Related papers: Fine Structure of Viral dsDNA Encapsidation
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
The complex physics of self-assembly in colloidal crystals on deformable interfaces and surfaces poses interesting possibilities for the designability and synthesis of next-generation metamaterials. The goal of this article is to…
Disclination configurations of a nematic liquid crystal are studied within a self-consistent molecular field theory. The theory is based on a tensor order parameter, and can accommodate anisotropic elastic energies without the known…
The ordering of rod-like particles in soft, deformable containers emerges from the interplay of anisotropic interactions, geometric confinement, and boundary compliance. This competition couples internal particle organization to container…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
We investigate the flat phase of $D$-dimensional crystalline membranes embedded in a $d$-dimensional space and submitted to both metric and curvature quenched disorders using a nonperturbative renormalization group approach. We identify a…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Spherical particles confined to a sphere surface cannot pack densely into a hexagonal lattice without defects. In this study, we use hard particle Monte Carlo simulations to determine the effects of continuously deformable shape anisotropy…
The ordering matrix, which was originally introduced by de Gennes, is a well-known mathematical device for describing orientational order of biaxial nematic liquid crystal. In this paper we propose a new interpretation of the ordering…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
How condensed-matter simulations depend on the number of molecules being simulated ($N$) is sometimes itself a valuable piece of information. Liquid crystals provide a case in point. Light scattering and $2d$-IR experiments on…
We present a combined x-ray diffraction and infrared spectroscopy study on the phase behavior and molecular dynamics of n-hexadecanol in its bulk state and confined in an array of aligned nanochannels of 8 nm diameter in mesoporous silicon.…
We calculate the entropic part of partition function of a bubble embedded in a double stranded DNA (dsDNA) by considering the total weights of possible configurations of a system of two single stranded DNA (ssDNA) of given length which…
Brownian motion provides access to hydrodynamic properties of nanoscale objects independent of their optical resolvability. Here, we present a diffusion-based approach to infer effective particle size distributions of DNA-functionalized…
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Local bond order parameters based on spherical harmonics, also known as Steinhardt order parameters, are often used to determine crystal structures in molecular simulations. Here we propose a modification of this method in which the complex…
In this paper we present a three-dimensional discrete model governing the deformation of a viral capsid, modelled as a regular icosahedron and subjected not to cross a given flat rigid surface on which it initially lies in correspondence of…