Related papers: The in silico macrophage: toward a better understa…
Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate…
The study of the interactions of living adherent cells with mechanically stable (visco)elastic materials enables understanding and exploiting physiological phenomena mediated by cell-extracellular communication. However, insight on the…
Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret…
Energy systems optimisation models are a leading tool for informing decisions in the energy transition. However, these models often remain opaque, and results are frequently presented without a clear discussion of their epistemic…
One of the ultimate goals in biology is to understand the design principles of biological systems. Such principles, if they exist, can help us better understand complex, natural biological systems and guide the engineering of de novo ones.…
Cells of the immune system are confronted with opposing pro- and anti-inflammatory signals. Dendritic cells (DC) integrate these cues to make informed decisions whether to initiate an immune response. Confronted with exogenous microbial…
In the field of environmental toxicology, rapid and precise assessment of the inflammatory response to pollutants in biological models is critical. This study leverages the power of deep learning to enable automated assessments of…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
Human pluripotent stem cells hold great promise for developments in regenerative medicine and drug design. The mathematical modelling of stem cells and their properties is necessary to understand and quantify key behaviours and develop…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Motile cilia are a striking example of functional cellular organelle, conserved across all the eukaryotic species. Motile cilia allow swimming of cells and small organisms and transport of liquids across epithelial tissues. Whilst the…
We derive a physiologically structured multiscale model for biofilm development. The model has components on two spatial scales, which induce different time scales into the problem. The macroscopic behavior of the system is modeled using…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
At present it is still quite difficult to match the vast knowledge on the behavior of individual tumor cells with macroscopic measurements on clinical tumors. On the modeling side, we already know how to deal with many molecular pathways…
In vitro transcription (IVT) plays a critical role in the manufacture of mRNA vaccines and therapeutics. Optimizing mRNA yield and ensuring product quality, such as capping efficiency and integrity, are essential but mechanistically…
Recent advancements in deep learning-based modeling of molecules promise to accelerate in silico drug discovery. A plethora of generative models is available, building molecules either atom-by-atom and bond-by-bond or fragment-by-fragment.…
Chimeric Antigen Receptor (CAR) T cell therapy has transformed immunotherapy for resistant cancers, yet it faces major limitations such as lack of persistence, toxicity, exhaustion, and antigen-negative relapse. Enhancing CAR T cells with…
Mathematical models are indispensable to the system biology toolkit for studying the structure and behavior of intracellular signaling networks. A common approach to modeling is to develop a system of equations that encode the known biology…
In this paper, we propose a new workflow to analyze macrophage motion during wound healing. These immune cells are attracted to the wound after an injury and they move showing both directional and random motion. Thus, first, we smooth the…