We describe a percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Tissues are considered as structures made of regular healthy, senescent, dead (
apoptotic) cells, and studied dynamically, with the ongoing processes including regular cell division to fill vacant sites left by dead cells, healthy cells becoming senescent or dying, and other processes. Statistical-mechanics description can provide patterns of time dependence and snapshots of morphological system properties. An illustrative application of the developed theoretical modeling approach is reported, confirming recent experimental findings that inhibition of senescence can lead to extended lifespan.
We model within the kinetic Monte Carlo method the initiation of neck formation and then later evolution of the resulting bridging regions for configurations involving small particles initially positioned fitted between large particles for situations
typical for sintering of FCC nanocrystals, e.g., noble-metal nanoparticles. Neck initiation mechanisms by layering or clustering are identified. The stability of the resulting bridging configurations depends on several parameters, notably, on the relative small to large particle size ratio, and we explain recent experimental findings on improved sintering achieved for certain bimodal size distributions.
We report a kinetic Monte Carlo modeling study of nanocrystal layer sintering. Features that are of interest for the dynamics of the layer as a whole, especially the morphology of the evolving structure, are considered. It is found that the kinetics
of sintering is not entirely a local process, with the layer morphology affected by the kinetics in a larger than few-particle neighborhood. Consideration of a single layer of particles makes the numerics manageable and allows visualization of the results, as well as numerical simulations of several realizations for statistical averaging of properties of interest. We identify optimal regimes for sintering, considering several particle size distributions and temperature control protocols.
We model shell formation of core-shell noble metal nanoparticles. A recently developed kinetic Monte Carlo approach is utilized to reproduce growth morphologies realized in recent experiments on core-shell nanoparticle synthesis, which reported smoot
h epitaxially grown shells. Specifically, we identify growth regimes that yield such smooth shells, but also those that lead to the formation of shells made of small clusters. The developed modeling approach allows us to qualitatively study the effects of temperature and supply the shell-metal atoms on the resulting shell morphology, when grown on a pre-synthesized nanocrystal core.
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 the
oretical 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 networks 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 multi-step information/signal processing systems.
Kinetic Monte Carlo approach is developed to study aspects of sintering of dispersed nanoparticles of bimodal size distributions. We explore mechanisms of neck development when sintering is initiated at elevated temperatures for nanosize crystalline
surfaces of particles of different sizes. Specifically, the role of smaller particles fitting between larger particles, on the sintering of the latter is considered. Formation of stable necks bridging particles at the nanoscale was found to be governed by layering or clustering mechanisms at the facing surfaces, with clustering leading to a much faster formation of the bridging structure. Temperature, particle sizes and local arrangement, as well as other geometrical factors were found to have a profound effect on sintering mediated by a smaller particle placed in a void between larger particles.
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 to make the gates response sigmoid in both inputs. New functional forms are developed for qua
ntifying 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 develop a framework for optimizing a novel approach to extending the linear range of bioanalytical systems and biosensors by utilizing two enzymes with different kinetic responses to the input chemical as their substrate. Data for the flow-injecti
on amperometric system devised for detection of lysine based on the function of L-Lysine-alpha-Oxidase and Lysine-2-monooxygenase are analyzed. Lysine is a homotropic substrate for the latter enzyme. We elucidate the mechanism for extending the linear response range and develop optimization techniques for future applications of such systems.
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 wh
en 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.
In this work we extend recent study of the properties of the dense packing of superdisks, by Y. Jiao, F. H. Stillinger and S. Torquato, Phys. Rev. Lett. 100, 245504 (2008), to the jammed state formed by these objects in random sequential adsorption.
The superdisks are two-dimensional shapes bound by the curves of the form |x|^(2p) + |y|^(2p) = 1, with p > 0. We use Monte Carlo simulations and theoretical arguments to establish that p = 1/2 is a special point at which the jamming density has a discontinuous derivative as a function of p. The existence of this point can be also argued for by geometrical arguments.
