Related papers: Kinetic Model for a Threshold Filter in an Enzymat…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
Linear thresholding systems have been used as a model of neural activation and more recently proposed as a model of gene regulation. Here we exhibit linear thresholding systems whose dynamics produce surprisingly long cycles.
Linear thresholding systems have been used as a model of neural activation and have more recently been proposed as a model of gene activation. Deterministic linear thresholding systems can be turned into non-deterministic systems by the…
In this paper we address a general parameter estimation methodology for an extended biokinetic degradation model [1] for poorly degradable micropollutants. In particular we concentrate on parameter estimation of the micropollutant…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
In this paper we consider deterministic limits of molecular stochastic systems with finite and infinite degrees of freedom. The method to obtain the deterministic vector field is based on the continuum limit of such microscopic systems…
The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate…
We report the first systematic study of designed two-input biochemical systems as information processing gates with favorable noise-transmission properties accomplished by modifying the gate's response from convex shape to sigmoid in both…
In this paper, the event-triggered resilient filtering problem is investigated for a class of two-dimensional systems with asynchronous-delay under binary encoding-decoding schemes with probabilistic bit flips. To reduce unnecessary…
The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the…
We use linear stability analysis and hybrid lattice Boltzmann simulations to study the dynamical behaviour of an active nematic confined in a channel made of viscoelastic material. We find that the quiescent, ordered active nematic is…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
We study the mechanics of a reversible decohesion (unzipping) of an elastic layer subjected to quasi-static end-point loading. At the micro level the system is simulated by an elastic chain of particles interacting with a rigid foundation…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
In this paper, we investigate a mathematical modeling of biochemical processes which makes it possible to determine the adaptation of a biosystem to open environmental conditions.
Microorganisms have developed complex regulatory features controlling their reaction and internal adaptation to changing environments. When modeling these organisms we usually do not have full understanding of the regulation and rely on…
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental…
The paper proposes a modular-based approach to constraint handling in process optimization and control. This is partly motivated by the recent interest in learning-based methods, e.g., within bioproduction, for which constraint handling…