All Publications of James F. Lutsko 
Generated Wed Mar 21 09:59:03 2018 
3907 citations, hindex: 33 as of March 21, 2018 
[106] 
Mike Sleutel, James Lutsko, and Alexander E. S. Van Driessche.
Mineral Growth beyond the Limits of Impurity Poisoning.
Crystal Growth and Design, 18:171, 2018.
[ bib 
DOI 
.pdf 
http ]
More often than not, minerals formed in nature are grown at low supersaturation and from sources that are impure with respect to the crystals’ main building blocks. Quite paradoxically, these conditions are in conflict with the established crystal growth theories that focus on the interplay between the crystal interface and impurities that are present in the growth medium. These theories predict a kinetic dead zone for the cases where low purity is combined with weak driving forces. Hints toward reconciling this apparent disparity have been given by the observation that a specific class of steps, socalled macrosteps, can circumvent the debilitating kinetic effects of impurities in ways that up until now are poorly understood. In this contribution, we examine the mechanism of crystal growth by means of kinetic Monte Carlo simulation at conditions close to impurityinduced kinetic arrest. In agreement with previous reports, we show that as a result of impurity binding to the crystal surface, steps spontaneously group into bunches and later condense into macrosteps. A kinetic analysis demonstrates that these macrosteps are able to evade crystal growth cessation under conditions where single steps are firmly pinned. We identify the mechanism of interstep cooperativity which leads to cessation evasion by macrosteps and demonstrate that it applies to a range of supersaturation and impurity concentration values. On the basis of these findings, we present a model that explains how minerals can grow from mother liquor solutions that would otherwise seem to be nonconducive to crystal growth.

[105] 
Julien Lam and James F. Lutsko.
Lattice induced crystallization of nanodroplets: the role of
finitesize effects and substrate properties in controlling polymorphism.
Nanoscale, 10:4921, 2018.
[ bib 
DOI 
.pdf 
http ]
Targeting specific technological applications requires the control of nanoparticle properties, especially the crystalline polymorph. Freezing a nanodroplet deposited on a solid substrate leads to the formation of crystalline structures. We study the inherent mechanisms underlying this general phenomenon by means of molecular dynamics simulations. Our work shows that different crystal structures can be selected by finely tuning the solid substrate lattice parameter. Indeed, while for our system, facecentered cubic is usually the most preponderant structure, the growth of two distinct polymorphs, hexagonal centered packing and bodycentered cubic, was also observed even when the solid substrate was facecentered cubic. Finally, we also demonstrated that the growth of hexagonal centered packing is conditioned by the appearance of large enough bodycentered cubic clusters thus suggesting the presence of a crossnucleation pathway. Our results provide insights into the impact of nanoscale effects and solid substrate properties towards the growth of polymorphic nanomaterials.

[104] 
Jean Pierre Boon and James F. Lutsko.
Temporal diffusion: From microscopic dynamics to generalised
FokkerPlanck and fractional equations.
J. Statistical Physics, 166:1441, 2017.
[ bib 
.pdf 
http ]
The temporal Fokker–Planck equation (Boon et al. in J Stat Phys 3/4: 527, 2003) or propagation–dispersion equation was derived to describe diffusive processes with temporal dispersion rather than spatial dispersion as in classical diffusion. We present two generalizations of the temporal Fokker–Planck equation for the first passage distribution function f j(r, t) of a particle moving on a substrate with time delays τ j . Both generalizations follow from the first visit recurrence relation. In the first case, the time delays depend on the local concentration, that is the time delay probability Pj is a functional of the particle distribution function and we show that when the functional dependence is of the power law type, Pj ∝ f ν−1 j , the generalized Fokker–Planck equation exhibits a structure similar to that of the nonlinear spatial diffusion equation where the roles of space and time are reversed. In the second case, we consider the situation where the time delays are distributed according to a power law, Pj ∝ τ −1−α j (with 0 <α< 2), in which case we obtain a fractional propagationdispersion equation which is the temporal analog of the fractional spatial diffusion equation (with space and time interchanged). The analysis shows how certain microscopic mechanisms can lead to nonGaussian distributions and nonclassical scaling exponents.

[103] 
Julien Lam and James F. Lutsko.
Solute particle near a nanopore: influence of size and surface
properties on the solventmediated forces.
Nanoscale, 9:17099, 2017.
[ bib 
DOI 
.pdf 
http ]
Nanoscopic pores are used in various systems to attract nanoparticles. In general the behaviour is a result of two types of interactions: the material specific affinity and the solventmediated influence also called the depletion force. The latter is more universal but also much more complex to understand since it requires modeling both the nanoparticle and the solvent. Here, we employed classical density functional theory to determine the forces acting on a nanoparticle near a nanoscopic pore as a function of its hydrophobicity and its size. A simple capillary model is constructed to predict those depletion forces for various surface properties. For a nanoscopic pore, complexity arises from both the specific geometry and the fact that hydrophobic pores are not necessarily filled with liquid. Taking all of these effects into account and including electrostatic effects, we establish a phase diagram describing the entrance and the rejection of the nanoparticle from the pore.

[102] 
James F. Lutsko, Alexander E. S. Van Driessche, Miguel A.
DuránOlivencia, Dominique Maes, and Mike Sleutel.
Step Crowding Effects Dampen the Stochasticity of Crystal Growth
Kinetics.
Phys. Rev. Lett., 116:015501, 2016.
[ bib 
.pdf 
http ]
Crystals grow by laying down new layers of material which can either correspond in size to the height of one unit cell (elementary steps) or multiple unit cells (macrosteps). Surprisingly, experiments have shown that macrosteps can grow under conditions of low supersaturation and high impurity density such that elementary step growth is completely arrested. We use atomistic simulations to show that this is due to two effects: the fact that the additional layers bias fluctuations in the position of the bottom layer towards growth and by a transition, as step height increases, from a 2D to a 3D nucleation mechanism.

[101] 
James F. Lutsko and Grégoire Nicolis.
Mechanism for the stabilization of protein clusters above the
solubility curve.
Soft Matter, 12:93, 2016.
[ bib 
.pdf 
http ]
Pan, Vekilov and Lubchenko [J. Phys. Chem. B, 2010, 114, 7620] have proposed that dense stable protein clusters appearing in weak protein solutions above the solubility curve are composed of protein oligomers. The hypothesis is that a weak solution of oligomer species is unstable with respect to condensation causing the formation of dense, oligomerrich droplets which are stabilized against growth by the monomer–oligomer reaction. Here, we show that such a combination of processes can be understood using a simple capillary model yielding analytic expressions for the cluster properties which can be model and show that it is consistent with the predictions of the capillary model. The viability of the used to interpret experimental data. We also construct a microscopic Dynamic Density Functional Theory mechanism is thus confirmed and it is shown how the radius of the stable clusters is related to physically www.rsc.org/softmatter interesting quantities such as the monomer–oligomer rate constants.

[100] 
James F. Lutsko.
Mechanism for the stabilization of protein clusters above the
solubility curve: The role of nonideal chemical reactions.
Journal of Physics Condensed Matter, 28:244020, 2016.
[ bib 
http ]
Dense protein clusters are known to play an important role in nucleation of protein crystals from dilute solutions. While these have generally been thought to be formed from a metastable phase, the observation of similar, if not identical, clusters above the critical point for the dilutesolution/strongsolution phase transition has thrown this into doubt. Furthermore, the observed clusters are stable for relatively long times. Because protein aggregation plays a central role in some pathologies, understanding the nature of such clusters is an important problem. One mechanism for the stabilization of such structures was proposed by Pan, Vekilov and Lubchenko and was investigated using a dynamical density functional theory model which confirmed the viability of the model. Here, we revisit that model and incorporate additional physics in the form of statedependent reaction rates. We show by a combination of numerical results and general arguments that the statedependent rates disrupt the stability mechanism. Finally, we argue that the statedependent reactions correct unphysical aspects of the model with ideal (stateindependent) reactions and that this necessarily leads to the failure of the proposed mechanism.

[99] 
James F. Lutsko and Miguel A. DuránOlivencia.
A Twoparameter Extension of Classical Nucleation Theory.
J. Phys. Cond. Matt., 27:235101, 2015.
[ bib 
.pdf 
http ]
A twovariable stochastic model for diffusionlimited nucleation is developed using a formalism derived from fluctuating hydrodynamics. The model is a direct generalization of the standard Classical Nucleation Theory. The nucleation rate and pathway are calculated in the weaknoise approximation and are shown to be in good agreement with direct numerical simulations for the weaksolution/strongsolution transition in globular proteins. We find that Classical Nucleation Theory underestimates the time needed for the formation of a critical cluster by two orders of magnitude and that this discrepancy is due to the more complex dynamics of the two variable model and not, as often is assumed, a result of errors in the estimation of the free energy barrier.

