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Search results for: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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MATHEMATICAL MODELING OF FLOOD MANAGEMENT SYSTEM IN THE CITY OF GDAŃSK, ORUŃSKI STREAM CASE STUDY
PublicationAim of the study This study analyses the efficiency of flood protection in a small urban catchment, based on a system of small reservoirs. Material and methods To assess the flood routing and surge reduction, a mathematical model of the river catchment was implemented. This was a lumped hydrological model, based on the SCS-CN method. Channel routing was performed, using kinematic wave equation. The sub-catchments have been determined...
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Mathematical modeling of hydrogen production performance in thermocatalytic reactor based on the intermetallic phase of Ni3Al
PublicationThe main goal of the following work is to adjust mathematical modelling for mass transfer, to specific conditions resulting from presence of chemical surface reactions in the flow of the mixture consisting of helium and methanol. The thermocatalytic devices used for decomposition of organic compounds incorporate microchannels coupled at the ends and heated to 500 oC at the walls regions. The results of the experiment were compared...
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Computing internodal conductivities in numerical modeling of two dimensional unsaturated flow on rectangular grid
PublicationW artykule porównano rozwiązania numeryczne dwuwymiarowego równania przepływu nienasyconego z użyciem różnych metod uśredniania współczynnika przewodności hydraulicznej między sąsiednimiwęzłami. Uwzględniono średnia arytmetyczną, geometryczną, "pod prad" oraz całkową, a także niedawno zaproponowany sposób uśredniania oparty na analizie przepływu ustalonego. Ten ostatni sposób okazałsię najbardziej uniwersalny, gdyż umożliwiał otrzymanie...
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Modeling of effect of plastic deformation on Barkhausen noise and magnetoacoustic emission in iron with 2% silicon
PublicationW modelowaniu zaadaptowano model Alessandro-Beatrice-Bertotti-Montorsi dla opisu ruchu granic nie-180 stopniowych oraz model Jiles-Atherton dla opisu wpływu plastycznej deformacji na natężenie efektu Barkhausena oraz emisji magnetoakustcznej.
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NOx emission from a two-stroke ship engine. Part 1: Modeling aspect
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Improvement of the Rhizoremediation efficiency of PAHs contaminated soil under cysteine treatment along with modeling
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Numerical modeling of cross-flow heat exchanger for air-conditioning purposes in preliminary study.
PublicationPraca przedstawia wyniki obliczeń numerycznych krzyżowego płytowo-rurowego wymiennika ciepła przeznaczonego do celów klimatyzacyjnych w początkowym etapie jego projektowania.
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Modeling the electrical characteristics of P3HT:PCBM bulk heterojunction solar cells: Influence of the interface recombination
PublicationThe interface recombination of charge carriers located in the material with lower permittivity (Szmytkowski 2009 Chem.Phys.Lett. 470 123) has been implemented for the first time to calculate the electrical characteristics of the donor-acceptor P3HT:PCBM bulk heterojunction solar cell. In order to estimate the photocurrent density in this system, a simple analytical formula has been derived. We have obtained a very good agreement...
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Sparse vector autoregressive modeling of audio signals and its application to the elimination of impulsive disturbances
PublicationArchive audio files are often corrupted by impulsive disturbances, such as clicks, pops and record scratches. This paper presents a new method for elimination of impulsive disturbances from stereo audio signals. The proposed approach is based on a sparse vector autoregressive signal model, made up of two components: one taking care of short-term signal correlations, and the other one taking care of long-term correlations. The method...
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Submerged objects modeling and storing in a global reference context using multiresolution spline technique,
PublicationContemporary records from multibeam sonars or even elevations from 3D shuttle radar topography missions feature high resolution. On the other hand, bathymetric models of a different resolution from different sensors are available as well, beginning from very high resolution MBS records and low resolution records coming from regular scattered measurements. Approximating and eventually visualizing the high volume scattered 3D raster...
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Decisional DNA for modeling and reuse of experiential clinical assessments in breast cancer diagnosis and treatment
PublicationClinical Decision Support Systems (CDSS) are active knowledge resources that use patient data to generate case specific advice. The fast pace of change of clinical knowledge imposes to CDSS the continuous update of the domain knowledge and decision criteria. Traditional approaches require costly tedious manual maintenance of the CDSS knowledge bases and repositories. Often, such an effort cannot be assumed by medical teams, hence...
