Modeling charge separation in charged nanochannels for single-molecule electrometry.

We model the transport of electrically charged solute molecules by a laminar flow within a nanoslit microfluidic channel with electrostatic surface potential. We derive the governing convection-diffusion equation, solve it numerically, and compare it with a Taylor-Aris-like approximation, which gives excellent results for small Péclet numbers. We discuss our results in light of designing an assay that can measure simultaneously the hydrodynamic size and electric charge of single molecules by tracking their motion in such nanoslit channels with electrostatic surface potential.

Stochastic rounding: implementation, error analysis and applications.

Stochastic rounding (SR) randomly maps a real number x to one of the two nearest values in a finite precision number system. The probability of choosing either of these two numbers is 1 minus their relative distance to x. This rounding mode was first proposed for use in computer arithmetic in the 1950s and it is currently experiencing a resurgence of interest. If used to compute the inner product of two vectors of length n in floating-point arithmetic, it yields an error bound with constant n u with high probability, where u is the unit round-off. This is not necessarily the case for round to nearest (RN), for which the worst-case error bound has constant nu. A particular attraction of SR is that, unlike RN, it is immune to the phenomenon of stagnation, whereby a sequence of tiny updates to a relatively large quantity is lost. We survey SR by discussing its mathematical properties and probabilistic error analysis, its implementation, and its use in applications, with a focus on machine learning and the numerical solution of differential equations.

Fluid Simulations Accelerated With 16 Bits: Approaching 4x Speedup on A64FX by Squeezing ShallowWaters.jl Into Float16.

Most Earth-system simulations run on conventional central processing units in 64-bit double precision floating-point numbers Float64, although the need for high-precision calculations in the presence of large uncertainties has been questioned. Fugaku, currently the world's fastest supercomputer, is based on A64FX microprocessors, which also support the 16-bit low-precision format Float16. We investigate the Float16 performance on A64FX with ShallowWaters.jl, the first fluid circulation model that runs entirely with 16-bit arithmetic. The model implements techniques that address precision and dynamic range issues in 16 bits. The precision-critical time integration is augmented to include compensated summation to minimize rounding errors. Such a compensated time integration is as precise but faster than mixed precision with 16 and 32-bit floats. As subnormals are inefficiently supported on A64FX the very limited range available in Float16 is 6 × 10-5 to 65,504. We develop the analysis-number format Sherlogs.jl to log the arithmetic results during the simulation. The equations in ShallowWaters.jl are then systematically rescaled to fit into Float16, using 97% of the available representable numbers. Consequently, we benchmark speedups of up to 3.8x on A64FX with Float16. Adding a compensated time integration, speedups reach up to 3.6x. Although ShallowWaters.jl is simplified compared to large Earth-system models, it shares essential algorithms and therefore shows that 16-bit calculations are indeed a competitive way to accelerate Earth-system simulations on available hardware.

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.

Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields.

BACKGROUND: Influx and clearance of substances in the brain parenchyma occur by a combination of diffusion and convection, but the relative importance of these mechanisms is unclear. Accurate modeling of tracer distributions in the brain relies on parameters that are partially unknown and with literature values varying by several orders of magnitude. In this work, we rigorously quantified the variability of tracer distribution in the brain resulting from uncertainty in diffusion and convection model parameters. METHODS: Using the convection-diffusion-reaction equation, we simulated tracer distribution in the brain parenchyma after intrathecal injection. Several models were tested to assess the uncertainty both in type of diffusion and velocity fields and also the importance of their magnitude. Our results were compared with experimental MRI results of tracer enhancement. RESULTS: In models of pure diffusion, the expected amount of tracer in the gray matter reached peak value after 15 h, while the white matter did not reach peak within 24 h with high likelihood. Models of the glymphatic system were similar qualitatively to the models of pure diffusion with respect to expected time to peak but displayed less variability. However, the expected time to peak was reduced to 11 h when an additional directionality was prescribed for the glymphatic circulation. In a model including drainage directly from the brain parenchyma, time to peak occured after 6-8 h for the gray matter. CONCLUSION: Even when uncertainties are taken into account, we find that diffusion alone is not sufficient to explain transport of tracer deep into the white matter as seen in experimental data. A glymphatic velocity field may increase transport if a large-scale directional structure is included in the glymphatic circulation.