Related papers: Symmetries of Electrostatic Interaction between DN…
The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an…
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes,…
We report on our theoretical investigations of the electronic states in a DNA molecule. We have used a two-leg charge ladder model where electron-electron interactions and the electron spin have been taken into account. The energy spectra…
A novel class of non-local interactions between bosons is found to favor a crystalline Bose-Einstein condensation ground state. By using both low energy effective field theory and variational wavefunction method, we compare this state not…
Using the fact that the neutrino mixing matrix $U = U^\dagger_{e}U_{\nu}$, where $U_{e}$ and $U_{\nu}$ result from the diagonalisation of the charged lepton and neutrino mass matrices, we analyse the predictions based on the sum rules which…
Nuclear pairing interaction plays a crucial role in both macroscopic-microscopic and fully macroscopic descriptions of nuclei. In the present study we discuss different pairing interactions (monopole and delta pairing forces) and the…
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
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…
The formation of nanoscale domains (NDs) in correlated liquids and the emerging collective magnetic properties have been suggested as key mechanisms governing ion transport under external magnetic fields (eMFs). However, the molecular-level…
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…
We utilize few-level model systems to analyze the polarization and phase properties of below-threshold harmonics generated from aligned molecules. In a two-level system, we find that the phase of emitted harmonics undergoes a distinct…
We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
We study phase separation in mixed monolayers of neutral and highly negatively charged lipids, induced by the addition of divalent positively charged counterions. We find good agreement between experiments on mixtures of pip2 and sopc and…
Realistic models of magnetic reconnection in the solar chromosphere must take into account that the plasma is partially ionized and that plasma conditions within any two magnetic flux bundles undergoing reconnection may not be the same.…
We analytically examine the pair interaction for parallel, discrete helices of charge. Symmetry arguments allow for the energy to be decomposed into a sum of terms, each of which has an intuitive geometric interpretation. Truncated Fourier…
We consider the two-dimensional two-component plasma, or Coulomb gas, consisting of $N$ positive and $N$ negative charges with logarithmic interaction. We introduce a suitable regularization of the interaction by smearing the charges over a…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…