Related papers: A Minimal Model of B-DNA
We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte…
Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN$^-$, K$^+$ and acetamide is improved vis-a-vis experimentally measured properties. Given…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
In this paper, we present an entropy-stable (ES) discretization using a nodal discontinuous Galerkin (DG) method for the ideal multi-ion magneto-hydrodynamics (MHD) equations. We start by performing a continuous entropy analysis of the…
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT)…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount…
We propose two sets of initial conditions for magnetohydrodynamics (MHD) in which both the velocity and the magnetic fields have spatial symmetries that are preserved by the dynamical equations as the system evolves. When implemented…
Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
By applying a slow curing process, we show that biomolecules can be incorporated via a simple process as liquid stable phases inside a polydimethylsiloxane (PDMS) matrix. The process is carried out under mild conditions with regards to…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
Our study aims at a better control and understanding of the transfer of a complex [DNA supercoiled plasmid - dodecyltrimethylammonium surfactant] layer from a liquid-vapour water interface onto a silicon surface without any additional…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the…