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The structural evolution of surface gratings on a glassy material is investigated by means of molecular simulations. The gratings provide a means to probe surface diffusion in the vicinity of the glass transition temperature. A theory by Mullins [J. Appl. Phys. 30, 77 (1959)] is used to extract qu-antitative measures of surface diffusivity that rely on calculation of grating amplitude as a function of time. The simulations are implemented in the context of a model binary glass mixture [S. S. Ashwin and S. Sastry, J. Phys.: Condens. Matter 15, S1253 (2003)]. We find that surface diffusion is faster than bulk diffusion by several orders of magnitude, consistent with recent experimental data for an organic glass former. The diffusivities extracted by the grating-decay approach are consistent with those estimated on the basis of mean-squared particle displacements. The grating-decay approach, however, is more efficient than traditional techniques based on Einstein's diffusion equation. Grating decay is also more versatile and is shown to be applicable in a variety of sample geometries. [ABSTRACT FROM AUTHOR]

We present a coarse grain representation for Gaussian chains in the presence of hard surfaces. Whereas a Gaussian chain in the bulk can be represented by a bead-spring model with a quadratic potential between adjacent beads, the presence of a surface reduces the number of allowed chain configurations and modifies the effective potential between the beads. We derive the corrected potentials for several surface geometries: a single wall, two parallel walls (slit), and a spherical or cylindrical object (nanoparticle). Those potentials can be used in any model that includes a Gaussian chain, regardless of the simulation method. As an illustration, we consider a coarse grain model of a polymeric melt and, using Monte Carlo simulations, we compute the density profiles for (i) a melt confined in a slit and (ii) a melt in the vicinity of a nanoparticle. The case of a polymeric solution confined within a slit is also addressed, and the proposed approach is shown to yield results in qualitative agreement with those obtained with field-theoretic simulations. [ABSTRACT FROM AUTHOR]

A growing body of experimental evidence indicates that the interaction between amyloid β peptide and lipid bilayer membranes plays an important role in the development of Alzheimer disease. Recent experimental evidence also suggests that trehalose, a simple disaccharide, reduces the toxicity of amyloid β peptide. Molecular simulations are used to examine the effect of trehalose on the conformational stability of amyloid β peptide in aqueous solution and its effect on the interaction between amyloid β peptide and a model phospholipid bilayer membrane. It is found that, in aqueous solution, the peptide exhibits a random coil conformation but, in the presence of trehalose, it adopts an alpha helical conformation. It is then shown that the insertion of amyloid β peptide into a membrane is more favorable when the peptide is folded into an α-helix than in a random coil conformation, thereby suggesting that trehalose promotes the insertion of α-helical amyloid β into biological membranes. [ABSTRACT FROM AUTHOR]

Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington’s disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a β-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded β-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable β-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability. [ABSTRACT FROM AUTHOR]

The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations. [ABSTRACT FROM AUTHOR]

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 [uppercase_phi_synonym](qN) 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 LD(t)∼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.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A model was developed for predicting the collapse behavior of photoresist structures due to the drying of rinse liquids during wet chemical processing. The magnitude of the capillary forces was estimated using the classical thermodynamics of surface tension, and the deformation of the structure was modeled using beam bending mechanics that accounts for both elastic and plastic modes of deformation. The two-dimensional model can predict the critical beam height of collapse as a function of the wetting behavior of the rinse liquid on the beam, the elastic and plastic mechanical properties of the polymeric photoresist, and the beam dimensions. Collapse behavior was predicted for polymer nanostructures with elastoplastic mechanical properties similar to those of bulk poly(methyl methacrylate). We have compared the collapse predictions from our model with the results of models that account only for elastic or plastic deformation behavior. Regimes in the elastic-plastic mechanical property space for which it is necessary to use the developed beam bending model have been highlighted. It is shown that in some cases the inclusion of both elastic and plastic mechanical properties is necessary for modeling the collapse behavior of polymer beams fabricated using the lithographic process. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The hydration of Na-saturated Wyoming-type montmorillonite is investigated by Monte Carlo simulations at constant stress in the NP[sub zz]T ensemble and at constant chemical potential in the μVT 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 Chávez-Páez 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 Å. The corresponding density is 0.32 g/ml. Sodium ions are coordinated with six molecules of water separated 2.30–2.33 Å. 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 Å from the central plane, with the hydrogen atoms in two outermost layers, 3.826 Å 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. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Monte Carlo simulations and dynamic field theory are used to study spherical particles suspended in a nematic liquid crystal. Within these two approaches, we investigate the binding of the defects to the particles, the adsorption of a particle at a solid surface, and two particles interacting with each other. Quantitative comparisons indicate good agreement between the two approaches. A Monte Carlo method based on the combination of canonical expanded ensemble simulations with a density-of-state formalism is used to determine the potential of mean force between one particle and a hard wall. On the other hand, the potential of mean force is evaluated using a dynamic field theory, where the time-dependent evolution of the second rank tensor includes two major aspects of liquid crystalline materials, namely the excluded volume and the long-range order elasticity. The results indicate an effective repulsive force that acts between the particle and the wall. Layer formation at the surface of the hard wall gives rise to local minima in the potential of mean force. The director profile for a particle at contact with a solid surface is characterized by a disclination line distorted and attracted towards the wall. The structure of the nematic for two particles at short distances is also investigated. Our results indicate a structure where the two particles are separated by a circular disclination line. The potential of mean force associated with this configuration indicates an effective attractive interaction between the two particles. [ABSTRACT FROM AUTHOR]

