Related papers: Computational Insight into the Complexation of DNA…
Carrier dynamics in metallic nanostructures is strongly influenced by their confining dimensions. Gold nanoparticles of size $\sim 2$ nm lie at the boundary separating metallic and non-metallic behavior. In this work, we report carrier…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
We report the studies of ultrafast electron nanocrystallography on size-selected Au nanoparticles (2-20 nm) supported on a molecular interface. Reversible surface melting, melting, and recrystallization were investigated with dynamical…
Evolutionary algorithms have long been used for optimization problems where the appropriate size of solutions is unclear a priori. The applicability of this methodology is here investigated on the problem of designing a nano-particle (NP)…
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…
Gold clusters Aun of size n = 2 to 12 atoms were studied by the density-functional theory with an ab-initio pseudopotential and a generalized gradient approximation. Geometry optimizations starting from a number of initial candidate…
Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular…
High intrinsic mobility and small, biologically-compatible size make single-walled carbon nanotubes (SWNTs) in demand for the next generation of electronic devices. Further, the wide range of available bandgaps due to changes in diameter…
In this paper, we derive a variance-driven Local-Effect-Model ($\sigma$-LEM) to predict radiosensitization due to gold nanoparticles (AuNP). Assuming that the number of Au photo-ionisations scales strictly with particle volume…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
We examine theoretically coherent electron transport through the single-molecule magnet Mn$_{12}$, bridged between Au(111) electrodes, using the non-equilibrium Green's function method and the density-functional theory. We analyze the…
Nanoparticle (NP)-protein complexes exhibit the correct identity of NP in biological media. Therefore, protein-NP interactions should be closely explored to understand and to modulate the nature of NPs in medical implementations. This…
Assemblies of closely separated gold nanoparticles exhibit a strong collective plasmonic response due to coupling of the plasmon modes of the individual nanostructures. In the context of self-assembly of nanoparticles, closed packed 2D…
The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal…
Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesis involves a complex system of solvents, ligands, and copper…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…
Gold nanoparticles (GNPs) constitute a breakthrough in modern chemistry. The recent success in the synthesis and total structure determination of the precise-composition GNPs provides exciting opportunities for fundamental studies and…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…