Related papers: Molecular dynamics simulation of multivalent ion m…
We consider a hybrid atom-ion system consisting of a pair of bosons interacting with a single ion in a quasi-one-dimensional trapping geometry. Building upon a model potential for the atom-ion interaction developed in earlier theoretical…
Molecular dynamics simulations and integral equation calculations of a simple equimolar mixture of diatomic molecules and monomers interacting via attractive and repulsive short-range potentials show the existence of pattern formation…
Recent experiments measuring the electrical conductivity of DNA molecules highlight the need for a theoretical model of ion transport along a charged surface. Here we present a simple theory based on the idea of unbinding of ion pairs. The…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
We study the dynamics of the contact between a pair of surfaces (with properties designed to mimic ruthenium) via molecular dynamics simulations. In particular, we study the contact between a ruthenium surface with a single nanoasperity and…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
We consider the driven dynamics of a probe particle moving through an assembly of particles with competing long-range repulsive and short-range attractive interactions, which form crystal, stripe, labyrinth, and bubble states as the ratio…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
Interfaces between two fluids are ubiquitous and of special importance for industrial applications, e.g., stabilisation of emulsions. The dynamics of fluid-fluid interfaces is difficult to study because these interfaces are usually…
Using an Atomic Force Microscope (AFM) we measure the interaction between two identically charged silica surfaces in the presence of saline solution. For pure NaCl the interaction is always repulsive. Upon addition of cobalt hexamine ions,…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
Electrokinetic flows of an aqueous NaCl solution in nanochannels with negatively charged surfaces are studied using molecular dynamics (MD) simulations. The four transport coefficients that characterise the response to weak electric and…
Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond…
Recent advances in nanofluidics have enabled the confinement of water down to a single molecular layer. Such monolayer electrolytes show promise in achieving bio-inspired functionalities through molecular control of ion transport. However,…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
We simulate the dynamics, including laser cooling, of 3D ion crystals confined in a Penning trap using a newly developed molecular dynamics-like code. The numerical integration of the ions' equations of motion is accelerated using the fast…
The physical nature of a frequency shift of hydrogen valence vibrations in a water molecule due to its interaction with neighbor molecules has been studied. Electrostatic forces connected with the multipole moments of molecules are supposed…
When a mixture is confined, one of the phases can condense out. This condensate, which is otherwise metastable in the bulk, is stabilized by the presence of surfaces. In a sphere-plane geometry, routinely used in atomic force microscope…