59,205 research outputs found
Modelling the Self-Assembly of Virus Capsids
We use computer simulations to study a model, first proposed by Wales [1],
for the reversible and monodisperse self-assembly of simple icosahedral virus
capsid structures. The success and efficiency of assembly as a function of
thermodynamic and geometric factors can be qualitatively related to the
potential energy landscape structure of the assembling system. Even though the
model is strongly coarse-grained, it exhibits a number of features also
observed in experiments, such as sigmoidal assembly dynamics, hysteresis in
capsid formation and numerous kinetic traps. We also investigate the effect of
macromolecular crowding on the assembly dynamics. Crowding agents generally
reduce capsid yields at optimal conditions for non-crowded assembly, but may
increase yields for parameter regimes away from the optimum. Finally, we
generalize the model to a larger triangulation number T = 3, and observe more
complex assembly dynamics than that seen for the original T = 1 model.Comment: 16 pages, 11 figure
Nature-Inspired Interconnects for Self-Assembled Large-Scale Network-on-Chip Designs
Future nano-scale electronics built up from an Avogadro number of components
needs efficient, highly scalable, and robust means of communication in order to
be competitive with traditional silicon approaches. In recent years, the
Networks-on-Chip (NoC) paradigm emerged as a promising solution to interconnect
challenges in silicon-based electronics. Current NoC architectures are either
highly regular or fully customized, both of which represent implausible
assumptions for emerging bottom-up self-assembled molecular electronics that
are generally assumed to have a high degree of irregularity and imperfection.
Here, we pragmatically and experimentally investigate important design
trade-offs and properties of an irregular, abstract, yet physically plausible
3D small-world interconnect fabric that is inspired by modern network-on-chip
paradigms. We vary the framework's key parameters, such as the connectivity,
the number of switch nodes, the distribution of long- versus short-range
connections, and measure the network's relevant communication characteristics.
We further explore the robustness against link failures and the ability and
efficiency to solve a simple toy problem, the synchronization task. The results
confirm that (1) computation in irregular assemblies is a promising and
disruptive computing paradigm for self-assembled nano-scale electronics and (2)
that 3D small-world interconnect fabrics with a power-law decaying distribution
of shortcut lengths are physically plausible and have major advantages over
local 2D and 3D regular topologies
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