Ras B. Pandey

Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules

The adsorption mechanism of twenty amino acids and four surfactants was examined on a {111} surface of gold in dilute aqueous solution using molecular dynamics simulation with a broadly applicable intermolecular potential CHARMM–METAL. All molecules are attracted to the surface between −3 and −26 kcal mol−1. The adsorption strength correlates with the degree of coordination of polarizable atoms (O, N, C) to multiple epitaxial sites. Therefore, the molecular size and geometry rather than the specific chemistry determine the adsorption energy. Large molecules with planar sp2 hybridized groups (Arg, Trp, Gln, Tyr, Asn, and PPh3) adsorb most strongly, followed by molecules with polar sp3 hybridized groups, and short molecules with sp3 hybridized alkyl groups exhibit least attraction. Conformationally flexible, extended molecules such as hexadecyltrimethylammonium bromide (CTAB) also showed significant attraction to the metal surface related to accommodation in epitaxial grooves and coordination with numerous epitaxial sites. Computational results are consistent with combinatorial binding experiments, observations in the growth and stabilization of metal nanoparticles, and ab initio data. The mechanism of adsorption conforms to soft epitaxy observed for peptides on metal surfaces (H. Heinz et al., J. Am. Chem. Soc., 2009, 131, 9704) and enables the de novo design of molecules for binding to a given metal surface. In addition to soft epitaxy, contributions to adsorption are possible by covalent bonding and induced charges.

Dynamic Modeling of Transport Process Systems

The Nature of Dynamic Systems. Basic Concepts in the Numerical Integration of Ordinary Differential Equations. Accuracy in the Numerical Integration of Ordinary Differential Equations. Stability in the Numerical Integration of Ordinary Differential Equations. Systems Modeled by Ordinary Differential Equations. Systems Modeled by First Order Partial Differential Equations. Systems Modeled by Second Order Partial Differential Equations. Systems Modeled by First/Second Order, Multidimensional andMultidomain Partial Differential Equations. Appendices 1-9. Index.

Diffusion on random systems above, below, and at their percolation threshold in two and three dimensions

A detailed Monte Carlo study is presented for classical diffusion (random walks) on randomL * L triangular andL * L* L simple cubic lattices, withL up to 4096 and 256, respectively. The speed of a Cyber 205 vector computer is found to be about one order of magnitude larger than that of a usual CDC Cyber 76 computer. To reach the asymptotic scaling regime, walks with up to 10 million steps were simulated, with about 1011 steps in total forL=256 at the percolation threshold. We review and extend the dynamical scaling description for the distance traveled as function of time, the diffusivity above the threshold, and the cluster radius below. Earlier discrepancies between scaling theory and computer experiment are shown to be due to insufficient Monte Carlo data. The conductivity exponent μ is found to be 2.0 ± 0.2 in three and 1.28 ± 0.02 in two dimensions. Our data in three dimensions follow well the finite-size scaling theory. Below the threshold, the approach of the distance traveled to its asymptotic value is consistent with theoretical speculations and an exponent 2/5 independent of dimensionality. The correction-to-scaling exponent atpc seems to be larger in two than in three dimensions.

Qualitative percolation study of free-radical cross-linking polymerization

SummarySimulations of a conceptually simple model for free-radical cross-linking polymerization have been performed in relation to experimental indications for (temporary) microgel particles. Many qualitative features ascribed to microgels show up in the simulation. In particular this model yields qualitative agreement with experiments on the conversion dependence of the number of pendant double bonds.

MICELLE FORMATION, RELAXATION TIME, AND THREE-PHASE COEXISTENCE IN A MICROEMULSION MODEL

Our Larson‐type microemulsion model for surfactant chains in oil–water solvents leads to long relaxation times as well as, for essential modifications, to a stable peak in the chain‐cluster size distribution. Transfer energies for surfactant chains moving to the oil–water interface, and characteristic micelle concentrations (CMC) as a function of chain length are compared with experiment.

Metastability With Probabilistic Cellular Automata in an HIV Infection

Assuming a small failure probability for the interleukin production, a discrete model of HIV infection leads to transitions between fixed points. Eventually all initial configurations for the cellular automata lead to the destruction of the immune system, i.e., to AIDS.

