Self-consistent generalized Langevin equation for colloid dynamics

Non-equilibrium view of the amorphous solidification of liquids with competing interactions

The interplay between short-range attractions and long-range repulsions (SALR) characterizes the so-called liquids with competing interactions, which are known to exhibit a variety of equilibrium and non-equilibrium phases. The theoretical description of the phenomenology associated with glassy or gel states in these systems has to take into account both the presence of thermodynamic instabilities (such as those defining the spinodal line and the so called λ line) and the limited capability to describe genuine non-equilibrium processes from first principles. Here, we report the first application of the non-equilibrium self-consistent generalized Langevin equation theory to the description of the dynamical arrest processes that occur in SALR systems after being instantaneously quenched into a state point in the regions of thermodynamic instability. The physical scenario predicted by this theory reveals an amazing interplay between the thermodynamically driven instabilities, favoring equilibrium macro- and micro-phase separation, and the kinetic arrest mechanisms, favoring non-equilibrium amorphous solidification of the liquid into an unexpected variety of glass and gel states.

Phase separation and dynamical arrest of protein solutions dominated by short-range attractions

The interplay of liquid-liquid phase separation (LLPS) and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as condensed matter physics, materials science, food engineering, and the pharmaceutical industry. In this context, protein solutions exhibit remarkable equilibrium and non-equilibrium behaviors. In the regime where attractive and repulsive forces compete, it has been demonstrated, for example, that the location of the dynamical arrest line seems to be independent of ionic strength, so that the arrest lines at different ionic screening lengths overlap, in contrast to the LLPS coexistence curves, which strongly depend on the salt concentration. In this work, we show that the same phenomenology can also be observed when the electrostatic repulsions are largely screened, and the range and strength of the attractions are varied. In particular, using lysozyme in brine as a model system, the metastable gas-liquid binodal and the dynamical arrest line as well as the second virial coefficient have been determined for various solution conditions by cloud-point measurements, optical microscopy, centrifugation experiments, and light scattering. With the aim of understanding this new experimental phenomenology, we apply the non-equilibrium self-consistent generalized Langevin equation theory to a simple model system with only excluded volume plus short-range attractions, to study the dependence of the predicted arrest lines on the range of the attractive interaction. The theoretical predictions find a good qualitative agreement with experiments when the range of the attraction is not too small compared with the size of the protein.

Structural relaxation, dynamical arrest, and aging in soft-sphere liquids

We investigate the structural relaxation of a soft-sphere liquid quenched isochorically (ϕ = 0.7) and instantaneously to different temperatures T_f above and below the glass transition. For this, we combine extensive Brownian dynamics simulations and theoretical calculations based on the non-equilibrium self-consistent generalized Langevin equation (NE-SCGLE) theory. The response of the liquid to a quench generally consists of a sub-linear increase of the α-relaxation time with system's age. Approaching the ideal glass-transition temperature from above (T_f > T^a), sub-aging appears as a transient process describing a broad equilibration crossover for quenches to nearly arrested states. This allows us to empirically determine an equilibration timescale t^eq(T_f) that becomes increasingly longer as T_f approaches T^a. For quenches inside the glass (T_f ≤ T^a), the growth rate of the structural relaxation time becomes progressively larger as T_f decreases and, unlike the equilibration scenario, τ_α remains evolving within the whole observation time-window. These features are consistently found in theory and simulations with remarkable semi-quantitative agreement and coincide with those revealed in a previous and complementary study [P. Mendoza-Méndez et al., Phys. Rev. 96, 022608 (2017)] that considered a sequence of quenches with fixed final temperature T_f = 0 but increasing ϕ toward the hard-sphere dynamical arrest volume fraction ϕ_HS ^a=0.582. The NE-SCGLE analysis, however, unveils various fundamental aspects of the glass transition, involving the abrupt passage from the ordinary equilibration scenario to the persistent aging effects that are characteristic of glass-forming liquids. The theory also explains that, within the time window of any experimental observation, this can only be observed as a continuous crossover.

