Related papers: A note on retrodiction and machine evolution
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. The Markov Chain Convergence Theorem and the Data Processing Inequality describe how the mutual…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The…
A qualitative model is presented, suggesting gravitational information is transduced into biological systems primarily by its effect on spatially organised membrane and cytoplasmic flows. Continuous low affinity interactions between…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Human languages have evolved to be structured through repeated language learning and use. These processes introduce biases that operate during language acquisition and shape linguistic systems toward communicative efficiency. In this paper,…
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Current interpretations rely on descriptive catalogues of…
Understanding and predicting the evolution of across complex systems remains a fundamental challenge due to the absence of unified and computationally testable frameworks. Here we propose the Recursive Hierarchical Network(RHN),…
How the very first nervous systems evolved remains a fundamental open question. Molecular and genomic techniques have revolutionized our knowledge of the molecular ingredients behind this transition but not yet provided a clear picture of…
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…