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Erban, Radek (19)

Chapman, S. Jonathan (5)Flegg, Mark B. (4)Franz, Benjamin (3)Kevrekidis, Ioannis G. (3)View MoreJournalBulletin of Mathematical Biology (4)SIAM Journal on Applied Mathematics (4)Physical Review E (2)SIAM Journal on Scientific Computing (2)The Journal of Chemical Physics (2)View MoreKAUST Grant NumberKUK-C1-013-04 (17)KUK-C1- 013-04 (1)KUK-Cl-013-04 (1)PublisherSociety for Industrial & Applied Mathematics (SIAM) (6)Springer Nature (6)AIP Publishing (3)American Physical Society (APS) (2)Elsevier BV (1)View MoreSubjectBrownian dynamics (2)Multiscale simulation (2)Travelling wave (2)Adaptive meshes (1)Bacterial chemotaxis (1)View MoreTypeArticle (17)Book Chapter (1)Conference Paper (1)Year (Issue Date)2015 (1)2014 (3)2013 (5)2012 (3)2011 (2)View MoreItem AvailabilityMetadata Only (18)Open Access (1)

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Convergence of methods for coupling of microscopic and mesoscopic reaction–diffusion simulations

Flegg, Mark B.; Hellander, Stefan; Erban, Radek (Journal of Computational Physics, Elsevier BV, 2015-05) [Article]

© 2015 Elsevier Inc. In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step δ. t (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered:. (i)δt→0 and h is fixed;(ii)δt→0 and h→0 such that δt/h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

Ergodic directional switching in mobile insect groups

Escudero, Carlos; Yates, Christian A.; Buhl, Jerome; Couzin, Iain D.; Erban, Radek; Kevrekidis, Ioannis G.; Maini, Philip K. (Physical Review E, American Physical Society (APS), 2010-07-29) [Article]

We obtain a Fokker-Planck equation describing experimental data on the collective motion of locusts. The noise is of internal origin and due to the discrete character and finite number of constituents of the swarm. The stationary probability distribution shows a rich phenomenology including nonmonotonic behavior of several order and disorder transition indicators in noise intensity. This complex behavior arises naturally as a result of the randomness in the system. Its counterintuitive character challenges standard interpretations of noise induced transitions and calls for an extension of this theory in order to capture the behavior of certain classes of biologically motivated models. Our results suggest that the collective switches of the group's direction of motion might be due to a random ergodic effect and, as such, they are inherent to group formation. © 2010 The American Physical Society.

Adaptive Finite Element Method Assisted by Stochastic Simulation of Chemical Systems

Cotter, Simon L.; Vejchodský, Tomáš; Erban, Radek (SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics (SIAM), 2013-01) [Article]

Stochastic models of chemical systems are often analyzed by solving the corresponding Fokker-Planck equation, which is a drift-diffusion partial differential equation for the probability distribution function. Efficient numerical solution of the Fokker-Planck equation requires adaptive mesh refinements. In this paper, we present a mesh refinement approach which makes use of a stochastic simulation of the underlying chemical system. By observing the stochastic trajectory for a relatively short amount of time, the areas of the state space with nonnegligible probability density are identified. By refining the finite element mesh in these areas, and coarsening elsewhere, a suitable mesh is constructed and used for the computation of the stationary probability density. Numerical examples demonstrate that the presented method is competitive with existing a posteriori methods. © 2013 Society for Industrial and Applied Mathematics.

Analysis of the Two-Regime Method on Square Meshes

Flegg, Mark B.; Chapman, S. Jonathan; Zheng, Likun; Erban, Radek (SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics (SIAM), 2014-01) [Article]

The two-regime method (TRM) has been recently developed for optimizing stochastic reaction-diffusion simulations [M. Flegg, J. Chapman, and R. Erban, J. Roy. Soc. Interface, 9 (2012), pp. 859-868]. It is a multiscale (hybrid) algorithm which uses stochastic reaction-diffusion models with different levels of detail in different parts of the computational domain. The coupling condition on the interface between different modeling regimes of the TRM was previously derived for onedimensional models. In this paper, the TRM is generalized to higher dimensional reaction-diffusion systems. Coupling Brownian dynamics models with compartment-based models on regular (square) two-dimensional lattices is studied in detail. In this case, the interface between different modeling regimes contains either flat parts or right-angle corners. Both cases are studied in the paper. For flat interfaces, it is shown that the one-dimensional theory can be used along the line perpendicular to the TRM interface. In the direction tangential to the interface, two choices of the TRM parameters are presented. Their applicability depends on the compartment size and the time step used in the molecular-based regime. The two-dimensional generalization of the TRM is also discussed in the case of corners. © 2014 Society for Industrial and Applied Mathematics.

