A quantitative information measure applied to texture perception attributes during mastication.

We have calculated an entropy or information measure of previously reported experimentally determined temporal dominance of sensations (TDS) data of texture attributes for two sets of emulsion filled gels throughout the mastication cycle. The samples were emulsion filled gels and two-layered emulsion filled gels. We find that the entropy measure follows an average curve, which is different for each set. The specifics of the entropy curve may serve as a fingerprint for the perception of a specific food sample.

DNA compaction and dynamic observation in a nanopore gated sub-attoliter silicon nanocavity.

Confinement of biopolymers inside volumes with micro- or nanoscale lateral dimensions is ubiquitous in nature. Investigating the behavior of biopolymers in a confined environment is essential to improve our basic understanding in life sciences. In this work, we present a nanopore gated sub-attoliter silicon nanocavity device, which allows DNA compaction similar to that in virus capsids. Single DNA molecules can be electrically driven into the nanocavity, and then get compacted inside the nanocavity under certain conditions. The dynamic fluctuations of the compacted DNA can be monitored via ionic current measurements. The mechanism for the DNA compaction is elucidated by varying the DNA length or concentration, voltage polarity, nanocavity dimensions and ionic strength. Furthermore, Brownian dynamics simulations reveal the dynamic fluctuations of the compacted DNA, which are reflected in the measured ionic current. Our nanocavity device is anticipated to provide a controlled environment in extremely small volumes for investigating the physics of confined biopolymers.

Mean-field theory of the interaction of the magnesium ion with biopolymers: the case of lysozyme.

A statistical theory is presented of the magnesium ion interacting with lysozyme under conditions where the latter is positively charged. Temporarily assuming magnesium is not noncovalently bound to the protein, I solve the nonlinear Poisson-Boltzmann equation accurately and uniformly in a perturbative fashion. The resulting expression for the effective charge, which is larger than nominal owing to overshooting, is subtle and cannot be asymptotically expanded at high ionic strengths that are practical. An adhesive potential taken from earlier work together with the assumption of possibly bound magnesium is then fitted to be in accord with measurements of the second virial coefficient by Tessier et al. The resulting numbers of bound magnesium ions as a function of MgBr[Formula: see text] concentration are entirely reasonable compared with densitometry measurements.

Electrostatic confinement and manipulation of DNA molecules for genome analysis.

Very large DNA molecules enable comprehensive analysis of complex genomes, such as human, cancer, and plants because they span across sequence repeats and complex somatic events. When physically manipulated, or analyzed as single molecules, long polyelectrolytes are problematic because of mechanical considerations that include shear-mediated breakage, dealing with the massive size of these coils, or the length of stretched DNAs using common experimental techniques and fluidic devices. Accordingly, we harness analyte "issues" as exploitable advantages by our invention and characterization of the "molecular gate," which controls and synchronizes formation of stretched DNA molecules as DNA dumbbells within nanoslit geometries. Molecular gate geometries comprise micro- and nanoscale features designed to synergize very low ionic strength conditions in ways we show effectively create an "electrostatic bottle." This effect greatly enhances molecular confinement within large slit geometries and supports facile, synchronized electrokinetic loading of nanoslits, even without dumbbell formation. Device geometries were considered at the molecular and continuum scales through computer simulations, which also guided our efforts to optimize design and functionalities. In addition, we show that the molecular gate may govern DNA separations because DNA molecules can be electrokinetically triggered, by varying applied voltage, to enter slits in a size-dependent manner. Lastly, mapping the Mesoplasmaflorum genome, via synchronized dumbbell formation, validates our nascent approach as a viable starting point for advanced development that will build an integrated system capable of large-scale genome analysis.

Unfolding Kinetics of a Wormlike Chain under Elongational Flow.

A simple theory of the unfolding kinetics of a semi-flexible polymer chain is presented in terms of a Kramers type picture for the energy of elongation. The hydrodynamic interactions are discussed in terms of slender body theory. It turns out that the elongation of the chain is basically linear in time and independent of the viscosity. The former prediction agrees with experiments on the stretching dynamics of DNA under planar elongational flow. Nevertheless, the theory overestimates the experimental rate by a significant amount for reasons that are unclear.

Compaction of isolated Escherichia coli nucleoids: Polymer and H-NS protein synergetics.

Escherichia coli nucleoids were compacted by the inert polymer polyethylene glycol (PEG) in the presence of the H-NS protein. The protein by itself appears to have little impact on the size of the nucleoids as determined by fluorescent microscopy. However, it has a significant impact on the nucleoidal collapse by PEG. This is quantitatively explained by assuming the H-NS protein enhances the effective diameter of the DNA helix leading to an increase in the depletion forces induced by the PEG. Ultimately, however, the free energy of the nucleoid itself turns out to be independent of the H-NS concentration. This is because the enhancement of the supercoil excluded volume is negligible. The experiments on the nucleoids are corroborated by dynamic light scattering and EMSA analyses performed on DNA plasmids in the presence of PEG and H-NS.

