Contents
1 Introduction . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . 94
2 Coarse-Grained Molecular Dynamics Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3 Self-Assembly of Lipids into Biological Membranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
4 Self-Assembly of Dendrimers into Complex Architectures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5 Response of Biological Membranes to Addition of Macromolecules . . . . . . . . . . . . . . .. . . . . . 100
6 Assembly of Multilamellar Vesicles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
7 Perspectives and Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
1 Introduction
In the early 1920s, physicists were struggling with the consequences of the birth of
quantum mechanics, and quantum chemistry did not exist as a discipline. It is not
surprising therefore that, notwithstanding Gilbert N. Lewis [1], there was some
confusion among chemists as to the nature of the chemical bond. One of the
consequences of this lack of understanding of the fundamentals of molecular structure
and bonding was that initially there was little appreciation for the notion that
Hermann Staudinger’s high molecular weight “macromolecules” really were manifestations of covalent-linked monomeric entities as opposed to simple “aggregates” of
monomers [2].
Nowadays we take for granted that both synthetic and natural polymers really are
macromolecules. In the decades since Hermann Staudinger’s 1953 Nobel Prize [3],
driven in part by the immense technological importance of macromolecules in
consumer products and advanced materials, a deep understanding has emerged of
the phenomenon of macromolecular “aggregation” that underpins the field of supramolecular chemistry, championed by Jean-Marie Lehn [4]. Biology is rife with
examples of the latter, which provides inspiration for novel materials development
based on either the spontaneous or directed self-assembly of macromolecules.
The year 1953 was important not only because of the Staudinger Nobel Prize, but
also because it was the year that the structure of the macromolecule DNA was reported
by James Watson and Francis Crick [5], which is the subject of another article in this
volume by Ned Seeman [6]. Yet another important milestone was recorded in 1953,
namely the first published use of a computer to carry out a simulation of liquid, albeit a
liquid composed of argon atoms [7]. This seminal work, which was carried out on the
famous MANIAC machine at Los Alamos National Laboratory, by Nick Metropolis
and collaborators, was never honored with a Nobel Prize, but nonetheless had an
enormous impact across the whole breadth of the physical and life sciences. Indeed, it
is inconceivable today that one would attempt a research program dealing with either
natural or synthetic macromolecules without the aid of computer simulation as a
complement to their design, synthesis, and characterization [8].
The present article deals with the use of large-scale computer simulation
techniques to investigate the self-assembly of modest-sized natural and synthetic
94
G. Fiorin et al.
1 Introduction . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . 94
2 Coarse-Grained Molecular Dynamics Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3 Self-Assembly of Lipids into Biological Membranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
4 Self-Assembly of Dendrimers into Complex Architectures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5 Response of Biological Membranes to Addition of Macromolecules . . . . . . . . . . . . . . .. . . . . . 100
6 Assembly of Multilamellar Vesicles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
7 Perspectives and Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
1 Introduction
In the early 1920s, physicists were struggling with the consequences of the birth of
quantum mechanics, and quantum chemistry did not exist as a discipline. It is not
surprising therefore that, notwithstanding Gilbert N. Lewis [1], there was some
confusion among chemists as to the nature of the chemical bond. One of the
consequences of this lack of understanding of the fundamentals of molecular structure
and bonding was that initially there was little appreciation for the notion that
Hermann Staudinger’s high molecular weight “macromolecules” really were manifestations of covalent-linked monomeric entities as opposed to simple “aggregates” of
monomers [2].
Nowadays we take for granted that both synthetic and natural polymers really are
macromolecules. In the decades since Hermann Staudinger’s 1953 Nobel Prize [3],
driven in part by the immense technological importance of macromolecules in
consumer products and advanced materials, a deep understanding has emerged of
the phenomenon of macromolecular “aggregation” that underpins the field of supramolecular chemistry, championed by Jean-Marie Lehn [4]. Biology is rife with
examples of the latter, which provides inspiration for novel materials development
based on either the spontaneous or directed self-assembly of macromolecules.
The year 1953 was important not only because of the Staudinger Nobel Prize, but
also because it was the year that the structure of the macromolecule DNA was reported
by James Watson and Francis Crick [5], which is the subject of another article in this
volume by Ned Seeman [6]. Yet another important milestone was recorded in 1953,
namely the first published use of a computer to carry out a simulation of liquid, albeit a
liquid composed of argon atoms [7]. This seminal work, which was carried out on the
famous MANIAC machine at Los Alamos National Laboratory, by Nick Metropolis
and collaborators, was never honored with a Nobel Prize, but nonetheless had an
enormous impact across the whole breadth of the physical and life sciences. Indeed, it
is inconceivable today that one would attempt a research program dealing with either
natural or synthetic macromolecules without the aid of computer simulation as a
complement to their design, synthesis, and characterization [8].
The present article deals with the use of large-scale computer simulation
techniques to investigate the self-assembly of modest-sized natural and synthetic
94
G. Fiorin et al.