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Journal articles on the topic 'Ensembles de Llgnes 3D'

Author: Grafiati

Published: 1 June 2024

Last updated: 31 July 2025

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1

Krishnamoorthy, Kothandam, and Cynthia G. Zoski. "Fabrication of 3D Gold Nanoelectrode Ensembles by Chemical Etching." Analytical Chemistry 77, no. 15 (2005): 5068–71. http://dx.doi.org/10.1021/ac050604r.

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Spettl, Aaron, Thomas Werz, Carl E. Krill, and Volker Schmidt. "Parametric Representation of 3D Grain Ensembles in Polycrystalline Microstructures." Journal of Statistical Physics 154, no. 4 (2013): 913–28. http://dx.doi.org/10.1007/s10955-013-0893-7.

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3

CAO, Li-Xin, Pei-Sheng YAN, Ke-Ning SUN, and W. Donald KIRK. "Development and Evaluation of Gold 3D Cylindrical Nanoelectrode Ensembles." Chinese Journal of Chemistry 25, no. 11 (2007): 1754–57. http://dx.doi.org/10.1002/cjoc.200790324.

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4

Gangaraju, Deepa, Sridhar Vadahanambi, and Hyun Park. "Correction: 3D graphene–carbon nanotube–nickel ensembles as anodes in sodium-ion batteries." RSC Advances 6, no. 106 (2016): 104665. http://dx.doi.org/10.1039/c6ra90109c.

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Di Pierro, Michele, Ryan R. Cheng, Erez Lieberman Aiden, Peter G. Wolynes, and José N. Onuchic. "De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture." Proceedings of the National Academy of Sciences 114, no. 46 (2017): 12126–31. http://dx.doi.org/10.1073/pnas.1714980114.

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Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be predicted de novo using epigenetic data derived from chromatin immunoprecipitation-sequencing (ChIP-Seq). We exploit the idea that chromosomes encode a 1D sequence of chromatin structural types. Interactions between these chromatin types determine the 3D structural ensemble of chromosomes through a process similar to phase separation. First, a neural network is used to infer the relation between the epigenetic marks present at a locus, as a

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De Leo, Manuela, Alexander Kuhn, and Paolo Ugo. "3D-Ensembles of Gold Nanowires: Preparation, Characterization and Electroanalytical Peculiarities." Electroanalysis 19, no. 2-3 (2007): 227–36. http://dx.doi.org/10.1002/elan.200603724.

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7

Heinrich, Julian, Michael Krone, Seán I. O'Donoghue, and Daniel Weiskopf. "Visualising intrinsic disorder and conformational variation in protein ensembles." Faraday Discuss. 169 (2014): 179–93. http://dx.doi.org/10.1039/c3fd00138e.

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Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination—however, they are present in many of the available 3D structures, where they exhibit a wide range of conformations, from ill-defined and highly flexible to well-defined upon binding to partner molecules, or upon post-translational modifications. Analysing such large conformational variations across ensembles of 3D structures can be complex and difficult; our g

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Wang, Shuang, Xiaolin Xie, Zhi Chen, et al. "DNA-Grafted 3D Superlattice Self-Assembly." International Journal of Molecular Sciences 22, no. 14 (2021): 7558. http://dx.doi.org/10.3390/ijms22147558.

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The exploitation of new methods to control material structure has historically been dominating the material science. The bottom-up self-assembly strategy by taking atom/molecule/ensembles in nanoscale as building blocks and crystallization as a driving force bring hope for material fabrication. DNA-grafted nanoparticle has emerged as a “programmable atom equivalent” and was employed for the assembly of hierarchically ordered three-dimensional superlattice with novel properties and studying the unknown assembly mechanism due to its programmability and versatility in the binding capabilities. In

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Janson, Giacomo, and Michael Feig. "Transferable deep generative modeling of intrinsically disordered protein conformations." PLOS Computational Biology 20, no. 5 (2024): e1012144. http://dx.doi.org/10.1371/journal.pcbi.1012144.

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Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. Molecular simulations are a valuable computational strategy for constructing structural ensembles of disordered proteins but are highly resource-intensive. Recently, machine learning approaches based on deep generative models that learn from simulation data have emerged as an efficient alternative for generating structural ensembles. However, such

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10

Ayyer, Kartik, P. Lourdu Xavier, Johan Bielecki, et al. "3D diffractive imaging of nanoparticle ensembles using an x-ray laser." Optica 8, no. 1 (2020): 15. http://dx.doi.org/10.1364/optica.410851.

