Two-Gaussian excitations model for the glass transition

We develop a modified "two-state" model with Gaussian widths for the site energies of both ground and excited states, consistent with expectations for a disordered system. The thermodynamic properties of the system are analyzed in configuration space and found to bridge the gap between simple two-state models ("logarithmic" model in configuration space) and the random energy model ("Gaussian" model in configuration space). The Kauzmann singularity given by the random energy model remains for very fragile liquids but is suppressed or eliminated for stronger liquids. The sharp form of constant-volume heat capacity found by recent simulations for binary mixed Lennard-Jones and soft-sphere systems is reproduced by the model, as is the excess entropy and heat capacity of a variety of laboratory systems, strong and fragile. The ideal glass in all cases has a narrow Gaussian, almost invariant among molecular and atomic glassformers, while the excited-state Gaussian depends on the system and its width plays a role in the thermodynamic fragility. The model predicts the possibility of first-order phase transitions for fragile liquids. The analysis of laboratory data for toluene and o-terphenyl indicates that fragile liquids resolve the Kauzmann paradox by a first-order transition from supercooled liquid to ideal-glass state at a temperature between T(g) and Kauzmann temperature extrapolated from experimental data. We stress the importance of the temperature dependence of the energy landscape, predicted by the fluctuation-dissipation theorem, in analyzing the liquid thermodynamics.     

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.     

Equilibrium density of states and thermodynamic properties of a model glass former

This paper presents an analysis of the thermodynamics of a model glass former. We have performed equilibrium sampling of a popular binary Lennard-Jones model, employing parallel tempering Monte Carlo to cover the crystalline, amorphous, and liquid regions of configuration space. Disconnectivity graphs are used to visualize the potential energy landscape in the vicinity of a crystalline geometry and in an amorphous region of configuration space. The crystalline global minimum is separated from the bulk of the minima by a large potential energy gap, leading to broken ergodicity in conventional simulations. Our sampling reveals crystalline global minima that are lower in potential energy than some of the previous candidates. We present equilibrium thermodynamic properties based on parallel tempering simulations, including heat capacities and free energy profiles, which depend explicitly on the crystal structure. We also report equilibrium melting temperatures.     

Preferential attachment during the evolution of a potential energy landscape

It has previously been shown that the network of connected minima on a potential energy landscape is scale-free, and that this reflects a power-law distribution for the areas of the basins of attraction surrounding the minima. Here, the aim is to understand more about the physical origins of these puzzling properties by examining how the potential energy landscape of a 13-atom cluster evolves with the range of the potential. In particular, on decreasing the range of the potential the number of stationary points increases and thus the landscape becomes rougher and the network gets larger. Thus, the evolution of the potential energy landscape can be followed from one with just a single minimum to a complex landscape with many minima and a scale-free pattern of connections. It is found that during this growth process, new edges in the network of connected minima preferentially attach to more highly connected minima, thus leading to the scale-free character. Furthermore, minima that appear when the range of the potential is shorter and the network is larger have smaller basins of attraction. As there are many of these smaller basins because the network grows exponentially, the observed growth process thus also gives rise to a power-law distribution for the hyperareas of the basins.     

The potential energy landscape contribution to the dynamic heat capacity

The dynamic heat capacity of a simple polymeric, model glassformer was computed using molecular dynamics simulations by sinusoidally driving the temperature and recording the resultant energy. The underlying potential energy landscape of the system was probed by taking a time series of particle positions and quenching them. The resulting dynamic heat capacity demonstrates that the long time relaxation is the direct result of dynamics resulting from the potential energy landscape. Moreover, the equilibrium (low frequency) portion of the potential energy landscape contribution to the heat capacity is found to increase rapidly at low temperatures and at high packing fractions. This increase in the heat capacity is explained by a statistical mechanical model based on the distribution of minima in the potential energy landscape.     

Thermodynamic anomalies in a lattice model of water

We investigate a lattice-fluid model of water, defined on a three-dimensional body centered cubic lattice. Model molecules possess a tetrahedral symmetry, with four equivalent bonding arms, aiming to mimic the formation of hydrogen bonds. The model is similar to the one proposed by Roberts and Debenedetti [J. Chem. Phys. 105, 658 (1996)], simplified in that no distinction between bond "donors" and "acceptors" is imposed. Bond formation depends both on orientation and local density. In the ground state, we show that two different ordered (ice) phases are allowed. At finite temperature, we analyze homogeneous phases only, working out phase diagram, response functions, the temperature of maximum density locus, and the Kauzmann line. We make use of a generalized first-order approximation on a tetrahedral cluster. In the liquid phase, the model exhibits several anomalous properties observed in real water. In the low temperature region (supercooled liquid), there are evidences of a second critical point and, for some range of parameter values, this scenario is compatible with the existence of a reentrant spinodal.     

