Biomedical subjects

Dmitry Bedrov

Publications and source records attributed to Dmitry Bedrov.

14 recordsLinked to original sources

PubMed2006

Molecular dynamics simulation study of the structure of poly(ethylene oxide) brushes on nonpolar surfaces in aqueous solution.

The structure of poly(ethylene oxide) (PEO, M(w) = 526) brushes of various grafting density (sigma) on nonpolar graphite and hydrophobic (oily) surfaces in aqueous solution has been studied using atomistic molecular dynamics simulations. Additionally, the influence of PEO-surface interactions on the brush structure was investigated by systematically reducing the strength of the (dispersion) attraction between PEO and the surfaces. PEO chains were found to adsorb strongly to the graphite surface due primarily to the relative strength of dispersion interactions between PEO and the atomically dense graphite compared to those between water and graphite. For the oily surface, PEO-surface and water-surface dispersion interactions are much weaker, greatly reducing the energetic driving force for PEO adsorption. This reduction is mediated to some extent by a hydrophobic driving force for PEO adsorption on the oily surface. Reduction in the strength of PEO-surface attraction results in reduced adsorption of PEO for both surfaces, with the effect being much greater for the graphite surface where the strong PEO-surface dispersion interactions dominate. At high grafting density (sigma approximately 1/R(g)(2)), the PEO density profiles exhibited classical brush behavior and were largely independent of the strength of the PEO-surface interaction. With decreasing grafting density (sigma < 1/R(g)(2)), coverage of the surface by PEO requires an increasingly large fraction of PEO segments resulting in a strong dependence of the PEO density profile on the nature of the PEO-surface interaction.

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PubMed2006

Water-induced interactions between carbon nanoparticles.

Molecular dynamics simulations were carried out in order to study the hydration of C60 fullerenes, carbon nanotubes, and graphene sheets in aqueous solution and the nature of water-induced interactions between these carbon nanoparticles. The hydration of these nonpolar carbon nanoparticles does not exhibit classical hydrophobic character due to the high density of surface atoms (carbon) resulting in strong water-surface dispersion interactions. Water was found to wet the nanoparticle surfaces independent of nanoparticle surface curvature, with the decrease in the extent of water-water hydrogen bonding with decreasing surface curvature being offset by stronger water-surface interactions. While all carbon nanoparticles investigated are anticipated to aggregate in water due to strong direct nanoparticle-nanoparticle interactions, the water-induced interactions between nanoparticles were found to be repulsive and, in contrast to the wetting behavior, were observed to exhibit strong dependence on surface curvature. The strength of the water-induced interaction between carbon nanoparticles was found to correlate well with the number of hydration water molecules displaced upon particle aggregation, which, relative to the amount of direct nanoparticle-nanoparticle contact engendered upon aggregation, decreases with decreasing surface curvature.

Carbon↗

PubMed2006

A novel mesophase formed by top-shaped molecules in the bulk and unsupported thin films: a molecular dynamics study.

We have used molecular dynamics simulations to investigate the ordering of top-shaped molecules in bulk phases and in unsupported thin films. Each rigid anisotropic molecule was composed of 11 Lennard-Jones interaction centers (beads). In an attempt to enhance the nematic stability in preference to smectic, the three central beads were assigned a larger Lennard-Jones diameter than the tail beads, giving the molecule a shape resembling a top. The molecular model was found to exhibit an unusual bulk mesophase with long-range orientational order and with molecular center-of-mass positions arranged in parallel interdigitated layers, with layer spacing smaller than half the length of the long axis of a molecule. However, despite the toplike molecular shape, no nematic phase was observed in the pressure range studied. Unsupported films of the isotropic liquid were cooled in order to locate a triple point between the novel mesophase, vapor, and isotropic liquid. At temperatures slightly above the triple point, enhanced surface ordering of molecules was found to occur in the unsupported film. At temperatures slightly below the triple point, the preferred molecular alignment in the unsupported film was parallel to the interface, in violation of arguments that have been proposed based on the relative enthalpies of various cleavage planes for close-packed structures.

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PubMed2006

Monte Carlo simulation study of the kinetics of brush formation by irreversible adsorption of telechelic polymers onto a solid substrate.