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11

Renner, Steffen, Mirko Hechenberger, Tobias Noeske, et al. "Suche nach Wirkstoff-Grundgerüsten mit 3D-Pharmakophorhypothesen und Ensembles neuronaler Netze." Angewandte Chemie 119, no. 28 (2007): 5432–35. http://dx.doi.org/10.1002/ange.200604125.

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12

Renner, Steffen, Mirko Hechenberger, Tobias Noeske, et al. "Searching for Drug Scaffolds with 3D Pharmacophores and Neural Network Ensembles." Angewandte Chemie International Edition 46, no. 28 (2007): 5336–39. http://dx.doi.org/10.1002/anie.200604125.

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13

Callegari, Francesca, Martina Brofiga, and Paolo Massobrio. "Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays." PLOS Computational Biology 19, no. 2 (2023): e1010825. http://dx.doi.org/10.1371/journal.pcbi.1010825.

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Nowadays, in vitro three-dimensional (3D) neuronal networks are becoming a consolidated experimental model to overcome most of the intrinsic limitations of bi-dimensional (2D) assemblies. In the 3D environment, experimental evidence revealed a wider repertoire of activity patterns, characterized by a modulation of the bursting features, than the one observed in 2D cultures. However, it is not totally clear and understood what pushes the neuronal networks towards different dynamical regimes. One possible explanation could be the underlying connectivity, which could involve a larger number of ne

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14

Gangaraju, Deepa, Sridhar Vadahanambi, and Hyun Park. "3D graphene–carbon nanotube–nickel ensembles as anodes in sodium-ion batteries." RSC Advances 6, no. 102 (2016): 99914–18. http://dx.doi.org/10.1039/c6ra15069a.

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15

Lenz, Samuel, David Hunger, and Joris van Slageren. "Strong coupling between resonators and spin ensembles in the presence of exchange couplings." Chemical Communications 56, no. 84 (2020): 12837–40. http://dx.doi.org/10.1039/d0cc04841k.

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16

He, Yi, Suhani Nagpal, Mourad Sadqi, Eva de Alba, and Victor Muñoz. "Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts." Bioinformatics 35, no. 7 (2018): 1234–36. http://dx.doi.org/10.1093/bioinformatics/bty755.

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Abstract Motivation Many proteins are partially disordered in physiological conditions and only fold, fully or partially, upon binding. Their structural analysis is challenging because the accessible information, typically chemical shifts (CS) from nuclear magnetic resonance experiments, are averages over broad ensembles of conformations. We aim to develop a database for the analysis of such data in terms of conformational distributions of the protein backbone rather than of individual high-resolution structures. Results Glutton is the largest available database linking CS and protein 3D struc

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Sreejithkumar, Vivek, Edward Schrom, and Ronald Germain. "3D extension of spatial patterning analysis of cellular ensembles (SPACE) to extract parameters for dynamic tumor modeling." Journal of Immunology 212, no. 1_Supplement (2024): 0245_4416. http://dx.doi.org/10.4049/jimmunol.212.supp.0245.4416.

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Abstract Investigating the cellular interactions within three-dimensional (3D) tumor microenvironments is essential for understanding tumor growth and progression. Building upon the success of our previous computational framework, SPACE, designed for spatial analysis of high-plex tissue images, we are developing 3D-SPACE. This innovation extends spatial pattern analysis to 3D volumetric tissue images. Volumetric images more accurately capture nuances of cellular arrangements and tissue structures, offering a more realistic representation of the tumor microenvironment. Applying 3D-SPACE to anal

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18

Spitz, François. "Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles." Seminars in Cell & Developmental Biology 57 (September 2016): 57–67. http://dx.doi.org/10.1016/j.semcdb.2016.06.017.

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19

Mollamahale, Y. Bahari, Mohammad Ghorbani, Masoumeh Ghalkhani, Manouchehr Vossoughi, and Abolghasem Dolati. "Highly sensitive 3D gold nanotube ensembles: Application to electrochemical determination of metronidazole." Electrochimica Acta 106 (September 2013): 288–92. http://dx.doi.org/10.1016/j.electacta.2013.05.084.

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20

Špelić, Ivana, Dubravko Rogale, and Alka Mihelić Bogdanić. "The Study on Effects of Walking on the Thermal Properties of Clothing and Subjective Comfort." Autex Research Journal 20, no. 3 (2020): 228–43. http://dx.doi.org/10.2478/aut-2019-0016.

