Random energy model for dynamics in supercooled liquids: N dependence

The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding

The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.

What does the instantaneous normal mode spectrum tell us about dynamical heterogeneity in glass-forming fluids?

We examine the instantaneous normal mode spectrum of model metallic and polymeric glass-forming liquids. We focus on the localized modes in the unstable part of the spectrum [unstable localized (UL) modes] and find that the particles making the dominant contribution to the participation ratio form clusters that grow upon cooling in a fashion similar to the dynamical heterogeneity in glass-forming fluids, i.e., highly mobile (or immobile) particles form clusters that grow upon cooling; however, a comparison of the UL mode clusters to the mobile and immobile particle clusters indicates that they are distinct entities. We also show that the cluster size provides an alternate method to distinguish localized and delocalized modes, offering a significant practical advantage over the finite-size scaling approach. We examine the trajectories of particles contributing most to the UL modes and find that they have a slightly enhanced mobility compared to the average, and we determine a characteristic time quantifying the persistence time of this excess mobility. This time scale is proportional to the structural relaxation time τ_α of the fluid, consistent with a prediction by Zwanzig [Phys. Rev. 156, 190 (1967)] for the lifetime of collective excitations in cooled liquids. Evidently, these collective excitations serve to facilitate relaxation but do not actually participate in the motion associated with barrier crossing events governing activated transport. They also serve as a possible concrete realization of the "facilitation" clusters postulated in previous modeling of glass-forming liquids.

Instantaneous normal modes and the protein glass transition

In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at approximately 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.

Understanding fragility in supercooled Lennard-Jones mixtures. II. Potential energy surface

The connection between isobaric fragility and the properties of high-order stationary points of the potential energy surface in different supercooled Lennard-Jones mixtures was investigated. The increase of effective activation energies upon supercooling appears to be driven by the increase of average potential energy barriers measured by the energy dependence of the fraction of unstable modes. Such an increase is sharper, the more fragile the mixture. Correlations between fragility and other properties of high-order stationary points, including the vibrational density of states and the localization features of unstable modes, are also discussed.

Diffusivity, excess entropy, and the potential-energy landscape of monatomic liquids

The connection between thermodynamic, transport, and potential-energy landscape features is studied for liquids with Lennard-Jones-type pair interactions using both microcanonical molecular-dynamics and isothermal-isobaric ensemble Monte Carlo simulations. Instantaneous normal-mode and saddle-point analyses of two variants of the monatomic Lennard-Jones liquid have been performed. The diffusivity is shown to depend linearly on several key properties of instantaneous and saddle configurations-the energy, the fraction of negative curvature directions, and the mean, maximum, and minimum eigenvalues of the Hessian. Since the Dzugutov scaling relationship also holds for such systems [Nature (London) 381, 137 (1996)], the exponential of the excess entropy, within the two-particle approximation, displays the same linear dependence on energy landscape properties as the diffusivity.

Determining landscape-based criteria for freezing of liquids

The correlation between statistical properties of the energy landscape and the number of accessible configurational states, as measured by the exponential of the excess entropy (e(Se)), are studied in the case of a simple Lennard-Jones-type liquid in the neighborhood of the thermodynamic freezing transition. The excess entropy Se is defined as the difference between the entropy of the liquid and that of the ideal gas under identical temperature and pressure conditions and is estimated using the pair correlation contribution, S2. Landscape properties associated with three categories of configurations are considered: instantaneous configurations, inherent saddles, and inherent minima. Landscape properties studied include the energy and the key parameters of the Hessian eigenvalue distribution as well as the mean distances between instantaneous configurations and the corresponding inherent saddles and minima. The signatures of the thermodynamic freezing transition are clearest in the case of inherent structure properties which show, as a function of e(S2), a pronounced change in slope in the vicinity of the solid-liquid coexistence. The mean distance between instantaneous and saddle configurations also shows a similar change in slope when the system crosses from the stable to the supercooled regime. In the case of inherent saddles, the minimum eigenvalue acts as a similar indicator of the thermodynamic freezing transition but the average and maximum eigenvalues do not carry similar signatures. In the case of instantaneous configurations, a weak indicator of the thermodynamic freezing transition is seen in the behavior of the fraction of negative curvature directions as a function of the exponential of the excess entropy.

