Related papers: Defects Can Increase the Melting Temperature of DN…
Density--functional simulations have been performed on Na$_{55}$, Na$_{92}$ and Na$_{142}$ clusters in order to understand the experimentally observed melting properties [M. Schmidt \textit{et al.}, Nature (London) \textbf{393}, 238…
We theoretically investigated the temperature fluctuations of DNA close to denaturation and observed a strong enhancement of these fluctuations at the critical temperature. Although in a much lower frequency range, such a sharp increase was…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to…
In this work, the structural and magnetic properties of the gold-coated FePt nanoparticles synthesized from high-temperature solution phase are presented. The amount of gold was optimized to obtain most of the FePt particles coated. The…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
We present direct evidence for a reversible phase transition of DNA-linked colloidal gold assemblies. Transmission electron microscopy and optical absorption spectroscopy are used to monitor the colloidal gold phase transition, whose…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
The phonon thermal contribution to the melting temperature of nano-particles is inspected. Unlike in periodic boundary condition, under a general boundary condition the integration volume of low energy phonon for a nano-particle is more…
Melting is a high temperature process that requires extensive sampling of configuration space, thus making melting temperature prediction computationally very expensive and challenging. Over the past few years, I have built two methods to…
At the nanoscale, materials exhibit unique properties that differ greatly from those of the bulk state. In the case of Ag$_x$Pt$_{1-x}$ nanoalloys, we aimed to study the solid-liquid transition of nanoparticles of different sizes and…
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…
The phonon thermal contribution to the melting temperature of nano-particles is inspected. The discrete summation of phonon states and its corresponding integration form as an approximation for a nano-particle or for a bulk system have been…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
In this work, the binding of native DNA to MoS$_{2}$ nanoflakes (FLs) was studied by using UV-visible absorption spectroscopy, thermal denaturation method, transmission electron microscopy (TEM), temperature-dependent dynamic light…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…