Related papers: Robust replication initiation from coupled homeost…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Homologous recombination facilitates the exchange of genetic material between homologous DNA molecules. This crucial process requires detecting a specific homologous DNA sequence within a huge variety of heterologous sequences. The…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We have developed a method combining microfluidics, time-lapsed single-molecule microscopy and automated image analysis allowing for the observation of an excess of 3000 complete cell cycles of exponentially growing Escherichia coli cells…
We consider an epidemiological model that includes waning and boosting of immunity. Assuming that repeated exposure to the pathogen fully restores immunity, we derive an SIRS-type model with discrete and distributed delays. First we prove…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
The tryptophan (trp) operon in E. coli codes for the proteins responsible for the synthesis of the amino acid tryptophan from chorismic acid, and has been one of the most well-studied gene networks since its discovery in the 1960s. The…
In permissive environments, E. coli can double its dry mass every 21 minutes. During this time, ribosomes, RNA polymerases, and the proteome are all doubled. Yet, the question of how to relate bacterial doubling time to other biologically…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
A major challenge in synthetic genetic circuit development is the inter-dependency between heterologous gene expressions by circuits and host's growth rate. Increasing heterologous gene expression increases burden to the host, resulting in…
Erythropoiesis is a mechanism for the production of red blood cells by cellular differentiation. It is based on amplification steps due to an interplay between renewal and differentiation in the successive cell compartments from stem cells…
The lac operon in Escherichia coli has been studied extensively and is one of the earliest gene systems found to undergo both positive and negative control. The lac operon is known to exhibit bistability, in the sense that the operon is…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Stochastic resonance is a counter-intuitive concept[1,2], ; the addition of noise to a noisy system induces coherent amplification of its response. First suggested as a mechanism for the cyclic recurrence of ice ages, stochastic resonance…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Developing networks of neural systems can exhibit spontaneous, synchronous activities called neural bursts, which can be important in the organization of functional neural circuits. Before the network matures, the activity level of a burst…