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Search results for: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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Simulation-Driven Antenna Modeling by Means of Response Features and Confined Domains of Reduced Dimensionality
PublicationIn recent years, the employment of full-wave electromagnetic (EM) simulation tools has become imperative in the antenna design mainly for reliability reasons. While the CPU cost of a single simulation is rarely an issue, the computational overhead associated with EM-driven tasks that require massive EM analyses may become a serious bottleneck. A widely used approach to lessen this cost is the employment of surrogate models, especially...
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Comparative analysis of various transformation techniques for voiceless consonants modeling
PublicationIn this paper, a comparison of various transformation techniques, namely Discrete Fourier Transform (DFT), Discrete Cosine Transform (DCT) and Discrete Walsh Hadamard Transform (DWHT) are performed in the context of their application to voiceless consonant modeling. Speech features based on these transformation techniques are extracted. These features are mean and derivative values of cepstrum coefficients, derived from each transformation....
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Reliable computationally-efficient behavioral modeling of microwave passives using deep learning surrogates in confined domains
PublicationThe importance of surrogate modeling techniques has been steadily growing over the recent years in high-frequency electronics, including microwave engineering. Fast metamodels are employed to speedup design processes, especially those conducted at the level of full-wave electromagnetic (EM) simulations. The surrogates enable massive system evaluations at nearly EM accuracy and negligible costs, which is invaluable in parameter...
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Modeling of entrained flow steam gasification of sewage sludge
PublicationProper management of sewage sludge becomes increasingly problematic due to legal requirements aiming at diminishing environmental impact, as well as rationalizing the utilization from the point of view of logistics. Steam gasification of sewage sludge can result in very good quality of the producer gas. So far, the works have been focused on the gasification in fixed bed gasifiers. However, this does not allow to take full advantage...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Retention modeling of some saccharides separated on an amino column.
PublicationUsing an amino column (Supelcosil LC-NH2) and different mixtures of acetonitrile-water, quantitative structure-retention relationship models are discussed. These models are based on computed molecular descriptors representing numerically structured features of some saccharides. The obtained results are underlining the lipophilicity/hydrophilicity balance, and how this is controlling the separation of the saccharides. The resulting...
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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SELECTED PROBLEMS OF MACHINE DYNAMICS (2024)
e-Learning CoursesThe course is devoted towards lectures assocuated with the novel issues of machine and structures dynamics. The following lectures will be given during the SPMD course: - introduction to selected problems of machine dynamics, - definition of the machine and structure working environment, - internal and external loads on machines and structures, - dynamics of machines and structures, - strength of machines and structures, - special...
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Adaptive Method for Modeling of Temporal Dependencies between Fields of Vision in Multi-Camera Surveillance Systems
PublicationA method of modeling the time of object transition between given pairs of cameras based on the Gaussian Mixture Model (GMM) is proposed in this article. Temporal dependencies modeling is a part of object re-identification based on the multi-camera experimental framework. The previously utilized Expectation-Maximization (EM) approach, requiring setting the number of mixtures arbitrarily as an input parameter, was extended with the...
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Recent advances in high-frequency modeling by means of domain confinement and nested kriging
PublicationDevelopment of modern high-frequency components and circuits is heavily based on full-wave electromagnetic (EM) simulation tools. Some phenomena, although important from the point of view of the system performance, e.g., EM cross-coupling effects, feed radiation in antenna arrays, substrate anisotropy, cannot be adequately accounted for using simpler means such as equivalent network representations. Consequently, the involvement...
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A new open-source software developed for numerical simulations usingdiscrete modeling methods
PublicationThe purpose of this work is to present the development of an open-source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [F. Donzé, S.A. Magnier, Formulation of a three-dimensional numerical model of brittle behavior, Geophys....
