Related papers: Mapping gene expression dynamics to developmental …
Biological systems are typically highly open, non-equilibrium systems that are very challenging to understand from a statistical mechanics perspective. While statistical treatments of evolutionary biological systems have a long and rich…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
Entropy plays a key role in statistical physics of complex systems, which in general exhibit diverse aspects of emergence on different scales. However, it still remains not fully resolved how entropy varies with the coarse-graining level…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an…
We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…
We measure different contributions to entropy production in a living functional epithelial tissue. We do this by extracting the functional dynamics of development while at the same time quantifying fluctuations. Using the translucent…
The concept of entropy in nonequilibrium macroscopic systems is investigated in the light of an extended equation of motion for the density matrix obtained in a previous study. It is found that a time-dependent information entropy can be…
The constituents of a complex system exchange information to function properly. Their signalling dynamics often leads to the appearance of emergent phenomena, such as phase transitions and collective behaviors. While information exchange…
The gap in statistics between multi-variate and time-series analysis can be bridged by using entropy statistics and recent developments in multi-dimensional scaling. For explaining the evolution of the sciences as non-linear dynamics, the…
The central goal of a dynamical theory of evolution is to abstract the mean evolutionary trajectory in the trait space by considering ecological processes at the level of the individual. In this work, we develop such a theory for a new…
Data from social media are providing unprecedented opportunities to investigate the processes that rule the dynamics of collective social phenomena. Here, we consider an information theoretical approach to define and measure the temporal…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Cellular phenotype is characterized by different components such as cell size, protein content and cell cycle time. These are global variables that are the outcome of multiple internal microscopic processes. Accordingly, they display some…
We consider discrete stochastic processes, modeled by classical master equations, on networks. The temporal growth of the lack of information about the system is captured by its non-equilibrium entropy, defined via the transition…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Understanding the development of adolescent behavioral and mental health outcomes requires integrating genetic predisposition, environmental exposures, and neurobiological processes over time. Here, we present a unified quantitative…
We propose to examine the predictability and the complexity characteristics of the Standard&Poor500 dynamics behaviors in a coarse-grained way using the symbolic dynamics method and under the prism of the Information theory through the…