Related papers: Modeling DNA loops using the theory of elasticity
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
The elastic properties of the double-stranded DNA handles used in optical tweezers experiments on biomolecules are customarily modeled by an extensible worm-like chain model. Fitting such model to experimental data however is no trivial…
The elasticity of DNA catenanes, i.e. multiply linked DNA rings, is investigated using the Gauss invariant as a minimal model for topology conservation. An effective elastic free energy as a function of the distance $R$ between segments…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical…
We propose an Ashkin-Teller like model for elastic response of DNA molecule to external force and torque. The base-stacking interaction is described in a simple and uniform way. We obtain the phase diagram of dsDNA, and in particular, the…
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
We study the influence of a structural disorder on the thermodynamical properties of 2D-elastic chains submitted to mechanical/topological constraint as loops. The disorder is introduced via a spontaneous curvature whose distribution along…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate 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.…
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…