Related papers: Viral genome structures are optimal for capsid ass…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…
While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present…
Two simple kinetic models of Quantum Size Effect-directed nanocluster self-assembly in circular atomic corrals are discussed. The models correspond to an adsorption (either a physisorption or a chemisorption) and an adsorption-diffusion…
Understanding heat transfer characteristics of phase change and enhancing thermal energy transport in nanoscale are of great interest in both theoretical and practical applications. In the present study, we investigated the nanoscale…
We model a macromolecule as an infinitely long Gaussian semi-flexible polymer chain and the conformations of the chain were realized in the nano cube using a cubic lattice. A modified version of the recursion relations is used to calculate…
Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n<72 identical…
In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
The ICTV develops, refines and maintains a universal virus taxonomy; Order is the highest taxon in the branching hierarchy of recognised viral taxa. Historically, ICTV (sub)committees have classified viruses on the basis of morphological…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…
Quantum thermodynamics is a promising route to unambiguous detections of Majorana bound states. Being fundamentally different from quantum transport, this approach reveals unique Majorana thermodynamic behavior and deepens our insight into…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
A method of Transitional Automorphic Mapping of the Genome on Itself (TAMGI) is aimed at combining detection and reconstruction of correlational and quasi-periodic motifs in the viral genomic RNA/DNA sequences. The motifs reconstructed by…
Particles with ligand-receptor contacts bind and unbind fluctuating "legs" to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such "nanoscale caterpillars" is a challenge, since binding events often…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between…
In cell membranes, proteins and lipids are organized into sub-micrometric nanodomains of varying size, shape and composition, performing specific functions. Despite their biological importance, the detailed morphology of these nanodomains…
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this…