New method to design diamond lattices and other crystals from
microscopic building blocks

Date:
September 14, 2020
Source:
Arizona State University
Summary:
Researchers describe a technique for using LEGO(R)-like elements at
the scale of a few billionths of a meter. Further, they are able to
cajole these design elements to self-assemble, with each LEGO(R)
piece identifying its proper mate and linking up in a precise
sequence to complete the desired nanostructure.



FULL STORY ==========================================================================
An impressive array of architectural forms can be produced from the
popular interlocking building blocks known as LEGOS(R). All that is needed
is a child's imagination to construct a virtually infinite variety of
complex shapes.


==========================================================================
In a new study appearing in the journal Physical Review Letters,
researchers describe a technique for using LEGO(R)-like elements at
the scale of a few billionths of a meter. Further, they are able to
cajole these design elements to self-assemble, with each LEGO(R) piece identifying its proper mate and linking up in a precise sequence to
complete the desired nanostructure.

While the technique described in the new study is simulated on computer,
the strategy is applicable to self-assembly methods common to the field of
DNA nanotechnology. Here, the equivalent of each LEGO(R) piece consists
of a nanostructures made out of DNA, the famous molecular repository
of our genetic code. The four nucleotides making up DNA -- commonly
labelled A, C, T & G - - stick to one another according to a reliable
rule: A nucleotides always pair with Ts and C nucleotides with Gs.

Using base-pairing properties allows researchers like Petr Sulc,
corresponding author of the new study, to design DNA nanostructures that
can take shape in a test tube, as if on autopilot.

"The possible number of ways how to design interactions between the
building blocks is enormous, something what is called a 'combinatorial explosion'" Sulc says. "It is impossible to individually check every
possible building block design and see if it can self-assemble into
the desired structure. In our work, we provide a new general framework
that can efficiently search the space of possible solutions and find
the one which self-assembles into the desired shape and avoids other
undesired assemblies." Sulc is a researcher at the Biodesign Center for Molecular Design and Biomimetics and ASU's School of Molecular Sciences
(SMS). He is joined by his colleague Luka's Kroc along with international collaborators Flavio Romano and John Russo from Italy.



==========================================================================
The new technique marks an important stepping stone in the
rapidly-developing field of DNA nanotechnology, where self-assembled
forms are finding their way into everything from nanoscale tweezers to cancer-hunting DNA robots.

Despite impressive advances, construction methods relying on molecular
self- assembly have had to contend with unintended bondings of building material. The challenges grow with the complexity of the intended
design. In many cases, researchers are perplexed as to why certain
structures self-assemble from a given set of elementary building blocks,
as the theoretical foundations of these processes are still poorly
understood.

To confront the problem, Sulc and colleagues have invented a clever
color- coding system that manages to restrict the base pairings to only
those appearing in the design blueprint for the final structure, with
alternate base- pairings forbidden.

The process works through a custom-designed optimization algorithm,
where the correct color code for self-assembly of the intended form
produces the target structure at an energy minimum, while excluding
competing structures.

Next, they put the system to work, using computers to design two crystal
forms of great importance to the field of photonics: pyrochlore and
cubic diamond.

The authors note that this innovative method is applicable to any
crystal structure.

To apply their theoretical framework, Sulc has started a new collaboration
with professors Hao Yan and Nick Stephanopoulos, his colleagues at
Biodesign and SMS. Together, they aim to experimentally realize some of
the structures that they were able to design in simulations.

"While the obvious application of our framework is in DNA nanotechnology,
our approach is general, and can be also used for example to design self-assembled structures out of proteins," Sulc says.


========================================================================== Story Source: Materials provided by Arizona_State_University. Original
written by Richard Harth. Note: Content may be edited for style and
length.


========================================================================== Journal Reference:
1. Flavio Romano, John Russo, Luka's Kroc, Petr Sulc. Designing Patchy
Interactions to Self-Assemble Arbitrary Structures. Physical Review
Letters, 2020; 125 (11) DOI: 10.1103/PhysRevLett.125.118003 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/09/200914115907.htm

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