Stochastic simulation of chemical reactions in spatially complex media

Discrete stochastic simulations, via techniques such as the Stochastic Simulation Algorithm (SSA) are a powerful tool for understanding the dynamics of chemical kinetics when there are low numbers of certain molecular species. However, an important constraint is the assumption of well-mixedness and homogeneity. In this paper, we show how to use Monte Carlo simulations to estimate an anomalous diffusion parameter that encapsulates the crowdedness of the spatial environment. We then use this parameter to replace the rate constants of bimolecular reactions by a time-dependent power law to produce an SSA valid in cases where anomalous diffusion occurs or the system is not well-mixed (ASSA). Simulations then show that ASSA can successfully predict the temporal dynamics of chemical kinetics in a spatially constrained environment.

Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation

Discrete stochastic simulations are a powerful tool for understanding the dynamics of chemical kinetics when there are small-to-moderate numbers of certain molecular species. In this paper we introduce delays into the stochastic simulation algorithm, thus mimicking delays associated with transcription and translation. We then show that this process may well explain more faithfully than continuous deterministic models the observed sustained oscillations in expression levels of hes1 mRNA and Hes1 protein.

Analysis of efficiency and optimization of plasmon energy coupling into nanofocusing metal wedges

In this paper, we investigate theoretically and numerically the efficiency of energy coupling from a plasmon generated by a grating coupler at one of the interfaces of a metal wedge into the plasmonic eigenmode (i.e., symmetric or quasisymmetric plasmon) experiencing nanofocusing in the wedge. Thus the energy efficiency of energy coupling into metallic nanofocusing structure is analyzed. Two different nanofocusing structures with the metal wedge surrounded by a uniform dielectric (symmetric structure) and with the metal wedge enclosed between a substrate and a cladding with different dielectricpermittivities (asymmetric structure) are considered by means of the geometrical optics (adiabatic) approximation. It is demonstrated that the efficiency of the energy coupling from the plasmon generated by the grating into the symmetric or quasisymmetric plasmon experiencing nanofocusing may vary between ∼50% to ∼100%. In particular, even a very small difference (of ∼1%–2%) between the permittivities of the substrate and the cladding may result in a significant increase in the efficiency of the energy coupling (from ∼50% up to ∼100%) into the plasmon experiencing nanofocusing. Distinct beat patterns produced by the interference of the symmetric (quasisymmetric) and antisymmetric (quasiantisymmetric) plasmons are predicted and analyzed with significant oscillations of the magnetic and electric field amplitudes at both the metal wedge interfaces. Physical interpretations of the predicted effects are based upon the behavior, dispersion, and dissipation of the symmetric (quasisymmetric) and antisymmetric (quasiantisymmetric) filmplasmons in the nanofocusing metal wedge. The obtained results will be important for optimizing metallic nanofocusing structures and minimizing coupling and dissipative losses.