On the mechanism of reorientational and structural relaxation in supercooled liquids: the role of border dynamics and cooperativity

Molecular dynamics simulation and analysis based upon the many-body potential energy landscape (PEL) are employed to characterize single molecule reorientation and structural relaxation, and their interrelation, in deeply supercooled liquid CS(2). The rotational mechanism changes from small-step Debye diffusion to sudden large angle reorientation (SLAR) as the temperature falls below the mode-coupling temperature T(c). The onset of SLAR is explained in terms of the PEL; it is an essential feature of low-T rotational dynamics, along with the related phenomena of dynamic heterogeneity and the bifurcation of slow and fast relaxation processes. A long trajectory in which the system is initially trapped in a low energy local minimum, and eventually escapes, is followed in detail, both on the PEL and in real space. During the trapped period, "return" dynamics occurs, always leading back to the trap. Structural relaxation is identified with irreversible escape to a new trap. These processes lead to weak and strong SLAR, respectively; strong SLAR is a clear signal of structural relaxation. Return dynamics involves small groups of two to four molecules, while a string-like structure composed of all the active groups participates in the escape. It is proposed that, rather than simple, nearly instantaneous, one-dimensional barrier crossings, relaxation involves activation of the system to the complex, multidimensional region on the borders of the basins of attraction of the minima for an extended period.

Fifth-order two-dimensional Raman spectroscopy of liquid water, crystalline ice Ih and amorphous ices: Sensitivity to anharmonic dynamics and local hydrogen bond network structure

The theoretical study of off-resonant fifth-order two-dimensional (2D)-Raman spectroscopy is made to analyze the intermolecular dynamics of liquid and solid water. The 2D-Raman spectroscopy is susceptible to the nonlinear anharmonic dynamics and local hydrogen bond structure in water. It is found that the distinct 2D-Raman response appears as the negative signal near the t(2) axis. The origin of this negative signal for t(2)<15 fs is from the nonlinear polarizability in the librational motions, whereas that for 30 fs<t(2)<150 fs is attributed to the anharmonic translational motions. It is found that the mechanical anharmonicity and nonlinear polarizability couplings among modes clearly can be observed as the sum- and difference-frequency peaks in the 2D-Raman spectrum (i.e., Fourier transforms of the response). The 2D-Raman spectroscopies of ice Ih and amorphous ices, i.e., low density, high density, and very high density amorphous ices, are also investigated. It is found that the 2D-Raman spectroscopy is very sensitive to the anisotropy of the structure of ice Ih. The strong hydrogen bond stretching band is seen in the 2D-Raman spectroscopy of the polarization directions parallel to the c axis, whereas the contributions of the librational motion can be also seen in the spectrum with the polarization directions parallel to the a axis. The 2D-Raman spectroscopy is also found to be also very sensitive to the differences in local hydrogen bond network structures in various amorphous phases.

Non-Gaussian energy landscape of a simple model for strong network-forming liquids: Accurate evaluation of the configurational entropy

