1-D Metal-Dielectric-Metal Grating Structure as an Ultra-Narrowband Perfect Plasmonic Absorber in the Visible and Its Application in Glucose Detection

The need for an easy to fabricate perfect and narrowband light absorber in the visible range of electromagnetic (EM) spectrum has always been in demand for many scientific and device applications. Here, we propose a metal-dielectric-metal (MDM) 1-D grating plasmonic structure as a perfect narrow band light absorber in the visible and its application in glucose detection. The proposed structure consists of a 1- D grating of gold on the top of a dielectric layer on a gold film. Optimization for dielectric grating index (n), grating thickness (t), grating width (W), and grating period (P) has been done to improve the performance of plasmonic structure by calculating its quality factor and figure-of-merit (FOM). The optimized plasmonic structure behaves as a perfect narrowband light absorber. The flexibility to work at a specific wavelength is also offered by the proposed structure through an appropriate selection of the geometrical parameters and refractive index of the dielectric grating. The equivalent RC model is used to understand different components of the proposed structure on the optical response. The absorption response of the structure is invariant to the incident angle. Moreover, the calculated absorbance of the proposed plasmonic structure is ~ 100% with a narrow full-width half maxima (FWHM) of ~ 2.8 nm. We have numerically demonstrated a potential application of the proposed MDM absorber as a plasmonic glucose sensor in the visible range with detection sensitivity in the range of 140 to 195 nm/RIU.

     

Illusion Properties in Perfect Cylindrical Devices

In this paper, illusion properties in a class of perfect cylindrical devices that contain a singular radial mapping have been reported. In these media, illusion can be implemented using alternating structure of only two kinds of metamaterial: zero index metamaterials and perfect electric conductors. Full-wave simulations in two dimensions have been performed to verify its functionality and its illusionary effects for TM polarization incident wave. The duality principle can be applied for TE polarization.

     

Dual-Band Infrared Perfect Absorber Based on a Ag-Dielectric-Ag Multilayer Films with Nanoring Grooves Arrays

In this paper, we demonstrate a dual-band metamaterial perfect absorber based on a Ag-dielectric-Ag multilayer nanostructure. The structure of top metal film covers nanoring grooves array. A dielectric layer has a function of confining electromagnetic fields. Theoretical analysis shows that two absorption peaks (1059 nm and 1304 nm) with the absorption of 99.2% and 99.9% have been achieved, respectively. The physical origin of perfect absorption peaks are related to the Fabry-Perot resonance effect and localized surface plasmon resonance (LSPR) of the nanoring grooves. Its perfect absorption and resonance wavelength can be well regulated by adjusting the relevant structural parameters. Additionally, the absorber demonstrates good operation angle-polarization-tolerance at wide incident angles (0–60°). We believe that our design has a promising application in plasmon-enhanced photovoltaic, optical absorption switching, and modulator optical communications in the infrared regime.

     

Numerical Study of an Au-ZnO-Al Perfect Absorber for a Color Filter with a High Quality Factor

In this research, a perfect absorber based on an Au-ZnO-Al structure was studied numerically. The wavelength-selective and angle-independent characteristics of the device were demonstrated by simulation. The roles of the top metallic layer and the middle dielectric layer in producing a wavelength-selective perfect absorber with a high quality factor were investigated. The direction for further improving the quality factor is also pointed out in this paper. The research will be helpful for understanding the origination of perfect absorption in these types of metal-insulator-metal structures and producing a color filter with a high quality factor.

     

Wideband Graphene-Based Fractal Absorber and its Applications as Switch and Inverter

In this paper, the idea of square fractal geometry has been utilized to introduce a tunable wideband graphene-based perfect plasmonic absorber in the near-infrared region. It consists of a MgF₂ layer and an array of gold squares fractal loaded on a graphene layer. In the designed absorber a single layer of graphene has been used instead of multilayered graphene structures. The structure is polarization-insensitive under normal incidence due to the geometric symmetry. The absorption and bandwidth of the structure are almost insensitive to the incident angle up to 15° and 45° for TE and TM polarizations, respectively. Moreover, by choosing appropriate structural parameters, the resonance wavelength of the desired plasmonic absorber can be controlled. The absorption of the introduced structure can be tuned by changing the chemical potential of the graphene. Therefore, the proposed fractal absorber can act as switch and inverter at λ = 1995 nm. Furthermore, the equivalent circuit model of the absorber has been derived to confirm the validity of the simulation results. The superiorities of our fractal absorber are wide full-width at half-maximum of 406 nm, multi-applicant, perfect absorption, and fabrication feasibility due to the simple structure with the maximum absorption tolerance error of 5.12%.

