Related papers: The End Restraint Method for Mechanically Perturbi…
Atomic-resolution imaging with scanning transmission electron microscopy is a powerful tool for characterizing the nanoscale structure of materials, in particular features such as defects, local strains, and symmetry-breaking distortions.…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
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…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
Using molecular simulations and a modified Classical Nucleation Theory, we study the nucleation, under flow, of a variety of liquids: different water models, Lennard-Jones and hard sphere colloids. Our approach enables us to analyze a wide…
Wrinkling of an inextensible elastic lining of an inner-lined tube under imposed pressure is considered. A simple equation modeling the elastic properties of the lining, the pressure, and the soft-substrate forces is derived. This equation…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
A detailed investigation of the structural and vibrational properties of various prestressed silicon nitride membranes patterned with one-dimensional photonic crystal structures is presented. The tensile stress-related deformation of the…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing…