2016
DOI: 10.1039/c6sm01156j
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Nonlinear machine learning and design of reconfigurable digital colloids

Abstract: Digital colloids, a cluster of freely rotating "halo" particles tethered to the surface of a central particle, were recently proposed as ultra-high density memory elements for information storage. Rational design of these digital colloids for memory storage applications requires a quantitative understanding of the thermodynamic and kinetic stability of the configurational states within which information is stored. We apply nonlinear machine learning to Brownian dynamics simulations of these digital colloids to… Show more

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Cited by 24 publications
(33 citation statements)
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References 59 publications
(139 reference statements)
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“…Previous computational work has elucidated fundamental entropic contributions of particle shape on self-assembly 17,18 and the transition dynamics of reconfigurable colloidal clusters. 19 The practical limitations to performing MD simulations of every system of interest are the computational costs of relaxing a system to equilibrium and the subsequent sampling of the equilibrium ensemble of states. Consequently, it is essential that the molecular models, computational algorithms, and computational hardware used to perform MD simulations are optimized to minimize the computational cost.…”
Section: Introductionmentioning
confidence: 99%
“…Previous computational work has elucidated fundamental entropic contributions of particle shape on self-assembly 17,18 and the transition dynamics of reconfigurable colloidal clusters. 19 The practical limitations to performing MD simulations of every system of interest are the computational costs of relaxing a system to equilibrium and the subsequent sampling of the equilibrium ensemble of states. Consequently, it is essential that the molecular models, computational algorithms, and computational hardware used to perform MD simulations are optimized to minimize the computational cost.…”
Section: Introductionmentioning
confidence: 99%
“…37,38,[51][52][53][54][55][56] Geometrically, this can be understood as the emergence of a small number of collective variables governing the long-time evolution of the system to which the remaining degrees of freedom are slaved. 37,38,[57][58][59] We and others have previously demonstrated that these collective variables can be determined from molecular simulation trajectories using nonlinear manifold learning, [37][38][39]51,[60][61][62][63][64][65][66][67][68][69][70][71][72][73] the particular variant of which we use here are diffusion maps. 60,[65][66][67][68] In a nutshell, the diffusion map approach constructs a random walk over the high-dimensional simulation trajectory with hopping probabilities based on the structural similarity of the constituent snapshots, then performs a spectral analysis of the harmonics of the resultant discrete Markov process to ascertain the effective dimensionality of the underlying "intrinsic manifold" and nonlinear collective variables with which to parameterize it.…”
Section: Diffusion Maps Manifold Learningmentioning
confidence: 99%
“…With regards to materials design, computer simulation serves to accelerate the exploration of the vast landscape of the design parameters, which may be beyond theoretical and experimental capacities currently accessible. We envision that the computational results and predictions will certainly benefit future endeavors with useful databases for data mining techniques to further accelerate the discovery of new materials [47,94,95].…”
Section: Discussionmentioning
confidence: 99%