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The effect of cohesive contacts or, equivalently, dynamical cross-linking on the equilibrium morphology of a polymer brush infiltrated by nanoparticles that are attracted to the polymer strands is studied for plane-grafted brushes using coarse-grained molecular dynamics and approximate statistical mechanical models. In particular, the Alexander-de Gennes (AdG) and Strong Stretching Theory (SST) mean-field theory (MFT) models are considered. It is found that for values of the MFT crosslink strength interaction parameter beyond a certain threshold, both AdG and SST models predict that the polymer brush will be in a compact state of nearly uniform density packed next to the grafting surface over a wide range of solution phase nanoparticle concentrations. Coarse grained molecular dynamics simulations confirm this prediction, for both small nanoparticles (nanoparticle volume = monomer volume) and large nanoparticles (nanoparticle volume = 27 × monomer volume). Simulation results for these cross-linked systems are compared with analogous results for systems with no cross-linking. At the same solution phase nanoparticle concentration, strong cross-linking results in additional compression of the brush relative to the non-crosslinked analog and, at all but the lowest concentrations, to a lesser degree of infiltration by nanoparticles. For large nanoparticles, the monomer density profiles show clear oscillations moving outwards from the grafting surface, corresponding to a degree of layering of the absorbed nanoparticles in the brush as they pack against the grafting surface. [ABSTRACT FROM AUTHOR]

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic [p.sub.f]/([cm.sup.3]/s/pore) and diffusion [p.sub.d] ([cm.sup.3]/s/Pore) permeability coefficients per pore of [H.sub.2] and [D.sub.2]O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of [H.sub.2]O and [D.sub.2]O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the [D.sub.2]O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of [H.sub.2]O vs. [D.sub.2]O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of [p.sub.j] for [D.sub.2]O is ~15% smaller than for [H.sub.2]O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient [P.sub.f] (cm/s) of [D.sub.2]O is ~21% lower than for [H.sub.2]O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of [D.sub.2]O compared to [H.sub.2]O in AQP1 is most likely due to the lower self diffusion constant of [D.sub.2]O.

The study presented empirical formulas for calculating the dielectric self-energy and ion-ion pair interactions in cylindrical ion channels. It concluded that use of effective ion-ion potentials greatly reduces the computer memory required to perform dynamic lattice Monte Carlo (DLMC) ion permeation simulations in dielectrically inhomogeneous environments, thus enabling treatment of larger system than a can be handled by numerically exact techniques.

The dynamic lattice Monte Carlo (DLMC) algorithm is used to conduct simulations of ion permeations through narrow model cylindrical channels to determine the time evolution of the ions in the system based on the evaluation of the electrostatic forces acting on each particle. Comparison of the results with those available from the Poisson-Nernst-Planck theory is reported to indicate large differences with the degree of variation increasing as the radius of the ion channel is reduced.

Properties of the wide-angle equation (WAEQ), a nonparaxial scalar wave equation used to propagate light through media characterized by inhomogeneous refractive-index profiles, are studied. In particular, it is shown that the WAEQ is not equivalent to the more complicated but more fundamental Helmholtz equation (HEQ) when the index of refraction profile depends on the position along the propagation axis. This includes all nonstraight waveguides. To study the quality of the WAEQ approximation, we present a novel method for computing solutions to the WAEQ. This method, based on a short-time iterative Lanczos (SIL) algorithm, can be applied directly to the full three-dimensional case, i.e., systems consisting of the propagation axis coordinate and two transverse coordinates. Furthermore, the SIL method avoids series-expansion procedures (e.g., Pade approximants) and thus convergence problems associated with such procedures. Detailed comparisons of solutions to the HEQ, WAEQ, and the paraxial equation (PEQ) are presented for two cases in which numerically exact solutions to the HEQ can be obtained by independent analysis, namely, (i) propagation in a uniform dielectric medium and (ii) propagation along a straight waveguide that has been tilted at an angle to the propagation axis. The quality of WAEQ and PEQ, compared with exact HEQ results, is investigated. Cases are found for which the WAEQ actually performs worse than the PEQ. OCIS codes: 230.7370, 350.5500.

A dynamic lattice Monte Carlo (DLMC) simulation approach to the description of ion transport in dielectric environments is reported. The performance of the method is verified by comparing the numerical results to exact solutions for simple geometries, and to mean field (Poisson-Nernst-Planck, PNP) theory in a system where PNP should provide a reasonable description.

