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Khan KIA, Kumar A, Gupta P, Yadav RS, Åkerman J, Muduli PK. Magnetodynamic properties of ultrathin films of Fe[Formula: see text]Sn[Formula: see text]-a topological kagome ferromagnet. Sci Rep 2024; 14:3487. [PMID: 38347066 DOI: 10.1038/s41598-024-53621-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Fe[Formula: see text]Sn[Formula: see text] is a topological kagome ferromagnet that possesses numerous Weyl points close to the Fermi energy, which can manifest various unique transport phenomena such as chiral anomaly, anomalous Hall effect, and giant magnetoresistance. However, the magnetodynamic properties of Fe[Formula: see text]Sn[Formula: see text] have not yet been explored. Here, we report, for the first time, the measurements of the intrinsic Gilbert damping constant ([Formula: see text]), and the effective spin mixing conductance (g[Formula: see text]) of Pt/Fe[Formula: see text]Sn[Formula: see text] bilayers for Fe[Formula: see text]Sn[Formula: see text] thicknesses down to 2 nm, for which [Formula: see text] is [Formula: see text], and g[Formula: see text] is [Formula: see text]. The films have a high saturation magnetization, [Formula: see text], and large anomalous Hall coefficient, [Formula: see text]. The large values of g[Formula: see text], together with the topological properties of Fe[Formula: see text]Sn[Formula: see text], make Fe[Formula: see text]Sn[Formula: see text]/Pt bilayers useful heterostructures for the study of topological spintronic devices.
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Affiliation(s)
- Kacho Imtiyaz Ali Khan
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Akash Kumar
- Applied Spintronics Group, Department of Physics, University of Gothenburg, Gothenburg, 412 96, Sweden
- Center for Science and Innovation in Spintronics, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Pankhuri Gupta
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ram Singh Yadav
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Johan Åkerman
- Applied Spintronics Group, Department of Physics, University of Gothenburg, Gothenburg, 412 96, Sweden.
- Center for Science and Innovation in Spintronics, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
| | - Pranaba Kishor Muduli
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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2
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Venkataraman P, Saini S. Ecological disruptive selection acting on quantitative loci can drive sympatric speciation. NPJ Syst Biol Appl 2024; 10:6. [PMID: 38225420 PMCID: PMC10789801 DOI: 10.1038/s41540-024-00332-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024] Open
Abstract
The process of speciation generates biodiversity. According to the null model of speciation, barriers between populations arise in allopatry, where, prior to biology, geography imposes barriers to gene flow. On the other hand, sympatric speciation requires that the process of speciation happen in the absence of a geographical barrier, where the members of the population have no spatial, temporal barriers. Several attempts have been made to theoretically identify the conditions in which speciation can occur in sympatry. However, these efforts suffer from several limitations. We propose a model for sympatric speciation based on adaptation for resource utilization. We use a genetics-based model to investigate the relative roles of prezygotic and postzygotic barriers, from the context of ecological disruptive selection, sexual selection, and genetic architecture, in causing and maintaining sympatric speciation. Our results show that sexual selection that acts on secondary sexual traits does not play any role in the process of speciation in sympatry and that assortative mating based on an ecologically relevant trait forces the population to show an adaptive response. We also demonstrate that understanding the genetic architecture of the trait under ecological selection is very important and that it is not required for the strength of ecological disruptive selection to be very high in order for speciation to occur in sympatry. Our results provide an insight into the kind of scenarios in which sympatric speciation can be demonstrated in the lab.
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Affiliation(s)
- Pavithra Venkataraman
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400 076, India.