[98] 
Miguel A. DuránOlivencia and James F. Lutsko.
Mesoscopic nucleation theory for confined systems: A
oneparameter model.
Phys. Rev. E, 91:022402, 2015.
[ bib 
.pdf 
http ]
Classical nucleation theory has been recently reformulated based on fluctuating hydrodynamics [J.F. Lutsko and M.A. DuránOlivencia, J. Chem. Phys. 138, 244908(2013)]. The present work extends this effort to the case of nucleation in confined systems such as small pores and vesicles. The finite available mass imposes a maximal supercritical cluster size and prohibits nucleation altogether if the system is too small. We quantity the effect of system size on the nuceation rate. We also discuss the effect of relaxing the capillarymodel assumption of zero interfacial width resulting in significant changes in the nucleation barrier and nucleation rate.

[97] 
Mike Sleutel, James F. Lutsko, Dominique Maes, and Alexander E. S. Van
Driessche.
Mesoscopic impurities expose a nucleationlimited regime of
crystal growth.
Phys. Rev. Lett., 114:245501, 2015.
[ bib 
.pdf 
http ]

[96] 
Miguel A. DuránOlivencia and James F. Lutsko.
Unification of classical nucleation theories via unified
ItôStratonovich stochastic equation.
Phys. Rev. E, 92:032407, 2015.
[ bib 
.pdf 
http ]
Classical nucleation theory (CNT) is the most widely used framework to describe the early stage of firstorder phase transitions. Unfortunately the different points of view adopted to derive it yield different kinetic equations for the probability density function, e.g. ZeldovichFrenkel or BeckerDöringTunitskii equations. Starting from a phenomenological stochastic differential equation a unified equation is obtained in this work. In other words, CNT expressions are recovered by selecting one or another stochastic calculus. Moreover, it is shown that the unified CNT thus obtained produces the same FokkerPlanck equation as that form a recent update of CNT [J.F. Lutsko and M.A. DuránOlivencia, J. Chem. Phys., 2013, 138, 244908] when mass transport is governed by diffusion. Finally, we derive a general inductiontime expression along with specific approximations of it to be used under different scenarios. In particular, when the masstransport mechanism is governed by direct impingement, volume diffusion, surface diffusion or interface transfer.

[95] 
Jean Pierre Boon and James F. Lutsko.
Molecular theory of anomalous diffusion  Application to
Fluorescence Correlation Spectroscopy.
J. Stat. Phys., 160:622635, 2015.
[ bib 
.pdf 
http ]
The nonlinear theory of anomalous diffusion is based on particle interactions giving an explicit microscopic description of diffusive processes leading to sub, normal, or superdiffusion as a result competitive effects between attractive and repulsive interactions. We present the explicit analytical solution to the nonlinear diffusion equation which we then use to compute the correlation function which is experimentally measured by correlation spectroscopy. The theoretical results are applicable in particular to the analysis of fluorescence correlation spectroscopy of marked molecules in biological systems. More specifically we consider the case of fluorescently labeled lipids and we find that the nonlinear correlation spectrum reproduces very well the experimental data indicating subdiffusive molecular motion of lipid molecules in the cell membrane.

[94] 
James F. Lutsko, Nélido GonzálezSegredo, Miguel A.
DuránOlivencia, Dominique Maes, Alexander E.S. Van Driessche, and Mike
Sleutel.
Crystal Growth Cessation Revisited  the physical basis of step
pinning.
Crystal Growth and Design, 14:61296134, 2014.
[ bib 
.pdf 
http ]
The growth of crystals from solution is a fundamental process of relevance to such diverse areas as Xraydiffraction structural determination and the role of mineralization in living organisms. A key factor determining the dynamics of crystallization is the effect of impurities on step growth. For over fifty years, all discussions of impuritystep interaction have been framed in the context of the CabreraVermilyea (CV) model for step blocking, which has nevertheless proven difficult to validate experimentally. Here we report on extensive computer simulations which clearly falsify the CV model, suggesting a more complex picture. While reducing to the CV result in certain limits, our approach is more widely applicable, encompassing nontrivial impuritycrystal interactions, mobile impurities and negative growth, among others.

[93] 
Mike Sleutel, Jim Lutsko, Alexander E. S. Van Driessche, Miguel A.
DuránOlivencia, and Dominique Maes.
Observing classical nucleation theory at work by monitoring
phase transitions with molecular precision.
Nature Communications, 5:5598, 2014.
[ bib 
.pdf 
.html ]
It is widely accepted that many phase transitions do not follow nucleation pathways as envisaged by the classical nucleation theory. Many substances can traverse intermediate states before arriving at the stable phase. The apparent ubiquity of multistep nucleation has made the inverse question relevant: does multistep nucleation always dominate singlestep pathways? Here we provide an explicit example of the classical nucleation mechanism for a system known to exhibit the characteristics of multistep nucleation. Molecular resolution atomic force microscopy imaging of the twodimensional nucleation of the protein glucose isomerase demonstrates that the interior of subcritical clusters is in the same state as the crystalline bulk phase. Our data show that despite having all the characteristics typically associated with rich phase behaviour, glucose isomerase 2D crystals are formed classically. These observations illustrate the resurfacing importance of the classical nucleation theory by revalidating some of the key assumptions that have been recently questioned.

[92] 
James F. Lutsko and Jean Pierre Boon.
Comment on “Possible divergences in Tsallis’
thermostatistics” by Plastino A. and Rocca M. C.
EuroPhys. Lett., 107:10003, 2014.
[ bib 
.pdf 
http ]
Questions concerning Platino and Rocca, EPL 104 6003 (2013).

[91] 
James F. Lutsko and Miguel A. DuránOlivencia.
Classical nucleation theory from a dynamical approach to
nucleation.
J. Chem. Phys., 138:244908, 2013.
[ bib 
DOI 
.pdf 
http ]
It is shown that diffusionlimited classical nucleation theory (CNT) can be recovered as a simple limit of the recently proposed dynamical theory of nucleation based on fluctuating hydrodynamics (Lutsko, JCP 136, 034509 (2012)). The same framework is also used to construct a more realistic theory in which clusters have finite interfacial width. When applied to the dilute solution/dense solution transition in globular proteins, it is found that the extension gives corrections to the the nucleation rate even for the case of small supersaturations due to changes in the monomer distribution function and to the excess free energy. It is also found that the monomer attachement/detachment picture breaks down at high supersaturations corresponding to clusters smaller than about 100 molecules. The results also confirm the usual assumption that most important corrections to CNT can be acheived by means of improved estimates of the free energy barrier. The theory also illustrates two topics that have received considerable attention in the recent literature on nucleation: the importance subdominant corrections to the capillary model for the free energy and of the correct choice of the reaction coordinate.

[90] 
James F. Lutsko.
Direct correlation function from the consistent
fundamentalmeasure free energies for hardsphere mixtures.
Phys. Rev. E, 87:014103, 2013.
[ bib 
DOI 
.pdf 
http ]
In a recent paper [ Phys. Rev. E 86 040102(R) (2012)], Santos presented a selfconsistency condition that can be used to limit the possible forms of fundamental measure theory. Here, the direct correlation function, resulting from the Santos functional, is derived, and it is found to be very close to the result of the White Bear density functional, except near the origin where it diverges.

[89] 
James F. Lutsko and Jean Pierre Boon.
Microscopic theory of anomalous diffusion based on particle
interactions.
Phys. Rev. E, 88:022108, 2013.
[ bib 
DOI 
.pdf 
http ]
We present a master equation formulation based on a Markovian random walk model that exhibits subdiffusion, classical diffusion, and superdiffusion as a function of a single parameter. The nonclassical diffusive behavior is generated by allowing for interactions between a population of walkers. At the macroscopic level, this gives rise to a nonlinear FokkerPlanck equation. The diffusive behavior is reflected not only in the mean squared displacement [〈r2(t)〉∼tγ with 0<γ≤1.5] but also in the existence of selfsimilar scaling solutions of the FokkerPlanck equation. We give a physical interpretation of sub and superdiffusion in terms of the attractive and repulsive interactions between the diffusing particles and we discuss analytically the limiting values of the exponent γ. Simulations based on the master equation are shown to be in agreement with the analytical solutions of the nonlinear FokkerPlanck equation in all three diffusion regimes.

[88] 
Jean Pierre Boon, James F. Lutsko, and Christopher Lutsko.
Microscopic approach to nonlinear reactiondiffusion: The case
of morphogen gradient formation.
Phys. Rev. E, 85:021126, 2012.
[ bib 
DOI 
.pdf 
http ]
We develop a microscopic theory for reactiondifusion (RD) processes based on a generalization of Einstein's master equation with a reactive term and we show how the mean field formulation leads to a generalized RD equation with nonclassical solutions. For the nth order annihilation reaction A+A+A+...+A>0, we obtain a nonlinear reactiondiffusion equation for which we discuss scaling and nonscaling formulations. We find steady states with either solutions exhibiting long range power law behavior (for n>α) showing the relative dominance of subdiffusion over reaction effects in constrained systems, or conversely solutions (for n<α<n+1) with finite support of the concentration distribution describing situations where diffusion is slow and extinction is fast. Theoretical results are compared with experimental data for morphogen gradient formation.

