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Biomedical subjects

J J de Pablo

Publications and source records attributed to J J de Pablo.

18 recordsLinked to original sources

A molecular view of melting in anhydrous phospholipidic membranes.

A high-flux backscattering spectrometer and a time-of-flight disk chopper spectrometer are used to probe the molecular mobility of model freeze-dried phospholipid liposomes at a range of temperatures surrounding the main melting transition. Using specific deuteration, quasielastic neutron scattering provides evidence that, in contrast to the hydrocarbon chains, the headgroups of the phospholipid molecules do not exhibit a sharp melting transition. The onset of motion in the tails is located at temperatures far below the calorimetric transition. Long-range motion is achieved through the onset of whole-lipid translation at the melting temperature. Atomistic simulations are performed on a multibilayer model at conditions corresponding to the scattering experiments. The model provides a good description of the dynamics of the system, with predictions of the scattering functions that agree with experimental results. The analysis of both experimental data and results of simulations supports a picture of a gradual melting of the heterogeneous hydrophobic domain, with part of the chains spanning increasingly larger volumes and part of them remaining effectively immobile until the thermodynamic phase transition occurs.

1,2-Dipalmitoylphosphatidylcholine↗

Order-parameter-based Monte Carlo simulation of crystallization.

A Monte Carlo simulation method is presented for simulation of phase transitions, with emphasis on the study of crystallization. The method relies on a random walk in order parameter Phi(q(N)) space to calculate a free energy profile between the two coexisting phases. The energy and volume data generated over the course of the simulation are subsequently reweighed to identify the precise conditions for phase coexistence. The usefulness of the method is demonstrated in the context of crystallization of a purely repulsive Lennard-Jones system. A systematic analysis of precritical and critical nuclei as a function of supercooling reveals a gradual change from a bcc to a fcc structure inside the crystalline nucleus as it grows at large degrees of supercooling. The method is generally applicable and is expected to find applications in systems for which two or more coexisting phases can be distinguished through one or more order parameters.

Journal Article↗

Improved density of states Monte Carlo method based on recycling of rejected states.

In this paper a new algorithm is presented that improves the efficiency of Wang and Landau algorithm or density of states (DOS) Monte Carlo simulations by employing rejected states. The algorithm is shown to have a performance superior to that of the original Wang-Landau [F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)] algorithm and the more recent configurational temperature DOS algorithm. The performance of the method is illustrated in the context of results for the Lennard-Jones fluid.

Journal Article↗

Potential of mean force between two nanometer-scale particles in a polymer solution.

Expanded ensemble density-of-states simulations and a connectivity altering algorithm are used to investigate the effective interactions that arise between nanoparticles suspended in polymer solutions. Our calculations with systems of long polymeric chains reveal oscillations in the effective polymer-induced interactions between the particles, even at low concentrations. The range of these interactions is considerably longer than originally anticipated, and their origin is traced back to the chain-end effects and density fluctuations that were absent in previous treatments of these systems.

Journal Article↗

Quenched disorder in a liquid-crystal biosensor: adsorbed nanoparticles at confining walls.

We analyze the response of a nematic liquid-crystal film, confined between parallel walls, to the presence of nanoscopic particles adsorbed at the walls. This is done for a variety of patterns of adsorption (random and periodic) and operational conditions of the system that can be controlled in experimental liquid-crystal-based devices. We compute simulated optical textures and the total optical output of the sensor between crossed polars, as well as the correlation function for the liquid-crystal tensor order parameter; we use these observables to discuss the gradual destruction of the original uniform orientation. For large concentrations of particles adsorbed in random patterns, the liquid crystal at the center of the sensor adopts a multidomain state, characterized by a small correlation length of the tensor order parameter, and also by a loss of optical anisotropy under observation through crossed polars. In contrast, for particles adsorbed in periodic patterns, the nematic at the center of the cell can remain in a monodomain orientation state, provided the patterns in opposite walls are synchronized.

Adsorption↗

Slow dynamics of thin nematic films in the presence of adsorbed nanoparticles.

