Related papers: Computational Theory of Biological Function I
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),…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
Molecular science is governed by the dynamics of electrons, atomic nuclei, and their interaction with electromagnetic fields. A reliable physicochemical understanding of these processes is crucial for the design and synthesis of chemicals…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
To better understand the deep significance of our best physical theories it could be interesting to compare our Universe with its models. It may happen that the differences between the model and reality can be made indistinguishable, to the…
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which…
According to the Church-Turing Thesis (CTT), effective formal behaviours can be simulated by Turing machines; this has naturally led to speculation that physical systems can also be simulated computationally. But is this wider claim true,…
Scientific computation is a discipline that combines numerical analysis, physical understanding, algorithm development, and structured programming. Several yottacycles per year on the world's largest computers are spent simulating problems…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional are required. In this work, a model based on deep…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
This paper introduces abstractions that are meaningful for computers and that can be built and used according to computers' own criteria, i.e., computable abstractions. It is analyzed how abstractions can be seen to serve as the building…
Despite differing from the human language processing mechanism in implementation and algorithms, current language models demonstrate remarkable human-like or surpassing language capabilities. Should computational language models be employed…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
This paper is a reflexion on the computability of natural language semantics. It does not contain a new model or new results in the formal semantics of natural language: it is rather a computational analysis of the logical models and…