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Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
The patterns observed on the body surface of living organisms have traditionally been attributed solely to ecological strategies. However, this study investigates a fascinating phenomenon in Pelodiscus sinensis, where patterns formed on the…
Layered materials (LMs) such as graphene or MoS$_2$ have recently attracted a great deal of interest. These materials offer unique functionalities due to their structural anisotropy characterized by weak van der Waals bonds along the…
A transfer matrix approach is used to study the electronic transport in graphene superlattices with long-range correlated barrier spacements. By considering the low-energy electronic excitations as massless Dirac fermions, we compute by…
Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
The elastic scattering of twisted electrons by diatomic molecules is studied within the framework of the non-relativistic first Born approximation. In this process, the coherent interaction of incident electrons with two molecular centers…
The linear-combination of fragment molecular orbitals with three-body correction (FMO3-LCMO) is examined for electron transfer (ET) coupling matrix elements and ET pathway analysis, with application to hole transfer between two triptophanes…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
We examine the ordering behavior of hard plate-like particle in a very narrow slit-like pore using the Parsons-Lee density functional theory and the restricted orientation approximation. We observe that the plates are orientationally…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…
The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional…
Understanding the nature of the interface between a biomaterial implant and the biological fluid is an essential step towards creating improved implant materials. This study examined a diamond-like carbon coating biomaterial, the surface…
Electron and hole separate-path transport is theoretically found in the pi-stacked organic layers and columns. This effect might be a solution for the charge recombination problem. The building molecules, named…
Laser writing with ultrashort pulses provides a potential route for the manufacture of three-dimensional wires, waveguides and defects within diamond. We present a transmission electron microscopy (TEM) study of the intrinsic structure of…
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this currently…