Related papers: Computational Theory of Biological Function I
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Computability logic is a formal theory of (interactive) computability in the same sense as classical logic is a formal theory of truth. This approach was initiated very recently in "Introduction to computability logic" (Annals of Pure and…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Computational mechanics is a method for discovering, describing and quantifying patterns, using tools from statistical physics. It constructs optimal, minimal models of stochastic processes and their underlying causal structures. These…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
This chapter provides a tutorial overview of first principles methods to describe the properties of matter at the ground state or equilibrium. It begins with a brief introduction to quantum and statistical mechanics for predicting the…
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…
Computing in the life sciences has undergone a transformative evolution, from early computational models in the 1950s to the applications of artificial intelligence (AI) and machine learning (ML) seen today. This paper highlights key…
The molecular computing has been successfully employed to solve more and more complex computation problems. However, as an important complex problem, the model checking are still far from fully resolved under the circumstance of molecular…
Computability theory is traditionally conceived as the theoretical basis of informatics. Nevertheless, numerous proposals transcend computability theory, in particular by emphasizing interaction of modules, or components, parts,…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
In this document we shows a first implementation and some preliminary results of a new theory, facing Machine Learning problems in the frameworks of Classical Mechanics and Variational Calculus. We give a general formulation of the problem…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Complexity theory offers a variety of concise computational models for computing boolean functions - branching programs, circuits, decision trees and ordered binary decision diagrams to name a few. A natural question that arises in this…
Physical processes are computations only when we use them to externalize thought. Computation is the performance of one or more fixed processes within a contingent environment. We reformulate the Church-Turing thesis so that it applies to…