Related papers: Characterizing large scale base composition struct…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
We propose a new type of SPDEs, singular or with regularized noises, motivated by a study of the fluctuation of the density field in a microscopic interacting particle system. They include a large scaling parameter $N$, which is the ratio…
During hierarchical clustering, smaller masses generally collapse earlier than larger masses and so are denser on the average. The core of a small mass halo could be dense enough to resist disruption and survive undigested, when it is…
The large scale distribution of galaxies in the universe displays a complex pattern of clusters, super-clusters, filaments and voids with sizes limited only by the boundaries of the available samples. A quantitative statistical…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
We apply the scale-length method to several three dimensional samples of the Two degree Field Galaxy Redshift Survey. This method allows us to map in a quantitative and powerful way large scale structures in the distribution of galaxies…
We propose to consider nonlinear fluctuations in the theory of liquid $^{4}$He deforming the commutation relations between the generalized coordinates and momenta. Generalized coordinates are coefficients of density fluctuations of Bose…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Impact parameter dependent dipole models are ideal tools for investigating the spatial structure of the proton. We investigate the incoherent $ep$ cross section in exclusive $J/\psi$ photoproduction as measured by HERA, and find that as…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory…
The structural properties of dense random packings of identical hard spheres (HS) are investigated. The bond order parameter method is used to obtain detailed information on the local structural properties of the system for different…
The large-scale distribution of cold dark matter halos is generally assumed to trace the large-scale distribution of matter. In a universe with multiple types of matter fluctuations, as is the case with massive neutrinos, the relation…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
We address the relation between long range correlations and charge transfer efficiency in aperiodic artificial or genomic DNA sequences. Coherent charge transfer through the HOMO states of the guanine nucleotide is studied using the…
Supersonic turbulence results in strong density fluctuations in the interstellar medium (ISM), which have a profound effect on the chemical structure. Particularly useful probes of the diffuse ISM are the ArH$^+$, OH$^+$, H$_2$O$^+$…
On large scales galaxies and their halos are usually assumed to trace the dark matter with a constant bias and dark matter is assumed to trace the linear density field. We test these assumption using several large N-body simulations with…