     

Numerical Investigation of the Instability-Based Power Emission from an Ungated Plasmonic HEMT Using Complete Hydrodynamic Model

The full-wave analysis of the Dyakonov–Shur instability in an ungated short-channel high electron mobility transistor (HEMT) is investigated in this paper. This mechanism causes the emission of electromagnetic radiations by the device. The accurate analysis of the device is important especially when large electric fields are present. Herein, to analyze such structures, the complete hydrodynamic model, which is the simultaneous solution of Maxwell’s equations and the first three moments of the Boltzmann transport equation, is used. This model well describes the electron-wave interactions by considering the transport parameter variations with the electron energy and temperature. These variations are especially considerable when the emitter operates at high electromagnetic fields and were not considered in previous studies. The obtained results demonstrate the oscillation current along the channel and consequently the radiated power of the device are severely influenced by the transport parameter variations. The developed analysis method describes the behavior of the device as a terahertz emitter more accurately than the available ones.

     

Terahertz Dual-Band Polarization Insensitive Electromagnetically Induced Transparency-Like Metamaterials

In this paper, an electromagnetically induced transparency-like metamaterial for terahertz is designed. The structure is based on cross-shaped and SRRs composite elements. It can achieve dual-frequency transparent window in a wide frequency band and is insensitive to electromagnetic wave polarization. The resonance points of transmission peaks are 198.55 and 254.18 GHz, respectively. The electromagnetic transmittance can reach 95.6% and 97.7%, respectively, which has excellent electromagnetic transmission effect. The measured results are in good agreement with the trend of simulation curve. At the same time, flexible polyimide with stable performance is selected as the base material of metamaterial dielectric, which can be widely used in microwave fields such as filters, sensors, and slow light devices.

     

Design of Polarization Independent SERS Substrate with Raman Gain Evaluated Using Purcell Factor

Surface-enhanced Raman scattering (SERS) is a very promising detection/diagnostic technique at trace levels as the molecules exhibit a significant increase in their Raman signals when they are attached or are in proximity to plasmonic structures. In this study, a numerical design of SERS substrate as a probe has been demonstrated for detection and diagnosis of blood, water and urea samples. The proposed nanospiral design is polarization independent, and it offers the enhancement of the electric field strength ~ 10⁹. The substrate design is based on 3D finite difference time domain simulations and is robust, versatile and sensitive even at low concentrations of the analyte. It works equally well when used in the reflection mode. In this study, the cavity quantum electrodynamics (CQED) Purcell factor has also been transposed to plasmonics. The Purcell factor in corroboration with CQED has been used to achieve efficient light–matter interaction at nanoscale by providing a more realistic result. It takes into account the randomness of incident wave polarizations and arbitrary orientations of interacting molecules. This gives a deeper insight into electromagnetic Raman gain in SERS and can be used to design novel SERS substrates.

     

Dielectrophoretic separation of monocytes from cancer cells in a microfluidic chip using electrode pitch optimization

This study proposes a microfluidic device capable of separating monocytes from a type of cancer cell that is called T-cell acute lymphoblastic leukemia (RPMI-8402) in a continuous flow using negative and positive dielectrophoretic forces. The use of both the hydrodynamic and dielectrophoretic forces allows the separation of RPMI-8402 from monocytes based on differences in their intrinsic electrical properties and sizes. The specific crossover frequencies of monocytes and RPMI-8402 cells have been obtained experimentally. The optimum ranges of electrode pitch-to-channel height ratio at the cross sections with different electrode widths have been generally calculated by numerical simulations of the gradients of the electric field intensities and calculation their effective values (root-mean-square). In the device, the cell sorting has been conducted empirically, and then, the separation performance has been evaluated by analyzing the images before and after dielectrophoretic forces applied to the cells. In this work, the design of a chip with 77 μm gold–titanium electrode pitch was investigated to achieve high purity of monocytes of 95.2%. The proposed device can be used with relatively low applied voltages, as low as 16.5 V (peak to peak). Thus, the design can be used in biomedical diagnosis and chemical analysis applications as a lab-on-chip platform. Also, it can be used for the separation of biological cells such as bacteria, RNA, DNA, and blood cells.

