Beyond molecules: Self-assembly of mesoscopic and macroscopic components

Whitesides, George M.; Boncheva, Mila

doi:10.1073/pnas.082065899

Cited by 1,450 publications

(1,077 citation statements)

References 65 publications

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“…However, it has to be taken into account that in self-organizing systems, small energy differences are important even for the formation of very large structures [38,83]; for instance, in biological membranes, the tiny energy differences between lipids in the edges and within bilayers are responsible for the spontaneous closure of vesicles and cell membranes [52]. On the other hand, it is reasonable to consider that a continuous helicoid gives a homogeneous dynamic strength to chromatin within chromatids.…”

Section: Discussionmentioning

confidence: 99%

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Daban

2014

J. R. Soc. Interface.

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The measurement of the dimensions of metaphase chromosomes in different animal and plant karyotypes prepared in different laboratories indicates that chromatids have a great variety of sizes which are dependent on the amount of DNA that they contain. However, all chromatids are elongated cylinders that have relatively similar shape proportions (length to diameter ratio approx. 13). To explain this geometry, it is considered that chromosomes are self-organizing structures formed by stacked layers of planar chromatin and that the energy of nucleosome-nucleosome interactions between chromatin layers inside the chromatid is approximately 3.6 Â 10 220 J per nucleosome, which is the value reported by other authors for internucleosome interactions in chromatin fibres. Nucleosomes in the periphery of the chromatid are in contact with the medium; they cannot fully interact with bulk chromatin within layers and this generates a surface potential that destabilizes the structure. Chromatids are smooth cylinders because this morphology has a lower surface energy than structures having irregular surfaces. The elongated shape of chromatids can be explained if the destabilizing surface potential is higher in the telomeres (approx. 0.16 mJ m 22 ) than in the lateral surface (approx. 0.012 mJ m 22 ). The results obtained by other authors in experimental studies of chromosome mechanics have been used to test the proposed supramolecular structure. It is demonstrated quantitatively that internucleosome interactions between chromatin layers can justify the work required for elastic chromosome stretching (approx. 0.1 pJ for large chromosomes). The high amount of work (up to approx. 10 pJ) required for large chromosome extensions is probably absorbed by chromatin layers through a mechanism involving nucleosome unwrapping.

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Section: Discussionmentioning

confidence: 99%

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Daban

2014

J. R. Soc. Interface.

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“…1 Self-assembly methods 1,2 are generally limited to creation of uniform 2D films. 3,4 Printing methods, 5,6 which have the potential for organizing nanostructures through creation of chemical templates, can rarely achieve patterning below 50 nm, and then controlling orientations of individual nanostructures is difficult.…”

Section: Introductionmentioning

confidence: 99%

Physical Controls on Directed Virus Assembly at Nanoscale Chemical Templates

et al. 2006

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Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In-situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, and drove 1D and 2D condensation at subcritical volume fractions. The growth kinetics followed a t 1/2 law controlled by the slow diffusion of viruses. The lateral expansion of virus clusters that initially form on the 1D templates following introduction of polyethylene glycol (PEG) into the solution suggests a significant role for weak

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“…gravitational, electrostatic, magnetic, capillary, etc. In the past, the driving force has been mostly capillary interaction [23]. An important point to note here that the choice of the driving force depends on several factors like scale and magnitude of the force, environmental compatibility and influence of the interactions on the function of the system.…”

Section: Design Of a Magnetic Self-assembly Systemmentioning

confidence: 99%

A Framework for Designing Novel Magnetic Tiles Capable of Complex Self-assemblies

Majumder

Reif

2008

Unconventional Computing

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Abstract. Self-assembly has been immensely successful in creating complex patterns at the molecular scale. However, the use of self-assembly techniques at the macroscopic level has so far been limited to the formation of simple patterns. For example, in a number of prior works, self-assembling units or tiles formed aggregates based on the polarity of magnetic pads on their sides. The complexity of the resulting assemblies was limited, however, due to the small variety of magnetic pads that were used: namely just positive or negative polarity. This paper addresses the key challenge of increasing the variety of magnetic pads for tiles, which would allow the tiles to self-assemble into more complex patterns. We introduce a barcode scheme which potentially allows for the generation of arbitrarily complex structures using magnetic self-assembly at the macro-scale. Development of a framework for designing such barcode schemes is the main contribution of the paper. We also present a physical model based on Newtonian mechanics and Maxwellian magnetics. Additionally, we present a preliminary software simulation system that models the binding of these tiles using magnetic interactions as well as external forces (e.g. wind) which provide energy to the system. Although we have not performed any physical experiments, nevertheless, we show that it is possible to use the simulation results to extract a higher level kinetic model that can be used to predict assembly yield on a larger scale and provide better insight into the dynamics of the real system.

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Beyond molecules: Self-assembly of mesoscopic and macroscopic components

Cited by 1,450 publications

References 65 publications

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Physical Controls on Directed Virus Assembly at Nanoscale Chemical Templates

A Framework for Designing Novel Magnetic Tiles Capable of Complex Self-assemblies

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