Recent experiments indicate that liquid crystals can be used to optically report the presence of biomolecules adsorbed at solid surfaces. In this work, numerical simulations are used to investigate the effects of biological molecules, modeled as spherical particles, on the structure and dynamics of nematic ordering. In the absence of adsorbed particles, a nematic in contact with a substrate adopts a uniform orientational order, imposed by the boundary conditions at this surface. It is found that the relaxation to this uniform state is slowed down by the presence of a small number of adsorbed particles. However, beyond a critical concentration of adsorbed particles, the liquid crystal ceases to exhibit uniform orientational order at long times. At this concentration, the domain growth is characterized by a first regime where the average nematic domain size LD obeys the scaling law LDt approximately t1/2; at long times, a slow dynamics regime is attained for which LD tends to a finite value corresponding to a metastable state with a disordered texture. The results of simulations are consistent with experimental observations.

Journal Article↗

Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels.

The conformation and diffusion of a single DNA molecule confined between two parallel plates are examined using both single molecule experiments and Brownian dynamics simulations accounting for hydrodynamic interactions. The degree of chain stretching and the diffusivity are characterized as a function of the chain confinement and the channel geometry. Good agreement is found between the simulations, experiments, and scaling theory predictions.

Computer Simulation↗

Polymer-particle mixtures: depletion and packing effects.

The structure of polymers in the vicinity of spherical colloids is investigated by Monte Carlo simulations and integral equation theory. Polymers are represented by a simple bead-spring model; only repulsive Lennard-Jones interactions are taken into account. Using advanced trial moves that alter chain connectivity, depletion and packing effects are analyzed as a function of chain length and density, both at the bond and the chain level. Chain ends segregate to the colloidal surface and polymer bonds orient parallel to it. In the dilute regime, the polymer chain length governs the range of depletion and has a negligible influence on monomer packing in dense polymer melts. Polymers adopt an ellipsoidal shape, with the larger axis parallel to the surface of the particle, as they approach larger colloids. The dimensions are perturbed within the range of the depletion layer.

Journal Article↗

Monte Carlo molecular simulation of the hydration of Na-montmorillonite at reservoir conditions.

The hydration of Na-saturated Wyoming-type montmorillonite is investigated by Monte Carlo simulations at constant stress in the NP(zz)T ensemble and at constant chemical potential in the microVT ensemble, at the sedimentary basin temperature of 353 K and pressure of 625 bar, equivalent to 2-4 km depth. The simulations use procedures established in Chavez-Paez et al. [J. Chem. Phys. 114, 1405 (2001)]. At these conditions, simulations predict a single stable form of 1,2-water layer Na-montmorillonite, containing 164.38 mg/g or 53.37 molecules/layer of adsorbed water and having a spacing of 12.72 A. The corresponding density is 0.32 g/ml. Sodium ions are coordinated with six molecules of water separated 2.30-2.33 A. Water molecules are closer to the central interlayer plane and the spacing is larger than that at 300 K and 1 bar. The interlayer configuration consists of two symmetrical layers of oriented water molecules 1.038 A from the central plane, with the hydrogen atoms in two outermost layers, 3.826 A apart, and the sodium ions on the central plane located between the water layers. The interlayer configuration can be considered to be a stable two-layer intermediate between the one- and two-layer hydrates. Our simulations do not predict formation of other hydrates of Na-montmorillonite at 353 K and 615 bar.

Journal Article↗

Defect structure around two colloids in a liquid crystal.

This Letter investigates the defect structures that arise between two colloidal spheres immersed in a nematic liquid crystal. Molecular simulations and a dynamic field theory are employed to arrive at molecular-level and mesoscopic descriptions of the systems of interest. At large separations, each sphere is surrounded by a Saturn ring defect. However, at short separations both theory and simulation predict that a third disclination ring appears in between the spheres, in a plane normal to the Saturn rings. This feature gives rise to an effective binding of the particles. The structures predicted by field theory and molecular simulations are consistent with each other.

Biosensing Techniques↗

Dynamic interaction between suspended particles and defects in a nematic liquid crystal.

