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Pablo G Debenedetti

Publications and source records attributed to Pablo G Debenedetti.

At least 19 recordsLinked to original sources
PubMed2006

Scaled particle theory for hard sphere pairs. I. Mathematical structure.

We develop an extension of the original Reiss-Frisch-Lebowitz scaled particle theory that can serve as a predictive method for the hard sphere pair correlation function g(r). The reversible cavity creation work is analyzed both for a single spherical cavity of arbitrary size, as well as for a pair of identical such spherical cavities with variable center-to-center separation. These quantities lead directly to a prediction of g(r). Smooth connection conditions have been identified between the small-cavity situation where the work can be exactly and completely expressed in terms of g(r), and the large-cavity regime where macroscopic properties become relevant. Closure conditions emerge which produce a nonlinear integral equation that must be satisfied by the pair correlation function. This integral equation has a structure which straightforwardly generates a solution that is a power series in density. The results of this series replicate the exact second and third virial coefficients for the hard sphere system via the contact value of the pair correlation function. The predicted fourth virial coefficient is approximately 0.6% lower than the known exact value. Detailed numerical analysis of the nonlinear integral equation has been deferred to the subsequent paper.

Journal Article↗
PubMed2006

Scaled particle theory for hard sphere pairs. II. Numerical analysis.

We use the extension of scaled particle theory presented in the accompanying paper [F. H. Stillinger et al., J. Chem. Phys. 125, 204504 (2006)] to calculate numerically the pair correlation function of the hard sphere fluid over the density range 0< or =rhosigma(3)< or =0.96. Comparison with computer simulation results reveals that the new theory is able to capture accurately the fluid's structure across the entire density range examined. The pressure predicted via the virial route is systematically lower than simulation results, while that obtained using the compressibility route is lower than simulation predictions for rhosigma(3)< or =0.67 and higher than simulation predictions for rhosigma(3)> or =0.67. Numerical predictions are also presented for the surface tension and Tolman length of the hard sphere fluid.

Journal Article↗
PubMed2006

Computational probes of molecular motion in the Lewis-Wahnstrom model for ortho-terphenyl.

We use molecular dynamics simulations to investigate translational and rotational diffusion in a rigid three-site model of the fragile glass former ortho-terphenyl, at 260 K< or =T< or =346 K and ambient pressure. An Einstein formulation of rotational motion is presented, which supplements the commonly used Debye model. The latter is shown to break down at supercooled temperatures as the mechanism of molecular reorientation changes from small random steps to large infrequent orientational jumps. We find that the model system exhibits non-Gaussian behavior in translational and rotational motion, which strengthens upon supercooling. Examination of particle mobility reveals spatially heterogeneous dynamics in translation and rotation, with a strong spatial correlation between translationally and rotationally mobile particles. Application of the Einstein formalism to the analysis of translation-rotation decoupling results in a trend opposite to that seen in conventional approaches based on the Debye formalism, namely, an enhancement in the effective rate of rotational motion relative to translation upon supercooling.

Journal Article↗
PubMed2006

Family of tunable spherically symmetric potentials that span the range from hard spheres to waterlike behavior.

We investigate the equation of state, diffusion coefficient, and structural order of a family of spherically symmetric potentials consisting of a hard core and a linear repulsive ramp. This generic potential has two characteristic length scales: the hard and soft core diameters. The family of potentials is generated by varying their ratio, lambda. We find negative thermal expansion (thermodynamic anomaly) and an increase of the diffusion coefficient upon isothermal compression (dynamic anomaly) for 0< or =lambda<6/7. As in water, the regions where these anomalies occur are nested domes in the (T, p) or (T, P) planes , with the thermodynamic anomaly dome contained entirely within the dynamic anomaly dome. We calculate translational and orientational order parameters (t and Q6), and project equilibrium state points onto the (t, Q6) plane, or order map. The order map evolves from waterlike behavior to hard-sphere-like behavior upon varying lambda between 4/7 and 6/7. Thus, we traverse the range of liquid behavior encompassed by hard spheres (lanbda=1) and waterlike (lambda approximately 4/7) with a family of tunable spherically symmetric potentials by simply varying the ratio of hard to soft-core diameters. Although dynamic and thermodynamic anomalies occur almost across the entire range 0< or=lambda< or=1, waterlike structural anomalies (i.e., decrease in both t and Q6 upon compression and strictly correlated T and Q6 in the anomalous region) occur only around lambda=4/7. Waterlike anomalies in structure, dynamics and thermodynamics arise solely due to the existence of two length scales, with their ratio lambda being the single control parameter, orientation-dependent interactions being absent by design.