On a fundamental description of the Kovacs' kinetic signatures in glass-forming systems

The time-evolution equation for the time-dependent static structure factor of the non-equilibrium self-consistent generalized Langevin equation (NE-SCGLE) theory was used to investigate the kinetics of glass-forming systems under isochoric conditions. The kinetics are studied within the framework of the fictive temperature (T_F) of the glassy structure. We solve for the kinetics of T_F(t) and the time-dependent structure factor and find that they are different but closely related by a function that depends only on temperature. Furthermore, we are able to solve for the evolution of T_F(t) in a set of temperature-jump histories referred to as the Kovacs' signatures. We demonstrate that the NE-SCGLE theory reproduces all the Kovacs' signatures, namely, intrinsic isotherm, asymmetry of approach, and memory effect. In addition, we extend the theory into largely unexplored, deep glassy state, regions that are below the notionally "ideal" glass temperature.

Waiting-time dependent non-equilibrium phase diagram of simple glass- and gel-forming liquids

Under numerous circumstances, many soft and hard materials are present in a puzzling wealth of non-equilibrium amorphous states, whose properties are not stationary and depend on preparation. They are often summarized in unconventional "phase diagrams" that exhibit new "phases" and/or "transitions" in which time, however, is an essential variable. This work proposes a solution to the problem of theoretically defining and predicting these non-equilibrium phases and their time-evolving phase diagrams, given the underlying molecular interactions. We demonstrate that these non-equilibrium phases and the corresponding non-stationary (i.e., aging) phase diagrams can indeed be defined and predicted using the kinetic perspective of a novel non-equilibrium statistical mechanical theory of irreversible processes. This is illustrated with the theoretical description of the transient process of dynamic arrest into non-equilibrium amorphous solid phases of an instantaneously quenched simple model fluid involving repulsive hard-sphere plus attractive square well pair interactions.

Tagged-particle dynamics in confined colloidal liquids

We present numerical results for the tagged-particle dynamics by solving the mode-coupling theory in confined geometry for colloidal liquids (cMCT). We show that neither the microscopic dynamics nor the type of intermediate scattering function qualitatively changes the asymptotic dynamics in vicinity of the glass transition. In particular, we find similar characteristics of confinement in the low-frequency susceptibility spectrum which we interpret as footprints of parallel relaxation. We derive predictions for the localization length and the scaling of the diffusion coefficient in the supercooled regime and discover a pronounced nonmonotonic dependence on the confinement length. For dilute liquids in the hydrodynamic limit we calculate an analytical expression for the intermediate scattering functions, which is in perfect agreement with event-driven Brownian dynamics simulations. From this, we derive an expression for persistent anticorrelations in the velocity autocorrelation function (VACF) for confined motion. Using numerical results of the cMCT equations for the VACF we also identify a crossover between different scalings corresponding to a transition from unconfined to confined behavior.

"Dense diffusion" in colloidal glasses: short-ranged long-time self-diffusion as a mechanistic model for relaxation dynamics

Despite decades of exploration of the colloidal glass transition, mechanistic explanation of glassy relaxation processes has remained murky. State-of-the-art theoretical models of the colloidal glass transition such as random first order transition theory, active barrier hopping theory, and non-equilibrium self-consistent generalized Langevin theory assert that relaxation reported at volume fractions above the ideal mode coupling theory prediction φg,MCT requires some sort of activated process, and that cooperative motion plays a central role. However, discrepancies between predicted and measured values of φg and ambiguity in the role of cooperative dynamics persist. Underlying both issues is the challenge of conducting deep concentration quenches without flow and the difficulty in accessing particle-scale dynamics. These two challenges have led to widespread use of fitting methods to identify divergence, but most a priori assume divergent behavior; and without access to detailed particle dynamics, it is challenging to produce evidence of collective dynamics. We address these limitations by conducting dynamic simulations accompanied by experiments to quench a colloidal liquid into the putative glass by triggering an increase in particle size, and thus volume fraction, at constant particle number density. Quenches are performed from the liquid to final volume fractions 0.56 ≤ φ ≤ 0.63. The glass is allowed to age for long times, and relaxation dynamics are monitored throughout the simulation. Overall, correlated motion acts to release dynamics from the glassy plateau - but only over length scales much smaller than a particle size - allowing self-diffusion to re-emerge; self-diffusion then relaxes the glass into an intransient diffusive state, which persists for φ < 0.60. We observe similar relaxation dynamics up to φ = 0.63 before achieving the intransient state. We find that this long-time self-diffusion is short-ranged: analysis of mean-square displacement reveals a glassy cage size a fraction of a particle size that shrinks with quench depth, i.e. increasing volume fraction. Thus the equivalence between cage size and particle size found in the liquid breaks down in the glass, which we confirm by examining the self-intermediate scattering function over a range of wave numbers. The colloidal glass transition can hence be viewed mechanistically as a shift in the long-time self-diffusion from long-ranged to short-ranged exploration of configurations. This shift takes place without diverging dynamics: there is a smooth transition as particle mobility decreases dramatically with concomitant emergence of a dense local configuration space that permits sampling of many configurations via local particle motion.