Gaussian excitations model for glass-former dynamics and thermodynamics

We describe a model for the thermodynamics and dynamics of glass-forming liquids in terms of excitations from an ideal glass state to a Gaussian manifold of configurationally excited states. The quantitative fit of this three parameter model to the experimental data on excess entropy and heat capacity shows that "fragile" behavior, indicated by a sharply rising excess heat capacity as the glass transition is approached from above, occurs in anticipation of a first-order transition--usually hidden below the glass transition--to a "strong" liquid state of low excess entropy. The distinction between fragile and strong behavior of glass formers is traced back to an order of magnitude difference in the Gaussian width of their excitation energies. Simple relations connect the excess heat capacity to the Gaussian width parameter, and the liquid-liquid transition temperature, and strong, testable, predictions concerning the distinct properties of energy landscape for fragile liquids are made. The dynamic model relates relaxation to a hierarchical sequence of excitation events each involving the probability of accumulating sufficient kinetic energy on a separate excitable unit. Super-Arrhenius behavior of the relaxation rates, and the known correlation of kinetic with thermodynamic fragility, both follow from the way the rugged landscape induces fluctuations in the partitioning of energy between vibrational and configurational manifolds. A relation is derived in which the configurational heat capacity, rather than the configurational entropy of the Adam-Gibbs equation, controls the temperature dependence of the relaxation times, and this gives a comparable account of the experimental observations without postulating a divergent length scale. The familiar coincidence of zero mobility and Kauzmann temperatures is obtained as an approximate extrapolation of the theoretical equations. The comparison of the fits to excess thermodynamic properties of laboratory glass formers, and to configurational thermodynamics from simulations, reveals that the major portion of the excitation entropy responsible for fragile behavior resides in the low-frequency vibrational density of states. The thermodynamic transition predicted for fragile liquids emerges from beneath the glass transition in case of laboratory water and the unusual heat capacity behavior observed for this much studied liquid can be closely reproduced by the model.     

Potential energy and free energy landscapes

Familiar concepts for small molecules may require reinterpretation for larger systems. For example, rearrangements between geometrical isomers are usually considered in terms of transitions between the corresponding local minima on the underlying potential energy surface, V. However, transitions between bulk phases such as solid and liquid, or between the denatured and native states of a protein, are normally addressed in terms of free energy minima. To reestablish a connection with the potential energy surface we must think in terms of representative samples of local minima of V, from which a free energy surface is projected by averaging over most of the coordinates. The present contribution outlines how this connection can be developed into a tool for quantitative calculations. In particular, stepping between the local minima of V provides powerful methods for locating the global potential energy minimum, and for calculating global thermodynamic properties. When the transition states that link local minima are also sampled we can exploit statistical rate theory to obtain insight into global dynamics and rare events. Visualizing the potential energy landscape helps to explain how the network of local minima and transition states determines properties such as heat capacity features, which signify transitions between free energy minima. The organization of the landscape also reveals how certain systems can reliably locate particular structures on the experimental time scale from among an exponentially large number of local minima. Such directed searches not only enable proteins to overcome Levinthal's paradox but may also underlie the formation of "magic numbers" in molecular beams, the self-assembly of macromolecular structures, and crystallization.     

Dielectric relaxation and elasticity during polymerization

A molecular kinetics-elasticity relation has been investigated by using real time dielectric spectroscopy of a diepoxide-triamine liquid mixture polymerizing at 298 K. As the liquid polymerized, the dielectric relaxation time tau increased linearly with the exponential of the known value of the instantaneous shear modulus G(infinity), in agreement with the elastic model for viscous flow but without the effect of temperature. Thus the structure-dependent effect on the Brownian motions are separated from the temperature-dependent effect. In this time-dependent process, increase in G(infinity) may be compensated by an increase in T, thereby keeping G(infinity) and tau constant. In the potential energy landscape paradigm, a polymerizing liquid's state point, like a normal liquid's on cooling, continuously shifts to deeper and lower energy minima of higher curvature, but the shift occurs irreversibly to other parts of the total energy landscape, thus adding a reaction coordinate to the landscape. A minimum in the energy landscape corresponding to a structure formed by polymerization may be identical to a minimum in another landscape corresponding to another structure.     