Insertion of spherical particles into a uniform nematic liquid crystal gives rise to the formation of topological defects. In the present work, we investigate how a spherical particle accompanied by its topological defects interacts with neighboring disclination lines. We perform two- and three-dimensional dynamic simulations to analyze the effect of a particle on the annihilation process of two disclination lines. The dynamics of the liquid crystal is described by a time-dependent evolution equation on the symmetric traceless order parameter that includes some of the salient features of liquid crystalline materials: excluded volume effects, or equivalently, short-range order elasticity and long-range order elasticity. At the surface of the particle, the liquid crystal is assumed to exhibit strong homeotropic anchoring. The particle is located between two disclination lines of topological charges +1/2 and -1/2. Two-dimensional simulations indicate that the topological defects bound to the particle mediate an interaction between the two disclination lines which increases the attraction between them. This result is confirmed by three-dimensional simulations that provide a complete description of the director field and of the order parameter around the particle. These simulations indicate that a spherical particle between two disclination lines can be surrounded by a Saturn ring, and suggest that the dynamic behavior of disclination lines could be used to report the structure of a defect around the particle.

Journal Article↗

Spherical particle immersed in a nematic liquid crystal: effects of confinement on the director field configurations.

The effects of confinement on the director field configurations are studied for a spherical particle immersed in a nematic liquid crystal. The liquid crystal is confined in a cylindrical geometry and the particle is located on the axis of symmetry. A finite element method is used to minimize the Frank free energy for various sizes of the system. The liquid crystal is assumed to possess strong anchoring at all the surfaces in the system. Two structures are examined for strong homeotropic anchoring at the surface of the particle: configuration with a Saturn ring disclination line and configuration with a satellite point defect (hedgehog defect). It is shown that the equilibrium locations of the Saturn ring and of the hedgehog point defect change with confinement. It is also found that confinement induces an increase in the elastic free energy that differs substantially with the type of topological defect under consideration. In particular, the evaluation of the total free energy that includes an approximate contribution for the core defect shows that, for micrometer-sized particles in confined systems, the Saturn ring configuration appears to be more stable than the hedgehog defect. This result is in contrast to the bulk situation, where the hedgehog is more stable than the Saturn ring, and it helps explain recent experimental observations of Saturn ring defects around confined micrometer-sized solid particles.

Journal Article↗

Phase equilibria of size-asymmetric primitive model electrolytes.

The low-temperature phase coexistence of size-asymmetric primitive model electrolyte solutions has been investigated by means of Monte Carlo simulations. Binodal curves and critical parameters are reported as a function of size ratio lambda = sigma(+)/sigma(-) in the range 0.05 to 1. Both the critical temperature and the critical density are found to decrease as lambda decreases. These trends are in conflict with available theoretical predictions. For highly asymmetric systems, the depression of the critical parameters is accompanied by the formation of large chainlike and ringlike structures, thereby giving rise to considerable finite-size effects.

Journal Article↗

Molecular simulation of ultrathin polymeric films near the glass transition.

Properties such as the glass transition temperature ( T(g)) and the diffusion coefficient of ultrathin polymeric films are shown to depend on the dimensions of the system. In this work, a hard-sphere molecular dynamics methodology has been applied to simulate such systems. We investigate the influence that substrates have on the behavior of thin polymer films; we report evidence suggesting that, depending on the strength of substrate-polymer interactions, the glass transition temperature for a thin film can be significantly lower or higher than that of the bulk.

Journal Article↗

Stabilization and preservation of Lactobacillus acidophilus in saccharide matrices.

Lyophilization and vacuum- or spray-drying are some of the most useful techniques for preserving foods, agricultural products, and pharmaceuticals. Biological materials, however, can be irreversibly damaged during these treatments. Therefore, it is essential to design protective agents to preserve protein activity and cell viability. In this paper we examine the use of alpha, alpha-trehalose-borate systems as protectants for Lactobacillus acidophilus during freeze- and vacuum-drying. Trehalose was found to be an effective protectant for freeze-dried and vacuum-dried samples, and it is equivalent to a protective formulation which is in current industrial use. It is known from our previous work on enzymes that the presence of borate can dramatically enhance the protective ability of trehalose. In this work, the addition of trehalose-borate to bacterial concentrate greatly improves the recovery of viable cells after storage. This improvement was seen in freeze-dried samples stored at 37 degrees C as well as for vacuum-dried samples held at room temperature. A tailored buffering strategy was tested to counteract the high pH resulting from the addition of borate to the mixture. Use of citric or lactic acids in combination with ammonium hydroxide gave a protectant solution with high pH (resulting in effective crosslinking between trehalose and borate) but a dry product with reduced pH upon rehydration (conducive to cell survival). These results raise exciting possibilities for protection of more labile prokaryotic species as well as simple eukaryotes.

