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Search results for: HIV-1 INTEGRASE, INHIBITORS, DOCKING, ACTIVE SITE, ALLOSTERIC SITE,MOLECULAR DYNAMICS
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Active shape models in practice
PublicationAutorzy wykonali uniwersalny system lokalizacji obiektów zawierający implementację aktywnych modeli kształtu, a przeprowadzone z użyciem tego systemu eksperymenty wykazały powżne wady badanej metody. W pracy przedstawiono zaobserwowane w praktyce problemy związane ze stosowaniem metody aktywnych modeli kształtu (ASM).
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Unsupervised machine-learning classification of electrophysiologically active electrodes during human cognitive task performance
PublicationIdentification of active electrodes that record task-relevant neurophysiological activity is needed for clinical and industrial applications as well as for investigating brain functions. We developed an unsupervised, fully automated approach to classify active electrodes showing event-related intracranial EEG (iEEG) responses from 115 patients performing a free recall verbal memory task. Our approach employed new interpretable...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 2. The N-methylpyrrolidinone+methanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez metanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Structure of partially reduced xPbO (1-x)SiO2 glasses: combined EXAFS and MD study
PublicationWykorzystując połączenie metody EXAFS (extended X-ray absorption finestructure) i symulacji MD (molecular dynamics) zbadano strukturęczęściowo zredukowanych szkieł ołowiowo-krzemianowych o różnejstechiometrii wyjściowej. W wyniku analizy uzyskano szczegółowyopis struktury lokalnej wokół atomów ołowiu i jej zmiany w funkcjiskładu szkła i poziomu redukcji. Określono również jaką tendencjędo aglomeracji w metaliczne klastry wykazują...
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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CCDC151 Mutations Cause Primary Ciliary Dyskinesia by Disruption of the Outer Dynein Arm Docking Complex Formation
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The impact of the distribution network reconfiguration on active power losses: Selected issues of UPGRID project realization
PublicationThe dynamic development of smart grids allows the use of remote controllable switches to change the configuration of the distribution network. The paper discusses the impact of the distribution system reconfiguration on active power losses, taking into account the typical daily load profiles. Based on modified IEEE 33-bus test distribution system the article presents the method of selection the appropriate sensitivity factor and...
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Active Dynamic Thermography imaging of wound healing processes in cardio surgery
PublicationThe surgery is a branch of medicine, that is integrally connected to wounds. Despite using sterile tools and compliance with aseptic rolls, some of the surgery wounds become infected. In clinical practice there is a lack of cheap, objective methods and tools for quantitative definition and estimation of the surgery wound healing progress. This paper presents preliminary results of Active Dynamic Thermography (ADT) parametric imaging...
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Molecular Biology of Meniscal Healing: A Narrative Review
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Active Dynamic Infrared Thermal Imaging in Burn Depth Evaluation
PublicationThe aim of this study was to find the relationship between active dynamic thermography (ADT) with cold excitation and burn depth. This new modality of evaluation of burns seems to be an attractive proposal for quantitative classification, allowing proper choice of burn wound treatment: conservative or surgical, especially compared with static thermography. The work was an in vivo experiment on domestic pigs, and a small number...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
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Stanowisko maślaka błotnego Suillus flavidus(Fr.: Fr.) J. S. Presl. w rezerwacie przyrody ''Mierzeja Sarbska'' koło Łeby = A site of bolete Suillus flavidus (Fr: Fr.)J.S. Presl. In Nature reserve ''Mierzeja Sarbska'' near Łeba Town
PublicationW pracy przedstawiono stanowisko maślaka błotnego zlokalizowane w rezerwacie przyrody ''mierzeja Sarbska'' koło Łeby oraz zamieszczono opis opis gatunku
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Synthesis of Cyano-Benzylidene Xanthene Synthons Using a Diprotic Brønsted Acid Catalyst, and Their Application as Efficient Inhibitors of Aluminum Corrosion in Alkaline Solutions
PublicationNovel cyano-benzylidene xanthene derivatives were synthesized using one-pot and condensation reactions. A diprotic Brønsted acid (i.e., oxalic acid) was used as an effective catalyst for the promotion of the synthesis process of the new starting xanthene–aldehyde compound. Different xanthene concentrations (ca. 0.1–2.0 mM) were applied as corrosion inhibitors to control the alkaline uniform corrosion of aluminum. Measurements were...
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Dynamics of Topology-dependent Water Purification by Siliceous Zeolite Membranes
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Structured deformation of granular material in the state of active earth pressure
PublicationThe paper focuses on the ability of granular materials to undergo structured deformation by analysing the data from the retaining wall model tests and discrete element simulations. The structured deformation means the movement of a granular material which produces a stable, regular pattern of multiple shear bands. The paper's primary purpose is to study this kind of deformation for the selected data representing the state of active...
