Related papers: A note on retrodiction and machine evolution
Since the Hadean era of Earth's history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical…
Molecular Communication (MC) is an important nanoscale communication paradigm, which is employed for the interconnection of the nanomachines (NMs) to form nanonetworks. A transmitter NM (TN) sends the information symbols by emitting…
Molecular communication between biological entities is a new paradigm in communications. Recently, we studied molecular communication between two nodes formed from synthetic bacteria. Due to high randomness in behavior of bacteria, we used…
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
In this paper, we present a communication protocol between a pair of biological nanomachines, transmitter and receiver, built upon molecular communications in an aqueous environment. In our proposal, the receiver, acting as a control node,…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Programming languages are engineered languages that allow to instruct a machine and share algorithmic information; they have a great influence on the society since they underlie almost every information technology artefact, and they are at…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
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.…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Significant advances have been made in artificial systems by using biological systems as a guide. However, there is often little interaction between computational models for emergent communication and biological models of the emergence of…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology. The biological nature of chemical signaling makes MC a promising methodology for interdisciplinary applications…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…