14 papers · ranked by Valyu relevance
Mahnoor N Gondal, Muhammad U Sultan, Ammar Arif, Abdul Rehman + 33 more
Multi-scale models integrating biomolecular data from genetic, transcriptional, and translational levels, coupled with extracellular microenvironments can assist in decoding the complex mechanisms underlying system-level diseases such as cancer. To investigate the emergent properties and clinical translation of such…
Mahnoor Naseer Gondal, Safee Ullah Chaudhary
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built on top of this data have the potential to provide specific insights…
Pariksheet Nanda, Maral Budak, Christian T. Michael, Kathryn Krupinsky + 1 more
Although infectious disease dynamics are often analyzed at the macro-scale, increasing numbers of drug-resistant infections highlight the importance of within-host modeling that simultaneously solves across multiple scales to effectively respond to epidemics. We review multiscale modeling approaches for complex…
T.J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier
Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular…
Valentin J. Maurer, Marc Siggel, Rasmus K. Jensen, Julia Mahamid + 2 more
Simulating entire cells represents the next frontier of computational biology. Achieving this goal requires methods that accurately reconstruct and simulate cellular membranes across spatial and temporal scales. Although three-dimensional electron microscopy enables detailed membrane visualization, dose limitations and…
Emad Alamoudi, Yannik Schälte, Robert Müller, Jörn Starruß + 4 more
Biological tissues are dynamic and highly organized. Multi-scale models are helpful tools to analyze and understand the processes determining tissue dynamics. These models usually depend on parameters that need to be inferred from experimental data to achieve a quantitative understanding, to predict the response to…
Meiron Zollmann, Boris Rubinsky, Alexander Liberzon, Alexander Golberg
Multi-scale macroalgae growth models are required for the efficient design of sustainable, economically viable and environmentally safe farms. Here, we develop a multi-scale model for Ulva sp. macroalgae growth and nitrogen sequestration in an intensive cultivation farm, regulated by temperature, light and nutrients.…
Adam Husar, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey + 4 more
Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes and surfaces of scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum…
Oriol Canela-Xandri, Samira Anbari, Javier Buceta
This document is an extended version of the main text where some details and results are fleshed out. Further details can be also found in the manual of the code and at TiFoSi’s website: http://tifosi.thesimbiosys.com. Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks…
Xiaoran Lai, Oliver M Geier, Thomas Fleischer, Øystein Garred + 10 more
Mathematical modeling and simulation have emerged as a potentially powerful, time and cost effective approach to personalized cancer treatment. The usefulness of mechanistic models to disentangle complex multi-scale cancer processes such as treatment response has been widely acknowledged. However, a major barrier for…
Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot + 2 more
Iterating between data-driven research and generative computational models is a powerful approach for emulating biological systems, testing hypotheses, and gaining a deeper understanding of these systems. We developed a hybrid agent-based model (ABM) that integrates a Cellular Potts Model (CPM) designed to investigate…
Kaoruko Higuchi, Tomoki Kazawa, Buntaro Sakai, Shigehiro Namiki + 2 more
A major challenge in neurosciences is the elucidation of neural mechanisms in brains that are crucial for the processing of sensory information and the generation of adaptive behavior. In conjunction with the ever-growing body of experimental data, computational simulations have become crucial in integrating…
James M. Osborne
In recent years, multi–cellular models, where cells are represented as individual interacting entities, are becoming ever popular. This has led to a proliferation of novel methods and simulation tools. The first aim of this paper is to review the numerical methods utilised by multi–cellular modelling tools and to…
Bence Bruncsics, Wesley J. Errington, Casim A. Sarkar
Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim, an application suite built around a configurational network…