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AbstractFormer studies done by other authors investigated the first- and second-layered air gaps beneath the clothing garments. None of the previous studies reported multidisciplinary clothing design testing approach linking both the objective measuring methods and subjective responses, while testing the thermal properties linked to a microclimatic volume formed between the layers of garments forming the ensemble. Neither was determined the limiting value of the microclimatic volume for outerwear garments, after which the thermal insulation will start to decrease due to convection. By taking t

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21

Kurta, R. P., M. Altarelli, and I. A. Vartanyants. "X-Ray Cross-Correlation Analysis of Disordered Ensembles of Particles: Potentials and Limitations." Advances in Condensed Matter Physics 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/959835.

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Angular X-ray cross-correlation analysis (XCCA) is an approach to study the structure of disordered systems using the results of X-ray scattering experiments. In this paper we summarize recent theoretical developments related to the Fourier analysis of the cross-correlation functions. Results of our simulations demonstrate the application of XCCA to two- and three-dimensional (2D and 3D) disordered ensembles of particles. We show that the structure of a single particle can be recovered using X-ray data collected from a 2D disordered system of identical particles. We also demonstrate that valua

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22

Hu, Haifeng, Lixin Cao, Qingchuan Li, Kan Ma, Peisheng Yan, and Donald W. Kirk. "Fabrication and modeling of an ultrasensitive label free impedimetric immunosensor for Aflatoxin B1based on poly(o-phenylenediamine) modified gold 3D nano electrode ensembles." RSC Advances 5, no. 68 (2015): 55209–17. http://dx.doi.org/10.1039/c5ra06300k.

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An ultrasensitive label free impedimetric immunosensor for AFB<sub>1</sub>detection was fabricated based on poly(o-phenylenediamine) (PoPD) electropolymerized film modified gold three dimensional nanoelectrode ensembles (3DNEEs).

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23

Akl, Hoda, Brooke Emison, Xiaochuan Zhao, Arup Mondal, Alberto Perez, and Purushottam D. Dixit. "GENERALIST: A latent space based generative model for protein sequence families." PLOS Computational Biology 19, no. 11 (2023): e1011655. http://dx.doi.org/10.1371/journal.pcbi.1011655.

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Generative models of protein sequence families are an important tool in the repertoire of protein scientists and engineers alike. However, state-of-the-art generative approaches face inference, accuracy, and overfitting- related obstacles when modeling moderately sized to large proteins and/or protein families with low sequence coverage. Here, we present a simple to learn, tunable, and accurate generative model, GENERALIST: GENERAtive nonLInear tenSor-factorizaTion for protein sequences. GENERALIST accurately captures several high order summary statistics of amino acid covariation. GENERALIST

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24

Hoff, Samuel, and Massimiliano Bonomi. "BPS2025 - Extracting protein ensembles from cryo-EM 2D data and reconstructed 3D maps." Biophysical Journal 124, no. 3 (2025): 383a. https://doi.org/10.1016/j.bpj.2024.11.2069.

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25

Fonseca, Rasmus, Dimitar V. Pachov, Julie Bernauer, and Henry van den Bedem. "Characterizing RNA ensembles from NMR data with kinematic models." Nucleic Acids Research 42, no. 15 (2014): 9562–72. http://dx.doi.org/10.1093/nar/gku707.

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Abstract Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles acc

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26

Weeks, Abbie, and Brett Byram. "Exploring the benefits of spatial and temporal block-wise filtering architectures." Journal of the Acoustical Society of America 152, no. 4 (2022): A280. http://dx.doi.org/10.1121/10.0016270.

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Spatial block-wise filtering architectures improve noise stationarity locally, making SVD-based filtering more robust (Song et al., 2017). Temporal block-wise filtering has been proposed to augment spatial block-wise methods for 3D Doppler data acquired via mechanical translation (Chen et al., 2021) and compensate for bulk motion in cardiac power Doppler imaging (Zhang et al., 2021). We combine spatial and temporal block-wise architectures to suppress noise through depth and better capture time-varying signals with power Doppler. We show that a combination of spatial and temporal block-wise me

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27

Cofaru, Ileana Ioana, Paul Dan Brîndaşu, and Nicolae Florin Cofaru. "Designing a Specialized Devices for Correction of the Axis Deviation at the Human Leg." Applied Mechanics and Materials 371 (August 2013): 662–66. http://dx.doi.org/10.4028/www.scientific.net/amm.371.662.

