We report numerical investigations of a three-dimensional model of diffusive growth of fine particles, the internal structure of which corresponds to different crystal lattices. A growing cluster (particle) is immersed in, and exchanges monomer building blocks with a surrounding medium of diffusing (off-lattice) monomers. On-surface dynamics of the latter is accounted for by allowing, in addition to detachment, monomer motion to the neighboring vacant crystal sites, according to probabilistic rules mimicking local thermalization. The key new feature of our model is the focus on the growth of a single cluster, emerging as a crystalline core, without development of defects that can control large-scale growth modes. This single, defect-free core growth is imposed by the specific dynamical rules assumed. Our results offer a possible explanation of the experimentally observed shape uniformity, i.e., fixed, approximately even-sized proportions, in synthesis of uniform colloids and nanoparticles. We demonstrate the basic principles of well-defined particle shape emergence in such growth. Specifically, several shapes are possible for a given crystal structure. Formation of shapes that follow the crystal symmetry and are uniform, can be a result of the nonequilibrium nature of the growth process. The shape of a growing particle can be controlled by varying the relative rates of kinetic processes, as well as by adjusting the concentration of monomers in the surrounding medium. ______________________________________________________________________________ Posted as e-print 0902.3243 at www.arxiv.org

We report the first realization of a biomolecular AND gate function with double-sigmoid response (sigmoid in both inputs). Two enzyme biomarker inputs activate the gate output signal which can then be used as indicating liver injury, but only when both of these inputs have elevated pathophysiological concentrations, effectively corresponding to logic-1 of the binary gate functioning. At lower, normal physiological concentrations, defined as logic-0 inputs, the liver-injury output levels are not obtained. High-quality gate functioning in handling of various sources of noise, on time scales of relevance to potential applications is enabled by utilizing "filtering" effected by a simple added biocatalytic process. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.

We consider growth of nanoclusters and nanopillars in a model of surface deposition and restructuring yielding morphologies of interest in designing catalysis applications. Kinetic Monte Carlo numerical modeling yields examples of the emergence of face centered cubic (fcc) symmetry surface features in Pt-type metal nanostructures, allowing evaluation of the fraction of the resulting active sites with desirable properties, such as (111)-like coordination, as well as suggesting the optimal growth regimes.

We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic cascade. New theoretical expressions are derived to allow simple, few-parameter modeling of network components concatenated in such cascades, both with and without filtering. The derived expressions are tested against experimental data obtained for the realized network's responses, measured optically, to variations of its input chemicals' concentrations with and without filtering processes. We also describe how the present modeling approach captures and explains several observations and features identified in earlier studies of enzymatic processes when they were considered as potential network components for multistep information/signal processing systems.

We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output, allowing the gate's response to be made sigmoid in both inputs. New functional forms are developed for quantifying the kinetics of such systems, specifically designed to model their response in terms of signal and information processing. These theoretical expressions are tested for the studied system, which also allows us to consider aspects of biochemical information processing such as noise transmission properties and control of timing of the chemical and physical steps.

We report the first systematic study of designed two-input biochemical systems as information processing gates with favorable noise transmission properties accomplished by modifying the gate's response from a convex shape to sigmoid in both inputs. This is realized by an added chemical "filter" process, which recycles some of the output back into one of the inputs. We study a system involving the biocatalytic function of the enzyme horseradish peroxidase, functioning as an AND gate. We consider modularity properties, such as the use of three different input chromogens that when oxidized yield signal detection outputs for various ranges of the primary input, hydrogen peroxide. We also examine possible uses of different filter effect chemicals (reducing agents) to induce the sigmoid response. A modeling approach is developed and applied to our data, allowing us to describe the enzymatic kinetics in the framework of a formulation suitable for evaluating the noise-handling properties of the studied systems as logic gates for information processing steps.

The first realization of a biomolecular OR gate function with double-sigmoid response (sigmoid in both inputs) is reported. Two chemical inputs activate the enzymatic gate processes resulting in the output signal: chromogen oxidation, which occurs when either one of the inputs or both are present (corresponding to the OR binary function), and can be optically detected.High-quality gate functioning in handling of sources of noise is enabled by "filtering" involving pH control with an added buffer. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.

Growth of nanoclusters and nanopillars is considered in a model of surface deposition of building blocks (atoms) diffusionally transported from solution to the forming surface structure.Processes of surface restructuring are also accounted for in the model, which then yields morphologies of interest in catalysis applications. Kinetic Monte Carlo numerical approach is utilized to explore the emergence of FCC-symmetry surface features in Pt-type metal nanostructures. Available results exemplify evaluation of the fraction of the resulting active sites with desirable properties for catalysis, such as (111)-like coordination, as well as suggest optimal growth regimes.