Search results for "Biological physics"
showing 10 items of 153 documents
A TDDFT-based Study on the Proton-DNA Collision
2019
The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrenfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of base pair linking to the DNA double helix was emulated by fixing the four O3' atoms responsible for the attachment. The base pair tends to dissociate into its main components, namely the phosphate groups, sugars and nitr…
Ionic conduction, rectification, and selectivity in single conical nanopores
2006
Modern track-etching methods allow the preparation of membranes containing a single charged conical nanopore that shows high ionic permselectivity due to the electrical interactions of the surface pore charges with the mobile ions in the aqueous solution. The nanopore has potential applications in electrically assisted single-particle detection, analysis, and separation of biomolecules. We present a detailed theoretical and experimental account of the effects of pore radii and electrolyte concentration on the current-voltage and current-concentration curves. The physical model used is based on the Nernst-Planck and Poisson equations. Since the validity of continuum models for the descriptio…
Orientational landscapes of peptides in membranes: prediction of (2)H NMR couplings in a dynamic context.
2009
Unlike soluble proteins, membrane polypeptides face an anisotropic milieu. This imposes restraints on their orientation and provides a reference that makes structure prediction tractable by minimalistic thermodynamic models. Here we use this framework to build orientational distributions of monomeric membrane-bound peptides and to predict their expected solid-state (2)H NMR quadrupolar couplings when labeled at specific side chain positions. Using a complete rigid-body sampling of configurations relative to an implicit lipid membrane, peptide free energy landscapes are calculated. This allows us to obtain probability distributions of the peptide tilt, azimuthal rotation, and depth of membra…
Mechanical Properties of Pore-Spanning Lipid Bilayers Probed by Atomic Force Microscopy
2006
AbstractWe measure the elastic response of a free-standing lipid membrane to a local indentation by using an atomic force microscope. Starting point is a planar gold-coated alumina substrate with a chemisorbed 3-mercaptopropionic acid monolayer displaying circular pores of very well defined and tunable size, over which bilayers composed of N,N,-dimethyl-N,N,-dioctadecylammonium bromide or 1,2-dioleoyl-3-trimethylammonium-propane chloride were spread. Centrally indenting these “nanodrums” with an atomic force microscope tip yields force-indentation curves, which we quantitatively analyze by solving the corresponding shape equations of continuum curvature elasticity. Since the measured respon…
How molecular knots can pass through each other
2014
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of knots on a single DNA strand.
Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers
2013
According to the lipid raft hypothesis, biological lipid membranes are laterally heterogeneous and filled with nanoscale ordered "raft" domains, which are believed to play an important role for the organization of proteins in membranes. However, the mechanisms stabilizing such small rafts are not clear, and even their existence is sometimes questioned. Here we report the observation of raft-like structures in a coarse-grained molecular model for multicomponent lipid bilayers. On small scales, our membranes demix into a liquid ordered (lo) and a liquid disordered (ld) phase. On large scales, phase separation is suppressed and gives way to a microemulsion-type state that contains nanometer si…
Calorimetric Behavior of Phosphatidylcholine/Phosphatidylethanolamine Bilayers is Compatible with the Superlattice Model
2012
Differential scanning calorimetry was used to study the phase behavior of binary lipid bilayers consisting of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) of varying acyl chain length. A two-state transition model was used to resolve the individual transition components, and the two-state transition enthalpy, the relative enthalpy, and the transition temperature of each component were plotted as a function of composition. Intriguingly, abrupt changes in these thermodynamic parameters were observed at or close to many "critical" X(PE) values predicted by the superlattice model proposing that phospholipids with different headgroups tend to adopt regular rather than random latera…
Silicatein conjugation inside nanoconfined geometries through immobilized NTA–Ni(ii) chelates
2013
The chemical modification and bioconjugation processes inside confined geometries by His-tagged silicatein promote sensitive changes in the polarity and surface charge density that mainly contribute to the ionic current rectification properties of the single conical nanopores.
Universal monomer dynamics of a two dimensional semi-flexible chain
2013
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square displacements (MSDs) of stiff chains growing like t^{3/4} with time due to bending motions, and the Rouse-like regime t^{2 \nu / (1+ 2\nu)} where \nu is the Flory exponent describing the radius R of a swollen flexible coil. We identify how the prefactors of these laws scale with the persistence length l_p, and show that a crossover from stiff to flexible behavior occurs at a MSD of order l^2_p (at a time proportional to l^3_p). A second crossover (to diffusive moti…
Sugar-induced stabilization of the monoolein Pn3m bicontinuous cubic phase during dehydration
2001
To explore the molecular mechanism of the protective function of sugars on cubic lipidic systems, the mesomorphic properties of the monoolein-water system, dehydrated in the presence of a series of sugars, have been studied by osmotic stress experiments. Two bicontinuous inverse cubic structures $(Pn3m$ and $\mathrm{Ia}3d)$ and a lamellar ${L}_{\ensuremath{\alpha}}$ phase form under dehydration in pure water. In sugar solutions, the $\mathrm{Pn}3m$ phase shows an extraordinary stability: as a function of sugar concentration, the lattice parameter decreases to very low values, but no phase transitions occur. Instead, the $\mathrm{Pn}3m$ to $\mathrm{Ia}3d$ phase transition is obtained by equi…