Protein boson peak originated from hydration-related multiple minima energy landscape

The boson peak is a broad peak found in the low-frequency region of inelastic neutron and Raman scattering spectra in many glassy materials, including biopolymers below approximately 200 K. Here, we give a novel insight into the origins of the protein boson peak, which may also be valid for materials other than proteins. Molecular simulation reveals that the structured water molecules around a protein molecule increase the number of local minima in the protein energy landscape, which plays a key role in the origin of the boson peak. The peak appears when the protein dynamics are trapped within a local energy minimum at cryogenic temperatures. This trapping causes very low frequency collective motions to shift to higher frequencies. We demonstrate that the characteristic frequency of such systems shifts higher as the temperature decreases also in model one-dimensional energy surfaces with multiple minima.     

Global perspectives on the energy landscapes of liquids, supercooled liquids, and glassy systems: the potential energy landscape ensemble

In principle, all of the dynamical complexities of many-body systems are encapsulated in the potential energy landscapes on which the atoms move--an observation that suggests that the essentials of the dynamics ought to be determined by the geometry of those landscapes. But what are the principal geometric features that control the long-time dynamics? We suggest that the key lies not in the local minima and saddles of the landscape, but in a more global property of the surface: its accessible pathways. In order to make this notion more precise we introduce two ideas: (1) a switch to a new ensemble that deemphasizes the concept of potential barriers, and (2) a way of finding optimum pathways within this new ensemble. The potential energy landscape ensemble, which we describe in the current paper, regards the maximum accessible potential energy, rather than the temperature, as a control variable. We show here that while this approach is thermodynamically equivalent to the canonical ensemble, it not only sidesteps the idea of barriers it allows us to be quantitative about the connectivity of a landscape. We illustrate these ideas with calculations on a simple atomic liquid and on the Kob-Andersen [Phys. Rev. E 51, 4626 (1995)] of a glass-forming liquid, showing, in the process, that the landscape of the Kob-Anderson model appears to have a connectivity transition at the landscape energy associated with its empirical mode-coupling transition. We turn to the problem of finding the most efficient pathways through potential energy landscapes in our companion paper.     

A realistic potential model for N-H vector diffusion in proteins

A realistic model for the potential energy for the diffusion of N-H vectors in a protein is proposed, massively modifying the simplistic models currently used in the literature. In particular, a quantitative and analytical connection between the order parameter of the N-H vector diffusion in a protein and the number of potential minima is established, offering a significant insight into the longstanding question of how protein dynamics is affected by the potential-energy landscape. The largest number of potential minima in a protein is estimated to be no more than around 25. In addition, the conformational entropies derived from classical statistical mechanics and quantum statistical mechanics are proved to be identical. Based on the presented theoretical formula, the number of potential minima for each residue of five representative proteins is evaluated and shows a good correlation between local structural flexibility and the number of potential minima.     

Hydrophobic collapse in (in silico) protein folding

A model of hydrophobic collapse, which is treated as the driving force for protein folding, is presented. This model is the superposition of three models commonly used in protein structure prediction: (1) 'oil-drop' model introduced by Kauzmann, (2) a lattice model introduced to decrease the number of degrees of freedom for structural changes and (3) a model of the formation of hydrophobic core as a key feature in driving the folding of proteins. These three models together helped to develop the idea of a fuzzy-oil-drop as a model for an external force field of hydrophobic character mimicking the hydrophobicity-differentiated environment for hydrophobic collapse. All amino acids in the polypeptide interact pair-wise during the folding process (energy minimization procedure) and interact with the external hydrophobic force field defined by a three-dimensional Gaussian function. The value of the Gaussian function usually interpreted as a probability distribution is treated as a normalized hydrophobicity distribution, with its maximum in the center of the ellipsoid and decreasing proportionally with the distance versus the center. The fuzzy-oil-drop is elastic and changes its shape and size during the simulated folding procedure.     

