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Energy Landscapes: Applications to Clusters,

Biomolecules and Glasses (Cambridge Molecular
Science)

Article  in  Journal of Statistical Physics · January 2007

DOI: 10.1007/s10955-006-9264-y

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Journal of Statistical Physics (

C 2006 )

DOI: 10.1007/s10955-006-9264-y

Book Review: Energy Landscapes: Applications to

Clusters, Biomolecules and Glasses (Cambridge
Molecular Science)

Energy Landscapes: Applications to Clusters, Biomolecules and Glasses

(Cambridge Molecular Science) by David J. Wales (Cambridge University Press,
2004).

David J. Wales’ book Energy Landscapes is itself a description of a landscape,

namely of the science of systems composed of a relatively small number of
atoms or molecules in which disorder plays a crucial role. The understanding and
mathematical properties of potential energy surfaces (PES) present an underlying
unifying theme of this type of system. The book is written in the form of a
treatise on the way dynamic and thermodynamic properties of various systems are
encoded in, and can be deduced from, the features of their respective potential (or
free) energy surfaces. It covers a whole slew of theoretical subjects introducing
the concept and characteristics of PES and then going all the way to important
applications in small clusters, biomolecules and glasses.
In many respects Wales’ book defines a whole new subject, even more—a
whole new field, and at the same time presents its state of the art description.
It is very ambitious in its scope, extremely broad in its subject matter, and by
necessity relatively uneven in its treatment. Nevertheless it is a superb and laudable
achievement, and I believe it will represent a resource on the subject of PES for
years to come.
With its onerous 692 pages and ten voluminous chapters with extensive and
exhaustive lists of references, Wales’ book is not an easy read. Though it is intended
for nonspecialists, graduate students and advanced undergrads alike, I doubt that
any part of the intended audience will be able to follow its broad strokes in their
entirety. This does not mean it is a dull book. On the contrary. Wales manages
to write in a very lively and engaging style that invites learning, while the really
superb illustrations that abound in the book enliven his presentation and urge the
reader to carry on. Though the encyclopedic breadth of the book might overawe an
unprepared reader, I am sure it will eventually make its mark by being the resource
on the subject of PES and their applications in various systems.

0022-4715

C 2006 Springer Science+Business Media, LLC
 Book Review

But what really fascinates me about Wales’ book is its inherent interdisci-
plinarity stemming from its excursions into the worlds of nano and bio. It moves
through a number of fields unifying them through the concept of PES. This is
probably also its most important and lasting achievement. The author has mostly
managed to strike a fine balance between the descriptive breadth of exposition and
mathematical details of each of the subject matters. The book is thus not unman-
ageably technical and should be at least in part accessible to a fairly broad and
wide ranging audience composed of physicists, physical chemists and molecular
biologists, while helping them to realize the underlying unity between different
contexts in which PES emerge as an important tool for understanding the dynamic
and thermodynamic behavior of different systems.
I can certainly wholeheartedly recommend it as an exhaustive guide and
treasure trove of resources in the fascinating worlds of PES. Though in its entirety
it is probably not suited for an advanced undergraduate or even a graduate course,
parts of it can serve as a very illuminating and helpful introduction not only to the
field of PES itself but also as an introduction to the study of molecular clusters such
as small water clusters, properties of biomolecules such as proteins and glassy as
well as disordered materials in general. All in all due to its encyclopedic breadth,
this book stands a bit off the beaten path, while remaining a laudable enterprise
and a first class achievement.
The subject matter of this treatise is varied and broad. As stated, the nature of
the exposition while not straying from some technical and mathematical fine points,
remains within the bounds of accessible. The first chapter, the Introduction, states
the motivation of the book: to present a unified and reasonably self-contained view
of potential and free energy surfaces together with their use in the study of clusters,
biomolecules, glasses and supercooled liquids. The structure and dynamics of
atomic and molecular clusters, folding of proteins and phenomenology of glasses
are all aspects of PES or FES. The most important features of PES are their
local minima, the global minimum and different transition states, with various
pathways between minima defined by the connectivity of the PES. The study of
atomic and molecular clusters of rare gas atoms, molecules, metal and non-metal
atoms, based on multilayer polyhedra is introduced as an example of the workings
of PES. Levinthal’s paradox as well as the phenomenology of proteins and protein
structure with energy landscapes in protein folding are introduced as an additional
example of the workings of PES. The dynamics, pressure effects and aging of
glasses and supercooled liquids serve as the last example of the phenomenology
of PES.
The second chapter is dedicated to the basis of the PES i.e. to the
Born-Oppenheimer approximation (BOA) and normal mode analysis. BOA is
fundamental to the introduction of PES since it allows us to ignore other degrees
of freedom such as electronic coordinates and to concentrate on the configurations
Book Review