We present a numerical study of the statistical properties of the potential energy landscape of a simple model for strong network-forming liquids. The model is a system of spherical particles interacting through a square-well potential, with an additional constraint that limits the maximum number of bonds Nmax per particle. Extensive simulations have been carried out as a function of temperature, packing fraction, and Nmax. The dynamics of this model are characterized by Arrhenius temperature dependence of the transport coefficients and by nearly exponential relaxation of dynamic correlators, i.e., features defining strong glass-forming liquids. This model has two important features: (i) Landscape basins can be associated with bonding patterns. (ii) The configurational volume of the basin can be evaluated in a formally exact way, and numerically with an arbitrary precision. These features allow us to evaluate the number of different topologies the bonding pattern can adopt. We find that the number of fully bonded configurations, i.e., configurations in which all particles are bonded to Nmax neighbors, is extensive, suggesting that the configurational entropy of the low temperature fluid is finite. We also evaluate the energy dependence of the configurational entropy close to the fully bonded state and show that it follows a logarithmic functional form, different from the quadratic dependence characterizing fragile liquids. We suggest that the presence of a discrete energy scale, provided by the particle bonds, and the intrinsic degeneracy of fully bonded disordered networks differentiates strong from fragile behavior.

Geometrical properties of the potential energy of the soft-sphere binary mixture

We report a detailed study of the stationary points (zero-force points) of the potential energy surface (PES) of a model structural glassformer. We compare stationary points found with two different algorithms (eigenvector following and square gradient minimization), and show that the mapping between instantaneous configuration and stationary points defined by those algorithms is as different as to strongly influence the instability index K versus temperature plot, which relevance in analyzing the liquid dynamics is thus questioned. On the other hand, the plot of K versus energy is much less sensitive to the algorithm employed, showing that the energy is the good variable to discuss geometric properties of the PES. We find new evidence of a geometric transition between a minima-dominated phase and a saddle-point-dominated one. We analyze the distances between instantaneous configurations and stationary points, and find that above the glass transition, the system is closer to saddle points than to minima.

Qualitative features of the two-dimensional Raman spectrum in liquids

The theory presented earlier [J. Kim and T. Keyes, Phys. Rev. E 66, 051110 (2002)] is analyzed to determine the information available from the two-dimensional Raman spectrum R((5))(t(2),t(1)) in liquids. The known spectra are well represented by the sum of two products of ordinary time correlations predicted by the theory. The shape of R((5)) is related in general to the values of simple same-time averages and concepts amenable to physical intuition. Using standard models for the time correlations entering the theory, specific analytic expressions for the spectrum are obtained depending on two parameters and a time scale, and the behavior of the spectrum is mapped out in the parameter space.

Distributions of inherent structure energies during aging

We perform extensive simulations of a binary mixture Lennard-Jones system subjected to a temperature jump in order to study the time evolution of fluctuations during aging. Analyzing data from 1500 different aging realizations, we calculate distributions of inherent structure energies for different aging times and contrast them with equilibrium. We find that the distributions initially become narrower and then widen as the system equilibrates. For deep quenches, fluctuations in the glassy system differ significantly from those observed in equilibrium. Simulation results are partially captured by theoretical predictions only when the final temperature is higher than the mode coupling temperature.

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.

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.

Potential-energy-landscape-based extended van der Waals equation

The inherent structures (IS) are the local minima of the 3N-dimensional potential energy surface, or landscape, of an N-atom system. Stillinger has given an exact IS formulation of thermodynamics. Here the implications for the equation of state are investigated. It is shown that the van der Waals (vdW) equation, with density-dependent a and b coefficients, holds if the averaged IS energy is close to its high-temperature plateau value. The density-dependence alone significantly enriches the equation of state. Furthermore, an additional "landscape" contribution to the pressure is found at lower T. The resulting extended vdW equation is capable of yielding a waterlike density anomaly, flat isotherms in the coexistence region vs vdW loops, and several other desirable features. The plateau IS energy, the width of the distribution of IS, and T(TOL), the "top of the landscape" temperature at which the plateau is reached, are simulated over a broad reduced density range, 2.0>or=rho>or=0.20, in the Lennard-Jones fluid. Fits to the data yield an explicit equation of state, which is argued to be plausible at high density. Nevertheless, a(rho(c)) and b(rho(c)), where rho(c) is the critical density, are in excellent agreement with the standard values obtained by fitting the vdW equation at the critical point.