Related papers: Microscopic Pathways to Helix Formation: Packing S…
The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…
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…
Generic interactions e.g. the Coulomb or other long ranged radially symmetric repulsive interactions between monomers of bead-spring model of a semi-flexible polymer induce instabilities in a initially straight polymer chain to form long…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Recently, it has been demonstrated [Magee et al., Phys. Rev. Lett. 96, 207802 (2006)] that isolated, square-well homopolymers can spontaneously break chiral symmetry and freeze into helical structures at sufficiently low temperatures. This…
Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…
The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, helix has a unique position. Helical structures are ubiquitous in nature and a helical shape…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
We present a molecular simulation study of the structure of linear dendronized polymers. We use excluded volume interactions in the context of a generic coarse-grained molecular model whose geometrical parameters are tuned to represent a…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical…
Using Langevin simulations, we find that simple 'generic' bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The…
We investigate the sedimentation of chiral particles in viscous fluid flow. We identify helical ribbons as simple particles with strong translation-rotation coupling whose symmetry ensures that the centers of mass, buoyancy, resistance, and…
Intimately connected to the rule of life, chirality remains a long-time fascination in biology, chemistry, physics and materials science. Chiral structures, e.g., nucleic acid and cholesteric phase developed from chiral molecules are common…
We investigate the emergence of chiral meso-structures in one-dimensional fluids consisting of stacked discotic particles and demonstrate that helical undulations are generated spontaneously from internal elastic stresses. The stability of…
The helix is a ubiquitous motif for biopolymers. We propose a heuristic, entropically based model that predicts helix formation in a system of hard spheres and semiflexible tubes. We find that the entropy of the spheres is maximized when…
We propose a potential for wormlike polymer chains which can be used to model the low-temperature conformational structures. We successfully reproduced helix ground states up to 6.5 helical loops, using the multicanonical Monte Carlo…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We study the phase behaviour of cholesteric liquid crystal shells with different geometries. We compare the cases of tangential and no anchoring at the surface, focussing on the former case, which leads to a competition between the…