Related papers: Viral genome structures are optimal for capsid ass…
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)…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains…
We propose a mesoscale model structure for the coronavirus nucleocapsid, assembled from the high resolution structures of the basic building blocks of the N-protein, CryoEM imaging and mathematical constraints for an overall quasi-spherical…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We report on the construction of multiarm colloidal molecules by tip-linking filamentous bacteriophages, functionalized either by biological engineering or chemical conjugation. The affinity for streptavidin of a genetically modified vector…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
A suspension of nanoparticles with very low volume fraction is found to assemble into a macroscopic cellular phase under the collective influence of AC and DC voltages. Systematic study of this phase transition shows that it was the result…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We study the microrheology of nanoparticle shells [Dinsmore et al. Science 298, 1006 (2002)] and viral capsids [Ivanovska et al. PNAS 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a…
Transport of microscopic objects across biological membranes usually involves membrane deformation to enclose the object followed by detachment of the engulfed particle. However, in artificial membranes, this last topological remodelling…
Self-assembly is a fundamental concept in biology and of significant interest to nanotechnology. Significant progress has been made in characterizing and controlling the properties of the resulting structures, both experimentally and…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…