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Search results for: RESIDUE ANALYSIS
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Chromogenic Substrates of Bovine β-Trypsin: The Influence of an Amino Acid Residue in P1 Position on Their Interaction with the Enzyme
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Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
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FPGA implementation of reverse residue conversion based on the new Chinese Remainder Theorem II- Part I
PublicationW pracy opisano implementację algorytmu konwersji z systemu resztowego do systemu binarnego opartą na nowej formie chińskiego twierdzenia o resztach określanego jako CRT II.Nowa forma CRT nie wymaga operacji modulo M , gdzie M jest zakresem liczbowym systemu resztowego, jednak wymagana jest pewna liczba mnożników. W środowisku FPGA jest zwykle dostępne są mnożniki, stąd mogą być one wykorzystane do realizacji konwertera. Głównym...
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Analysis of chiral pharmaceutical residues in influent and effluent samples at racemic and enantiomeric level using liquid chromatography-tandem mass spectrometry
PublicationIn this work, two different chromatographic methods for seasonal monitoring of pharmaceutical residue in wastewater samples were developed. In the case of enantiomeric separation of selected compounds, LC-MS technique combining with vancomycin based chiral stationary phase was used. The performance of chiral analysis enabled to monitor the pharmaceutical contamination at the enantiomeric level. The d-SPE procedure was developed...
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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
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Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
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Raman and surface-enhanced Raman spectroscopy investigation of vasopressin analogues containing 1-aminocyclohexane-1-carboxylic acid residue
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FPGA implementation of reverse residue conversion based on the new Chinese Remainder Theorem II- Part II,- Experimantal results
PublicationW pracy opisano realizację sprzętową konwertera z systemu resztowego do systemu binarnego. Konwerter jest oparty na nowej formie chińskiego twierdzenia o resztach CRT II. Teoretyczne aspekty takiej konwersji przedstawiono w części I. Implementację konwertera wykonano w środowisku Xilinx FPGA. Zaprezentowano ogólną architekturę konwertera, a także opisano realizację wybranych bloków. Podano ilość koniecznych zasobów sprzętowych...
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A study on the protection of methionine and the reduction of methionine sulfoxide in methionine-containing analogues of the growth-modeling factor Gly-His-Lys
PublicationThe protection of methionine and the reduction of methionine sulfoxide in methionine-containing analogues of Gly-His-Lys are described. The peptides were synthesized by a solid-phase method using the standard Fmoc procedure. Simultaneous deprotection of the peptide side chain and liberation from the resin were achieved using an appropriate TFA cocktail. The TFA cocktail was selected to minimize oxidation of the methionine residue....
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Macrocyclic derivatives of imidazole as chromoionophores for bismuth(III)/lead(II) pair
Publication18-membered diazomacrocycles with imidazole or 4-methylimidazole residue as a part of macrocycle were used as chromoionophores in bismuth(III) and lead(II) dual selective optodes for the first time. Cellulose triacetate membranes doped with macrocyclic chromoionophores are bismuth(III) and lead(II) selective with color change from orange/red to different shades of blue and violet, respectively. Results obtained for model and real...
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Determination of pharmaceuticals in fish: method optimization and occurrence in different species from Mediterranean rivers
PublicationThe multi-residue analytical method developed, based on accelerated solvent extraction, gel permeation chromatography purification and UPLC-MS/MS analysis allowed the simultaneous determination of 21 pharmaceuticals. Recoveries obtained for most of the target compounds were higher than 50%. The application of UPLC-MS/MS operating in the MRM mode, with two transitions monitored for each compound, provided good sensitivity and selectivity....
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Study on effectiveness of PVC/β-diketone sorbent in removing residue of Zn(II), Cr(III) and Ni(II) from post-galvanic wastewater
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Characteristics of volatile organic compounds emission profiles from hot road bitumens
PublicationA procedure for the investigation and comparison of volatile organic compounds (VOCs) emission profiles to the atmosphere from road bitumens with various degrees of oxidation is proposed. The procedure makes use of headspace analysis and gas chromatography with universal as well as selective detection, including gas chromatography–mass spectrometry (GC–MS). The studies revealed that so-called vacuum residue, which is the main component...
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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Binuclear Co(II), Zn(II) and Cd(II) tri-tert-butoxysilanethiolates. Synthesis, crystal structure and spectroscopic studies.
PublicationA series of Co(II), Zn(II) and Cd(II) complexes have been synthesized in reaction of respective metal tri-tert-butoxysilanethiolates with pyrazine 1 and 2 and 1,2-bis(2-pyridyl)ethylene 3–5. All compounds have been characterized by single-crystal X-ray structure determination, elemental analysis, FT-IR and thermogravimetry. Obtained complexes are bimetallic with the formula of [M{SSi(OtBu)3}2(μ-L)]2 and metal ions bridged by N,N′-spacer....