Mode-coupling theory of the glass transition for colloidal liquids in slit geometry

We provide a detailed derivation of the mode-coupling equations for a colloidal liquid confined by two parallel smooth walls. We introduce irreducible memory kernels for the different relaxation channels thereby extending the projection operator technique to colloidal liquids in slit geometry. Investigating both the collective dynamics as well as the tagged-particle motion, we prove that the mode-coupling functional assumes the same form as in the Newtonian case corroborating the universality of the glass-transition singularity with respect to the microscopic dynamics.

Glassy dynamics in asymmetric binary mixtures of hard spheres

We perform a systematic and detailed study of the glass transition in highly asymmetric binary mixtures of colloidal hard spheres, combining differential dynamic microscopy experiments, event-driven molecular dynamics simulations, and theoretical calculations, exploring the whole state diagram and determining the self-dynamics and collective dynamics of both species. Two distinct glassy states involving different dynamical arrest transitions are consistently described, namely, a double glass with the simultaneous arrest of the self-dynamics and collective dynamics of both species, and a single glass of large particles in which the self-dynamics of the small species remains ergodic. In the single-glass scenario, spatial modulations in the collective dynamics of both species occur due to the structure of the large spheres, a feature not observed in the double-glass domain. The theoretical results, obtained within the self-consistent generalized Langevin equation formalism, are in agreement with both simulations and experimental data, thus providing a stringent validation of this theoretical framework in the description of dynamical arrest in highly asymmetric mixtures. Our findings are summarized in a state diagram that classifies the various amorphous states of highly asymmetric mixtures by their dynamical arrest mechanisms.

Long-term aging behaviors in a model soft colloidal system

Colloidal and molecular systems share similar behaviors near to the glass transition volume fraction or temperature. Here, aging behaviors after volume fraction up-jump (induced by performing temperature down-jumps) conditions for a PS-PNIPAM/AA soft colloidal system were investigated using light scattering (diffusing wave spectroscopy, DWS). Both aging responses and equilibrium dynamics were investigated. For the aging responses, long-term experiments (100 000 s) were performed, and both equilibrium and non-equilibrium behaviors of the system were obtained. In the equilibrium state, as effective volume fraction increases (or temperature decreases), the colloidal dispersion displays a transition from the liquid to a glassy state. The equilibrium α-relaxation dynamics strongly depend on both the effective volume fraction and the initial mass concentration for the studied colloidal systems. Compared with prior results from our lab [X. Di, X. Peng and G. B. McKenna, J. Chem. Phys., 2014, 140, 054903], the effective volume fractions investigated spanned a wider range, to deeper into the glassy domain. The results show that the α-relaxation time τ_α of the samples aged into equilibrium deviate from the classical Vogel-Fulcher-Tammann (VFT)-type expectations and the super-Arrhenius signature disappears above the glass transition volume fraction. The non-equilibrium aging response shows that the time for the structural evolution into equilibrium and the α-relaxation time are decoupled. The DWS investigation of the aging behavior after different volume fraction jumps reveals a different non-equilibrium or aging behavior for the considered colloidal systems compared with either molecular glasses or the macroscopic rheology of a similar colloidal dispersions.

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics

Background

The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors.

Methods

We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with “imperfect” reaction rates.

Results

The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates.