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400 076, India
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3
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Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023; 8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2-64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants' impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
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Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilie F Rustad
- Department of Medial Genetics, Oslo University Hospital, Oslo, Norway
| | - Vernon Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, Norway
| | - Laura Orellana
- Protein Dynamics and Mutation lab, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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Sherekar S, Todankar CS, Viswanathan GA. Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response. NPJ Syst Biol Appl 2023; 9:57. [PMID: 37973854 PMCID: PMC10654705 DOI: 10.1038/s41540-023-00318-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Cell-to-cell variability during TNFα stimulated Tumor Necrosis Factor Receptor 1 (TNFR1) signaling can lead to single-cell level pro-survival and apoptotic responses. This variability stems from the heterogeneity in signal flow through intracellular signaling entities that regulate the balance between these two phenotypes. Using systematic Boolean dynamic modeling of a TNFR1 signaling network, we demonstrate that the signal flow path variability can be modulated to enable cells favour apoptosis. We developed a computationally efficient approach "Boolean Modeling based Prediction of Steady-state probability of Phenotype Reachability (BM-ProSPR)" to accurately predict the network's ability to settle into different phenotypes. Model analysis juxtaposed with the experimental observations revealed that NFκB and PI3K transient responses guide the XIAP behaviour to coordinate the crucial dynamic cross-talk between the pro-survival and apoptotic arms at the single-cell level. Model predicted the experimental observations that ~31% apoptosis increase can be achieved by arresting Comp1 - IKK* activity which regulates the NFκB and PI3K dynamics. Arresting Comp1 - IKK* activity causes signal flow path re-wiring towards apoptosis without significantly compromising NFκB levels, which govern adequate cell survival. Priming an ensemble of cancerous cells with inhibitors targeting the specific interaction involving Comp1 and IKK* prior to TNFα exposure could enable driving them towards apoptosis.
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Affiliation(s)
- Shubhank Sherekar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Chaitra S Todankar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Ganesh A Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India.
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Mondal D, Mahapatra SR, Derrico AM, Rai RK, Paudel JR, Schlueter C, Gloskovskii A, Banerjee R, Hariki A, DeGroot FMF, Sarma DD, Narayan A, Nukala P, Gray AX, Aetukuri NPB. Modulation-doping a correlated electron insulator. Nat Commun 2023; 14:6210. [PMID: 37798279 PMCID: PMC10556139 DOI: 10.1038/s41467-023-41816-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Correlated electron materials (CEMs) host a rich variety of condensed matter phases. Vanadium dioxide (VO2) is a prototypical CEM with a temperature-dependent metal-to-insulator (MIT) transition with a concomitant crystal symmetry change. External control of MIT in VO2-especially without inducing structural changes-has been a long-standing challenge. In this work, we design and synthesize modulation-doped VO2-based thin film heterostructures that closely emulate a textbook example of filling control in a correlated electron insulator. Using a combination of charge transport, hard X-ray photoelectron spectroscopy, and structural characterization, we show that the insulating state can be doped to achieve carrier densities greater than 5 × 1021 cm-3 without inducing any measurable structural changes. We find that the MIT temperature (TMIT) continuously decreases with increasing carrier concentration. Remarkably, the insulating state is robust even at doping concentrations as high as ~0.2 e-/vanadium. Finally, our work reveals modulation-doping as a viable method for electronic control of phase transitions in correlated electron oxides with the potential for use in future devices based on electric-field controlled phase transitions.
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Affiliation(s)
- Debasish Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Smruti Rekha Mahapatra
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Rajeev Kumar Rai
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
| | - Jay R Paudel
- Department of Physics, Temple University, Philadelphia, PA, USA
| | | | | | - Rajdeep Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Atsushi Hariki
- Department of Physics and Electronics, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Frank M F DeGroot
- Utrecht University, Inorganic Chemistry and Catalysis Group Universiteitsweg 99, Utrecht, The Netherlands
| | - D D Sarma
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Awadhesh Narayan
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Pavan Nukala
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
| | - Alexander X Gray
- Department of Physics, Temple University, Philadelphia, PA, USA.
| | - Naga Phani B Aetukuri
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India.
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6
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Sreenivasan V, Kumar S, Pestilli F, Talukdar P, Sridharan D. GPU-accelerated connectome discovery at scale. Nat Comput Sci 2022; 2:298-306. [PMID: 38177824 PMCID: PMC10766542 DOI: 10.1038/s43588-022-00250-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/21/2022] [Indexed: 01/06/2024]
Abstract
Diffusion magnetic resonance imaging and tractography enable the estimation of anatomical connectivity in the human brain, in vivo. Yet, without ground-truth validation, different tractography algorithms can yield widely varying connectivity estimates. Although streamline pruning techniques mitigate this challenge, slow compute times preclude their use in big-data applications. We present 'Regularized, Accelerated, Linear Fascicle Evaluation' (ReAl-LiFE), a GPU-based implementation of a state-of-the-art streamline pruning algorithm (LiFE), which achieves >100× speedups over previous CPU-based implementations. Leveraging these speedups, we overcome key limitations with LiFE's algorithm to generate sparser and more accurate connectomes. We showcase ReAl-LiFE's ability to estimate connections with superlative test-retest reliability, while outperforming competing approaches. Moreover, we predicted inter-individual variations in multiple cognitive scores with ReAl-LiFE connectome features. We propose ReAl-LiFE as a timely tool, surpassing the state of the art, for accurate discovery of individualized brain connectomes at scale. Finally, our GPU-accelerated implementation of a popular non-negative least-squares optimization algorithm is widely applicable to many real-world problems.
