Related papers: Single-cell approaches to cell competition: high-t…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell…
The intratumor heterogeneity has been recognized to characterize cancer cells impairing the efficacy of cancer treatments. We here propose an extension of constraint-based modeling approach in order to simulate metabolism of cell…
Aberrantly regulated cell motility is a hallmark of cancer cells. A hybrid agent-based model has been developed to investigate the synergistic and antagonistic cell motility-impacting effects of three microenvironment variables…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
Complex systems in science and engineering sometimes exhibit behavior that changes across different regimes. Traditional global models struggle to capture the full range of this complex behavior, limiting their ability to accurately…
A recent burst of dynamic single-cell growth-division data makes it possible to characterize the stochastic dynamics of cell division control in bacteria. Different modeling frameworks were used to infer specific mechanisms from such data,…
Competition for a limited resource is the hallmark of many complex systems, and often, that resource turns out to be the physical space itself. In this work, we study a novel model designed to elucidate the dynamics and emergence in complex…
Quantization problem in digital control system have attracted more and more attention in these years. Normally, a quantized variable is regarded as a perturbed copy of the unquantized variable in the research of quantization effect, but…
Competing risk models are survival models with several events of interest acting in competition and whose occurrence is only observed for the event that occurs first in time. This paper presents a Bayesian approach to these models in which…
Cellular development follows a stochastic yet rule-governed trajectory, though the underlying principles remain elusive. Here, we propose that cellular development follows paths of least action, aligning with foundational physical laws that…
Single-cell gene expression measurements encode variability spanning molecular noise, cell-to-cell heterogeneity, and technical artifacts. Mechanistic stochastic models provide powerful approaches to disentangle these sources, yet inferring…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
A simple cellular automata model for a two-group war over the same territory is presented. It is shown that a qualitative advantage is not enough for a minority to win. A spatial organization as well a definite degree of aggressiveness are…
A cell routinely responds to one of many competing environmental cues. A fundamental question is whether the cell follows the cue prioritized by its internal signaling network or the cue that carries the most external information. We…
The paper aims to discuss statistical properties of the multi-agent based model of competitive growth. Each of the agents is described by growth (or decay) rule of its virtual "mass" with the rate affected by the interaction with other…