Biomedical subjects

E Orlandini

Publications and source records attributed to E Orlandini.

At least 19 recordsLinked to original sources

PubMed2006

Permeative flows in cholesterics: shear and Poiseuille flows.

By using a lattice Boltzmann scheme that solves the Beris-Edwards equations of motion describing liquid-crystal hydrodynamics, we study the response of cholesterics to shear and Poiseuille flows. The geometry we focus on is a flow along the direction of the helical axis, which is known to give rise to permeation. For both shear and Poiseuille flow we find that the boundary conditions on the director field are crucial in determining the rheological properties of the liquid crystal. For helices pinned at the boundaries, a small forcing leads to a large viscosity increase whereas a stronger forcing induces a sharp decrease towards the Newtonian value. This shear thinning behavior is in agreement with experiments and previous analytic results. If, on the other hand, the director is free to rotate at the walls, different behaviors are found depending on the symmetry of the steady-state primary flow. Some of the cases considered are compared to a similar imposed flow but with the helix lying perpendicular to the plates, for which no viscosity increase is observed.

Journal Article↗

PubMed2006

Knotting of random ring polymers in confined spaces.

Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with effective strategies for simplifying the geometrical complexity of ring conformations without altering their knot type. By these means we extend previous studies and characterize in detail how the probability to form a given prime or composite knot behaves in terms of the number of ring segments N and confining radius R. For 50 < or =N < or =450 we show that the probability of forming a composite knot rises significantly with the confinement, while the occurrence probability of prime knots are, in general, nonmonotonic functions of 1R. The dependence of other geometrical indicators, such as writhe and chirality, in terms of R and N is also characterized. It is found that the writhe distribution broadens as the confining sphere narrows.

Computer Simulation↗

PubMed2005

Rheology of cholesteric blue phases.

Cholesteric blue phases are a spectacular example of disclination line networks. Here we numerically investigate their response to an imposed Poiseuille flow. We show that shear forces bend and twist and can unzip the disclination lines. Under gentle forcing the network opposes the flow and the apparent viscosity is large. With increased forcing we find strong shear thinning corresponding to the disruption of the network. As the viscosity starts to drop, the imposed flow sets the network into motion. Disclinations break up and re-form with their neighbors along the flow.

Journal Article↗

PubMed2004

Entangled polymers in condensed phases.

We present Monte Carlo results on a model of polymers in a condensed phase, over a range of monomer densities. We imagine cutting a cube out of the system. This cube will typically have several polymer molecules running through its interior, and starting and ending on the boundary. These subchains will be mutually entangled and we present a way to assess the extent of entanglement complexity as a function of the monomer density and the number of subchains in the cube. The model is a set of k self-avoiding and mutually avoiding walks, properly embedded in the cube.

Journal Article↗

PubMed2004

Lattice Boltzmann algorithm for three-dimensional liquid-crystal hydrodynamics.

We describe a lattice Boltzmann algorithm to simulate liquid-crystal hydrodynamics in three dimensions. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be considered. Backflow effects and the hydrodynamics of topological defects are naturally included in the simulations, as are viscoelastic effects such as shear-thinning and shear-banding. We describe the implementation of velocity boundary conditions and show that the algorithm can be used to describe optical bounce in twisted nematic devices and secondary flow in sheared nematics with an imposed twist.

Journal Article↗

PubMed2004

Interplay between shear flow and elastic deformations in liquid crystals.

We study shear flow in liquid crystal cells with elastic deformations using a lattice Boltzmann scheme that solves the full, three-dimensional Beris-Edwards equations of hydrodynamics. We consider first twisted and hybrid aligned nematic cells, in which the deformation is imposed by conflicting anchoring at the boundaries. We find that backflow renders the velocity profile non Newtonian, and that the director profile divides into two regions characterized by different director orientations. We next consider a cholesteric liquid crystal, in which a twist deformation is naturally present. We confirm the presence of secondary flow for small shear rates, and are able to follow the dynamical pathway of shear-induced unwinding, for higher shear rates. Finally, we analyze how the coupling between shear and elastic deformation can affect shear banding in an initially isotropic phase. We find that for a nematic liquid crystal, elastic distortions may cause an asymmetry in the dynamics of band formation, whereas for a cholesteric, shear can induce twist in an initially isotropic sample.

Journal Article↗

PubMed2004

Permeative flows in cholesteric liquid crystals.

