Related papers: Arginine-Phosphate Salt Bridges Between Histones a…
The emerging interest in van der Waals heterostructures as new materials for opto-electronics and photonics poses questions about their stability and structure-property relations. In the framework of density-functional and many-body…
Salt bridges are known to be important for the stability of protein conformation, but up to now it has been difficult to study their geometry in solution. Here we characterize the spatial structure of a model salt bridge between guanidinium…
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the…
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,…
Atomic Force Microscopy analysis is employed to study the geometrical and topological properties of $3000$kbp DNA molecules fixed in mica substrates with $MgCl_{2}$. We found that the aggregates on the substrate surface for certain salt…
The interactions between different layers in van der Waals heterostructures have a significant impact on the electronic and optical characteristics. By utilizing the intrinsic dipole moment of Janus transition metal dichalcogenides (TMDs),…
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the…
The role of defects in van der Waals heterostructures made of graphene and hexagonal boron nitride (h-BN) is studied by a combination of ab initio and model calculations. Despite the weak van der Waals interaction between layers, defects…
We performed density functional theory (DFT) calculations for a bi-layered heterostructure combining a graphene layer with a MoS2 layer with and without intercalated Li atoms. Our calculations demonstrate the importance of the van der Waals…
The first principles approaches, density functional theory (DFT) and quantum Monte Carlo, have been used to examine the balance between van der Waals (vdW) forces and hydrogen (H) bonding in ambient and high pressure phases of ice. At…
The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD)…
We investigate interlayer adhesion and relaxation at interfaces between graphene and hexagonal boron nitride (hBN) monolayers in van der Waals heterostructures. The adhesion potential between graphene and hBN is calculated as a function of…
Density functional theory is used to investigate the interactions between a layer of magnesium hydroxide, Mg(OH)2, the magnesium (Mg) surface Mg(0001), and the three amino acids glycine, proline and glutamine. The aim is to improve the…
We report first-principles calculations for a ferroelectric organic crystal of phenazine and chloranilic acid molecules. Weak intermolecular interactions are properly treated by using a second version of van der Waals density functional…
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…
We used the binding energy-bond-charge model to study the atomic bonding and electrical properties of the two-dimensional graphene/BN van der Waals heterostructure. We manipulated its atomic bonding and electrical properties by…
The two-dimensional transition metal carbide/nitride family (MXenes) has garnered significant attention due to their highly customizable surface functional groups. Leveraging modern material science techniques, the customizability of MXenes…
Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…