Biomedical subjects

Irene Yarovsky

Publications and source records attributed to Irene Yarovsky.

8 recordsLinked to original sources

PubMed2006

Density functional theory study of hydrogen bonding in ionic molecular materials.

Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials.(1) In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.

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PubMed2006

Classical molecular dynamics study of [60]fullerene interactions with silica and polyester surfaces.

This study examines the interaction of neutral and charged fullerenes with model silica and polyester surfaces. Molecular dynamics simulations at 298 K indicate that van der Waals forces are sufficiently strong in most cases to cause physisorption of the neutral fullerene particle onto the surfaces. The fullerenes are unable to penetrate the rigid silica surface but are generally able to at least partially infiltrate the flexible polymer surface by opening surface cavities. The introduction of charge to the fullerene generally leads to an increase in both the separation distance and Work of Separation with silica. However, the charged fullerenes generally exhibit significantly closer and stronger interactions with polyester films, with a distinct tendency to absorb into the "bulk" of the polymer. The separation distance and Work of Separation of C60 with each of the surfaces also depend greatly on the sign, magnitude, and localization of the charge on the particle. Cross-linking of the polyester can improve resistance to the neutral fullerene. Functionalization of the polyester surface (F and OH substituents) has been shown to prevent the C60 from approaching as close to the polyester surface. Fluorination leads to improved resistance to positively charged fullerenes, compared to the unmodified polyester. However, hydroxylation generally enables greater adhesion of charged fullerenes to the surface due to H-bonding and electrostatic attraction.

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PubMed2006

Effect of S arrangement on Fe(110) properties at 1/3 monolayer coverage: a DFT study.

Using density functional theory calculations, we compare the relative stabilities and properties of different arrangements of S on Fe(110) at a 1/3 monolayer coverage, including two observed experimentally. For all studied arrangements, S is adsorbed in the three high-symmetry adsorption sites: 4-fold hollow, 3-fold hollow, bridge, and atop sites. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are determined and compared. The most stable overlayer arrangement corresponds to the overlayer seen by experiment after dissociative adsorption of H2S and has S adsorbed in 4-fold hollow sites. In the other arrangements, the S atoms are located closer to each other on the surface reducing the stability of the overlayer. S causes a minor adsorbate-induced reconstruction of the Fe surface and quenches the magnetic moment of the Fe atoms it bonds to directly. It adsorbs as an electropositive species, causing a positive work function change and forms polar covalent bonds to the surface.

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PubMed2005

Electric field effects on insulin chain-B conformation.

The response of proteins to different forms of stress continues to be a topic of major interest, especially with the proliferation of electromagnetic devices conjectured to have detrimental effects on human health. In this paper, we have performed molecular dynamics simulations on insulin chain-B under the influence of both static and oscillating electric fields, ranging from 10(7) to 10(9) V/m. We have found that both variants have an effect on the normal behavior of the protein, with oscillating fields being more disruptive to the structure as compared to static fields of similar effective strength. The application of a static field had a stabilizing effect on the secondary structure, restricting the inherent flexibility that is crucial for insulin's biological activity.

Computer Simulation↗

PubMed2005

Adhesion between graphite and modified polyester surfaces: a theoretical study.

This study examines the adhesion of graphite to functionalized polyester surfaces using a range of qualitative and quantitative measures of theoretical adhesion. Modifications to the polyester surfaces include the addition of hydroxyl, carboxyl, or fluorine substituents with coverages of 0.4 and 0.9 groups per nm(2). In each case, the introduction of substituents to the surface of the polyester was calculated to lead to reduced adhesion to graphite. Effects of surface relaxation on adhesion are studied by employing different simulation protocols. The theoretical results suggest one mechanism to reduce adhesion to carbonaceous solids is to increase atomic roughness using strongly hydrophilic or alternatively strongly hydrophobic substituents.

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PubMed2005

Effect of sulfur coverage on Fe(110) adhesion: a DFT study.

The effect of adsorbed S at different coverages on the adhesion of Fe(110) surfaces in match and mismatch is examined using density functional theory (DFT). S is adsorbed in atop, bridge, and 4-fold hollow sites on one side of the interface in c(2 x 2) and p(1 x 1) arrangements, corresponding to coverages of 1/2 and 1 monolayer, respectively. The calculated adhesion energy values at different interfacial separations are fitted to the universal binding energy relation, and the effect of the S coverages on the adhesive strength is analyzed. The effect of relaxation of the interfaces at equilibrium is also investigated, and the resulting interfacial structures and related magnetic and charge density properties are compared.

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PubMed2005

Coverage-dependent adsorption of atomic sulfur on Fe(110): a DFT study.

Adsorption of atomic sulfur at different coverages on the Fe(110) surface is examined using density functional theory (DFT) in order to investigate the effect that adsorbate-adsorbate interactions may have on the surface properties. S is adsorbed in the high-symmetry adsorption sites: 4-fold hollow, bridge, and atop sites in the following surface arrangements: c(2 x 2) and p(1 x 1) which correspond to coverages of 1/2 and 1 monolayer, respectively. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are examined and compared to our previous study of S adsorbed at 1/4 monolayer coverage and p(2 x 2) arrangement [Spencer et al. Surf. Sci. 2003, 540, 420]. It was found that S forms polar covalent bonds to the surface. The bonding goes from being S-Fe dominated at the low coverages to being S-S dominated at the higher coverages where the S atoms are located closer together on the surface and interact with each other.

Journal Article↗

PubMed2004

"Exact" surface free energies of iron surfaces using a modified embedded atom method potential and lambda integration.

Previously a new universal lambda-integration path and associated methodology was developed for the calculation of "exact" surface and interfacial free energies of solids. Such a method is in principle applicable to any intermolecular potential function, including those based on ab initio methods, but in previous work the method was only tested using a relatively simple embedded atom method iron potential. In this present work we apply the new methodology to the more sophisticated and more accurate modified embedded atom method (MEAM) iron potential, where application of other free- energy methods would be extremely difficult due to the complex many-body nature of the potential. We demonstrate that the new technique simplifies the process of obtaining "exact" surface free energies by calculating the complete set of these properties for the low index surface faces of bcc and fcc solid iron structures. By combining these data with further calculations of liquid surface tensions we obtain the first complete set of exact surface free energies for the solid and liquid phases of a realistic MEAM model system. We compare these predictions to various experimental and theoretical results.

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