003. NU Research Institutes & Centres
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Item Open Access 2D nucleation of CdSe on FTO/glass(The 6th International Conference on Nanomaterials and Advanced Energy Storage Systems. Institute of Batteries LLP, Nazarbayev University, and PI “National Laboratory Astana”., 2018-08-08) Khussurova, Gulnur; Puzikova, Darya; Dergacheva, Margarita; Urazov, KazhmuhanCadmium selenide is an important photovoltaic material due to its high absorption coefficient and optimal band gap (1.7 eV) for efficient absorption and conversion of solar radiation. The influence of nanostructures on the behavior of CdSe anodes in photovoltaic cells leads to an interest in the study of its electrochemical deposition process and the peculiarities of nucleation and growth of semiconductor precipitation. However, the growth processes in the electrochemical deposition of cadmium selenide remain little investigated....Item Open Access 3D PRINTING OF HIGH-PERFORMANCE ELECTRODES FOR ALL-SOLID-STATE RECHARGEABLE LITHIUM-ION BATTERIES(National Laboratory Astana, 2022-08) Nnwaogu, Emmanuel Chisom; Nurpeissova, Arailym; Kalimuldina, Gulnur; Bakenov, ZhumabayThree-Dimensional (3D) electrode architecture of lithium-ion batteries (LIBs) is a new generation energy storage system with high energy and high-power capacity to satisfy high consumer demands, especially for its application in biomedical, electrical vehicles, and portable electronics.Item Metadata only 5 Patient specific in situ 3D printing(Woodhead Publishing, 2017-01-01) Akilbekova, Dana; Mektepbayeva, Damel; Dana, AkilbekovaAbstract In this chapter, we will focus on how 3D printer technology is transforming traditional medicine into a personalized approach, giving an overview of the technology advancement and its clinical applications. First, we will discuss why personalization in medicine is required, its benefits for the patients and how 3D printing technology can address this need for the patient specific treatment solutions. Basic capabilities of 3D printers and the three most common 3D printing technologies used in medical applications will be covered as well. The second section focuses on current and potential medical applications of 3D printing. The main medical applications can be arranged into three categories: (1) 3D bioprinting of organs and tissues; (2) patient specific medical devices: prosthetics and implants; and (3) 3D models for surgical preparation. Here, we will discuss 3D printing of living cells, in situ 3D bioprinting directly to the defect site, some successful cases of the implantation of various 3D constructs and the production of precise anatomical models for surgical trainings. Lastly, we will highlight challenges and emerging technology developments for the printing of functional organ constructs and medical devices.Item Open Access A design for large-area fast photo-detectors with transmission-line readout and waveform sampling(In Real Time Conference, 2009. RT'09. 16th IEEE-NPSS (pp. 49-61). IEEE., 2009) Adams, B.; Anderson, J. T.; Attenkofer, K.; Bogdan, M.; Byrum, K.; Drake, G.; Insepov, Z.We present a preliminary design and the results of simulation for a photo-detector module to be used in applications requiring the coverage of areas of many square meters with time resolutions less than 10 picoseconds and position resolutions of less than a millimeter for charged particles. The source of light is Cherenkov light in a radiator/window; the amplification is provided by panels of micro-pores functionalized to act as microchannel plates (MCPs). The good time and position resolution stems from the use of an array of parallel 50 Ω transmission lines (strips) as the collecting anodes. The anode strips feed multi-GS/sec sampling chips which digitize the pulse waveform at each end of the strip, allowing a measurement of the time from the average of the two ends, and a 2-dimensional position measurement from the difference of times on a strip, and, in the orthogonal direction, the strip number, or a centroid of the charges deposited on adjacent strips. The module design is constructed so that large areas can be `tiled' by an array of modules.Item Open Access A General Model of Vacuum Arcs in Linacs(Proceedings of NAPAC2016, Chicago, IL, USA, 2017-01) Norem, J.; Insepov, Z.We are developing a general model of breakdown and gradient limits that applies to accelerators, along