Related papers: A structural model for the Coronavirus Nucleocapsi…
Nucleic acids such as mRNA have emerged as a promising therapeutic modality with the capability of addressing a wide range of diseases. Lipid nanoparticles (LNPs) as a delivery platform for nucleic acids were used in the COVID-19 vaccines…
A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human, and human-to-animal transmission of…
This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types…
A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that consitute the capsids and…
One of the frontiers of nanotechnology is advancing beyond the periodic self-assembly of materials. Icosahedral quasicrystals, aperiodic in all directions, represent one of the most challenging targets that have yet to be experimentally…
Blueprints of polyhedral cages with icosahedral symmetry made of circular DNA molecules are provided. The basic rule is that every edge of the cage is met twice in opposite directions by the DNA strand, and vertex junctions are realised by…
A new approach to solve quasicrystalline atomic structures in 3-dimensional (3D) real space is presented: The atomic pair distribution function (PDF) of face centred icosahedral Ho9Mg26Zn65 [a(6D) = 2x5.18(3)A was obtained from in-house…
When a thin sheet is crushed into a small three-dimensional volume, it invariably forms a structure with a low volume fraction but high resistance to further compression. Being a far-from-equilibrium process, forced crumpling is not…
Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole…
Spherical multi-layered structures are prevalent in numerous biological systems and engineered applications, including tumor spheroids, layered tissues, and multi-shell nanoparticles for targeted drug delivery. Despite their widespread…
An explicit quark model, based on a mean field description of non-overlapping nucleon bags bound by the self-consistent exchange of $\sigma$, $\omega$ and $\rho$ mesons, is used to investigate the properties of both nuclear and neutron…
Creating materials with structure that is independently controllable at a range of scales requires breaking naturally occurring hierarchies. Breaking these hierarchies can be achieved via the decoupling of building block attributes from…
In a recent computational study, we found highly structured ground states for coarse-grained polymers adsorbed to ultrathin nanowires in a certain model parameter region. Those tubelike configurations show, even at a first glance, exciting…
Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Nanoscrolls consist of sheets rolled up into a papyrus-like form. Their open ends produce great radial flexibility, which can be exploited for a large variety of applications, from actuators to hydrogen storage. They have been successfully…
The building blocks of life, amino acids and nucleobases, are believed to have been synthesized in the extreme conditions that prevail in space starting from simple molecules containing hydrogen, carbon, oxygen and nitrogen. However, the…
The sharp rise in medical tomography examinations has created a demand for automated systems that can reliably extract informative features for downstream tasks such as tumor characterization. Although 3D volumes contain richer information…