Efe Ilker

Bio: Efe Ilker is an academic researcher from PSL Research University. The author has contributed to research in topics: Metamaterial & Phase transition. The author has an hindex of 11, co-authored 28 publications receiving 758 citations. Previous affiliations of Efe Ilker include Max Planck Society & Case Western Reserve University.

Extreme sensitivity biosensing platform based on hyperbolic metamaterials

Abstract: Optical sensor technology offers significant opportunities in the field of medical research and clinical diagnostics, particularly for the detection of small numbers of molecules in highly diluted solutions. Several methods have been developed for this purpose, including label-free plasmonic biosensors based on metamaterials. However, the detection of lower-molecular-weight (<500 Da) biomolecules in highly diluted solutions is still a challenging issue owing to their lower polarizability. In this context, we have developed a miniaturized plasmonic biosensor platform based on a hyperbolic metamaterial that can support highly confined bulk plasmon guided modes over a broad wavelength range from visible to near infrared. By exciting these modes using a grating-coupling technique, we achieved different extreme sensitivity modes with a maximum of 30,000 nm per refractive index unit (RIU) and a record figure of merit (FOM) of 590. We report the ability of the metamaterial platform to detect ultralow-molecular-weight (244 Da) biomolecules at picomolar concentrations using a standard affinity model streptavidin-biotin.

Phase-change-material-based low-loss visible-frequency hyperbolic metamaterials for ultrasensitive label-free biosensing

Abstract: DOI: 10.1002/adom.201900081 The extreme anisotropic permittivity of hyperbolic metamaterials (HMMs) represent a unique opportunity to realize effective bulk metastructures with extraordinary optical properties over a broad frequency range from visible to terahertz.[1] HMMs are artificial uniaxial materials that exhibit hyperbolic dispersion because the out of plane dielectric constant (εzz = ε⊥) has an opposite sign to the in-plane dielectric constants (εxx = εyy = εll). HMMs can be classified into two types based on the sign of their dielectric components, i.e., type I (−ε⊥ and εll) and type II (ε⊥ and −εll). In comparison to isotropic materials showing elliptical dispersion, HMMs support propagation of optical modes across the structure with infinitely large momentum (high-k modes) in the effective medium limit,[2,3] irrespective of Hyperbolic metamaterials (HMMs) have emerged as a burgeoning field of research over the past few years as their dispersion can be easily engineered in different spectral regions using various material combinations. Even though HMMs have comparatively low optical loss due to a single resonance, the noble-metal-based HMMs are limited by their strong energy dissipation in metallic layers at visible frequencies. Here, the fabrication of noble-metal-free reconfigurable HMMs for visible photonic applications is experimentally demonstrated. The low-loss and active HMMs are realized by combining titanium nitride (TiN) and stibnite (Sb2S3) as the phase change material. A reconfigurable plasmonic biosensor platform based on active Sb2S3–TiN HMMs is proposed, and it is shown that significant improvement in sensitivity is possible for small molecule detection at low concentrations. In addition, a plasmonic apta-biosensor based on a hybrid platform of graphene and Sb2S3–TiN HMM is developed and the detection and real-time binding of thrombin concentration as low as 1 × 10−15 m are demonstrated. A biosensor operating in the visible range has several advantages including the availability of sources and detectors in this region, and ease of operation particularly for point-of-care applications. Hyperbolic Metamaterials

Enhancing the Angular Sensitivity of Plasmonic Sensors Using Hyperbolic Metamaterials.

Abstract: Surface plasmon resonance (SPR) sensors operate mainly on prism and grating coupling techniques, with spectral and angular scans being the two major interrogation schemes. Among them, the angular scan technique has several advantages including higher measurement precision owing to its higher signal-to-noise ratio. The currently available SPR sensor arrangements provide a maximum angular sensitivity of 500°–600° per RIU. Here, we report the study of grating coupled-hyperbolic metamaterial (GC-HMM) sensors with high angular sensitivity. The experimental studies show extraordinary angular sensitivities from visible to near infrared (NIR) wavelengths by exciting bulk plasmon polaritons associated with hyperbolic metamaterials, with a maximum of 7000° per RIU. This angular-scan plasmonic biosensor has been used for the detection of low molecular weight biomolecules such as biotin (244 Da) and high molecular weight macromolecules such as Cowpea mosaic virus (CPMV, 5.6 × 106 Da) at ultralow concentrations. The miniaturized sensing device can be integrated with microfluidic systems for the development of next-generation biosensors for lab-on-a-chip and point-of-care applications.

