Related papers: Passively parallel regularized stokeslets
Inexpensive numerical methods are key to enable simulations of systems of a large number of particles of different shapes in Stokes flow. Several approximate methods have been introduced for this purpose. We study the accuracy of the…
We present the results of direct numerical simulations of heavy particle transport in homogeneous, isotropic, fully developed turbulence, up to resolution $512^3$ ($R_\lambda\approx 185$). Following the trajectories of up to 120 million…
In this paper, we introduce a nonlinear stochastic model to describe the propagation of information inside a computer processor. In this model, a computational task is divided into stages, and information can flow from one stage to another.…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Rectified flow (Liu et al., 2022; Liu, 2022; Wu et al., 2023) is a method for defining a transport map between two distributions, and enjoys popularity in machine learning, although theoretical results supporting the validity of these…
For many biological systems that involve elastic structures immersed in fluid, small length scales mean that inertial effects are also small, and the fluid obeys the Stokes equations. One way to solve the model equations representing such…
Ciliary flows are generated by a vast array of eukaryotic organisms, from unicellular algae to mammals, and occur in a range of different geometrical configurations. We employ a point torque -- or `rotlet' -- model to capture the…
We are concerned with the simulation and optimization of large-scale gas pipeline systems in an error-controlled environment. The gas flow dynamics is locally approximated by sufficiently accurate physical models taken from a hierarchy of…
Stream Processing (SP) has evolved as the leading paradigm to process and gain value from the high volume of streaming data produced e.g. in the domain of the Internet of Things. An SP system is a middleware that deploys a network of…
We present a method called Manifold Interpolating Optimal-Transport Flow (MIOFlow) that learns stochastic, continuous population dynamics from static snapshot samples taken at sporadic timepoints. MIOFlow combines dynamic models, manifold…
Background. It is assumed that the introduction of stochastic in mathematical model makes it more adequate. But there is virtually no methods of coordinated (depended on structure of the system) stochastic introduction into deterministic…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
An efficient algorithm for computing the terms appearing in the Generalised Kolmogorov Equation (GKE) written for the indefinite plane channel flow is presented. The algorithm, which features three distinct strategies for parallel…
Simulations of over $10^3$ hydrodynamically coupled solid spheres are performed to investigate collective motion of linear trains and regular square arrays of particles suspended in a fluid bounded by two parallel walls. Our novel…
Extending well-structured transition systems to incorporate a probabilistic scheduling rule, we define a new class of stochastic well-structured transition systems that includes population protocols, chemical reaction networks, and many…
Monitoring small groups of sheep in spontaneous evolution in the field, we decipher behavioural rules that sheep follow at the individual scale in order to sustain collective motion. Individuals alternate grazing mode at null speed and…