Historically physics was first known as ‘natural philosophy’ and research was carried out by purely theoretical (or philosophical) investigation. True progress was obviously limited by the lack of real knowledge of whether or not a given theory really applied to nature. Eventually experimental investigation became an accepted form of research although it was always limited by the physicist's ability to prepare a sample for study or to devise techniques to probe for the desired properties. With the advent of computers it became possible to carry out simulations of models which were intractable using ‘classical’ theoretical techniques. In many cases computers have, for the first time in history, enabled physicists not only to invent new models for various aspects of nature but also to solve those same models without substantial simplification. In recent years computer power has increased quite dramatically, with access to computers becoming both easier and more common (e.g. with personal computers and workstations), and computer simulation methods have also been steadily refined. As a result computer simulations have become another way of doing physics research. They provide another perspective; in some cases simulations provide a theoretical basis for understanding experimental results, and in other instances simulations provide ‘experimental’ data with which theory may be compared. There are numerous situations in which direct comparison between analytical theory and experiment is inconclusive. For example, the theory of phase transitions in condensed matter must begin with the choice of a Hamiltonian, and it is seldom clear to what extent a particular model actually represents real material on which experiments are done.

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.