Related papers: Modeling sRNA-regulated Plasmid Maintenance
The toxins associated with infectious diseases are potential targets for inhibitors which have the potential for prophylactic or therapeutic use. Many antibodies have been generated for this purpose, and the objective of this study was to…
Measurements of the thermal conductance of single-molecule junctions have recently been reported for the first time. It is presently unclear, how much the heat transport can be controlled through molecule-internal effects. The search for…
Cross-protection, which refers to a process whereby artificially inoculating a plant with a mild strain provides protection against a more aggressive isolate of the virus, is known to be an effective tool of disease control in plants. In…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Each and every biological function in living organism happens as a result of protein-protein interactions.The diseases are no exception to this. Identifying one or more proteins for a particular disease and then designing a suitable…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
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…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…
Collective excitations in topologically non-trivial systems have attracted considerable attention in recent years. Here we study plasmons in the Su-Schrieffer-Heeger model whose low-energy electronic band is only partially filled, such that…
The segregation of plasmids in a bacterial population is investigated. Hereby, a dynamical model is formulated in terms of a size-structured population using a hyperbolic partial differential equation incorporating non-local terms (the…
The interactions between tumor cells and the immune system play a crucial role in cancer evolution. In this study, we explore how these interactions influence cancer progression by modeling the relationships among naive T cells, effector T…
In vertebrates, insufficient availability of calcium and phosphate ions in extracellular fluids leads to loss of bone density and neuronal hyper-excitability. To counteract this problem, calcium ions are present at high concentrations…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
Some microbial organisms are known to randomly slip into and out of hibernation, irrespective of environmental conditions [1]. In a (genetically) uniform population a typically very small subpopulation becomes metabolically inactive whereas…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…