Browsing by Author "Li, Z."

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Open Access
Chiral metamaterials with negative refractive index based on four "U" split ring resonators
(American Institute of Physics, 2010-08-23) Li, Z.; Zhao, R.; Koschny, T.; Kafesaki, M.; Alici, K. B.; Colak, E.; Caglayan, H.; Özbay, Ekmel; Soukoulis, C. M.
A uniaxial chiral metamaterial is constructed by double-layered four "U" split ring resonators mutually twisted by 90°. It shows a giant optical activity and circular dichroism. The retrieval results reveal that a negative refractive index is realized for circularly polarized waves due to the large chirality. The experimental results are in good agreement with the numerical results.
Open Access
Chiral metamaterials: from optical activity and negative refractive index to asymmetric transmission
(IOP Publishing, 2013-01-30) Li, Z.; Mutlu, M.; Özbay, Ekmel
We summarize the progress in the development and application of chiral metamaterials. After a brief review of the salient features of chiral metamaterials, such as giant optical activity, circular dichroism, and negative refractive index, the common method for the retrieval of effective parameters for chiral metamaterials is surveyed. Then, we introduce some typical chiral structures, e.g., chiral metamaterial consisting of split ring resonators, complementary chiral metamaterial, and composite chiral metamaterial, on the basis of the studies of the authors’ group. The coupling effect during the construction of bulk chiral metamaterials is mentioned and discussed. We introduce the application of bianisotropic chiral structures in the field of asymmetric transmission. Finally, we mention a few directions for future research on chiral metamaterials.
Open Access
Chiral Structures: Manipulation of Asymmetric Transmission in Planar Chiral Nanostructures by Anisotropic Loss (Advanced Optical Materials 7/2013)
(2013) Li, Z.; Gokkavas, M.; Özbay, Ekmel
Asymmetric transmissions of circularly polarized optical waves can be achieved when the waves are incident normal to planar chiral structures, provided that the structures are anisotropic and lossy. In order to clarify how the factor of loss affects the asymmetric transmission, Z. Li, M. Gokkavas, and E. Ozbay studied a typical planar chiral structure by using an optical lumped element model. On page 482, they found that the anisotropy of loss, instead of the whole loss, plays a crucial role for achieving asymmetric transmission. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Open Access
Complementary chiral metamaterials with giant optical activity and negative refractive index
(American Institute of Physics, 2011-04-20) Li, Z.; Alici, K. B.; Colak, E.; Özbay, Ekmel
A complementary bilayer cross-wire chiral metamaterial is proposed and studied experimentally and numerically. It exhibits giant optical activity and a small circular dichroism. The retrieval results reveal that a negative refractive index is realized for right circularly polarized waves due to the strong chirality. Our numerical results show that the mechanism of the chiral behavior at the resonance of lower frequency can be interpreted as the coupling effects between two sets of mutually twisted virtual magnetic dipoles, while the resonance of higher frequency shows complicated nonlocal features.
Open Access
Composite chiral metamaterials with negative refractive index and high values of the figure of merit
(Optical Society of America, 2012) Li, Z.; Caglayan, H.; Alici, K. B.; Kafesaki, M.; Soukoulis, C. M.; Özbay, Ekmel
A composite chiral metamaterial (CCMM) is designed and studied both numerically and experimentally. The CCMM is constructed by the combination of a continuous metallic wires structure and a purely chiral metamaterial (CMM) that consists of conjugated Rosettes. For the CMM, only very small, useful bands of negative index can be obtained for circularly polarized waves. These bands are all above the chiral resonance frequencies because of the high value of the effective parameter of relative permittivity epsilon. After the addition of the continuous metallic wires, which provide negative permittivity, the high value of epsilon can be partially compensated. Thus, a negative index band for the left circularly polarized wave that is below the chiral resonance frequency is obtained for the CCMM. At the same time, a negative index band for the right circularly polarized wave that is above the chiral resonance frequency is also obtained. Furthermore, both negative index bands correspond to the transmission peaks and have high values of the figure of merit. Therefore, the CCMM design that is proposed here is more suitable than the CMM for the construction of chiral metamaterials with a negative index. (C) 2012 Optical Society of America
Open Access
Coupling effect between two adjacent chiral structure layers
(Optical Society of America, 2010-03-01) Li, Z.; Caglayan, H.; Colak, E.; Zhou, J.; Soukoulis, C. M.; Özbay, Ekmel
A pair of mutually twisted metallic cross-wires can produce giant optical activity. When this single chiral layer is stacked layer by layer in order to build a thick chiral metamaterial, strong coupling effects are found between the two adjacent chiral layers. We studied these coupling effects numerically and experimentally. The results show that the existing coupling between chiral layers can make the chiral properties of a two-layered chiral metamaterial different from the constituting single chiral layers. It is explained qualitatively that the coupling effects are generated from the coupling of metallic cross-wires belonging to different chiral layers. Our experimental results are in good agreement with the simulation results. ©2010 Optical Society of America
Open Access
Determination of the effective constitutive parameters of bianisotropic metamaterials from reflection and transmission coefficients
(American Physical Society, 2009) Li, Z.; Aydin, K.; Özbay, Ekmel
We propose a method to retrieve the effective constitutive parameters of a slab of bianisotropic metamaterial from reflection and transmission coefficients (or scattering parameters). In our retrieval method, only the scattering parameters in one propagation direction are used. Analytical inversion equations are derived in order to retrieve the effective parameters of the permittivity, permeability, and magnetoelectric coupling coefficient of the bianisotropic metamaterial. To demonstrate the validity of the method, we used it to retrieve the parameters of four different metamaterials, among which two were normal media without bianisotropy and the other two were bianisotropic media. In using our retrieval method, including bianisotropy, the intrinsic differences between a normal medium and a bianisotropic medium were illustrated clearly. Our simulation and retrieval results also corroborate the conclusions of the previously published literature.