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Mathematical Modeling of the Impact Range of Sewage Discharge on the Vistula Water Quality in the Region of Włocławek
PublicationThe paper presents results of analysis of the industrial sewage discharge influence at km 688 + 250 of the Vistula River on water quality. During the analysis, two-dimensional models of flow, impurities and temperature transport were used. Hydrological conditions of the analyzed section of the river, characteristic flows and bathymetry of the riverbed in the first instance were defined. Calculations of velocity distribution at...
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A new approach to modeling of selected human respiratory system diseases, directed to computer simulations
PublicationThis paper presents a new versatile approach to model severe human respiratory diseases via computer simulation. The proposed approach enables one to predict the time histories of various diseases via information accessible in medical publications. This knowledge is useful to bioengineers involved in the design and construction of medical devices that are employed for monitoring of respiratory condition. The approach provides the...
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Geospatial Modeling of the Tombolo Phenomenon in Sopot using Integrated Geodetic and Hydrographic Measurement Methods
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Accurate modeling of layout parasitic to forecast EMI emitted from a DC-DC converter.
PublicationThis paper illustrates how to account for all parasitic due to the layout of a power converter (inductive and capacitive), in order to forecast electromagnetic interferences (EMI). The method is generic, and is validated here in the simple example of a DC-DC converter, realized on different technologies: insulated metal substrate (IMS), printed circuit board (PCB). In addition, several layouts aspects will be investigated. Conclusions...
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Comparative modeling of shear zone patterns in granular bodies with finite and discrete element method
PublicationW artykule przedstawiono wyniki numeryczne naporu piasku na ściankę szczelną. Obliczenia wykonano stosując metodę elementów dyskretnych i skończonych na bazie mikropolarnego hipoplastycznego prawa materiałowego. Porównanie obu podejść wykonano na poziomie makro i mikro. Wyniki numeryczne porównano także z wynikami doświadczalnymi.
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Shape and force control of cable structures with minimal actuators and actuation
PublicationShape adjustment and stress control can be considered as one of the effective parameters in prestressed cable structures since such structures are widely constructed nowadays due to their characteristics. The assembly errors and applied loads hugely affect the cables’ nodal positions and stress due to their delicacy. The former could disturb the shape, which affects the appearance and the function of the structure. In contrast,...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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Fast surrogate-assisted frequency scaling of planar antennas with circular polarisation
PublicationIn this work, the problem of computationally efficient frequency scaling (re-design) of circular polarisation antennas is addressed using surrogate-assisted techniques. The task is challenging and requires the identification of the optimum geometry parameters to enable the operation of the re-designed structure at a selected (required) centre frequency. This involves handling several performance figures such as the antenna gain,...
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Performance Analysis of the "Intelligent" Kirchhoff- Law - Johnson-Noise Secure Key Exchange
PublicationThe Kirchhoff-law - Johnson-noise (KLJN) secure key distribution system provides a way of exchanging theoretically secure keys by measuring random voltage and current through the wire connecting two different resistors at Alice’s and Bob’s ends. Recently new advanced protocols for the KLJN method have been proposed with enhanced performance. In this paper, we analyze the KLJN system and compare with the „intelligent” KLJN (iKLJN)...
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Computationally Efficient Surrogate-Assisted Design of Pyramidal-Shaped 3D Reflectarray Antennas
PublicationReflectarrays (RAs) have been attracting considerable interest in the recent years due to their appealing features, in particular, a possibility of realizing pencil-beam radiation patterns, as in the phased arrays, but without the necessity of incorporating the feeding networks. These characteristics make them attractive solutions, among others, for satellite communications or mobile radar antennas. Notwithstanding, available microstrip...
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Numerical Estimate of the Spectral Resonance Structure Frequency Scale of Natural ULF Magnetic Field
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Robust Parameter Estimation and Output Prediction for Reactive Carrier-Load Nonlinear Dynamic Networks
PublicationIn this paper an extension of on-line model simplification technique for a class of networked systems, namely reactive carrier-load nonlinear dynamic networked system (RCLNDNS), kept within point-parametric model (PPM) framework is addressed. The PPM is utilised to acquire a piece wise constant time-varying parameter linear structure for the RCLNDNS suitable for the on-line one step ahead prediction that may be applied to monitoring...