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Deciphering the Molecular Mechanism of Substrate-Induced Assembly of Gold Nanocube Arrays toward an Accelerated Electrocatalytic Effect Employing Heterogeneous Diffusion Field Confinement
PublicationThe complex electrocatalytic performance of gold nanocubes (AuNCs) is the focus of this work. The faceted shapes of AuNCs and the individual assembly processes at the electrode surfaces define the heterogeneous conditions for the purpose of electrocatalytic processes. Topographic and electron imaging demonstrated slightly rounded AuNC (average of 38 nm) assemblies with sizes of ≤1 μm, where the dominating patterns are (111) and...
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ESTIMATION OF NONSTATIONARY HARMONIC SIGNALS AND ITS APPLICATION TO ACTIVE CONTROL OF MRI NOISE
PublicationA new adaptive comb filtering algorithm, capable of tracking the fundamental frequency and amplitudes of different frequency components of a nonstationary harmonic signal embedded in white measurement noise, is proposed. Frequency tracking characteristics of the new scheme are studied analytically, proving (under Gaussian assumptions and optimal tuning) its statistical efficiency for quasi-linear frequency changes. Laboratory tests...
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Application of specific cell permeable cathepsin G inhibitors resulted in reduced antigen processing in primary dendritic cells
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Rozstaw rys według PN-EN 1992-1-1:2008 oraz PN-B 03264:2002
PublicationW pracy opisano mechanizm powstawania rys dla osiowo rozciąganego pręta żelbetowego. Na tej podstawie określono maksymalny i minimalny rozstaw rys, konfrontując otrzymane wyniki z procedurami podanymi w normie europejskiej PN-EN 1992-1-1:2008 oraz w normie polskiej PN-B 03264:2002. Przedstawiono praktyczne wnioski do projektowania, wynikajace z przeprowadzonej analizy.
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Badania przyczyn uszkodzenia zaworu 1"
PublicationWykonano badania przyczyn uszkodzenia zaworu 1" ze stopu miedzi. Wykonano badania metalograficzne makro i mikroskopowe, w tym z wykorzystaniem analizy EDX. Sformułowano wnioski.
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Enhanced switched parasitic antenna with switched active monopoles for indoor positioning systems
PublicationThis paper presents the concept of enhanced reduced-size steerable antenna array with two rows of switched active and passive elements. Designed array is similar to ESPAR antenna but it has a set of switched monopoles instead of central one. It is intended for 2.4 GHz ISM applications with emphasis on indoor positioning systems (IPS). Proposed antenna provides improved radiation parameters and reduced dimensions in comparison to...
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Comparable analysis of PID controller settings in order to ensure reliable operation of active foil bearings
PublicationIn comparison to the traditional solutions, active bearings offer great operating flexibility, ensure better operating conditions over a wider range of rotational speeds and are safe to use. In order to ensure optimum bearing performance a bearing control system is used that adapts different geometries during device operation. The selection of optimal controller parameters requires the use of modern optimization methods that make...
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublicationAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublicationTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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BIOGAS PRODUCTION FROM BAKERY WASTES -DYNAMICS, RETENTION TIME AND BIOGAS POTENTIAL
PublicationThis paper presents results of bakery-waste methane-fermentation. The scope of the study covers the determination of basic physicochemical parameters, process dynamics and retention time as well as biogas composition and biogas efficiency. Methane fermentation process was carried out in accordance with German Standard DIN 38414 S8 and under condition of 38°C. Conclusion: bakery wastes have big potential for biogas production.
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Periodic Properties of 1D FE Discrete Models in High Frequency Dynamics
PublicationFinite element discrete models of various engineering 1D structures may be considered as structures of certain periodic characteristics. The source of this periodicity comes from the discontinuity of stress/strain field between the elements. This behaviour remains unnoticeable, when low frequency dynamics of these structures is investigated. At high frequency regimes, however, its influence may be strong enough to dominate calculated...
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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Selected anionic and cationic surface active agents determined in river sediments – the Klodnica catchment
PublicationSurface active agents (SAAs) are specific compounds that contain hydrophilic/ hydrophobic group in their molecules named as amphiphilic structures. According to charge on the hydrophilic part of surfactants they can be classified into three main groups: anionic, cationic and non-ionic compounds. Due to the amphiphilic structure of SAAs they have specific properties (e.g. ability to adsorption at different surfaces, reduction of...
