Molecular dynamics simulation study of the dynamics of fluids at solid-liquid interfaces

The dynamics of fluids at solid-liquid interfaces is investigated. In particular, we consider a simple Lennard-Jones fluid as well as a melt of hexadecane chains. For the Lennard-Jones fluid, the numerical results are compared with analytical calculations based on the diffusion equation, which shows that the numerical results can very well by described by the solution of the diffusion equation for reflecting surfaces. The diffusion coefficient is practically independent of the position within the film, although the fluid is inhomogeneous perpendicular to the surface. In contrast, the dynamics of the centers of mass of hexadecane molecules perpendicular to repulsive surfaces is severely slowed down due to their extended and anisotropic nature and cannot be described by a single particle diffusion equation.     

Diffusion on ruffled membrane surfaces

We present a position Langevin equation for overdamped particle motion on rough two-dimensional surfaces. A Brownian dynamics algorithm is suggested to evolve this equation numerically, allowing for the prediction of effective (projected) diffusion coefficients over corrugated surfaces. In the case of static surface roughness, we find that a simple area-scaling prediction for the projected diffusion coefficient leads to seemingly quantitative agreement with numerical results. To study the effect of dynamic surface evolution on the diffusive process, we consider particle diffusion over a thermally fluctuating elastic membrane. Surface fluctuation has the effect of increasing the effective diffusivity toward a limiting annealed-surface value discussed previously. We argue that protein motion over cell surfaces spans a variety of physical regimes, making it impossible to identify a single approximation scheme appropriate to all measurements of interest.     

Molecular dynamics simulations of polymer transport in nanocomposites

Molecular dynamics simulations on the Kremer-Grest bead-spring model of polymer melts are used to study the effect of spherical nanoparticles on chain diffusion. We find that chain diffusivity is enhanced relative to its bulk value when polymer-particle interactions are repulsive and is reduced when polymer-particle interactions are strongly attractive. In both cases chain diffusivity assumes its bulk value when the chain center of mass is about one radius of gyration R(g) away from the particle surface. This behavior echoes the behavior of polymer melts confined between two flat surfaces, except in the limit of severe confinement where the surface influence on polymer mobility is more pronounced for flat surfaces. A particularly interesting fact is that, even though chain motion is strongly speeded up in the presence of repulsive boundaries, this effect can be reversed by pinning one isolated monomer onto the surface. This result strongly stresses the importance of properly specifying boundary conditions when the near surface dynamics of chains are studied.     

Structure and Dynamics of Adsorbed Dopamine on Solvated Carbon Nanotubes and in a CNT Groove

Advanced carbon microelectrodes, including many carbon-nanotube (CNT)-based electrodes, are being developed for the in vivo detection of neurotransmitters such as dopamine (DA). Our prior simulations of DA and dopamine-o-quinone (DOQ) on pristine, flat graphene showed rapid surface diffusion for all adsorbed species, but it is not known how CNT surfaces affect dopamine adsorption and surface diffusivity. In this work, we use molecular dynamics simulations to investigate the adsorbed structures and surface diffusion dynamics of DA and DOQ on CNTs of varying curvature and helicity. In addition, we study DA dynamics in a groove between two aligned CNTs to model the spatial constraints at the junctions within CNT assemblies. We find that the adsorbate diffusion on a solvated CNT surface depends upon curvature. However, this effect cannot be attributed to changes in the surface energy roughness because the lateral distributions of the molecular adsorbates are similar across curvatures, diffusivities on zigzag and armchair CNTs are indistinguishable, and the curvature dependence disappears in the absence of solvent. Instead, adsorbate diffusivities correlate with the vertical placement of the adsorbate’s moieties, its tilt angle, its orientation along the CNT axis, and the number of waters in its first hydration shell, all of which will influence its effective hydrodynamic radius. Finally, DA diffuses into and remains in the groove between a pair of aligned and solvated CNTs, enhancing diffusivity along the CNT axis. These first studies of surface diffusion on a CNT electrode surface are important for understanding the changes in diffusion dynamics of dopamine on nanostructured carbon electrode surfaces.     

Brownian diffusion close to a polymer brush

In an effort to control particle diffusion near surfaces, we have studied the dynamics of colloidal hard spheres and soft compliant star copolymers on surfaces coated with polymer brushes using evanescent wave dynamic light scattering. The same experiments provide information on the brush structure and confined particle motion. The penetration into dense polydisperse brushes is size- and solvent-dependent.     

