Related papers: Transient crosslinking kinetics optimize gene clus…
Transient networks comprised of polymers connected by short-lived bonds are a common design theme for both biological and synthetic materials. Transient bonds can provide mechanical rigidity, while still allowing for visco-elastic flows on…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this…
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…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Cell motility and tissue morphogenesis depend crucially on the dynamic remodelling of actomyosin networks. An actomyosin network consists of an actin polymer network connected by crosslinker proteins and motor protein myosins that generate…
Network of nonlinear dynamical elements often show clustering of synchronization by chaotic instability. Relevance of the clustering to ecological, immune, neural, and cellular networks is discussed, with the emphasis of partially ordered…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
A review is given on the studies of formation of light clusters and heavier fragments in heavy-ion collisions at incident energies from several tens of MeV/nucleon to several hundred MeV/nucleon, focusing on dynamical aspects and on…
Living systems often exhibit internal driving: active, molecular processes drive nonequilibrium phenomena such as metabolism or migration. Active gels constitute a fascinating class of internally driven matter, where molecular motors exert…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…