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Wyniki wyszukiwania dla: PROTEIN-STRUCTURE MODELING, COARSE GRAINING, UNRES MODEL OF POLYPEPTIDE CHAINS, MOLECULAR DYNAMICS, DATA-ASSISTED SIMULATIONS
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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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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Numerical Investigation on Dynamic Performance of a Multi-storey Steel Structure Model and Comparison with Experimental Results
PublikacjaShaking table testing is the most commonly adopted method to simulate earthquake forces. This approach allows us to analyze the dynamic performance and provides a valuable insight into the dynamics of building structures, which helps to improve their future safety and reliability. The present study aims to conduct a numerical evaluation of dynamic response of a multi-storey steel structure model, which was previously examined during...
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Numerical investigation on dynamic performance of a multi-storey steel structure model and comparison with experimental results
PublikacjaShaking table testing is the most commonly adopted method to simulate earthquake forces. This approach allows us to analyze the dynamic performance and provides a valuable insight into the dynamics of building structures, which helps to improve their future safety and reliability. The present study aims to conduct a numerical evaluation of dynamic response of a multi-storey steel structure model, which was previously examined during...
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Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives
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User satisfaction model
PublikacjaRaport techniczny - opis metody ''User Satisfaction Methods'' wykorzystywanej w projektowaniu komunikacji człowiek-komputer oraz doskonaleniu interfejsu użytkownika.
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Reliable Microwave Modeling By Means of Variable-Fidelity Response Features
PublikacjaIn 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...
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Novel primosomal protein B from Clostridium pasteurianum
PublikacjaPriB 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...
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Novel primosomal protein B from Clostridium pastuerianum
PublikacjaPriB 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...
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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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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Model Correction and Optimization Framework for Expedited EM-Driven Surrogate-Assisted Design of Compact Antennas
PublikacjaDesign of compact antennas is a numerically challenging process that heavily relies on electromagnetic (EM) simulations and numerical optimization algorithms. For reliability of simulation results, EM models of small radiators often include connectors which—despite being components with fixed dimensions—significantly contribute to evaluation cost. In this letter, a response correction method for antenna models without connector,...
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Molecular biology GT
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A Triplet-Learnt Coarse-to-Fine Reranking for Vehicle Re-identification
PublikacjaVehicle re-identification refers to the task of matching the same query vehicle across non-overlapping cameras and diverse viewpoints. Research interest on the field emerged with intelligent transportation systems and the necessity for public security maintenance. Compared to person, vehicle re-identification is more intricate, facing the challenges of lower intra-class and higher inter-class similarities. Motivated by deep...
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Dynamics of quantum entanglement
PublikacjaA model of discrete dynamics of entanglement of a bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied by an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of subsystems. For some mixed states...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublikacjaBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Dynamics of a simplified HPT model in relation to 24h TSH profiles
PublikacjaWe propose a simplified mathematical model of the hypothalamus-pituitary-thyroid (HPT) axis in an endocrine system. The considered model is a modification of the model proposed by Mukhopadhyay and Bhattacharyya in [10]. Our system of delay differential equations reconstructs the HPT axis in relation to 24h profiles of human in physiological conditions. Homeostatic control of the thyroid-pituitary axis is considered by using...
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A simple model of circular hydraulic pump
PublikacjaRozpatrzono warunki powstawania osiowosymetrycznego uskoku hydraulicznego. Przedstawiono model, w którym rozpatrzono obecność dodatkowych strat w równaniu Bernoulliego. Przyczyniają się one do powstawania dodatkowego wiru w miejscu uskoku. Porównanie z wynikami badań eksperymentalnych potwierdza słuszność przyjętych tez.
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User-assisted methodology targeted for building structure interpretable QSPR models for boosting CO2 capture with ionic liquids
PublikacjaTask-specific ionic liquid (IL) is an emerging class of compounds that may be environmentally friendly. Properly selected, these compounds may be green alternative to amine solutions and can replace them in post-combustion carbon dioxide (CO2) capture processes on an industrial scale. However, owing to the vast diversity of ions and their possible combinations, laboratory research is time consuming and expensive. Therefore, computational...
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Numerical heat transfer model in skin burn depth simulations
PublikacjaW artykule przedstawiono numeryczny model wymiany ciepła zachodzącej w tkance skórnej . Wyniki symulacji na modelu zostały porównane z wynikami pomiarów In vivo na zwierzętach.
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A compartment model of alveolar–capillary oxygen diffusion with ventilation–perfusion gradient and dynamics of air transport through the respiratory tract
PublikacjaThis paper presents a model of alveolar–capillary oxygen diffusion with dynamics of air transport through the respiratory tract. For this purpose electrical model representing the respiratory tract mechanics and differentia equations representing oxygen membrane diffusion are combined. Relevant thermodynamic relations describing the mass of oxygen transported into the human body are proposed as the connection between these models,...
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Optical method supported by machine learning for dynamics of C‐reactive protein concentrations changes detection in biological matrix samples
PublikacjaIn this article we present the novel spectroscopy method supported with machine learning for real-time detection of infectious agents in wastewater. In the case of infectious diseases, wastewater monitoring can be used to detect the presence of inflammation biomarkers, such as the proposed C-reactive protein, for monitoring inflammatory conditions and mass screening during epidemics for early detection in communities of concern,...
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Selected Problems of Machine Dynamics
Kursy OnlineThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Copper containing protein sites - structure, properties and models
PublikacjaEnzymy organizmów żywych katalizują wiele reakcji stosowanych w przemyśle chemicznym. Przykładem potencjalnego zastosowania enzymu w produkcji jest synteza L-Dopy przy udziale tyrozynazy. Ze względu na możliwe praktyczne zastosowanie w katalizie, otrzymano i opisano wiele prostych modeli miejsc aktywnych enzymów. W artykule opisano niektóre modele białek zawierających miedź.
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The structure of the data flow in integrated urban traffic management systems – the case of TRISTAR system
PublikacjaThe purpose of the article is to offer some insight into the data flow architecture in the Tri-City’s integrated traffic management system called TRISTAR. To that end selected elements of TRISTAR are identified and described as well as the structure for collecting and exchanging data within different sub-systems. Finally, the article highlights how the TRISTAR system can be extended by adding new elements and modules.
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On the Origin of Protein Superfamilies and Superfolds
PublikacjaDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublikacjaThe experimental analysis of the wood chip removing system during its redesigning in the existing sliding table circular saw and computational fluid dynamic (CFD) numerical simulations of the air flow process is presented in the paper. The attention was focused on the extraction hood and the bottom shelter of the actual existing system. The main aim was to perform experimental research on the pressure distribution inside the...
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Ontological Model for Contextual Data Defining Time Series for Emotion Recognition and Analysis
PublikacjaOne of the major challenges facing the field of Affective Computing is the reusability of datasets. Existing affective-related datasets are not consistent with each other, they store a variety of information in different forms, different formats, and the terms used to describe them are not unified. This paper proposes a new ontology, ROAD, as a solution to this problem, by formally describing the datasets and unifying the terms...
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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Molecular-dynamics simulation of clustering processes in sea-ice floes
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Data on solutions of Hes1 system
Dane BadawczeHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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Synthesis, Molecular Structure, Anticancer Activity, and QSAR Study of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)Benzenesulfonamide Derivatives
PublikacjaA series of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)benzenesulfonamides were synthesized from 4-amino-N-(aryl/heteroaryl)benzenesulfonamides and 2,5-dimethoxytetrahydrofuran. All the synthesized compounds were evaluated for their anticancer activity on HeLa, HCT-116, and MCF-7 human tumor cell lines. Compound 28, bearing 8-quinolinyl moiety, exhibited the most potent anticancer activity against the HCT-116, MCF-7, and HeLa cell lines,...
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Multilevel pharmacokinetics-driven modeling of metabolomics data
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Spirometry measurement model - the diagnostic purpose support
Publikacjathe paper presents a new model of respiratory mechanism based on the spirometry measurements. the spirometry test assesses the efficiency of the lung ventilation. the respiratory system functioning is based on the ventilation mechanism. thus the quality of the lung depends on the quality of lung ventilation. modelling of the respiratory system supports a diagnostic process. the model parameter estimates are obtained on the basis...
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Accelerated multi-objective design optimization of antennas by surrogate modeling and domain segmentation
PublikacjaMulti-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...
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Damaged plasticity model - seismic analysis of structure of the Petronas Twin Towers (Kuala Lumpur) in Malaysia
PublikacjaThe article presents numerical simulations for the modelling of seismic impact on the structure of Petronas Twin Towers (Kuala Lumpur) in Malaysia with application of two methods. The Response Spectrum method, in which a spectrum of the structure's responses to an earthquake's impact is generated and the Acceletogram (BETA) method, in which we generate dynamic load in the form of a diagram of the connection between acceleration...