Open Access
Enhanced transmission and directivity from metallic subwavelength apertures with nonuniform and nonperiodic grooves
(AIP Publishing LLC, 2008) Li, Z.; Caglayan, H.; Colak, E.; Özbay, Ekmel
Nonuniform and nonperiodic grooves are used to enhance the transmission and directivity of emissions from a single metallic subwavelength aperture. By using nonuniform and nonperiodic grooves, the amplitude and phase of the diffracted power flow from each groove can be adjusted properly. As a result, the transmission and emission directivity can be further improved when compared to apertures with uniform and periodic grooves. Our experimental results are in good agreement with the finite difference time domain simulation results.
Open Access
Enhanced transmission through a subwavelength aperture using metamaterials
(AIP Publishing LLC, 2009-08-04) Cakmak, A. O.; Aydin, K.; Colak, E.; Li, Z.; Bilotti, F.; Vegni, L.; Özbay, Ekmel
We report an enhanced transmission through a single circular subwavelength aperture that is incorporated with a split ring resonator (SRR) at the microwave regime. Transmission enhancement factors as high as 530 were observed in the experiments when the SRR was located in front of the aperture in order to efficiently couple the electric field component of the incident electromagnetic wave at SRR’s electrical resonance frequency. The experimental results were supported by numerical analyses. The physical origin of the transmission enhancement phenomenon was discussed by examining the induced surface currents on the structures.
Open Access
Experimental and numerical study of omega type bianisotropic metamaterials combined with a negative permittivity medium
(Elsevier BV, 2008) Aydin, K.; Li, Z.; Bilge, S.; Özbay, Ekmel
We report on the transmission properties of the omega (Ω) type metamaterials. Transmission through the periodic Ω-only and Ω-wire metamaterials are studied experimentally and numerically. A resonance band gap is observed for the periodic Ω medium around the resonance frequency of the single Ω unit cell. A transmission band is observed below the resonance band gap, when the periodic Ω structure is embedded in a negative permittivity medium composed of thin metallic wire arrays. We also studied the effect of periodicity on the transmission spectra of Ω type metamaterials.
Open Access
Fano resonances in THz metamaterials composed of continuous metallic wires and split ring resonators
(Optical Society of America, 2014) Li, Z.; Cakmakyapan, S.; Butun, B.; Daskalaki, C.; Tzortzakis, S.; Yang, X.; Özbay, Ekmel
We demonstrate theoretically and experimentally that Fano resonances can be obtained in terahertz metamaterials that are composed of periodic continuous metallic wires dressed with periodic split ring resonators. An asymmetric Fano lineshape has been found in a narrow frequency range of the transmission curve. By using a transmission line combined with lumped element model, we are able to not only fit the transmission spectra of Fano resonance which is attributed to the coupling and interference between the transmission continuum of continuous metallic wires and the bright resonant mode of split ring resonators, but also reveal the capacitance change of the split ring resonators induced frequency shift of the Fano resonance. Therefore, the proposed theoretical model shows more capabilities than conventional coupled oscillator model in the design of Fano structures. The effective parameters of group refractive index of the Fano structure are retrieved, and a large group index more than 800 is obtained at the Fano resonance, which could be used for slow light devices. (C) 2014 Optical Society of America
Open Access
Generation of an axially asymmetric bessel-like beam from a metallic subwavelength aperture
(American Physical Society, 2009) Li, Z.; Alici, K. B.; Caglayan, H.; Özbay, Ekmel
An electromagnetic nondiffractive Bessel-like beam from a subwavelength aperture is generated by placing a metallic circular gratinglike structure in front of the aperture. When the incident wave is linearly polarized, the beam is axially asymmetric. The beam possesses fluctuating, but approximately uniform, intensity distribution along its longitudinal axis. The full width at half maximum of the beam remains less than two wavelengths over nearly ten wavelengths. Our experimental results are in good agreement with the simulation results and analytical results. © 2009 The American Physical Society.
