Related papers: Modeling sRNA-regulated Plasmid Maintenance
Harnessing the topology of ring polymers as a design motif in functional nanomaterials is becoming a promising direction in the field of soft matter. For example, the ring topology of DNA plasmids prevents the relaxation of excess twist…
Studies on the role of fluctuations in signal propagation and on gene regulation in monoclonal bacterial population have been extensively pursued based on the machinery of two-component system. The bacterial two-component system shows noise…
Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial…
Nuclear pore complexes are constantly confronted by large fluxes of macromolecules and macromolecular complexes that need to get into and out of the nucleus. Such bi-directional traffic occurring in a narrow channel can easily lead to…
The SARS-CoV-2 RNA pseudoknot is a promising target for antiviral intervention, as it regulates the efficiency of $-$1 programmed ribosomal frameshifting ($-$1 PRF), a mechanism that is essential for viral protein synthesis. The pseudoknot…
We propose a numerical method for the Vlasov-Poisson-Fokker-Planck model written as an hyperbolic system thanks to a spectral decomposition in the basis of Hermite functions with respect to the velocity variable and a structure preserving…
For predicting cancer survival outcomes, standard approaches in clinical research are often based on two main modalities: pathology images for observing cell morphology features, and genomic (e.g., bulk RNA-seq) for quantifying gene…
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…
Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counter-defense mechanisms of specific phages. These…
Non Regression Testing (NRT) aims to check if software modifications result in undesired behaviour. Suppose the behaviour of the application previously known, this kind of test makes it possible to identify an eventual regression, a bug.…
The formation of Internal Transport Barrier (ITB) is studied in HL-2A plasmas by means of nonlinear gyrokinetic simulations. A new paradigm for the ITB formation is proposed in which different physics mechanisms play a different role…
Chemotaxis is a fundamental guidance mechanism of cells and organisms, responsible for attracting microbes to food, embryonic cells into developing tissues, immune cells to infection sites, animals towards potential mates, and…
Machine learning models of cellular interaction dynamics hold promise for understanding cell behavior. Natural killer (NK) cell cytotoxicity is a prominent example of such interaction dynamics and is commonly studied using time-resolved…
We develop a time and space dependent predator-prey model. The predators' equation is a non local hyperbolic balance law, while the diffusion of prey obeys a parabolic equation, so that predators "hunt" for prey, while prey diffuse. A…
Despite their dynamic nature, certain chromatin marks must be maintained over the long term. This is particulary true for histone 3 lysine 9 (H3K9) trimethylation, that is involved in the maintenance of healthy differentiated cellular…
This paper studies the decay of an objective functional using a new control technique within Pontryagin's framework. Convergence analysis is carried out on the infinite-dimensional space of Tokamak plasma dynamical state as described by…
It is shown, that plasmonic metamaterial nanostructures could be used to reduce the electron-phonon scattering rate, by providing an alternative, fast electron-plasmon scattering channel. Since the plasmon-phonon and plasmon-photon…
Myxobacteria aggregate and generate fruiting bodies in the soil to survive under starvation conditions. Considering soil as a porous medium, the biological mechanism and dynamic behavior of myxobacteria and slime (chemoattractants) affected…
Plasmids are major players in Horizontal Gene Transfer mechanisms, hence they are highly variable in their gene content and length. We propose a model for the fitness of a plasmid as a function of its length, which predicts diminishing…
Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or…