[87] 
James F. Lutsko.
A dynamical theory of nucleation for colloids and
macromolecules.
J. Chem. Phys., 136:034509, 2012.
[ bib 
DOI 
.pdf 
http ]
A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential equations for the evolution of order parameters are given. The conditions under which the elements of Classical Nucleation Theory are recovered are determined. The theory provides a justification and extension of more heuristic equilibrium approaches based solely on the free energy. It is illustrated by application to the lowconcentration/highconcentration transition in globular proteins where a novel twostep mechanism is identified where the first step involves the formation of longwavelength density fluctuations and the second step is the actual nucleation event occuring within the fluctuation.

[86] 
James F. Lutsko.
Nucleation of colloids and macromolecules: Does the nucleation
pathway matter?
J. Chem. Phys., 136:134402, 2012.
[ bib 
DOI 
.pdf 
http ]
A recent description of diffusionlimited nucleation based on fluctuating hydrodynamics that extends classical nucleation theory predicts a very nonclassical twostep scenario whereby nucleation is most likely to occur in spatially extended, lowamplitude density fluctuations. In this paper, it is shown how the formalism can be used to determine the maximum probability of observing any proposed nucleation pathway, thus allowing one to address the question as to their relative likelihood, including of the newly proposed pathway compared to classical scenarios. Calculations are presented for the nucleation of highconcentration droplets in a lowconcentration solution of globular proteins and it is found that the relative probabilities (new theory compared to classical result) for reaching a critical nucleus containing Nc molecules scales as e−Nc/3 thus indicating that for all but the smallest nuclei, the classical scenario is extremely unlikely.

[85] 
James F. Lutsko.
On the role of metastable intermediate states in the homogeneous
nucleation of solids from solution.
Adv. Chem. Phys., 151:137172, 2012.
[ bib 
.pdf 
http ]
The role of metastable liquid phases in vaporcrystal nucleation is studied using Density Functional Theory(DFT). The model gives a semiquantitatively accurate description of both the vaporliquidsolid phase diagram for both simple fluids (LennardJones interactions) and of the lowdensity/highdensity/crystal phase diagram for model globular proteins (ten WoldeFrenkel interaction). The density profile is characterized by two local order parameters, the average density and the crystallinity. The bulk free energy model is supplemented by squaredderivative terms in these order parameters to account for inhomogeneities thus producing a model similar in spirit to phasefield theory. It is shown that for both interaction models, the vaporcrystal part of the phasediagram can be separated into regions for which metastable liquid phases are more or less stable than the vapor, but always less stable than the solid. The former case allows for the possibility of double nucleation whereby liquid droplets nucleate from the vapor followed by a separate nucleation of the solid phase within the liquid droplets. Whether or not this actually occurs depends on the relative free energy barriers for vaporsolid and vaporliquid nucleation and it is shown that for simple fluids, double nucleation is indeed favored at sufficiently large supersaturation. Finally, by studying the minimum free energy path from the vapor to the solid, the separate possibility of transient nucl 
[84] 
James F. Lutsko.
Nucleation of colloids and macromolecules in a finite volume.
J. Chem. Phys., 137:154903, 2012.
[ bib 
DOI 
http ]
A recently formulated description of homogeneous nucleation for Brownian particles in the overdamped limit based on fluctuating hydrodynamics is used to determine the nucleation pathway, characterized as the most likely path (MLP), for the nucleation of a denseconcentration droplet of globular protein from a dilute solution in a small, finite container. The calculations are performed by directly discretizing the equations for the MLP and it is found that they confirm previous results obtained for infinite systems: the process of homogeneous nucleation begins with a longwavelength, spatiallyextended concentration fluctuation that it condenses to form the precritical cluster. This is followed by a classical growth processes. The calculations show that the postcritical growth involves the formation of a depletion zone around the cluster whereas no such depletion is observed in the precritical cluster. The approach therefore captures dynamical effects not found in classical Density Functional Theory studies while consistently describing the formation of the precritical cluster.

[83] 
James F. Lutsko.
A dynamical theory of homogeneous nucleation for colloids and
macromolecules.
J. Chem. Phys., 135:161101, 2011.
[ bib 
DOI 
.pdf 
http ]
Homogeneous nucleation is formulated within the context of fluctuating hydrodynamics. It is shown that for a colloidal or macromolecular system in the strong damping limit the most likely path for nucleation can be determined by gradient descent in density space governed by a nontrivial metric fixed by the dynamics. The theory provides a justification and extension of more heuristic equilibrium approaches based solely on the free energy. It is illustrated by application to liquidvapor nucleation where it is shown that, in contrast to most free energybased studies, the smallest clusters correspond to long wavelength, small amplitude perturbations.

[82] 
James F. Lutsko.
Density functional theory of inhomogeneous liquids. IV.
Squaredgradient approximation and classical nucleation theory.
J. Chem. Phys., 134:164501, 2011.
[ bib 
DOI 
.pdf 
http ]
The squaredgradient approximation to the modifiedcore Van der Waals density functional theory model is developed. A simple, explicit expression for the SGA coefficient involving only the bulk equation of state and the interaction potential is given. The model is solved for planar interfaces and spherical clusters and is shown to be quantitatively accurate in comparison to computer simulations. An approximate technique for solving the SGA based on piecewiselinear density profiles is introduced and is shown to give reasonable zerothorder approximations to the numerical solution of the model. The piecewiselinear models of spherical clusters are shown to be a natural extension of classical nucleation theory and serve to clarify some of the nonclassical effects previously observed in liquid–vapor nucleation. Nucleation pathways are investigated using both constrained energyminimization and steepestdescent techniques.

[81] 
James F. Lutsko and Jean Pierre Boon.
Questioning the validity of nonextensive thermodynamics for
classical Hamiltonian systems.
EuroPhysics Letters, 95:20006, 2011.
[ bib 
DOI 
.pdf 
.pdf ]
We examine the nonextensive approach to the statistical mechanics of Hamiltonian systems with H = T +V, where T is the classical kinetic energy. Our analysis starts from the basics of the formalism by applying the standard variational method for maximizing the entropy subject to the average energy and normalization constraints. The analytical results show i) that the nonextensive thermodynamics formalism should be called into question to explain experimental results described by extended exponential distributions exhibiting long tails, i.e. qexponentials with q >1, and ii) that in the thermodynamic limit the theory is only consistent in the range 0 q 1 where the distribution has finite support, thus implying that configurations with, e.g., energy above some limit have zero probability, which is at variance with the physics of systems in contact with a heat reservoir. We also discuss the (qdependent) thermodynamic temperature and the generalized specific heat.

[80] 
Jean Pierre Boon and James F. Lutsko.
Nonextensive formalism and continuous Hamiltonian systems.
Physics Letters A, 375:329334, 2011.
[ bib 
DOI 
.pdf 
http ]
A recurring question in nonequilibrium statistical mechanics is what deviation from standard statistical mechanics gives rise to nonBoltzmann behavior and to nonlinear response, which amounts to identifying the emergence of “statistics from dynamics” in systems out of equilibrium. Among several possible analytical developments which have been proposed, the idea of nonextensive statistics introduced by Tsallis about 20 years ago was to develop a statistical mechanical theory for systems out of equilibrium where the Boltzmann distribution no longer holds, and to generalize the Boltzmann entropy by a more general function Sq while maintaining the formalism of thermodynamics. From a phenomenological viewpoint, nonextensive statistics appeared to be of interest because maximization of the generalized entropy Sq yields the qexponential distribution which has been successfully used to describe distributions observed in a large class of phenomena, in particular power law distributions for q > 1. Here we reexamine the validity of the nonextensive formalism for continuous Hamiltonian systems. In particular we consider the qideal gas, a model system of quasiparticles where the effect of the interactions are included in the particle properties. On the basis of exact results for the qideal gas, we find that the theory is restricted to the range q < 1, which raises the question o 
[79] 
James F Lutsko, Julien Laidet, and Patrick Grosfils.
Phase behavior of a confined nanodroplet in the grandcanonical
ensemble: the reverse liquid–vapor transition.
J. Phys.: Cond. Matt., 22(3):035101, 2010.
[ bib 
.pdf 
http ]
The equilibrium density distribution and thermodynamic properties of a LennardJones fluid confined to nanosized spherical cavities at a constant chemical potential was determined using Monte Carlo simulations. The results describe both a single cavity with semipermeable walls as well as a collection of closed cavities formed at the constant chemical potential. The results are compared to calculations using classical density functional theory (DFT). It is found that the DFT calculations give a quantitatively accurate description of the pressure and structure of the fluid. Both theory and simulation show the presence of a 'reverse' liquid–vapor transition whereby the equilibrium state is a liquid at large volumes but becomes a vapor at small volumes.

