Optimization methods for side-chain positioning and macromolecular docking

This dissertation proposes new optimization algorithms targeting protein-protein docking which is an important class of problems in computational structural biology. The ultimate goal of docking methods is to predict the 3-dimensional structure of a stable protein-protein complex. We study two specific problems encountered in predictive docking of proteins. The first problem is Side-Chain Positioning (SCP), a central component of homology modeling and computational protein docking methods. We formulate SCP as a Maximum Weighted Independent Set (MWIS) problem on an appropriately constructed graph. Our formulation also considers the significant special structure of proteins that SCP exhibits for docking. We develop an approximate algorithm that solves a relaxation of MWIS and employ randomized estimation heuristics to obtain high-quality feasible solutions to the problem. The algorithm is fully distributed and can be implemented on multi-processor architectures. Our computational results on a benchmark set of protein complexes show that the accuracy of our approximate MWIS-based algorithm predictions is comparable with the results achieved by a state-of-the-art method that finds an exact solution to SCP. The second problem we target in this work is protein docking refinement. We propose two different methods to solve the refinement problem. The first approach is based on a Monte Carlo-Minimization (MCM) search to optimize rigid-body and side-chain conformations for binding. In particular, we study the impact of optimally positioning the side-chains in the interface region between two proteins in the process of binding. We report computational results showing that incorporating side-chain flexibility in docking provides substantial improvement in the quality of docked predictions compared to the rigid-body approaches. Further, we demonstrate that the inclusion of unbound side-chain conformers in the side-chain search introduces significant improvement in the performance of the docking refinement protocols. In the second approach, we propose a novel stochastic optimization algorithm based on Subspace Semi-Definite programming-based Underestimation (SSDU), which aims to solve protein docking and protein structure prediction. SSDU is based on underestimating the binding energy function in a permissive subspace of the space of rigid-body motions. We apply Principal Component Analysis (PCA) to determine the permissive subspace and reduce the dimensionality of the conformational search space. We consider the general class of convex polynomial underestimators, and formulate the problem of finding such underestimators as a Semi-Definite Programming (SDP) problem. Using these underestimators, we perform a biased sampling in the vicinity of the conformational regions where the energy function is at its global minimum. Moreover, we develop an exploration procedure based on density-based clustering to detect the near-native regions even when there are many local minima residing far from each other. We also incorporate a Model Selection procedure into SSDU to pick a predictive conformation. Testing our algorithm over a benchmark of protein complexes indicates that SSDU substantially improves the quality of docking refinement compared with existing methods

Multiple sclerosis Lesion Detection via Machine Learning Algorithm based on converting 3D to 2D MRI images

In the twenty first century, there have been various scientific discoveries which have helped in addressing some of the fundamental health issues. Specifically, the discovery of machines which are able to assess the internal conditions of individuals has been a significant boost in the medical field. This paper or case study is the continuation of a previous research which aimed to create artificial models using support vector machines (SVM) to classify MS and normal brain MRI images, analyze the effectiveness of these models and their potential to use them in Multiple Sclerosis (MS) diagnosis. In the previous study presented at the Cognitive InfoCommunication (CogInfoCom 2019) conference, we intend to show that 3D images can be converted into 2D and by considering machine learning techniques and SVM tools. The previous paper concluded that SVM is a potential method which can be involved during MS diagnosis, however, in order to confirm this statement more research and other potentially effective methods should be included in the research and need to be tested. First, this study continues the research of SVM used for classification and Cellular Learning Automata (CLA), then it expands the research to other method such as Artificial Neural Networks (ANN) and k-Nearest Neighbor (k-NN) and then compares the results of these

Dual-Band RFID Tag Antenna Based on the Hilbert-Curve Fractal for HF and UHF Applications

A novel single-radiator card-type tag is proposed which is constructed using a series Hilbert-curve loop and matched stub for high frequency (HF)/ultra high frequency (UHF) dual-band radio frequency identification (RFID) positioning applications. This is achieved by merging the series Hilbert-curve for implementing the HF coil antenna, and square loop structure for implementing the UHF antenna to form a single RFID tag radiator. The RFID tag has directivity of 1.75 dBi at 25 MHz, 2.65 dBi at 785 MHz, 2.82 MHz at 835 MHz and 2.75 dBi at 925 MHz. The tag exhibits circular polarisation with -3 dB axial-ratio bandwidth of 14, 480, 605 and 455 MHz at 25, 785, 835 and 925 MHz, respectively. The radiation characteristics of the RFID tag is quasi-omnidirectional in its two orthogonal planes. Impedance matching circuits for the HF/UHF dual-band RFID tag are designed for optimal power transfer with the microchip. The resulting dual-band tag is highly compact in size and possesses good overall performance which makes it suitable for diverse applications

Bandwidth extension of planar antennas using embedded slits for reliable multiband RF communications

In this paper a technique is described to extend the impedance bandwidth of patch antennas without compromising their size. This is accomplished by embedding capacitive slits in the rectangular patch with a truncated ground-plane, and exciting the antenna through a meandered strip-line feed. The proposed antenna was fabricated on standard FR-4 substrate with permittivity of 4.6, thickness of 0.8 mm and loss-tangent of 0.001. The performance of the prototype antenna was verified through measurements. Characteristics of the antenna include an impedance bandwidth of 5.25 GHz (800 MHz–6.05 GHz) for VSWR<2 corresponding to a fractional bandwidth of 153.28%, peak gain of 5.35 dBi, radiation efficiency of 84.12% at 4.45 GHz, and low cross-polarization. These attributes make the antenna applicable for stable and reliable multiband applications in the UHF, L, S and major part of C-bands. The antenna offers advantages of low cost, low profile, ease of manufacturing, durability and conformability

