Related papers: How Cations Change Peptide Structure
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated…
We employed density functional theory-based ab initio molecular dynamics simulations to examine the hydration structure of several common alkali and alkali earth metal cations. We found that the commonly used atom pairwise dispersion…
Ionic behaviors, including ion distributions and hydration characteristics at solid-liquid interfaces, are important research interests in many important applications, such as electric double-layer capacitors and water lubrication. Here, we…
Correlations between electrons and the effective dimensionality are crucial factors that shape the properties of an interacting electron system. For example, the onsite Coulomb repulsion, U, may inhibit, or completely block the intersite…
The electronic structure in unconventional superconductors holds a key to understand the momentum-dependent pairing interactions and the resulting superconducting gap function. In superconducting Fe-based chalcogenides, there have been…
We predict new forms of carbon consisting of one and two dimensional networks of interlinked single wall carbon nanotubes, some of which are energetically more stable than van der Waals packing of the nanotubes on a hexagonal lattice. These…
Advances in research have sparked an increasing curiosity in understanding the plasmonic excitation properties of molecular-scale systems. Polycyclic aromatic hydrocarbons, as the fundamental building blocks of graphene, have been…
Biological water is an ionic solution containing both monovalent and divalent ions. However, the effects of divalent ions on the dynamics of biological water remain largely unknown. Here, we investigate how the transport dynamics of water…
Hybrid perovskites with mixed organic cations such as methylammonium and formamidinium have attracted interest due to their improved stability and capability to tune their properties varying the composition. In this work we report on the…
The supramolecular assembly of lipids into bilayer membranes is essential for cellular structure and function. However, the impact of lipid structural variations such as acyl chain length, degree of unsaturation, and headgroup type on…
Physical quilities such as electronic, mechanical, thermal, and optical properties of Al and P codoped silicene forming AlSi$_6$P nanosheets are investigated by first-principle calculations within density functional theory. A particular…
The quantum size effect has a significant impact on electrons, such that it can even change their topologically protected properties. An example of this phenomenon is the gap opening in the topologically protected gapless surface state in…
A two-dimensional (2D) material, formed for example by a self-assembled molecular monolayer or by a single layer of a van der Walls material, can couple efficiently with photonic nanocavities, potentially reaching the strong coupling…
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (80%), RNA (10%), and a number of different proteins (10%). These nucleoid proteins act as regulators of gene expression…
Using confocal-microscopy we investigate the structure of binary mixtures of colloidal hard spheres with size ratio q=0.61. As a function of the packing fraction of the two particle species, we observe a marked change of the dominant…
Nanoparticle gels have attracted considerable attention due to their highly tunable properties. One strategy for producing nanoparticle gels involves using strong local attractions between polymeric molecules, such as DNA hybridization or…
Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely the formation of salt bridges between arginine residues in…
In this work, we addressed the effects of Y$^{3+}$ and Nd$^{3+}$ cations on the adsorption of the whey protein $\beta$-lactoglobulin (BLG) at air-water interfaces as a function of electrolyte concentration. Both cations caused very similar…
Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between…