Related papers: Process Bigraphs and the Architecture of Compositi…
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…
Biofilms are bacterial aggregates that grow on moist surfaces. Thin homogeneous biofilms naturally formed on the walls of conducts may serve as biosensors, providing information on the status of microsystems (MEMS) without disrupting them.…
There is significant interest in using existing repositories of biological entities, relationships, and models to automate biological model assembly and extension. Current methods aggregate human-curated biological information into…
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…
Bioprocesses are central to modern biotechnology, enabling sustainable production in pharmaceuticals, specialty chemicals, cosmetics, and food. However, developing high-performing processes is costly and complex, requiring iterative,…
In biology, arborized structures are well represented and typically complex for visualization and analysis. In order to have a profound understanding of the topology of arborized 3D biological model, higher level abstraction is needed. We…
Diagrams are essential tools for problem-solving and communication as they externalize conceptual structures using spatial relationships. But when picking a diagramming framework, users are faced with a dilemma. They can either use a highly…
The Open Knowledgebase of Interatomic Models (OpenKIM) project is a framework intended to facilitate access to standardized implementations of interatomic models for molecular simulations along with computational protocols to evaluate them.…
Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
A trend across most areas where simulation-driven development is used is the ever increasing size and complexity of the systems under consideration, pushing established methods of modeling and simulation towards their limits. This paper…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward…
Microfiltration technology is a widely used engineering strategy for fresh water production and water treatment. The major concern in many applications is the formation of a biological fouling layer leading to increased hydraulic resistance…
Simulation models have been described using different perspectives, or worldviews. In the process interaction world view (PI), every entity is modeled by a sequence of actions describing its life cycle, offering a comprehensive model that…
Hypercomplex image processing extends conventional techniques in a unified paradigm encompassing algebraic and geometric principles. This work leverages quaternions and the two-dimensional orthogonal planes split framework (splitting of a…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
In Business Process Management (BPM), process modelling has been solved in various ways. However, there are no commonly accepted modelling tools (languages). Some of them are criticized for their inability to capture both the lifecycle,…