticles. The methodology is applied to C(60) and to carbonaceous nanoparticles produced in combustion environments. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The CG models are shown to reproduce accurately the structural properties of the nanoparticle systems studied, while allowing for MD simulations of much larger self-assembled nanoparticle systems.

Models, Molecular↗

PubMed2005

Cyclodehydrogenation reactions to cyclopentafused polycyclic aromatic hydrocarbons.

B3LYP/6-31G(d,p) electronic structure calculations are employed to elucidate the reaction mechanisms for the conversion of the alternant C(18)H(12) polycyclic aromatic hydrocarbon benzo[c]phenanthrene into the nonalternant C(18)H(10) PAHs cyclopenta[cd]pyrene and benzo[ghi]fluoranthene. Isomerization reactions such as 5/6-ring switching and hydrogen atom scrambling are analyzed. Bay region chemistry, involving the rupture of one benzene ring followed by the formation of a new five-membered ring, is also studied, together with the mechanism for the formation of an aryne. The rearrangement of the latter yields annelated cyclopentadienylidenecarbene, which is then trapped intramolecularly.

Journal Article↗

PubMed2003

Modeling aerosol formation in opposed-flow diffusion flames.

The microstructures of atmospheric pressure, counter-flow, sooting, flat, laminar ethylene diffusion flames have been studied numerically by using a new kinetic model developed for hydrocarbon oxidation and pyrolysis. Modeling results are in reasonable agreement with experimental data in terms of concentration profiles of stable species and gas-phase aromatic compounds. Modeling results are used to analyze the controlling steps of aromatic formation and soot growth in counter-flow configurations. The formation of high molecular mass aromatics in diffusion controlled conditions is restricted to a narrow area close to the flame front where these species reach a molecular weight of about 1000 u. Depending on the flame configuration, soot formation is controlled by the coagulation of nanoparticles or by the addition of PAH to soot nuclei.

Aerosols↗