Analysis of a Stochastic Chemical System Close to a SNIPER Bifurcation of Its Mean-Field Model

Erban, Radek; Chapman, S. Jonathan; Kevrekidis, Ioannis G.; Vejchodský, Tomáš (SIAM Journal on Applied Mathematics, Society for Industrial & Applied Mathematics (SIAM), 2009-01) [Article]

A framework for the analysis of stochastic models of chemical systems for which the deterministic mean-field description is undergoing a saddle-node infinite period (SNIPER) bifurcation is presented. Such a bifurcation occurs, for example, in the modeling of cell-cycle regulation. It is shown that the stochastic system possesses oscillatory solutions even for parameter values for which the mean-field model does not oscillate. The dependence of the mean period of these oscillations on the parameters of the model (kinetic rate constants) and the size of the system (number of molecules present) are studied. Our approach is based on the chemical Fokker-Planck equation. To gain some insight into the advantages and disadvantages of the method, a simple one-dimensional chemical switch is first analyzed, and then the chemical SNIPER problem is studied in detail. First, results obtained by solving the Fokker-Planck equation numerically are presented. Then an asymptotic analysis of the Fokker-Planck equation is used to derive explicit formulae for the period of oscillation as a function of the rate constants and as a function of the system size. © 2009 Society for Industrial and Applied Mathematics.

Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

Lipková, Jana; Zygalakis, Konstantinos C.; Chapman, S. Jonathan; Erban, Radek (SIAM Journal on Applied Mathematics, Society for Industrial & Applied Mathematics (SIAM), 2011-01) [Article]

A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K. (IEEE Transactions on Parallel and Distributed Systems, Institute of Electrical and Electronics Engineers (IEEE), 2012-02) [Article]

We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system's size. © 2006 IEEE.

Multistability in planar liquid crystal wells

Luo, Chong; Majumdar, Apala; Erban, Radek (Physical Review E, American Physical Society (APS), 2012-06-08) [Article]

A planar bistable liquid crystal device, reported in Tsakonas, is modeled within the Landau-de Gennes theory for nematic liquid crystals. This planar device consists of an array of square micrometer-sized wells. We obtain six different classes of equilibrium profiles and these profiles are classified as diagonal or rotated solutions. In the strong anchoring case, we propose a Dirichlet boundary condition that mimics the experimentally imposed tangent boundary conditions. In the weak anchoring case, we present a suitable surface energy and study the multiplicity of solutions as a function of the anchoring strength. We find that diagonal solutions exist for all values of the anchoring strength W≥0, while rotated solutions only exist for W≥W c>0, where W c is a critical anchoring strength that has been computed numerically. We propose a dynamic model for the switching mechanisms based on only dielectric effects. For sufficiently strong external electric fields, we numerically demonstrate diagonal-to-rotated and rotated-to-diagonal switching by allowing for variable anchoring strength across the domain boundary. © 2012 American Physical Society.

From Individual to Collective Behavior of Unicellular Organisms: Recent Results and Open Problems

Xue, Chuan; Othmer, Hans G.; Erban, Radek (AIP Conference Proceedings, AIP Publishing, 2009-09-23) [Conference Paper]

The collective movements of unicellular organisms such as bacteria or amoeboid (crawling) cells are often modeled by partial differential equations (PDEs) that describe the time evolution of cell density. In particular, chemotaxis equations have been used to model the movement towards various kinds of extracellular cues. Well-developed analytical and numerical methods for analyzing the time-dependent and time-independent properties of solutions make this approach attractive. However, these models are often based on phenomenological descriptions of cell fluxes with no direct correspondence to individual cell processes such signal transduction and cell movement. This leads to the question of how to justify these macroscopic PDEs from microscopic descriptions of cells, and how to relate the macroscopic quantities in these PDEs to individual-level parameters. Here we summarize recent progress on this question in the context of bacterial and amoeboid chemotaxis, and formulate several open problems.

Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release

Flegg, Mark B.; Rüdiger, Sten; Erban, Radek (The Journal of Chemical Physics, AIP Publishing, 2013-04-17) [Article]

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. © 2013 American Institute of Physics.

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