Related papers: The Cell Physiome: What do we need in a computatio…
We present multiscale models of cancer tumor invasion with components at the molecular, cellular, and tissue levels. We provide biological justifications for the model components, present computational results from the model, and discuss…
Characterizing the dynamic interactive patterns of complex systems helps gain in-depth understanding of how components interrelate with each other while performing certain functions as a whole. In this study, we present a novel multimodal…
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
This chapter sheds light on the synaptic organization of the brain from the perspective of computational neuroscience. It provides an introductory overview on how to account for empirical data in mathematical models, implement such models…
Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underly many morphogenetic events and involve spatial gradients in active cellular forces…
In the past 40 years, single-molecule techniques have been rapidly developed and widely applied in numerous fields of biology researches, offering new insights that conventional biochemical assays cannot discover. In this review, to help…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
The electrophysiology of betacells is at the origin of insulin secretion. Betacells exhibit a complex behaviour upon stimulation with glucose including repeated and uninterrupted bursting. Mathematical modelling is most suitable to improve…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
Scientific research is a major driving force in a knowledge based economy. Income, health and wellbeing depend on scientific progress. The better we understand the inner workings of the scientific enterprise, the better we can prompt,…
Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the…
In this paper, we will show that the recently introduced graphical model: Conditional Random Fields (CRF) provides a template to integrate micro-level information about biological entities into a mathematical model to understand their…
Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…