Related papers: Predictive landscapes hidden beneath biological ce…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Stability landscapes are useful for understanding the properties of dynamical systems. These landscapes can be calculated from the system's dynamical equations using the physical concept of scalar potential. Unfortunately, for most…
Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems,…
Central to the artificial life endeavour is the creation of artificial systems spontaneously generating properties found in the living world such as autopoiesis, self-replication, evolution and open-endedness. While numerous models and…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
Cellular automata are arrays of finite state machines that can exist in a finite number of states. These machines update their states simultaneously based on specific local rules that govern their interactions. This framework provides a…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
In view of ever-changing conditions both in the external world and in intrinsic brain states, maintaining the robustness of computations poses a challenge, adequate solutions to which we are only beginning to understand. At the level of…
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model…
State-space models are dynamical systems defined by a latent and an observed process. In ecology, stochastic state-space models in discrete time are most often used to describe the imperfectly observed dynamics of population sizes or animal…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
This paper points out some key drawbacks of today's modeling and control underlying hierarchical electric power system operations and planning as the hidden roadblocks on the way to decarbonization. We suggest that these can be overcome by…
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…
How do cellular automata behave in the limit of a very large number of cells? Is there a continuum limit with simple properties? We attack this problem by mapping certain classes of automata to quantum field theories for which powerful…
Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of…
We discuss a characterization of complexity based on successive approximations of the probability density describing a system by means of maximum entropy methods, thereby quantifying the respective role played by different orders of…