INTRODUCTION

The combination of improved experimental capability, great advances in computer performance, and the development of new algorithms from computer science have led to quite sophisticated methods for the study of certain biomolecules, in particular of folded protein structures. One such technique, called ‘threading,’ picks out small pieces of the primary structure of a protein whose structure is unknown and examines extensive databases of known protein structures to find similar pieces of primary structure. One then guesses that this piece will have the same folded structure as that in the known structure. Since pieces do not all fit together perfectly, an effective force field is used to ‘optimize’ the resultant structure, and Monte Carlo methods have already begun to play a role in this approach. (There are substantial similarities to ‘homology modeling’ approaches to the same, or similar, problems.) Of course, the certainty that the structure is correct comes primarily from comparison with experimental structure determination of crystalized proteins. One limitation is thus that not all proteins can be crystalized, and, even if they can, there is no assurance that the structure will be the same in vivo. Threading algorithms have, in some cases, been extraordinarily successful, but since they do not make use of the interactions between atoms it would be useful to complement this approach by atomistic simulations. (For an introductory overview of protein structure prediction, see Wooley and Ye (2007).) Biological molecules are extremely large and complex; moreover, they are usually surrounded by a large number of water molecules.

INTRODUCTION

In most of the discussion presented so far in this book, the quantum character of atoms and electrons has been ignored. The Ising spin models have been an exception, but since the Ising Hamiltonian is diagonal (in the absence of a transverse magnetic field!), all energy eigenvalues are known and the Monte Carlo sampling can be carried out just as in the case of classical statistical mechanics. Furthermore, the physical properties are in accord with the third law of thermodynamics for Ising-type Hamiltonians (e.g. entropy S and specific heat vanish for temperature T → 0, etc.) in contrast to the other truly classical models dealt with in previous chapters (e.g. classical Heisenberg spin models, classical fluids and solids, etc.) which have many unphysical low temperature properties. A case in point is a classical solid for which the specific heat follows the Dulong–Petit law, C = 3NkB, as T → 0, and the entropy has unphysical behavior since S → −∞. Also, thermal expansion coefficients tend to non-vanishing constants for T → 0 while the third law implies that they must be zero. While the position and momentum of a particle can be specified precisely in classical mechanics, and hence the groundstate of a solid is a perfectly rigid crystal lattice (motionless particles localized at the lattice points), in reality the Heisenberg uncertainty principle forbids such a perfect rigid crystal, even at T → 0; due to zero point motions which ‘smear out’ the particles over some region around these lattice points.

INTRODUCTION AND PERSPECTIVE

In the preceding chapters of this book we have dealt extensively with equilibrium properties of a wide variety of models and materials. We have emphasized the importance of insuring that equilibrium has been reached, and we have discussed the manner in which the system may approach the correct distribution of states, i.e. behavior before it comes to equilibrium. This latter topic has been treated from the perspective of helping us understand the difficulties of achieving equilibrium. The theory of equilibrium behavior is well developed and in many cases there is extensive, reliable experimental information available.

In this chapter, however, we shall consider models which are inherently non-equilibrium! This tends to be rather uncharted territory. For some cases theory exists, but it has not been fully tested. In other situations there is essentially no theory to rely upon. In some instances the simulation has preceded the experiment and has really led the way in the development of the field. As in the earlier chapters, for pedagogical reasons we shall concentrate on relatively simple models, but the presentation can be generalized to more complex systems.

DRIVEN DIFFUSIVE SYSTEMS (DRIVEN LATTICE GASES)

Over two decades ago a deceptively simple modification of the Ising lattice gas model was introduced (Katz et al., 1984) as part of an attempt to understand the behavior of superionic conductors.

WHAT IS A MONTE CARLO SIMULATION?

In a Monte Carlo simulation we attempt to follow the ‘time dependence’ of a model for which change, or growth, does not proceed in some rigorously predefined fashion (e.g. according to Newton's equations of motion) but rather in a stochastic manner which depends on a sequence of random numbers which is generated during the simulation. With a second, different sequence of random numbers the simulation will not give identical results but will yield values which agree with those obtained from the first sequence to within some ‘statistical error’. A very large number of different problems fall into this category: in percolation an empty lattice is gradually filled with particles by placing a particle on the lattice randomly with each ‘tick of the clock’. Lots of questions may then be asked about the resulting ‘clusters’ which are formed of neighboring occupied sites. Particular attention has been paid to the determination of the ‘percolation threshold’, i.e. the critical concentration of occupied sites for which an ‘infinite percolating cluster’ first appears. A percolating cluster is one which reaches from one boundary of a (macroscopic) system to the opposite one. The properties of such objects are of interest in the context of diverse physical problems such as conductivity of random mixtures, flow through porous rocks, behavior of dilute magnets, etc. Another example is diffusion limited aggregation (DLA) where a particle executes a random walk in space, taking one step at each time interval, until it encounters a ‘seed’ mass and sticks to it.

INTRODUCTION

In the previous chapters of this text we have examined a wide variety of Monte Carlo methods in depth. Although these are exceedingly useful for many different problems in statistical physics, there are some circumstances in which the systems of interest are not well suited to Monte Carlo study. Indeed there are some problems which may not be treatable by stochastic methods at all, since the time-dependent properties as constrained by deterministic equations of motion are the subject of the study. The purpose of this chapter is thus to provide a very brief overview of some of the other important simulation techniques in statistical physics. Our goal is not to present a complete list of other methods or even a thorough discussion of these methods which are included but rather to offer sufficient background to enable the reader to compare some of the different approaches and better understand the strengths and limitations of Monte Carlo simulations.

