Related papers: Modeling sRNA-regulated Plasmid Maintenance
Discrete-time models are the traditional approach for capturing population dynamics of a host-parasitoid system. Recent work has introduced a semi-discrete framework for obtaining model update functions that connect host-parasitoid…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Transforming Growth Factor-beta (TGF-beta) signalling is an important regulator of cellular growth and differentiation. The principal intracellular mediators of TGF-beta signalling are the Smad proteins, which upon TGF-beta stimulation…
We model, analyze, and simulate a novel run-and-tumble model with autochemotaxis, biologically inspired by the phytoplankton Heterosigma akashiwo. Developing a fundamental understanding of planktonic movements and interactions through…
A bacterial colony may develop a small number of cells genetically identical to, but phenotypically different from other normally growing bacteria. These so-called persister cells keep themselves in a dormant state and thus are insensitive…
Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, differentiation…
This paper presents a predictive control strategy based on neural network model of the plant is applied to Continuous Stirred Tank Reactor (CSTR). This system is a highly nonlinear process; therefore, a nonlinear predictive method, e.g.,…
The phenomenon of cell sorting/segregation, by which cells organise spatially into clusters of specific cell type or function, is essential for tissue morphogenesis. This self-organization process involves an interplay between mechanical,…
Along the pathogenesis of Mycobacterium Tuberculosis (MTB), hypoxia-induced dormancy is a process involving the oxygen-depleted environment encountered inside the lung granuloma, where bacilli enter a viable, non-replicating state termed as…
The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
In order to contribute to the understanding of runaway electron generation mechanisms during tokamak disruptions, a test particle tracker is introduced in the JOREK 3D non-linear MHD code, able to compute both full and guiding center…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
Many studies have shown that the protection of the host $\it{Acyrthosiphon~pisum}$ (Hemiptera, Aphididae) against the parasitoid $\it{Aphidius~ervi}$ (Hymenoptera, Braconidae) is conferred by the interaction between the secondary…
Coherent control of OH-free radicals interacting with the spin-triplet state of a DNA molecule is investigated. A model Hamiltonian for molecular spin singlet-triplet resonance is developed. We illustrate that the spin-triplet state in DNA…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
The ability of water to dissolve biomolecules is crucial for our life. It has been shown that protein has a profound effect on the behavior of water in its hydration shell, which in turn affects the structure and function of the protein.…
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…
We present a general framework to study the effect of killing sources on moving particles, trafficking inside biological cells. We are merely concerned with the case of spine-dendrite communication, where the number of calcium ions, modeled…