[78]  Patrick Grosfils and James F. Lutsko. LowDensity/HighDensity Liquid Phase Transition for Model Globular Proteins. Langmuir, 26(11):85108516, 2010. [ bib  .pdf  http ] 
[77] 
James F. Lutsko, Vasileios Basios, Gregoire Nicolis, John J. Kozak, Mike
Sleutel, and Dominique Maes.
Kinetic rougheninglike transition with finite nucleation
barrier.
J. Chem. Phys., 132(3):035102, 2010.
[ bib 
DOI 
.pdf 
http ]
Recent observations of the growth of protein crystals have identified two different growth regimes. At low supersaturation, the surface of the crystal is smooth and increasing in size due to the nucleation of steps at defects and the subsequent growth of the steps. At high supersaturation, nucleation occurs at many places simultaneously, the crystal surface becomes rough, and the growth velocity increases more rapidly with increasing supersaturation than in the smooth regime. Kinetic roughening transitions are typically assumed to be due to the vanishing of the barrier for twodimension nucleation on the surface of the crystal. We show here, by means of both analytic meanfield models and kinetic Monte Carlo simulations, that a transition between different growth modes reminiscent of kinetic roughening can also arise as a kinetic effect occurring at finite nucleation barriers. Keywords: crystal growth; Monte Carlo methods; nucleation; proteins; reaction kinetics 
[76] 
James F. Lutsko.
Recent Developments in Classical Density Functional Theory.
Adv. Chem. Phys., 144:1, 2010.
[ bib ]
The Density Functional approach to equilibrium statistical mechanics is reviewed. Topics covered include the basic theory behind Density Functional Theory, exact density functionals in low dimension, and theories based on effective liquid approximations. Particular attention is given to more recent developments such as Fundamental Measure Theory for hardspheres, Dynamical Density Functional Theory and the determination of state transition pathways.

[75] 
James F. Lutsko, Vasileios Basios, Grégoire Nicolis, Tom P. Caremans,
Alexander Aerts, Johan A. Martens, Christine E. A. Kirschhock, and Titus S.
van Erp.
Kinetics of intermediatemediated selfassembly in nanosized
materials: A generic model.
J. Chem. Phys., 132(16):164701, 2010.
[ bib 
DOI 
.pdf 
http ]
We propose in this paper a generic model of a nonstandard aggregation mechanism for selfassembly processes of a class of materials involving the mediation of intermediates consisting of a polydisperse population of nanosized particles. The model accounts for a long induction period in the process. The proposed mechanism also gives insight on future experiments aiming at a more comprehensive picture of the role of selforganization in selfassembly processes. Keywords: nanostructured materials; numerical analysis; selfassembly 
[74] 
Patrick Grosfils and James F. Lutsko.
Dependence of the liquidvapor surface tension on the range of
interaction: A test of the law of corresponding states.
J. Chem. Phys., 130(5):054703+, 2009.
[ bib 
.pdf 
http ]
The planar surface tension of coexisting liquid and vapor phases of a fluid of LennardJones atoms is studied as a function of the range of the potential using both Monte Carlo simulations and Density Functional Theory. The interaction range is varied from r_{c}^{*} = 2.5 to r_{c}^{*} = 6 and the surface tension is determined for temperatures ranging from T^{*} = 0.7 up to the critical temperature in each case. The results are shown to be consistent with previous studies. The simulation data are welldescribed by Guggenheim's law of corresponding states but the agreement of the theoretical results depends on the quality of the bulk equation of state. Keywords: lutsko 
[73] 
J. F. Lutsko, J. P. Boon, and P. Grosfils.
Is the Tsallis entropy stable?
EPL (Europhysics Letters), 86(4):40005+, 2009.
[ bib 
DOI 
.pdf 
http ]
The question of whether the Tsallis entropy is Leschestable is revisited. It is argued that when physical averages are computed with the escort probabilities, the correct application of the concept of Leschestability requires use of the escort probabilities. As a consequence, as shown here, the Tsallis entropy is unstable but the thermodynamic averages are stable. We further show that Lesche stability as well as thermodynamic stability can be obtained if the homogeneous entropy is used as the basis of the formulation of nonextensive thermodynamics. In this approach, the escort distribution arises naturally as a secondary structure. Keywords: lutsko 
[72] 
J. F. Lutsko.
Reply to the Comment by M. Iwamatsu.
EPL (Europhysics Letters), 86(2):26002+, 2009.
[ bib 
DOI 
.pdf 
http ]
Keywords: lutsko 
[71] 
Wm. G. Hoover, Carol G. Hoover, and James F. Lutsko.
Microscopic and macroscopic stress with gravitational and
rotational forces.
Phys. Rev. E, 79:036709, Mar 2009.
[ bib 
DOI 
http ]
Many recent papers have questioned Irving and Kirkwood’s atomistic expression for stress. In Irving and Kirkwood’s approach both interatomic forces and atomic velocities contribute to stress. It is the velocitydependent part that has been disputed. To help clarify this situation we investigate (i) a fluid in a gravitational field and (ii) a steadily rotating solid. For both problems we choose conditions where the two stress contributions, potential and kinetic, are significant. The analytic forcebalance solutions of both these problems agree very well with a smoothparticle interpretation of the atomistic IrvingKirkwood stress tensor.

[70] 
James F. Lutsko and Jean P. Boon.
Generalized diffusion: A microscopic approach.
Phys. Rev. E, 77(5), 2008.
[ bib 
DOI 
.pdf 
http ]
The FokkerPlanck equation for the probability f(r,t) to find a random walker at position r at time t is derived for the case that the probability to make jumps depends nonlinearly on f(r,t). The result is a generalized form of the classical FokkerPlanck equation where the effects of drift, due to a violation of detailed balance, and of external fields are also considered. It is shown that in the absence of drift and external fields a scaling solution, describing anomalous diffusion, is possible only if the nonlinearity in the jump probability is of the power law type [ f(r,t)], in which case the generalized FokkerPlanck equation reduces to the porous media equation. Monte Carlo simulations are shown to confirm the theoretical results. Keywords: lutsko 
[69] 
James F. Lutsko.
Density functional theory of inhomogeneous liquids. III.
Liquidvapor nucleation.
J. Chem. Phys., 129(124):244501+, 2008.
[ bib 
.pdf 
http ]
The process of nucleation of vapor bubbles from a superheated liquid and of liquid droplets from a supersaturated vapor is investigated using the ModifiedCore van der Waals model Density Functional Theory (Lutsko, JCP 128, 184711 (2008)). A novel approach is developed whereby nucleation is viewed as a transition from a metastable state to a stable state via the minimum free energy path which is identified using the nudged elasticband method for exploring free energy surfaces. This allows for the unbiased calculation of the properties of sub and supercritical clusters, as well as of the critical cluster. For LennardJones fluids, the results compare well to simulation and support the view that even at high supersaturation nucleation proceeds smoothly rather than via spinodallike instabilities as has been suggested recently. Keywords: lutsko 
[68] 
James F. Lutsko.
Density functional theory of inhomogeneous liquids. II. A
fundamental measure approach.
J. Chem. Phys., 128(18), 2008.
[ bib 
.pdf 
http ]
Previously, it has been shown that the direct correlation function for a Lennard–Jones fluid could be modeled by a sum of that for hardspheres, a meanfield tail, and a simple linear correction in the core region constructed so as to reproduce the (known) bulk equation of state of the fluid [Lutsko, J. Chem. Phys. 127, 054701 (2007)]. Here, this model is combined with ideas from the fundamental measure theory to construct a density functional theory for the free energy. The theory is shown to accurately describe a range of inhomogeneous conditions including the liquid vapor interface, the fluid in contact with a hard wall, and a fluid confined in a slit pore. The theory gives quantitatively accurate predictions for the surface tension, including its dependence on the potential cutoff. It also obeys two important exact conditions: That relating the direct correlation function to the functional derivative of the free energy with respect to density and the wall theorem. Keywords: lutsko 
[67] 
J. F. Lutsko.
Theoretical description of the nucleation of vapor bubbles in a
superheated fluid.
EPL (Europhysics Letters), 83(4):46007+, 2008.
[ bib 
DOI 
.pdf 
http ]
The nucleation of vapor bubbles within a superheated fluid is studied using density functional theory. The nudged elastic band technique is used to find the minimum energy pathway from the metastable uniform liquid to the stable uniform gas thus emphasizing the analogy between the the nucleation problem and that of chemical reactions. The result is both an accurate determination of the critical nucleus and an unbiased description of the density profile at various points along the path between the free energy extrema. This calculation is compared to two other methods: the use of parametrized profiles and constrained minimization of the free energy. The results indicate that the recent claim, based on the constraint method, that bubble nucleation and growth involves an activated instability is incorrect. Keywords: lutsko_epl_2008 
[66] 
James F. Lutsko.
Density functional theory of inhomogeneous liquids. I. The
liquidvapor interface in LennardJones fluids.
J. Chem. Phys., 127:054701, 2007.
[ bib 
.pdf ]
A simple model is proposed for the direct correlation function (DCF) for simple fluids consisting of a hardcore contribution, a simple parametrized core correction, and a meanfield tail. The model requires as input only the free energy of the homogeneous fluid, obtained, e.g., from thermodynamic perturbation theory. Comparison to the DCF obtained from simulation of a LennardJones fluid shows this to be a surprisingly good approximation for a wide range of densities. The model is used to construct a density functional theory for inhomogeneous fluids which is applied to the problem of calculating the surface tension of the liquidvapor interface. The numerical values found are in good agreement with simulation.