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The presented article is an original contribution which implies the design of a specialized device for high tybial osteotomy (HTO) optimization. In the papers are presented the sources that imply HTO, the axial deviations of the human lower member from the correct position. This sources are the gonarthosys owed to the usage of the knees cartilages or owed to some diseases (such as the Blount disease) and the vicious consolidated fractures. After presenting the needs to realize such a specialized device for HTO, the principal requests the device shall fulfill are underlined. Starting from these

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28

Rangan, Ramya, Andrew M. Watkins, Jose Chacon, et al. "De novo3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures." Nucleic Acids Research 49, no. 6 (2021): 3092–108. http://dx.doi.org/10.1093/nar/gkab119.

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AbstractThe rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5′ UTR; the reverse complement of the 5′ U

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29

Bashir, Shazab, Arfan Jaffar, Muhammad Rashid, Sheeraz Akram, and Sohail Masood Bhatti. "Intelligent recognition of human activities using deep learning techniques." PLOS One 20, no. 4 (2025): e0321754. https://doi.org/10.1371/journal.pone.0321754.

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Recognition of Human Actions (HAR) Portrays a crucial significance in various applications due to its ability for analyzing behaviour of humans within videos. This research investigates HAR in Red, Green, and Blue, or RGB videos using frameworks for deep learning. The model’s ensemble method integrates the forecasts from two models, 3D-AlexNet-RF and InceptionV3 Google-Net, to improve accuracy in recognizing human activities. Each model independently predicts the activity, and the ensembles method merges these predictions, often using voting or averaging, to produce a more accurate and reliabl

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30

SONI, AMEET, and JUDE SHAVLIK. "PROBABILISTIC ENSEMBLES FOR IMPROVED INFERENCE IN PROTEIN-STRUCTURE DETERMINATION." Journal of Bioinformatics and Computational Biology 10, no. 01 (2012): 1240009. http://dx.doi.org/10.1142/s0219720012400094.

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Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a

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31

Wu, Jiong, and Xiaoying Tang. "Brain segmentation based on multi-atlas and diffeomorphism guided 3D fully convolutional network ensembles." Pattern Recognition 115 (July 2021): 107904. http://dx.doi.org/10.1016/j.patcog.2021.107904.

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32

Bahari Mollamahalle, Yaser, Mohammad Ghorbani, and Abolghasem Dolati. "Electrodeposition of long gold nanotubes in polycarbonate templates as highly sensitive 3D nanoelectrode ensembles." Electrochimica Acta 75 (July 2012): 157–63. http://dx.doi.org/10.1016/j.electacta.2012.04.119.

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33

Cui, Yinan, and Nasr Ghoniem. "Influence of Size on the Fractal Dimension of Dislocation Microstructure." Metals 9, no. 4 (2019): 478. http://dx.doi.org/10.3390/met9040478.

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Three-dimensional (3D) discrete dislocation dynamics simulations are used to analyze the size effect on the fractal dimension of two-dimensional (2D) and 3D dislocation microstructure. 2D dislocation structures are analyzed first, and the calculated fractal dimension ( n 2 ) is found to be consistent with experimental results gleaned from transmission electron microscopy images. The value of n 2 is found to be close to unity for sizes smaller than 300 nm, and increases to a saturation value of ≈1.8 for sizes above approximately 10 microns. It is discovered that reducing the sample size leads t

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34

Ben Ahmed, Kaoutar, Lawrence O. Hall, Dmitry B. Goldgof, and Robert Gatenby. "Ensembles of Convolutional Neural Networks for Survival Time Estimation of High-Grade Glioma Patients from Multimodal MRI." Diagnostics 12, no. 2 (2022): 345. http://dx.doi.org/10.3390/diagnostics12020345.

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Glioma is the most common type of primary malignant brain tumor. Accurate survival time prediction for glioma patients may positively impact treatment planning. In this paper, we develop an automatic survival time prediction tool for glioblastoma patients along with an effective solution to the limited availability of annotated medical imaging datasets. Ensembles of snapshots of three dimensional (3D) deep convolutional neural networks (CNN) are applied to Magnetic Resonance Image (MRI) data to predict survival time of high-grade glioma patients. Additionally, multi-sequence MRI images were us

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35

Randrup, Jørgen. "Correlated fission fragment angular momenta." EPJ Web of Conferences 292 (2024): 08007. http://dx.doi.org/10.1051/epjconf/202429208007.