Conclusions

Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

Dynamic equivalences in the hard-sphere dynamic universality class

We perform systematic simulation experiments on model systems with soft-sphere repulsive interactions to test the predicted dynamic equivalence between soft-sphere liquids with similar static structure. For this we compare the simulated dynamics (mean squared displacement, intermediate scattering function, α-relaxation time, etc.) of different soft-sphere systems, between them and with the hard-sphere liquid. We then show that the referred dynamic equivalence does not depend on the (Newtonian or Brownian) nature of the microscopic laws of motion of the constituent particles, and hence, applies independently to colloidal and to atomic simple liquids. Finally, we verify another more recently proposed dynamic equivalence, this time between the long-time dynamics of an atomic liquid and its corresponding Brownian fluid (i.e., the Brownian system with the same interaction potential).

Equilibration and aging of dense soft-sphere glass-forming liquids

The recently developed nonequilibrium extension of the self-consistent generalized Langevin equation theory of irreversible relaxation [Ramírez-González and Medina-Noyola, Phys. Rev. E 82, 061503 (2010); Ramírez-González and Medina-Noyola, Phys. Rev. E 82, 061504 (2010)] is applied to the description of the irreversible process of equilibration and aging of a glass-forming soft-sphere liquid that follows a sudden temperature quench, within the constraint that the local mean particle density remains uniform and constant. For these particular conditions, this theory describes the nonequilibrium evolution of the static structure factor S(k;t) and of the dynamic properties, such as the self-intermediate scattering function F(S)(k,τ;t), where τ is the correlation delay time and t is the evolution or waiting time after the quench. Specific predictions are presented for the deepest quench (to zero temperature). The predicted evolution of the α-relaxation time τ(α)(t) as a function of t allows us to define the equilibration time t(eq)(φ), as the time after which τ(α)(t) has attained its equilibrium value τ(α)(eq)(φ). It is predicted that both, t(eq)(φ) and τ(α)(eq)(φ), diverge as φ→φ((a)), where φ((a)) is the hard-sphere dynamic-arrest volume fraction φ((a))(≈0.582), thus suggesting that the measurement of equilibrium properties at and above φ((a)) is experimentally impossible. The theory also predicts that for fixed finite waiting times t, the plot of τ(α)(t;φ) as a function of φexhibits two regimes, corresponding to samples that have fully equilibrated within this waiting time (φ≤φ((c))(t)), and to samples for which equilibration is not yet complete (φ≥φ((c))(t)). The crossover volume fraction φ((c))(t) increases with t but saturates to the value φ((a)).

General nonequilibrium theory of colloid dynamics

A nonequilibrium extension of Onsager's canonical theory of thermal fluctuations is employed to derive a self-consistent theory for the description of the statistical properties of the instantaneous local concentration profile n(r,t) of a colloidal liquid in terms of the coupled time-evolution equations of its mean value n(r,t) and of the covariance [Formula in text] of its fluctuations δn(r,t)=n(r,t)-n(r,t). These two coarse-grained equations involve a local mobility function b(r,t) which, in its turn, is written in terms of the memory function of the two-time correlation function [Formula in text]. For given effective interactions between colloidal particles and applied external fields, the resulting self-consistent theory is aimed at describing the evolution of a strongly correlated colloidal liquid from an initial state with arbitrary mean and covariance n(0)(r) and σ(0)(r,r') toward its equilibrium state characterized by the equilibrium local concentration profile n(eq)(r) and equilibrium covariance σ(eq)(r,r'). This theory also provides a general theoretical framework to describe irreversible processes associated with dynamic arrest transitions, such as aging, and the effects of spatial heterogeneities.

Aging of a homogeneously quenched colloidal glass-forming liquid

The nonequilibrium self-consistent generalized Langevin equation theory of colloid dynamics is used to describe the nonstationary aging processes occurring in a suddenly quenched model colloidal liquid with hard-sphere plus short-ranged attractive interactions, whose static structure factor and van Hove function evolve irreversibly from the initial conditions before the quench to a final dynamically arrested state. The comparison of our numerical results with available simulation data are highly encouraging.

Single master curve for self-diffusion coefficients in distinctly different glass-forming liquids

An existence of a single master curve for the long-time self-diffusion coefficients D(S)(L)(T) in diversely different glass-forming liquids is predicted over wide temperature T ranges above the glass transition point T(g) by analyzing various experimental and simulation data consistently from a unified point of view based on the mean-field theory recently developed. In order to scale those data appropriately, the power-law dependence of the α- and the β-relaxation times on D(S)(L) is used. Then, it is shown that any equilibrium data for self-diffusion of atom in different systems are all collapsed onto a singular function f(T(f)((α))/T) , where T(f)((α)) is a fictive singular temperature of atom α. Thus, we emphasize that any equilibrium self-diffusion data can be described by a single master curve f(x) above T(g)(>T(f)), while the data out of equilibrium start to deviate from f(x) around T(g).

