Related papers: Molecular simulation analysis of structural variat…
The continuum-rod model has emerged as an efficient tool to describe the long-length-scale structural-deformations of DNA which are critical to understanding the nature of many biological processes such as gene expression. However, a…
We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane…
We study phase behaviours of lipid--bilayer vesicles functionalised by ligand--receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo…
We investigate pores in fluid membranes by molecular dynamics simulations of an amphiphile-solvent mixture, using a molecular coarse-grained model. The amphiphilic membranes self-assemble into a lamellar stack of amphiphilic bilayers…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…
Capillary thinning of polymeric fluids is central to biological and industrial processes, yet the mechanisms governing thinning dynamics remain unresolved, especially for semi-flexible polymers. Using ideal solutions of semi-flexible DNA,…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Complexes of cationic and neutral lipids and DNA (lipoplexes) are emerging as promising vectors for gene therapy applications. Their appeal stems from their non pathogenic nature and the fact that they self-assemble under conditions of…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them,…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has…
Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…
We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective…
Lipid nanoparticles (LNPs) are a leading platform in the delivery of RNA-based therapeutics, playing a pivotal role in the clinical success of mRNA vaccines and other nucleic acid drugs. Their performance in RNA encapsulation and delivery…
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…