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Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
Biological activities are often seen entrained onto the day-night and other celestial mechanical cycles (e.g., seasonal and lunar), but studies on the origin of life have largely not accounted for such periodic external environmental…
This thesis is designed to be a self-contained exposition of the neurobiological and mathematical aspects of sensory perception, memory, and learning with a bias towards olfaction. The final chapters introduce a new approach to modeling…
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…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
The origin of life is often approached through the lens of replication, heredity, or molecular specificity. This paper proposes a thermodynamic framework in which the emergence of life is driven by the persistence of reaction pathways that…
Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling…
Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have…
Self-regulation of living tissue as an example of self-organization phenomena in hierarchical systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
Autophagy is an intracellular degradation process that employs complex membrane dynamics to isolate and break down cellular components. However, many unanswered questions remain concerning remodeling of autophagic membranes. Here, we focus…
A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case,…
One of the major goals of nanobionics and bottom-up synthetic biology is the development of artificial cell organelles for the creation of cell-like structures operating similar to biological systems with a minimalistic set of building…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place --…
The sciences of complexity present some recurrent themes: the emergence of qualitatively new behaviors in dissipative systems out of equilibrium, the aparent tendency of complex system to lie at the border of phase transitions and…
Based on laboratory based growth of plant-like structures from inorganic materials, we present new theory for the emergence of plant structure at a range of scales dictated by levels of ionization (charge density), which can be traced…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
The emergence of biomolecular homochirality is a critically important question about life phenomenon and the origins of life. In a previous paper (arXiv:1309.1229), I tentatively put forward a new hypothesis that the emergence of a single…