[65] 
Jean Pierre Boon and James F. Lutsko.
From Einstein to generalized diffusion.
AIP Conference Proceedings, 965(1):157164, 2007.
[ bib 
DOI 
.pdf 
http ]
We show that from a generalization of Einstein's master equation for the random walk one obtains a generalized equation for diffusion processes. The master equation is generalized by making the particle jump probability Pj(r) a functional of the particle distribution function f(r,t). If one demands that the resulting generalized diffusion equation admits of scaling solutions: f(r;t) = t−gamma/2phi(r/tgamma/2), a power law Pj(r)[proportional]f(r)alpha−1 (with alpha>1) follows, and the solutions exhibit qexponential forms which are found to be in agreement with the results of MonteCarlo simulations, providing a microscopic basis validating the nonlinear diffusion equation. We also show that the phenomenological porous media equation is an approximation to the generalized advectiondiffusion equation. Keywords: statistical mechanics; FokkerPlanck equation; diffusion; probability; master equation; transport processes 
[64] 
J. P. Boon and J. F. Lutsko.
Nonlinear diffusion from Einstein's master equation.
EPL (Europhysics Letters), 80(6):60006 (4pp), 2007.
[ bib 
.pdf 
http ]
We generalize Einstein's master equation for randomwalk processes by considering that the probability for a particle at position r to make a jump of length j lattice sites, Pj(r), is a functional of the particle distribution function f(r, t). By multiscale expansion, we obtain a generalized advectiondiffusion equation. We show that the power law Pj(r)[?]f(r)a1 (with a>1) follows from the requirement that the generalized equation admits scaling solutions (f(r;t)=t[?]gph(r/tg)). The solutions have a qexponential form and are found to be in agreement with the results of Monte Carlo simulations, so providing a microscopic basis validating the nonlinear diffusion equation. Although its hydrodynamic limit is equivalent to the phenomenological porous media equation, there are extra terms which, in general, cannot be neglected as evidenced by the Monte Carlo computations.

[63] 
James F. Lutsko.
ChapmanEnskog expansion about nonequilibrium states with
application to the sheared granular fluid.
Phys. Rev. E, 73:021302, 2006.
[ bib 
arXiv 
eprint 
.pdf 
http ]
The ChapmanEnskog method of solution of kinetic equations, such as the Boltzmann equation, is based on an expansion in gradients of the deviations of the hydrodynamic fields from a uniform reference state (e.g., local equilibrium). This paper presents an extension of the method so as to allow for expansions about arbitrary, farfromequilibrium reference states. The primary result is a set of hydrodynamic equations for studying variations from the arbitrary reference state which, unlike the usual NavierStokes hydrodynamics, does not restrict the reference state in any way. The method is illustrated by application to a sheared granular gas which cannot be studied using the usual NavierStokes hydrodynamics.

[62] 
James F. Lutsko and Grégoire Nicolis.
Theoretical Evidence for a Dense Fluid Precursor to
Crystallization.
Phys. Rev. Lett., 96:046102, 2006.
Also appeared in February 15, 2006 issue of Virtual Journal of
Biological Physics Research.
[ bib 
arXiv 
eprint 
.pdf 
http ]
We present classical density functional theory calculations of the freeenergy landscape for fluids below their triple point as a function of density and crystallinity. We find that, both for a model globular protein and for a simple atomic fluid modeled with a LennardJones interaction, it is freeenergetically easier to crystallize by passing through a metastable dense fluid in accord with the Ostwald rule of stages but in contrast to the alternative of ordering and densifying at once as assumed in the classical picture of crystallization.

[61] 
James F. Lutsko.
First principles derivation of Ginzburg–Landau free energy
models for crystalline systems.
Physica A, 366:229242, 2006.
[ bib 
.pdf ]
The expression of the free energy density of a classical crystalline system as a gradient expansion in terms of a set of order parameters is developed using classical density functional theory. The goal here is to extend and complete an earlier derivation by Löwen et al. [Europhys. Lett. 9 (1989) 791]. The limitations of the resulting expressions are also discussed including the boundary conditions needed for finite systems and the fact that the results cannot, at present, be used to take into account elastic relaxation.

[60] 
Jean Pierre Boon and James F. Lutsko.
Generalized diffusion equation.
Physica A, 368:5562, 2006.
[ bib 
.pdf ]
Modern analyses of diffusion processes have proposed nonlinear versions of the Fokker–Planck equation to account for nonclassical diffusion. These nonlinear equations are usually constructed on a phenomenological basis. Here, we introduce a nonlinear transformation by defining the qgenerating function which, when applied to the intermediate scattering function of classical statistical mechanics, yields, in a mathematically systematic derivation, a generalized form of the advection–diffusion equation in Fourier space. Its solutions are discussed and suggest that the qgenerating function approach should be a useful method to generalize classical diffusive transport formulations.

[59] 
James F. Lutsko.
Hydrodynamics of an endothermic gas with application to bubble
cavitation.
J. Chem. Phys., 125:164319, 2006.
[ bib 
.pdf ]
The hydrodynamics for a gas of hard spheres which sometimes experience inelastic collisions resulting in the loss of a fixed, velocityindependent, amount of energy Delta is investigated with the goal of understanding the coupling between hydrodynamics and endothermic chemistry. The homogeneous cooling state of a uniform system and the modified NavierStokes equations are discussed and explicit expressions given for the pressure, cooling rates, and all transport coefficients for D dimensions. The NavierStokes equations are solved numerically for the case of a twodimensional gas subject to a circular piston so as to illustrate the effects of the enegy loss on the structure of shocks found in cavitating bubbles. It is found that the maximal temperature achieved is a sensitive function of Delta with a minimum occurring near the physically important value of Delta 12 000 K 1 eV.

[58] 
James F. Lutsko.
Properties of nonfcc hardsphere solids predicted by density
functional theory.
Phys. Rev. E, 74:021121, 2006.
[ bib 
.pdf ]
The free energies of the fcc, bcc, hcp, and simple cubic phases for hard spheres are calculated as a function of density using the fundamental measure theory models of Rosenfeld et al. [Phys. Rev. E 55, 4245 (1997)], Tarazona [Phys. Rev. Lett. 84, 694 (2001)], and Roth et al. [J. Phys.: Condens. Matter 14, 12063 (2002)] in the Gaussian approximation. For the fcc phase, the present work confirms the vanishing of the Lindemann parameter (i.e., vanishing of the width of the Gaussians) near close packing for all three models and the results for the hcp phase are nearly identical. For the bcc phase and for packing fractions above eta 0.56, all three theories show multiple solid structures differing in the widths of the Gaussians. In all three cases, one of these structures shows the expected vanishing of the Lindemann parameter at close packing, but this physical structure is only thermodynamically favored over the unphysical structures in the Tarazona theory and even then, some unphysical behavior persists at lower densities. The simple cubic phase is stabilized in the model of Rosenfeld et al. for a range of densities and in the Tarazona model only very near close packing.

[57] 
James F. Lutsko.
GinzburgLandau theory of the liquidsolid interface and
nucleation for hard spheres.
Phys. Rev. E, 74:021603, 2006.
[ bib 
.pdf ]
The GinzburgLandau free energy functional for hard spheres is constructed using the fundamental measure theory approach to density functional theory as a starting point. The functional is used to study the liquidfcc solid planer interface and the properties of small solid clusters nucleating within a liquid. The surface tension for planer interfaces agrees well with simulation and it is found that the properties of the solid clusters are consistent with classical nucleation theory.

[56] 
James F. Lutsko.
Transport properties of dense dissipative hardsphere fluids for
arbitrary energy loss models.
Phys. Rev. E, 72:021306, 2005.
[ bib 
eprint 
.pdf 
http ]
The solution of the Enskog equation for the onebody velocity distribution of a moderately dense arbitrary mixture of inelastic hard spheres undergoing planar shear flow is described. A generalization of the Grad moment method, implemented by means of a novel generating function technique, is used so as to avoid any assumptions concerning the size of the shear rate. The result is illustrated by using it to calculate the pressure, normal stresses, and shear viscosity of a model polydisperse granular fluid in which grain size, mass, and coefficient of restitution vary among the grains. The results are compared to a numerical solution of the Enskog equation as well as moleculardynamics simulations. Most bulk properties are well described by the Enskog theory and it is shown that the generalized moment method is more accurate than the simple (Grad) moment method. However, the description of the distribution of temperatures in the mixture predicted by Enskog theory does not compare well to simulation, even at relatively modest densities.

[55] 
James F. Lutsko and Gregoire Nicolis.
The effect of the range of interaction on the phase diagram of a
globular protein.
J. Chem. Phys., 122:244907, 2005.
[ bib 
eprint 
.pdf 
http ]
Thermodynamic perturbation theory is applied to the model of globular proteins studied by ten Wolde and Frenkel [P. R. ten Wolde and D. Frenkel Science 77, 1975 (1997)] using computer simulation. It is found that the reported phase diagrams are accurately reproduced. The calculations show how the phase diagram can be tuned as a function of the length scale of the potential.