with other high field applications such as power grids and laser ablation. We have considered connections with failure modes of integrated circuits, sheath properties of dense, non-Debye plasmas and applications of capillary wave theory to rf breakdown in linacs. In contrast to much of the rf breakdown effort that considers one physical mechanism or one experimental geometry, we find an enormous volume of relevant material in the literature that helps to constrain our model and suggest experimental tests.Item Open Access A Low-Cost Open-Source 3-D-Printed Three-Finger Gripper Platform for Research and Educational Purposes(IEEE Access, 2015-06-02) Telegenov, Kuat; Tlegenov, Yedige; Shintemirov, AlmasRobotics research and education have gained significant attention in recent years due to increased development and commercial deployment of industrial and service robots. A majority of researchers working on robot grasping and object manipulation tend to utilize commercially available robot-manipulators equipped with various end effectors for experimental studies. However, commercially available robotic grippers are often expensive and are not easy to modify for specific purposes. To extend the choice of robotic end effectors freely available to researchers and educators, we present an open-source lowcost three-finger robotic gripper platform for research and educational purposes. The 3-D design model of the gripper is presented and manufactured with a minimal number of 3-D-printed components and an off-the-shelf servo actuator. An underactuated finger and gear train mechanism, with an overall gripper assembly design, are described in detail, followed by illustrations and a discussion of the gripper grasping performance and possible gripper platform modifications. The presented open-source gripper platform computer-aided design model is released for downloading on the authors research lab website(www.alaris.kz) and can be utilized by robotics researchers and educators as a design platform to build their own robotic end effector solutions for research and educational purposes.Item Open Access A model of rf breakdown arcs(Fermilab, 2008) Insepov, Z.; Bross, A.; Qian, Z.; Norem, J.; Huang, D.; Veitzer, S.; Torun, Y.This paper presents a rst iteration of a model that attempts to describe all aspects of breakdown in rf cavities and provides some estimates of the parameters and parameter ranges involved, as an aid to producing more precise models and more useful experiments. The model describes how breakdown events can be triggered, how they grow, it identi es the power source for their rapid growth, mechanisms that limit their growth, how they are extinguished and how they can be mitigated. We also discuss applications to superconducting rf and high pressure gas structures. The model relies heavily on previous experiments with 805 and 201 MHz warm copper cavities, and pre-liminary plasma modeling using the code OOPIC Pro. We compare estimates from the model with experimental data where this is possible. Because of the geometrical dependence of all parameters, the wide range of experiments being performed, the wide range of experimental parameters in a given breakdown event and the lack of extensive systematic parameter searches at this stage in our studies, it is diffcult to present precise results. We are constrained to showing what mechanisms are involved, the strength of these mechanisms and how they interact to produce the experimental data. We are primarily interested in the development and dynamics of the arc, magnetic and gas effects and insights on how to avoid arcing in all environments.Item Open Access A New Multiscale Approach to Nuclear Fuel Simulations: Atomistic Validation of Kinetic Method(Transactions of the American Nuclear Society, 2010) Insepov, Z.; Rest, J.; Hofman, G. L.; Yacout, A.; Norman, G. E.; Starikov, S. A.; Stegailov, V. V.A key issue for fuel behavior codes is their sensitivity to values of various materials properties, many of which have large uncertainties or have not been measured. Kinetic mesoscale models, such as those developed at Argonne National Laboratory within the past decade, are directly comparable to data obtained from in-reactor experiments. In the present paper, a new multiscale concept is proposed that consists of using atomistic simulation methods to verify the kinetic approach. The new concept includes kinetic