Related papers: A Theory of Differentiation with Dynamic Clusterin…
Experimental results often do not assess network structure; rather, the network structure is inferred by the dynamics of the nodes. From the dynamics of the nodes one then constructs a network of functional relations, termed the functional…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
Recent advances in classical density functional theory are combined with stochastic process theory and rare event techniques to formulate a theoretical description of nucleation, including crystallization, that can predict nonclassical…
Many natural and engineered complex networks have intricate mesoscopic organization, e.g., the clustering of the constituent nodes into several communities or modules. Often, such modularity is manifested at several different hierarchical…
Through in-depth thinking and reasoning about the conditions required for cells to maintain unchanged material distribution, it is concluded that life metabolic reactions require high information content. However, the self-replication of a…
Network of nonlinear dynamical elements often show clustering of synchronization by chaotic instability. Relevance of the clustering to ecological, immune, neural, and cellular networks is discussed, with the emphasis of partially ordered…
Many fields, such as neuroscience, are experiencing the vast proliferation of cellular data, underscoring the need for organizing and interpreting large datasets. A popular approach partitions data into manageable subsets via hierarchical…
We explore the interplay of network structure, topology, and dynamic interactions between nodes using the paradigm of distributed synchronization in a network of coupled oscillators. As the network evolves to a global steady state,…
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…
A new model that describes adsorption and clustering of particles on a surface is introduced. A {\it clustering} transition is found which separates between a phase of weakly correlated particle distributions and a phase of strongly…
We rigorously prove a form of disorder-resistance for a class of one-dimensional cellular automaton rules, including some that arise as boundary dynamics of two-dimensional solidification rules. Specifically, when started from a random…
We propose a kind of reaction-diffusion equations for cell differentiation, which exhibits the Turing instability. If the diffusivity of some variables is set to be infinity, we get coupled competitive reaction-diffusion equations with a…
We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…
Probably the most fundamental processes for biological systems is their ability to create themselves through the use of cell division and cell differentiation. In this work a simple physical model is proposed for biological cell division.…
Cells achieve size homeostasis by regulating their division timing based on their size, added size, and cell cycle time. Previous research under steady-state conditions demonstrated the robustness of these mechanisms. However, their dynamic…
In this paper, we bring together our efforts in identifying and understanding nonequilibrium phase segregation driven by active processes in the living cell, with special focus on the segregation of cell membrane components driven by active…
Recent experimental and theoretical studies suggest that crystallization and glass-like solidification are useful analogies for understanding cell ordering in confluent biological tissues. It remains unexplored how cellular ordering…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…