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An Efficient Clustering Algorithm Using Stochastic Association Model and Its Implementation Using Nanostructures

Takashi Morie, Tomohiro Matsuura, Makoto Nagata, Atsushi Iwata
2001 Neural Information Processing Systems  
This paper describes a clustering algorithm for vector quantizers using a "stochastic association model". It offers a new simple and powerful softmax adaptation rule.  ...  Simulation results demonstrate that the new algorithm can achieve efficient adaptation as high as the "neural gas" algorithm, which is reported as one of the most efficient clustering methods.  ...  Masataka Hirose for his support and encouragement.  ... 
dblp:conf/nips/MorieMNI01 fatcat:z4uzyoa7fjcbricks2ocabeika

A stochastic view on surface inhomogeneity of nanoparticles

R. A. J. Post, D. van der Zwaag, G. Bet, S. P. W. Wijnands, L. Albertazzi, E. W. Meijer, R. W. van der Hofstad
2019 Nature Communications  
Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution.  ...  Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles.  ...  ), resulting from the EM-algorithm based on the simulated localizations and associated uncertainties.  ... 
doi:10.1038/s41467-019-09595-y pmid:30971686 pmcid:PMC6458121 fatcat:k5xbvofssfeo7ooekgrp45jvgm

Graph-based simulated annealing: a hybrid approach to stochastic modeling of complex microstructures

O Stenzel, D Westhoff, I Manke, M Kasper, D P Kroese, V Schmidt
2013 Modelling and Simulation in Materials Science and Engineering  
The model is based on a hybrid approach, where in a first step a graph model is developed using ideas from stochastic geometry.  ...  A stochastic model is proposed for the efficient simulation of complex 3-dimensional microstructures consisting of two different phases.  ...  energy is associated with its surface area.  ... 
doi:10.1088/0965-0393/21/5/055004 fatcat:gcqej2cla5huxjmp6lqmwbfn6u

A Transfer Learning Approach for Improved Classification of Carbon Nanomaterials from TEM Images

Qixiang Luo, Elizabeth A Holm, Chen Wang
2020 Nanoscale Advances  
The extensive use of carbon nanomaterials such as carbon nanotubes/nanofibers (CNTs/CNFs) in industrial settings has raised concerns over the potential health risks associated with occupational exposure  ...  We also greatly appreciate the important open-source Python libraries Keras 50 and Scikit-Learn 51 for supporting our implementation and work.  ...  Conflicts of interest The ndings and conclusions in this report are those of the authors and do not necessarily represent the views of the National Institute for Occupational Safety and Health.  ... 
doi:10.1039/d0na00634c fatcat:zrqfkdoqjbf5xgsdd57kizqtou

Finite-temperature Simulations for Magnetic Nanostructures [article]

M.A. Novotny, D.T. Robb, S.M. Stinnett, G. Brown, P.A. Rikvold
2006 arXiv   pre-print
In addition, we discuss other topics of current interest in the modeling of magnetic hysteresis in nanostructures, including kinetic Monte Carlo simulations of dynamic phase transitions and First-Order  ...  We examine different models and methods for studying finite-temperature magnetic hysteresis in nanoparticles and ultrathin films.  ...  DMR-0120310 and DMR-0444051, and by the DOE Office of Science through the Computational Materials Science Network of BES-DMSE.  ... 
arXiv:cond-mat/0501692v2 fatcat:wrrkkw5anbgvpiyxol7drlvyii

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

Toshifumi Mori, Shinji Saito
2015 Journal of Chemical Physics  
Currently, our focuses are following research subjects. (1) Coupled cluster theory for excited states of large system We develop the coupled cluster theories and their efficient computational algorithm  ...  Figure 1 . 1 (a) Algorithm of density matrix renormalization group (DMRG) and (b) Its application to manganese cluster. ,28o) reported by Pierloot et al. [M. Radon, E. Broclawik, and K.  ...  To overcome these diseases, it is essential to understand amyloid genesis and disruption. We perform such MD simulations of amyloid fibrils.  ... 
doi:10.1063/1.4916641 pmid:25854260 fatcat:74aylkw3sfhfrnqxtaiih4uuly

Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters

Haralampos N. Miras, Cole Mathis, Weimin Xuan, De-Liang Long, Robert Pow, Leroy Cronin
2020 Proceedings of the National Academy of Sciences of the United States of America  
A stochastic model confirms the presence of an autocatalytic network involving molecular recognition and assembly processes, where the larger clusters are the only products stabilized by the cycle, isolated  ...  – nanostructure.  ...  Götz Bucher for allowing us to access to the stopped-flow UV-vis, and Dr. Nicola Bell and Dr. James Taylor for comments on the manuscript.  ... 
doi:10.1073/pnas.1921536117 pmid:32371490 fatcat:nax63z565bflrdsplrfqgf56le

Designing the self-assembly of arbitrary shapes using minimal complexity building blocks [article]

Joakim Bohlin, Andrew J. Turberfield, Ard A. Louis, Petr Šulc
2022 arXiv   pre-print
Finally, we use coarse-grained DNA simulations to investigate the realisation of multicomponent shapes using DNA nanostructures as building blocks.  ...  Using a novel pipeline, we explore the design spaces for a set of structures of various sizes and complexities.  ...  We thank Michael Matthies for his help with the design and assembly of DNA nanostructures and to Flavio Romano, Lukáš Kroc, Lorenzo Rovigatti and John Russo for helpful discussions and their contributions  ... 
arXiv:2207.06954v1 fatcat:nz3v7zq6nfcwnpobtnybvlwjka