Ammonium Hydroxide↗

Simulation of phase transitions in fluids.

This review provides a discussion of recent techniques for simulation of phase equilibria of complex fluids. Monte Carlo methods are emphasized over molecular dynamics methods. We describe recent developments, such as the use of expanded-ensemble, tempering, or histogram reweighting techniques. Our discussion of such developments is aimed at a general audience and is intended to provide an overview of the main advantages and limitations of each particular technique. References are provided to allow interested readers to identify and trace back most recent applications of a particular simulation technique. We conclude with general guidelines regarding selection of suitable simulation methods for particular problems and systems of interest.

Journal Article↗

Stabilization of lactate dehydrogenase following freeze thawing and vacuum-drying in the presence of trehalose and borate.

PURPOSE: The purpose of this work was to investigate the effects of trehalose and trehalose/sodium tetraborate mixtures on recovery of lactate dehydrogenase (LDH) activity following freeze-thawing and centrifugal vacuum-drying/rehydration. The storage stability of LDH under conditions of either high relative humidity or high temperature was also studied. METHODS: LDH was prepared in buffered aqueous formulations containing trehalose alone and trehalose/"borate" mixtures. Enzymatic activity was measured immediately following freeze-thawing and vacuum-drying/rehydration processes, and also after vacuum-dried formulations were stored in either high humidity or high temperature environments. Also, glass transition temperatures (Tg) were measured for both freeze-dried and vacuum-dried formulations. RESULTS: The Tg values of freeze-dried trehalose/borate mixtures are considerably higher than that of trehalose alone. Freezing and vacuum-drying LDH in the presence of 300 mM trehalose resulted in the recovery of 80% and 65% of the original activity, respectively. For vacuum-dried mixtures, boron concentrations below 1.2 mole boron/ mole trehalose had no effect on recovered LDH. After several weeks storage in either humid (100% relative humidity) or warm (45 degrees C) environments, vacuum-dried formulations that included trehalose and borate showed greater enzymatic activities than those prepared with trehalose alone. We attribute this stability to the formation of a chemical complex between trehalose and borate. CONCLUSIONS: The high Tg values of trehalose/borate mixtures offer several advantages over the use of trehalose alone. Most notable is the storage stability under conditions of high temperature and high relative humidity. In these cases, formulations that contain trehalose and borate are superior to those containing trehalose alone. These results have practical implications for long-term storage of biological materials.

Borates↗

Thermophysical properties of trehalose and its concentrated aqueous solutions.

PURPOSE: To address the lack of fundamental thermophysical data for trehalose and its aqueous systems by measuring equilibrium and non-equilibrium properties of such systems. METHODS/RESULTS: Differential scanning calorimetry (DSC) and dynamic mechanical analysis were used to measure glass transition temperatures of trehalose and its solutions. X-ray diffractometry was used to verify the structure of amorphous trehalose. Controlled-stress rheometry was used to measure viscosity of several aqueous trehalose systems at ambient and sub-ambient temperatures. Over this temperature range, the density of these solutions was also measured with a vibrating tube densimeter. The equilibrium phase diagram of aqueous trehalose was determined by measuring the solubility and freezing point depression. CONCLUSIONS: Our solubility measurements, which have allowed long times for attainment of chemical equilibrium, are substantially different from those reported earlier that used different techniques. Our measurements of the glass transition temperature of trehalose are higher than reported values. A simple model for the glass transition is presented to describe our experimental observations.

Calorimetry, Differential Scanning↗