     

Tunable and Multichannel Terahertz Perfect Absorber Due to Tamm Plasmons with Topological Insulators

In this paper, Tamm plasmons with topological insulators in a composite structure consisting of Bi₂Se₃, spacer layer, and one-dimensional photonic crystal (1DPC) have been demonstrated theoretically. The perfect absorption has been realized in the terahertz regime because of the optical Tamm states (OTSs) excited at the interface between Bi₂Se₃ and 1DPC. The perfect absorption can be realized for both TE and TM waves, and it is noted that the perfect absorption can be obtained at any incident angle by simultaneously changing the wavelength of incident light for TE-polarizations. Moreover, the perfect absorption can be realized at different wavelengths with the change of the chemical potential and the thickness of Bi₂Se₃. The thickness and the dielectric constant of the spacer layer will also play a vital role in the performance of the perfect absorber. Especially, the multichannel perfect absorption phenomenon can be achieved by choosing the appropriate thickness of the spacer layer. This tunable and multichannel terahertz perfect absorber has great application potential in the solar energy, photodetection, and THz biosensor.

     

Molecular dynamics simulation of liquid water under the influence of an external electric field

Molecular dynamics simulations of liquid water were performed at 258K and a density of 1.0?g/cm³ under various applied external electric field, ranging 0～10¹⁰?V/m. The influence of external field on structural and dynamical properties of water was investigated. The simple point charge (SPC) model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bonds structure. With increasing field strength, water system has a more perfect structure, which is similar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected since the self-diffusion coefficient was very large. The self-diffusion coefficient decreases remarkably with increasing strength of electric field and the self-diffusion coefficient is anisotropic.     

Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

The Na⁺-translocating NADH:quinone oxidoreductase (Na⁺-NQR) is the major Na⁺ pump in aerobic pathogens such as Vibrio cholerae. The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na⁺-NQR. While the mechanisms underlying Na⁺-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na⁺-NQR. An in silico model of the NqrB–D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na⁺-NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB–D interface underwent a non-physiological transition after 350 ns.

     

Molecular Dynamics Simulation of Nucleation and Growth of a Binary Quasicrystal

Abstract

The quasicrystal structure is considered to be a new type of ordered phase because its Fourier transform has Laue spots with icosahedral symmetry, which is inconsistent with crystal structure. Computer simulation of the formation process of a quasicrystal was performed by the molecular dynamics method. On the basis of the Strandburg type of quasicrystal model, we developed an algorithm of the formation process of binary quasicrystal reflecting the procedure as realistically as possible. The Fourier transform of some of the obtained structures has shown decagonal symmetry although the spots are rather diffused. It has been shown that the potential parameter and experimental condition should be limited to produce a perfect quasicrystal structure.     

A Strong to Fragile Transition in a Model of Liquid Silica

Abstract

The transport properties of an ionic model for liquid silica [1] at high temperatures and pressure are investigated using molecular dynamics simulations. With increasing pressure, a clear change from “strong” to “fragile” behaviour (according to Angell's classification of glass-forming liquids) is observed, albeit only on the small viscosity range that can be explored in MD simulations. This change is related to structural changes, from an almost perfect four-fold coordination to an imperfect five or six-fold coordination.     

Molecular insight into conformational transformation of human glucokinase: conventional and targeted molecular dynamics

Abstract

Glucokinase (GK) plays a key role in the regulation of hepatic glucose metabolism. An unusual mechanism of positive cooperativity of monomeric GK containing only a single binding site for glucose is very interesting and still unclear. The activation process of GK is associated with a large-scale conformational change from the inactive to the active state. Here, conventional and targeted molecular dynamics simulations were used to study the conformational dynamics of GK in the stable configurations and in the transition from active to inactive state. Three phases of the structural reorganization of GK were detected. The first step is a transformation of GK from the active state to the intermediate structure, where the cleft between the domains is open, but alpha helix 13 is still inside the small domain. From this point, there are two alternative paths. One path leads to the inactive state through the release of helix 13 from the inside of small domain to the outside. Other path goes back to the active state. Simulation results reveal the critical role of helix 13 in the transformation of GK from the open state to inactive one and the influence of the loop 2 on the protein transformation between the open and the closed active states. Principal component analysis and covariance matrix analysis were carried out to analyze the dynamics of protein. Importance of hydrogen bonds in the stability of the closed conformation is shown. Overall, our simulations provide new information about the dynamics of GK and its structural transformation.

