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DOE OSTI2020

Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations

Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Partitioned exponential methods for coupled multiphysics systems

Multiphysics problems involving two or more coupled physical phenomena are ubiquitous in science and engineering. This work develops a new partitioned exponential approach for the time integration of multiphysics problems. After a possible semi-discretization in space, the class of problems under consideration is modeled by a system of ordinary differential equations where the right-hand side is a summation of two component functions, each corresponding to a given set of physical processes. The partitioned-exponential methods proposed herein evolve each component of the system via an exponential integrator, and information between partitions is exchanged via coupling terms. Here, the traditional approach to constructing exponential methods, based on the variation-of-constants formula, is not directly applicable to partitioned systems. Rather, our approach to developing new partitioned-exponential families is based on a general-structure additive formulation of the schemes. Two method formulations are considered, one based on a linear-nonlinear splitting of the right hand component functions, and another based on approximate Jacobians. The paper develops classical (non-stiff) order conditions theory for partitioned exponential schemes based on particular families of T-trees and B-series theory. Several practical methods of third order are constructed that extend the Rosenbrock-type and EPIRK families of exponential integrators. Several implementation optimizations specific to the application of these methods to reaction-diffusion systems are also discussed. Numerical experiments reveal that the new partitioned-exponential methods can perform better than traditional unpartitioned exponential methods on some problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Stochastic self-tuning hybrid algorithm for reaction-diffusion systems

Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Furthermore, its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Kinetic model describing self-limiting CO 2 diffusion in supported amine adsorbents

A reaction–diffusion shrinking core model describing the decay in diffusivity of supported amine sorbents upon CO 2 sorption under both simulated direct air capture and point source capture conditions is described. The decay in CO 2 diffusivity is associated with crosslinking in the aminopolymer samples and general pore blockage in the amino-silane derived samples, which occurs as CO 2 is adsorbed. The model is used to extract four kinetic parameters that govern the CO 2 uptake kinetics and working capacity: an apparent reaction rate constant, an initial effective diffusivity, and two dimensionless decay parameters. Ideally, an initially reaction limited system would allow for direct determination of the intrinsic reaction rate constant; however, sorption experiments suggest mass transfer resistances related to gas mixing, external boundary layers and intraparticle diffusion are present. Reaction rate constants are determined and agree well with theoretical values predicted with the Eyring equation parameterized using density functional theory energies from literature sources. The kinetic performance is expressed as the average effective diffusivity as a function of average conversion, which can be correlated to the dispersion of sorption sites on the support and the morphology of the active sorbent phase. Four supports are impregnated or grafted with amines, SBA-15, single-walled zeolite nanotubes (ZNT), Syloid SiO 2 , and γ-Al 2 O 3 . Due to its pore structure, γ-Al 2 O 3 supported amines can be modeled at the μm scale or at the nm scale, where the shell balance is on the μm-sized macroporous particle aggregate or on the nm-sized amine film on the surface of the Al 2 O 3 nanoparticles, which comprise the spherical particle aggregates. Faster diffusion rates are maintained under 400 ppm rather than 10% CO 2 due to a slower reaction rate giving a slower decay in diffusivity. In conclusion, this work provides a first principles kinetic analysis of CO 2 sorption where previous models are semi-empirical and use arbitrary kinetic parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