Non-equilibrium relaxation and near-arrest dynamics in colloidal suspensions

In this work we propose a theory to describe the irreversible diffusive relaxation of the local concentration of a colloidal dispersion that proceeds toward its stable thermodynamic equilibrium state, but which may in the process be trapped in metastable or dynamically arrested states. The central assumption of this theory is that the irreversible relaxation of the macroscopically observed mean value [Formula: see text] of the local concentration of colloidal particles is described by a diffusion equation involving a local mobility b(*)(r,t) that depends not only on the mean value [Formula: see text] but also on the covariance [Formula: see text] of the fluctuations [Formula: see text]. This diffusion equation must hence be solved simultaneously with the relaxation equation for the covariance σ(r,r';t), and here we also derive the corresponding relaxation equation. The dependence of the local mobility b(*)(r,t) on the mean value and the covariance is determined by a self-consistent set of equations involving now the spatially and temporally non-local time-dependent correlation functions, which in a uniform system in equilibrium reduces to the self-consistent generalized Langevin equation (SCGLE) theory of colloid dynamics. The resulting general theory considers the possibility that these relaxation processes occur under the influence of external fields, such as gravitational forces acting in the process of sedimentation. In this paper, however, we describe a simpler application, in which the system remains spatially uniform during the irreversible relaxation process, and discuss the general features of the glass transition scenario predicted by this non-equilibrium theory.

Universality in multicomponent glass-forming liquids near the glass transition

The slow dynamics of a single particle in multicomponent glass-forming systems including fragile and strong glasses is studied from a unified point of view. The simulation results on two different systems, bulk glass-forming Cu60Ti20Zr20 melt and network-forming SiO2 , melt are analyzed by the mean-field theory (MFT) recently proposed and are compared with other systems near the glass transition. It is shown that the simulation results for the mean-square displacement are all collapsed into a master curve given by MFT if a long-time self-diffusion coefficient has the same value in each system. It is also shown that each long-time self-diffusion coefficient is described well by a singular function predicted recently from first principles. Thus, we conclude that there exists a simple universal mechanism near the glass transition even among any diversely different glass-forming systems.

Glass transition in soft-sphere dispersions

The concept of dynamic equivalence among mono-disperse soft-sphere fluids is employed in the framework of the self-consistent generalized Langevin equation (SCGLE) theory of colloid dynamics to calculate the ideal glass transition phase diagram of model soft-sphere colloidal dispersions in the softness-concentration state space. The slow dynamics predicted by this theory near the glass transition is compared with available experimental data for the decay of the intermediate scattering function of colloidal dispersions of soft-microgel particles. Increasing deviations from this simple scheme occur for increasingly softer potentials, and this is studied here using the Rogers-Young static structure factor of the soft-sphere systems as the input of the SCGLE theory, without assuming a priori the validity of the equivalence principle above.

Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase

This article describes a numerical solution of the steady-state Poisson-Boltzmann-Smoluchowski (PBS) and Poisson-Nernst-Planck (PNP) equations to study diffusion in biomolecular systems. Specifically, finite element methods have been developed to calculate electrostatic interactions and ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to the wild-type and several mutated avian influenza neurominidase crystal structures. The calculated rates show very good agreement with recent experimental studies. Furthermore, these finite element methods require significantly fewer computational resources than existing particle-based Brownian dynamics methods and are robust for complicated geometries. The key finding of biological importance is that the electrostatic steering plays the important role in the drug binding process of the neurominidase.