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Synthesis of disubstituted 1,3,4,9-tetrahydropyrano-[3,4-b]indole-1-acetic acids derivatives
Publication1,3,4,9-tetrahydropyrano[3,4-b ]indole-1-acetic acid derivatives are of interest for pharmaceutical research as a core structure for synthesis of biological active substance - Etodolac (selective Cyclooxygenase-2 inhibitor, which belongs to the Non-steroidal Anti-inflammatory Drug, NSAID, that shows a clin-ically effective analgesic and anti-inflammatory activity). Here the way of synthesis of two 1,3,4,9-tetrahydropyrano[3,4-b...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublicationWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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A Comprehensive Review: Applications of the Kozeny–Carman Model in Engineering with Permeability Dynamics
PublicationIn this review article, we investigate the dynamic nature of the Kozeny–Carman Model concerning permeability and its application in engineering contexts. Providing insights into the changing dynamics of permeability within mining, petroleum, and geotechnical engineering, among other engineering applications. While some are complex and require additional modifcations to be applicable, others are simple and still function in specifc...
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Single-phase power electronics transformer with active functions for smart grid
PublicationThis paper presents the control of one cell of a modular single-phase power electronics transformer with active functions for meeting the smart grid concept. In this way, the converter could be used not only as a conventional transformer but also for grid such as reactive power, harmonic elimination and energy storage. The topology of the cell is composed by a bidirectional converter with three stages: a half bridge in the input...
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Vibration Diagnostics of Rolling Mills Based on Nonlinear Effects in Dynamics
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Improvement of Oxygen Electrode Performance of Intermediate Temperature Solid Oxide Cells by Spray Pyrolysis Deposited Active Layers
PublicationIntermediate temperature solid oxide fuel cells oxygen electrodes are modified by active interfacial layers. Spray pyrolysis is used to produce thin (≈500 nm) layers of mixed ionic and electronic conductors: Sm0.5Sr0.5CoO3−δ (SSC), La0.6Sr0.4CoO3−δ (LSC), La0.6Sr0.4Co0.2Fe0.8O3−δ (LSCF), and Pr6O11 (PrOx) on the electrode–electrolyte interface. The influence of the annealing temperature on the electrode polarization (area specific...
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Molecular structure and electrochemical properties of alkyldithiocarbamates.
PublicationZastosowano klasyczne metody elektroanalityczne do badania właściwości redoks ditiokarbaminianów litu w środowisku dimetylosulfotlenku. Użyto elektrody z platyny i węgla szklistego. Badane związki zsyntezowano z N,N'-dimetyloetylenodiaminy, do której podstawiono jedną lub dwie grupy ditiokarbonylowe na drodze reakcji z CS2 w środowisku alkalicznym. Stwierdzono, że elektrochemiczne utlenianie ditiokarbaminianów przebiega z udziałem...
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Using River Formation Dynamics Algorithm in Mobile Robot Navigation
PublicationRiver Formation Dynamics is a heuristic optimization algorithm based on the manner, in which drops of water form the river bed. The idea is to imitate the movement of drops on the edges between given nodes thus performing a search based on their height, which is modified through the mechanism of soil erosion and sediment deposition. In this way decreasing gradients are constructed, and these are followed by subsequent drops to...
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Probing the Magnetic Anisotropy of Co(II) Complexes Featuring Redox-Active Ligands
PublicationCoordination complexes that possess large magnetic anisotropy (otherwise known as zero-field splitting, ZFS) have possible applications in the field of magnetic materials, including single molecule magnets (SMMs). Previous studies have explored the role of coordination number and geometry in controlling the magnetic anisotropy and SMM behavior of high-spin (S = 3/2) Co(II) complexes. Building upon these efforts, the present work...
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A new approach to active noise and vibration control - [Part II: unknown frequency case]
PublicationThis paper presents a new approach to rejection of complex-valued sinusoidal disturbances acting at the output of a discrete-time stable linear plant with unknown and possibly timevarying dynamics. It is assumed that both the instantaneous frequency of the sinusoidal disturbance and its amplitude may be slowly varying with time and that the output signal is contaminated with wideband measurement noise. It is not assumed that a...
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Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase
PublicationDue to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine...
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Microarrays and Dynamics of Fluorescent Dyes
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Dynamics of Changes in The Urban Space
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Statistical Dynamics of the Rolling Mills
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Lattice dynamics of CuAu-orderedCuInSe2
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Fast bubble dynamics and sizing
PublicationSingle bubble sizing is usually performed by measuring the resonant bubble response using the Dual Frequency Ultrasound Method. However, in practice, the use of millisecond-duration chirp-like waves yields nonlinear distortions of the bubble oscillations. In comparison with the resonant curve obtained under harmonic excitation, it was observed that the bubble dynamic response shifted by up to 20 percent of the resonant frequency...