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Empirical modelling often aims for the simplest model consistent with the data. A new technique is presented which quantifies the consistency of the model dynamics as a function of location in state space. As is well-known, traditional…
Periodically forced turbulence is used as a test case to evaluate the predictions of two-equation and multiple-scale turbulence models in unsteady flows. The limitations of the two-equation model are shown to originate in the basic…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
We analyse a collection of empirical networks in a wide spectrum of disciplines and show that strong non-normality is ubiquitous in network science. Dynamical processes evolving on non-normal networks exhibit a peculiar behaviour, as…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
The question of how irreversibility can emerge as a generic phenomena when the underlying mechanical theory is reversible has been a long-standing fundamental problem for both classical and quantum mechanics. We describe a mechanism for the…
Complex, oscillatory data arises from a large variety of biological, physical, and social systems. However, the inherent oscillation and ubiquitous noise pose great challenges to current methodology such as linear and nonlinear time series…
A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…
Rhythmic data are ubiquitous in the life sciences. Biologists need reliable statistical tests to identify whether a particular experimental treatment has caused a significant change in a rhythmic signal. When these signals display…
We disclose the generality of the intrinsic mechanisms underlying multistability in reciprocally inhibitory 3-cell circuits composed of simplified, low-dimensional models of oscillatory neurons, as opposed to those of a detailed Hodgkin-…
Economic models may exhibit incompleteness depending on whether or not they admit certain policy-relevant features such as strategic interaction, self-selection, or state dependence. We develop a novel test of model incompleteness and…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Diffusion models generate structure by progressively transforming noise into data, yet the mechanisms underlying this transition remain poorly understood. In this work, we show that pattern formation in trained diffusion models can be…
Pituitary gonadotropins play an essential and pivotal role in the control of human and animal reproduction within the hypothalamic-pituitary-gonadal (HPG) axis. The computational modeling of pituitary gonadotropin signaling encompasses…
An approach to fault isolation that exploits vastly incomplete models is presented. It relies on separate descriptions of each component behavior, together with the links between them, which enables focusing of the reasoning to the relevant…
We reexamine the classical linear regression model when the model is subject to two types of uncertainty: (i) some of covariates are either missing or completely inaccessible, and (ii) the variance of the measurement error is undetermined…
The evolutionary biology of aging is fundamental to understanding the mechanisms of aging and how to develop anti-aging treatments. Thus far most evolutionary theory concerns the genetics of aging with limited physiological integration.…
The fluctuation theorems have remained one of the cornerstones in the study of systems that are driven far out of equilibrium, and they provide strong constraints on the fraction of trajectories that behave atypically in light of the second…
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…