Related papers: Multi-shell model of ion-induced nucleic acid cond…
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological…
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important…
The hypothesis of composite $XHe$ dark atoms offers a compelling framework to address the challenges in direct dark matter particles detection, as their neutral, atom-like configuration evades conventional experimental signatures. A…
We formulate a general three-dimensional semiclassical model for the study of correlated multielectron escape during fragmentation of molecules driven by intense infrared laser pulses, while fully accounting for the magnetic field of the…
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…
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…
In recent years, short DNA duplexes have been studied as an interesting self-assembling system and a building block for DNA-based nanotechnologies. Numerical simulation studies for the determination of the full phase diagram of short…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
We formulate a three-dimensional semi-classical model to treat three-electron escape dynamics in a strongly-driven linear triatomic molecule, HeH$_{2}^{+}$. Our model includes the Coulomb singularities. Hence, to avoid unphysical…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative…
Graphite is a ubiquitous electrode material with particular promise for use in e.g., energy storage and desalination devices, but very little is known about the properties of the graphite-electrolyte double layer at technologically relevant…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Tasker type III polar terminations of ionic crystals carry a net surface charge as well as a dipole moment and are fundamentally unstable. In contact with electrolytes, such polar surfaces can be stabilized by adsorption of counter ions…
We introduce a shell-model theory that combines traditional spherical states, which yield a diagonal representation of the usual single-particle interaction, with collective configurations that track deformations, and test the validity of…
In this study, molecular dynamic simulations are employed to investigate the nucleation of NaCl crystal in solutions. According to the simulations, the dissolved behaviors of NaCl in water are dependent on ion concentrations. With…
Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets…
Electrochemical devices often consist of multicomponent electrolyte solutions. Two processes influence the overall dynamics of these devices: the formation of electrical double layers and chemical conversion due to redox reactions. However,…
The shell correction is proposed in the improved isospin dependent quantum molecular dynamics (ImIQMD) model, which plays an important role in heavy-ion fusion reactions near Coulomb barrier. By using the ImIQMD model, the static and…