Related papers: Chirality modifies the interaction between knots
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Coarse-grained simulations are used to demonstrate that knotted filaments in shear flow at zero Reynolds number exhibit remarkably rich dynamic behaviour. For stiff filaments that are weakly deformed by the shear forces, the knotted…
An extensive study of single block copolymer knots containing two kinds of monomers $A$ and $B$ is presented. The knots are in a solution and their monomers are subjected to short range interactions that can be attractive or repulsive. In…
We optimize the nucleon-nucleon interaction from chiral effective field theory at next-to-next- to-leading order. The resulting new chiral force NNLOopt yields \chi^2 \approx 1 per degree of freedom for laboratory energies below…
The origin and function of chirality in DNA, proteins, and other building blocks of life represent a central question in biology. Observations of spin polarization and magnetization associated with electron transport through chiral…
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…
We study a two-dimensional chiral active crystal composed of underdamped chiral active particles. These particles, characterized by intrinsic handedness and persistence, interact via linear forces derived from harmonic potentials. Chirality…
A model for filament buckling at finite temperatures is presented. Starting from the classical worm-like chain model under constant compression, we use a mean-field approach for filament inextensibility to find the complete partition…
We use computer simulations to compare the dynamical behaviour of torus and even-twist knots in polymers under tension. The knots diffuse through a mechanism similar to reptation. Their friction coefficients grow linearly with average knot…
The interaction between intense light-matter not only promotes emerging applications in quantum and nonlinear optics but also facilitates changes in material properties. Plasmons can significantly enhance not only molecular chirality but…
We consider the ground state and the elementary excitations of an array of spin-Peierls chains coupled by elastic and magnetic interactions. It is expected that the effect of the magnetic interchain coupling will be to reduce the…
The spin dynamics of electrons in chiral molecular systems remain a topic of intense interest, particularly regarding whether geometric chirality inherently induces spin polarization in current-carrying electrons. In this work, we employ ab…
Chirality, an intrinsic handedness, is one of the most intriguing fundamental phenomena in nature. Materials composed of chiral molecules find broad applications in areas ranging from nonlinear optics and spintronics to biology and…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The assembly of filamentous bundles with controlled diameters is common in biological systems and desirable for the development of nanomaterials. We discuss dynamical simulations and free energy calculations on patchy spheres with chiral…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…