Related papers: Compound Poisson Statistics and Models of Clusteri…
We explore the effects of overdispersed DNA lesion distribution on the shapes of cell surviving curves of mammalian cells exposed to hadrons at various doses. To provide a theoretical framework in resolving discrepancies between…
Classically, Bayesian clustering interprets each component of a mixture model as a cluster. The inferred clustering posterior is highly sensitive to any inaccuracies in the kernel within each component. As this kernel is made more flexible,…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
We address theoretically aggregation of DNA segments by multivalent polyamines such as spermine and spermidine. In experiments, the aggregation occurs above a certain threshold concentration of multivalent ions. We demonstrate that the…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
Clustering is one of the most widely used procedures in the analysis of microarray data, for example with the goal of discovering cancer subtypes based on observed heterogeneity of genetic marks between different tissues. It is well-known…
Epigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
The production of two double strand breaks in spatially separated locations on the DNA molecule can cause the loss of a whole DNA loop, which can be of substantial length depending on the geometrical position of the two damaged sites and…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The Poisson distribution is the probability distribution of the number of independent events in a given period of time. Although the Poisson distribution appears ubiquitously in various stochastic dynamics of gene expression, both as…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable worm-like chain model. Here we show, by means of analytical results and computer…
$\alpha$-clustering study since the pioneering discovery of $^{12}$C+$^{12}$C molecular resonances half a century ago. Our knowledge on physics of nuclear molecules has increased considerably and nuclear clustering remains one of the most…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
We present a comprehensive approach to the modeling, performance analysis, and design of clustered molecular nanonetworks in which nano-machines of different clusters release an appropriate number of molecules to transmit their sensed…