Open Access
A global reference for human genetic variation
(Nature Publishing Group, 2015) Auton, A.; Abecasis, G. R.; Altshuler, D. M.; Durbin, R. M.; Bentley, D. R.; Chakravarti, A.; Clark, A. G.; Donnelly, P.; Eichler, E. E.; Flicek, P.; Gabriel, S. B.; Gibbs, R. A.; Green, E. D.; Hurles, M. E.; Knoppers, B. M.; Korbel, J. O.; Lander, E. S.; Lee, C.; Lehrach, H.; Mardis, E. R.; Marth, G. T.; McVean, G. A.; Nickerson, D. A.; Schmidt, J. P.; Sherry, S. T.; Wang, J.; Wilson, R. K.; Boerwinkle, E.; Doddapaneni, H.; Han, Y.; Korchina, V.; Kovar, C.; Lee, S.; Muzny, D.; Reid, J. G.; Zhu, Y.; Chang, Y.; Feng, Q.; Fang, X.; Guo, X.; Jian, M.; Jiang, H.; Jin, X.; Lan, T.; Li, G.; Li, J.; Li, Y.; Liu, S.; Liu, X.; Lu, Y.; Ma, X.; Tang, M.; Wang, B.; Wang, G.; Wu, H.; Wu, R.; Xu, X.; Yin, Y.; Zhang, D.; Zhang, W.; Zhao, J.; Zhao, M.; Zheng, X.; Gupta, N.; Gharani, N.; Toji, L. H.; Gerry, N. P.; Resch, A. M.; Barker, J.; Clarke, L.; Gil, L.; Hunt, S. E.; Kelman, G.; Kulesha, E.; Leinonen, R.; McLaren, W. M.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Smith, R. E.; Streeter, I.; Thormann, A.; Toneva, I.; Vaughan, B.; Zheng-Bradley, X.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Sudbrak, R.; Albrecht, M. W.; Amstislavskiy, V. S.; Borodina, T. A.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, Marie-Laure; Fulton, L.; Ananiev, V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Church, D.; Cohen, R.; Cook, C.; Garner, J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez, J.; Meric, P.; O'Sullivan, C.; Ostapchuk, Y.; Phan, L.; Ponomarov, S.; Schneider, V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang, H.; Balasubramaniam, S.; Burton, J.; Danecek, P.; Keane, T. M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker, J.; Quail, M.; Davies, C. J.; Gollub, J.; Webster, T.; Wong, B.; Zhan, Y.; Campbell, C. L.; Kong, Y.; Marcketta, A.; Yu, F.; Antunes, L.; Bainbridge, M.; Sabo, A.; Huang, Z.; Coin, L. J. M.; Fang, L.; Li, Q.; Li, Z.; Lin, H.; Liu, B.; Luo, R.; Shao, H.; Xie, Y.; Ye, C.; Yu, C.; Zhang, F.; Zheng, H.; Zhu, H.; Alkan, C.; Dal, E.; Kahveci, F.; Garrison, E. P.; Kural, D.; Lee, W. P.; Leong, W. F.; Stromberg, M.; Ward, A. N.; Wu, J.; Zhang, M.; Daly, M. J.; DePristo, M. A.; Handsaker, R. E.; Banks, E.; Bhatia, G.; Del Angel, G.; Genovese, G.; Li, H.; Kashin, S.; McCarroll, S. A.; Nemesh, J. C.; Poplin, R. E.; Yoon, S. C.; Lihm, J.; Makarov, V.; Gottipati, S.; Keinan, A.; Rodriguez-Flores, J. L.; Rausch, T.; Fritz, M. H.; Stütz, A. M.; Beal, K.; Datta, A.; Herrero, J.; Ritchie, G. R. S.; Zerbino, D.; Sabeti, P. C.; Shlyakhter, I.; Schaffner, S. F.; Vitti, J.; Cooper, D. N.; Ball, E. V.; Stenson, P. D.; Barnes, B.; Bauer, M.; Cheetham, R. K.; Cox, A.; Eberle, M.; Kahn, S.; Murray, L.; Peden, J.; Shaw, R.; Kenny, E. E.; Batzer, M. A.; Konkel, M. K.; Walker, J. A.; MacArthur, D. G.; Lek, M.; Herwig, R.; Ding, L.; Koboldt, D. C.; Larson, D.; Ye, K.; Gravel, S.; Swaroop, A.; Chew, E.; Lappalainen, T.; Erlich, Y.; Gymrek, M.; Willems, T. F.; Simpson, J. T.; Shriver, M. D.; Rosenfeld, J. A.; Bustamante, C. D.; Montgomery, S. B.; De La