Journal Article↗
PubMed2006

Fluid-phase behavior of binary mixtures in which one component can have two critical points.

We investigate theoretically the binary fluid-phase behavior of mixtures in which one water-like component can have two critical points. We consider three equal-sized nonpolar solutes that differ in the strength of their dispersive interactions (a1 < a2 < a3, where a denotes the van der Waals attractive parameter). In each case, we compare the phase behavior predicted using two sets of parameters for water: one giving rise to a pure component low-temperature liquid-liquid transition terminating at a critical point (two-critical-point parameter set), and one in which no such second critical point exists (singularity-free parameter set). Regardless of the parameter values used, we find five mixture critical lines. Using the two-critical-point parameter set, we find that a critical line originates at water's second critical point for aqueous mixtures involving solutes 1, 2, or 3. For mixtures involving solutes 1 or 2, this line extends towards low pressures and high temperatures as the solute mole fraction increases, and is closely related to the critical line originating at water's ordinary vapor-liquid critical point: these two critical lines are loci of upper and lower consolute points corresponding to the same liquid-liquid transition. In mixtures involving solute 2, the critical locus emanating from water's second critical point is shifted to higher temperatures compared to mixtures involving solute 1, and extends up to T approximately 310 K at moderate pressures (ca. 200 bars). This suggests the possibility of an experimentally accessible manifestation of the existence of a second critical point in water. For binary mixtures involving solutes 1 or 2, changing the water parameters from the two critical points to the singularity-free case causes the disappearance of a lower consolute point at moderate pressures. For binary mixtures involving solute 3, the differences between two-critical-point and singularity-free behaviors occur only in the experimentally difficult-to-probe low-temperature and high-pressure region.

Journal Article↗
PubMed2006

Effect of pressure on the phase behavior and structure of water confined between nanoscale hydrophobic and hydrophilic plates.

We perform systematic molecular dynamics simulations of water confined between two nanoscale plates at T = 300K. We investigate the effect of pressure (-0.15 GPa< or = P< or =0.2GPa) and plate separation (0.4 nm < or =d < or =1.6 nm) on the phase behavior of water when the plates are either hydrophobic or hydrophilic. When water is confined between hydrophobic plates, capillary evaporation occurs between the plates at low enough P. The threshold value of d at which this transition occurs decreases with P (e.g., 1.6 nm at P approximately equal to -0.05 GPa, 0.5 nm at P approximately equal to 0.1 GPa), until, at high P, no capillary evaporation occurs. For d approximately equal to 0.6 nm and P > or =0.1 GPa, the system crystallizes into a bilayer ice. A P-d phase diagram showing the vapor, liquid, and bilayer ice phases is proposed. When water is confined by hydrophilic (hydroxylated silica) plates, it remains in the liquid phase at all P and d studied. Interestingly, we observe for this case that even at the P at which bulk water cavitates, the confined water remains in the liquid state. We also study systematically the state of hydration at different P for both kinds of plates. For the range of conditions studied here, we find that in the presence of hydrophobic plates the effect of P is to enhance water structure and to push water molecules toward the plates. The average orientation of water molecules next to the hydrophobic plates does not change upon pressurization. In contrast, in the presence of hydrophilic plates, water structure is insensitive to P. Hence, our results suggest that upon pressurization, hydrophobic plates behave as "soft" surfaces (in the sense of accommodating pressure-dependent changes in water structure) while hydrophilic walls behave as "hard" surfaces.

Journal Article↗
PubMed2006

Computational characterization of the sequence landscape in simple protein alphabets.

We characterize the "sequence landscapes" in several simple, heteropolymer models of proteins by examining their mutation properties. Using an efficient flat-histogram Monte Carlo search method, our approach involves determining the distribution in energy of all sequences of a given length when threaded through a common backbone. These calculations are performed for a number of Protein Data Bank structures using two variants of the 20-letter contact potential developed by Miyazawa and Jernigan [Miyazawa S, Jernigan WL. Macromolecules 1985;18:534], and the 2-monomer HP model of Lau and Dill [Lau KF, Dill KA. Macromolecules 1989;22:3986]. Our results indicate significant differences among the energy functions in terms of the "smoothness" of their landscapes. In particular, one of the Miyazawa-Jernigan contact potentials reveals unusual cooperative behavior among its species' interactions, resulting in what is essentially a set of phase transitions in sequence space. Our calculations suggest that model-specific features can have a profound effect on protein design algorithms, and our methods offer a number of ways by which sequence landscapes can be quantified.

