Organic matter from Artic sea ice loss alters bacterial community structure and function

Continuing losses of multi-year sea ice (MYI) across the Arctic are resulting in first-year ice (FYI) dominating the Arctic ice pack. Melting FYI provides a strong seasonal pulse of dissolved organic matter (DOM) into surface waters; however, the biological impact of this DOM input is unknown. Here we show that DOM additions cause significant and contrasting changes in under-ice bacterioplankton abundance, production and species composition. Utilization of DOM was influenced by molecular size, with 10-100 kDa and >100 kDa DOM fractions promoting rapid growth of particular taxa, while uptake of sulfur and nitrogen-rich low molecular weight organic compounds shifted bacterial community composition. These results demonstrate the ecological impacts of DOM released from melting FYI, with wideranging consequences for the cycling of organic matter across regions of the Arctic Ocean transitioning from multi-year to seasonal sea ice as the climate continues to warm

Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo

Efficient uncertainty quantification algorithms are key to understand the propagation of uncertainty—from uncertain input parameters to uncertain output quantities—in high resolution mathematical models of brain physiology. Advanced Monte Carlo methods such as quasi Monte Carlo (QMC) and multilevel Monte Carlo (MLMC) have the potential to dramatically improve upon standard Monte Carlo (MC) methods, but their applicability and performance in biomedical applications is underexplored. In this paper, we design and apply QMC and MLMC methods to quantify uncertainty in a convection‐diffusion model of tracer transport within the brain. We show that QMC outperforms standard MC simulations when the number of random inputs is small. MLMC considerably outperforms both QMC and standard MC methods and should therefore be preferred for brain transport models

OPTIMIZATION OF HOPF BIFURCATION POINTS

We introduce a numerical technique for controlling the location and stability properties of Hopf bifurcations in dynamical systems. The algorithm consists of solving an optimization problem constrained by an extended system of nonlinear partial differential equations that characterizes Hopf bifurcation points. The flexibility and robustness of the method allows us to advance or delay a Hopf bifurcation to a target value of the bifurcation parameter, as well as controlling the oscillation frequency with respect to a parameter of the system or the shape of the domain on which solutions are defined. Numerical applications are presented in systems arising from biology and fluid dynamics, such as the FitzHugh-Nagumo model, Ginzburg-Landau equation, Rayleigh-Bénard convection problem, and Navier-Stokes equations, where the control of the location and oscillation frequency of periodic solutions is of high interest

Efficient white noise sampling and coupling for multilevel Monte Carlo with nonnested meshes

When solving stochastic partial differential equations (SPDEs) driven by additive spatial white noise, the efficient sampling of white noise realizations can be challenging. Here, we present a new sampling technique that can be used to efficiently compute white noise samples in a finite element method (FEM) and multilevel Monte Carlo (MLMC) setting. The key idea is to exploit the finite element matrix assembly procedure and factorize each local mass matrix independently, hence avoiding the factorization of a large matrix. Moreover, in an MLMC framework, the white noise samples must be coupled between subsequent levels. We show how our technique can be used to enforce this coupling even in the case of nonnested mesh hierarchies. We demonstrate the efficacy of our method with numerical experiments. We observe optimal convergence rates for the finite element solution of the elliptic SPDEs of interest in 2D and 3D and we show convergence of the sampled field covariances. In an MLMC setting, a good coupling is enforced and the telescoping sum is respected

Automated adjoints of coupled PDE-ODE systems

Mathematical models that couple partial differential equations (PDEs) and spatially distributed ordinary differential equations (ODEs) arise in biology, medicine, chemistry, and many other fields. In this paper we discuss an extension to the FEniCS finite element software for expressing and efficiently solving such coupled systems. Given an ODE described using an augmentation of the Unified Form Language (UFL) and a discretization described by an arbitrary Butcher tableau, efficient code is automatically generated for the parallel solution of the ODE. The high-level description of the solution algorithm also facilitates the automatic derivation of the adjoint and tangent linearization of coupled PDE-ODE solvers. We demonstrate the capabilities of the approach on examples from cardiac electrophysiology and mitochondrial swelling

Efficient white noise sampling and coupling for multilevel Monte Carlo with nonnested meshes

When solving stochastic partial differential equations (SPDEs) driven by additive spatial white noise, the efficient sampling of white noise realizations can be challenging. Here, we present a new sampling technique that can be used to efficiently compute white noise samples in a finite element method (FEM) and multilevel Monte Carlo (MLMC) setting. The key idea is to exploit the finite element matrix assembly procedure and factorize each local mass matrix independently, hence avoiding the factorization of a large matrix. Moreover, in an MLMC framework, the white noise samples must be coupled between subsequent levels. We show how our technique can be used to enforce this coupling even in the case of nonnested mesh hierarchies. We demonstrate the efficacy of our method with numerical experiments. We observe optimal convergence rates for the finite element solution of the elliptic SPDEs of interest in 2D and 3D and we show convergence of the sampled field covariances. In an MLMC setting, a good coupling is enforced and the telescoping sum is respected

FFC: The FEniCS form compiler

One of the key features of FEniCS is automated code generation for the general and efficient solution of finite element variational problems. This automated code generation relies on a form compiler for offline or just-in-time compilation of code for individual forms. Two different form compilers are available as part of FEniCS. This chapter describes the form compiler FFC. The other form compiler, SFC, is described in Chapter 15

Automated adjoints of coupled PDE-ODE systems

Mathematical models that couple partial differential equations (PDEs) and spatially distributed ordinary differential equations (ODEs) arise in biology, medicine, chemistry, and many other fields. In this paper we discuss an extension to the FEniCS finite element software for expressing and efficiently solving such coupled systems. Given an ODE described using an augmentation of the Unified Form Language (UFL) and a discretization described by an arbitrary Butcher tableau, efficient code is automatically generated for the parallel solution of the ODE. The high-level description of the solution algorithm also facilitates the automatic derivation of the adjoint and tangent linearization of coupled PDE-ODE solvers. We demonstrate the capabilities of the approach on examples from cardiac electrophysiology and mitochondrial swelling

Efficient white noise sampling and coupling for multilevel Monte Carlo with nonnested meshes

When solving stochastic partial differential equations (SPDEs) driven by additive spatial white noise, the efficient sampling of white noise realizations can be challenging. Here, we present a new sampling technique that can be used to efficiently compute white noise samples in a finite element method (FEM) and multilevel Monte Carlo (MLMC) setting. The key idea is to exploit the finite element matrix assembly procedure and factorize each local mass matrix independently, hence avoiding the factorization of a large matrix. Moreover, in an MLMC framework, the white noise samples must be coupled between subsequent levels. We show how our technique can be used to enforce this coupling even in the case of nonnested mesh hierarchies. We demonstrate the efficacy of our method with numerical experiments. We observe optimal convergence rates for the finite element solution of the elliptic SPDEs of interest in 2D and 3D and we show convergence of the sampled field covariances. In an MLMC setting, a good coupling is enforced and the telescoping sum is respected