Vega, F. M.; Byrnes, J. K.; Carroll, A. W.; DeGorter, M. K.; Lacroute, P.; Maples, B. K.; Martin, A. R.; Moreno-Estrada, A.; Shringarpure, S. S.; Zakharia, F.; Halperin, E.; Baran, Y.; Cerveira, E.; Hwang, J.; Malhotra, A.; Plewczynski, D.; Radew, K.; Romanovitch, M.; Zhang, C.; Hyland, F. C. L.; Craig, D. W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A. A.; Sinari, S. A.; Squire, K.; Xiao, C.; Sebat, J.; Antaki, D.; Gujral, M.; Noor, A.; Ye, K.; Burchard, E. G.; Hernandez, R. D.; Gignoux, C. R.; Haussler, D.; Katzman, S. J.; Kent, W. J.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E. T.; Devine, S. E.; Kang, H. M.; Kidd, J. M.; Blackwell, T.; Caron, S.; Chen, W.; Emery, S.; Fritsche, L.; Fuchsberger, C.; Jun, G.; Li, B.; Lyons, R.; Scheller, C.; Sidore, C.; Song, S.; Sliwerska, E.; Taliun, D.; Tan, A.; Welch, R.; Wing, M. K.; Zhan, X.; Awadalla, P.; Hodgkinson, A.; Li, Y.; Shi, X.; Quitadamo, A.; Lunter, G.; Marchini, J. L.; Myers, S.; Churchhouse, C.; Delaneau, O.; Gupta-Hinch, A.; Kretzschmar, W.; Iqbal, Z.; Mathieson, I.; Menelaou, A.; Rimmer, A.; Xifara, D. K.; Oleksyk, T. K.; Fu, Y.; Liu, X.; Xiong, M.; Jorde, L.; Witherspoon, D.; Xing, J.; Browning, B. L.; Browning, S. R.; Hormozdiari, F.; Sudmant, P. H.; Khurana, E.; Tyler-Smith, C.; Albers, C. A.; Ayub, Q.; Chen, Y.; Colonna, V.; Jostins, L.; Walter, K.; Xue, Y.; Gerstein, M. B.; Abyzov, A.; Balasubramanian, S.; Chen, J.; Clarke, D.; Fu, Y.; Harmanci, A. O.; Jin, M.; Lee, D.; Liu, J.; Mu, X. J.; Zhang, J.; Zhang, Y.; Hartl, C.; Shakir, K.; Degenhardt, J.; Meiers, S.; Raeder, B.; Casale, F. P.; Stegle, O.; Lameijer, E. W.; Hall, I.; Bafna, V.; Michaelson, J.; Gardner, E. J.; Mills, R. E.; Dayama, G.; Chen, K.; Fan, X.; Chong, Z.; Chen, T.; Chaisson, M. J.; Huddleston, J.; Malig, M.; Nelson, B. J.; Parrish, N. F.; Blackburne, B.; Lindsay, S. J.; Ning, Z.; Zhang, Y.; Lam, H.; Sisu, C.; Challis, D.; Evani, U. S.; Lu, J.; Nagaswamy, U.; Yu, J.; Li, W.; Habegger, L.; Yu, H.; Cunningham, F.; Dunham, I.; Lage, K.; Jespersen, J. B.; Horn, H.; Kim, D.; Desalle, R.; Narechania, A.; Sayres, M. A. W.; Mendez, F. L.; Poznik, G. D.; Underhill, P. A.; Mittelman, D.; Banerjee, R.; Cerezo, M.; Fitzgerald, T. W.; Louzada, S.; Massaia, A.; Yang, F.; Kalra, D.; Hale, W.; Dan, X.; Barnes, K. C.; Beiswanger, C.; Cai, H.; Cao, H.; Henn, B.; Jones, D.; Kaye, J. S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio, P. N.; Parker, M.; Rotimi, C. N.; Royal, C. D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Via, M.; Wang, Y.; Yang, H.; Yang, L.; Zhu, J.; Bodmer, W.; Bedoya, G.; Cai, Z.; Gao, Y.; Chu, J.; Peltonen, L.; Garcia-Montero, A.; Orfao, A.; Dutil, J.; Martinez-Cruzado, J. C.; Mathias, R. A.; Hennis, A.; Watson, H.; McKenzie, C.; Qadri, F.; LaRocque, R.; Deng, X.; Asogun, D.; Folarin, O.; Happi, C.; Omoniwa, O.; Stremlau, M.; Tariyal, R.; Jallow, M.; Joof, F. S.; Corrah, T.; Rockett, K.; Kwiatkowski, D.; Kooner, J.; Hien, T. T.; Dunstan, S. J.; ThuyHang, N.; Fonnie, R.; Garry, R.; Kanneh, L.; Moses, L.; Schieffelin, J.; Grant, D. S.; Gallo, C.; Poletti, G.; Saleheen, D.; Rasheed, A.; Brooks, L. D.; Felsenfeld, A. L.; McEwen, J. E.; Vaydylevich, Y.; Duncanson, A.; Dunn, M.; Schloss, J. A.