The irreversible adsorption of telechelic polymer chains from solution and melts onto solid substrates has been studied using the bond fluctuation Monte Carlo model. Complex brush formation kinetics dominated by diffusion of chains to the substrate at short times (diffusion-limited regime or DLR) and by penetration of chains through the maturing brush at longer times (penetration-limited regime or PLR) were observed. During the entire adsorption process, the rate of chain adsorption decreases monotonically with time. In the DLR, characterized by a maximum in the concentration of singly bound chains and a rapidly increasing fraction of doubly bound chains (loops), this decrease is due primarily to the depletion of free chains near the substrate and the formation of concentration gradients of free (nonadsorbed) chains in the bulk solution. The DLR and PLR are separated by an intermediate regime during which the brush becomes dominated by doubly bound chains and both penetration of the maturing brush and diffusion of chains to the brush surface play a role in determining the kinetics of brush growth. The PLR is characterized by steep gradients of free chains within the growing brush and the disappearance of concentration gradients for free chains in the bulk solution. In the PLR, the concentration of singly bound chains is low and decreases slowly while surface coverage and the fraction of doubly bound chains increase slowly. The rates of adsorption of new chains and the formation of loops in the PLR slow dramatically with increasing surface coverage and increasing chain length and less dramatically with decreasing bulk concentration.

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PubMed2006

Thermal relaxation mechanism and role of chemical functionalization in fullerene solutions.

Using molecular-dynamics simulations we investigate thermal relaxation of C60 and C84 molecules suspended in octane liquid. Pristine fullerenes exhibit relatively slow relaxation due to weak thermal coupling with the liquid. A comparison of the interfacial transport characteristics obtained from relaxation simulations with those obtained from equilibrium simulations and fluctuation-dissipation theorem analysis demonstrates that the relaxation process involves two main steps: (i) energy flow from high- to low-frequency modes within the fullerene, and (ii) energy flow from low-frequency fullerene modes to the liquid. Functionalization of fullerenes with alkene chains leads to significant reduction of the thermal relaxation time. The relaxation time of functionalized fullerenes becomes independent from the functionalizing chain length beyond approximately 10 carbon segments; this can be understood in terms of thermal conductivity along the chain and heat transfer between the chain and the solvent.

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PubMed2005

A molecular-dynamics simulation study of solvent-induced repulsion between C60 fullerenes in water.

Molecular-dynamics simulations of a single C(60) fullerene and pairs of C(60) fullerenes in aqueous solution have been performed for the purpose of obtaining improved understanding of the nature of solvent-induced interactions between C(60) fullerenes in water. Our simulations reveal repulsive solvent-induced interactions between two C(60) fullerenes in aqueous solution in contrast to the associative effects observed for conventional nonpolar solutes. A decomposition of the solvent-induced potential of mean force between fullerenes into entropy and energy (enthalpy) contributions reveals that the water-induced repulsion between fullerenes is energetic in origin, contrasting strongly to entropy-driven association observed for conventional nonpolar solutes. The dominance of energy in the solvent-induced interactions between C(60) fullerenes arises primarily from the high atomic density of the C(60) molecule, resulting in strong C(60)-water van der Waals attraction that is reduced upon association of the fullerenes. The water-induced repulsion is found to decrease with increasing temperature due largely to an increasing contribution from a relatively weak entropy-driven association.

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PubMed2005

Equilibrium sampling of self-associating polymer solutions: a parallel selective tempering approach.

We present a novel simulation algorithm based on tempering a fraction of relaxation-limiting interactions to accelerate the process of obtaining uncorrelated equilibrium configurations of self-associating polymer solutions. This approach consists of tempering (turning off) the attractive interactions for a fraction of self-associating groups determined by a biasing field h. A number of independent configurations (replicas) with overlapping Hamiltonian distributions in the expanded (NVTh) ensemble with constant NVT but different biasing fields, forming a chain of Hamiltonians, were simulated in parallel with occasional attempts to exchange the replicas associated with adjacent fields. Each field had an associated distribution of tempered interactions, average fraction of tempered interactions, and structural decorrelation time. Tempering parameters (number of replicas, fields, and exchange frequencies) were chosen to obtain the highest efficiency in sampling equilibrium configurations of a self-association polymer solution based on short serial simulation runs and a statistical model. Depending on the strength of the relaxation-limiting interactions, system size, and thermodynamic conditions, the algorithm can be orders of magnitude more efficient than conventional canonical simulation and is superior to conventional temperature parallel tempering.

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PubMed2005

Molecular dynamics simulation study of the role of evenly spaced poly(ethylene oxide) tethers on the aggregation of C60 fullerenes in water.

The aggregation behavior of C60 fullerenes and C60 fullerenes with six symmetrically tethered poly(ethylene oxide) oligomers [(PEO)-6-C60] in aqueous solutions has been studied using implicit solvent molecular dynamics simulations. Our simulations reveal that while the attraction between two (PEO)-6-C60 fullerenes in aqueous solution is stronger and longer range than that between two bare C60 fullerenes, the (PEO)-6-C60 fullerenes do not phase-separate in water but rather aggregate in chain-like clusters at concentrations where unmodified fullerenes completely phase-separate.

Letter↗

PubMed2005

Molecular dynamics simulation study of the alpha- and beta-relaxation processes in a realistic model polymer.

