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Biomedical subjects

K Kroy

Publications and source records attributed to K Kroy.

8 recordsLinked to original sources

Binding of TmHU to single dsDNA as observed by optical tweezers.

Optical tweezers are employed to study the action of the histone-like protein from Thermotoga maritima (TmHU) on DNA at a single molecule level. Binding and disruption of TmHU to and from DNA are found to take place in discrete steps of 4-5 nm length and a net binding enthalpy of about 16kBT. This is in reasonable agreement with a microscopic model that estimates the extension of the binding sites of the protein and evaluates the energetics mainly for bending of the DNA in the course of interaction.

Bacterial Proteins↗

Microrheology probes length scale dependent rheology.

We exploit the power of microrheology to measure the viscoelasticity of entangled F-actin solutions at different length scales from 1 to 100 microm over a wide frequency range. We compare the behavior of single probe-particle motion to that of the correlated motion of two particles. By varying the average length of the filaments, we identify fluctuations that dissipate diffusively over the filament length. These provide an important relaxation mechanism of the elasticity between 0.1 and 30 rad/sec.

Actins↗

Non-equilibrium behavior of sticky colloidal particles: beads, clusters and gels.

To understand the non-equilibrium behavior of colloidal particles with short-range attraction, we studied salt-induced aggregation of lysozyme. Optical microscopy revealed four regimes: bicontinuous texture, 'beads', large aggregates, and transient gelation. The interaction of a metastable liquid-liquid binodal and an ergodic to non-ergodic transition boundary inside the equilibrium crystallization region can explain our findings.

Colloids↗

Cluster mode-coupling approach to weak gelation in attractive colloids.

Mode-coupling theory (MCT) predicts the arrest of colloids in terms of their volume fraction, and the range and depth of the interparticle attraction. We discuss how the effective values of these parameters evolve under cluster aggregation. We argue that weak gelation in colloids can be idealized as a two-stage ergodicity breaking: first at short scales (approximated by the bare MCT) and then at larger scales (governed by MCT applied to clusters). The competition between the arrest and phase separation is considered in relation to recent experiments. We predict a long-lived "semiergodic" phase of mobile clusters, showing logarithmic relaxation close to the gel line.

Journal Article↗

Continuum saltation model for sand dunes.

We derive a phenomenological continuum saltation model for aeolian sand transport that can serve as an efficient tool for geomorphological applications. The coupled differential equations for the average density and velocity of sand in the saltation layer reproduce both the known equilibrium relations for the sand flux and the time evolution of the sand flux as predicted by microscopic saltation models. The three phenomenological parameters of the model are a reference height for the grain-air interaction, an effective restitution coefficient for the grain-bed interaction, and a multiplication factor characterizing the chain reaction caused by the impacts leading to a typical time or length scale of the saturation transients. We determine the values of these parameters by comparing our model with wind tunnel measurements. Our main interest are out of equilibrium situations where saturation transients are important, for instance at phase boundaries (ground/sand) or under unsteady wind conditions. We point out that saturation transients are indispensable for a proper description of sand flux over structured terrain, by applying the model to the windward side of an isolated dune, thereby resolving recently reported discrepancies between field measurements and theoretical predictions.

Journal Article↗

Desmin filaments studied by quasi-elastic light scattering.

We studied polymers of desmin, a muscle-specific type III intermediate filament protein, using quasi-elastic light scattering. Desmin was purified from chicken gizzard. Polymerization was induced either by 2 mM MgCl(2) or 150 mM NaCl. The polymer solutions were in the semidilute regime. We concluded that the persistence length of the filaments is between 0.1 and 1 microm. In all cases, we found a hydrodynamic diameter of desmin filaments of 16-18 nm. The filament dynamics exhibits a characteristic frequency in the sense that correlation functions measured on one sample but at different scattering vectors collapse onto a single master curve when time is normalized by the experimentally determined initial decay rate.

Animals↗

Analysis of the F-actin binding fragments of vinculin using stopped-flow and dynamic light-scattering measurements.

Using amino acids 884-1066 and 884-1012 expressed from chicken vinculin as fusion proteins with schistosomal glutathione S-transferase, we determined the binding kinetics of the protein fragments with F-actin. We established by the stopped-flow method a two-step binding process: an initial rapid reaction followed by a slower process. The latter is attributed to F-actin cross-linking and/or bundling, which was previously detected by viscometry and electron microscopy [Johnson, R. P. & Craig, S. W. (1995) Nature 373, 261-264]. This is also supported by dynamic light-scattering measurements, indicating dramatic changes in the internal actin filament dynamics, i.e. in bending undulations due to thermal noise. The similar size of the binding reaction for both fusion proteins with F-actin indicates that the F-actin binding site(s) on vinculin are located between residues 884-1012. No binding of pure glutathione S-transferase or its fusion protein with vinculin peptide 1012-1066 with F-actin was detected by either method.

Actins↗