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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins
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Investigation of long-range dependencies in the stochastic part of daily GPS solutions
PublicationThe long-range dependence (LRD) of the stochastic part of GPS-derived topocentric coordinates change (North, East, Up) results with relatively high autocorrelation values with a focus on self-similarity. One of the reasons for such self-similarity in the GPS time series are noises that are commonly recognised to prevail in the form of the flicker noise model. To prove the self-similarity of the stochastic part of GPS time series...
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Distinction of clenbuterol intake from drug or contaminated food of animal origin in a controlled administration trial – the potential of enantiomeric separation for doping control analysis
PublicationThe differentiation of clenbuterol abuse and unintentional ingestion by contaminated meat is crucial with respect to the valuation of an adverse analytical finding in human sports doping control. The proportion of the two enantiomers of clenbuterol may serve as potential discriminating parameter. For the determination of the individual enantiomers, specific methods were developed and validated for the different matrices under investigation...
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Pyrrole bearing diazocrowns: Selective chromoionophores for lead(II) optical sensing
PublicationDiazocrowns of 18-, 21- and 23-membered rings with pyrrole residue as a part of macrocycle were for the first time used as chromoionophores in lead(II) selective optodes. Sensing properties of optodes depend on the type of macrocycle, namely its size and the type of linker: oligoether or hydrocarbon chain. The best results were obtained for optode bearing 18-membered crown with oligoether linker showing linear response range of...
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Interactions of fish gelatin and chitosan in uncrosslinked and crosslinked with EDC films: FT-IR study
PublicationFilms based on fish gelatin, chitosan and blend of fish gelatin and chitosan before and after cross-linking with EDC have been characterized by FT-IR spectroscopy. The FT-IR spectrum of fish gelatin film showed the characteristic amide I, amide II and amide III bands, and the FT-IR spectrum of chitosan film confirmed that the polymer was only a partially deacetylated product, and included CH3-C=O and NH2 groups, the latter both...
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Mono- and polynuclear Co(II) silanethiolates with aliphatic diamines
PublicationFour Co(II) complexes, [Co{SSi(OtBu)3}2(dmpda)] 1, [Co{SSi(OtBu)3}2(bda)2]n2 [Co{SSi(OtBu)3}2(pda)2]n3 and [Co{SSi(OtBu)3}2(hda)2]n4 [dmpda = 3-(dimethylamino)-1-propylamine; bda = 1.4-butanediamine; pda = 1.5-pentanediamine; had = 1.6-hexanediamine] have been synthesized and characterized using X-ray diffraction. Complex 1 is mononuclear and contains Co(II) coordinated by dmpda molecule in chelating mode, whereas compounds 3 and...
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Sewage sludge co-pyrolysis with agricultural/forest residues: A comparative life-cycle assessment
PublicationThis study aims to determine the sustainability and energy efficiency of co-pyrolysis scenarios as treatment processes for municipal sewage sludge through a life cycle assessment (LCA). In addition, sensitivity and energy recovery analyses are conducted to determine the possible methods for optimizing the co-pyrolysis process from a circular bioeconomy perspective. Corncob and wood residue have been selected as potential co-feed...
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Mechanical Properties, Microstructure and Surface Quality of Polypropylene Green Composites as a Function of Sunflower Husk Waste Filler Particle Size and Content
PublicationAgricultural waste is a still untapped source of materials that can, in case of proper utilization, significantly improve the sustainability of polymers and their composites. In this work, polymer composites based on isotactic polypropylene were produced incorporating ground sunflower husk in the amount of 10 wt% and 20 wt%. The work’s main objective is to evaluate how preliminary fractioning of this agricultural waste filler affects...
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Utilization of rapeseed pellet from fatty acid methyl esters production as an energy source
PublicationRapeseed pellet – crushed seed residue from oil extraction is a by-product of fatty acid methyl esters production process. As other types of biomass, it can either be burned directly in furnaces or processed to increase its energetic value. Biomass is renewable, abundant and has domestic usage; the sources of biomass can help the world reduce its dependence on petroleum products, fossil coal and natural gas. Energetically effective...