A tree swaying in a turbulent wind: a scaling analysis.

A tentative scaling theory is presented of a tree swaying in a turbulent wind. It is argued that the turbulence of the air within the crown is in the inertial regime. An eddy causes a dynamic bending response of the branches according to a time criterion. The resulting expression for the penetration depth of the wind yields an exponent which appears to be consistent with that pertaining to the morphology of the tree branches. An energy criterion shows that the dynamics of the branches is basically passive. The possibility of hydrodynamic screening by the leaves is discussed.

Presentation of large DNA molecules for analysis as nanoconfined dumbbells.

The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multi-pronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties-but tressed by molecular simulations-we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green's function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the "Odijk regime" does indeed start when the confinement dimensions size are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.

Characterization of Escherichia coli nucleoids released by osmotic shock.

Nucleoids were isolated by osmotic shock from Escherichia coli spheroplasts at relatively low salt concentrations and in the absence of detergents. Sucrose-protected cells, made osmotically sensitive by growth in the presence of ampicillin or by digestion with low lysozyme concentrations (50-5 µg/ml), were shocked by 100-fold dilution of the sucrose buffer. Liberated nucleoids stained with 4',6-diamidino-2-phenylindole dihydrochloride hydrate (DAPI), the dimeric cyanine dye TOTO-1, or fluorescent DNA-binding protein appeared as cloud-like structures, in the absence of phase contrast. Because UV-irradiation disrupted the DAPI-stained nucleoids within 5-10 s, they were imaged by time-lapse microscopy with exposure times less than 2 s. The volume of nucleoids isolated from ampicillin- or low-lysozyme spheroplasts and minimally exposed to UV (<2 s) was on average ∼42 µm(3). Lysozyme at concentrations above 1 µg/ml in the lysate compacted the nucleoids. Treatment with protease E or K (20-200 µg/ml) and sodium dodecyl sulfate (SDS; 0.001-0.01%) caused a twofold volume increase and showed a granular nucleoid at the earliest UV-exposure; the expansion could be reversed with 50 µM ethidium bromide, but not with chloroquine. While DNase (1 µg/ml) caused a rapid disruption of the nucleoids, RNase (0.1-400 µg/ml) had no effect. DAPI-stained nucleoids treated with protease, SDS or DNase consisted of granular substructures at the earliest exposure similar to UV-disrupted nucleoids obtained after prolonged (>4 s) UV irradiation. We interpret the measured volume in terms of a physical model of the nucleoid viewed as a branched DNA supercoil crosslinked by adhering proteins into a homogeneous network.

Depletion theory and the precipitation of protein by polymer.

The depletion theory of nanoparticles immersed in a semidilute polymer solution is reinterpreted in terms of depleted chains of polymer segments. Limitations and extensions of mean-field and scaling theories are discussed. An explicit expression for the interaction between two small spheres is also reviewed. The depletion free energy for a particle of general shape is given in terms of the capacitance or effective Stokes radius. This affords a reasonable explanation for the effect of polymer on protein precipitation.

Scaling theory of DNA confined in nanochannels and nanoslits.

A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on itself giving rise to a global persistence length that may be very large owing to entropic deflection. Moreover, there is an orientational excluded-volume effect between the DNA segments imposed solely by the nanoconfinement. These two effects cause the chain statistics to be intricate leading to nontrivial power laws for the chain extension in the intermediate regimes. It is stressed that DNA confinement within nanochannels differs from that in nanoslits because the respective orientational excluded-volume effects are not the same.

Collective diffusion coefficient of proteins with hydrodynamic, electrostatic, and adhesive interactions.

A theory is presented for lambdaC, the coefficient of the first-order correction in the density of the collective diffusion coefficient, for protein spheres interacting by electrostatic and adhesive forces. An extensive numerical analysis of the Stokesian hydrodynamics of two moving spheres is given so as to gauge the precise impact of lubrication forces. An effective stickiness is introduced and a simple formula for lambdaC in terms of this variable is put forward. A precise though more elaborate approximation for lambdaC is also developed. These and numerically exact expressions for lambdaC are compared with experimental data on lysozyme at pH 4.5 and a range of ionic strengths between 0.05M and 2M.

A single-molecule barcoding system using nanoslits for DNA analysis.

Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro- and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.

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.

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.

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.

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.

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.

Diffusion of water and sodium counter-ions in nanopores of a ß-lactoglobulin crystal: a molecular dynamics study.

The dynamics of water and sodium counter-ions (Na(+)) in a C222(1) orthorhombic ß-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm(2) ns(-1), when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.