Related papers: Mesoscopic helical models for DNA
We present a family of Virtual Element Methods for three-dimensional linear elasticity problems based on the Hellinger-Reissner variational principle. A convergence and stability analysis is developed. Moreover, using the hybridization…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Neurocognitive disorders, such as Alzheimer's and Parkinson's, have a wide social impact. These proteinopathies involve misfolded proteins accumulating into neurotoxic aggregates. Mathematical and computational models describing the…
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…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
The equations for strands of rigid charge configurations interacting nonlocally are formulated on the special Euclidean group, SE(3), which naturally generates helical conformations. Helical stationary shapes are found by minimizing the…
Phase-field methods offer a versatile computational framework for simulating large-scale morphological evolution. However, the applicability and predictability of phase-field models are inherently limited by their ad hoc nature, and there…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
In this paper we have investigated, through computer simulations, dislocation nucleation and dislocation dynamics in a heterostructure system with the lattice-mismatch interface, i.e. a system with internal strain. In particular, we have…
The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
We develop a mesoscopic lattice model to study the morphology formation in interacting ternary mixtures with evaporation of one component. As concrete application of our model, we wish to capture morphologies as they are typically arising…
We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Magnetic gels are composite materials, consisting of a polymer matrix and embedded magnetic particles. Those are mechanically coupled to each other, giving rise to the magnetostrictive effects as well as to a controllable overall elasticity…