From energy to cellular forces in the Cellular Potts Model: An algorithmic approach

EG Rens, L Edelstein-Keshet - PLoS computational biology, 2019 - journals.plos.org
Single and collective cell dynamics, cell shape changes, and cell migration can be
conveniently represented by the Cellular Potts Model, a computational platform based on …

Computational structural biology: successes, future directions, and challenges

R Nussinov, CJ Tsai, A Shehu, H Jang - Molecules, 2019 - mdpi.com
Computational biology has made powerful advances. Among these, trends in human health
have been uncovered through heterogeneous 'big data'integration, and disease-associated …

Modeling, simulations, and optimization of smooth muscle cell tissue engineering for the production of vascular grafts

Y Elsayed, C Lekakou, P Tomlins - Biotechnology and …, 2019 - Wiley Online Library
The paper presents a transient, continuum, two‐phase model of the tissue engineering in
fibrous scaffolds, including transport equations for the flowing culture medium, nutrient and …

Data-driven spatio-temporal modelling of glioblastoma

ACS Jørgensen, CS Hill, M Sturrock… - Royal Society …, 2023 - royalsocietypublishing.org
Mathematical oncology provides unique and invaluable insights into tumour growth on both
the microscopic and macroscopic levels. This review presents state-of-the-art modelling …

Bridging the gap between individual-based and continuum models of growing cell populations

MAJ Chaplain, T Lorenzi, FR Macfarlane - Journal of Mathematical Biology, 2020 - Springer
Continuum models for the spatial dynamics of growing cell populations have been widely
used to investigate the mechanisms underpinning tissue development and tumour invasion …

Temporally resolved concentration profiling via computationally limited, distributed sensor nodes

ML Manion, J Doctor, AT Liu - AIChE Journal, 2024 - Wiley Online Library
Accurate mapping of chemical concentrations in reactor networks remains an obstacle to
establish complete systems‐level insight and control. This issue extends beyond traditional …

Colloidal State Machines as Smart Tracers for Chemical Reactor Analysis

G Zhang, JF Yang, S Yang, AM Brooks… - Advanced Intelligent …, 2023 - Wiley Online Library
A widely utilized tool in reactor analysis is passive tracers that report the residence time
distribution, allowing estimation of the conversion and other properties of the system …

Derivation of continuum models from discrete models of mechanical forces in cell populations

P Lötstedt - Journal of Mathematical Biology, 2021 - Springer
In certain discrete models of populations of biological cells, the mechanical forces between
the cells are center based or vertex based on the microscopic level where each cell is …

Multiscale modeling in systems biology: methods and perspectives

A Coulier - 2021 - diva-portal.org
In the last decades, mathematical and computational models have become ubiquitous to the
field of systems biology. Specifically, the multiscale nature of biological processes makes the …

Modeling binary and graded cone cell fate patterning in the mouse retina

KC Eldred, C Avelis, RJ Johnston Jr… - PLoS computational …, 2020 - journals.plos.org
Nervous systems are incredibly diverse, with myriad neuronal subtypes defined by gene
expression. How binary and graded fate characteristics are patterned across tissues is …