First-principles design of nanomachines

Abstract

Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations.anisotropy ͉ Frenet frame ͉ globular proteins ͉ molecular switching S ignificant advances in laboratory techniques for tailoring and processing materials at the atomic scale have resulted in nanotechnology becoming an increasingly mature field with great promise. One of the exciting goals of the field is the design of powerful machines, such as functional entities that can switch reversibly between distinct geometries (1-4). Such machines would not only be of great use on their own but also could yield novel emergent behavior upon networking them together (5). The existence of life in its myriad forms provides a proof-of-concept of what one might aspire to accomplish with nanotechnology.Proteins are complex water-soluble chain molecules made up of tens or hundreds of 20 types of naturally occurring amino acids and exhibit conformational switching (6) triggered by influences such as ligand binding. At the nanoscale, thermal fluctuations yield forces with magnitudes comparable with those involved in chemical reactions catalyzed by the proteins (7). How might one design a machine whose functionality is structure based? In its simplest form, we seek an object that takes on just a few distinct geometries in a reproducible manner and is able to switch reversibly between them because of thermal fluctuations. Such a situation would allow external stabilizing influences to favor a given conformation over the others and allow for the development of powerful machines at the nanoscale.A collection of hard spheres constitutes the simplest model of matter and exhibits both a crystalline phase and a fluid phase on varying the density of spheres (8). A linear chain of hard spheres is the simplest connected object with the fewest constraints and, thus, the greatest flexibility (9). Such a chain, at high temperatures or when there are no interactions promoting compaction, would occupy a random-coil phase in which all self-avoiding conformations are equally likely. This situation is not conducive for machine design. In the presence of intersphere interactions promoting compaction and when there are no frustrating influences from the sphere tethering, one would expect a generic compact phase in which, at least locally, the preferred conformation is that of a face-centered cubic (fcc) lattice. It was conjectured by Kepler, and proven more recently by Hales, that the fcc structure provides for optimal packing of unconst...

Sequence dependent aggregation of peptides and fibril formation

“…1a,b). The latter are approximately given by the inverse direction to the normal vector 45 at the chain's local position. The new constraint requires that two residues i and j make a hydrophobic contact if n i · c ij < 0.5 and n j · c ji < 0.5 where n i and n j are the normal vectors of the Frenet frames associated with bead i and j, respectively; c ij is an unit vector pointing from bead i to bead j; and c ji = −c ij .…”

The elixir phase of chain molecules

“…While, to the best of our knowledge, the elixir phase has not been identified in any previous studies, the model studied here, but with parameters poising the system outside the elixir phase, has been found to exhibit the characteristics of a machine by spontaneously switching between two distinct geometries, a single helix, and a double helix, merely because of thermal fluctuations . A consequence of the existence of the elixir phase is that it can be exploited for the creation of nifty artificially made interacting nanomachines.…”

“…The overlap between adjoining main‐chain spheres results in an entropic stiffness because of the reduction in the ability to bend the chain . A hint that such symmetry breaking could be important is provided by the extreme case of a chain of coins, which, in the continuum limit, has a tube‐like geometry . And, as is well‐known, a garden hose is often wound into a helical geometry in a hardware store.…”

Effect ofN-methyl amide linkage on hydrogen bonding behavior and water transport properties of partiallyN-methylated random aromatic copolyamides

“…Their outstanding properties arise from their rigid aromatic backbone and secondary amide linkages in the trans conformation, which result in the extended rod‐like polymer structure that interacts with each other via strong π‐π stackings and hydrogen bondings, and produce a sheet structure . On the other hand, aromatic oligoamides containing the three‐center hydrogen bonding to disrupt the intermolecular hydrogen bondings provide a highly planar molecular backbone and fold into a specific secondary structure such as molecular crescents, helices, and macrocycles . For the poly( p ‐benzamide), the attachment of triethylene glycol chains to the aromatic rings improved their organosolubility and produced a completely flat polymer backbone due to the disruption of hydrogen bonding by the three‐center hydrogen bonding .…”