Disability and therapeutic response in paediatric neuromyelitis optica spectrum disorder: A case series from Iran

                                                                                         ABSTRACT Objectives:The characteristics of paediatric neuromyelitis optica spectrum disorder (NMOSD) may indicate the degree of disability and identify factors that predict the response to treatment.Materials &amp; MethodsAmong 114 NMOSD patients in an acquired demyelinating syndromes registry at the Sina Hospital, in Tehran, Iran, 10 paediatric NMOSD patients with longitudinal follow-up from 2005 to 2016 were retrospectively identified. The median time between disease onset and diagnosis was 18 months (range 1-108 months).ResultsAll patients had a relapsing course, which resulted in disability in six with severe visual impairment and functional blindness in one and impaired ambulation in five patients during follow-up. Azathioprine (AZA) was first drug of choice for prophylaxis, but in five patients new attacks occurred and therapy was switched to rituximab (RTX) with no further relapses after median two years (range 1-3 y) follow-up.Conclusion:Paediatric onset of NMOSD was associated with severe attacks and poor response in 50 % of cases to AZA, RTX seemed to decrease the relapse rate

Planar Antennas with Enhanced Bandwidth and Radiation Characteristics

Wireless companies want next-generation gadgets to download at rates of gigabits per second. This is because there is an exponential growth in mobile traffic, however, existing digital networks and devices will not be efficient enough to handle this much growth. In order to realize this requirement, the next generation of wireless communication devices will need to operate over a much larger frequency bandwidth. In this chapter, novel wideband and ultra-wideband (UWB) antennas that are based on loading the background plane of a monopole radiator with concentric split-ring resonators are presented. It is shown that this modification improves the fractional bandwidth of the antenna from 41 to 87%; in particular, the operational bandwidth of the proposed antennas is double that of a conventional monopole antenna of the same size

Periodic array of complementary artificial magnetic conductor metamaterials-based multiband antennas for broadband wireless transceivers

This study presents the empirical results of a low-profile light-weight antenna based on a periodic array of the complementary artificial magnetic conductor metamaterial structure, which is realised by loading the antenna with E-shaped slits and inductive microstrip lines grounded using metallic via-holes. The finalised prototype antenna operates over a broadband of 0.41–4.1 GHz, which corresponds to a fractional bandwidth of 165.84%, and has dimensions of 40mm × 35mm × 1.6mm or 0.054λo × 0.047λo × 0.0021λo, where λo is free-space wavelength at operating frequency of 410 MHz. The finalised antenna has a peak gain and radiation efficiency of 4.45 dBi and 85.8%, respectively, at 2.76 GHz. At the lower operating frequency of 410 MHz, the gain and radiation efficiency are 1.05 dBi and 32.5%, respectively, which is normally highly challenging to realise with very small antennas. The planar nature of antenna enables easy integration with wireless transceivers

Traveling-wave antenna based on metamaterial transmission line structure for use in multiple wireless communication applications

This paper introduces a left-handed metamaterial traveling-wave antenna (TWA) based on metamaterial transmission-line structure to enhance the gain and radiation efficiency of the antenna without trading on its fractional bandwidth. The antenna consists of a series of coupled unit-cells comprising ‘‘X-shaped” slots which are inductively terminated to ground. Effective aperture of the antenna can be increased by increasing the number of unit-cells. The consequence of this is enhanced gain and radiation efficiency performance with no adverse affect on its fractional bandwidth. The antenna’s characterizing parameters were extracted using 3D electromagnetic simulation tool (HFSSTM), and the antenna was fabricated using standard PCB manufacturing techniques on a 1.6 mm thick dielectric substrate with permittivity of 2.2. The antenna operates from 0.4 GHz to 4.7 GHz. The antenna has an electrical size of 0.017Lamda_o x 0.006Lamda_o x 0.002Lamda_o, where Lamda_o is free space wavelength at 400 MHz. The proposed antenna is significantly smaller than its conventional counterparts. Antenna’s measured optimum gain and radiation efficiency are 2 dBi and 65%, respectively, at 2.5 GHz. These features make the antenna attractive for use in multiple wireless communication applications

Metamaterial Based Ultra-Wideband Antennas for Portable Wireless Applications

Antennas are essential for wireless communication systems. The size of a conventional antenna is dictated mainly by its operating frequency. With the advent of ultra-wideband systems (UWB), the size of antennas has become a critical issue in the design of portable wireless devices. Consequently, research and development of suitably small and highly compact antennas are challenging and have become an area of great interest among researchers and radio frequency (RF) design engineers. Various approaches have been reported to reduce the physical size of RF antennas including using high permittivity substrates, shorting pins, reactive components, and more recently, metamaterials (MTM) based on composite right-/left-handed transmission-lines (CRLH-TLs). MTM exhibit unique electromagnetic response that cannot be found in the nature. In this chapter, the properties of CRLH-TL are used to synthesize novel and highly compact planar UWB antennas with radiation properties suitable for wireless mobile devices and systems