arXiv subjects

O. N. Mesquita

Publications and source records attributed to O. N. Mesquita.

7 recordsLinked to original sources

arXiv2014

Shape reconstruction and height fluctuations of red blood cells using defocusing microscopy

In this paper the bright-field defocusing microscopy (DM) technique is presented. DM is able to obtain quantitative information of each plane/surface of pure phase objects, as live unlabeled cells, and its application to red blood cells (RBCs) is demonstrated. Based on contrast, simple methods to obtain thickness profile and three dimensional (3D) total reconstruction of RBCs are proposed and the actual height profiles of upper and lower surface-membranes (lipid bilayer$/$cytoskeleton) of discocyte and stomatocyte red cells are presented as examples. In addition, using the mean square contrast fluctuation and modeling the RBC membranes fluctuations spectra as dependent of a bending modulus $(κ_c)$, a surface tension $(σ)$ and a confining potential $(γ)$ term, slowly varying quantities along the cell radius, a genetic algorithm (GA) is used and the radial height fluctuations of each surface-membrane are accessed, separately. The radial behaviors of $κ_c$, $σ$ and $γ$ are also obtained, allowing the discussion of physical aspects of the RBC membrane.

physics.bio-ph↗

arXiv2014

Total 3D imaging of phase objects using defocusing microscopy: application to red blood cells

We present Defocusing Microscopy (DM), a bright-field optical microscopy technique able to perform total 3D imaging of transparent objects. By total 3D imaging we mean the determination of the actual shapes of the upper and lower surfaces of a phase object. We propose a new methodology using DM and apply it to red blood cells subject to different osmolality conditions: hypotonic, isotonic and hypertonic solutions. For each situation the shape of the upper and lower cell surface-membranes (lipid bilayer/cytoskeleton) are completely recovered, displaying the deformation of RBCs surfaces due to adhesion on the glass-substrate. The axial resolution of our technique allowed us to image surface-membranes separated by distances as small as 300 nm. Finally, we determine volume, superficial area, sphericity index and RBCs refractive index for each osmotic condition.

physics.bio-ph↗

arXiv2010

DNA-psoralen: single-molecule experiments and first principles calculations

The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a certain critical concentration is reached, above which it abruptly decreases and remains approximately constant. The contour length of the complexes exhibits no such discontinuous behavior. By fitting the relative increase of the contour length to the neighbor exclusion model, we obtain the exclusion number and the intrinsic intercalating constant of the psoralen-DNA interaction. Ab initio calculations are employed in order to provide an atomistic picture of these experimental findings.

physics.bio-ph↗

arXiv2007

Transition on the entropic elasticity of DNA induced by intercalating molecules

We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from zero up to 2 pN. Our results show that the persistence length of the DNA-drug complexes increases strongly as the drug concentration increases up to some critical value. Above this critical value, the persistence length decreases abruptly and remains practically constant for larger drug concentrations. The contour length of the molecules increases monotonically and saturates as drugs concentration increases. Measured in- tercalants critical concentrations for the persistence length transition coincide with reported values for the helix-coil transition of DNA-drug complexes, obtained from sedimentation experiments.

physics.bio-ph↗

arXiv2006

Towards absolute calibration of optical tweezers

Aiming at absolute force calibration of optical tweezers, following a critical review of proposed theoretical models, we present and test the results of MDSA (Mie-Debye-Spherical Aberration) theory, an extension of a previous (MD) model, taking account of spherical aberration at the glass/water interface. This first-principles theory is formulated entirely in terms of experimentally accessible parameters (none adjustable). Careful experimental tests of the MDSA theory, undertaken at two laboratories, with very different setups, are described. A detailed description is given of the procedures employed to measure laser beam waist, local beam power at the transparent microspheres trapped by the tweezers, microsphere radius and the trap transverse stiffness, as a function of radius and height in the (inverted microscope) sample chamber. We find generally very good agreement with MDSA theory predictions, for a wide size range, from the Rayleigh domain to large radii, including the values most often employed in practice, and at different chamber heights, both with objective overfilling and underfilling. The results asymptotically approach geometrical optics in the mean over size intervals, as they should, and this already happens for size parameters not much larger than unity. MDSA predictions for the trapping threshold, position of stiffness peak, stiffness variation with height, multiple equilibrium points and `hopping' effects among them are verified. Remaining discrepancies are ascribed to focus degradation, possibly arising from objective aberrations in the infrared, not yet included in MDSA theory.

physics.optics↗

arXiv2004

Recoiling DNA Molecule: Simulation & Experiment

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between computer simulated recoil curves, generated from the corresponding Langevin equation, and experimental recoils is used to assure the validity of data analysis.

physics.bio-ph↗

arXiv1999

Molecular dynamic simulation of directional crystal growth

We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach experimentally, being an important tool for further experimental and theoretical developments in the area of crystal growth.

cond-mat.stat-mech↗