Related papers: Irregular model DNA particles self-assemble into a…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
DNA Self-Assembly has emerged as an interdisciplinary field with many intriguing applications such DNA bio-sensor, DNA circuits, DNA storage, drug delivery etc. Tile assembly model of DNA has been studied for various computational…
In 1987-89 were synthesized soluble nano-composites of polyacetylene (NPA) with an abnormally high intensity of Raman scattering and high stability under laser radiation. Here we demonstrate that the key pre-condition to the outstanding…
We examine nanoparticles (NPs) forming polyhedral sections of the ideal cubic lattice, simple (sc), body centered (bcc), and face centered (fcc) cubic, which are confined by facets characterized by densest and second densest {h k l}…
We say that a triangle $T$ tiles a polygon $A$, if $A$ can be dissected into finitely many nonoverlapping triangles similar to $T$. We show that if $N>42$, then there are at most three nonsimilar triangles $T$ such that the angles of $T$…
We investigate finite 3-nets embedded in a projective plane over a (finite or infinite) field of any characteristic p. Such an embedding is regular when each of the three classes of the 3-net comprises concurrent lines, and irregular…
The surface curvature of membranes, interfaces, and substrates plays a crucial role in shaping the self-assembly of particles adsorbed on these surfaces. However, little is known about the interplay between particle anisotropy and surface…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
In this thesis the formation and properties of a polymer gel on and at a surface are investigated. The gel under investigation is defined as a three-dimensional network of "phantom" macromolecules that form permanent links with one another…
From the perspective of network analysis, the ubiquitous networks are comprised of regular and irregular components, which makes uncovering the complexity of network structures to be a fundamental challenge. Exploring the regular…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and…
We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the…
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…