Controlling the speed and trajectory of evolution with counterdiabatic driving

Abstract: The pace and unpredictability of evolution are critically relevant in a variety of modern challenges, such as combating drug resistance in pathogens and cancer, understanding how species respond to environmental perturbations like climate change and developing artificial selection approaches for agriculture. Great progress has been made in quantitative modelling of evolution using fitness landscapes, allowing a degree of prediction for future evolutionary histories. Yet fine-grained control of the speed and distributions of these trajectories remains elusive. We propose an approach to achieve this using ideas originally developed in a completely different context—counterdiabatic driving to control the behaviour of quantum states for applications like quantum computing and manipulating ultracold atoms. Implementing these ideas for the first time in a biological context, we show how a set of external control parameters (that is, varying drug concentrations and types, temperature and nutrients) can guide the probability distribution of genotypes in a population along a specified path and time interval. This level of control, allowing empirical optimization of evolutionary speed and trajectories, has myriad potential applications, from enhancing adaptive therapies for diseases to the development of thermotolerant crops in preparation for climate change, to accelerating bioengineering methods built on evolutionary models, like directed evolution of biomolecules. The unpredictability of evolution makes it difficult to deal with drug resistance because over the course of a treatment there may be mutations that we cannot predict. The authors propose to use quantum methods to control the speed and distribution of potential evolutionary outcomes.

Hyperbolic metamaterials-based plasmonic biosensor for fluid biopsy with single molecule sensitivity

Abstract: Plasmonic sensors are one of the most powerful optical biosensors, which can be used for the detection of small numbers of molecules at ultra-low concentrations. However, the detection of dilute analytes of low molecular weight (<500 Da) is still a challenging task using currently available plasmonic biosensors. Here, we demonstrate the detection of both lower and heavier molecular weight biomolecules close to single molecule level using a novel plasmonic biosensor platform based on hyperbolic metamaterials. We show experimentally the extraordinary spectral and angular sensitivities of the biosensor platform, from visible to near infrared (NIR) wavelengths, by exciting the bulk plasmon polaritons associated with hyperbolic metamaterials.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Plasmonic Surface Lattice Resonances: A Review of Properties and Applications

Abstract: When metal nanoparticles are arranged in an ordered array, they may scatter light to produce diffracted waves. If one of the diffracted waves then propagates in the plane of the array, it may couple the localized plasmon resonances associated with individual nanoparticles together, leading to an exciting phenomenon, the drastic narrowing of plasmon resonances, down to 1–2 nm in spectral width. This presents a dramatic improvement compared to a typical single particle resonance line width of >80 nm. The very high quality factors of these diffractively coupled plasmon resonances, often referred to as plasmonic surface lattice resonances, and related effects have made this topic a very active and exciting field for fundamental research, and increasingly, these resonances have been investigated for their potential in the development of practical devices for communications, optoelectronics, photovoltaics, data storage, biosensing, and other applications. In the present review article, we describe the basic phy...

SERS-Activated Platforms for Immunoassay: Probes, Encoding Methods, and Applications

Abstract: Owing to their excellent multiplexing ability, high sensitivity, and large dynamic range, immunoassays using surface-enhanced Raman scattering (SERS) as the readout signal have found prosperous applications in fields such as disease diagnosis, environmental surveillance, and food safety supervision. Various ever-increasing demands have promoted SERS-based immunoassays from the classical sandwich-type ones to those integrated with fascinating automatic platforms (e.g., test strips and microfluidic chips). As recent years have witnessed impressive progress in SERS immunoassays, we try to comprehensively cover SERS-based immunoassays from their basic working principles to specific applications. Focusing on several basic elements in SERS immunoassays, typical structures of SERS nanoprobes, productive optical spectral encoding strategies, and popular immunoassay platforms are highlighted, followed by their representative biological applications in the last 5 years. Moreover, despite the vast advances achieved ...

Plasmonic Biosensing Focus Review

Abstract: Plasmonic biosensing has been used for fast, real-time, and label-free probing of biologically relevant analytes, where the main challenges are to detect small molecules at ultralow concentrations and produce compact devices for point-of-care (PoC) analysis. This review discusses the most recent, or even emerging, trends in plasmonic biosensing, with novel platforms which exploit unique physicochemical properties and versatility of new materials. In addition to the well-established use of localized surface plasmon resonance (LSPR), three major areas have been identified in these new trends: chiral plasmonics, magnetoplasmonics, and quantum plasmonics. In describing the recent advances, emphasis is placed on the design and manufacture of portable devices working with low loss in different frequency ranges, from the infrared to the visible.

Photonic crystals: Emerging biosensors and their promise for point-of-care applications

Abstract: Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.