Search
Filters
total: 9474
-
Catalog
- Publications 8021 available results
- Journals 112 available results
- Conferences 18 available results
- People 116 available results
- Projects 4 available results
- Laboratories 1 available results
- Research Equipment 1 available results
- e-Learning Courses 129 available results
- Events 2 available results
- Open Research Data 1070 available results
displaying 1000 best results Help
Search results for: ambiguous restraints, coarse-grained models, nmr-assisted protein-structure modeling, unres
-
Strategies for feature-assisted development of topology agnostic planar antennas using variable-fidelity models
PublicationDesign of antennas for contemporary applications presents a complex challenge that integrates cognitive-driven topology development with the meticulous adjustment of parameters through rigorous numerical optimization. Nevertheless, the process can be streamlined by emphasizing the automatic determination of structure geometry, potentially reducing the reliance on traditional methods that heavily rely on engineering insight in the...
-
Diffusion process modeling by using fractional-order models
Publication -
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...
-
High-resolution microscopy assisted mechanical modeling of ultrafine electrospun network
Publication -
Reliable Microwave Modeling By Means of Variable-Fidelity Response Features
PublicationIn this work, methodologies for low-cost and reliable microwave modeling are presented using variable-fidelity response features. The two key components of our approach are: (i) a realization of the modeling process at the level of suitably selected feature points of the responses (e.g., S-parameters vs. frequency) of the structure at hand, and (ii) the exploitation of variable-fidelity EM simulation data, also for the response...
-
Efficient Surrogate Modeling and Design Optimization of Compact Integrated On-Chip Inductors Based on Multi-Fidelity EM Simulation Models
PublicationHigh-performance and small-size on-chip inductors play a critical role in contemporary radio-frequency integrated circuits. This work presents a reliable surrogate modeling technique combining low-fidelity EM simulation models, response surface approximations based on kriging interpolation, and space mapping technology. The reported method is useful for the development of broadband and highly accurate data-driven models of integrated...
-
Biopolyols obtained via microwave-assisted liquefaction of lignin: structure, rheological, physical and thermal properties
PublicationThe present study examined the application of polyols obtained via microwave-assisted liquefaction of lignin in the production of rigid polyurethane foam. Lignin was liquefed in crude glycerol and 1,4-butanediol at diferent temperatures (130–170 °C), without a catalyst and using various biomass concentrations (15 and 30 wt%). The physicochemical properties, process yield, and FTIR-based identifcation of the obtained polyols were...
-
Enhanced trap-assisted recombination in organic semiconductors
PublicationAn analytical model to describe the interaction of excitons and charge transfer states with deep traps is formulated for the case of molecular materials. Here, we have considered the influence of a trap-assisted recombination on this phenomenon. The final expression for the effective recombination rate has been derived from the Shockley–Read–Hall theory and kinetic equations which characterize different photophysical processes....
-
Numerical modeling of wave-seabed-structure interaction.
PublicationPraca doktorska przedstawia propozycję nowoczesnego rozwiązania obciążeń hydraulicznych przy uwzględnieniu nieliniowych oddziaływań pomiędzy falą wodną, przepuszczalnym dnem i porowatą konstrukcją morską. Nabrzeże pionowe, falochron podwodny i falochron kompozytowy były obiektem eksperymentów numerycznych, których wyniki były weryfikowane przy użyciu wyników laboratoryjnych (niszczących i nieniszczących). Krótki przegląd bieżącej...
-
The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
-
The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
-
MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publication—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
-
Results of modeling of pharmaceuticals mixtures toxicity with deviation ratio and best-fit functions models using Aliivibrio fischeri bacterium as model organism
Open Research DataThe research was concerned with verifying the impact of mixtures of nine pharmaceuticals against a selected organism, i.e., the bacterium Aliivibrio fischeri. A. fisheri is used as a model organism in the monitoring of acute toxicity in environmental and reference samples in Microtox® systems. Tested pharmaceuticals, namely: diclofenac (sodium salt),...
-
Justyna Signerska-Rynkowska dr inż.
PeopleI am currently an assistant professor (adjunct) at Gdansk University of Technology (Department of Differential Equations and Mathematics Applications). My scientific interests include dynamical systems theory, chaos theory and their applications to modeling of biological phenomena, especially to neurosciences. In June 2013 I completed PhD in Mathematics at the Institute of Mathematics of Polish Academy of Sciences (IMPAN) (thesis...
-
NMR dispersion studies of poly(ethylene oxide)/sodium montmorillonitenanocomposites
PublicationPraca prezentuje wyniki badań dotyczące struktury nanokompozytów opartych na matrycy poli(tlenku etylenu) zawierającej montmorylonit sodowy. Układy zawierające PEO/MMT scharakteryzowano metodami NMR (Fast Field Cycling NMR), DSC oraz XRD.
-
Introductory modeling for decision-making using AMPL
e-Learning CoursesIntroductory modeling for decision-making using AMPL
-
Modeling projects for decision-making using AMPL
e-Learning CoursesModeling projects for decision-making using AMPL
-
Modeling of pharmaceuticals mixtures toxicity with deviation ratio and best-fit functions models
PublicationThe present study deals with assessment of ecotoxicological parameters of 9 drugs (diclofenac (sodium salt), oxytetracycline hydrochloride, fluoxetine hydrochloride, chloramphenicol, ketoprofen, progesterone, estrone, androstenedione and gemfibrozil), present in the environmental compartments at specific concentration levels, and theirmutual combinations by couples against Microtox® and XenoScreen YES/YAS® bioassays. As the quantitative...
-
Structure-property relationships in peroxide-assisted blends of poly(ε-caprolactone) and poly(3-hydroxybutyrate)
PublicationPoly(ε-caprolactone) and poly(3-hydroxybutyrate) (PCL/PHB) blends in two weight ratios (75/25 and 50/50) were reactively compatibilized in the presence of di-(2-tert-butyl-peroxyisopropyl)-benzene and dicumyl peroxide as free radical initiators. Rheological, mechanical, thermal properties and morphological features, as well as the chemical structure of PCL/PHB blends were investigated. It was found that regardless of PCL/PHB blend...
-
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
-
Synthesis, crystal structure, and high-resolution NMR spectroscopy of methyl 3-azido-2,3-dideoxy-4,6-di-O-p-tolylsulfonyl-α-D-xylo-hexopyranoside
PublicationOpisano syntezę 3-azydo-2,3-dideoksy-4,6-di-O-p-toluenosulfonylo- i 6-O-p-toluenosulfonylo-alfa-D-ksylo-heksopiranozydów. Dla obu związków i ich prekursorów wykonano wysokorozdzielczą spektroskopię 1H i 13C NMR. Strukturę tytułowego związku określono metodą rentgenowskiej analizy strukturalnej. W pracy dyskutuje się wpływ grup ochronnych przy atomach tlenu na przesunięcia chemiczne sąsiadujących atomów w węglowej i protonowej spektroskopii...
-
LC-MS and LC-NMR as Complementary Techniques for the Determination of Pharmaceuticals in Dosage Formulations
PublicationPharmaceuticals contain not only pharmacologically active compounds but also a range of excipients. The danger exists that impurities may also be present in such drugs, which may adversely affect their efficacy and even endanger patient health and life. Monitoring the composition of pharmaceutical products is therefore essential. The trace amounts of such impurities in pharmaceuticals are often identified and determined with liquid...
-
Numerical Modeling of Hydrosystems 2024/2025
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
-
Numerical Modeling of Hydrosystems 2024/2025
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
-
Numerical Modeling of Hydrosystems 2023/2024
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
-
Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
-
Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
-
NEW EXPERIENCES IN DIKE CONSTRUCTION WITH SOIL-ASH COMPOSITESAND FINE-GRAINED DREDGED MATERIALS
PublicationThe supporting structure inside a coastal dike is often made of dredged non-uniform sand with good compaction proper-ties. Due to the shortage of natural construction material for both coastal and river dikes and the surplus of different processed mate-rials, new experiments were made with sand-ash mixtures and fine-grained dredged materials to replace both dike core and dikecover materials resulting in economical, environmentally...
-
Charge-assisted N(+)–H···(−)S hydrogen bonds in the crystal structure of selected diammonium thiophenolates.
PublicationNew salts of thiophenol with three flexible aliphatic diamines H2N(CH2)nNH2 (n = 2, 4 and 6) have been synthesized and characterized by elemental analyses, IR spectroscopy and X-ray crystallography in order to analyze their supramolecular architecture. Structural analyses indicate that in the crystals, proton transfer has occurred, with the –SH group giving (+)N–H···S(−) hydrogen bonding interaction. The structure of compound 1...
-
Kriging Models for Microwave Filters
PublicationSurrogate modeling of microwave filters’ response is discussed. In particular, kriging is used to model either the scattering parameters of the filter or the rational representation of the filter’s characteristics. Surrogate models for these two variants of kriging are validated in solving a microwave filter optimization problem. A clear advantage of surrogate models based on the rational representation over the models based on scattering...
-
Ultrasound assisted extraction
PublicationThe use of green and sustainable extraction techniques is very popular topic in the multidisciplinary area of chemistry, biology and technology. There is no doubt that extraction constitutes a very important step of analytical procedures of separation, detection, identification and determination of wide spectrum analytes from samples characterized by complex and very often nonhomogeneous composition of matrix. Traditional techniques...
-
The effect of sunscreen 4‐methylbenzylidene camphor in different and reproductive models, its bioaccumulation and molecular effects on ligand‐receptor interaction, and protein expression
Publication4-Methylbenzylidene camphor (4-MBC) is a photo-absorbing UV filter prevalently used in cosmetics, which can be absorbed into circulation and cause systemic effects. 4-MBC is continued to be released in the environment despite the growing knowledge about its bioaccumulation and endocrine disrupting effects. Previous reviews have mentioned UV-filter together but this review considers 4-MBC alone, due to its prevalence and concerning...
-
NMR-Based Structural Insight into DNA G-Quadruplex
PublicationEmerging as a promising area in anticancer research, noncanonical DNA structures such as G-quadruplexes are studied using NMR spectroscopy. NOESY spectra reveals crucial interactions between ligands and G-quadruplexes, helping to understand non-covalent binding mechanisms. This knowledge is essential for rational drug design targeting these structures.
-
Expedited Variable-Resolution Surrogate Modeling of Miniaturized Microwave Passives in Confined Domains
PublicationDesign of miniaturized microwave components is largely based on computational models, primarily, full-wave electromagnetic (EM) simulations. EM analysis is capable of giving an accurate account for cross-coupling effects, substrate and radiation losses, or interactions with environmental components (e.g., connectors). Unfortunately, direct execution of EM-based design tasks such as parametric optimization or uncertainty quantification,...
-
TIME SERIES MODELING (PG_00063724)
e-Learning CoursesEffectively uses in-depth knowledge of economic time series analysis methods, applying the results of analyzes to formulate forecasts. Subject contents: 1. Classical time series analysis (trend, cyclical fluctuations) 2. Exponential smoothing models 3. Holt and Winters model 4. Stochastic processes and time series 5. Characteristics of stochastic processes 6. Process spectrum autocorrelation functions 7. Study of the stationarity...
-
Arbutin: Isolation, X-ray structure and computional studies
PublicationArbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were...
-
Quantitative structure-(chromatographic) retention relationship models for dissociating compounds
Publication -
Attributional and attentional patterns in the perception of ambiguous harmful encounters involving peer and authority figures
Publication -
Synthesis, structure and properties of novel poly(hydroxyurethane)s obtained by non-isocyanate route
PublicationNon-isocyanate polyurethanes (NIPUs) can be synthesized by polyaddition of five-membered bis(cyclic carbonate)s and primary diamines. NIPUs are an alternative for the commonly used (in the form of foams, elastomers, coatings or fibers) in the industry polyurethanes obtained using toxic and moisture sensitive diisocyanates, polyols and low-molecular weight chain extenders. The main aim of this work was to synthesize non-isocyanate...
-
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,...
-
GRAPHICAL MODELS
Journals -
STOCHASTIC MODELS
Journals -
Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
Publication -
Biomolecular NMR Assignments
Journals -
JOURNAL OF BIOMOLECULAR NMR
Journals -
Characterization of metabolites in different kiwifruit varieties by NMR and fluorescence spectroscopy
PublicationIt is known from our previous studies that kiwifruits, which are used in common human diet, have preventive properties of coronary artery disease. This study describes a combination of 1H NMR spectroscopy, multivariate data analyses and fluorescence measurements in differentiating of some kiwifruit varieties, their quenching and antioxidant properties. A total of 41 metabolites were identified by comparing with literature data...
-
Numerical Modeling of Hydrosystems 2022/2023 (summer)
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
-
Numerical Modeling of Hydrosystems 2022/2023 (winter)
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
-
Synthesis, the crystal structure, and high-resolution NMR spectroscopy of methyl 4-O-acetyl-3-azido-2,3,6-trideoxy-6-iodo-ŕ-D-arabino-hexopyranoside
PublicationW wyniku wieloetapowej syntezy otrzymano glikozyd metylowy 4-O-acetylo-3-azydo-2,3,6-trideoksy-6-jodo-ŕ-D-arabino-heksopyranozy. Związek wykazuje konformację 4C1, co wykazano na podstawie wysokorozdzielczej spektroskopii1H i 13C NMR oraz rentgenowskiej analizy strukturalnej monokryształu. W pracy scharakteryzowano również 7 nowych związków otrzymanych jako produkty pośrednie i uboczne.
-
A simple model of the trap-assisted recombination with the excitonic Auger mechanism
PublicationWe present a simple model of the trap-assisted recombination combined with the excitonic Auger mechanism. It has been shown that only six independent transitions of electrons and holes should be taken into account to describe a combination of the Shockley–Read–Hall (SRH) recombination with this excitonic process. This is in opposition to a well-known model of the SRH mechanism with the free carriers Auger effect via deep states,...