membranes are inhomogeneous mixtures of different lipids. The thermodynamic
and mechanical properties of membranes have been modeled by assuming the
presence of “lipid rafts,” i.e., microdomains with enhanced concentration of certain
constituent lipids. Currently, an extensive characterization of lipid rafts by experiment is cumbersome. It is also debatable whether MD simulations possess the
required accuracy to predict the formation of such structures. Nevertheless, experimental techniques such as microscopy and computational methods such as CG
simulations are now converging to the same scales of length and time. It is highly
likely that CG models will become progressively more accurate by complementing
measured properties with computational predictions.
Finally, one must consider that many of the supramolecular structures discussed
here, and others of similar complexity, are often produced outside thermodynamic
equilibrium yet they are effectively treated as the “native” structure of a macromolecular assembly because of the insurmountable time scales required to transition
between different phases. On the other hand, this complication is particularly challenging for systems where processing drives them into nonequilibrium states that
demonstrate relatively long relaxation time-scales (e.g., days to months). MD simulations of macromolecules in liquid solutions have so far relied on the notion that
thermodynamic exchange between all relevant states could always be achieved within
the time scale of the laboratory. However, supramolecular structures are formed over a
broad range of time scales, sometimes beyond those that allow one to gather a
quantitative understanding. A paramount example is that of the crystallization of
macromolecules. The study of slow-forming supramolecular structures demands an
even higher predictive power from MD simulations, and a continued effort to perfect
both CG models as well as the technology required to use them.
References
1. Chemical Heritage Foundation (2010) Chemistry in history: Gilbert Newton Lewis. Chemical
Heritage Foundation, Philadelphia. http://www.chemheritage.org/discover/online-resources/
chemistry-in-history/themes/molecular-synthesis-structure-and-bonding/lewis.aspx.
2. Deußing G, Weber M (2012) Topic of the month: The life and work of Hermann Staudinger.
Guido Deußing, Neuss. http://www.k-online.de/cipp/md_k/custom/pub/content,oid,35205/
lang,2/ticket,g_u_e_s_t/~/February_2012_Life_and_work_of_Hermann_Staudinger_part_1.html.
3. Nobelprize.org (2013) The Nobel Prize in Chemistry 1953. Nobel Media AB, Stockholm.
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1953/.
4. Nobelprize.org (2013) Jean-Marie Lehn – biographical. Nobel Media AB, Stockholm. http://
www.nobelprize.org/nobel_prizes/chemistry/laureates/1987/lehn-bio.html.
5. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids – a structure for deoxyribose nucleic acid. Nature 171(4356):737–738
6. Seeman NC (2014) Another important 60th anniversary. Covalent and supramolecular macromolecules with complex architecture. Adv Polym Sci. doi:10.1007/12_2013_243
7. Metropolis N et al (1953) Equation of state calculations by fast computing machines. J Chem
Phys 21(6):1087–1092
8. Percec V et al (2010) Self-assembly of Janus dendrimers into uniform dendrimersomes and
other complex architectures. Science 328(5981):1009–1014
Computer Simulation of Self-Assembling Macromolecules
105
and mechanical properties of membranes have been modeled by assuming the
presence of “lipid rafts,” i.e., microdomains with enhanced concentration of certain
constituent lipids. Currently, an extensive characterization of lipid rafts by experiment is cumbersome. It is also debatable whether MD simulations possess the
required accuracy to predict the formation of such structures. Nevertheless, experimental techniques such as microscopy and computational methods such as CG
simulations are now converging to the same scales of length and time. It is highly
likely that CG models will become progressively more accurate by complementing
measured properties with computational predictions.
Finally, one must consider that many of the supramolecular structures discussed
here, and others of similar complexity, are often produced outside thermodynamic
equilibrium yet they are effectively treated as the “native” structure of a macromolecular assembly because of the insurmountable time scales required to transition
between different phases. On the other hand, this complication is particularly challenging for systems where processing drives them into nonequilibrium states that
demonstrate relatively long relaxation time-scales (e.g., days to months). MD simulations of macromolecules in liquid solutions have so far relied on the notion that
thermodynamic exchange between all relevant states could always be achieved within
the time scale of the laboratory. However, supramolecular structures are formed over a
broad range of time scales, sometimes beyond those that allow one to gather a
quantitative understanding. A paramount example is that of the crystallization of
macromolecules. The study of slow-forming supramolecular structures demands an
even higher predictive power from MD simulations, and a continued effort to perfect
both CG models as well as the technology required to use them.
References
1. Chemical Heritage Foundation (2010) Chemistry in history: Gilbert Newton Lewis. Chemical
Heritage Foundation, Philadelphia. http://www.chemheritage.org/discover/online-resources/
chemistry-in-history/themes/molecular-synthesis-structure-and-bonding/lewis.aspx.
2. Deußing G, Weber M (2012) Topic of the month: The life and work of Hermann Staudinger.
Guido Deußing, Neuss. http://www.k-online.de/cipp/md_k/custom/pub/content,oid,35205/
lang,2/ticket,g_u_e_s_t/~/February_2012_Life_and_work_of_Hermann_Staudinger_part_1.html.
3. Nobelprize.org (2013) The Nobel Prize in Chemistry 1953. Nobel Media AB, Stockholm.
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1953/.
4. Nobelprize.org (2013) Jean-Marie Lehn – biographical. Nobel Media AB, Stockholm. http://
www.nobelprize.org/nobel_prizes/chemistry/laureates/1987/lehn-bio.html.
5. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids – a structure for deoxyribose nucleic acid. Nature 171(4356):737–738
6. Seeman NC (2014) Another important 60th anniversary. Covalent and supramolecular macromolecules with complex architecture. Adv Polym Sci. doi:10.1007/12_2013_243
7. Metropolis N et al (1953) Equation of state calculations by fast computing machines. J Chem
Phys 21(6):1087–1092
8. Percec V et al (2010) Self-assembly of Janus dendrimers into uniform dendrimersomes and
other complex architectures. Science 328(5981):1009–1014
Computer Simulation of Self-Assembling Macromolecules
105