Information physics fundamentals of nanophotonics

Makoto Naruse, Naoya Tate, Masashi Aono, Motoichi Ohtsu
2013 Reports on progress in physics (Print)  
Furthermore, the spatio-temporal dynamics of optical excitation transfer and its inherent stochastic attributes are utilized for solution searching, paving the way to a novel computing paradigm that exploits  ...  A stochastic analysis of light-assisted material formation is also presented, where an information-based approach provides a deeper understanding of the phenomena involved, such as self-organization.  ...  discussions over several years, in particular T Kawazoe, T Yatsui, W Nomura, H Hori, K Kobayashi, K Akahane, N Yamamoto, T Inoue, F Peper, K Leibnitz, M Hoga, Y Ohyagi, L B Kish, C Lienau, E Runge, S Huant and  ... 
doi:10.1088/0034-4885/76/5/056401 pmid:23574991 fatcat:oknba3yyvbfijj52xxlilyf5ym

Towards a framework for designing applications onto hybrid nano/CMOS fabrics

Catherine Dezan, Ciprian Teodorov, Loïc Lagadec, Michael Leuchtenburg, Teng Wang, Pritish Narayanan, Andras Moritz
2009 Microelectronics Journal  
After an overview of common requirements, physical models, and associated techniques, a case study in the context of NASIC fabrics is used to illustrate some of the concepts.  ...  It integrates fault-tolerant techniques and fabric-related density transformations with more conventional design automation techniques.  ...  Adaptive generic algorithms include general purpose optimization heuristics like simulated annealing or genetic algorithms and algorithms for FPGAs like Pathfinder and PLA clustering as the ones implemented  ... 
doi:10.1016/j.mejo.2008.07.072 fatcat:te4h6zgiincqfnngggutvziuia

A Review of Statistical Methods for Quality Improvement and Control in Nanotechnology

Jye-Chyi Lu, Shuen-Lin Jeng, Kaibo Wang
2009 Journal of QualityTechnology  
Topics include experimental design, uncertainty modeling, process optimization and monitoring, and areas for future research efforts.  ...  Besides advances in physics, chemistry, biology, and other science-based technologies, the use of statistical methods has also helped the rapid development of nanotechnology in terms of data collection  ...  Lu's research was partially supported by the US National Science Foundation under the award 0400071.  ... 
doi:10.1080/00224065.2009.11917770 fatcat:izaiqisx6nftpdmqvceghmjpgq

Spatial modeling of the 3D morphology of hybrid polymer-ZnO solar cells, based on electron tomography data

O. Stenzel, H. Hassfeld, R. Thiedmann, L. J. A. Koster, S. D. Oosterhout, S. S. van Bavel, M. M. Wienk, J. Loos, R. A. J. Janssen, V. Schmidt
2011 Annals of Applied Statistics  
Its parameters are fitted to image data gained by electron tomography (ET), where adaptive thresholding and stochastic segmentation have been used to represent morphological features of the considered  ...  Such materials are used, for example, in photoactive layers of hybrid polymer zinc oxide solar cells. The model is based on ideas from stochastic geometry and spatial statistics.  ...  In the next step a stochastic algorithm [see Thiedmann et al. (2011) ] is used to efficiently represent the set B by a union of spheres, which is denoted by B .  ... 
doi:10.1214/11-aoas468 fatcat:ea3f3j2qc5glzb4tibtfrrgcgm

Modified genetic algorithms to model cluster structures in medium-size silicon clusters

Victor E. Bazterra, Ofelia Oña, María C. Caputo, Marta B. Ferraro, Patricio Fuentealba, Julio C. Facelli
2004 Physical Review A. Atomic, Molecular, and Optical Physics  
This paper presents the results obtained using a genetic algorithm (GA) to search for stable structures of medium size silicon clusters.  ...  In this work the GA uses a semiempirical energy function to find the best cluster structures, which are further optimized using density-functional theory.  ...  METHODOLOGY In any GA implementation it is necessary to define a genome with enough information to calculate the associated fitness function.  ... 
doi:10.1103/physreva.69.053202 fatcat:3ohhevt4q5hexib7xj3p3y4sv4

Mapping the stochastic response of nanostructures

S. Pattamatta, R. S. Elliott, E. B. Tadmor
2014 Proceedings of the National Academy of Sciences of the United States of America  
Here, we explore a new method based on constructing an "equilibrium map" (akin to a phase diagram) that efficiently and systematically explores a nanostructure's stochastic, rate-dependent response to  ...  Instead, we construct an equilibrium map (EM) for the nanostructure, analogous to a phase diagram for bulk materials, which fully characterizes its response.  ...  Materials and Methods The algorithms and pseudocodes implemented in the current version of the BFB code used in the construction of the EM are described in ref. 41 .  ... 
doi:10.1073/pnas.1402029111 pmid:24733929 pmcid:PMC4035991 fatcat:ekwagl6gq5hkrg47arbxhfshhy

Multiscale in modelling and validation for solar photovoltaics

Tareq Abu Hamed, Nadja Adamovic, Urs Aeberhard, Diego Alonso-Alvarez, Zoe Amin-Akhlaghi, Matthias Auf der Maur, Neil Beattie, Nikola Bednar, Kristian Berland, Stefan Birner, Marco Califano, Ivana Capan (+70 others)
2018 EPJ Photovoltaics  
Therefore, multiscale modeling has found particular interest in the photovoltaics community, as a tool to advance the field beyond its current limits.  ...  including nanostructured regions.  ...  Matthias Auf der Maur coordinated the manuscript preparation and submission. All authors contributed to the discussions, ongoing work and presented results.  ... 
doi:10.1051/epjpv/2018008 fatcat:5ywv2jo5qjbctaraxv3fjrtlyi
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