Search results for "biological physics"
showing 10 items of 153 documents
Synthetic nanopores with fixed charges: An electrodiffusion model for ionic transport
2003
Synthetic nanopores with fixed charges exhibit ionic equilibrium and transport properties that resemble those displayed by biological ion channels. We present an electrodiffusion model based on the Nernst-Planck flux equations, which allows for a qualitative description of the steady state ionic transport through a nanopore when the membrane fixed charges and all mobile carriers (including the water ions) are properly taken into account. In particular, we study the current-voltage curve, the electrical conductance, the reversal potential (a measure of the nanopore ionic selectivity), as well as the flux inhibition by protons and divalent cations in the nanopore. The model clearly shows how …
Trapping of 27 bp–8 kbp DNA and immobilization of thiol-modified DNA using dielectrophoresis
2006
Dielectrophoretic trapping of six different DNA fragments, sizes varying from the 27 to 8416 bp, has been studied using confocal microscopy. The effect of the DNA length and the size of the constriction between nanoscale fingertip electrodes on the trapping efficiency have been investigated. Using finite element method simulations in conjunction with the analysis of the experimental data, the polarizabilities of the different size DNA fragments have been calculated for different frequencies. Also the immobilization of trapped hexanethiol- and DTPA-modified 140 nm long DNA to the end of gold nanoelectrodes was experimentally quantified and the observations were supported by density functiona…
Diamond Magnetic Microscopy of Malarial Hemozoin Nanocrystals.
2019
Magnetic microscopy of malarial hemozoin nanocrystals was performed using optically detected magnetic resonance imaging of near-surface diamond nitrogen-vacancy centers. Hemozoin crystals were extracted from $Plasmodium$-$falciparum$-infected human blood cells and studied alongside synthetic hemozoin crystals. The stray magnetic fields produced by individual crystals were imaged at room temperature as a function of applied field up to 350 mT. More than 100 nanocrystals were analyzed, revealing the distribution of their magnetic properties. Most crystals ($96\%$) exhibit a linear dependence of stray field magnitude on applied field, confirming hemozoin's paramagnetic nature. A volume magneti…
Elastic Properties and Line Tension of Self-Assembled Bilayer Membranes
2013
The elastic properties of a self-assembled bilayer membrane are studied using the self-consistent field theory, applied to a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents. Examining the free energy of bilayer membranes with different geometries allows us to calculate their bending modulus, Gaussian modulus, two fourth-order membrane moduli, and the line tension. The dependence of these parameters on the microscopic characteristics of the amphiphilic chain, characterized by the volume fraction of the hydrophilic component, is systematically studied. The theoretical predictions are compared with the results from a simple monolayer model, whic…
Noncovalent force spectroscopy using wide-field optical and diamond-based magnetic imaging
2019
A realization of the force-induced remnant magnetization spectroscopy (FIRMS) technique of specific biomolecular binding is presented where detection is accomplished with wide-field optical and diamond-based magnetometry using an ensemble of nitrogen-vacancy (NV) color centers. The technique may be adapted for massively parallel screening of arrays of nanoscale samples.
Deconvolution of the Effects of Binary Associations and Collective Assemblies on the Rheological Properties of Entangled Side-Chain Supramolecular Po…
2019
The properties and function of supramolecular polymer networks are determined not only by pairwise interchain transient associations but also by chain entanglement and nanoscopic phase separation of the associative groups. To unravel the impact and interplay of these different factors, we devise a set of model supramolecular polymer networks in which the number of entanglements and the density of associative groups are systematically varied. Rheological data show that by increasing the density of associative groups, the plateau modulus grows to a steady level and extends over a distinct frequency range. This is credited to the presence of binary associations with unique partner exchange tim…
Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields
2012
AbstractPolymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional “bond fluctuation model”. It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluct…
Proton dynamics in bacterial spores, a neutron scattering investigation
2014
International audience; Results from first neutron scattering experiments on bacterial spores are reported. The elastic intensities and mean square displacements have a non-linear behaviour as function of temperature, which is in agreement with a model presenting more pronounced variations at around 330 K (57 • C) and 400 K (127 • C). Based on the available literature on thermal properties of bacterial spores, mainly referring to differential scanning calorimetry, they are suggested to be associated to main endothermic transitions induced by coat and/or core bacterial response to heat treatment.
FLUCTUATIONS IN LIPID BILAYERS: ARE THEY UNDERSTOOD?
2013
We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local "protrusions" and/or density fluctuations. Such models provide an excellent basis for describing the fluctuations of tensionless bilayers in the fluid phase at a quantitative level. However, this description is found to fail for membranes in the gel phase and for membranes subject to high tensions. The fluctuations of tilted gel membranes show a signature of the modulated ripple structure, which is a nearby phase observed in the pretransition regime betw…
Gyrification from constrained cortical expansion
2014
The exterior of the mammalian brain - the cerebral cortex - has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated a…