Microrheology of semiflexible filament solutions based on relaxation simulations.

We present an efficient computational methodology to obtain the viscoelastic response of dilute solutions of semiflexible filaments. By considering an approach based on the fluctuation-dissipation theorem, we were able to evaluate the dynamical properties of probe particles immersed in solutions of semiflexible filaments from relaxation simulations with a relatively low computational cost and higher precision in comparison to those based on stochastic dynamics. We used a microrheological approach to obtain the complex shear modulus and the complex viscosity of the solution through its compliance which was obtained directly from the dynamical properties of a probe particle attached to an effective medium described by a mesoscopic model, i.e., an effective filament model (EFM). The relaxation simulations were applied to assess the effects of the bending energy on the viscoelasticity of the semiflexible filament solutions, and our methodology was validated by comparing the numerical results to the experimental data on DNA and collagen solutions.

Size-dependent bandgap and particle size distribution of colloidal semiconductor nanocrystals.

A new analytical expression for the size-dependent bandgap of colloidal semiconductor nanocrystals is proposed within the framework of the finite-depth square-well effective mass approximation in order to provide a quantitative description of the quantum confinement effect. This allows one to convert optical spectroscopic data (photoluminescence spectrum and absorbance edge) into accurate estimates for the particle size distributions of colloidal systems even if the traditional effective mass model is expected to fail, which occurs typically for very small particles belonging to the so-called strong confinement limit. By applying the reported theoretical methodologies to CdTe nanocrystals synthesized through wet chemical routes, size distributions are inferred and compared directly to those obtained from atomic force microscopy and transmission electron microscopy. This analysis can be used as a complementary tool for the characterization of nanocrystal samples of many other systems such as the II-VI and III-V semiconductor materials.

Dodecyltrimethylammonium bromide surfactant effects on DNA: Unraveling the competition between electrostatic and hydrophobic interactions.

We present a new study on the interaction of the DNA molecule with the surfactant dodecyltrimethylammonium bromide (DTAB), performed mainly with optical tweezers. Single-molecule force spectroscopy experiments performed in the low-force entropic regime allowed a robust characterization of the DNA-DTAB interaction, unveiling how the surfactant changes the mechanical properties of the biopolymer, the binding parameters, and the competition of the two mechanisms involved in the interaction: electrostatic attraction between the cationic surfactant heads and the negative phosphate backbone of the DNA and hydrophobic interactions between the tails of the bound DTAB molecules, which can result in DNA compaction in solution depending on the quantity of bound surfactant. Finally, force clamp experiments with magnetic tweezers and gel electrophoresis assays confirm that DTAB compacts DNA depending not only on the surfactant concentration but also on the conformation of the biopolymer in solution. The present study provides new insights on general aspects of the DNA-surfactant complexes formation, contributing to the fundamental knowledge of the physics of such interactions.

ß-Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters.

Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a ß-cyclodextrin polymer (poly-ß-CD) with λ-DNA. The polymers are obtained by the reaction of ß-CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-ß-CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-ß-CD concentration (<300µM). On the other hand, significant alterations were observed in the persistence length that identifies two binding modes corresponding to the clustering of ∼2.6 and ∼14 polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric ß-CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) ß-CD. These results show that the polymerization of the ß-CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.