Related papers: Coevolution of membranes and channels: A possible …
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
It is undeniable that life as we know it depends on liquid water. It is difficult to imagine any biochemical machinery that does not require water. On Earth, life adapts to the most diverse environments and, once established, it is very…
A theoretical study of cell evolution is presented here. By using a toolbox containing an intracellular catalytic reaction network model and a mutation-selection process, four distinct phases of self-organization were unveiled. First, the…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
A mechanism of the replication of proto-RNAs in oligomer world is proposed. The replication is carried out by a minimum cycle which is sustained by a ligase and a helicase. We expect that such a cycle actually worked in the primordial soup…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
The origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements…
We discuss some of the cosmological constraints on the evolution and persistence of life in the Universe and in hypothetical universes other than our own. We highlight the role played by the age and size of the universe, and discuss the…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
Morphological change of bilayer membrane in vivo is not a spontaneous procedure but modulated by various types of proteins in general. Most of these modulations are associated with the localization of related proteins in the crowded lipid…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
I describe the non-equilibrium thermodynamics and the photochemical mechanisms which may have been involved in the dissipative structuring, proliferation and evolution of the fundamental molecules at the origin of life from simpler and more…
This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the…
Conceptualizing planetary habitability depends on understanding how living organisms originated and what features of environments are essential to foster abiogenesis. Estimates of the abundance of life's building blocks are confounded by…
I show that exoplanets can be used to test origins scenarios. Origins scenarios start with certain initial conditions, proceed via a network of chemical reactions and, if successful, result in a chemistry that is closer to a living system…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…
A simple model of species origin resulted from dynamic features of a population, solely, is developed. The model is based on the evolution optimality in space distribution, and the selection is gone over the mobility. Some biological issues…