rate-equations for radiation damage, energetics and kinetics of defects, and gas/defect-driven swelling of fuels as a function of temperature and burnup. The quantum and classical atomistic simulation methods are applied to increase our understanding of radiation damage and defect formation and growth processes and to calculate the probabilities of elemental processes and reactions that are applicable to irradiated nuclear materials.Item Metadata only A new step in the development of Zn/LiFePO4 aqueous battery(2017-01-01) Molkenova, A.; Belgibayeva, A.; Ibrayeva, D.; Sultanov, M.; Zhumagali, S.; Akhmetova, N.; Hara, T.; Bakenov, Z.; A., MolkenovaAbstract In recent years, aqueous batteries have gained much attention due to their low production cost and exceptional safety compared to commercial Li-ion battery systems. Three-dimensional (3D) structure could be promising to enhance these batteries energy capacity. In this work, the electrochemical performance of 3D Zn electrode, developed for aqueous rechargeable Zn/LiFePO4 (Zn/LFP) battery system, was studied. Formation of uniformly coated Zn metal on the three-dimensionally organized carbon fibers was verified by field emission scanning electron microscopy (FE-SEM). The electrochemical performance of the battery with this anode was tested for over 50 cycles, where the initial capacity decayed by 11%. Further, poly(methyl methacrylate) (PMMA) and poly(p-phenylene oxide) (PPO) polymer coatings were extensively investigated as a potential separator for the 3D aqueous battery system. Cyclability of PMMA-coated Zn anode was better than that of “plane” Zn; however, the initial capacity of 3D Zn anode was lower than that for the counterpart system.Item Open Access A novel approach for determining the optimal number of independent components for reproducible cancer transcriptomes data analysis(National Laboratory Astana, Nazarbayev University, 2017-09-15) Kairov, U.; Cantini, L.; Greco, A.; Molkenov, A.; Czerwinska, U.; Barillot, E.; Zinovyev, A.Item Open Access A Personal View on a Zero Carbon Future(International Scientific and University Conference. "Climate Change and CO2 Emission Reduction" 12-13 July, 2017, 2017-07-12) Winter, AxelItem Open Access A real-time multiplex PCR assay for the detection of Salmonella Enteritidis(National Laboratory Astana, Nazarbayev University, 2017-09-15) Tarlykov, P.; Atavlieva, S.; Ramanculov, E.Item Open Access A simple approach to synthesize novel sulfur/graphene oxide/multiwalled carbon nanotube composite cathode for high performance lithium/sulfur batteries(Ionics. Springer-Verlag Berlin Heidelberg 2016, 2016-04-30) Yuan, Guanghui; Zhao, Yan; Jin, Huafeng; Bakenov, ZhumabayA sulfur/graphene oxide/multiwalled carbon nanotube (S/GO/MWNT) composite was synthesized via a simple ultrasonic mixing method followed by heat treatment. By taking advantage of this solution-based self-assembly synthesis route, poisonous and noxious reagents and complicated fabrication processes are rendered unnecessary, thereby simplifying its manufacturing and decreasing the cost of the final product. Transmission and scanning electronic microscopy observations indicated the formation of the threedimensional interconnected S/GO/MWNTcomposite through the environmentally friendly process...Item Open Access A targeted sequencing reveal overlapping pattern of genetic variants in patients with cardiomyopathy with cardiac arrhythmias in Kazakhstan(2016-05) Akilzhanova, A.; Guelly, Ch.; Abilova, Zh.; Rakhimova, S.; Akhmetova, A.; Kairov, U.; Nuralinov, O.; Rashbayeva, G.; Trajanoski, S.; Zhumadilov, Zh.; Bebosynova, M.Ventricular tachycardia (VT) is a common symptom in cardiac disorders of different etiology. Abnormalities of ion channels are attributed to mutations in the genes encoding the channel protein and cause altered function of channels, which can predispose to arrhythmias. Due to the high incidence of cardiovascular disorders in Kazakhstan, we enrolled a study cohort of 95 patients of different clinical phenotypes of cardiomyopathies, including DCM, idiopathic VT but also patients with myocardial infarction as a consequence of coronary heart disease. The common denominator among the three main groups was the occurrence of severe episodes of VT in all patients. Using targeted resequencing, we investigated 96 cardiomyopathy associated candidate-genes in this cohort with the aim to detect rare and