MOLECULAR DYNAMICS

Integrationmethods (microcanonical ensemble)

Molecular dynamics methods are those techniques which are used to numerically integrate coupled equations of motion for a system which may be derived, e.g. in the simplest case from Lagrange's equations or Hamilton's equations. Thus, the approach chosen is to deal with many interacting atoms or molecules within the framework of classical mechanics. We begin this discussion with consideration of systems in which the number of particles N, the system volume V, and the total energy of the system E are held constant.

FLUIDS

NVTensemble and the virial theorem

The examination of the equation of state of a two-dimensional model fluid (the hard disk system) was the very first application of the importance sampling Monte Carlo method in statistical mechanics (Metropolis et al., 1953), and since then the study of both atomic and molecular fluids by Monte Carlo simulation has been a very active area of research. Remember that statistical mechanics can deal well analytically with very dilute fluids (ideal gases!), and it can also deal well with crystalline solids (making use of the harmonic approximation and perfect crystal lattice periodicity and symmetry), but the treatment of strongly correlated dense fluids (and their solid counterparts, amorphous glasses) is much more difficult. Even the description of short range order in fluids in a thermodynamic state far away from any phase transition is a non-trivial matter (unlike the lattice models discussed in the last chapter, where far away from phase transitions the molecular field approximation, or a variant thereof, is usually both good enough and easily worked out, and the real interest is generally in phase transition problems).

The discussion in this chapter will consider only symmetric particles, and for the consideration of hard rods, spherocylinders, etc., the reader is referred elsewhere (Frenkel and Smit, 1996).

Within the contents of this book we have attempted to elucidate the essential features of Monte Carlo simulations and their application to problems in statistical physics. We have attempted to give the reader practical advice as well as to present theoretically based background for the methodology of the simulations as well as the tools of analysis. New Monte Carlo methods will be devised and will be used with more powerful computers, but we believe that the advice given to the reader in Section 4.8 will remain valid.

In general terms we can expect that progress in Monte Carlo studies in the future will take place along two different routes. First, there will be a continued advancement towards ultra high resolution studies of relatively simple models in which critical temperatures and exponents, phase boundaries, etc., will be examined with increasing precision and accuracy. As a consequence, high numerical resolution as well as the physical interpretation of simulational results may well provide hints to the theorist who is interested in analytic investigation. On the other hand, we expect that there will be a tendency to increase the examination of much more complicated models which provide a better approximation to physical materials. As the general area of materials science blossoms, we anticipate that Monte Carlo methods will be used to probe the often complex behavior of real materials. This is a challenge indeed, since there are usually phenomena which are occurring at different length and time scales.

COMMENTARY

In the preceding chapters we described the application of Monte Carlo methods in numerous areas that can be clearly identified as belonging to physics. Although the exposition was far from complete, it should have sufficed to give the reader an appreciation of the broad impact that Monte Carlo studies has already had in statistical physics. A more recent occurrence is the application of these methods in non-traditional areas of physics related research. More explicitly, we mean subject areas that are not normally considered to be physics at all but which make use of physics principles at their core. In some cases physicists have entered these arenas by introducing quite simplified models that represent a ‘physicist's view’ of a particular problem. Often such descriptions are oversimplified, but the hope is that some essential insight can be gained as is the case in many traditional physics studies. (A recent, provocative perspective of the role of statistical physics outside of physics has been presented by Stauffer (2004).) In other cases, however, Monte Carlo methods are being applied by non-physicists (or ‘recent physicists’) to problems that, at best, have a tenuous relationship to physics. This chapter is to serve as a brief glimpse of applications of Monte Carlo methods ‘outside’ of physics. The number of such studies will surely grow rapidly; and even now, we wish to emphasize that we will make no attempt to be complete in our treatment.

INTRODUCTION

Modern Monte Carlo methods have their roots in the 1940s when Fermi, Ulam, von Neumann, Metropolis and others began considering the use of random numbers to examine different problems in physics from a stochastic perspective (Cooper (1989); this set of biographical articles about S. Ulam provides fascinating insight into the early development of the Monte Carlo method, even before the advent of the modern computer). Very simple Monte Carlo methods were devised to provide a means to estimate answers to analytically intractable problems. Much of this work is unpublished and a view of the origins of Monte Carlo methods can best be obtained through examination of published correspondence and historical narratives. Although many of the topics which will be covered in this book deal with more complex Monte Carlo methods which are tailored explicitly for use in statistical physics, many of the early, simple techniques retain their importance because of the dramatic increase in accessible computing power which has taken place during the last two decades. In the remainder of this chapter we shall consider the application of simple Monte Carlo methods to a broad spectrum of interesting problems.

COMPARISONS OF METHODS FOR NUMERICAL INTEGRATION OF GIVEN FUNCTIONS

Simple methods

One of the simplest and most effective uses for Monte Carlo methods is the evaluation of definite integrals which are intractable by analytic techniques. (See the book by Hammersley and Handscomb (1964) for more mathematical details.)