A random-walk simulation of microdialysis is used to examine how a reaction that consumes analyte in the medium external to the probe affects the extraction and recovery processes. The simulations suggest that such a reaction can promote the extraction process while simultaneously inhibiting the recovery process, which appears to be consistent with recent experimental evidence of asymmetry in the extraction and recovery of the neurotransmitter, dopamine, during brain microdialysis. This suggests that quantitative microdialysis strategies that rely on the extraction fraction as a measure of the probe recovery value, such as the no-net-flux method, will produce an underestimate of the analyte concentration in the external medium when that analyte is consumed by a reaction in the external medium. Furthermore, if experimental conditions arise under which the kinetics of the reaction are changed, then changes in the extraction and recovery processes are likely to occur as well. The implications of these theoretical findings for the quantitative interpretation of in vivo microdialysis results obtained for the neurotransmitter dopamine are examined.

An algorithm for propagating semiclassical Gaussian wave packets using electronic structure data computed 'on the fly' in the course of propagation is presented. Its feasibility for condensed phase systems is demonstrated by calculation of Franck-Condon absorption and emission spectra.

A recently introduced optimal control theory method for optical waveguide design is applied to Y-branch waveguides and Mach-Zehnder modulators. The method simultaneously optimizes many parameters in a chosen design scheme; computational effort scales mildly with the number of parameters considered. Significant improvement in guiding efficiency relative to intuitively reasonable initial parameter choices is obtained in all cases.

Polymer-nanoparticle composites are a promising new class of materials for creation of controllable nano-patterned surfaces and nanopores. We use coarse-grained molecular dynamics simulations augmented with analytical theory to study the structural transitions of surface grafted polymer layers (brushes) induced by infiltration of nanoparticles that are attracted to the polymers in the layer. We systematically compare two different polymer brush geometries: one where the polymer chains are grafted to a planar surface and the other where the chains are grafted to the inside of a cylindrical nanochannel. We perform a comprehensive study of the effects of the material parameters such as the polymer chain length, chain grafting density, nanoparticle size, strength of attraction between nanoparticles and polymer monomers, and, in the case of the cylindrically grafted brush, the radius of the cylinder. We find a very general behavioral motif for all geometries and parameter values: the height of the polymer brush is non-monotonic in the nanoparticle concentration in solution. As the nanoparticle concentration increases, the brush height first decreases and after passing through a minimum value begins to increase, resulting in the swelling of the nanoparticle infused brush. These morphological features may be useful for devising tunable "smart" nano-devices whose effective dimensions can be reversibly and precisely adjusted by changing the nanoparticle concentration in solution. The results of approximate Self-Consistent Field Theory (SCFT) calculations, applicable in the regime of strong brush stretching, are compared to the simulation results. The SCFT calculations are found to be qualitatively, even semi-quantitatively, accurate when applied within their intended regime of validity, and provide a useful and efficient tool for modeling such materials. [ABSTRACT FROM AUTHOR]

An approximation scheme is developed to compute Brownian motion according to the Langevin equation for a molecular system moving in a harmonic force field (corresponding to a quadratic potential energy surface) and characterized by one or more rigid internal fragments. This scheme, which relies on elements of the rotation translation block (RTB) method for computing vibrational normal modes of large molecules developed by Sanejouand and co-workers [Biopolymers 34, 759 (1994); Proteins: Struct., Funct., Genet. 41, 1 (2000)], provides a natural and efficient way to freeze out the small amplitude, high frequency motions within each rigid fragment. The number of dynamical degrees of freedom in the problem is thereby reduced, often dramatically. To illustrate the method, the relaxation kinetics of the small membrane-bound ion channel protein gramicidin-A, subjected to an externally imposed impulse, is computed. The results obtained from all-atom dynamics are compared to those obtained using the RTB-Langevin dynamics approximation (treating eight indole moieties as internal rigid fragments): good agreement between the two treatments is found. [ABSTRACT FROM AUTHOR]

The rotation and translation block (RTB) method of Durand et al. [Biopolymers 34, 759 (1994)] and Tama et al. [Proteins 41, 1 (2000)] provides an appealing way to calculate low-frequency normal modes of large biomolecules by restricting the space of motions to exclude internal motions of preselected rigid fragments within the molecule. These fragments are modeled essentially as rigid bodies and the need to calculate high-frequency relative motions of the atoms that form them is obviated in a natural way. Here we extend the RTB approach into a method for computing the classical (Newtonian) dynamics of a biomolecule, or any large molecule, with effective rigid-body constraints applied to a prechosen set of internal molecular fragments. This method, to be termed RTB dynamics, is easy to implement, conserves the total energy of the system, does not require the construction of the matrix of second spatial derivatives of the potential-energy function (Hessian matrix), and can be used to compute the classical dynamics of a system moving in an arbitrary anharmonic force field. An elementary numerical application to signal propagation in the small membrane-bound polypeptide gramicidin-A is presented for illustration purposes. [ABSTRACT FROM AUTHOR]