In this work a novel Monte Carlo method is developed to simulate the equilibrium thermodynamic properties of strongly associating fluids. The highly anisotropic nature of intermolecular interactions in these fluids makes conventional simulation techniques of little use. By introducing biased sampling techniques we are able to explore configuration space efficiently, thereby obtaining reliable estimates for the thermodynamic properties, including phase equilibria, of model systems. The results of our simulations are used to assess the accuracy and validity of various theories for associating fluids. [ABSTRACT FROM AUTHOR]

We have studied the kinematics and rheological properties of undiluted polymers by modeling the fluids as a collection of interacting Kramers freely jointed bead–rod chains with anisotropic friction using Brownian dynamics simulations. The anisotropic friction depends on the instantaneous configuration of the system. The resulting stochastic differential equations have multiplicative noise. The correlation of the ‘‘Langevin’’ Brownian forces appearing in these equations turns out to be anisotropic as well. The excluded volume effect, often ignored in kinetic theory, plays an important role in the behavior of short polymer chains. The chain kinematics may be distorted in its absence. In this work, we also discuss the effects of two types of excluded volume (EV) forces (hard-sphere and soft-repulsive forces) on rheological properties of concentrated polymer solutions. [ABSTRACT FROM AUTHOR]

The assembly of lamella-forming block copolymer blend thin films on chemically nanopatterned striped surfaces was monitored in real time with small angle x-ray scattering (SAXS) in transmission mode. The strongest diffraction from the assembled grating structure was detected after 4.5 min of annealing as the temperature was ramped from 100 to 240 °C at a rate of about 20 °C/min. Real-space images were also obtained from samples annealed for specific times using top-down scanning electron microscopy (SEM) and this identified structures formed during annealing that are unique to the block copolymer blends. The data are compared to previously reported SEM and molecular simulation studies with pure block copolymers. Because it can be used in real time and probes the entire film thickness, transmission SAXS proved to be a useful tool for better understanding the block copolymer annealing process. [ABSTRACT FROM AUTHOR]

Monte Carlo simulations have been used to predict the interlayer basal separations of sodium-saturated Wyoming clays at constant stress (NP[sub zz]T ensemble) and at constant chemical potential (μVT ensemble). These simulations use the Ewald summation technique to incorporate long-range Coulombic interactions in the calculation of the total potential energy and the pressure tensor. A comparison is made between the use of one, two, and three sheets of clay. It is shown that, for small separations, at least two separate clay sheets must be used to avoid system-size effects. The stable interlamellar separations are determined by combining results from isostress-isothermal and grand canonical simulations. It is shown that, consistent with experiments, at the temperature and pressure studied here, the cations in the interlayer are hydrated, except at the smallest basal separations. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We have performed Monte Carlo simulations of a three-dimensional quenched-annealed system on a cubic lattice with nearest-neighbor interactions. A small fraction of the lattices sites are blocked, thereby creating a quenched matrix. Histogram reweighting techniques are applied to investigate the critical behavior of the system. We have studied lattice sizes ranging from L=10 to L=18. For each size, we have evaluated the number of matrix replicas necessary to obtain statistically meaningful results. This number, determined by analyzing the convergence of the histograms, ranged from 50 for the smallest system sizes to 200 for the largest sizes. We have evaluated the critical temperature, the fourth cumulant of Binder et al. [K. K. Kaski, K. Binder, and J. D. Gunton, Phys. Rev. B 29, 3996 (1984)], and the critical exponents 1/ν and β/ν. The estimated critical temperature is only slightly lower than that of the three-dimensional Ising model. The simulated critical exponents, however, differ significantly from those for Ising-class three- and two-dimensional systems. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A continuum theory is used to study the interactions between nanoparticles suspended in nematic liquid crystals. The free energy functional that describes the system is minimized using an Euler-Lagrange approach and an unsymmetric radial basis function method. It is shown that nanoparticle liquid-crystal mediated interactions can be controlled over a large range of magnitudes through changes of the anchoring energy and the particle diameter. The results presented in this work serve to reconcile past discrepancies between theoretical predictions and experimental observations, and suggest intriguing possibilities for directed nanoparticle self-assembly in liquid crystalline media., (© 2012 American Chemical Society)

A growing body of experimental evidence indicates that the interaction between amyloid beta peptide and lipid bilayer membranes plays an important role in the development of Alzheimer disease. Recent experimental evidence also suggests that trehalose, a simple disaccharide, reduces the toxicity of amyloid beta peptide. Molecular simulations are used to examine the effect of trehalose on the conformational stability of amyloid beta peptide in aqueous solution and its effect on the interaction between amyloid beta peptide and a model phospholipid bilayer membrane. It is found that, in aqueous solution, the peptide exhibits a random coil conformation but, in the presence of trehalose, it adopts an alpha helical conformation. It is then shown that the insertion of amyloid beta peptide into a membrane is more favorable when the peptide is folded into an alpha-helix than in a random coil conformation, thereby suggesting that trehalose promotes the insertion of alpha-helical amyloid beta into biological membranes.

A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.

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.

The conformation and dynamics of a single DNA molecule undergoing oscillatory pressure-driven flow in microfluidic channels is studied using Brownian dynamics simulations, accounting for hydrodynamic interactions between segments in the bulk and between the chain and the walls. Oscillatory flow provides a scenario under which the polymers may remain in the channel for an indefinite amount of time as they are stretched and migrate away from the channel walls. We show that by controlling the chain length, flow rate and oscillatory flow frequency, we are able to manipulate the chain extension and the chain migration from the channel walls. The chain stretch and the chain depletion layer thickness near the wall are found to increase as the Weissenberg number increases and as the oscillatory frequency decreases.

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.

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.

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.

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.

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.

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.

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., (Copyright 2000 Academic Press.)

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.

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.

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.