Related papers: The Control of Branching Morphogenesis
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
During embryonic development tissue morphogenesis and signaling are tightly coupled. It is therefore important to simulate both tissue morphogenesis and signaling simultaneously in in silico models of developmental processes. The resolution…
Obstructions influence the growth and expansion of bodies in a wide range of settings -- but isolating and understanding their impact can be difficult in complex environments. Here, we study obstructed growth/expansion in a model system…
A curious feature of organ and organoid morphogenesis is that in certain cases, spatial oscillations in the thickness of the growing "film" are out-of-phase with the deformation of the slower-growing "substrate," while in other cases, the…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
In this paper, a special sequence of controlled branching processes is considered. We provide a simple set of sufficient conditions for the weak convergence of such processes to a weak solution to a kind of continuous branching processes…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
Cell formation problem is among the first obstacles the designer of cellular production systems must overcome. This paper presents a critical analysis of the various criteria and constraints considered in the literature. The objective is to…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both…
Physical fundamentals of the self-organizing theory for the system with varying constraints are considered. A variation principle, specifically the principle of dynamic harmonization as a generalization of the Gauss-Hertz principle for the…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
This review paper presents the known results on the asymptotics of the survival probability and limit theorems conditioned on survival of critical and subcritical branching processes in IID random environments. The key assumptions of the…
We have performed a statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli. The analysis reveals that operons that regulate each other and operons that are coregulated tend…
Morphogenesis is the ensemble of processes that determines form, shape and patterns in organisms. Based on a reaction-diffusion theoretical setting and some prototype reaction schemes, we make a review of the models and experiments that…