4,069 research outputs found
Turing instabilities in general systems
We present necessary and sufficient conditions on the stability matrix of a general n(S2)-dimensional reaction-diffusion system which guarantee that its uniform steady state can undergo a Turing bifurcation. The necessary (kinetic) condition, requiring that the system be composed of an unstable (or activator) and a stable (or inhibitor) subsystem, and the sufficient condition of sufficiently rapid inhibitor diffusion relative to the activator subsystem are established in three theorems which form the core of our results. Given the possibility that the unstable (activator) subsystem involves several species (dimensions), we present a classification of the analytically deduced Turing bifurcations into p (1 h p h (n m 1)) different classes. For n = 3 dimensions we illustrate numerically that two types of steady Turing pattern arise in one spatial dimension in a generic reaction-diffusion system. The results confirm the validity of an earlier conjecture [12] and they also characterise the class of so-called strongly stable matrices for which only necessary conditions have been known before [23, 24]. One of the main consequences of the present work is that biological morphogens, which have so far been expected to be single chemical species [1-9], may instead be composed of two or more interacting species forming an unstable subsystem
STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB
Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.\ud
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Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2
Dynamic p-enrichment schemes for multicomponent reactive flows
We present a family of p-enrichment schemes. These schemes may be separated
into two basic classes: the first, called \emph{fixed tolerance schemes}, rely
on setting global scalar tolerances on the local regularity of the solution,
and the second, called \emph{dioristic schemes}, rely on time-evolving bounds
on the local variation in the solution. Each class of -enrichment scheme is
further divided into two basic types. The first type (the Type I schemes)
enrich along lines of maximal variation, striving to enhance stable solutions
in "areas of highest interest." The second type (the Type II schemes) enrich
along lines of maximal regularity in order to maximize the stability of the
enrichment process. Each of these schemes are tested over a pair of model
problems arising in coastal hydrology. The first is a contaminant transport
model, which addresses a declinature problem for a contaminant plume with
respect to a bay inlet setting. The second is a multicomponent chemically
reactive flow model of estuary eutrophication arising in the Gulf of Mexico.Comment: 29 pages, 7 figures, 3 table
Well-posedness and exponential equilibration of a volume-surface reaction-diffusion system with nonlinear boundary coupling
We consider a model system consisting of two reaction-diffusion equations,
where one species diffuses in a volume while the other species diffuses on the
surface which surrounds the volume. The two equations are coupled via a
nonlinear reversible Robin-type boundary condition for the volume species and a
matching reversible source term for the boundary species. As a consequence of
the coupling, the total mass of the two species is conserved. The considered
system is motivated for instance by models for asymmetric stem cell division.
Firstly we prove the existence of a unique weak solution via an iterative
method of converging upper and lower solutions to overcome the difficulties of
the nonlinear boundary terms. Secondly, our main result shows explicit
exponential convergence to equilibrium via an entropy method after deriving a
suitable entropy entropy-dissipation estimate for the considered nonlinear
volume-surface reaction-diffusion system.Comment: 31 page
Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting
The efficiency of exact simulation methods for the reaction-diffusion master
equation (RDME) is severely limited by the large number of diffusion events if
the mesh is fine or if diffusion constants are large. Furthermore, inherent
properties of exact kinetic-Monte Carlo simulation methods limit the efficiency
of parallel implementations. Several approximate and hybrid methods have
appeared that enable more efficient simulation of the RDME. A common feature to
most of them is that they rely on splitting the system into its reaction and
diffusion parts and updating them sequentially over a discrete timestep. This
use of operator splitting enables more efficient simulation but it comes at the
price of a temporal discretization error that depends on the size of the
timestep. So far, existing methods have not attempted to estimate or control
this error in a systematic manner. This makes the solvers hard to use for
practitioners since they must guess an appropriate timestep. It also makes the
solvers potentially less efficient than if the timesteps are adapted to control
the error. Here, we derive estimates of the local error and propose a strategy
to adaptively select the timestep when the RDME is simulated via a first order
operator splitting. While the strategy is general and applicable to a wide
range of approximate and hybrid methods, we exemplify it here by extending a
previously published approximate method, the Diffusive Finite-State Projection
(DFSP) method, to incorporate temporal adaptivity
Travelling waves in a nonlinear degenerate diffusion model for bacterial pattern formation
We study a reaction diffusion model recently proposed in [5] to describe the spatiotemporal evolution of the bacterium Bacillus subtilis on agar plates containing nutrient. An interesting mathematical feature of the model, which is a coupled pair of partial differential equations, is that the bacterial density satisfies a degenerate nonlinear diffusion equation. It was shown numerically that this model can exhibit quasi-one-dimensional constant speed travelling wave solutions. We present an analytic study of the existence and uniqueness problem for constant speed travelling wave solutions. We find that such solutions exist only for speeds greater than some threshold speed giving minimum speed waves which have a sharp profile. For speeds greater than this minimum speed the waves are smooth. We also characterise the dependence of the wave profile on the decay of the front of the initial perturbation in bacterial density. An investigation of the partial differential equation problem establishes,via a global existence and uniqueness argument, that these waves are the only long time solutions supported by the problem. Numerical solutions of the partial differential equation problem are presented and they confirm the results of the analysis
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