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THE INFLUENCE OF THE URBAN DESIGN ON THE AIR EXCHANGE IN CITIES. SELECTED PROBLEMS IN POLISH REALITY
PublicationThe progress of the architecture and urbanism raises problems requiring interdisciplinary research conducted with the use of advanced experimental techniques and computer simulation. The fields of this research include aerodynamics, especially in intensively developed area of Environmental Wind Engineering (EWE). Aerodynamic phenomena occurring around buildings have a significant impact on the quality of the climate in the cities....
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Dependence between Ionic Liquid Structure and Mechanism of Visible-Light-Induced Activity of TiO2 Obtained by Ionic-Liquid-Assisted Solvothermal Synthesis
PublicationBecause of the tremendous structural diversityof ionic liquids (ILs), simple transfer of observations performed for one IL used for IL-TiO2 preparation on different samples is not possible. Therefore, four ionic liquids, all containing distinct nitrogen-bearing organic cations (pyridinium, pyrrolidinium, ammonium, imidazolium), were used for the first time for the preparation of IL-TiO2 composites. The role of the individual IL...
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Combined Single Neuron Unit Activity and Local Field Potential Oscillations in a Human Visual Recognition Memory Task
PublicationGOAL: Activities of neuronal networks range from action potential firing of individual neurons, coordinated oscillations of local neuronal assemblies, and distributed neural populations. Here, we describe recordings using hybrid electrodes, containing both micro- and clinical macroelectrodes, to simultaneously sample both large-scale network oscillations and single neuron spiking activity in the medial temporal lobe structures...
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Independence in uniform linear triangle-free hypergraphs
PublicationThe independence number a(H) of a hypergraph H is the maximum cardinality of a set of vertices of H that does not contain an edge of H. Generalizing Shearer’s classical lower bound on the independence number of triangle-free graphs Shearer (1991), and considerably improving recent results of Li and Zang (2006) and Chishti et al. (2014), we show a new lower bound for a(H) for an r-uniform linear triangle-free hypergraph H with r>=2.
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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FORECASTING EXCHANGE RATES IN THE PROCESS OF THE ASSESSMENT OF CONSUMER RISK BANKRUPTCY IN CENTRAL EUROPE
PublicationThis paper focuses on the issue of forecasting the fluctuation of exchange rates as part of the early warning system against the risk of consumer bankruptcy. The author identified the main macroeconomic factors affecting the level of bankruptcies for households in Poland. The fluctuation of exchange rates, which directly affects the deterioration of the economic situation of borrowers who have opened credit accounts in a foreign...
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Prediction of manoeuvring abilities of 10000 DWT pod-driven coastal tanker
PublicationThis paper aims to present a new approach in the prediction of manoeuvring abilities of pod-driven ships. A new mathematical model of motions based on MMG methodology was developed and a new type of description of forces acting on azimuth drives is presented. Captive model tests of medium-size coastal tanker and pod open water tests were carried out in CTO S.A. (Ship Design and Research Centre S.A.) to obtain hull hydrodynamic derivatives...
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Simultaneous Optimization of Unicast and Anycast Flows and Replica Location in Survivable Optical Networks
PublicationDotychczasowe prace z zakresu ochrony sieci przed awariami dotyczyły przypadku transmisji unicast. W niniejszym artykule rozważamy problem ochrony transmisji anycast (jeden-do-jednego-z-wielu). Jako wariant ochrony stosujemy podejście pojedynczej ścieżki zabezpieczającej (ang. path protection), chroniącej przed awarią pojedynczego węzła.Wprowadzono nowe modele programowania całkowitoliczbowego optymalnego znajdowania tras oraz...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Charge density wave and crystalline electric field effects in TmNiC2
PublicationSingle crystals of TmNiC2 were grown by the optical floating-zone technique and were investigated by x-ray diffraction (XRD), thermal expansion, electrical resistivity, specific heat, and magnetic susceptibility measurements. Single-crystal XRD reveals the formation of a commensurate charge density wave (CDW) characterized by a CDW modulation vector q2c = (0.5, 0.5, 0.5), which is accompanied by a symmetry change from the orthorhombic...
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Application of Diffusion Models in the Analysis of Financial Markets: Evidence on Exchange Traded Funds in Europe
PublicationExchange traded funds (ETFs) are financial innovations that may be considered as a part of the index financial instruments category, together with stock index derivatives. The aim of this paper is to explore the trajectories and formulates predictions regarding the spread of ETFs on the financial markets in six European countries. It demonstrates ETFs’ development trajectories with regard to stock index futures and options that...
