Related papers: Characterising DNA T-motifs by Simulation and Expe…
Layered two-dimensional (2D) materials exhibit unique properties, expanding opportunities in material design. We investigate MX$_2$ transition metal dichalcogenides (TMDCs) (M = Mo, W; X = S, Se, Te) in homo- and heterobilayers with…
For layered materials, the interlayer stacking is a critical degree of freedom tuning electronic properties, while its microscopic characterization faces great challenges. The transition-metal dichalcogenide 1T-TaS$_2$ represents a novel…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…
DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
Coupling between axial and torsional degrees of freedom often modifies the conformation and expression of natural and synthetic filamentous aggregates. Recent studies on chiral single-walled carbon nanotubes and B-DNA reveal a reversal in…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we…