Molecular dynamics simulations of a melt of freely rotating chains of 1,4-polybutadiene (FRC-PBD) have been performed over a wide range of temperature. Removal of the dihedral barriers in FRC-PBD allows for complete resolution of the Johari-Goldstein beta process from the primary alpha process in the simulation time window. We find that relaxation in the beta regime occurs as the result of large-angle excursions of all backbone dihedrals. While during the beta process each dihedral visits all available states, the complete relaxation of torsional autocorrelation function (alpha process) occurs only when the polymer matrix shows significant motion and each dihedral populates all states with equilibrium probability.

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PubMed2005

Repulsive solvent-induced interaction between C60 fullerenes in water.

The role of water-fullerene interactions in the behavior of C60 in aqueous solution was investigated utilizing realistic Lennard-Jones (LJ) and repulsive Weeks-Chandler-Anderson (WCA) potentials. Strong water-fullerene dispersion interactions in the LJ potential dramatically influence the hydration of the fullerene promoting the formation of a high-density hydration shell of water. In contrast to the WCA potential, the water liquid phase between fullerenes remains stable with decreasing fullerene separation, resulting in a repulsive solvent-induced contribution to the fullerene potential of mean force.

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PubMed2004

A molecular dynamics simulation study of the alpha-relaxation in a 1,4-polybutadiene melt as probed by the coherent dynamic structure factor.

The dynamic coherent structure factor Scoh(q,t) for a 1,4-polybutadiene (PBD) melt has been investigated using atomistic molecular dynamics simulations. The relaxation of Scoh(q,t) at q = 1.44 angstroms(-1) and q = 2.72 angstroms(-1), corresponding to the first and second peaks in the static structure factor for PBD, was studied in detail over a wide range of temperature. It was found that time-temperature superposition holds for the alpha-relaxation for both q values over a wide temperature range and that the alpha-relaxation can be well described by a stretched (Kohlrauch-William-Watts) exponential with temperature independent but q dependent amplitude and stretching exponent. The alpha-relaxation times for both q values were found to exhibit the same non-Arrhenius temperature dependence, indicating that the same physical processes are responsible for relaxation on both length scales. The alpha-relaxation time was found to depend strongly upon the dynamical range of data utilized in determining the relaxation time, accounting for qualitative discrepancies between alpha-relaxation times reported here and those extracted for PBD from experimentally measured Scoh(q,t).

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PubMed2004

Anomalous pressure dependence of the structure factor in 1,4-polybutadiene melts: a molecular dynamics simulation study.

Neutron scattering has shown the first diffraction peak in the structure factor of a 1,4-polybutadiene melt under compression to move to larger q values as expected but to decrease significantly in intensity. Simulations reveal that this behavior does not result from loss of structure in the polymer melt upon compression but rather from the generic effects of differences in the pressure dependence of the intermolecular and intramolecular contributions to the melt structure factor and differences in the pressure dependence of the partial structure factors for carbon-carbon and carbon-deuterium intermolecular correlations. This anomalous pressure dependence is not seen for protonated melts.

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PubMed2003

Structural relaxation and dynamic heterogeneity in a polymer melt at attractive surfaces.

Molecular dynamics simulations of polymer melts at flat and structured surfaces reveal that, for the former, slow dynamics and increased dynamic heterogeneity for an adsorbed polymer is due to densification of the polymer in a surface layer, while, for the latter, the energy topography of the surface plays the dominant role in determining dynamics of interfacial polymer. The dramatic increase in structural relaxation time for polymer melts at the attractive structured surface is largely the result of dynamic heterogeneity induced by the surface and does not resemble dynamics of a bulk melt approaching T(g).

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PubMed2002

A revised quantum chemistry-based potential for poly(ethylene oxide) and its oligomers in aqueous solution.

We have conducted a high-level quantum chemistry study of the interactions of 1,2-dimethoxyethane (DME) with water for complexes representing both hydrophilic and hydrophobic hydration. It was found that our previous quantum chemistry-based force field for poly(ethylene oxide) (PEO) and its oligomers in aqueous solution did a poor job in describing the hydrophobic binding of water to the ether, consistent with our recent calculations of the excess free energy and entropy of hydration of DME. Our original force field was revised to more accurately reproduce the interaction of water with the carboneous portions of DME. Molecular dynamics simulations of aqueous DME solutions using the revised quantum chemistry-based potential yielded good agreement with experiment for excess free energy, enthalpy, and volume as well as excess solution viscosity and the self-diffusion of water. Comparison with our original potential revealed that the relatively hydrophobic ether-water interactions in the new potential strongly reduced the favorable excess free energy and enthalpy but have relatively little influence on the excess entropy for dilute DME solutions. Other properties of DME and PEO solutions including conformational populations and dynamics, solution viscosity, hydrogen bonding, water translational and rotational diffusion and neutron structure factor as a function of solution composition were found to be largely unchanged from those obtained using the original potential.

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