We use lattice Boltzmann simulations to solve the Beris-Edwards equations of motion for a cholesteric liquid crystal subjected to Poiseuille flow along the direction of the helical axis (permeative flow). The results allow us to clarify and extend the approximate analytic treatments currently available. We find that if the cholesteric helix is pinned at the boundaries there is an enormous viscosity increase. If, instead, the helix is free the velocity profile is flattened, but the viscosity is essentially unchanged. We highlight the importance of secondary flows, and, for higher flow velocities, we identify a flow-induced double twist structure in the director field--reminiscent of the texture characteristic of blue phases.

Colloids↗

PubMed2004

Biological qualification of blood units: considerations about the effects of sample's handling and storage on stability of nucleic acids.

BACKGROUND: In transfusional setting introduction of nucleic amplification technique (NAT) for HBV-DNA, HCV-RNA and HIV-RNA in biological qualification of blood units suggest some problems. At first the opportunity to operate on mini-pool, at second the need to store the samples at +4 degrees C. The authors therefore have tried to estimate the impact of these conditions on the operativity of NAT testing in the transfusional setting. METHODS: The following parameters has been estimated: distribution of viral-load in untreated subjects, stability of nucleic acids during storage at +4 degrees C, stability of nucleic acids after repeated cycles of freezing and defrosting, robustness of the test to the cross-contamination, definition of the detection-limit (95%). Quantitative tests has been performed by using the following kits: Cobas Amplicor HBV Monitor, Cobas Amplicor HCV Monitor, Cobas Amplicor HIV Monitor; the qualitative tests has been performed by using the following kits: Ampliscreen HBV, Ampliscreen HCV 2,0, Ampliscreen HIV 1,5 all supplied by Roche Molecular System (Brancburg, NJ). RESULTS: Viral load in untreated subjects showed wide variation for HBV, HCV and HIV. HBV has been demonstrated much stable to the conservation +4 degrees C also until 168 h while for HCV and HIV a greater decrease of the viral-load was observed. For all and three virus the conservation to +4 degrees C until 72 h does not seem to involve meaningful fall in the viral-load. A remarkable reduction of the viral-load has been observed after five cycles of freezing and defrosting. All the tests showed a good robustness to cross-contamination. The detection-limit (95%) was 8 U/ml for HBV, 21 U/ml for HCV and 27 copy/ml for HIV. CONCLUSIONS: Samples for NAT testing, can be stored until 72 h to +4 degrees C without appreciable lowering of the viral-load. Repeated cycles of changes of state should be avoided. The tests showed a good robustness to cross-contamination. NAT tests for biological qualification of blood units had a minimal sensibility around 50 (copy/unit/ml). In our experience the detection-limit (95%) was 21 U/ml for HCV, 27 copies/ml for HIV, 8 U/ml for HBV. The availability of NAT test for HBV-DNA, HCV-RNA e HIV-RNA, sensitive and reliable, together with epidemiological data, suggest the opportunity to place side by side, in the biological qualification of the blood units, to add the tests for HBV-DNA and HIV-RNA to the test for HCV-RNA mandatory by low, in Italy in the biological qualification of blood units.

Blood Preservation↗

PubMed2003

RNA denaturation: excluded volume, pseudoknots, and transition scenarios.

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

Models, Chemical↗

PubMed2003

Polymer theta-point as a knot delocalization transition.

We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localized in the high temperature swollen regime, but become delocalized in the low temperature globular phase. Precisely at the collapse transition, the knots are weakly localized. Some of our results can be interpreted in terms of the theory of polymer networks, which allows one to conjecture exact exponents for the knot length probability distributions.

Journal Article↗

PubMed2003

Interstrand distance distribution of DNA near melting.

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga-type model that includes self-avoiding interactions. At the transition temperature and for a large distance r, the distribution decays as 1/r(kappa) with kappa=1+(c-2)/nu. Here nu is the self-avoiding walk correlation length exponent and c is the exponent associated with the entropy of an open loop in the chain. Results for the distribution function just below the melting point are also presented. Numerical simulations that fully take into account the self-avoiding interactions are in good agreement with the scaling approach.

Journal Article↗

PubMed2003

Response to a plaque control regimen on different levels of gingival inflammation.