Interaction of micrometer-scale particles with nanotextured surfaces in shear flow

Dynamic particle adhesion from flow over collecting surfaces with nanoscale heterogeneity occurs in important natural systems and current technologies. Accurate modeling and prediction of the dynamics of particles interacting with such surfaces will facilitate their use in applications for sensing, separating, and sorting colloidal-scale objects. In this paper, the interaction of micrometer-scale particles with electrostatically heterogeneous surfaces is analyzed. The deposited polymeric patches that provide the charge heterogeneity in experiments are modeled as 11-nm disks randomly distributed on a planar surface. A novel technique based on surface discretization is introduced to facilitate computation of the colloidal interactions between a particle and the heterogeneous surface based on expressions for parallel plates. Combining these interactions with hydrodynamic forces and torques on a particle in a low Reynolds number shear flow allows particle dynamics to be computed for varying net surface coverage. Spatial fluctuations in the local surface density of the deposited patches are shown responsible for the dynamic adhesion phenomena observed experimentally, including particle capture on a net-repulsive surface.     

ADSORPTION DYNAMICS OF MACROPOROUS POLYMERIC ADSORBENT I. The Studies on the Particle Diffusion Mass-Transfer Process

1 INTRODUCTIONBoyd et al established the foundation of ion-exchange dynamics based on the Fick's Law intothe process of ion-exchange diffusion at firstll]. At present time, most of studies for themacroporous adsorption resin are focus on the synthesis of new adsorbent, observing the effectof some conditions on the adsorption capacity and adsorption selectivity. But there are nopedicular studies on the aspect of adsorption dynamics, such as mass-transfer rate, mass-transfermechanism and so…     

Isometric graphing and multidimensional scaling for reaction-diffusion modeling on regular and fractal surfaces with spatiotemporal pattern recognition

Heterogeneous surface reactions exhibiting complex spatiotemporal dynamics and patterns can be studied as processes involving reaction-diffusion mechanisms. In many realistic situations, the surface has fractal characteristics. This situation is studied by isometric graphing and multidimensional scaling (IGMDS) of fractal surfaces for extracting geodesic distances (i.e., shortest scaled distances that obtain edges of neighboring surface nodes and their interconnections) and the results obtained used to model effects of surface diffusion with nonlinear reactions. Further analysis of evolved spatiotemporal patterns may be carried out by IGMDS because high-dimensional snapshot data can be efficiently projected to a transformed subspace with reduced dimensions. Validation of the IGMDS methodology is carried out by comparing results with reduction capabilities of conventional principal component analysis for simple situations of reaction and diffusion on surfaces. The usefulness of the IGMDS methodology is shown for analysis of complex patterns formed on both regular and fractal surfaces, and using generic nonlinear reaction-diffusion systems following FitzHugh Nagumo and cubic reaction kinetics. The studies of these systems with nonlinear kinetics and noise show that effects of surface disorder due to fractality can become very relevant. The relevance is shown by studying properties of dynamical invariants in IGMDS component space, viz., the Lyapunov exponents and the KS entropy for interesting situations of spiral formation and turbulent patterns.     

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level.     

Nonadiabatic Dynamics of Hydrogen Diffusion on Cu(001): Classical Mapping Model with Multistate Projection Window in Real Space

Diffusion of atomic hydrogen on metallic surfaces is a longstanding research topic of both fundamental and practical interests. However, full understanding of the microscopic mechanisms and development of effective strategy for surface dynamics control at the molecular level remain elusive. In this paper, we propose a new nonadiabatic multistate model for surface diffusion based on a real space decomposition scheme by generalizing the classical mapping theory of Meyer and Miller. The model suggests a general multistate perspective on real-time surface dynamics by mapping it into spatially disjointed windowing functions, which feature the explicit nonadiabatic controllability. Within this framework, the first nonadiabatic molecular dynamics simulation is performed for atomic hydrogen diffusion on the Cu(001) surface, and the nonequilibrium effect of lattice distortion is studied.     