[54]  K. Yoshimoto, G. J. Papakonstantopoulos, J. F. Lutsko, and J. J. de Pablo. Statistical calculation of elastic moduli for atomistic models. Phys. Rev. B, 71:184108, 2005. [ bib  .pdf ] 
[53] 
J. F. Lutsko and J. P. Boon.
Nonextensive diffusion as nonlinear response.
Euro. Phys. Lett., 71(6):906911, 2005.
[ bib 
eprint 
.pdf 
.html ]
The porousmedia equation has been proposed as a phenomenological ”nonextensive” generalization of classical diffusion. Here, we show that a very similar equation can be derived, in a systematic manner, for a classical fluid by assuming nonlinear response, i.e. that the diffusive flux depends on gradients of a power of the concentration. The present equation distinguishes from the porousmedia equation in that it describes generalized classical diffusion, i.e. with r/sqrt(Dt scaling, but with a generalized Einstein relation, and with powerlaw probability distributions typical of nonextensive statistical mechanics.)

[52] 
James F. Lutsko.
Kinetic theory and hydrodynamics of dense, reacting fluids far
from equilibrium.
J. Chem. Phys., 120:6325, 2004.
[ bib 
eprint 
.pdf 
http ]
The kinetic theory for a fluid of hard spheres which undergo endothermic and/or exothermic reactions with mass transfer is developed. The exact balance equations for concentration, density, velocity, and temperature are derived. The Enskog approximation is discussed and used as the basis for the derivation, via the Chapman–Enskog procedure, of the Navier–Stokes reaction equations under various assumptions about the speed of the chemical reactions. It is shown that the phenomenological description consisting of a reaction–diffusion equation with a convective coupling to the Navier–Stokes equations is of limited applicability.

[51] 
James F. Lutsko.
Rheology of dense polydisperse granular fluids under shear.
Phys. Rev. E, 70:061101, 2004.
[ bib 
.pdf 
http ]
The solution of the Enskog equation for the onebody velocity distribution of a moderately dense arbitrary mixture of inelastic hard spheres undergoing planar shear flow is described. A generalization of the Grad moment method, implemented by means of a novel generating function technique, is used so as to avoid any assumptions concerning the size of the shear rate. The result is illustrated by using it to calculate the pressure, normal stresses, and shear viscosity of a model polydisperse granular fluid in which grain size, mass, and coefficient of restitution vary among the grains. The results are compared to a numerical solution of the Enskog equation as well as moleculardynamics simulations. Most bulk properties are well described by the Enskog theory and it is shown that the generalized moment method is more accurate than the simple (Grad) moment method. However, the description of the distribution of temperatures in the mixture predicted by Enskog theory does not compare well to simulation, even at relatively modest densities.

[50] 
P. Gaspard and J. Lutsko.
Imploding shock wave in a fluid of hardcore particles.
Phys. Rev. E, 70:026306, 2004.
[ bib 
.pdf ]
We report the study of a fluid of harddisk particles in a contracting cavity. Under supersonic contraction speed, a shock wave converges to the center of the cavity where it implodes, creating a central peak in temperature. The dynamics of the fluid is studied by solving the Euler and NavierStokes equations, as well as by molecular dynamics simulations and the Enskog direct simulation Monte Carlo method. The value of the maximum temperature reached at the center of the cavity is systematically investigated with the different methods which give consistent results. Moreover, we develop a scaling theory for the maximum temperature based on the selfsimilar solutions of Euler's equations and meanfreepath considerations. This scaling theory provides a comprehensive scheme for the interpretation of the numerical results. In addition, the effects of the imploding shock wave on an passively driven isomerization reaction A[r harp over l]B are also studied.

[49] 
Jean Pierre Boon, Patrick Grosfils, and James F. Lutsko.
PropagationDispersion Equation.
J. Stat. Phys., 113(34):527  548, 2003.
[ bib 
eprint 
.pdf 
http ]
A propagationdispersion equation is derived for the first passage distribution function of a particle moving on a substrate with time delays. The equation is obtained as the hydrodynamic limit of the first visit equation, an exact microscopic finite difference equation describing the motion of a particle on a lattice whose sites operate as timedelayers. The propagationdispersion equation should be contrasted with the advectiondiffusion equation (or the classical Fokker–Planck equation) as it describes a dispersion process in time (instead of diffusion in space) with a drift expressed by a propagation speed with nonzero bounded values. The temporal dispersion coefficient is shown to exhibit a form analogous to Taylor's dispersivity. Physical systems where the propagationdispersion equation applies are discussed.

[48] 
J. P. Boon, P. Grosfils, and J. F. Lutsko.
Temporal diffusion.
Euro. Phys. Lett., 63:186192, 2003.
[ bib 
eprint 
.html ]
We consider the general problem of the firstpassage distribution of particles whose displacements are subject to time delays. We show that this problem gives rise to a propagationdispersion equation which is obtained as the largedistance (hydrodynamic) limit of the exact microscopic firstvisit equation. The propagationdispersion equation should be contrasted with the advectiondiffusion equation as the roles of space and time are reversed, hence the name temporal diffusion, which is a generic behavior encountered in an important class of systems.

[47] 
J. W. Dufty, J. J. Brey, and J. Lutsko.
Diffusion in a granular fluid. I. Theory.
Phys. Rev. E, 65:051303, 2002.
[ bib 
.pdf 
http ]
Many important properties of granular fluids can be represented by a system of hard spheres with inelastic collisions. Traditional methods of nonequilibrium statistical mechanics are effective for analysis and description of the inelastic case as well. This is illustrated here for diffusion of an impurity particle in a fluid undergoing homogeneous cooling. An appropriate scaling of the Liouville equation is described such that the homogeneous cooling ensemble and associated time correlation functions map to those of a stationary state. In this form the familiar methods of linear response can be applied, leading to GreenKubo and Einstein representations of diffusion in terms of the velocity and meansquare displacement correlation functions. These correlation functions are evaluated approximately using a cumulant expansion and from kinetic theory, providing the diffusion coefficient as a function of the density and the restitution coefficients. Comparisons with results from moleculardynamics simulation are given in the following companion paper.

[46] 
J. Lutsko, J. J. Brey, and J. W. Dufty.
Diffusion in a granular fluid. II. Simulation.
Phys. Rev. E, 65:051304, 2002.
[ bib 
.pdf 
http ]
The linearresponse description for impurity diffusion in a granular fluid undergoing homogeneous cooling is developed in the preceding paper. The formally exact Einstein and GreenKubo expressions for the selfdiffusion coefficient are evaluated there from an approximation to the velocity autocorrelation function. These results are compared here to those from moleculardynamics simulations over a wide range of density and inelasticity, for the particular case of selfdiffusion. It is found that the approximate theory is in good agreement with simulation data up to moderate densities and degrees of inelasticity. At higher density, the effects of inelasticity are stronger, leading to a significant enhancement of the diffusion coefficient over its value for elastic collisions. Possible explanations associated with an unstable long wavelength shear mode are explored, including the effects of strong fluctuations and mode coupling.

[45] 
J. F. Lutsko and J. W. Dufty.
Longranged correlations in sheared fluids.
Phys. Rev. E, 66:041206, 2002.
[ bib 
.pdf 
http ]
The presence of longranged correlations in a fluid undergoing uniform shear flow is investigated. An exact relation between the density autocorrelation function and the densitymometum correlation function implies that the former must decay more rapidly than 1/r, in contrast to predictions of simple modecoupling theory. Analytic and numerical evaluation of a nonperturbative modecoupling model confirms a crossover from 1/r behavior at ”small” r to a stronger asymptotic powerlaw decay. The characteristic length scale is [script l][approximate]sqrt( lambda[sub 0]/a), where lambda0 is the sound damping constant and a is the shear rate.

[44]  J. F. Lutsko. Atomicscale structure of hardcore fluids under shear flow. Phys. Rev. E, 66:051109, 2002. [ bib ] 
[43] 
James F. Lutsko.
Velocity Correlations and the Structure of Nonequilibrium
HardCore Fluids.
Phys. Rev. Lett., 86:3344, 2001.
[ bib 
.pdf 
http ]
A model for the pairdistribution function of nonequilibrium hardcore fluids is proposed based on a model for the effect of velocity correlations on the structure. Good agreement is found with molecular dynamics simulations of granular fluids and of sheared elastic hard spheres. It is argued that the incorporation of velocity correlations are crucial to correctly modeling atomic scale structure in nonequilibrium fluids.

[42] 
James F. Lutsko.
Model for the atomicscale structure of the homogeneous cooling
state of granular fluids.
Phys. Rev. E, 63:061211, 2001.
[ bib 
.pdf 
www: ]
The effect of velocity correlations on the equaltime density autocorrelation function, e.g., the pair distribution function (PDF), of a hardsphere fluid undergoing shear flow is investigated. The PDF at contact is calculated within the Enskog approximation and is shown to be in good agreement with molecular dynamics simulations for shear rates below the shearinduced ordering transition. These calculations are used to construct a nonequilibrium generalized meanspherical approximation for the PDF at finite separations, which is also found to agree well with the simulation data.

