PubMed Health⌕ Search

Biomedical subjects

Theo Odijk

Publications and source records attributed to Theo Odijk.

8 recordsLinked to original sources
PubMed2006

DNA confined in nanochannels: hairpin tightening by entropic depletion.

A theory is presented of the elongation of double-stranded DNA confined in a nanochannel based on a study of the formation of hairpins. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The DNA in the hairpin remains double-stranded. The free energy of the hairpin is significantly larger than what one would expect if this entropic effect were unimportant. As a result, the distance between hairpins or the global persistence length is often tens of micrometer long and may even reach millimeter sizes for 10 nm thin channels. The hairpin shape and size and the DNA elongation are computed for nanoslits and circular and square nanochannels. A comparison with experiment is given.

Computer Simulation↗
PubMed2006

Application of the optimized Baxter model to the hard-core attractive Yukawa system.

We perform Monte Carlo simulations on the hard-core attractive Yukawa system to test the optimized Baxter model that was introduced by Prinsen and Odijk [J. Chem. Phys. 121, 6525 (2004)] to study a fluid phase of spherical particles interacting through a short-range pair potential. We compare the chemical potentials and pressures from the simulations with analytical predictions from the optimized Baxter model. We show that the model is accurate to within 10% over a range of volume fractions from 0.1 to 0.4, interaction strengths up to three times the thermal energy, and interaction ranges from 6% to 20% of the particle diameter, and performs even better in most cases. We furthermore establish the consistency of the model by showing that the thermodynamic properties of the Yukawa fluid computed via simulations may be understood on the basis of one similarity variable, the stickiness parameter defined within the optimized Baxter model. Finally, we show that the optimized Baxter model works significantly better than an often used, naive method determining the stickiness parameter by equating the respective second virial coefficients based on the attractive Yukawa and Baxter potentials.

Journal Article↗
PubMed2006

Fluid-crystal coexistence for proteins and inorganic nanocolloids: Dependence on ionic strength.

We investigate theoretically the fluid-crystal coexistence of solutions of globular charged nanoparticles such as proteins and inorganic colloids. The thermodynamic properties of the fluid phase are computed via the optimized Baxter model P. Prinsen and T. Odijk [J. Chem. Phys. 121, 6525 (2004)]. This is done specifically for lysozyme and silicotungstates for which the bare adhesion parameters are evaluated via the experimental second virial coefficients. The electrostatic free energy of the crystal is approximated by supposing the cavities in the interstitial phase between the particles are spherical in form. In the salt-free case a Poisson-Boltzmann equation is solved to calculate the effective charge on a particle and a Donnan approximation is used to derive the chemical potential and osmotic pressure in the presence of salt. The coexistence data of lysozyme and silicotungstates are analyzed within this scheme, especially with regard to the ionic-strength dependence of the chemical potentials. The latter agree within the two phases provided some upward adjustment of the effective charge is allowed for.

Journal Article↗
PubMed2005

Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid.

To study the dynamics and organization of the DNA within isolated Escherichia coli nucleoids, we track the movement of a specific DNA region. Labeling of such a region is achieved using the Lac-O/Lac-I system. The Lac repressor-GFP fusion protein binds to the DNA section where tandem repeats of the Lac operator are inserted, which allows us to monitor the motion of the DNA. The movement of such a GFP spot is followed at 48 ms temporal resolution during 12s. The spots are found to diffuse within a confined space, so that the nucleoid appears to behave like a viscoelastic network. The distribution of the "particle" position in time can be fitted to a Gaussian function indicating that the motion of the particle is Brownian. An average self-diffusion constant Ds=0.12 microm(2) s-1 is derived via the time auto-correlation functions of the displacement and is compatible with the collective diffusion coefficient measured previously by dynamic light scattering. Restriction of a DNA sequence to a small region of the nucleoid is tentatively related to the existence of so-called supercoiling domains.

Chromosomes, Bacterial↗
PubMed2005

Single-particle tracking of oriC-GFP fluorescent spots during chromosome segregation in Escherichia coli.

DNA regions close to the origin of replication were visualized by the green fluorescent protein (GFP)-Lac repressor/lac operator system. The number of oriC-GFP fluorescent spots per cell and per nucleoid in batch-cultured cells corresponded to the theoretical DNA replication pattern. A similar pattern was observed in cells growing on microscope slides used for time-lapse experiments. The trajectories of 124 oriC-GFP spots were monitored by time-lapse microscopy of 31 cells at time intervals of 1, 2, and 3 min. Spot positions were determined along the short and long axis of cells. The lengthwise movement of spots was corrected for cell elongation. The step sizes of the spots showed a Gaussian distribution with a standard deviation of approximately 110 nm. Plots of the mean square displacement versus time indicated a free diffusion regime for spot movement along the long axis of the cell, with a diffusion coefficient of 4.3+/-2.6x10(-5) microm2/s. Spot movement along the short axis showed confinement in a region of the diameter of the nucleoid ( approximately 800 nm) with an effective diffusion coefficient of 2.9+/-1.7x10(-5) microm2/s. Confidence levels for the mean square displacement analysis were obtained from numerical simulations. We conclude from the analysis that within the experimental accuracy--the limits of which are indicated and discussed--there is no evidence that spot segregation requires any other mechanism than that of cell (length) growth.

Algorithms↗
PubMed2004

Optimized Baxter model of protein solutions: electrostatics versus adhesion.

A theory is set up of spherical proteins interacting by screened electrostatics and constant adhesion, in which the effective adhesion parameter is optimized by a variational principle for the free energy. An analytical approach to the second virial coefficient is first outlined by balancing the repulsive electrostatics against part of the bare adhesion. A theory similar in spirit is developed at nonzero concentrations by assuming an appropriate Baxter model as the reference state. The first-order term in a functional expansion of the free energy is set equal to zero which determines the effective adhesion as a function of salt and protein concentrations. The resulting theory is shown to have fairly good predictive power for the ionic-strength dependence of both the second virial coefficient and the osmotic pressure or compressibility of lysozyme up to about 0.2 volume fraction.

Adhesiveness↗
PubMed2004

Statics and dynamics of condensed DNA within phages and globules.

Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages under the assumption that the DNA globule has a uniform density. A new electrostatic model is introduced for computing the osmotic pressure of rod-like polyelectrolytes at very high concentrations. At intermediate packing, a reptation model is considered for DNA diffusing within a toroidal globule. Under tight-packing conditions a model of Coulomb sliding friction is proposed. A general discussion is given of our current understanding of the statics and dynamics of confined DNA in the context of the following experiments: characterization of the liquid crystalline phases, X-ray scattering by phages, osmotic-stress measurements, cyclization within globules and single-molecule determination of the loading forces.

Bacteriophages↗