Communicated by Ramaswamy H. Sarma     

Theoretical models for branch formation in plants

Various branch architectures are observed in living organisms including plants. Branch formation has traditionally been an area of interest in the field of developmental biology, and theoretical approaches are now commonly used to understand the complex mechanisms involved. In this review article, we provide an overview of theoretical approaches including mathematical models and computer simulations for studying plant branch formation. These approaches cover a wide range of topics. In particular, we focus on the importance of positional information in branch formation, which has been especially revealed by theoretical research in plants including computations of developmental processes.

     

XXIst century magnetotherapy

Abstract

This paper discusses the state of the art therapeutic application of magnetic and electromagnetic fields (EMF) in treatment of various medical problems – from pain relief to musculoskeletal trauma, to vascular and endocrine disorders. The paper describes problems related to physical parameters of used fields, biophysical dosimetry, clinical protocols, and safety of the device operators. Clinical benefits and mechanisms of action are also discussed.     

Molecular dynamics simulation of the size-dependent morphological stability of cubic shape silver nanoparticles

The morphological stability of sharp-edged silver nanoparticles is examined by the classical molecular dynamics (MD) simulations. The crystalline structure and the perfect fcc atom packing of a series of silver nanocubes (AgNC) of different sizes varying from 63 up to 1099 atoms are compared against quasi-spherical nanoparticles of the same sizes at temperature 303 K. Our MD simulations demonstrate that starting from the preformed perfect crystalline structures the cubic shape is preserved for AgNCs composed of 365–1099 atoms. Surprisingly, the rapid loss of the cubic shape morphology and transformation into the non-fcc-structure are found for smaller AgNCs composed of less than ~256 atoms. No such loss of the preformed crystalline structure is seen for quasi-spherical nanoparticles composed of 38–1007 atoms. The analysis of the temperature dependence and the binding energy of outermost Ag surface atoms suggests that the loss of the perfect cubic shape, rounding and smoothing of sharp edges and corners are driven by the tendency towards the increase in their coordination number. In addition, we revealed that AgNC₁₀₉₉ partially loses its sharp edges and corners in the aqueous environment; however, the polymer coating with poly(vinyl alcohol) (PVA) was able to preserve the well-defined cubic morphology. Finally, these results help improve the understanding of the role of surface capping agents in solution phase synthesis of Ag nanocubes.     

An improved procedure for transformingArabidopsis thaliana (Landsbergerecta) root explant

Agrobacterium tumefaciens-mediated transformation has been widely used in molecular characterization of genes inArabidopsis thaliana. A number of procedures have been developed for transformation ofArabidopsis explants usingAgrobacterium. This paper describes an improved protocol for transformation ofArabidopsis thaliana root explants. Most significantly, using this protocol one can achieve efficient root regeneration of transformation in Landsbergerecta, an ecotype which is widely used in genetic and molecular analyses and which has been difficult to transform in the past. Additional modifications allow easy production of roots for transformation and regeneration of large numbers of transformation t shoots.     

Precision medicine in human heart modeling

Precision medicine is a new frontier in healthcare that uses scientific methods to customize medical treatment to the individual genes, anatomy, physiology, and lifestyle of each person. In cardiovascular health, precision medicine has emerged as a promising paradigm to enable cost-effective solutions that improve quality of life and reduce mortality rates. However, the exact role in precision medicine for human heart modeling has not yet been fully explored. Here, we discuss the challenges and opportunities for personalized human heart simulations, from diagnosis to device design, treatment planning, and prognosis. With a view toward personalization, we map out the history of anatomic, physical, and constitutive human heart models throughout the past three decades. We illustrate recent human heart modeling in electrophysiology, cardiac mechanics, and fluid dynamics and highlight clinically relevant applications of these models for drug development, pacing lead failure, heart failure, ventricular assist devices, edge-to-edge repair, and annuloplasty. With a view toward translational medicine, we provide a clinical perspective on virtual imaging trials and a regulatory perspective on medical device innovation. We show that precision medicine in human heart modeling does not necessarily require a fully personalized, high-resolution whole heart model with an entire personalized medical history. Instead, we advocate for creating personalized models out of population-based libraries with geometric, biological, physical, and clinical information by morphing between clinical data and medical histories from cohorts of patients using machine learning. We anticipate that this perspective will shape the path toward introducing human heart simulations into precision medicine with the ultimate goals to facilitate clinical decision making, guide treatment planning, and accelerate device design.