Glass-liquid-glass reentrance in mono-component colloidal dispersions

The self-consistent generalized Langevin equation (SCGLE) theory of colloid dynamics is employed to describe the ergodic-non-ergodic transition in model mono-disperse colloidal dispersions whose particles interact through hard-sphere plus short-ranged attractive forces. The ergodic-non-ergodic phase diagram in the temperature-concentration state space is determined for the hard-sphere plus attractive Yukawa model within the mean spherical approximation for the static structure factor by solving a remarkably simple equation for the localization length of the colloidal particles. Finite real values of this property signals non-ergodicity and determines the non-ergodic parameters f(k) and f(s)(k). The resulting phase diagram for this system, which involves the existence of reentrant (repulsive and attractive) glass states, is compared with the corresponding prediction of mode coupling theory. Although both theories coincide in the general features of this phase diagram, there are also clear qualitative differences. One of the most relevant is the SCGLE prediction that the ergodic-attractive glass transition does not preempt the gas-liquid phase transition, but always intersects the corresponding spinodal curve on its high-concentration side. We also calculate the ergodic-non-ergodic phase diagram for the sticky hard-sphere model to illustrate the dependence of the predicted SCGLE dynamic phase diagram on the choice of one important constituent element of the SCGLE theory.

Theory of dynamic arrest in colloidal mixtures

We present a first-principles theory of dynamic arrest in colloidal mixtures based on the multicomponent self-consistent generalized Langevin equation theory of colloid dynamics [M. A. Chávez-Rojo and M. Medina-Noyola, Phys. Rev. E 72, 031107 (2005); M. A. Chávez-Rojo and M. Medina-Noyola, Phys. Rev. E76, 039902 (2007)]. We illustrate its application with a description of dynamic arrest in two simple model colloidal mixtures: namely, hard-sphere and repulsive Yukawa binary mixtures. Our results include observation of the two patterns of dynamic arrest, one in which both species become simultaneously arrested and the other involving the sequential arrest of the two species. The latter case gives rise to mixed states in which one species is arrested while the other species remains mobile. We also derive the ("bifurcation" or fixed-point") equations for the nonergodic parameters of the system, which takes the surprisingly simple form of a system of coupled equations for the localization length of the particles of each species. The solution of this system of equations indicates unambiguously which species is arrested (finite localization length) and which species remains ergodic (infinite localization length). As a result, we are able to draw the entire ergodic-nonergodic phase diagram of the binary hard-sphere mixture.

Simplified self-consistent theory of colloid dynamics

One of the main elements of the self-consistent generalized Langevin equation (SCGLE) theory of colloid dynamics [Phys. Rev. E 62, 3382 (2000); 72, 031107 (2005)] is the introduction of exact short-time moment conditions in its formulation. The need to previously calculate these exact short-time properties constitutes a practical barrier for its application. In this Brief Report, we report that a simplified version of this theory, in which this short-time information is eliminated, leads to the same results in the intermediate and long-time regimes. Deviations are only observed at short times, and are not qualitatively or quantitatively important. This is illustrated by comparing the two versions of the theory for representative model systems.

Dynamic arrest within the self-consistent generalized Langevin equation of colloid dynamics

This paper presents a recently developed theory of colloid dynamics as an alternative approach to the description of phenomena of dynamic arrest in monodisperse colloidal systems. Such theory, referred to as the self-consistent generalized Langevin equation (SCGLE) theory, was devised to describe the tracer and collective diffusion properties of colloidal dispersions in the short- and intermediate-time regimes. Its self-consistent character, however, introduces a nonlinear dynamic feedback, leading to the prediction of dynamic arrest in these systems, similar to that exhibited by the well-established mode coupling theory of the ideal glass transition. The full numerical solution of this self-consistent theory provides in principle a route to the location of the fluid-glass transition in the space of macroscopic parameters of the system, given the interparticle forces (i.e., a nonequilibrium analog of the statistical-thermodynamic prediction of an equilibrium phase diagram). In this paper we focus on the derivation from the same self-consistent theory of the more straightforward route to the location of the fluid-glass transition boundary, consisting of the equation for the nonergodic parameters, whose nonzero values are the signature of the glass state. This allows us to decide if a system, at given macroscopic conditions, is in an ergodic or in a dynamically arrested state, given the microscopic interactions, which enter only through the static structure factor. We present a selection of results that illustrate the concrete application of our theory to model colloidal systems. This involves the comparison of the predictions of our theory with available experimental data for the nonergodic parameters of model dispersions with hard-sphere and with screened Coulomb interactions.

Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations

This article describes the numerical solution of the time-dependent Smoluchowski equation to study diffusion in biomolecular systems. Specifically, finite element methods have been developed to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to the mouse acetylcholinesterase (mAChE) monomer and several tetramers. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different time steps. Calculated rates show very good agreement with experimental and theoretical steady-state studies. Furthermore, these finite element methods require significantly fewer computational resources than existing particle-based Brownian dynamics methods and are robust for complicated geometries. The key finding of biological importance is that the rate accelerations of the monomeric and tetrameric mAChE that result from electrostatic steering are preserved under the non-steady-state conditions that are expected to occur in physiological circumstances.

Self-consistent generalized Langevin equation for colloidal mixtures

A self-consistent theory of collective and tracer diffusion in colloidal mixtures is presented. This theory is based on exact results for the partial intermediate scattering functions derived within the framework of the generalized Langevin equation formalism, plus a number of conceptually simple and sensible approximations. The first of these consists of a Vineyard-like approximation between collective and tracer diffusion, which writes the collective dynamics in terms of the memory function related to tracer diffusion. The second consists of interpolating this only unknown memory function between its two exact limits at small and large wave vectors; for this, a phenomenologically determined, but not arbitrary, interpolating function is introduced: a Lorentzian with its inflection point located at the first minimum of the partial static structure factor. The small wave-vector exact limit involves a time-dependent friction function, for which we take a general approximate result, previously derived within the generalized Langevin equation formalism. This general result expresses the time-dependent friction function in terms of the partial intermediate scattering functions, thus closing the system of equations into a fully self-consistent scheme. This extends to mixtures a recently proposed self-consistent theory developed for monodisperse suspensions [Yeomans-Reyna and Medina-Noyola, Phys. Rev. E 64, 066114 (2001)]. As an illustration of its quantitative accuracy, its application to a simple model of a binary dispersion in the absence of hydrodynamic interactions is reported.

Finite element solution of the steady-state Smoluchowski equation for rate constant calculations

This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been developed to solve the steady-state Smoluchowski equation to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to mouse acetylcholinesterase. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different reaction criteria. The calculated rates were compared with experimental data and show very good agreement when the correct reaction criterion is used. Additionally, these finite element methods require significantly less computational resources than existing particle-based Brownian dynamics methods.

Self-diffusion in a system of interacting Langevin particles

The behavior of the self-diffusion constant of Langevin particles interacting via a pairwise interaction is considered. The diffusion constant is calculated approximately within a perturbation theory in the potential strength about the bare diffusion constant. It is shown how this expansion leads to a systematic double expansion in the inverse temperature beta and the particle density rho. The one-loop diagrams in this expansion can be summed exactly and we show that this result is exact in the limit of small beta and rhobeta constants. The one-loop result can also be resummed using a semiphenomenological renormalization group method which has proved useful in the study of diffusion in random media. In certain cases the renormalization group calculation predicts the existence of a diverging relaxation time signaled by the vanishing of the diffusion constant, possible forms of divergence coming from this approximation are discussed. Finally, at a more quantitative level, the results are compared with numerical simulations, in two dimensions, of particles interacting via a soft potential recently used to model the interaction between coiled polymers.

Self-consistent theory of collective Brownian dynamics: theory versus simulation

A recently developed theory of collective diffusion in colloidal suspensions is tested regarding the quantitative accuracy of its description of the dynamics of monodisperse model colloidal systems without hydrodynamic interactions. The idea is to exhibit the isolated effects of the direct interactions, which constitute the main microscopic relaxation mechanism, in the absence of other effects, such as hydrodynamic interactions. Here we compare the numerical solution of the fully self-consistent theory with the results of Brownian dynamics simulation of the van Hove function G(r,t) and/or the intermediate scattering function F(k,t) of four simple model systems. Two of them are representative of short-ranged soft-core repulsive interactions [(sigma/r)(mu), with mu>>1], in two and in three dimensions. The other two involve long-ranged repulsive forces in two (dipolar, r(-3) potential) and in three (screened Coulomb, or repulsive Yukawa interactions) dimensions. We find that the theory, without any sort of adjustable parameters or rescaling prescriptions, provides an excellent approximate description of the collective dynamics of these model systems, particularly in the short- and intermediate-time regimes. We also compare our results with those of the single exponential approximation and with the competing mode-mode coupling theory.