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Robotic cutting of soft materials is critical for applications such as food processing, household automation, and surgical manipulation. As in other areas of robotics, simulators can facilitate controller verification, policy learning, and…
Intra-tumour phenotypic heterogeneity limits accuracy of clinical diagnostics and hampers the efficiency of anti-cancer therapies. Dealing with this cellular heterogeneity requires adequate understanding of its sources, which is extremely…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
The discrete class algorithm presented in this paper is an efficient simulation tool for stochastic processes governed by a reasonably small set of transition rates. The algorithm is presented, its performance compared to prevailing methods…
Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using…
The Segment Anything Model (SAM) has garnered significant attention for its versatile segmentation abilities and intuitive prompt-based interface. However, its application in medical imaging presents challenges, requiring either substantial…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
This paper introduces a new behavioral system model with distinct external and internal signals possibly evolving on different time scales. This allows to capture abstraction processes or signal aggregation in the context of control and…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
We introduce the Composable Involution Delay Model (CIDM) for fast and accurate digital simulation. It is based on the Involution Delay Model (IDM) [F\"ugger et al., IEEE TCAD 2020], which has been shown to be the only existing candidate…
Recent years have witnessed the rapid development of acceleration techniques for diffusion models, especially caching-based acceleration methods. These studies seek to answer two fundamental questions: "When to cache" and "How to use…
We consider solving distributed consensus optimization problems over multi-agent networks. Current distributed methods fail to capture the heterogeneity among agents' local computation capacities. We propose DISH as a distributed hybrid…
Many biological systems are governed by difference equations and exhibit discrete-time dynamics. Examples include the size of a population when generations are non-overlapping, and the incidence of a disease when infections are recorded at…
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion…
Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication.…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results:…
This paper enhances the Diffuse Interface Method (DIM) for simulating compressible multiphase flows across all Mach numbers by addressing the accuracy challenges posed at low Mach regimes. A correction to the Riemann solver is introduced,…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…