[41]  Victor MedinaChico, Alberto Suárez, and James F. Lutsko. Backpropagation in Decision Trees for Regression. In Proceedings of the 12th European Conference on Machine Learning, volume 2167 of Lecture Notes In Computer Science, pages 348359, 2001. [ bib ] 
[40]  A. Suarez and J.F. Lutsko. Globally optimal fuzzy decision trees for classification and regression. IEEE Transactions on Pattern Analysis and Machine Intelligence, 21:1280, 1999. [ bib ] 
[39] 
James F. Lutsko.
Viscoelastic effects from the Enskog equation for uniform shear
flow.
Phys. Rev. E, 58:434, 1998.
[ bib 
.pdf 
http ]
The Enskog kinetic equation for hard spheres is the only tractable theory with which the transport properties of a moderately dense gas can be studied. However, relatively little is known about its solutions outside the linear regime. In this paper two approximate nonlinear solutions of the Enskog equation for uniform shear flow are presented: a perturbative solution to second order in the shear rate and to fourth order in velocity moments and a ”nonperturbative” moment solution to all orders in the shear rate and to second order in the velocity moments. A comparison to the results of nonequilibrium moleculardynamics simulations shows that the perturbative results give good estimates of the quadratic corrections to the pressure tensor while the nonperturbative solution gives a semiquantitative description of viscoelastic effects including shear thinning and the normal stresses over a wide range of shear rates. The relevance of these results to the construction of kinetic models of the Enskog equation is also discussed.

[38] 
J. M. Montanero, A. Santos, M. Lee, J. W. Dufty, and J. F. Lutsko.
Stability of uniform shear flow.
Phys. Rev. E, 57:546556, 1998.
[ bib 
.pdf 
http ]
The stability of idealized computer shear flow at long wavelengths is studied in detail. A hydrodynamic analysis at the level of the NavierStokes equation for small shear rates is given to identify the origin and universality of an instability at any finite shear rate for sufficiently long wavelength perturbations. The analysis is extended to larger shear rates using a low density model kinetic equation. Direct Monte Carlo simulation of this equation is compared with a hydrodynamic description including nonNewtonian rheological effects. The hydrodynamic description of the instability is in good agreement with the direct Monte Carlo simulation for t<50t0, where t0 is the mean free time. Longer time simulations up to 2000t0 are used to identify the asymptotic state as a spatially nonuniform quasistationary state. Finally, preliminary results from molecular dynamics simulation showing the instability are presented and discussed.

[37] 
James F. Lutsko.
Approximate Solution of the Enskog Equation Far from
Equilibrium.
Phys. Rev. Lett., 78:243, 1997.
[ bib 
.pdf 
http ]
A moment method is used to solve the Enskog equation for the steadystate distribution under conditions of uniform shear flow. Comparison to nonequilibrium molecular dynamics demonstrates that the lowest order solution gives a good quantitative description of nonlinear effects such as shear thinning and normal stresses in a moderately dense fluid. The results are used as a basis in the formulation of a simple and quantitatively accurate kinetic model of the Enskog equation.

[36] 
James F. Lutsko.
Molecular Chaos, Pair Correlations, and ShearInduced Ordering
of Hard Spheres.
Phys. Rev. Lett., 77:2225, 1996.
[ bib 
.pdf 
http ]
We present results of molecular dynamics simulations that show that the shearinduced ordering of hard spheres is preceded by the apparent decrease to zero (in certain directions) of the anisotropic pairdistribution function (PDF) at contact. This precursor to the ordering is explained on the basis of a careful interpretation of the meaning of ”molecular chaos” in hardsphere systems. An ansatz is proposed to model the nonequilibrium PDF at finite separations and is shown to compare well with simulations.

[35] 
M. Lee, J. W. Dufty, J. M. Montanero, A. Santos, and J. F. Lutsko.
Long Wavelength Instability for Uniform Shear Flow.
Phys. Rev. Lett., 76:27022705, 1996.
[ bib 
.pdf 
http ]
Uniform shear flow is a prototype nonequilibrium state admitting detailed study at both the macroscopic and microscopic levels via theory and computer simulation. It is shown that the hydrodynamic equations for this state have a long wavelength instability. This result is obtained first from the NavierStokes equations and shown to apply at both low and high densities. Next, higher order rheological effects are included using a model kinetic theory. The results are compared favorably to those from Monte Carlo simulation.

[34]  James F. Lutsko and Bart Kuijpers. Simulated annealing and the determination of nearoptimal decision trees. In P. Cheeseman and R.W.Oldford, editors, Selecting Models from Data. SpringerVerlag, 1994. [ bib ] 
[33]  Kris Dockx and James F. Lutsko. SA/GA: Survival of the fittest in Alaska. In P. Cheeseman and R.W.Oldford, editors, Selecting Models from Data. SpringerVerlag, 1994. [ bib ] 
[32]  P. Van Sina, J. F. Lutsko, and W. De Clercq. A casebased expert system for the design of control schemes in chemical plants. In F. Moser et al., editor, ESCAPE3, pages 97101. Pergamon Press, 1993. [ bib ] 
[31] 
C. F. Tejero, J. F. Lutsko, J. L. Colot, and M. Baus.
Thermodynamic properties of the fluid, fcc, and bcc phases of
monodisperse chargestabilized colloidal suspensions within the Yukawa
model.
Phys. Rev. A, 46:33733379, 1992.
[ bib 
.pdf 
http ]
The thermodynamic properties of the Yukawa model for colloidal suspensions are determined theoretically from the RogersYoung integral equation for the fluid phase and from a recently introduced van der Waals–like theory for the solid phases. Very good agreement with the Monte Carlo simulations of Meijer and Frenkel [J. Chem. Phys. 94, 2269 (1991)] is found for both the fluid and the (fccbcc) solid phases. The location of the twophase coexistences, however, is shown to involve such small freeenergy and density changes that no definite statements about the phase diagram are possible within the present accuracy.

[30]  E. Aurell, U. Frisch, J. Lutsko, and M. Vergassola. On the multifractal properties of the energy dissipation derived from turbulence data. J. Fluid Mech., 238:467, 1992. [ bib ] 
[29] 
J. F. Lutsko.
Reformulation of nonperturbative densityfunctional theories of
classical nonuniform systems.
Phys. Rev. A, 43:41244130, 1991.
[ bib 
.pdf 
http ]
It is shown that most nonperturbative densityfunctional theories of classical systems can be reformulated as secondorder truncations of exact perturbative expansions, thus eliminating the ad hoc nature of such theories. This reformulation is used as a basis for discussion as to why some theories work better than others when applied to hard spheres, why most theories perform poorly for continuous potentials, and in what direction they might be modified so as to improve their performance

[28]  Marc Baus and James F. Lutsko. Statistical mechanical theories of freezing: Where do we stand? Physica A, 176(1):2836, 1991. [ bib ] 
[27] 
J F Lutsko and M Baus.
The freezing of soft spheres from a simple hardsphere
perturbation theory.
J. Phys.: Condens. Matter, 3(33):65476552, 1991.
[ bib ]
It is shown that a simple perturbation expansion around the free energy of a (BCC/FCC) hardsphere crystal leads to accurate predictions for the (BCC/FCC) freezing of soft spheres interacting via the inversepower potential, V(r)= epsilon ( sigma /r)n, for all values of n including the extreme case of the onecomponent plasma (n=1). In particular, the authors find that for 1<or=n<or=6 there is both a fluidBCC and BCCFCC transition whereas for n>6 the BCC phase is unstable and only the fluidFCC transition survives, in agreement with the computer simulations.

[26]  J.F. Lutsko, JP. Boon, and J.A. Somers. Lattice Gas Simulations of Viscous Fingering in a Porous Medium. In Numerical methods for the Simulation of Multiphase and Complex Flows. SpringerVerlag, 1991. [ bib ] 
[25] 
J. F. Lutsko and M. Baus.
Nonperturbative densityfunctional theories of classical
nonuniform systems.
Phys. Rev. E, 41:66476661, 1990.
[ bib 
.pdf 
http ]
We propose an approximation to the densityfunctional theory of classical nonuniform systems that reproduces all the formal properties of the free energy and requires only the direct correlation function of the uniform system as input. By introducing additional assumptions into this theory a direct relation can be established with most of the existing nonperturbative theories. When the theory is worked out for the case of the hardsphere solid, very good agreement is found with the computer simulations. The free energies, pressures, and fluidsolid coexistence data are reproduced to within the error bars of the simulations. The theory also predicts stable bcc and sc phases that could play a role in the final nucleation of the equilibrium fcc phase.

[24] 
J. F. Lutsko and M. Baus.
Can the thermodynamic properties of a solid be mapped onto those
of a liquid?
Phys. Rev. Lett., 64:761763, 1990.
[ bib 
.pdf 
http ]
A new approximation to the densityfunctional theory of classical nonuniform systems is proposed and worked out for the case of the hardsphere solid. The theory satisfies all the formal properties of the free energy and requires only the direct correlation function of the uniform system as input. the agreement with the computer simulations of the fcc hardsphere solid is excellent: The resulting free energies, pressures, and fluidsolid coexistence data are reproduced to within the error bars of the simulations. The theory also predicts stable bcc and sc phases which could facilitate the final nucleation into the equilibrium fcc phase.