Toward absolute density of states calculations for proteins

The density of states (DOS), which gives the number of conformations with a particular energy E, is a prerequisite in computing most thermodynamic quantities and in elucidating important biological processes such as the mechanism of protein folding. However, current methods for computing DOS of large systems such as proteins generally yield only the ratios of microstate counts for different energies, which could yield absolute conformation counts if the total number of conformations in phase space is known, thus motivating this work. Here, the total number of energy minima of 50-mer polyalanine, whose size corresponds to naturally occurring small proteins, was estimated under an all-atom potential energy function based on the cumulative distribution function (CDF) of conformational differences to be approximately 10(38). This estimate can place any DOS function, such as the Gaussian DOS distribution in the random energy model, on an absolute scale. Comparing the absolute conformational counts from a Gaussian DOS function with those from the CDF derived from quenched molecular dynamics ensembles shows that the former are far greater than the latter, indicating far fewer low-energy minima actually exist. In addition to showing how CDF and relative DOS calculations can yield absolute DOS for a discrete system, we also show how they can yield absolute DOS for continuous variable systems to a specified atomic variance. In the context of protein folding, knowing this phase-space "volume" of conformations in a DOS function, as well as characteristic transition times, constrains the set of possible folding mechanisms.     

The free energy of the metastable supersaturated vapor via restricted ensemble simulations

Pressure, excess chemical potential, and excess free energy, with respect to ideal gas data at different densities of the supersaturated Lennard-Jones particle vapor at the reduced temperature 0.7 are obtained by the restricted canonical ensemble Monte Carlo simulation method [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)]. The excess free energy values depend upon the constraints imposed on the system with local minima exhibited for densities below the spinodal density and monotonic variation for densities larger than the spinodal density. The results are compared with a molecular dynamics simulation study [A. Linharton et al., J. Chem. Phys. 122, 144506 (2005)] on the same system. The current study verifies the conclusion drawn by the simulation work that clustering of Lennard-Jones atoms exists even in the vicinity of spinodal. Our method gives an alternative to molecular dynamic simulations for the determination of equilibrium properties of a metastable fluid, especially close to the spinodal, and does not require a very large system to carry out the simulation.     

Characterizing the first steps of amyloid formation for the ccbeta peptide

We employ constant-temperature and replica exchange molecular dynamics to survey the free energy landscape of the ccbeta peptide using a united-atom potential and an implicit solvent representation. Starting from the experimental coiled-coil structure we observe alpha to beta conversion on increasing the temperature, in agreement with experiment. Various beta-sheet trimers are identified as free energy minima, including one that closely resembles the amyloid beta-sheet model previously proposed from experimental data. We characterize two alternative pathways leading to beta-sheets. The first proceeds via direct alpha to beta conversion without dissociation of the trimer, and the second can be classified as a dissociation/reassociation pathway.     

Symmetric double-well potential model and its application to vibronic spectra: studies of inversion modes of ammonia and nitrogen-vacancy defect centers in diamond

In this paper, we have studied the vibronic transitions between two symmetric double-well potentials by proposing a model Hamiltonian consisting of a harmonic oscillator and a parturition described by a Gaussian function that leads to a double minima potential with a barrier between the two energy minima. Making use of the contour integral form of Hermite polynomials, we present a new formula that can calculate Franck-Condon factors of the system rigorously. The simulated vibronic spectra of ammonia and the negatively charged nitrogen-vacancy center in diamond are presented as an application of the formula.     

Shear-induced disappearances of energy minima and plastic deformation in polymer glasses

The potential energy landscape of a polymer glass is examined with regard to plastic deformation under shear strain. Shear strain is found to cause the disappearance of local potential energy minima, as determined by the decrease to zero of the curvature of the local minima. If the local energy minimum which the system is in disappears, the system becomes mechanically unstable and is forced to relax to an alternate energy minimum. This mechanical instability, which leads to a discontinuous change in system properties, is inherently irreversible—the new local minimum will not disappear, in general, when the strains are reversed. These disappearances of local energy minima and the associated irreversible relaxations lead to plastic deformation in polymer glasses.     

Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the "inherent structure entropy." The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics.     

Thermodynamic behavior and structural properties of an aqueous sodium chloride solution upon supercooling

We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk quantities. We study the isotherms and the isochores for both the aqueous solution and bulk water. The comparison of the phase diagrams shows that thermodynamic properties of the solution are not merely shifted with respect to the bulk. Moreover, from the analysis of the thermodynamic curves, both the spinodal line and the temperatures of maximum density curve can be calculated. The spinodal line appears not to be influenced by the presence of ions at the chosen concentration, while the temperatures of maximum density curve displays both a mild shift in temperature and a shape modification with respect to bulk. Signatures of the presence of a liquid-liquid critical point are found in the aqueous solution. By analyzing the water-ion radial distribution functions of the aqueous solution, we observe that upon changing density, structural modifications appear close to the spinodal. For low temperatures, additional modifications appear also for densities close to that corresponding to a low density configurational energy minimum.