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Nuclear fission produces fragments whose spins are coupled to each other as well as to the relative fragment motion due to angular momentum conservation. Statistical ensembles of such spins can readily be obtained by either direct microcanonical sampling or by sampling of the associated normal modes of rotation. The spin-spin opening angle distribution is illustrated for both 3D and 2D spin scenarios and it is demonstrated how recent calculations with various models can be well reproduced by the statistical results under different assumptions about the scission geometry.

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36

Forcellini, Davide, Marco Tanganelli, and Stefania Viti. "Response Site Analyses of 3D Homogeneous Soil Models." Emerging Science Journal 2, no. 5 (2018): 238. http://dx.doi.org/10.28991/esj-2018-01148.

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The seismic excitation at the surface can be determined through Site Response Analyses (SRA) as to account for the specific soil properties of the site. However, the obtained results are largely affected by the model choice and setting, and by the depth of the considered soil layer. This paper proposes a refined 3D analytical approach, by the application of OPENSEES platform. A preliminary analysis has been performed to check the model adequacy as regards the mesh geometry and the boundary conditions. After the model setting, a SRA has been performed on various soil profiles, differing for the

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37

Puzyrev, Dmitry, Kirsten Harth, Torsten Trittel, and Ralf Stannarius. "Machine Learning for 3D Particle Tracking in Granular Gases." Microgravity Science and Technology 32, no. 5 (2020): 897–906. http://dx.doi.org/10.1007/s12217-020-09800-4.

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Abstract Dilute ensembles of granular matter (so-called granular gases) are nonlinear systems which exhibit fascinating dynamical behavior far from equilibrium, including non-Gaussian distributions of velocities and rotational velocities, clustering, and violation of energy equipartition. In order to understand their dynamic properties, microgravity experiments were performed in suborbital flights and drop tower experiments. Up to now, the experimental images were evaluated mostly manually. Here, we introduce an approach for automatic 3D tracking of positions and orientations of rod-like parti

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KHAKI, MILAD, MEGAN ROUSSY, NASIM MORTAZAVI, ROGELIO LUNA, ADAM SACHS, and JULIO MARTINEZ-TRUJILLO. "Using decoders to understand working memory representations of 3D space in primate prefrontal neuronal ensembles." Journal of Vision 20, no. 11 (2020): 1474. http://dx.doi.org/10.1167/jov.20.11.1474.

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39

Fosco, C. D., and L. E. Oxman. "A non Abelian effective model for ensembles of magnetic defects in 3D Yang–Mills theory." Journal of Physics A: Mathematical and Theoretical 46, no. 33 (2013): 335401. http://dx.doi.org/10.1088/1751-8113/46/33/335401.

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Cao, Lixin, Peisheng Yan, Kening Sun, and Donald W Kirk. "Gold 3D Brush Nanoelectrode Ensembles with Enlarged Active Area for the Direct Voltammetry of Daunorubicin." Electroanalysis 21, no. 10 (2009): 1183–88. http://dx.doi.org/10.1002/elan.200804526.

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41

Kruggel-Emden, Harald, Erdem Simsek, Siegmar Wirtz, and Viktor Scherer. "A Comparative Numerical Study of Particle Mixing on Different Grate Designs Through the Discrete Element Method." Journal of Pressure Vessel Technology 129, no. 4 (2006): 593–600. http://dx.doi.org/10.1115/1.2767338.

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Based on LEAT’s discrete element codes, granular flow and mixing on conveying equipment are studied in two and three dimensions. Discrete element simulations, which are briefly introduced, provide detailed information on particle positions and velocities over time. This information is used to derive quantities characterizing the dynamic process of mixing. The main focus of the study presented is the mixing process of inhomogeneous particle ensembles on different grate types. For this purpose, the introduced mixing parameters are used to compare the mixing in a 3D situation with the correspondi

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Tang, Wai Shing, Gabriel Monteiro da Silva, Henry Kirveslahti, et al. "A topological data analytic approach for discovering biophysical signatures in protein dynamics." PLOS Computational Biology 18, no. 5 (2022): e1010045. http://dx.doi.org/10.1371/journal.pcbi.1010045.

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Identifying structural differences among proteins can be a non-trivial task. When contrasting ensembles of protein structures obtained from molecular dynamics simulations, biologically-relevant features can be easily overshadowed by spurious fluctuations. Here, we present SINATRA Pro, a computational pipeline designed to robustly identify topological differences between two sets of protein structures. Algorithmically, SINATRA Pro works by first taking in the 3D atomic coordinates for each protein snapshot and summarizing them according to their underlying topology. Statistically significant to

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43

Mantasa, Dedi, and Yos Sudarman. "PENGGUNAAN APLIKASI BASIC GUITAR CHORDS 3D PADA PEMBELAJARAN SENI BUDAYA (MUSIK) DI KELAS VII SMP NEGERI 3 KECAMATAN HARAU." Jurnal Sendratasik 9, no. 3 (2020): 41. http://dx.doi.org/10.24036/jsu.v9i1.109436.