Amino Acid Sequence↗
PubMed2005

Generating inherent structures of liquids: comparison of local minimization algorithms.

Properties of minima obtained by two different local minimization algorithms, the conjugate gradient and the limited-memory Broyden-Fletcher-Goldfarb-Shanno, are compared for a liquid whose particles interact via a modified Lennard-Jones pair interaction. The average properties of inherent structures obtained by the two minimization procedures are shown to agree within statistical error, though for a given starting configuration the two algorithms may not quench to identical minima.

Journal Article↗
PubMed2005

Novel computational probes of diffusive motion.

Self-diffusion constants, D, and the atomic-level processes that produce them have been investigated numerically for the binary-mixture Lennard-Jones (BMLJ) model and for liquid silica as described by the Van Beest-Kramer-Van Santen interaction model. The primary conceptual tool for this study is the joint probability distribution for single particles as a function of initial velocity and positional displacement at a given later instant. Self-diffusion constants can be expressed exactly in terms of this probability function. The numerical simulations for the BMLJ case reveal an unusual temperature effect; in contrast to the high-temperature behavior, particles with high initial velocities experience disproportionate retardation in forward displacement. In the silica modeling simulations, diffusive processes have been compared at constant-temperature "isodiffusive" pairs of states, demonstrating a significant role played by the amount of local tetrahedral order that is present in the medium.

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PubMed2005

Effects of nonpolar solutes on the thermodynamic response functions of aqueous mixtures.

We investigate the effect of adding nonpolar solutes at atmospheric pressure on water's temperature of maximum density, isothermal compressibility, and isobaric heat capacity, using a statistical mechanical model of water solutions [H. S. Ashbaugh, T. M. Truskett, and P. G. Debenedetti, J. Chem. Phys. 116, 2907 (2002)]. We find that the temperature of maximum density increases with solute hydrophobicity, as characterized by its size, and decreases with its van der Waals attractive parameter a, in agreement with experiment. We predict similar trends for the addition of solutes on the isothermal compressibility and isobaric heat capacity: solute hydrophobicity causes an upward shift in water's anomalies, whereas dispersive interactions as measured by the solute's van der Waals attractive parameter shift the anomalies to lower temperatures. The locus along which the competing contributions of solute size sigma and interaction strength a to the shift in water's response functions balance each other obeys the scaling relationship sigma6 approximately a.

Algorithms↗
PubMed2005

Structural order in glassy water.

We investigate structural order in glassy water by performing classical molecular dynamics simulations using the extended simple point charge (SPC/E) model of water. We perform isochoric cooling simulations across the glass transition temperature at different cooling rates and densities. We quantify structural order by orientational and translational order metrics. Upon cooling the liquid into the glassy state, both the orientational order parameter Q and translational order parameter tau increase. At T=0 K, the glasses fall on a line in the Q-tau plane or order map. The position of this line depends only on density and coincides with the location in the order map of the inherent structures (IS) sampled upon cooling. We evaluate the energy of the IS, eIS(T), and find that both order parameters for the IS are proportional to eIS. We also study the structural order during the transformation of low-density amorphous ice (LDA) to high-density amorphous ice (HDA) upon isothermal compression and are able to identify distinct regions in the order map corresponding to these glasses. Comparison of the order parameters for LDA and HDA with those obtained upon isochoric cooling indicates major structural differences between glasses obtained by cooling and glasses obtained by compression. These structural differences are only weakly reflected in the pair correlation function. We also characterize the evolution of structural order upon isobaric annealing, leading at high pressure to very-high density amorphous ice (VHDA).

Journal Article↗
PubMed2005

A computational study of hydration, solution structure, and dynamics in dilute carbohydrate solutions.