BACKGROUND: The purpose of the present study was to evaluate the effectiveness of an oral hygiene regimen in subjects presenting with substantially different severity of plaque-associated gingivitis. METHODS: The study population was selected from among a large pool of subjects undergoing an experimental gingivitis trial. At completion of the 21-day plaque accumulation period, 2 sub-groups of subjects were identified on the basis of uppermost and lowest quartile for Gingival Index (GI), respectively classified as highly-inflamed (Hinf; n=17; GI: 1.07+/-0.10) and slightly-inflamed (Sinf; n=22; GI: 0.28+/-0.09) groups. An oral hygiene regimen, based on use of amine fluoride/stannous fluoride-containing toothpaste and mouthrinse, was then prescribed for 21 days. RESULTS: Plaque Index (PI), GI, gingival crevicular fluid (GCF) and Angulated Bleeding Index (AngBI) significantly decreased after treatment in both HInf and SInf groups (p<0.001). However, PI (0.77+/-0.41 vs 0.43+/-0.33, p<0.01), GI (0.23+/-0.30 vs 0.08+/-0.11, p<0.05), GCF (15.23 +/-7.11 vs 7.66+/-2.93, p<0.0000) remained significantly greater in the Hinf group compared to the Sinf group. CONCLUSIONS: These results suggest that 1) an oral hygiene regimen based on amine/stannous fluoride-containing toothpaste and mouthrinse is effective in reducing plaque-associated gingivitis, regardless of pre-existing severity of gingival inflammation; 2) the level of improvement in gingival status, however, is dependent on the pre-existing severity of the inflammatory condition.

Adult↗

PubMed2002

Optimal potentials for predicting inter-helical packing in transmembrane proteins.

A set of pairwise contact potentials between amino acid residues in transmembrane helices was determined from the known native structure of the transmembrane protein (TMP) bacteriorhodopsin by the method of perceptron learning, using Monte Carlo dynamics to generate suitable "decoy" structures. The procedure of finding these decoys is simpler than for globular proteins, since it is reasonable to assume that helices behave as independent, stable objects and, therefore, the search in the conformational space is greatly reduced. With the learnt potentials, the association of the helices in bacteriorhodopsin was successfully simulated. The folding of a second TMP (the helix-dimer glycophorin A) was then accomplished with only a refinement of the potentials from a small number of decoys.

Amino Acids↗

PubMed2001

Dynamical scaling of the DNA unzipping transition.

We report studies of the dynamics of a set of exactly solvable lattice models for the force-induced DNA unzipping transition. Besides yielding the whole equilibrium phase diagram, which reveals a reentrance, these models enable us to characterize the dynamics of the process starting from a nonequilibrium initial condition. The thermal melting of DNA displays a model dependent time evolution. On the contrary, the dynamical mechanism for the unzipping by force is very robust and the scaling behavior is independent of the details of the description and, hence, superuniversal.

DNA↗

PubMed2001

Peculiar scaling of self-avoiding walk contacts.

The nearest neighbor contacts between the two halves of an N-site lattice self-avoiding walk offer an unusual example of scaling random geometry: for N-->infinity they are strictly finite in number but their radius of gyration R(c) is power law distributed proportional to R(-tau)(c), where tau>1 is a novel exponent characterizing universal behavior. A continuum of diverging length scales is associated with the R(c) distribution. A possibly superuniversal tau = 2 is also expected for the contacts of a self-avoiding or random walk with a confining wall.

Journal Article↗

PubMed2001

Phase ordering in nematic liquid crystals.

We study the kinetics of the nematic-isotropic transition in a two-dimensional liquid crystal by using a lattice Boltzmann scheme that couples the tensor order parameter and the flow consistently. Unlike in previous studies, we find that the time dependences of the correlation function, energy density, and number of topological defects obey dynamic scaling laws with growth exponents that, within the numerical uncertainties, agree with the value 1/2 expected from simple dimensional analysis. We find that these values are not altered by the hydrodynamic flow. In addition, by examining shallow quenches, we find that the presence of orientational disorder can inhibit amplitude ordering.

Journal Article↗

PubMed2001

Lattice Boltzmann simulations of liquid crystal hydrodynamics.

We describe a lattice Boltzmann algorithm to simulate liquid crystal hydrodynamics. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be considered. Backflow effects and the hydrodynamics of topological defects are naturally included in the simulations, as are non-Newtonian flow properties such as shear thinning and shear banding.

Journal Article↗

PubMed2001

Zipping and collapse of diblock copolymers.

Using exact enumeration methods and Monte Carlo simulations, we study the phase diagram relative to the conformational transitions of a diblock copolymer in two dimensions. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that, depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen phase to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed, and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.

Journal Article↗