Related papers: A note on retrodiction and machine evolution
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Combinatorial evolution and forecasting of system requirements is examined. The morphological model is used for a hierarchical requirements system (i.e., system parts, design alternatives for the system parts, ordinal estimates for the…
Plants and insects communicate using chemical signals like volatile organic compounds (VOCs). A plant encodes information using different blends of VOCs, which propagate through the air to represent different symbolic information. This…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
The spectacular successes of recurrent neural network models where key parameters are adjusted via backpropagation-based gradient descent have inspired much thought as to how biological neuronal networks might solve the corresponding…
We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted…
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts…
Hierarchies are the hidden backbones of complex systems and their analysis allows for a deeper understanding of their structure and how they evolve. We consider languages also to be complex adaptive systems with several intricate networks…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not…
In computer interfaces in general, especially in information retrieval tasks, it is important to be able to quickly find and retrieve information. State of the art approach, used, for example, in search engines, is not effective as it…
Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, modern neural architectures designed for learning…
This paper investigates the application of the transformer architecture in protein folding, as exemplified by DeepMind's AlphaFold project, and its implications for the understanding of so-called large language models. The prevailing…
Molecular signalling in living cells occurs at low copy numbers and is thereby inherently limited by the noise imposed by thermal diffusion. The precision at which biochemical receptors can count signalling molecules is intimately related…