[23]  M. D. Kluge, D. Wolf, J. F. Lutsko, and S. R. Phillpot. Formalism for the calculation of local elastic constants at grain boundaries by means of atomistic simulation. J. App. Phys., 67:2370, 1990. [ bib ] 
[22]  S. R. Phillpot, D. Wolf, and J. F. Lutsko. Anomalous elastic behavior in superlattices of twist grain boundaries in silicon. J. App. Phys., 67:6747, 1990. [ bib ] 
[21]  D. Wolf, P. R. Okamoto, S. Yip, J. F. Lutsko, and M. Kluge. Thermodynamic parallels between solidstate amorphization and melting. Journal of Materials Research, 5(2):286301, 1990. [ bib ] 
[20] 
James F. Lutsko, J. W. Dufty, and S. P. Das.
Fluctuations and dissipation in a fluid under shear: Linear
dynamics.
Phys. Rev. A, 39:1311, 1989.
[ bib 
.pdf 
http ]
A set of nonlinear Langevin equations for fluctuations of the local conserved densities in a fluid under shear is proposed. These equations are a model for the extension of hydrodynamics to very short wavelengths at liquid densities. The hydrodynamic modes associated with the linearized equations are studied as a function of wave vector and shear rate. The degeneracy of the viscous shear modes is lifted by the shear, and one of these modes combines with the heat mode to form a propagating pair. As an example of nonequilibrium fluctuations, the dynamic structure factor is calculated for several values of frequency and wave vector. At large shear rates one pair of propagating modes becomes unstable at a wavelength of the order of the particle size. This instability is suggested as a possible explanation for a shearinduced disorderorder transition seen in computer simulations. Nonlinear modecoupling effects are studied elsewhere.

[19] 
S. R. Phillpot, J. F. Lutsko, D. Wolf, and S. Yip.
Moleculardynamics study of latticedefectnucleated melting in
silicon.
Phys. Rev. B, 40:28312840, 1989.
[ bib 
.pdf 
http ]
The hightemperature behavior of both a highangle twist grain boundary and a free surface on the (110) plane of silicon are investigated using molecular dynamics and the StillingerWeber potential. It is found that, above the thermodynamic melting point, melting is nucleated at the grain boundary or surface and propagates through the system with a velocity that increases with temperature. We conclude that, due to the relatively fast nucleation times, melting in real crystals should be initiated at grain boundaries and surfaces, a conclusion that is entirely in accord with experiment.

[18] 
J. F. Lutsko, D. Wolf, S. R. Phillpot, and S. Yip.
Moleculardynamics study of latticedefectnucleated melting in
metals using an embeddedatommethod potential.
Phys. Rev. B, 40:28412855, 1989.
[ bib 
.pdf 
http ]
The hightemperature behavior of a highangle twist grain boundary, a free surface, and planar arrays of voids of various sizes, all on the (001) plane in copper, are studied through moleculardynamics simulation using an embeddedatommethod potential. Independently, we determine the thermodynamic melting point, Tm of this potential through an analysis of the free energies of a perfect crystal and the liquid phase. It is found that an ideal crystal consisting of nearly 1000 atoms may be superheated over 200 K above Tm while the introduction of any of the defects listed above nucleates melting at any temperature above Tm. We conclude that nucleation of the liquid phase at extrinsic defects is the most rapid, and therefore the dominant, mechanism of melting.

[17]  J. F. Lutsko. Generalized expressions for the calculation of elastic constants by computer simulation. J. App. Phys., 65:2991, 1989. [ bib ] 
[16]  D. Wolf and J. F. Lutsko. Origin of the supermodulus effect in metallic superlattices. J. App. Phys., 66:1961, 1989. [ bib ] 
[15]  D. Wolf and J. F. Lutsko. On the geometrical relationship between tilt and twist grainboundaries. Zeitschrift fur Kristallographie, 189(34):239262, 1989. [ bib ] 
[14]  D. Wolf and J. F. Lutsko. Structurallyinduced elastic anomalies in a superlattice of (001) twist grainbooundaries. Journal of Materials Research, 4(6):14271443, 1989. [ bib ] 
[13]  S. R. Phillpot, J. F. Lutsko, and D. Wolf. Nucleation and kinetics of thermodynamic melting  a moleculardynamics study of grainboundary induced melting in silicon. Solid State Communications, 70(3):265268, 1989. [ bib ] 
[12]  J. F. Lutsko, D. Wold, S. R. Phillpot, and S. Yip. On the relevance of extrinsic defects to melting  a moleculardynamics study using an embedded atom potential. Scripta Metallurgica, 23(3):333338, 1989. [ bib ] 
[11] 
D. Wolf and J. F. Lutsko.
Structurally induced supermodulus effect in superlattices.
Phys. Rev. Lett., 60:11701173, 1988.
[ bib 
.pdf 
http ]
It is suggested that the “supermodulus effect” observed for compositionmodulated superlattices arises from the presence of the structurally disordered solid interfaces and not necessarily from electronic structure effects.

[10] 
J. F. Lutsko, D. Wolf, S. Yip, S. R. Phillpot, and T. Nguyen.
Moleculardynamics method for the simulation of bulksolid
interfaces at high temperatures.
Phys. Rev. B, 38:1157211581, 1988.
[ bib 
.pdf 
http ]
A new method for the moleculardynamics simulation of bulk planar interfaces at high temperatures is presented. The method uses the basic ParrinelloRahman (constantstress) scheme, modified for the application to inhomogeneous systems. Since our computational cell contains only one interface with twodimensional (2D) periodic border conditions, we are able to study isolated interfaces all the way up to melting. The interaction between boundaries which may lead to their annihilation at higher temperatures, which is a problem when 3D periodic borders are applied, is thus avoided. As an application, the method is used to study the stability of a grain boundary at high temperatures. Observations on a possible connection between grainboundary migration and “premelting” are discussed.

[9] 
J. F. Lutsko, D. Wolf, and S. Yip.
Molecular dynamics calculation of free energy.
J. Chem. Phys., 88:6525, 1988.
[ bib 
http ]
The results of a systematic study of a recently proposed method by Frenkel and Ladd for calculating free energies via molecular dynamics are reported. Internal measures of the error, the effect of varying parameters, and comparison of the relative computational efficiency of the method compared to other methods is considered. In particular, agreement with the quasiharmonic method is shown for temperatures up to 75% of melting.

[8]  J. F. Lutsko. Stress and elastic constants in anisotropic solids: Molecular dynamics techniques. J. App. Phys., 64:1152, 1988. [ bib ] 
[7]  J. F. Lutsko, D. Wolf, and S. Yip. Free energy calculation via MD  Methodology and application to bicrystals. J.ournal de Physique, 49(C5):375379, 1988. [ bib ] 
[6]  J. F. Lutsko and D. Wolf. A moleculardynamics study of grainboundary behavior at elevated temperatures using an embedded atom potential. Scripta Metallurgica, 22(12):19231928, DEC 1988. [ bib ] 
[5] 
J. F. Lutsko and J. W. Dufty.
Possible Instability for ShearInduced OrderDisorder
Transition.
Phys. Rev. Lett., 57:27752778, 1986.
[ bib 
.pdf 
http ]
A simple fluid in uniform isothermal shear flow is studied for conditions used in recent nonequilibrium computer simulations. The shorttime dynamics for the local conserved densities is found to be unstable at large shear rates for wave vectors near the peak of the structure factor. The critical shear rates obtained are similar to those for an orderdisorder transition observed in the computer simulations.

[4]  James W. Dufty and James F. Lutsko. Nonlinear Transport and Mode Coupling in Fluids Under Shear. In J. CasasVazquez, editor, Recent Developments in Nonequilibrium Statistical, pages 4784, Berlin, 1986. SpringerVerlag. [ bib ] 
[3] 
J. Lutsko and J. W. Dufty.
Hydrodynamic fluctuations at large shear rate.
Phys. Rev. A, 32:3040, 1985.
[ bib 
.pdf 
http ]
The nonlinear NavierStokesLangevin equations are used to describe fluctuations in a compressible fluid with uniform shear flow. The hydrodynamic modes for small deviations from the macroscopic nonequilibrium state are calculated, including linear mode coupling of the fluctuating variables with the macroscopic velocity field. The associated correlation functions are determined with the full nonlinear dependence on shear rate required for long times and/or large shear rate. The stationary and joint probability densities are also constructed from the associated FokkerPlanck equation. As an application of these results, the lowestorder modecoupling contributions to the renormalized shear viscosity are evaluated.

[2] 
J. Lutsko and J. W. Dufty.
Modecoupling contributions to the nonlinear shear viscosity.
Phys. Rev. A, 32:12291231, 1985.
[ bib 
.pdf 
http ]
Three different results for the nonanalytic dependence of the shear viscosity on shear rate have been given. This discrepancy is resolved by an independent calculation based on the nonlinear NavierStokesLangevin equations. The relationship to previous calculations and reasons for the differences are described.

[1]  James W. Dufty and James F. Lutsko. Structure and Stability of Hydrodynamic Modes for Shear Flow. Kinam, 6:169181, 1985. [ bib ] 
This file was generated by bibtex2html 1.98.