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Load introduction to composite columns revisited—Significance of force allocation and shear connection stiffness
PublicationThe AISC 360-16 Specification recommends that the design shear force between parts of a composite column in the load introduction area shall be calculated based on the force allocation at ultimate limit state. Applicability of this straightforward method to the load levels that usually arise in slender composite columns is questionable, as this capacity-based force allocation is only true when the axial force is equal to the plastic...
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Effect of Pin Shape on Thermal History of Aluminum-Steel Friction Stir Welded Joint: Computational Fluid Dynamic Modeling and Validation
PublicationThis article studied the effects of pin angle on heat generation and temperature distribution during friction stir welding (FSW) of AA1100 aluminum alloy and St-14 low carbon steel. A validated computational fluid dynamics (CFD) model was implemented to simulate the FSW process. Scanning electron microscopy (SEM) was employed in order to investigate internal materials’ flow. Simulation results revealed that the mechanical work...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Protein thermal stabilization in aqueous solutions of osmolytes
PublicationProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Dynamic characteristics of the proton exchange membrane fuel cell module
PublicationThe paper describes a fuel cell based system and its performance. The system is based on two fuel cell units, DC/DC converter, DC/AC inverter, microprocessor control unit, load unit, bottled hydrogen supply system and a set of measurement instruments. In the study presented in the paper a dynamic response of the proton exchange membrane (PEM) fuel cell system to unit step change load as well as to periodical load changing cycles...
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Dynamic Nanoimpedance Characterization of the Atomic Force Microscope Tip-Surface Contact
PublicationNanoimpedance measurements, using the dynamic impedance spectroscopy technique, were carried out during loading and unloading force of a probe on three kinds of materials of different resistivity. These materials were: gold, boron-doped diamond, and AISI 304 stainless steel. Changes of impedance spectra versus applied force were registered and differences in the tip-to-sample contact character on each material were revealed. To...
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Reactive extrusion of biodegradable aliphatic polyesters in the presence of free-radical-initiators: A review
PublicationNowadays, growing attention is being paid to the environment and sustainability, what fully justified research works focused on modification of biodegradable polymers and their composites. In this field of research reactive extrusion seems to be the most promising approach, which fits well to sustainable development strategy. In In the present work, the in-situ modification of biodegradable aliphatic polyesters and the compatibilization...
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Bibliometric analysis and literature review of ultrasound-assisted degradation of organic pollutants
PublicationUltrasound as a clean, efficient, and cheap technique gains special attention in wastewater treatment. Ultrasound alone or coupled with hybrid processes have been widely studied for the treatment of pollutants in wastewater. Thus, it is essential to conduct a review about the research development and trends on this emerging technique. This work presents a bibliometric analysis of the topic associated with multiple tools such as...
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An adaptive-noise Augmented Kalman Filter approach for input-state estimation in structural dynamics
PublicationThe establishment of a Digital Twin of an operating engineered system can increase the potency of Structural Health Monitoring (SHM) tools, which are then bestowed with enhanced predictive capabilities. This is particularly relevant for wind energy infrastructures, where the definition of remaining useful life is a main driver for assessing the efficacy of these systems. In order to ensure a proper representation of the physical...
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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Identification of residual force in static load tests on instrumented screw displacement piles
PublicationOccurrence of the so-called residual force of an unknown value significantly disturbs interpretation of static load tests performed on piles equipped with additional measuring instruments. Screw displacement piles are the piling technology in which the residual force phenomenon is very common. Its formation mechanism is closely related to the installation method of this type of piles, which initiates generation of negative pile...
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Microwave-assisted synthesis of zinc derivatives of potato starch
PublicationZincatated potato starch was prepared in a solid-state, microwave-assisted reaction using generated in situ sodium tetrahydroxozincate [Na2Zn(OH)4]. For comparison, zincatation of starch was also carriedout on convectional heating. Depending on the irradiation conditions, the products of either mono- or crosslinking esterification were formed. Higher power applied at shorter exposition offered products ofmonoesterification, and...
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Molecular simulation study of cooperativity in hydrophobic association
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Construction and purification of his6-Thermus thermophilus MutS protein
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublicationGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...