Force Induced DNA Melting

When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA which is a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA start melting abruptly/smoothly after a critical force depending on the pulling direction. The critical force fm, at which DNA melts completely decreases as the temperature of the system is increased. The melting force in case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the cases of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to different base pair sequence. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.Comment: 23 pages, 9 figures, accepted for publication in J. Phys.: Condens. Matte

Translocation and encapsulation of siRNA inside carbon nanotubes

We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics (MD) simulations with explicit solvent. We use Umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles shows that siRNA gains free energy while translocating inside CNT and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time \tau decreases with the increase of CNT diameter with a critical diameter of 24 \AA for the translocation. In contrast, double strand DNA (dsDNA) of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.Comment: Accepted for the Journal of Chemical Physics; 24 pages, 6 figures and 1 tabl

Elasticity of DNA and the effect of Dendrimer Binding

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus {\gamma}_1 of dsDNA in quantitative agreement with the literature value. The bend angle distribution P({\theta}) of the dsDNA also has a Gaussian form and allows to extract a persistence length, L_p of 43 nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.Comment: 21 pages, 5 figure

Modeling Interlayer Interactions and Phonon Thermal Transport in Silicene Bilayer

We develop an accurate interlayer pairwise potential derived from the \textit{ab-initio} calculations and investigate the thermal transport of silicene bilayers within the framework of equilibrium molecular dynamics simulations. The electronic properties are found to be sensitive to the temperature with the opening of the band gap in the $\Gamma$$\rightarrow$M direction. The calculated phonon thermal conductivity of bilayer silicene is surprisingly higher than that of monolayer silicene, contrary to the trends reported for other classes of 2D materials like graphene and hBN bilayers. This counterintuitive behavior of the bilayer silicene is attributed to the interlayer interaction effects and inherent buckling, which lead to a higher group velocity in the LA$_1$/LA$_2$ phonon modes. The thermal conductivity of both the mono- and bilayer silicene decreases with temperature as $\kappa\sim T^{-0.9}$ because of the strong correlations between the characteristic timescales of heat current autocorrelation function and temperature ($\tau\sim T^{-0.75}$). The mechanisms underlying phonon thermal transport in silicene bilayers are further established by analyzing the temperature induced changes in acoustic group velocity.Comment: To appear in Phys. Rev.

Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3′end1–3′end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5′end1–5′end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3′end1–3′end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break

Dramatic changes in DNA Conductance with stretching: Structural Polymorphism at a critical extension

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out multiscale modeling, to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 $\AA$ or 17 %) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32$\AA$ (84 %) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We find that the dramatically different conductance behaviors for two different pulling protocols arise from the nature of how hydrogen bonds of DNA base pairs break

Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3′end1–3′end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5′end1–5′end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3′end1–3′end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break