纳米镍团簇表面性质及能量的分子动力学研究

在单分散金属纳米粒子制备过程中,金属烧结现象需要尽量避免。烧结与诸多因素有关,其中金属纳米粒子的表面性质和能量对烧结作用有着重要影响。本工作利用分子动力学,以4种不同粒径的金属Ni纳米团簇为研究对象,在COMPASS力场下对不同温度下其表面积、扩散性质、表面能以及比表面能等进行了计算。结果显示,随着温度从300K升至1000K,纳米团簇的表面积稍微增加了约5%,表面层扩散系数显著增加了约3个数量级,表面能量升高了约15%,同时表面层与体相的能量差明显增加了近3倍。比表面能定义为增加单位表面积所引起的表面能的增量。计算结果表明,700K时团簇的比表面能比镍熔点处的表面张力高出约3个数量级,预示着团簇烧结具有强大的推动力。比表面能随温度升高以及粒径增大而下降,与热力学原理相一致。     

LSPR Imaging: Simultaneous Single Nanoparticle Spectroscopy and Diffusional Dynamics

A wide-field localized surface plasmon resonance (LSPR) imaging method using a liquid crystal tunable filter (LCTF) is used to measure the scattering spectra of multiple Ag nanoparticles in parallel. This method provides the ability to characterize moving Ag nanoparticles by measuring the scattering spectra of the particles while simultaneously tracking their motion. Consequently, single particle diffusion coefficients can be determined. As an example, several single Ag nanoprisms are tracked, the LSPR scattering spectrum of each moving particle is obtained, and the single particle diffusion coefficient is determined from its trajectory. Coupling diffusion information with spectral information in real time is a significant advance and addresses many scientific problems, both fundamental and biological, such as cell membrane protein diffusion, functional plasmonic distributions, and nanoparticle growth mechanisms.     

Hydration and dewetting near graphite-CH(3) and graphite-COOH plates

The dynamics of water near the nanoscale hydrophobic (graphite-CH(3)) and hydrophilic (graphite-COOH) plates has been studied in detail with molecular dynamics simulations in this paper. It is shown that these designed surfaces (by growing a layer of methyl or carboxyl groups on top of graphite) can have a significant impact on the neighboring water dynamics, with the hydrophilic carboxyl surface having even more profound effects. The water hydrogen bond lifetime is much longer near both types of surfaces than that in the bulk, while on the other hand the water diffusion constant is much smaller than that in the bulk. The difference in the diffusion constant can be as large as a factor of 8 and the difference in the hydrogen bond lifetime can be as large as a factor of 2, depending on the distance from the surface. Furthermore, the water molecules in the first solvation shell of surface atoms show a strong bias in hydroxyl group orientation near the surface, confirming some of the previous findings. Finally, the possible water dewetting transition between two graphite-CH(3) plates and the effect of the strength of the solute-solvent attractions on the water drying transition are investigated. The relationship among the dewetting transition critical distance, van der Waals potential well depth, and water contact angle on the graphite-CH(3) surface is also analyzed on the basis of a simple macroscopic theory, which can be used to predict the dewetting transition critical distance.     

ADSORPTION DYNAMICS OF MACROPOROUS POLYMERIC ADSORBENT 1．The Studies on the Particle Diffusion Mass—Transfer Process

The adsorption dynamics for phenol in aqueous solution of the adsorbent based on polystyrene was studied.In order to distinguish with the Boyd quasi-homogeneous model of the inner structure of ion-exchanger,the particle diffusion model including surface diffustion model and porediffusion model was suggested which is suitable to the macroporous adsorbent.The diffusiondetermination step of the adsorption pocess was established and the effective diffusion coefficient was also determined.The influence of surface diffusion and pore difusion on the particle diffusion rate was investigated qualitatively.All of these were very important to improve the structure of the macroporous adsorbent in order to improve the mass-transfer rate.     

Simulating surface diffusion and surface growth in ceramics

We examine the movement of ion pairs on the surfaces of simple oxides. Using temperature-accelerated dynamics the elementary processes involved are identified and the activation energies of these used as input to kinetic Monte Carlo simulations. Results are presented for the motion of BaO and SrO ion pairs on the (100) surfaces of BaO and SrO, respectively, and the formation of island pairs on these surfaces is studied. The simulations reveal the importance of exchange mechanisms in surface diffusion and growth of oxides. The importance of such reactions has been recognised previously for metallic surfaces but not for ionic systems, where it has been assumed that ionic surface diffusion is surface diffusion via the hopping motion of ion pairs from one surface site to another. Exchange mechanisms can dominate transport processes both on terraces and steps for both homoepitaxial and heteroepitaxial growth. We suggest the unavoidable mixing when an exchange mechanism operates must be considered when attempting to grow sharp interfaces in oxide nanostructures.     

