Related papers: Extrusion of chromatin loops by a composite loop e…
We present several models of the magnetic structure of solar coronal mass ejections (CMEs). First, we model CMEs as expanding force-free magnetic structures. While keeping the internal magnetic field structure of the stationary solutions,…
An expurgating linear function (ELF) is a linear outer code that disallows the low-weight codewords of the inner code. ELFs can be designed either to maximize the minimum distance or to minimize the codeword error rate (CER) of the…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
Motivated by the well-known fractal packing of chromatin, we study the Rouse-type dynamics of elastic fractal networks with embedded, stochastically driven, active force monopoles and force dipoles that are temporally correlated. We…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
Organic solar cells (OSCs) have recently shown a rapid improvement in their performance, bringing power conversion efficiencies (PCEs) closer to the point where commercial applications of the technology become viable. However, the low…
Cell migration is crucial to many physiological and pathological processes. During migration, a cell adapts its morphology, including the overall morphology and nucleus morphology, in response to various cues in complex microenvironments,…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Previous studies have found that coronal loops have a nearly uniform thickness, which seems to disagree with the characteristic expansion of active region magnetic fields. This is one of the most intriguing enigmas in solar physics. We here…
We found evidence of dynamic scaling in the spreading of MDCK monolayer, which can be characterized by the Hurst exponent ${\alpha} = 0.86$ and the growth exponent ${\beta} = 0.73$, and theoretically and experimentally clarified the…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
The nuclear morphology of eukaryotic cells is determined by the interplay between the lamina forming the nuclear skeleton, the chromatin inside the nucleus and the coupling with the cytoskeleton. Nuclear alterations are often associated…
The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop…
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to…
A simple lattice model describing the recombination dynamics in visible light emitting porous Silicon is presented. In the model, each occupied lattice site represents a Si crystal of nanometer size. The disordered structure of porous…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Multi Expression Programming (MEP) is a Genetic Programming variant that uses linear chromosomes for solution encoding. A unique feature of MEP is its ability of encoding multiple solutions of a problem in a single chromosome. In this paper…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…