Cellular automata approach to interacting cellular network models for the dynamics of cell population in an early HIV infection

In order to understand the evolution of cell population in an early HIV infection (AIDS), a network model of interacting cellular elements, such as macrophages, viruses, T4 cells, and T8 cells, is introduced for a cell mediated response. In a simplified discrete representation of binary cells, boolean expressions are used to describe their interactions and concentrations. Two different interaction models are considered and flows of configurations are studied in their configurational phase space. In the mean field (or infinite range interacting network) treatment, one interaction gives two fixed points describing the extreme limits of “immuno-competence” and “immunodeficiency”; in addition, it gives rise to a periodic cycle consisting of an “infected”, a “severely infected”, and a “susceptible” state. The other interaction leads to seven fixed points, two of which are the same as those in the first. The third fixed point represents a “severely infected” state, and the remaining four describe “susceptible” states of varying order. Growth and decay of cellular elements are then studied on a simple cubic lattice where nearest neighbor interactions are treated by inhomogeneous cellular automata using computer simulations. In order to take into account the sporadic growth of virions, an interaction latency parameter B is introduced, and the decline of immunocompetence as a function of B is discussed. A detail study is presented for the crossover between an immunodeficient and an immunocompetent state as a function of the initial concentration of the host cells and latency/dilution.

Kinetics and Jamming Coverage in a Random Sequential Adsorption of Polymer Chains

Studying the kinetics of random sequential adsorption(RSA) has attracted a considerable interest in recentyears [1–18] because of its enormous applications [19–24]in the adsorption processes involving a variety of speciesfrom a point-like particle to a protein-like complex struc-ture in physical, chemical, and biological systems. Someof the examples include binding of ligands on polymerchains, coating, designing composites, chemisorption, ph-ysisorption, and reaction of molecular species includingglobular protein on surfaces and interfaces, etc. Theseadsorption processes may be divided into two categories:(1) annealed adsorption where the species are mobile (athermal equilibration for the interacting adsorbants) be-forethey settleontothe surface–acooperativesequentialadsorption. (2) Quenched adsorption where the adsorp-tion occurs without subsequent diffusion or desorption.We consider the latter category known as random se-quential adsorption.The problem of RSA in one dimension [19,25–27] iswell understood with exact results for some adsorptionprocesses. Understanding the growth of coverage in twodimensions with the RSA lacks rigorous results by ana-lytical methods due to their intractabilities especially forobjects with polydisperse shapes. Therefore, computersimulations remain one of the primary tools to investi-gate these problems. Numerical results [2] and theoreti-cal analyses [3,4] for the deposition of disks on continuumsuggest that the coverage follows the Feder’s law [2] atlarge time,θ(t) ≈ θ

Bioassembled Layered Silicate-Metal Nanoparticle Hybrids

Here we report on the bioenabled assembly of layered nanohybrids using peptides identified with regard to their affinity to the nanoparticle surface. A dodecamer peptide termed M1, determined from a phage peptide display library, was found to bind to the surface of a layered aluminosilicate (montmorillonite, MMT). Fusion of a metal binding domain to the M1 peptide or the M1 peptide by itself was able to direct the growth of metal nanoparticles, such as gold and cobalt-platinum, respectively, on the MMT. This method of producing hybrid nanoclay materials will have utility in catalytic, optical, biomedical, and composite materials applications.

Sol–gel phase transitions in thermoreversible gels: Onset of gelation and melting

A Monte Carlo simulation model is proposed to study the phase transition and the structural evolution of thermoreversible gels with the coexistence of phase separation and gelation processes. Our model includes the mobility of all the species and the reversibility of bonds of the clusters formed due to cross‐linking reactions. These features provide a more realistic description of a polymer–solvent system. We attempt to elucidate the effects of interactions, solvents, polymer fraction, etc. on the phase behaviors of the thermoreversible gel. Sol‐to‐gel transition is studied in detail as a function of temperature, and the related critical exponents are evaluated. Two different energy parameters are used to describe the gelation and the melting processes. The collective structure factors are calculated, and their dynamic behaviors are analyzed. The competing effects of the phase separation and the network formation on the structural evolutions of the gel are discussed.