Dynamics of water confined in the interdomain region of a multidomain protein

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.     

Adsorption on Heterogeneous Regular Surfaces

Quantifying the role of surface shape and physicochemical surface conditions on the interfacial reactivity of particles and substrates is fundamental to a multitude of natural and engineered surface adsorption phenomena. We consider continuum/jump regime adsorption at the gas or liquid interface of arbitrary regular solid surfaces with heterogeneous surface features. In particular, the 3-D boundary value problem (based on Laplace's diffusion equation) is converted into a 2-D integral equation for the adsorbate concentration at the particle surface. This accommodates numerical descretization via the implementation of 2-D Gauss-Legendre quadratures on an arrangement of high- and low-adsorption patch trace sites constructed to completely cover the particle surface. A generalized computer program is developed to solve the resulting linear algebra problem for the unkown local adsorption current densities. We investigate the role of various distributions of high- and low-adsorption sites for a generalized class of spheres which includes the DNA-like shaped twisted spheres. The biological implications of the role of surface curvature on interfacial adsorption/reactivity at particle surfaces are also discussed. Copyright 2001 Academic Press.     

Boundary homogenization for trapping by patchy surfaces

We analyze trapping of diffusing particles by nonoverlapping partially absorbing disks randomly located on a reflecting surface, the problem that arises in many branches of chemical and biological physics. We approach the problem by replacing the heterogeneous boundary condition on the patchy surface by the homogenized partially absorbing boundary condition, which is uniform over the surface. The latter can be used to analyze any problem (internal and external, steady state, and time dependent) in which diffusing particles are trapped by the surface. Our main result is an expression for the effective trapping rate of the homogenized boundary as a function of the fraction of the surface covered by the disks, the disk radius and trapping efficiency, and the particle diffusion constant. We demonstrate excellent accuracy of this expression by testing it against the results of Brownian dynamics simulations. (c) 2004 American Institute of Physics.     

Electrostatically confined nanoparticle interactions and dynamics

We report integrated evanescent wave and video microscopy measurements of three-dimensional trajectories of 50, 100, and 250 nm gold nanoparticles electrostatically confined between parallel planar glass surfaces separated by 350 and 600 nm silica colloid spacers. Equilibrium analyses of single and ensemble particle height distributions normal to the confining walls produce net electrostatic potentials in excellent agreement with theoretical predictions. Dynamic analyses indicate lateral particle diffusion coefficients approximately 30-50% smaller than expected from predictions including the effects of the equilibrium particle distribution within the gap and multibody hydrodynamic interactions with the confining walls. Consistent analyses of equilibrium and dynamic information in each measurement do not indicate any roles for particle heating or hydrodynamic slip at the particle or wall surfaces, which would both increase diffusivities. Instead, lower than expected diffusivities are speculated to arise from electroviscous effects enhanced by the relative extent (kappaa approximately 1-3) and overlap (kappah approximately 2-4) of electrostatic double layers on the particle and wall surfaces. These results demonstrate direct, quantitative measurements and a consistent interpretation of metal nanoparticle electrostatic interactions and dynamics in a confined geometry, which provides a basis for future similar measurements involving other colloidal forces and specific biomolecular interactions.     

Nuclear Dynamics and Electronic Effects of Hydrogen on Solid Surfaces

Hydrogen is involved in a variety of chemical processes on surfaces. While hydrogen exhibits vibrational and rotational dynamics in its adsorption state, it in some cases undergoes diffusion into the substrate as well as on the surface, and participates in chemical reactions. Furthermore, hydrogen exchanges an electron with surfaces having a significant effect on the surface electronic structure. In this personal account, we review our recent studies on surface nuclear dynamics of hydrogen, hydrogen transport across surfaces, catalytic hydrogenation/isotope exchange reactions, and charge transfer between the surface and hydrogen by using a depth‐resolved technique of nuclear reaction analysis and a quantum‐state‐selective detection of resonance enhanced multiphoton ionization in combination with surface science techniques. As a future prospect, we refer to ultraslow μ spin rotation spectroscopy for a direct probe of the hydrogen charge state at surfaces.