Related papers: On the remote interaction of biological objects wi…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
Predicting the evolution of a large system of units using its structure of interaction is a fundamental problem in complex system theory. And so is the problem of reconstructing the structure of interaction from temporal observations. Here,…
It is shown how to take advantage of the frequent occurrence of double-strand breaks in the genome of prokaryotic cells, in order to reduce their high efficient reproductive capability. The analysis examines the physical status of the free…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself.
Energy transport is of central importance in understanding a wide variety of transitions of physical states in nature. Recently, the coherence and noise have been identified for their existence and key roles in energy transport processes,…
It is well-established that the provenance of a scientific result is important, sometimes more important than the actual result. For computational analyses that involve visualization, this provenance information may contain the steps…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Experimental realizations of such systems include colloids grafted with complementary single-stranded DNA (ssDNA), and particles…
Bacterial quorum sensing is the communication that takes place between bacteria as they secrete certain molecules into the intercellular medium that later get absorbed by the secreting cells themselves and by others. Depending on cell…
Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most…
This work bridges the technical concepts underlying distributed computing and blockchain technologies with their profound socioeconomic and sociopolitical implications, particularly on academic research and the healthcare industry. Several…
How to artificially encode observer in universal information coding structure like DNA ? It requires naturally creating information Bits and natural encoding triplet code enables recognizing other encoded information. These Bits become…
Models of coevolution have recently been studied, in which a species is defined by a genome in the form of a bitstring, and the interactions between species i and j are given by a fixed matrix with independent, randomly distributed elements…
The genome is a unique identifier for human individuals. The genome also contains highly sensitive information, creating a high potential for misuse of genomic data (for example, genetic discrimination). In this paper, I investigated how…
Individuals are always limited by some inelastic resources, such as time and energy, which restrict them to dedicate to social interaction and limit their contact capacity. Contact capacity plays an important role in dynamics of social…
We discuss the similarity of the degeneration structure of the genetic code with a pure number theoretic -- ``divisors code.'' The most interesting thing about our observation is not that there is a connection between number theory and the…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
In the brain, information is encoded, transmitted and used to inform behaviour at the level of timing of action potentials distributed over population of neurons. To implement neural-like systems in silico, to emulate neural function, and…