Related papers: Molecular simulation analysis of structural variat…
We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…
We present a theoretical study of the physical properties of cationic lipid-DNA (CL-DNA) complexes - a promising synthetically based nonviral carrier of DNA for gene therapy. The study is based on a coarse-grained molecular model, which is…
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…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
We introduce a simple model for DNA-cationic-lipid complexes in which galleries between planar bilayer lipid lamellae contain DNA 2D smectic lattices that couple orientationally and positionally to lattices in neighboring galleries. We…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
We advanced a previously reported model for the \textit{in situ} scattering data analysis of coexisting lipid domains in free-floating multilamellar vesicles. Based on the scattering density profile of the individual domains we considered…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
We consider DNA-cationic lipid complexes that form lamellar stacks of lipid bilayers with parallel DNA strands intercalated in between. We calculate the electrostatically induced elastic deformations of the lipid bilayers. It is found that…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the…
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 use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal model based on the physical idea that constraints…
The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid…
Recent advancements in deep learning-based modeling of molecules promise to accelerate in silico drug discovery. A plethora of generative models is available, building molecules either atom-by-atom and bond-by-bond or fragment-by-fragment.…
A cell dynamics method for domain separation of diblock copolymers (DBCPs) interacting with nanoparticles (NPs) whose diffusion coefficients depend on chain configuration is proposed for self-assembly of DBCP/NP composites. Increasing NP…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…