of the molecules as a whole. This chapter deals with a formal mathematical intro-
duction of BOA and its limitations together with some simple examples of PES
and some of its basic properties such as PES crossings and its consequences.
Symmetry considerations are dealt with in the third chapter. Symmetry is a
key player in the description and analysis of PES and is introduced through the not
impenetrably technical essentials of the group theory. Molecular symmetry groups
of rigid and non-rigid molecules and especially the polytetrahedral packing and the
geometric description of packing in bulk systems is discussed through symmetry
considerations.
Features of the landscape are dealt with in the fourth chapter with the same
heading. The stationary points of the PES are introduced and analyzed in terms
of local minima and transition states. The classification of the stationary states
is based upon the properties of the matrix of the second derivatives (the Hessian
matrix), especially its eigenvalues. Thus the transition state is defined as a station-
ary state with a Hessian that has a single negative eigenvalue and is connected to
different local minima by steepest descent pathways. Branch points, geometrical
symmetry selection rules, and (McIver—Stanton) symmetry transition rules are
also introduced and explained as well in this chapter.
The following chapter is dedicated to a description of the landscape. In order
to understand the features of PES, which is a 3N dimensional function where N
is the number of particles, one needs to devise aids to facilitate visualizing the
energy landscape. Two appropriate visualization aids introduced in this chapter
are: monotonic sequences and disconnectivity graphs. The monotonic sequence
is a sequence of local minima and correposnding transition states along which
the energy constantly decreases. This concept also defines the basin or folding
funnel—a sequence of states that leads to the same local minimum. On the other
hand the disconnectivity graphs are defined as superbasins at a certain fixed
value of energy such that PES pathways between them never exceed this fixed
energy. Lennard-Jones clusters, C(60) fullerenes and Lennard-Jones polymers are
discussed as examples of use of these visualization aids. Disconnectivity graphs
can also be understood in terms of the small world networks.
The sixth chapter explores the landscape and is based on methods to locate
and characterize different features of PES including the global minimum of the
surface as well as higher index saddles that have more then a single negative
eigenvalue. These methods include molecular dynamics (MD), Monte-Carlo sim-
ulations (MC) and stochastic dynamics together with various techniques of biased
sampling.
The seventh chapter deals with properties of the landscape. Both dynamic and
thermodynamic properties of the various systems can be obtained from the sta-
tionary points sampled from PES. The superposition approximation is especially
valuable in this respect since it allows one to write the partition function in terms
 Book Review

of contributions from different local minima in the classical and quantum limit.
An approach based on the master equation to dynamics through paths between
different local minima and transtion states allows the use of the PES features in the
dynamical context. This chapter also deals with and introduces the role of catas-
trophe theory in understanding the role that the features of PES play in dynamics
and thermodynamics of various systems.
Chapter eight deals with various molecular or atomic clusters. It builds on
the introduction to atomic and molecular clusters in the first chapter and proceeds
with a more detailed description of the nature and properties of clusters. Finite size
effects, thermodynamic stability and phase transitions of clusters are discussed in
detail. Cluster simulations with Lennard—Jones interactions are used to intro-
duce their structure and properties of the corresponding PES that can show, in the
most simple version, a single or a double-funnel landscape. Cluster simulations
with Morse interactions are used to discuss the importance of the range of in-
teratomic potential that separates the Lennard—Jones from the Morse clusters in
terms of thermodynamic and dynamic properties. Additional interesting examples
of atomic and molecular clusters are the alkali halide clusters, the buckminster-
fullerene and especially and most importantly water clusters which are discussed
in considerable detail.
The ninth chapter is dedicated to PES in biomolecules. Biomolecules are
in many respects quite similar to other molecular clusters. Computer simulations
are used as a primary tool to understand and predict protein structure ab initio.
More coarse-grained lattice and off-lattice models such as the random energy
model are also used to understand features of protein structure such as frustration.
Structure of various polypeptides and proteins is used as examples of protein PES
in order to discuss the relation between the PES properties such as disconnectivity
graphs and protein structure.
The subject matter of the last chapter is that of glasses and supercooled liquids.
Apart from discussing the connection between the glass transition temperature and
the features of PES this chapter introduces also some of the theories of the glassy
state such as the free volume theory and the mode coupling theory of the glass
transition. It also deals with models based on the spin glass theories, though
spin glasses are quite different from ordinary glasses since they assume a regular
lattice. Simulation of glasses and superposition description of glasses in terms of
inherent structures as embodied by the PES is introduced next in order to connect
the transition states and pathways between local minima in glasses with molecular
rearrangement mechanisms.
Once again this is in many respects a beautiful, well conceived and most
informative book. It moves elegantly and engagingly through various fields of the-
oretical physics, physical chemistry and molecular biology to expose and explain
the unifying workings of the potential energy surfaces and along the way finds
Book Review

an elegant and meaningful connection, on a most fundamental level, between the

worlds of nano and bioscience in a way hardly attempted before.

Rudi Podgornik
Section on Molecular Biophysics,
Laboratory of Physical and Structural Biology,
National Institute of Child Health and Human Development,
National Institutes of Health, Bldg. 9,
Room 1E-116, 9 Memorial Dr. Bethesda, MD 20892-0924
E-mail: [email protected]

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