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Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological…
Flow transport in confined spaces is ubiquitous in technological processes, ranging from separation and purification of pharmaceutical ingredients by microporous membranes and drug delivery in biomedical treatment to chemical and biomass…
Self-generated gradients have atttracted a lot of attention in the recent biological literature. It is considered as a robust strategy for a group of cells to find its way during a long journey. This note is intended to discuss various…
The managed-metabolism hypothesis suggests that a cooperation barrier must be overcome if self-producing chemical organizations are to transition from non-life to life. This barrier prevents un-managed, self-organizing, autocatalytic…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Self-organization phenomena in ensembles of self-propelled particles open pathways to the synthesis of new dynamic states not accessible by traditional equilibrium processes. The challenge is to develop a set of principles that facilitate…
A mystery about the origins of life is which molecular structures $-$ and what spontaneous processes $-$ drove the autocatalytic transition from simple chemistry to biology? Using the HP lattice model of polymer sequence spaces leads to the…
For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare,…
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…
Autocatalysis is thought to have played an important role in the earliest stages of the origin of life. An autocatalytic cycle (AC) is a set of reactions that results in stoichiometric increase in its constituent chemicals. When the…
The observed single-handedness of biological amino acids and sugars has long been attributed to autocatalysis. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross inhibition of the two chiral…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
Living organisms are molecular systems with self-sustained dynamics via energy conversion through molecular cooperation, resulting in highly complex macroscopic behaviors. Construction of such autonomous macroscopic dynamics at a molecular…
Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we…
Life can be viewed as a localized chemical system that sits on, or in the basin of attraction of, a metastable dynamical attractor state that remains out of equilibrium with the environment. Such a view of life allows that new living states…
Complex interactions between cellular systems and their surrounding extracellular matrices are emerging as important mechanical regulators of cell functions such as proliferation, motility, and cell death, and such cellular systems are…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…