We present a new approach for simulating the motions of flexible polyelectrolyte chains based on the continuous kink-jump Monte Carlo technique coupled to a lattice field theory based calculation of the Poisson-Boltzmann (PB) electrostatic free energy ''on the fly.'' This approach is compared to the configurational-bias Monte Carlo technique, in which the chains are grown on a lattice and the PB equation is solved for each configuration with a linear scaling multigrid method to obtain the many-body free energy. The two approaches are used to calculate end-to-end distances of charged polymer chains in solutions with varying ionic strengths and give similar numerical results. The configurational-bias Monte Carlo/multigrid PB method is found to be more efficient, while the kink-jump Monte Carlo method shows potential utility for simulating nonequilibrium polyelectrolyte dynamics. [ABSTRACT FROM AUTHOR]

A recently developed Floquet theory-based formalism for computing electron transport through a molecular bridge coupled to two metal electrodes in the presence of a monochromatic ac radiation field is applied to an experimentally relevant system, namely a xylyl-dithiol molecule in contact at either end with gold electrodes. In this treatment, a nondissipative tight-binding model is assumed to describe the conduction of electric current. Net current through the wire is calculated for two configurations of the electrode-wire-electrode system. In one, symmetric, configuration, the electrodes are close (∼2 Å) and equidistant from the bridge molecule. In the other, asymmetric configuration, one electrode is farther away (∼ 5 Å), representing the tip of a scanning tunneling microscope located at this distance from the bridge molecule (the other end being chemisorbed to a gold substrate). For both configurations, electron current is calculated for a range of experimental inputs, including dc bias and the intensity and frequency of the laser. Via absorption/emission of photons, resonant conditions may be achieved under which electron transport is significantly enhanced compared to the unilluminated analog. Calculations show that this can be accomplished with experimentally accessible laser field strengths. [ABSTRACT FROM AUTHOR]

This paper considers electron transport through a molecular bridge coupled to two metal electrodes in the presence of a monochromatic radiation field. Current flow through the wire is calculated within a nondissipative one-electron tight binding model of the quantum dynamics. Using Floquet theory, the field-driven molecular wire is mapped to an effective time-in dependent quantum system characterized by a tight-binding Hamiltonian with the same essential structure as the nondriven analog. Thus, Green's Function methods for computing current flow through the wire, which have been profitably applied to the molecular wire problem in the absence of driving, can also be used to analyze the corresponding field-driven system. Illustrative numerical calculations on a simple model system are presented. [ABSTRACT FROM AUTHOR]

Three-dimensional dynamic Monte Carlo simulations of polymer translocation through a cylindrical hole in a planar slab under the influence of an external driving force are performed. The driving force is intended to emulate the effect of a static electric field applied in an electrolytic solution containing charged monomer particles, as is relevant to the translocation of certain biopolymers through protein channel pores embedded in cell membranes. The time evolution of the probability distribution of the translocation coordinate (the number of monomers that have passed through the pore) is extracted from three-dimensional (3-D) simulations over a range of polymer chain lengths. These distributions are compared to the predictions of a 1-D Smoluchowski equation model of the translocation coordinate dynamics. Good agreement is found, with the effective diffusion constant for the 1-D Smoluchowski model being nearly independent of chain length. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) and Brownian dynamics (BD) simulations are integrated to analyze the ion conduction, charge selectivity and halothane modulation mechanisms in Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC). Halothane is shown to perturb salt bridges in GLIC that is important for channel gating and open-channel stability, but has no major impact on the single ion potential of mean force (PMF) profiles.

A generalization of the model to the case of a nondegenerate three-level system coupled to a high-dimensional bath is considered, such a model system has direct relevance to a large class of donor-bridge-acceptor electron transfer processes. Numerically exact path integral calculations to the predictions of second-order time-local relaxation theory are compared because the quantum dynamics of this system cannot be computed analytically.

An analytically solvable model of multilevel condensed-phase quantum dynamics relevant to vibrational relaxation and electron transfer is presented. It is demonstrated that for N>2 the long-time steady-state system site occupation probabilities are not the same for all sites, that is, they are distributed in a non-Boltzmann manner, which depends on the initial conditions and the number of levels in the system.