Related papers: Biological Organization and Negative Entropy: Base…
In this philosophical paper, we explore computational and biological analogies to address the fine-tuning problem in cosmology. We first clarify what it means for physical constants or initial conditions to be fine-tuned. We review…
Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic, and mounting experimental evidence raises the intriguing…
The remarkable range of biological forms in and around us, such as the undulating shape of a leaf or flower in the garden, the coils in our gut, or the folds in our brain, raise a number of questions at the interface of biology, physics and…
Entropy estimation is of practical importance in information theory and statistical science. Many existing entropy estimators suffer from fast growing estimation bias with respect to dimensionality, rendering them unsuitable for…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
Self-organizing complex systems typically are comprised of a large number of frequently similar components or events. Through their process, a pattern at the global-level of a system emerges solely from numerous interactions among the…
We introduce an ambidextrous view of stochastic dynamical systems, comparing their forward-time and reverse-time representations and then integrating them into a single time-symmetric representation. The perspective is useful theoretically,…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
A model to describe the arising of new structures in an initial homogeneous biological system is proposed. The essay is motivated by the intention to work on a non-equilibrium situation grouping together several mechanisms and processes as:…
Entropy, its production, and its change in a dynamical system can be understood from either a fully stochastic dynamic description or from a deterministic dynamics exhibiting chaotic behavior. By taking the former approach based on the…
A central aim of physics is to describe the dynamics of physical systems. Schrodinger's equation does this for isolated quantum systems. Describing the time evolution of a quantum system that interacts with its environment, in its most…
We develop an axiomatic reconstruction of thermodynamics based entirely on two primitive components: a description of what aspects of a system are observed and a reference measure that encodes the underlying descriptive convention. These…
Many biological systems perform close to their physical limits, but promoting this optimality to a general principle seems to require implausibly fine tuning of parameters. Using examples from a wide range of systems, we show that this…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
This work is concerned with the minimization of quantum entropies under local constraints of density, current, and energy. The problem arises in the work of Degond and Ringhofer about the derivation of quantum hydrodynamical models from…
Since its origin in the thermodynamics of the 19th century, the concept of entropy has also permeated other fields of physics and mathematics, such as Classical and Quantum Statistical Mechanics, Information Theory, Probability Theory,…
Trying to identify the entropy production within a cell has been part of debates and studies in the last century. First the idea was to make a resemblance of a cell with a Carnot engine, which is the most thermodynamically perfect machine.…
A basic idea in optimal transport is that optimizers can be characterized through a geometric property of their support sets called cyclical monotonicity. In recent years, similar "monotonicity principles" have found applications in other…
"Self-organization" has become a watchword in developmental biology, characterizing observations in which embryonic or induced stem cells of animals replicate morphological steps and outcomes seen in intact embryos. While the term was…