相关论文: Biology is a constructive physics
The evolution of complexity has been a central theme for Biology and Artificial Life (Bonner, 1988; Bedau et al., 2000). Complexification has been interpreted in different ways: as a process of diversification between evolving units…
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…
The evolution of a gas can be described by different models depending on the observation scale. A natural question, raised by Hilbert in his sixth problem, is whether these models provide consistent predictions. In particular, for rarefied…
Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…
Following the development of the selectionist theory of the immune system, there was an attempt to characterize many biological mechanisms as being "selectionist" as juxtaposed to "instructionist." But this broad definition would group…
In a recent paper Andrei N. Soklakov explained the foundations of the Lagrangian formulation of classical particle mechanics by means of Kolmogorov complexity. In the present paper we use some of Soklakov ideas in order to derive the second…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
Constructor theory seeks to express all fundamental scientific theories in terms of a dichotomy between possible and impossible physical transformations - those that can be caused to happen and those that cannot. This is a departure from…
In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers <> but also extainers ><,…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
The purpose of this paper is to abstractly describe the notion of a generative mechanism that implements a code and to provide a number of examples including the DNA-RNA machinery that implements the genetic code, Chomsky's Principles &…
Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
Mnay models situated in the current research landscape of modelling and simulating social processes have roots in physics. This is visible in the name of specialties as Econophysics or Sociophysics. This chapter describes the history of…
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
We introduce a non-growth model that generates the power-law distribution with the Zipf exponent. There are N elements, each of which is characterized by a quantity, and at each time step these quantities are redistributed through binary…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…