Related papers: The End Restraint Method for Mechanically Perturbi…
Exploiting elastic instability in thin films has proven a robust method for creating complex patterns and structures across a wide range of lengthscales. Even the simplest of systems, an elastic membrane with a lattice of pores, under…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
The dynamics of a nucleate cell in shear flow is of great relevance in cancer cells and circulatory tumor cells where they dominate the dynamics of blood. Buoyed by the success of Giant Unilamellar vesicles in explaining the dynamics of…
We systematically investigate the neutron-skin thickness of neutron-rich nuclei within a compressible droplet model, which includes several parameters characterizing the surface tension and the equation of state (EOS) of asymmetric nuclear…
We propose a computational framework, Hetero-EUCLID, for segmentation and parameter identification to characterize the full hyperelastic behavior of all constituents of a heterogeneous material. In this work, we leverage the Bayesian-EUCLID…
We study different configurations of permanent magnets and ferromagnetic circuit, in order to optimize the magnetic field for the so-called ``magnetic tweezers'' technique, for studing mechanical properties of DNA molecules. The magnetic…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
In order to improve the accuracy of molecular dynamics simulations, classical force fields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a…
We had combined the Neukirch-Marko model that describes the extension, torque and supercoiling in single, stretched and twisted DNA of infinite contour length, with a form of the free energy suggested by Sinha and Samuels to describe short…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…
Atomically thin films, like transition metal dichalcogenides, can now be synthesized at wafer scale, achieving the same extreme aspect ratio (~10^8) that a sheet of paper would have if it covered an entire city. Yet, the intrinsic (i.e.…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
Transport of microscopic objects across biological membranes usually involves membrane deformation to enclose the object followed by detachment of the engulfed particle. However, in artificial membranes, this last topological remodelling…
Eukaryote cells have a flexible shape, which dynamically changes according to the function performed by the cell. One mechanism for deforming the cell membrane into the desired shape is through the expression of curved membrane proteins.…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…
The cell nucleus is enveloped by a complex membrane, whose wrinkling has been implicated in disease and cellular aging. The biophysical dynamics and spectral evolution of nuclear wrinkling during multicellular development remain poorly…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…