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The intracellular release of calcium from the endoplasmic reticulum is controlled by ion channels. The resulting calcium signals exhibit a rich spatio-temporal signature, which originates at least partly from microscopic fluctuations. While stochasticity in the gating transition of ion channels has been incorporated into many models, the distribution of calcium is usually described by deterministic reaction-diffusion equations. Here we test the validity of the latter modeling approach by using two different models to calculate the frequency of localized calcium signals (calcium puffs) from clustered IP3 receptor channels. The complexity of the full calcium system is here limited to the basic opening mechanism of the ion channels and, in the mathematical reduction simplifies to the calculation of a first passage time. Two models are then studied: (i) a hybrid model, where channel gating is treated stochastically, while calcium concentration is deterministic and (ii) a fully stochastic model with noisy channel gating and Brownian calcium ion motion. The second model utilises the recently developed two-regime method [M. B. Flegg, S. J. Chapman, and R. Erban, 'The two-regime method for optimizing stochastic reaction-diffusion simulations,' J. R. Soc., Interface 9, 859-868 (2012)] in order to simulate a large domain with precision required only near the Ca2+ absorbing channels. The expected time for a first channel opening that results in a calcium puff event is calculated. It is found that for a large diffusion constant, predictions of the interpuff time are significantly overestimated using the model (i) with a deterministic non-spatial calcium variable. It is thus demonstrated that the presence of diffusive noise in local concentrations of intracellular Ca2+ ions can substantially influence the occurrence of calcium signals. The presented approach and results may also be relevant for other cell-physiological first-passage time problems with small ligand concentration and high cooperativity. [ABSTRACT FROM AUTHOR]

We develop a computationally efficient method for the theoretical analysis of thermophoresis of nanoparticles and adatoms on crystalline surfaces (thermal tweezers) for efficient parallel nanofabrication. The analysis of surface diffusion of particles or adatoms in the presence of strong temperature gradients is conducted through the direct determination of probability distributions for diffusing particles, using the numerical solution of the Smoluchowski diffusion equation with varying (temperature-dependent) diffusion constant. The local values of the diffusion constant are determined from the Fokker–Planck equation for the considered crystalline potential of the substrate and local temperature. Steady-state and nonsteady-state particle distributions on the surface are obtained and analyzed in the presence of optically-induced strong temperature gradients. Detailed comparison of this approach with the previously obtained results from the Monte Carlo simulations of the Langevin equation is conducted, demonstrating high computational efficiency, and accuracy of the new method in the high-friction regime. Applicability conditions for the developed method are also determined and discussed. [ABSTRACT FROM AUTHOR]