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Fast, sensitive and reliable multi-residue method for routine determination of 34 pesticides from various chemical groups in water samples by using dispersive liquid – liquid microextraction coupled with gas chromatography – mass spectrometry
PublicationA simple and efficient dispersive liquid-liquid microextraction technique (DLLME) was developed by using a mixture of two solvents: 40 μL of tetrachlorethylene (extraction solvent) and 1.0 mL of methanol (disperser solvent), which was rapidly injected with a syringe into 10mL ofwater sample. Some important parameters affecting the extraction efficiency, such as type and volume of solvents, water sample volume, extraction time,...
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Solventless and solvent-minimized sample preparation techniques for determining currently used pesticides in water samples: A review
PublicationThe intensification of agriculture means that increasing amounts of toxic organic and inorganic compounds are entering the environment. The pesticides generally applied nowadays are regarded as some of the most dangerous contaminants of the environment. Their presence in the environment, especially in water, is hazardous because they cause human beings to become more susceptible to disease. For these reasons, it is essential to...
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Unexpected Z/E isomerism of N-methyl-O-phosphothioyl benzohydroxamic acids, their oxyphilic reactivity and inertness to amines
PublicationThiophosphinoylation of N-methyl p-substituted benzohydroxamic acids using disulfanes (method A) or diphenylphosphinothioyl chloride (method B) provides only one conformer of the respective O-phosphothioyl derivative (Xray and NMR analysis). Undergoing the P-transamidoxylation reaction is an evidence of the reversibility of thiophosphinoylation. Only those products containing strong EWG substituents in the aroyl residue or bulky...
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Investigation of volatile low molecular weight compounds formed during continuous reclaiming of ground tire rubber
PublicationGround tire rubber was thermo-mechanically reclaimed at different temperature conditions (80, 120, 160 °C) using a co-rotating twin screw extruder. The progress of ground tire rubber reclaiming was evaluated with specific mechanical energy, sol fraction and thermogravimetric analysis. Volatile organic compounds (VOCs) including volatile sulfur compounds (VCSs) released from ground tire rubber and ground tire rubber after reclaiming...
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Entrained Flow Plasma Gasification of Sewage Sludge–Proof-of-Concept and Fate of Inorganics
PublicationSewage sludge is a residue of wastewater processing that is biologically active and consists of water, organic matter, including dead and living pathogens, polycyclic aromatic hydrocarbons, and heavy metals, as well as organic and inorganic pollutants. Landfilling is on the decline, giving way to more environmentally friendly utilisation routes. This paper presents the results of a two-stage gasification–vitrification system, using...
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Sample preparation techniques for determination of pesticide residues in food samples
PublicationPesticides are very important in increasing the efficiency and quality of agricultural production. They are applied in many spheres of life, not only in agriculture, and their applications are expanding. Despite their numerous merits, pesticides are some of the most toxic substances contaminating our environment and have a negative impact on the human health. Properties of pesticides such as stability, ability to bioaccumulation...
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Digital structures for high-speed signal processing
PublicationThe work covers several issues of realization of digital structures for pipelined processing of real and complex signals with the use of binary arithmetic and residue arithmetic. Basic rules of performing operations in residue arithmetic are presented along with selected residue number systems for processing of complex signals and computation of convolution. Subsequently, methods of conversion of numbers from weighted systems to...
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Nitrogen transformation during fermentation in agricultural biogas plants
PublicationThe aim of the present study was to determine changes in the organic nitrogen fraction in the liquid fraction of the digestate during laboratory tests of mono- and co-digestion. Three agricultural wastes were tested: distillery residue, cattle slurry and corn silage. In the mono-fermentation tests, the initial total nitrogen concentration depended on the feedstock used. As a result of the hydrolysis and ammonification of the organic...
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Sustainable Chemically Modified Mater-Bi/Poly(ε-caprolactone)/Cellulose Biocomposites: Looking at the Bulk through the Surface
PublicationSustainable polymer composites are progressively under development in a technological paradigm shift from "just use more and more" to "convert into value-added products". The bio-based blends based on Mater-Bi bio-plastic (A) and poly(ε-caprolactone) (B), at a weight ratio of 70:30 (A:B) were developed, followed by the addition of UFC100 cellulose (C) filler to yield 70/30 (w/w) (A:B)/C sustainable biocomposites. The effects of...
