Related papers: Spontaneous RNA condensation into nanoring structu…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to…
Predicting the spatial configuration of gas molecules in nanopores of shale formations is crucial for fluid flow forecasting and hydrocarbon reserves estimation. The key challenge in these tight formations is that the majority of the pore…
We investigate the self-assembly of amphiphilic nanocubes under rest and shear using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These particles combine both interaction and shape anisotropy, making them…
Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Nanoscale confinement of molecules in a fluid can result in enhanced viscosity, local fluidic order, or collective motion. Confinement also affects ion transport and/or the rate and equilibrium concentration in a chemical reaction, all of…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell $-$ functions that are inherently connected to their physical properties. A remarkable aspect of such condensates is that…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
The jumping-droplet condensation, namely the out-of-plane jumping of condensed droplets upon coalescence, has been a promising technical innovation in the fields of energy harvesting, droplet manipulation, thermal management, etc., yet is…
We review here the physics of capillary condensation of liquids in confined media, with a special regard to the application in nanotechnologies. The thermodynamics of capillary condensation and thin film adsorption are first exposed along…
RNA molecules in living cells form what look like liquid droplets formed by liquid/liquid phase separation. But unlike the molecules in conventional phase separating mixtures, RNA molecules are transported by molecular motors that consume…
We study the effects of droplet finite size on the structure of nanogel particles synthesized by random crosslinking of molecular polymers diluted in nanoemulsions. For this, we use a bead-spring computer model of polymer-like structures…
X-ray diffraction experiments were performed on MnO confined in mesoporous silica SBA-15 and MCM-41 matrices with different channel diameters. The measured patterns were analyzed by profile analysis and compared to numerical simulations of…