Related papers: A Simple Comparison of Biochemical Systems Theory …
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
Life cycle analysis (LCA) has emerged as a vital tool for assessing the environmental impacts of products, processes, and systems throughout their entire lifecycle. It provides a systematic approach to quantifying resource consumption,…
We discuss the conceptual differences between the Broad Histogram (BHM) and reweighting methods in general, and particularly the so-called Multicanonical (MUCA) approaches. The main difference is that BHM is based on microcanonical,…
A decade ago, Abdulla, Ben Henda and Mayr introduced the elegant concept of decisiveness for denumerable Markov chains [1]. Roughly speaking, decisiveness allows one to lift most good properties from finite Markov chains to denumerable…
Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set…
Dynamical systems describe the changes in processes that arise naturally from their underlying physical principles, such as the laws of motion or the conservation of mass, energy or momentum. These models facilitate a causal explanation for…
Ordered chains (such as chains of amino acids) are ubiquitous in biological cells, and these chains perform specific functions contingent on the sequence of their components. Using the existence and general properties of such sequences as a…
Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
A large number of biological systems - from bacteria to sheep - can be described as ensembles of self-propelled agents (active particles) with a complex internal dynamic that controls the agent's behavior: resting, moving slow, moving fast,…
The Software Transactional Memory (STM) model is an original approach for controlling concurrent accesses to ressources without the need for explicit lock-based synchronization mechanisms. A key feature of STM is to provide a way to group…
Data scientists and statisticians are often at odds when determining the best approach, machine learning or statistical modeling, to solve an analytics challenge. However, machine learning and statistical modeling are more cousins than…
A general theoretical framework is derived for the recently developed multi-state trajectory (MST) approach from the time dependent Schr\"odinger equation, resulting in equations of motion for coupled nuclear-electronic dynamics equivalent…
Trajectory mutual information is frequently used to quantify information transfer in biochemical systems. Tractable solutions of the trajectory mutual information can be obtained via the widely used Linear-Noise Approximation (LNA) using…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
The synthetic control method is a an econometric tool to evaluate causal effects when only one unit is treated. While initially aimed at evaluating the effect of large-scale macroeconomic changes with very few available control units, it…
We study a stochastic two-species chemical reaction system with two mechanisms. One mechanism consists of chemical interactions which govern the overall drift of species amounts in the system; the other mechanism consists of resampling,…
This paper investigates the role of size in biological organisms. More specifically, how the energy demand, expressed by the metabolic rate, changes according to the mass of an organism. Empirical evidence suggests a power-law relation…