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In frameworks of the scaling theory of phase transitions and critical phenomena the quantitative dependence of macroscopic properties on nanostructural parameters in a polymeric material is revealed. The draw ratios at neck and at break are…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
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…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
Using high-resolution confocal rheometry, we study the shear profiles of well-entangled DNA solutions under large amplitude oscillatory shear (LAOS) in a rectilinear planar shear cell. With increasing Weissenberg number (Wi), we observe…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
\textbf{Background}: Identifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a…
How local stresses propagate through polymeric fluids, and, more generally, how macromolecular dynamics give rise to viscoelasticity are open questions vital to wide-ranging scientific and industrial fields. Here, to unambiguously connect…
Super-resolution microscopy is crucial for imaging sub-wavelength biological structures. However, most techniques rely on nonlinear saturation or stochastic switching of emitters, limiting imaging speed and increasing phototoxicity. Here,…
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to…
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…