Related papers: Structure of DNA-Functionalized Dendrimer Nanopart…
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide…
The rapid development of fabrication of functional high-quality graphene-like nanoribbons has increasingly reliant on integration of diverse nanofabrication platforms. The demand for innovative techniques to enable the exploration and…
The increasing threat of uranium contamination to environmental and human health due to its radiotoxicity demands the development of novel and efficient adsorbents for remediation. In this study, we investigated the potential of…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance…
The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
Optimal characterization of the mechanical properties of both cells and their surrounding is an issue of major interest. Indeed, cell function and development are strongly influenced by external stimuli. Furthermore, a change in cell…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
Dendronized polymers consist of an elastic backbone with a set of iterated branch structures (dendrimers)attached at every base point of the backbone. The conformations of such molecules depend on the elastic deformation of the backbone and…
We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC)…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Surface enhanced Raman scattering (SERS) process results in a tremendous increase of Raman scattering cross section of molecules adsorbed to plasmonic metals and influenced by numerous physico-chemical factors such as geometry and optical…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
Using density functional theory calculations, we investigated the properties of few-layer silicene nanosheets, namely bilayers and trilayers, functionalized with group-III or group-V atoms of the periodic table. We considered the…