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Affiliation(s)
| | - Sawan Kumar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Franco Pestilli
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
| | - Partha Talukdar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India
| | - Devarajan Sridharan
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India.
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
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7
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Patil AB, Vijay N. Repetitive genomic regions and the inference of demographic history. Heredity (Edinb) 2021; 127:151-166. [PMID: 34002046 PMCID: PMC8322061 DOI: 10.1038/s41437-021-00443-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Inference of demographic histories using whole-genome datasets has provided insights into diversification, adaptation, hybridization, and plant-pathogen interactions, and stimulated debate on the impact of anthropogenic interventions and past climate on species demography. However, the impact of repetitive genomic regions on these inferences has mostly been ignored by masking of repeats. We use the Populus trichocarpa genome (Pop_tri_v3) to show that masking of repeat regions leads to lower estimates of effective population size (Ne) in the distant past in contrast to an increase in Ne estimates in recent times. However, in human datasets, masking of repeats resulted in lower estimates of Ne at all time points. We demonstrate that repeats affect demographic inferences using diverse methods like PSMC, MSMC, SMC++, and the Stairway plot. Our genomic analysis revealed that the biases in Ne estimates were dependent on the repeat class type and its abundance in each atomic interval. Notably, we observed a weak, yet consistently significant negative correlation between the repeat abundance of an atomic interval and the Ne estimates for that interval, which potentially reflects the recombination rate variation within the genome. The rationale for the masking of repeats has been that variants identified within these regions are erroneous. We find that polymorphisms in some repeat classes occur in callable regions and reflect reliable coalescence histories (e.g., LTR Gypsy, LTR Copia). The current demography inference methods do not handle repeats explicitly, and hence the effect of individual repeat classes needs careful consideration in comparative analysis. Deciphering the repeat demographic histories might provide a clear understanding of the processes involved in repeat accumulation.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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Abstract
Hydrodynamic collapse of a central air-cavity during the recoil phase of droplet impact on a superhydrophobic sieve leads to satellite-free generation of a single droplet through the sieve. Two modes of cavity formation and droplet ejection have been observed and explained. The volume of the generated droplet scales with the pore size. Based on this phenomenon, we propose a drop-on-demand printing technique. Despite significant advancements in inkjet technology, enhancement in mass-loading and particle-size have been limited due to clogging of the printhead nozzle. By replacing the nozzle with a sieve, we demonstrate printing of nanoparticle suspension with 71% mass-loading. Comparatively large particles of 20 μm diameter are dispensed in droplets of ~80 μm diameter. Printing is performed for surface tension as low as 32 mNm-1 and viscosity as high as 33 mPa∙s. In comparison to existing techniques, this way of printing is widely accessible as it is significantly simple and economical.
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Affiliation(s)
- Chandantaru Dey Modak
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Arvind Kumar
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Abinash Tripathy
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India
- Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, CH-8092, Zurich, Switzerland
| | - Prosenjit Sen
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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9
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Abstract
Manipulation of colloidal objects with light is important in diverse fields. While performance of traditional optical tweezers is restricted by the diffraction-limit, recent approaches based on plasmonic tweezers allow higher trapping efficiency at lower optical powers but suffer from the disadvantage that plasmonic nanostructures are fixed in space, which limits the speed and versatility of the trapping process. As we show here, plasmonic nanodisks fabricated over dielectric microrods provide a promising approach toward optical nanomanipulation: these hybrid structures can be maneuvered by conventional optical tweezers and simultaneously generate strongly confined optical near-fields in their vicinity, functioning as near-field traps themselves for colloids as small as 40 nm. The colloidal tweezers can be used to transport nanoscale cargo even in ionic solutions at optical intensities lower than the damage threshold of living micro-organisms, and in addition, allow parallel and independently controlled manipulation of different types of colloids, including fluorescent nanodiamonds and magnetic nanoparticles.
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Affiliation(s)
- Souvik Ghosh
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Ambarish Ghosh
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
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