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. © 2015 Macmillan Publishers Limited. All rights reserved.
Open Access
Highly asymmetric transmission of linearly polarized waves realized with a multilayered structure including chiral metamaterials
(IOP Publishing, 2014) Li, Z.; Mutlu, M.; Özbay, Ekmel
We numerically and experimentally demonstrate highly asymmetric transmission of linearly polarized waves with a multilayered metallic structure. The whole structure has a subwavelength thickness and consists of a thin slab of chiral metamaterial sandwiched between two 90° twisted linear polarizers. The chiral metamaterial is made of two sets of twisting cross wires that can rotate the polarization by 90° at resonance, and the two linear polarizers are simple metallic grating polarizers. The operation principle of the whole structure can be well interpreted by using the Jones matrix method. Our experimental results also verify that chiral metamaterials can be safely integrated into complex structures and treated as an effective medium as long as their resonant modes are not affected by the environment.
Open Access
Highly directional emission from photonic crystals with a wide bandwidth
(AIP Publishing LLC, 2007) Li, Z.; Aydin, K.; Özbay, Ekmel
The authors numerically and experimentally demonstrated highly directional emission from photonic crystals. This was achieved by first splitting the incident electromagnetic wave into multiple beams using photonic crystal waveguide structures. The beams were then emitted out of the surface of a photonic crystal with the same phase, which resulted in a highly directional radiation pattern. The measured half power beam width was 4.8°, which was in good agreement with the calculated value of 4.1°. In contrast to the traditional beaming structures, their design did not involve gratinglike structures, which resulted in a wider operation bandwidth.
Open Access
An integrated map of genetic variation from 1,092 human genomes
(Nature Publishing Group, 2012) Altshuler, D.M.; Durbin, R.M.; Abecasis G.R.; Bentley, D.R.; Chakravarti, A.; Clark, A.G.; Donnelly P.; Eichler, E.E.; Flicek P.; Gabriel, S.B.; Gibbs, R.A.; Green, E.D.; Hurles, M.E.; Knoppers, B.M.; Korbel J.O.; Lander, E.S.; Lee, C.; Lehrach H.; Mardis, E.R.; Marth G.T.; McVean G.A.; Nickerson, D.A.; Schmidt J.P.; Sherry, S.T.; Wang, J.; Wilson, R.K.; Dinh H.; Kovar, C.; Lee, S.; Lewis L.; Muzny, D.; Reid J.; Wang, M.; Fang X.; Guo X.; Jian, M.; Jiang H.; Jin X.; Li G.; Li J.; Li Y.; Li, Z.; Liu X.; Lu, Y.; Ma X.; Su, Z.; Tai, S.; Tang, M.; Wang, B.; Wang G.; Wu H.; Wu, R.; Yin, Y.; Zhang W.; Zhao J.; Zhao, M.; Zheng X.; Zhou, Y.; Gupta, N.; Clarke L.; Leinonen, R.; Smith, R.E.; Zheng-Bradley X.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Sudbrak, R.; Albrecht, M.W.; Amstislavskiy V.S.; Borodina, T.A.; Lienhard, M.; Mertes F.; Sultan, M.; Timmermann, B.; Yaspo, M.-L.; Fulton L.; Fulton, R.; Weinstock G.M.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Auton, A.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang Y.; Yu J.; Coin L.J.M.; Fang L.; Li Q.; Li, Z.; Lin H.; Liu, B.; Luo, R.; Qin, N.; Shao H.; Wang, B.; Xie, Y.; Ye, C.; Yu, C.; Zhang F.; Zheng H.; Zhu H.; Garrison, E.P.; Kural, D.; Lee W.