Related papers: Structuring of counterions around dna double helix…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
Molecular dynamics simulations are used to study the local dynamics of counterion-charged polymer association at charge densities above and below the counterion condensation threshold. Surprisingly, the counterions form weakly-interacting…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
Neutron and x-ray powder diffraction have been used to investigate the crystal structures of a sample of the newly-discovered superconducting sodium cobaltate deuterate compound with composition Na0.31(3)CoO2o1.25(2)D2O and its anhydrous…
The production of two double strand breaks in spatially separated locations on the DNA molecule can cause the loss of a whole DNA loop, which can be of substantial length depending on the geometrical position of the two damaged sites and…
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to ongoing experimental and theoretical…
Highly concentrated aqueous lithium chloride solutions were investigated by classical molecular dynamics (MD) and reverse Monte Carlo (RMC) simulations. At first MD calculations were carried out applying twenty-nine combinations of…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The electrostatic interactions of phosphate groups and counter ions critically affect the structure, function and reactivity of DNA or RNA. We present a joint experimental-theoretical investigation of dimethyl phosphate (DMP-) in aqueous…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in…
Aggregation of two oppositely charged colloids in salty water is studied. We focus on the role of Coulomb interaction in strongly asymmetric systems in which the charge and size of one colloid is much larger than the other one. In the…
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…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Understanding transport behavior in nanoconfined environments is critical to many natural and engineering systems, including cementitious materials, yet its molecular-level mechanisms remain poorly understood. Here, molecular dynamics (MD)…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…