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AbstractThis study aims to describe the activities of Culture and Arts (music) teachers in grade VII of SMP Negeri 3 Harau District, Lima Puluh Kota Regency in implementing music instruction using the Basic Guitar Chords 3D application for learning guitar at school. The use of this guitar playing application provides an opportunity for students to learn guitar playing virtually with a different learning atmosphere from how guitar learning was theoretically and practically conducted before.This study uses references to results from relevant research and several theoretical studies especially th

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Blanchard, Aaron T., Joshua M. Brockman, Khalid Salaita, and Alexa L. Mattheyses. "Variable incidence angle linear dichroism (VALiD): a technique for unique 3D orientation measurement of fluorescent ensembles." Optics Express 28, no. 7 (2020): 10039. http://dx.doi.org/10.1364/oe.381676.

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Schmalhorst, Philipp S., and Andreas Bergner. "A Grid Map Based Approach to Identify Nonobvious Ligand Design Opportunities in 3D Protein Structure Ensembles." Journal of Chemical Information and Modeling 60, no. 4 (2020): 2178–88. http://dx.doi.org/10.1021/acs.jcim.0c00051.

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46

Lin, Jing, Xiansong Wang, Guangxia Shen, and Daxiang Cui. "3D Plasmonic Ensembles of Graphene Oxide and Nobel Metal Nanoparticles with Ultrahigh SERS Activity and Sensitivity." Journal of Nanomaterials 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/7689357.

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We describe a comparison study on 3D ensembles of graphene oxide (GO) and metal nanoparticles (silver nanoparticles (AgNPs), gold nanoparticles (GNPs), and gold nanorods (GNRs)) for surface-enhanced Raman scattering (SERS) application. For the first time, GNRs were successfully assembled on the surfaces of GO by means of electrostatic interactions without adding any surfactant. The SERS properties of GO/AgNPs, GO/GNPs, and GO/GNRs were compared using 2-mercaptopyridine (2-Mpy) as probing molecule. We found that GO/AgNPs and GO/GNPs substrates are not suitable for detecting 2-Mpy due to the ver

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Osmer, Patrick S., Gatikrushna Singh, and Kathleen Boris-Lawrie. "A New Approach to 3D Modeling of Inhomogeneous Populations of Viral Regulatory RNA." Viruses 12, no. 10 (2020): 1108. http://dx.doi.org/10.3390/v12101108.

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Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of expe

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Kulkarni, Prakash, Vitor B. P. Leite, Susmita Roy, et al. "Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma." Biophysics Reviews 3, no. 1 (2022): 011306. http://dx.doi.org/10.1063/5.0080512.

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Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs co

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Shumyantseva, V. V., T. V. Bulko, E. V. Suprun, and A. I. Archakov. "Electrochemical sensor systems based on one dimensional (1D) nanostructures for analysis of bioaffinity interactions." Biomeditsinskaya Khimiya 59, no. 2 (2013): 209–18. http://dx.doi.org/10.18097/pbmc20135902209.

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It was shown that modification of screen printed graphite electrodes with gold nanoparticles (AuNPs) decorated Pb nanowires (PbNWs) demonstrates the enhancement of sensor’s analytical characteristics such as effective surface area, electro catalytic properties and heterogeneous electron transfer kinetics. The reason for such improvement may be the synergistic effect of AuNPs and PbNWs. Nanowires ensembles on electrode surface were employed for the detection of hemeproteins cytochrome P450 2B4, cytochrome c , and cardiac myoglobin in human plasma. Composite materials based on nanoparticles with

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Teber, S. "Thermodynamic and statistical properties of charged topological defects." Journal de Physique IV 12, no. 9 (2002): 235–36. http://dx.doi.org/10.1051/jp4:20020403.

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We focus on the statistical and thermodynamic properties of systems with competing long-range interactions. The studies are based on the physics of quasi-one dimensional system with special interest towards their topological defects, the so-called solitons. We have been considering ensembles of solitons resulting from the degeneracy of the ground state of the system. This is the case of various charge density-wave systems such as polyacetylene-like polymers where the solitons are the non-trivial excitations connecting different ground-states. We have been interested in particular with a one co

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