-P.; Fung Leong W.; Ward, A.N.; Wu J.; Zhang, M.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Shi X.; Von Grotthuss, M.; Zhang, C.; Daly, M.J.; Depristo, M.A.; Banks, E.; Bhatia G.; Carneiro, M.O.; Del Angel G.; Genovese G.; Handsaker, R.E.; Hartl, C.; McCarroll, S.A.; Nemesh J.C.; Poplin, R.E.; Schaffner, S.F.; Shakir, K.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Cheol Kim, K.; Rausch, T.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; Gottipati, S.; Keinan, A.; Rodriguez-Flores J.L.; Sabeti P.C.; Grossman, S.R.; Tabrizi, S.; Tariyal, R.; Cooper, D.N.; Ball, E.V.; Stenson P.D.; Barnes, B.; Bauer, M.; Keira Cheetham, R.; Cox, T.; Eberle, M.; Kahn, S.; Murray L.; Peden J.; Shaw, R.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Herwig, R.; Shriver, M.D.; Bustamante, C.D.; Byrnes J.K.; De La Vega F.M.; Gravel, S.; Kenny, E.E.; Kidd J.M.; Maples, B.K.; Moreno-Estrada, A.; Zakharia F.; Halperin, E.; Baran, Y.; Craig, D.W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Squire, K.; Xiao, C.; Sebat J.; Bafna V.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; James Kent W.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E.T.; Lappalainen, T.; Devine, S.E.; Liu X.; Maroo, A.; Tallon L.J.; Rosenfeld J.A.; Michelson L.P.; Min Kang H.; Anderson P.; Angius, A.; Bigham, A.; Blackwell, T.; Busonero F.; Cucca F.; Fuchsberger, C.; Jones, C.; Jun G.; Li Y.; Lyons, R.; Maschio, A.; Porcu, E.; Reinier F.; Sanna, S.; Schlessinger, D.; Sidore, C.; Tan, A.; Kate Trost, M.; Awadalla P.; Hodgkinson, A.; Lunter G.; Marchini J.L.; Myers, S.; Churchhouse, C.; Delaneau O.; Gupta-Hinch, A.; Iqbal, Z.; Mathieson I.; Rimmer, A.; Xifara, D.K.; Oleksyk, T.K.; Fu, Y.; Liu X.; Xiong, M.; Jorde L.; Witherspoon, D.; Xing J.; Browning, B.L.; Alkan C.; Hajirasouliha I.; Hormozdiari F.; Ko, A.; Sudmant P.H.; Chen, K.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Tyler-Smith, C.; Albers, C.A.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Li H.; Scally, A.; Walter, K.; Xue, Y.; Zhang, Y.; Gerstein, M.B.; Abyzov, A.; Balasubramanian, S.; Chen J.; Clarke, D.; Fu, Y.; Habegger L.; Harmanci, A.O.; Jin, M.; Khurana, E.; Jasmine Mu X.; Sisu, C.; Degenhardt J.; Stütz, A.M.; Keira Cheetham, R.; Church, D.; Michaelson J.J.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Mu X.J.; Fowler G.; Hale W.; Kalra, D.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Vaughan, B.; Ananiev V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Cohen, R.; Cook, C.; Garner J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez J.; Meric P.; O'Sullivan, C.; Ostapchuk, Y.; Phan L.; Ponomarov, S.; Schneider V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang H.; Barnes, K.C.; Beiswanger, C.; Cai H.; Cao H.; Gharani, N.; Henn, B.; Jones, D.; Kaye J.S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Reich, D.; Rotimi, C.N.; Royal, C.D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Toji L.H.; Via, M.; Wang Y.; Yang H.; Yang L.; Zhu J.; Bodmer W.; Bedoya G.; Ming, C.Z.; Yang G.; Jia You, C.; Peltonen L.; Garcia-Montero, A.; Orfao, A.; Dutil J.; Martinez-Cruzado J.C.; Brooks L.D.; Felsenfeld, A.L.; McEwen J.E.; Clemm, N.C.; Duncanson, A.; Dunn, M.; Guyer, M.S.; Peterson J.L.; Lacroute P.
By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. © 2012 Macmillan Publishers Limited. All rights reserved.
Open Access
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
(Nature Publishing Group, 2014) Delaneau O.; Marchini J.; McVeanh G.A.; Donnelly P.; Lunter G.; Marchini J.L.; Myers, S.; Gupta-Hinch, A.; Iqbal, Z.; Mathieson I.; Rimmer, A.; Xifara, D.K.; Kerasidou, A.; Churchhouse, C.; Altshuler, D.M.; Gabriel, S.B.; Lander, E.S.; Gupta, N.; Daly, M.J.; DePristo, M.A.; Banks, E.; Bhatia G.; Carneiro, M.O.; Del Angel G.; Genovese G.; Handsaker, R.E.; Hartl, C.; McCarroll, S.A.; Nemesh J.C.; Poplin, R.E.; Schaffner, S.F.; Shakir, K.; Sabeti P.C.; Grossman, S.R.; Tabrizi, S.; Tariyal, R.; Li H.; Reich, D.; Durbin, R.M.; Hurles, M.E.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Scally, A.; Walter, K.; Xue, Y.; Zhang, Y.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Chris, T.-S.; Abecasis G.R.; Kang H.M.; Anderson P.; Blackwell, T.; Busonero F.; Fuchsberger, C.; Jun G.; Maschio, A.; Porcu, E.; Sidore, C.; Tan, A.; Trost, M.K.; Bentley, D.R.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Bauer, M.; Cheetham, R.K.; Cox, T.; Eberle, M.; Murray L.; Shaw, R.; Chakravarti, A.; Clark, A.G.; Keinan, A.; Rodriguez-Flores J.L.; De LaVega F.M.; Degenhardt J.; Eichler, E.E.; Flicek P.; Clarke L.; Leinonen, R.; Smith, R.E.; Zheng-Bradley X.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Gibbs, R.A.; Dinh H.; Kovar, C.; Lee, S.; Lewis L.; Muzny, D.; Reid J.; Wang, M.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang, Y.; Yu J.; Fowler G.; Hale W.; Kalra, D.; Green, E.D.; Knoppers, B.M.; Korbel J.O.; Rausch, T.; Sttz, A.M.; Lee, C.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Von Grotthuss, M.; Zhang, C.; Shi X.; Lehrach H.; Sudbrak, R.; Amstislavskiy V.S.; Lienhard, M.; Mertes F.; Sultan, M.; Timmermann, B.; Yaspo, M.L.; Herwig, S.R.; Mardis, E.R.; Wilson, R.K.; Fulton L.; Fulton, R.; Weinstock G.M.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Marth G.T.; Garrison, E.P.; Kural, D.; Lee W.-P.; Leong W.F.; Ward, A.N.; Wu J.; Zhang, M.; Nickerson, D.A.; Alkan, C.; Hormozdiari F.; Ko, A.; Sudmant P.H.; Schmidt J.P.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Sherry, S.T.; Xiao, C.; Church, D.; Ananiev V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Cohen, R.; Cook, C.; Garner J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez J.; Meric P.; Ostapchuk, Y.; Phan L.; Ponomarov, S.; Schneider V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang H.; Wang J.; Fang X.; Guo X.; Jian, M.; Jiang H.; Jin X.; Li G.; Li J.; Li, Y.; Liu X.; Lu, Y.; Ma X.; Tai, S.; Tang, M.; Wang, B.; Wang G.; Wu H.; Wu, R.; Yin, Y.; Zhang W.; Zhao J.; Zhao, M.; Zheng X.; Lachlan H.; Fang L.; Li Q.; Li, Z.; Lin H.; Liu, B.; Luo, R.; Shao H.; Wang, B.; Xie, Y.; Ye, C.; Yu, C.; Zheng H.; Zhu H.; Cai H.; Cao H.; Su, Y.; Tian, Z.; Yang H.; Yang L.; Zhu J.; Cai, Z.; Wang J.; Albrecht, M.W.; Borodina, T.A.; Auton, A.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Kim, K.C.; Gottipati, S.; Jones, D.; Cooper, D.N.; Ball, E.V.; Stenson P.D.; Barnes, B.; Kahn, S.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Shriver, M.D.; Bustamante, C.D.; Gravel, S.; Kenny, E.E.; Kidd J.M.; Lacroute P.; Maples, B.K.; Moreno-Estrada, A.; Zakharia F.; Henn, B.; Sandoval, K.; Byrnes J.K.; Halperin, E.; Baran, Y.; Craig, D.W.; Christoforides, A.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Homer, N.; Squire, K.; Sebat J.; Bafna V.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; Kent W.J.