common variations in these genes associated with VT molecular basisItem Metadata only Aberrant base excision repair pathway of oxidatively damaged DNA: Implications for degenerative diseases(Free Radical Biology and Medicine, 2017-06-01) Talhaoui, Ibtissam; Matkarimov, Bakhyt T.; Tchenio, Thierry; Zharkov, Dmitry O.; Saparbaev, Murat K.; Ibtissam, TalhaouiAbstract In cellular organisms composition of DNA is constrained to only four nucleobases A, G, T and C, except for minor DNA base modifications such as methylation which serves for defence against foreign DNA or gene expression regulation. Interestingly, this severe evolutionary constraint among other things demands DNA repair systems to discriminate between regular and modified bases. DNA glycosylases specifically recognize and excise damaged bases among vast majority of regular bases in the base excision repair (BER) pathway. However, the mismatched base pairs in DNA can occur from a spontaneous conversion of 5-methylcytosine to thymine and DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved special DNA repair systems that target the non-damaged DNA strand in a duplex to remove mismatched regular DNA bases. Mismatch-specific adenine- and thymine-DNA glycosylases (MutY/MUTYH and TDG/MBD4, respectively) initiated BER and mismatch repair (MMR) pathways can recognize and remove normal DNA bases in mismatched DNA duplexes. Importantly, in DNA repair deficient cells bacterial MutY, human TDG and mammalian MMR can act in the aberrant manner: MutY and TDG removes adenine and thymine opposite misincorporated 8-oxoguanine and damaged adenine, respectively, whereas MMR removes thymine opposite to O6-methylguanine. These unusual activities lead either to mutations or futile DNA repair, thus indicating that the DNA repair pathways which target non-damaged DNA strand can act in aberrant manner and introduce genome instability in the presence of unrepaired DNA lesions. Evidences accumulated showing that in addition to the accumulation of oxidatively damaged DNA in cells, the aberrant DNA repair can also contribute to cancer, brain disorders and premature senescence. For example, the aberrant BER and MMR pathways for oxidized guanine residues can lead to trinucleotide expansion that underlies Huntington's disease, a severe hereditary neurodegenerative syndrome. This review summarises the present knowledge about the aberrant DNA repair pathways for oxidized base modifications and their possible role in age-related diseases.Item Open Access Aberrant DNA glycosylase-initiated repair pathway of free radicals induced DNA damage: implications for age-related diseases and natural aging(Biopolymers and Cell. doi: http://dx.doi.org/10.7124/bc.000943, 2017) Matkarimov, B.; Saparbaev, M.Aerobic cellular respiration generates reactive oxygen species (ROS), which can damage macro-molecules including lipids, proteins and DNA. It was proposed that aging is a consequence of accumulation of naturally occurring unrepaired oxidative DNA damage. In human cells, approximately 2000 to 8000 DNA lesions occur per hour in each cell, i.e. 40000 to 200000 per cell per day. DNA repair systems are able to discriminate between regular and modified bases. For example, DNA glycosylases specifically recognize and excise damaged bases among vast majority of regular bases in the base excision repair (BER) pathway. However, mismatched pairs between two regular bases occur due to spontaneous conversion of 5-methylcytosine to thymine and DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved special DNA repair systems that target the non-damaged DNA strand in a duplex to remove mismatched regular DNA bases. Base excision repair (BER) and mismatch repair (MMR) pathways initiated by mismatch-specific adenine- and thymine-DNA glycosylases (MutY/MUTYH and TDG/MBD4, respectively) can recognize and remove normal DNA bases in mismatched DNA duplexes. Under certain circumstances in DNA repair deficient cells bacterial MutY and human TDG can act in an aberrant manner: MutY and TDG remove Adenine and Thymine opposite to misincorporated 8-oxoguanine and damaged Adenine, respectively. These unusual activities lead either to mutations or futile DNA repair, thus indicating that the DNA repair pathways which target non-damaged DNA strand can act in an aberrant manner and introduce genome instability in the presence of unrepaired DNA lesions. Both accumulation