Related papers: Molecular dynamics simulations of a single strande…
The fluidic behavior of water at the micro/nano scale is studied by using of single DNA molecules as a model system. Stable curved DNA patterns with spans about one micron were generated by using of water flows, and observed by Atomic Force…
We propose an aqueous functionalized molybdenum disulfide nanoribbon suspended over a solid electrode as the first capacitive displacement sensor aimed at determining the DNA sequence. The detectable sequencing events arise from the…
Thermodynamic probes can be used to deduce microscopic internal dynamics of nanoscale quantum systems. Several direct entropy measurement protocols based on charge transport measurements have been proposed and experimentally applied to…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
Interest in studying the interaction of small molecules with DNA is caused by the need to develop new, highly effective, and low-toxic drugs for cancer treatment. The strong and highly specific binding of thionine with DNA makes it a…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing-wave spectroscopy (DWS) to investigate the…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix,…
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on…
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the…
We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown…