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Wyniki wyszukiwania dla: ambiguous restraints, coarse-grained models, nmr-assisted protein-structure modeling, unres
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublikacjaShort 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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NMR study of the complexes of tris(oxaalkyl) borates with SbCl5
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Effect of the template-assisted electrodeposition parameters on the structure and magnetic properties of Co nanowire arrays
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Modeling of Human Tissue for Medical Purposes
PublikacjaThe paper describes the possibilities offered for medicine by modeling of human tissue using virtual and augmented reality. It also presents three proposals of breast modeling for the use in clinical practice. These proposals are the result of arrangements of medical and computer scientists team (the authors) and will be pursued and implemented in the near future. There is included also a brief description of the most popular methods...
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Protein & Cell
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PROTEIN JOURNAL
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Modeling emotions for affect-aware applications
PublikacjaThe chapter concerns emotional states representation and modeling for software systems, that deal with human affect. A review of emotion representation models is provided, including discrete, dimensional and componential models. The paper provides also analysis of emotion models used in diverse types of affect-aware applications: games, mood trackers or tutoring systems. The analysis is supported with two design cases. The study...
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Probabilistic Analysis of Structure Models using Target Random Sampling (TRS)
PublikacjaThe work presents testing methods of sensitivity and reliability of mechanical or structural systems. All computations concerned the case of Zigler column, a simple model of a compressed column involving two random variables only. A conclusion was drawn that the standard Monte Carlo method, its reduction variants and the response surface method allow to assess the sensitivity of structural response to the variation of random structural...
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Accurate simulation-driven modeling and design optimization of compact microwave structures
PublikacjaCost efficient design optimization of microwave structures requires availability of fast yet reliable replacement models so that multiple evaluations of the structure at hand can be executed in reasonable timeframe. Direct utilization of full-wave electromagnetic (EM) simulations is often prohibitive. On the other hand, accurate data-driven modeling normally requires a very large number of training points and it is virtually infeasible...
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Influence of bulky 3,3′-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublikacjaWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublikacjaWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Models of Structures in Didactics
PublikacjaThe final aim of teaching students subjects, such as structural mechanics, reinforced concrete, and steel structures is to teach them how structures work in a given building as well as to provide them with skills enabling them to calculate and design structures. The behavioral model of the structure, contrary to the architectural model, which focuses mainly on the external form of the building, shows workings from both the static...
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Rapid dimension scaling of triple-band antennas by means of inverse surrogate modeling
PublikacjaGeometry scaling of antennas, i.e., finding optimum dimensions of the structure for given operating conditions and material parameters is an important yet challenging problem. In this paper, we discuss fast dimension scaling of triple-band antennas with respect to operating frequencies. We adopt the inverse surrogate modeling approach where the surrogate model is a function of the three operating frequencies of the antenna and...
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Arginine-, d-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies
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Modelling gene expression of a self-regulating protein
PublikacjaWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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A structure and simulation-driven design of compact CPW-fed UWB antenna
PublikacjaIn this letter, a structure of a miniaturized ultra-wideband CPW-fed antenna and its design proce-dure are presented. The antenna is a modified version of the design previously proposed in the literature, with additional degrees of freedom introduced in order to improve the structure flexibility. The small size is achieved by executing a rigorous optimization procedure that consists of two stages: (i) smart random search carried...
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JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Application of chemometric modeling for ionic liquid-based ultrasonic-assisted dispersive liquid-liquid microextraction: Analysis of fosetyl-aluminum in fruit and vegetable samples
PublikacjaThis manuscript presents a new method for selective extraction and determination of fosetyl-aluminum in fruits and vegetable samples based on ultrasonic-assisted dispersive liquid-liquid microextraction method using ionic liquids (IL-UA-DLLME). A UV-Visible spectrophotometer was used for detection and quantification. Plants used for sample collection were grown under controlled conditions in a greenhouse. Central composite design...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublikacjaMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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15 N NMR and FTIR studies of 2,4-dinitroanilines and their salts
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Modeling external carbon addition in combined N-P activated sludge systems with an extension of the IWA Activated Sludge Models
PublikacjaThe aim of this study was to expand the IWA Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic...
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Modeling external carbon addition in combined N-P activated sludge systems with an extension of the IWA Activated Sludge Models
PublikacjaThe aim of this study was to expand the IWA Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic...
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublikacjaIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Modeling BIM Objects From Point Clouds. Examples
PublikacjaThe article presents several ways to obtain BIM (Building Information Modeling) models from point clouds using standard commands in Revit 2018. In Revit geometric forms are possible to obtain in project, family or conceptual environments. Efficient modeling requires knowledge of methods of creating families and components in these environments and ways to combine them. Modeling methods with system and loadable families are presented,...
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Rapid EM-driven antenna dimension scaling through inverse modeling
PublikacjaIn this letter, a computationally feasible technique for dimension scaling of antenna structures is introduced. The proposed methodology is based on inverse surrogate modeling where the geometry parameters of the antenna structure of interest are explicitly related to the operating frequency. The surrogate model is identified based on a few antenna designs optimized for selected reference frequencies. For the sake of computational...
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Proteins Structure Models in the Evaluation of Novel Variant (C.472_477del) in the MOCS2 Gene
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Journal of Chemical Information and Modeling
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bio-based polyester polyols - chemical structure of Miniatura 4 proper samples
Dane BadawczePresented results are related with project MINIATURA 4 realization. At the document, the chemical structure of bio-based polyester polyols (poly(propylene-co-propan-1,2,3-triol succinate)s) are presented as analysis of FTIR and H NMR spectroscopy.
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublikacjaBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Fundamentals of Data-Driven Surrogate Modeling
PublikacjaThe primary topic of the book is surrogate modeling and surrogate-based design of high-frequency structures. The purpose of the first two chapters is to provide the reader with an overview of the two most important classes of modeling methods, data-driven (or approx-imation), as well as physics-based ones. These are covered in Chap-ters 1 and 2, respectively. The remaining parts of the book give an exposition of the specific aspects...
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Inverse surrogate modeling for low-cost geometry scaling of microwave and antenna structures
PublikacjaPurpose–The purpose of this paper is to investigate strategies for expedited dimension scaling ofelectromagnetic (EM)-simulated microwave and antenna structures, exploiting the concept of variable-fidelity inverse surrogate modeling.Design/methodology/approach–A fast inverse surrogate modeling technique is described fordimension scaling of microwave and antenna structures. The model is established using referencedesigns obtained...
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Study of Aliphatic Polyurethanes by the Low-Field 1H NMR Relaxometry Method with the Inversion of the Integral Transformation
PublikacjaIn this paper, the distributions of the 1H nuclear magnetic resonance (NMR) spin–lattice and spin–spin relaxation times are used to characterize the mobility of different sections of macromolecules of aliphatic polyurethanes and the cross-linking density of polymer chains. The NMR relaxometry method with inversion of integral transformation is applied to study the effect of poly (ethylene glycol) and glycerol phosphate calcium...
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
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Local Conformation and Cocrystallization Phenomena in Renewable Diaminoisoidide-Based Polyamides Studied by FT-IR, Solid State NMR, and WAXD
PublikacjaBiobased polyamides synthesized from diaminoisoidide (DAII), 1,4-diaminobutane, and sebacic acid are investigated by FT-IR, 13C{1H} magic-angle spinning/cross-polarization (CP/MAS) NMR spectroscopy, and WAXD. Their molecular conformation and mobility undergo distinct changes as a function of temperature and diaminoisoidide content in the compositions. The presence of randomly distributed diaminoisoidide (DAII) in the polyamides...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
Kursy Online{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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Polymeric materials in medicine – structure and desing 2023/24
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A structure and design of a novel compact UWB MIMO antenna
PublikacjaIn the paper, a concept and design procedure of a novel compact MIMO slot antenna is presented. In order to achieve a better filling of available space, individual antennas are constrained to a triangular shape and optimized for a reduced size. The MIMO structure is then assembled using the two of previously designed antennas in orthogonal arrangement. Surrogate-assisted numerical optimization involving variable-fidelity electromagnetic...
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OIL-ASSISTED THERMO-MECHANICAL RECLAMATION OF GROUND TIRE RUBBER
PublikacjaNowadays, it is crucial to seek for the methods of by-products and waste utilization, considering both environmental and economic factors. The example of waste material generated in the massive amounts, which requires the attention is ground tire rubber generated during recycling of post-consumer car tires. It can be applied as a filler into different polymer matrices, but to enhance its effectivity proper modifications should...
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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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Kriging-assisted hybrid reliability design and optimization of offshore wind turbine support structure based on a portfolio allocation strategy
PublikacjaIn recent years, offshore wind power generation technology has developed rapidly around the world, making important contributions to the further development of renewable energy. When designing an Offshore Wind Turbine (OWT) system, the uncertainties in parameters and different types of constraints need to be considered to find the optimal design of these systems. Therefore, the Reliability-Based Design Optimization (RBDO) method...
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Domain segmentation for low-cost surrogate-assisted multi-objective design optimisation of antennas
PublikacjaAbstract: Information regarding the best possible design trade-offs of an antenna structure can be obtained through multiobjective optimisation (MO). Unfortunately, MO is extremely challenging if full-wave electromagnetic (EM) simulation models are used for performance evaluation. Yet, for the majority of contemporary antennas, EM analysis is the only tool that ensures reliability. This study introduces a procedure for accelerated...
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A DSC and NMR-Relaxation study of the molecular mobility of water protons interacting with chemically modified starches
PublikacjaChanges in the mobility of water protons in the chemically modified starches (CMS)–water system are studied by differential scanning calorimetry and NMR relaxation. The amounts of unfrozen water at negative temperatures and additional (after gelation) unfrozen for CMS are lower than those for native starch. The proton spin–spin relaxation time T2 for CMS samples, conventionally attributed to the water fraction in starch granules,...
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Grand Challenges on the Theory of Modeling and Simulation
PublikacjaModeling & Simulation (M&S) is used in many different fields and has made many significant contributions. As a field in its own right, there have been many advances in methodologies and technologies. In 2002 a workshop was held in Dagstuhl, Germany, to reflect on the grand challenges facing M&S. Ten years on, a series of M& S Grand Challenge activities are marking a decade of progress and are providing an opportunity to reflect...
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Dynamic Bayesian Networks for Symbolic Polyphonic Pitch Modeling
PublikacjaSymbolic pitch modeling is a way of incorporating knowledge about relations between pitches into the process of an- alyzing musical information or signals. In this paper, we propose a family of probabilistic symbolic polyphonic pitch models, which account for both the “horizontal” and the “vertical” pitch struc- ture. These models are formulated as linear or log-linear interpo- lations of up to fi ve sub-models, each of which is...
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Discrete modeling of micro-structure evolution during concrete fracture using DEM
PublikacjaW artykule pokazano wyniki dyskretne DEM dla betonu poddanego ściskaniu i rozciąganiu jednoosiowemu. Wyniki siła-przemieszczenie i zarysowania porównano z doświadczeniami. Szczególną uwagę zwrócono na zjawiska mikrostrukturalne podczas zarysowania na poziomie kruszywa.
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Flow Process Models for Pipeline Diagnosis
PublikacjaThis chapter examines the problem of modeling and parameterization of the transmission pipeline flow process. First, the base model for discrete time is presented, which is a reference for other developed models. Then, the diagonal approximation (AMDA) method is proposed, in which the tridiagonal sub-matrices of the recombination matrix are approximated by their diagonal counterparts, which allows for a simple determination of...