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E.T.; Lappalainen, T.; Devine, S.E.; Liu X.; Maroo, A.; Tallon L.J.; Rosenfeld J.A.; Michelson L.P.; Angius, A.; Cucca F.; Sanna, S.; Bigham, A.; Jones, C.; Reinier F.; Li, Y.; Lyons, R.; Schlessinger, D.; Awadalla P.; Hodgkinson, A.; Oleksyk, T.K.; Martinez-Cruzado J.C.; Fu, Y.; Liu X.; Xiong, M.; Jorde L.; Witherspoon, D.; Xing J.; Browning, B.L.; Hajirasouliha I.; Chen, K.; Albers, C.A.; Gerstein, M.B.; Abyzov, A.; Chen J.; Fu, Y.; Habegger L.; Harmanci, A.O.; Mu X.J.; Sisu, C.; Balasubramanian, S.; Jin, M.; Khurana, E.; Clarke, D.; Michaelson J.J.; OSullivan, C.; Barnes, K.C.; Gharani, N.; Toji L.H.; Gerry, N.; Kaye J.S.; Kent, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Rotimi, C.N.; Royal, C.D.; Tishkoff, S.; Via, M.; Bodmer W.; Bedoya G.; Yang G.; You, C.J.; Garcia-Montero, A.; Orfao, A.; Dutil J.; Brooks L.D.; Felsenfeld, A.L.; McEwen J.E.; Clemm, N.C.; Guyer, M.S.; Peterson J.L.; Duncanson, A.; Dunn, M.; Peltonen L.
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.
Open Access
Laser-ablation assisted strain engineering of gold nanoparticles for selective electrochemical CO2 reduction
(Royal Society of Chemistry, 2022-04-19) Zhang, C.; Zhang, W.; Karadaş, Ferdi; Low, J.; Long, R.; Liang, C.; Wang, J.; Li, Z.; Xiong, Y.
Strain engineering can endow versatile functions, such as refining d-band center and inducing lattice mismatch, on catalysts for a specific reaction. To this end, effective strain engineering for introducing strain on the catalyst is highly sought in various catalytic applications. Herein, a facile laser ablation in liquid (LAL) strategy is adopted to synthesize gold nanoparticles (Au NPs) with rich compressive strain (Au-LAL) for electrochemical CO2 reduction. It is demonstrated that the rich compressive strain can greatly promote the electrochemical CO2 reduction performance of Au, achieving a CO partial current density of 24.9 mA cm−2 and a maximum CO faradaic efficiency of 97% at −0.9 V for Au-LAL, while it is only 2.77 mA cm−2 and 16.2% for regular Au nanoparticles (Au-A). As revealed by the in situ Raman characterization and density functional theory calculations, the presence of compressive strain can induce a unique electronic structure change in Au NPs, significantly up-shifting the d-band center of Au. Such a phenomenon can greatly enhance the adsorption strength of Au NPs toward the key intermediate of CO2 reduction (i.e., *COOH). More interestingly, we demonstrate that, an important industrial chemical feedstock, syngas, can be obtained by simply mixing Au-LAL with Au-A in a suitable ratio. This work provides a promising method for introducing strain in metal NPs and demonstrates the important role of strain in tuning the performance and selectivity of catalysts.
Open Access
Manipulation of Asymmetric Transmission in Planar Chiral Nanostructures by Anisotropic Loss
(Wiley, 2013) Li, Z.; Gokkavas, M.; Özbay, Ekmel
Planar chiral structures may provide asymmetric transmission for circularly polarized optical waves at normal incidence if the structures are anisotropic and lossy, but the role of loss has not yet been clarified. Here, a typical planar chiral structure is studied, and the mechanism of asymmetric transmission is analyzed. It is demonstrated for the first time that asymmetric transmission can be manipulated by changing the anisotropy of loss.
Open Access
Quantum dots on vertically aligned gold nanorod monolayer: plasmon enhanced fluorescence
(Royal Society of Chemistry, 2014) Peng, B.; Li, Z.; Mutlugun, E.; Martinez, P. L. H.; Li, D.; Zhang, Q.; Gao, Y.; Demir, Hilmi Volkan; Xiong, Q.
CTAB-coated Au nanorods were directly self-assembled into a vertically aligned monolayer with highly uniform hot spots through a simple but robust approach. By coupling with CdSe/ZnS quantum dots, a maximum enhancement of 10.4 is achieved due to: increased excitation transition rate, radiative rate, and coupling efficiency of emission to the far field.