Related papers: Complete integrability of information processing b…
Although G\"odel's incompleteness theorem made mathematician recognize that no axiomatic system could completely prove its correctness and that there is an eternal hole between our knowledge and the world, physicists so far continue to work…
A subjective expected utility policy making centre, managing complex, dynamic systems, needs to draw on the expertise of a variety of disparate panels of experts and integrate this information coherently. To achieve this, diverse supporting…
We address the problem of estimating unknown model parameters and state variables in stochastic reaction processes when only sparse and noisy measurements are available. Using an asymptotic system size expansion for the backward equation we…
Statistical mechanics is generalized on the basis of an additive information theory for incomplete probability distributions. The incomplete normalization $\sum_{i=1}^wp_i^q=1$ is used to obtain generalized entropy $S=-k\sum_{i=1}^wp_i^q\ln…
We review the statistical mechanics approach to the study of the emerging collective behavior of systems of heterogeneous interacting agents. The general framework is presented through examples is such contexts as ecosystem dynamics and…
The boundaries between physical and social networks have narrowed with the advent of the Internet and its pervasive platforms. This has given rise to a complex adaptive information ecosystem where individuals and machines compete for…
Mathematical models of physical systems are subject to many uncertainties such as measurement errors and uncertain initial and boundary conditions. After accounting for these uncertainties, it is often revealed that discrepancies between…
Estimating rate coefficients from complex chemical reactions is essential for advancing detailed chemistry. However, the stiffness inherent in real-world atmospheric chemistry systems poses severe challenges, leading to training instability…
In the previous papers (Kui\'{c} et al. in Found Phys 42:319-339, 2012; Kui\'{c} in arXiv:1506.02622, 2015), it was demonstrated that applying the principle of maximum information entropy by maximizing the conditional information entropy,…
We develop a statistical toolbox for a quantitative model evaluation of stochastic reaction-diffusion systems modeling space-time evolution of biophysical quantities on the intracellular level. Starting from space-time data $X_N(t,x)$, as,…
The statistics of fluctuations on large regions of space encodes universal properties of many-body systems. At equilibrium, it is described by thermodynamics. However, away from equilibrium such as after quantum quenches, the fundamental…
Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
The significance of statistical physics concepts such as entropy extends far beyond classical thermodynamics. We interpret the similarity between partitions in statistical mechanics and partitions in Bayesian inference as an articulation of…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
Theoretical results regarding two-dimensional ordinary-differential equations (ODEs) with second-degree polynomial right-hand sides are summarized, with an emphasis on limit cycles, limit cycle bifurcations and multistability. The results…
Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
Thermodynamics (in concert with its sister discipline, statistical physics) can be regarded as a data reduction scheme based on partitioning a total system into a subsystem and a bath that weakly interact with each other. The ubiquity and…
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…
There is no compelling reason imposing that the methods of statistical mechanics should be restricted to the dynamical systems which follow the usual Boltzmann-Gibbs prescriptions. More specifically, ubiquitous natural and artificial…