We report results from a molecular simulation study of the structure and dynamics of water near single carbohydrate molecules (glucose, trehalose, and sucrose) at 0 and 30 degrees C. The presence of a carbohydrate molecule has a number of significant effects on the microscopic water structure and dynamics. All three carbohydrates disrupt the tetrahedral arrangement of proximal water molecules and restrict their translational and rotational mobility. These destructuring effects and slow dynamics are the result of steric constraints imposed by the carbohydrate molecule and of the ability of a carbohydrate to form stable H bonds with water, respectively. The carbohydrates induce a pronounced decoupling between translational and rotational motions of proximal water molecules.

Journal Article↗
PubMed2005

Alternative view of self-diffusion and shear viscosity.

By performing an elementary transformation, the conventional velocity autocorrelation function expression for the temperature and density dependent self-diffusion constant D(T,rho) has been reformulated to emphasize how initial particle momentum biases final mean displacement. Using collective flow variables, an analogous expression has been derived for 1/eta(T,rho), the inverse of shear viscosity. The Stokes-Einstein relation for liquids declares that D and T/eta should have a fixed ratio as T and rho vary, but experiment reveals substantial violations for deeply supercooled liquids. Upon analyzing the self-diffusion and viscous flow processes in terms of configuration space inherent structures and kinetic transitions between their basins, one possible mechanism for this violation emerges. This stems from the fact that interbasin transitions become increasingly Markovian as T declines, and though self-diffusion is possible in a purely Markovian regime, shear viscosity in the present formulation intrinsically relies on successive correlated transitions.

Journal Article↗
PubMed2005

Computational investigation of order, structure, and dynamics in modified water models.

Model liquids have been constructed to study the role of local structure in the anomalous properties of liquid water. The intermolecular potentials were modified by increasing the weight of the Lennard-Jones term relative to the electrostatic term in the SPC/E model for water. The resulting family of liquids varies from SPC/E water to a Lennard-Jones-like liquid. Properties were measured as a function of density and temperature. The local structure was described by two order parameters, one measuring the tetrahedral order and the other measuring the translational order. The translational order parameter was found to be large for both tetrahedral and Lennard-Jones liquids, but to go through a minimum as the potentials were modified, demonstrating that the two types of structure are incompatible. Just as in water several properties (e.g., the translational diffusion coefficient, entropy) exhibit anomalous density dependence as a result of the breakdown of local tetrahedrality, we observed nonmonotonic behavior of the translational diffusion constant and reorientational relaxation rate as the fluids were transformed from tetrahedral to Lennard-Jones-like. This is also an indication of the incompatibility between Lennard-Jones and water-like structure.

Journal Article↗
PubMed2004

Simultaneous determination of structural and thermodynamic effects of carbohydrate solutes on the thermal stability of ribonuclease A.

This communication describes a new technique for the study of the effects of carbohydrates on the thermal stability of proteins. This approach combines capillary electrophoresis (CE) and protein charge ladders, collections of proteins that differ incrementally in number of chemically modified charged groups, to provide information on both the thermodynamics (i.e., the free energy, DeltaGN-D, of denaturation), and structural changes (i.e., the effective hydrodynamic radius, RH, of proteins in both the native and denatured states) associated with stability. This information, obtained in a single set of electrophoresis experiments, allows a simple microscopic interpretation of the effects of carbohydrate solutes on protein stability. We use this technique to show that the stabilization of ribonuclease A at pH 8.4 by sucrose and fructose can be explained entirely by the contribution these solutes make to the entropy of formation of the protein-solution interface. There is no need, in this case, to refer to quasichemical concepts such as preferential hydration, binding, or exchange of solutes with water at specific sites on the protein to account for the stabilizing effects observed.

Enzyme Stability↗
PubMed2004

Thermodynamics and the glass transition in model energy landscapes.

We determine the liquid-state thermodynamics for a model energy landscape corresponding to soft spheres with a mean-field attraction. We consider two approximations, in which the distribution of potential energy minima is either Gaussian or binomial, and for each we calculate the liquid spinodal, binodal, and "effective" glass transition locus. The resulting models provide a unified description of the liquid state across the complete range from low-temperature glassiness to high-temperature instability with respect to the vapor phase.

Journal Article↗
PubMed2004

Saddles in the energy landscape: extensivity and thermodynamic formalism.

We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system size, as well as several approximations for the properties of low-order saddles (i.e., those with only a few unstable directions). We then cast the canonical partition function in a saddle-explicit form and develop, for the first time, a rigorous energy landscape approach capable of reproducing trends observed in simulations, in particular, the temperature dependence of the energy and fractional order of sampled saddles.

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