Related papers: Spontaneous Domain Formation in Spherically-Confin…
A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and…
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…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
Inspired to understand the complex spectrum of space-filling organizations the dsDNA genome within the capsid of bacterial viruses, we study a minimal, coarse-grained model of single chains densely-packed into a finite spherical volume. We…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
Competing ground states may lead to topologically constrained excitations such as domain walls or quasiparticles, which govern metastable states and their dynamics. Domain walls and more exotic topological excitations are well studied in…
Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
Bose-Einstein condensates of dilute atomic gases, characterized by a macroscopic population of the quantum mechanical ground state, are a new, weakly interacting quantum fluid. In most experiments condensates in a single weak field seeking…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance…
Observations indicate galaxies are distributed in a filament-dominated web-like structure. Numerical experiments at high and low redshift of viable structure formation theories also show filament-dominance. We present a simple quantitative…
Electrostatic interactions play a central role in the assembly of single-stranded RNA viruses. Under physiological conditions of salinity and acidity, virus capsid assembly requires the presence of genomic material that is oppositely…
Polymer filaments form the foundation of biology from cell scaffolding to DNA. Their study and fabrication play an important role in a wide range of processes from tissue engineering to molecular machines. We present a simple method to…
Electroporation is a physical method to induce the uptake of therapeutic drugs and DNA, by eukaryotic cells and tissues. The phenomena behind electro-mediated membrane permeabilization to plasmid DNA have been shown to be significantly more…
We investigate ordering properties of two-dimensional granular materials using several shapes created by welding ball bearings together. Ordered domains form much more easily in two than in three dimensions, even when configurations lack…
Spherical confinement can act either stabilizing or destabilizing on the collapsed state of a semi-flexible polymer. General free-energy arguments suggest that the order of the unconstrained collapse transition is the distinguishing factor:…