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Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from…
This communication is both a pedagogical note for understanding polyatomic modelling in kinetic theory and a ''cheat sheet'' for a series of corresponding concepts and formulas. We explain, detail and relate three possible approaches for…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
This scientific paper explores two distinct approaches for identifying and approximating the simulation model, particularly in the context of the snap process crucial to medical device assembly. Simulation models play a pivotal role in…
We present a mathematical model of polymer bilayers that undergo large bending deformations when actuated by non-mechanical stimuli such as thermal effects. The simple model captures a large class of nonlinear bending effects and can be…
We propose a method of describing a phase transition in a cell fluid model with pair interaction potential that includes repulsive and attractive parts. An exact representation of the grand partition function of this model is obtained in…
Camouflaged objects are typically assimilated into their backgrounds and exhibit fuzzy boundaries. The complex environmental conditions and the high intrinsic similarity between camouflaged targets and their surroundings pose significant…
One strategy to scale up ML-driven science is to increase wet lab experiments' information density. We present a method based on a neural extension of compressed sensing to function space. We measure the activity of multiple different…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
The effective mixing behavior of solutes in porous media is fundamentally connected to the development of a local mixing interface between the two initial solutions, which is characterized by a complex lamellar structure. The deformation of…
Brain surface analysis is essential to neuroscience, however, the complex geometry of the brain cortex hinders computational methods for this task. The difficulty arises from a discrepancy between 3D imaging data, which is represented in…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Cellular tissue behavior is a multiscale problem. At the cell level, out of equilibrium, biochemical reactions drive physical cell-cell interactions in a typical active matter process. Cell modeling computer simulations are a robust tool to…
Local drug delivery has received much recognition in recent years, yet it is still unpredictable how drug efficacy depends on physicochemical properties and delivery kinetics. The purpose of the current study is to provide a useful…
We propose a model describing liquid-solid phase coexistence in mixed lipid membranes by including explicitly the occurrence of a rippled phase. For a single component membrane, we employ a previous model in which the membrane thickness is…
The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…