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Removal of Volatile Organic Compounds (VOCs) from Air: Focus on Biotrickling Filtration and Process Modeling
PublicationBiotrickling filtration is a well-established technology for the treatment of air polluted with odorous and volatile organic compounds (VOCs). Besides dozens of successful industrial applications of this technology, there are still gaps in a full understanding and description of the mechanisms of biotrickling filtration. This review focuses on recent research results on biotrickling filtration of air polluted with single and multiple...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Limitations of WSSUS modeling of stationary underwater acoustic communication channel
PublicationPerformances of underwater acoustic communication (UAC) systems are strongly related to specific propagation conditions of the underwater channel. Due to their large variability, there is a need for adaptive matching of the UAC systems signaling to the transmission properties of the channel. This requires a knowledge of instantaneous channel characteristics, in terms of the specific parameters of stochastic models. The wide-sense...
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Adsorption onto zeolites: molecular perspective
Publication2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent...
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublicationFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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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
PublicationThis 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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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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<title>Cavity control system advanced modeling and simulations for TESLA linear accelerator and free electron laser</title>
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Joanna Raczek dr inż.
PeopleEmployment 2003 -- 2019: Faculty of Applied Physics and Mathematics, Gdańsk University of Technology. 2019 - present: Faculty of Electronic, Informatics and Telecominications, Gdańsk University of Technology. Education May 2007: Doctor of Philosophy in Mathematics, University of Gdańsk. Doctoral dissertation: "Paired domination and doubly domination in graphs". Supervisor: dr hab. Jerzy Topp. 2000 -- 2004 Bachelor of Science...
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Indirect adaptive controller based on a self-structuring fuzzy system for nonlinear modeling and control
PublicationIn this paper, a unified nonlinear modeling and control scheme is presented. A self-structuring Takagi-Sugeno (T-S) fuzzymodel is used to approximate the unknown nonlinear plant based on I/O data collected on-line. Both the structure and theparameters of the T-S fuzzy model are updated by an on-line clustering method and a recursive least squares estimation(RLSE) algorithm. The rules of the fuzzy model can be added, replaced or...
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular Dynamics Studies on Amyloidogenic Proteins
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The comparison of semiempirical and ab initio molecular modeling methods in activity and property evaluation of selected antimicrobial sulfonamides
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Half-Order Modeling of Saturated Synchronous Machine
PublicationNoninteger order systems are used to model diffusion in conductive parts of electrical machines as they lead to more compact and knowledge models but also to improve their precision. In this paper a linear half-order impedance model of a ferromagnetic sheet deduced from the diffusion of magnetic field is briefly introduced. Then, from physical considerations and finite elements simulation, the nonlinear half-order impedance model...
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Hearing aid operating in acoustical free field
PublicationAparatowanie bardzo małych dzieci (od 5 miesiąca życia) za pomocą standardowych protez słuchu natrafia na wiele trudności natury praktycznej. Dotyczy to procesu dopasowania aparatu słuchowego, czyli doboru jego ustawień stosownie do aktualnych charakterystyk ubytku słuchu dzieci. Tymczasem wczesne aparatowanie jest zagadnieniem o ogromnym zanczeniu dla rozwoju słuchu, mowy i ogólnej inteligencji dziecka. Referat prezentuje uzyskane...
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Modeling of luminance distribution in CAVE-type virtual reality systems
PublicationAt present, one of the most advanced virtual reality systems are CAVE-type (Cave Automatic Virtual Environment) installations. Such systems are usually consisted of four, five or six projection screens and in case of six screens arranged in form of a cube. Providing the user with a high level of immersion feeling in such systems is largely dependent of optical properties of the system. The modeling of physical phenomena plays nowadays...
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Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublicationIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
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Modeling of a Quasi-Resonant DC Link Inverter Dedicated to Common-Mode Voltage and Ground Current Reduction
PublicationIn this paper, the modeling methodology of the AC drive system with a Parallel Quasi-Resonant DC Link Inverter (PQRDCLI) is described. A presented modeling approach is an attractive tool used for the effective evaluation of a common-mode (CM) voltage and grounds current reduction methods. Designed models of inverter, induction machine (IM), and cable are simple, thus the methods for parameter extraction are not complicated. Verification...
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Numerical Modeling of Cone Penetration Test in Slightly Overconsolidated Clay with Arbitrary Lagrangian-Eulerian Formulation
PublicationIn this paper the results of the cone penetration test (CPT) modeling with the arbitrary Lagrangian-Eulerian (ALE) formulation provided by Abaqus software package have been presented. The study compares the cone resistance and sleeve friction obtained in numerical analysis with values measured in soundings performed in the uniform layer of clayey soil in the Koszalin area. The clay layer was found to be slightly overconsolidated...
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A Goal-Oriented Error Estimator for Reduced Basis Method Modeling of Microwave Devices
PublicationThis letter proposes a novel a-posteriori error estimator suitable for the reduced order modeling of microwave circuits. Unlike the existing error estimators based on impedance function residuals, the new one exploits the residual error associated with the computation of the scattering matrix. The estimator can be effectively used in the Reduced Basis Method (RBM) to automatically generate reduced-order models. The results of numerical...
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Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins
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Exchange
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Numerical modeling and experimental validation of full-scale segment to support design of novel GFRP footbridge
PublicationThe paper contains analysis of full-scaled three meters long segment of a novel composite footbridge. Both numerical modeling and experimental validation were performed. Analyzed object is a shell type sandwich channel-like structure made of composite sandwich with GFRP laminates as a skin and PET foam as a core. Several static load schemes were performed including vertical and horizontal forces. In FEM analysis multilayered laminate...
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APPLICATION OF RESPONSE SURFACE MODELING FOR OPTIMIZATION AND DETERMINATION OF MALONDIALDIALDEHYDE BY VORTEX-ASSISTED DISPERSIVE LIQUID-LIQUID MICROEXTRACTION AND GC-FID
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Electronic structure and magnetism of samarium and neodymium adatoms on free-standing graphene
PublicationThe electronic structure of selected rare-earth atoms adsorbed on a free-standing graphene was investigated using methods beyond the conventional density functional theory (DFT+U, DFT +HIA, and DFT+ED). The influence of the electron correlations and the spin-orbit coupling on the magnetic properties has been examined. The DFT+U method predicts both atoms to carry local magnetic moments (spin and orbital) contrary to a nonmagnetic...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublicationW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
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Exchange-traded products in Germany: development and substitution of exchange-traded funds, exchange-traded commodities and exchange-traded notes.
PublicationResearch background: Exchange-traded products (ETPs) are one of the most rapidly growing categories of financial products. Their fast development has been boosted by innovative features. Three main categories of ETPs are exchange-traded funds (ETFs), exchange-traded commodities (ETCs) and exchange-traded notes (ETNs). ETCs and ETNs remain least known, even though their number on some stock exchanges is high. In Europe, Germany...
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Data set generation at novel test-rig for validation of numerical models for modeling granular flows
PublicationSignificant effort has been exerted on developing fast and reliable numerical models for modeling particulate flow; this is challenging owing to the complexity of such flows. To achieve this, reliable and high-quality experimental data are required for model development and validation. This study presents the design of a novel test-rig that allows the visualization and measurement of particle flow patterns during the collision...
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Zdzisław Kowalczuk prof. dr hab. inż.
PeopleZdzislaw Kowalczuk received his M.Sc. degree in 1978 and Ph.D. degree in 1986, both in Automatic Control from Technical University of Gdańsk (TUG), Gdańsk, Poland. In 1993 he received his D.Sc. degree (Dr Habilitus) in Automatic Control from Silesian Technical University, Gliwice, Poland, and the title of Professor from the President of Poland in 2003. Since 1978 he has been with Faculty of Electronics, Telecommunications and Informatics...
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Accelerated multi-objective design optimization of antennas by surrogate modeling and domain segmentation
PublicationMulti-objective optimization yields indispensable information about the best possible design trade-offs of an antenna structure, yet it is challenging if full-wave electromagnetic (EM) analysis is utilized for performance evaluation. The latter is a necessity for majority of contemporary antennas as it is the only way of achieving acceptable modeling accuracy. In this paper, a procedure for accelerated multi-objective design of...