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Chromatographic behavior of a new hybrid type RP material containing silica bonded 1,3-alternate 25,27-bis-[cyanopropyloxy]-26,28-bis-[3-propyloxy]-calix[4]arene
PublicationA novel 1,3-alternate 25,27-bis-[cyanopropyloxy]-26,28-bis-[3-propyloxy]-calix[4]arene-bonded silica gel stationary phase (CalixPrCN) was prepared and it's structure was confirmed by ATR-FTIR spectroscopy and elemental analysis. The CalixPrCN phase was characterized in terms of their surface coverage, hydrophobic selectivity, aromatic selectivity, shape selectivity, hydrogen bonding capacity, residue metal content, and silanol...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Pipelined Two-Operand Modular Adders
PublicationPipelined two-operand modular adder (TOMA) is one of basic components used in digital signal processing (DSP) systems that use the residue number system (RNS). Such modular adders are used in binary/residue and residue/binary converters, residue multipliers and scalers as well as within residue processing channels. The structure of pipelined TOMAs is usually obtained by inserting an appropriate number of pipeline register layers within...
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Asfalteny jako fazy stacjonarne w chromatografii cieczowej w normalnych układach faz
PublicationRozprawa doktorska dotyczy zbadania możliwości wykorzystania asfaltenów wydzielonych z: próżniowej pozostałości ropy naftowej, produktów jej utleniania i naturalnego asfaltu jako fazy stacjonarnej na powierzchni sorpcyjnej żelu krzemionkowego do rozdzielania nisko polarnych organicznych związków chemicznych w warunkach chromatografii cieczowej w normalnych układach faz, w odniesieniu do żelu krzemionkowego jako nośnika. Opracowano...
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Layer-by-layer polymer deposited fabrics with superior flame retardancy and electrical conductivity
PublicationSmart and multifunctional textiles and fabrics are progressively developing, such that multifunctional fabrics are becoming more widespread. We elaborated herein multi-layered flax fabrics with superior flame retardancy and conductivity, which revealed fireproof feature while keeping conductivity during burning. The flax fabric was reinforced by layer-by-layer (LbL) deposition of sodium polyacrylate (SPA), polyethylenimine (PEI),...
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Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline
PublicationThe role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hin- dering a potentially important avenue in the rational drug de- sign. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity....
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Optical recognition elements: macrocyclic imidazole chromoionophores entrapped in silica xerogel
PublicationMaterials containing new chromoionophores consisting of crown residue and azole moiety as partsof macrocycles were encapsulated by the sol-gel procedure in silica xerogel matrices and proposed aschemical recognition elements especially for such metal ions as Li+, Cs+ and Cu2+. Action of these recognition elements is in principle based on changes of reflectance. The recognition elements containing 21-membered chromogenic...
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The PRNS butterfly in the FPGA technology
PublicationW publikcaji zaprezentowano koncepcję realizacji motylka konwesji wejściowej w Wielomianowym Systemie Resztowym (Polynoamil Residue Number System, PRNS). Omówiono wykorzystanie reprezentacji liczb w systemie diminished-1 w prezentowanym rozwiązaniu oraz przedstawiono wynik syntezy ukłądu w środowisku Xilinx ISE.
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(1H-Pyrazole-[kappa]N)bis(tri-tert-butoxysilanethiolato-[kappa]2O,S)cadmium
PublicationThe CdII atom in the title complex, [Cd(C12H27O3SSi)2-(C3H4N2)], is penta-coordinated by two O and two S atoms from the O,S-chelating silanethiolate residue and one pyrazole N atom in a distorted trigonal-bipyramidal geometry. The pyrazole ligand forms an intramolecular N-H---O hydrogen bond.
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Low-Cost Surrogate Models for Microwave Filters
PublicationA novel low-cost kriging-based multivariable parametric macromodeling technique for microwave filters is presented. Kriging is used to model both the residues and poles of a microwave filter's reflection coefficient, and the zeros of the transmission coefficient. The proposed residue-pole-zero (RPZ) technique is demonstrated to efficiently model a high dimensional (8D) microwave filter with pseudoelliptic characteristics.
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RNS/TCS CONVERTER DESIGN USING HIGH-LEVEL SYNTHESIS IN FPGA
PublicationAn experimental high-level synthesis (HLS) of the residue number system (RNS) to two’s-complement system (TCS) converter in the Vivado Xilinx FPGA environment is shown. The assumed approach makes use of the Chinese Remainder Theorem I (CRT I). The HLS simplifies and accelerates the design and implementation process, moreover the HLS synthesized architecture requires less hardware by about 20% but the operational frequency is smaller...
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The prns butterfly synthesis in the FPGA
Publicationw pracy przedstawiono sprzętową implementację elementarnych obliczeń, określanych jako obliczenia motylkowe, dla splotu realizowanego z użyciem wielomianowego systemu resztowego(ang. polynomial residue number system - prns). obliczenia są wykonywane z zastosowaniem reprezentacji systemu diminished-1. opisano syntezę układu realizującego obliczenie motylkowe w środowisku xilinx w układzie virtex 4. podano również wymaganą ilość...