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Ahmer Bin Hafeez
OsobyI have experience in Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Furthermore, I have hands-on experience with Bioinformatics software. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational...
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Delay induced oscillations in gene expression of Hes1 protein model
PublikacjaW pracy został omówiony model produkcji białka Hes1. Stężenie Hes1 jest kontrolowane przez ujemne sprzężenie zwrotne wbudowane w białko i jego mRNA. Przeprowadzona analiza potwierdziła znane wyniki numeryczne, że oscylacje wywołane są przez opóźnienie. Pokazaliśmy również, że jeśli współczynnik Hilla jest większy niż 1, to istnieje krytyczna wartość opóźnienia, dla której ma miejsce bifurkacja Hopfa i pojawiają się rozwiązania...
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Data Model Development for Security Information Sharing in Smart Grids
PublikacjaThe smart grid raises new security concerns which require novel solutions. It is commonly agreed that to protect the grid, the effective collaboration and information sharing between the relevant stakeholders is prerequisite. Developing a security information sharing platform for the smart grid is a new research direction which poses several challenges related to the highly distributed and heterogeneous character of the grid. In...
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The protocol for using elastic wall model in modeling blood flow within human artery
PublikacjaMedical diagnostic tools will play a major role in the future for an effective patient treatment and reduction their mortality, related to the cardiovascular system diseases (CVDs). There is an urgent need for developing diagnostic procedure to be robust, reliable, accurate and efficient, in the framework of a paradigm shift. Application of numerical techniques is seen as a perspective tool for such purpose. Nevertheless, existing...
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Executing Multiple Simulations in the MERPSYS Environment
PublikacjaThe chapter investigates the steps necessary to perform a simulation instance in the MERPSYS environment and discusses potential limitations in case when vast numbers of simulations are required. An extended architecture is proposed which includes a JMS-based simulation queue and multiple distributed simulators, overcoming the potential bottlenecks. The chapter introduces also methods for preparing suites of multiple simulations...
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On dynamics of origami-inspired rod
PublikacjaWe discuss the dynamics of a relatively simple origami-inspired structure considering discrete and continuum models. The latter was derived as a certain limit of the discrete model. Here we analyze small in-plane deformations and related equations of infinitesimal motions. For both models, dispersion relations were derived and compared. The comparison of the dispersion relations showed that the continuum model can capture the behavior...
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High-resolution microscopy assisted mechanical modeling of ultrafine electrospun network
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Molecular geometry of hexachlorobenzene
Dane BadawczePresented data shows molecular geometry of the ground singlet state of hexachlorobenzene and hexachlorobenzene with potassium atom in 10 angstrom distance. The geometry was obtained via MP2 and CCSD calculations using balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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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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Application of MARKAL model to optimisation of electricity generation structure in Poland in the long-term time horizon Part I - concept of the model
PublikacjaIn this paper, which inaugurates a series of papers on this subject, a concept is proposed of a power system development model with regard to the technological structure of electricity generation in Poland, in the long-term time perspective – until 2060. The model is based on the mathematical structure of the MARKAL optimization package. The paper presents a brief description of the tool used in the model research. In addition,...
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GIS for processing multidimensional marine data in SAAS model
PublikacjaGeographic Information Systems (GIS) have always been a useful tool for visualization and processing of geospatial data. However, their capabilities of analysis non-standard information such as hydroacoustic soundings has thus far been very limited. This paper proposes a general-purpose GIS which uses techniques such as OLAP, WCS and WCPS for processing of multidimensional spatio-temporal data. The versatility of the GIS is exemplified...
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Experimental and Numerical Analysis of Air Trapping in a Porous Medium with Coarse Textured Inclusions
PublikacjaThe paper presents a 2D upward infiltration experiment performed on a model porous medium consisting of fine sand background with two inclusions made of coarser sands. The purpose of the experiment was to investigate the effects of structural air trapping, which occurs during infiltration as a result of heterogeneous material structure. The experiment shows that a significant amount of air becomes trapped in each of the inclusions. Numerical...
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Bistability in a One-Dimensional Model of a Two-Predators-One-Prey Population Dynamics System
PublikacjaIn this paper, we study a classical two-predators-one-prey model. The classical model described by a system of three ordinary differential equations can be reduced to a one-dimensional bimodalmap. We prove that this map has at most two stable periodic orbits. Besides, we describe the bifurcation structure of the map. Finally, we describe a mechanism that leads to bistable regimes. Taking this mechanism into account, one can easily...