of oxidative DNA damage in cells and the aberrant DNA repair can contribute to cancer, brain disorders and premature senescence.Item Open Access Aberrant repair initiated by mismatch-specific thymine-DNA glycosylases provides a mechanism for the mutational bias observed in CpG islands(Nucleic Acids Research, 2014-04-01) Talhaoui, Ibtissam; Couve, Sophie; Gros, Laurent; Ishchenko, Alexander A.; Matkarimov, Bakhyt; Saparbaev, Murat K.The human thymine-DNA glycosylase (TDG) initiates the base excision repair (BER) pathway to remove spontaneous and induced DNA base damage. It was first biochemically characterized for its ability to remove T mispaired with G in CpG context. TDG is involved in the epigenetic regulation of gene expressions by protecting CpG-rich promoters from de novo DNA methylation. Here we demonstrate that TDG initiates aberrant repair by excising T when it is paired with a damaged adenine residue in DNA duplex. TDG targets the non-damaged DNA strand and efficiently excises T opposite of hypoxanthine (Hx), 1,N6-ethenoadenine, 7,8-dihydro-8-oxoadenine and abasic site in TpG/CpX context, where X is a modified residue. In vitro reconstitution of BER with duplex DNA containing Hx•T pair and TDG results in incorporation of cytosine across Hx. Furthermore, analysis of the mutation spectra inferred from single nucleotide polymorphisms in human population revealed a highly biased mutation pattern within CpG islands (CGIs), with enhanced mutation rate at CpA and TpG sites. These findings demonstrate that under experimental conditions used TDG catalyzes sequence context-dependent aberrant removal of thymine, which results in TpG, CpA→CpGmutations, thus providing a plausible mechanism for the putative evolutionary origin of the CGIs in mammalian genomes.Item Open Access Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli(BIOCHEMISTRY, BIOPHYSICS AND MOLECULAR BIOLOGY, 2018-12-15) Zutterling, Caroline; Mursalimov, Aibek; alhaoui, Ibtissam; Koshenov, Zhanat; Akishev, Zhiger; Bissenbaev, Amangeldy K.; Mazon, Gerard; Geacintov, Nicolas E.; Gasparutto, Didier; Groisman, Regina; Zharkov, Dmitry O.; Matkarimov, Bakhyt T.; Saparbaev, MuratDNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway....Item Open Access Abstract Book of The 8th International Conference on Nanomaterials and Advanced Energy Storage Systems(The 8th International Conference on Nanomaterials and Advanced Energy Storage Systems; Nazarbayev University; National Laboratory Astana; Institute of Batteries, 2020-08)The INESS 2020 topics covered the following and related areas: advanced nanomaterials for energy application, advanced energy storage, conversion and saving systems, materials for electrochemical sensor and electroanalytical applications, catalysis and fuel cells, battery monitoring and management systems, battery safety and utilization, development of electric vehicles and stationary energy storage. The scientists and students from Japan, Korea, France, Germany, China, Russia, Canada, UAE, UK, Turkey and Kazakhstan reviewed and discussed the recent progress and problems in materials science, nanotechnologies, ecology, renewable energy, energy storage systems and modeling methods in these fields.Item Open Access Accelerated Parameter Estimation with DALE X(NURIS; Energetic Cosmos Laboratory, 2017-05-08) Daniel, Scott F.; Linder, Eric V.We consider methods for improving the estimation of constraints on a high-dimensional parameter space with a computationally expensive likelihood function. In such cases Markov chain Monte Carlo (MCMC) can take a long time to converge and concentrates on finding the maxima rather than the often-desired confidence con-tours for accurate error estimation. We employ DALEχ(Direct Analysis of Limits via the Exterior ofχ2) for determining confidence contours by minimizing a cost function parametrized to incentivize points in parameter space which are both on the confidence limit and far from previously sampled points. We compare DALEχ to the nested sampling algorithm implemented in MultiNest on a toy likelihood function that is highly non-Gaussian and non-linear in the mapping between parameter values and χ2. We find that in high-dimensional cases DALEχfinds the same confidence limit as Multi-Nest using roughly an order of magnitude fewer evaluations of the likelihood function.DALE χ is open-source and available athttps://github.com/danielsf/Dalex.git.