Related papers: Molecular dynamics simulation of multivalent ion m…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
We examine the effective force between two nanometer scale solutes in water by Molecular Dynamics simulations. Macroscopic considerations predict a strong reduction of the hydrophobic attraction between solutes when the latter are charged.…
Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents, provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics…
Using molecular dynamics simulations, we have determined that the nature of dynamical heterogeneity in jammed liquids is very sensitive to short-ranged attractions. Weakly attractive systems differ little from dense hard-sphere and…
In solution, electrically like-charged particles can experience a strong and long-ranged attraction that leads to the formation of stable, slowly reorganizing clusters. The attractive force underpinning this spontaneous organization process…
Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
The nucleation of gas hydrates is of great interest in flow assurance, global energy demand, and carbon capture and storage. A complex molecular understanding is critical to control hydrate nucleation and growth in the context of potential…
We investigate the dynamics of colloids at a fluid interface driven by attractive capillary interactions. At submillimeter length scales, the capillary attraction is formally analogous to two-dimensional gravity. In particular it is a…
Chemistry occurring at or near the surfaces of aqueous droplets and thin films in the atmosphere influences air quality and climate. Molecular dynamics simulations are becoming increasingly useful for gaining atomic-scale insight into the…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
We study colloidal particle dynamics of a model glass system using confocal and fluorescence microscopy as the sample evolves from a hard-sphere glass to a liquid with attractive interparticle interactions. The transition from hard-sphere…
Using molecular dynamic simulations we study a system of particles interacting through a continuous core-softened potentials consisting of a hard core, a shoulder at closest distances and an attractive well at further distance. We obtain…
We study closed liquid membranes that segregate into three phases due to differences in the chemical and physical properties of its components. The shape and in-plane membrane arrangement of the phases are coupled through phase-specific…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
In this work we investigate the Fe$_3$O$_4$(001) surface/water interface by combining several theoretical approaches, ranging from a hybrid functional method (HSE06) to density-functional tight-binding (DFTB) to molecular mechanics (MM).…
The 3'-monofunctional adduct of cisplatin and d(CTCTG*G*TCTC)2 duplex DNA in solvent with explicit counter ions and water molecules were subjected to MD- simulation with AMBER force field on a nanosecond time scale. In order to simulate the…
One of the most progressive methods of cancer treatment is ion beam therapy. The simulations of water radiolysis show that in the cell medium the most long-living species are hydrogen peroxide (H$_2$O$_2$) molecules. But up to the present…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…