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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Ammine(2-ethylpyridine-κN)bis(tri-tert-butoxysilanethiolato-κS)cobalt(II)
PublicationTytułowy związek [Co(C12H27O3SSi)2(C7H9N)(NH3)] został otrzymany w reakcji dimerycznego amoniakalnego tri-tert-butoksysilanotiolanu kobaltu(II) z 2-etylopirydyną. Atom kobaltu w otrzymanym związku jest koordynowany przez dwa atomy siarki, jedną resztę 2-etylopirydyny i jedną cząsteczkę amoniaku. Dzięki specyficznemu przestrzennemu ustawieniu ligandów, dodatkowo tworzy się wiązanie wodorowe wewnątrz cząsteczkowe N-H - S
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Electronic structure and rovibrational predissociation of the 2^1Π state in KLi
PublicationAdiabatic potential energy curves of the 3^1Σ^+, 3^3Σ^+, 2^1Π and 2^3Π states correlating for large internuclear distance with the K(4s) + Li(2p) atomic asymptote were calculated. Very good agreement between the calculated and the experimental curve of the 2^1Π state allowed for a reliable description of the dissociation process through a small (∼20 cm−1 for J = 0) potential energy barrier. The barrier supports several rovibrational...
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Classification of Covid-19 using Differential Evolution Chaotic Whale Optimization based Convolutional Neural Network
PublicationCOVID-19, also known as the Coronavirus disease-2019, is an transferrable disease that spreads rapidly, affecting countless individuals and leading to fatalities in this worldwide pandemic. The precise and swift detection of COVID-19 plays a crucial role in managing the pandemic's dissemination. Additionally, it is necessary to recognize COVID-19 quickly and accurately by investigating chest x-ray images. This paper proposed a...
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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
PublicationIn 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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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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A Quality Model for UML tools
PublicationJakość narzędzi UML wpływa na efektywność wykonywania zadań związanych z modelowaniem systemów w procesie wytwarzania oprogramowania. Celem badań prezentowanych w tym referacie jest wyodrębnienie kryteriów jakości narzędzi UML. Omówiono rolę narzędzi UML w projekcie informatycznym, a następnie zaprezentowano szereg kryteriów jakości narzędzi UML wraz z aspektami oceny oraz opisem ankiety, która służy do oceny narzędzi względem...
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The elasto-viscoplstic Chaboche model
PublicationW artykule przedstawiono rozwoj i numeryczną aplikacje sprężysto-lepkoplastycznego modelu Chabocha. Przedstawione są także szczegółowe opisy kilkunastu wariantów modelu Chaboche'a wraz z parametrami materiałowymi.
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublicationControlled ovarian stimulation is tailored to the patient based on clinical parameters but estimating the number of retrieved metaphase II (MII) oocytes is a challenge. Here, we have developed a model that takes advantage of the patient’s genetic and clinical characteristics simultaneously for predicting the stimulation outcome. Sequence variants in reproduction-related genes identified by next-generation sequencing were matched...
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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...
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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...
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High accuracy hydroacoustic system to study codend model parameters
PublicationWażnym zadaniem projektantów narzędzi połowowych jest stworzenie efektywnych narzędzi połowowych działających selektywnie poprzez optymalizacje ich geometrii. Hydroakustyczny system pomiaru geometrii modeli worków dorszowych opisany w artykule został zaprojektowany dla opracowania konstrukcji worka dorszowego na potrzeby rybołówstwa na Morzu Bałtyckim.System składa się z 10 par przetworników ultradźwiękowych, mikroprocesorowego...
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Novel 2-(2-alkylthiobenzenesulfonyl)-3-(phenylprop-2-ynylideneamino)guanidine derivatives as potent anticancer agents – Synthesis, molecular structure, QSAR studies and metabolic stability
PublicationA series of new 2-(2-alkylthiobenzenesulfonyl)-3-(phenylprop-2-ynylideneamino)guanidine derivatives have been synthesized and evaluated in vitro by MTT assays for their antiproliferative activity against cell lines of colon cancer HCT-116, cervical cancer HeLa and breast cancer MCF-7. The obtained results indicated that these compounds display prominent cytotoxic effect. The best anticancer properties have been observed for derivatives...
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The structure of knowledge resources supporting a model of IT technologies architecture = Struktury zasobów wiedzy wspierających model architektury technologii IT
PublicationThis paper introduces an abstract model for tools used in the software engineering process. The main goal of the research is to develop a universal model which allows a description of tools used in the process. The model supports a decision making process and gives an option to choose the best tooling for the situation. The model considers many factors including, but not exclusive to, the company structure, project environment...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Modelling gene expression of a self-regulating protein
PublicationWe 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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Redox State Sensitive Spectroscopy of the Model Compound [(H-dcbpy)(2)Ru-II(NCS)(2)](2-) (dcbpy=2,2 '-Bipyridine-4,4 '-dicarboxylato)
PublicationThe charge transfer reaction mechanism in a ruthenium polypyridine model complex with isothiocyanato ligands, i.e., [(H-dcbpy)(2)Ru(NCS)(2)](2-) 2Bu(4)N(+) (Ru2H) (dcbpy = 2,2'-bipyridine-4,4'-dicarboxylato), has been investigated by combining UV-vis absorption, resonance Raman spectroscopy, and electrochemical methods. Understanding the photophysics of light-harvesting complexes of this class is an indispensable prerequisite to...
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Improving the Accuracy in Sentiment Classification in the Light of Modelling the Latent Semantic Relations
PublicationThe research presents the methodology of improving the accuracy in sentiment classification in the light of modelling the latent semantic relations (LSR). The objective of this methodology is to find ways of eliminating the limitations of the discriminant and probabilistic methods for LSR revealing and customizing the sentiment classification process (SCP) to the more accurate recognition of text tonality. This objective was achieved...
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High quality speech codec employing sines+noise+transients model
PublicationA method of high quality wideband speech signal representation employing sines+transients+noise model is presented. The need for a wideband speech coding approach as well as various methods for analysis and synthesis of sines, residual and transient states of speech signal is discussed. The perceptual criterion is applied in the proposed approach during encoding of sines amplitudes in order to reduce bandwidth requirements and...
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A review on computer‐aided chemogenomics and drug repositioning for rational COVID ‐19 drug discovery
PublicationApplication of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development...
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Conspiracy beliefs about groups benefitting from the COVID-19 pandemic moderate the relationship between fear of COVID-19 and subjective assessment of the efficacy of preventive measures
PublicationDrawing on the protective motivation theory and parallel response model, in this cross-sectional, questionnaire-based study (N = 212) performed on the general public (age 18-65), we aimed to test the potential interaction effects of fear of COVID-19 and conspiracy beliefs about groups benefitting from the COVID-19 pandemic in predicting subjective assessment of the efficacy of three COVID-19 preventive measures. The results...
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Algebraic periods of self-maps of a rational exterior space of rank 2
PublicationArtykuł stanowi kompletny opis okresów algebraicznych dla odwzorowań wymiernej przestrzeni zewnętrznej rangi 2 w siebie.
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Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublicationAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe 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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Evaluating Performance and Accuracy Improvements for Attention-OCR
PublicationIn this paper we evaluated a set of potential improvements to the successful Attention-OCR architecture, designed to predict multiline text from unconstrained scenes in real-world images. We investigated the impact of several optimizations on model’s accuracy, including employing dynamic RNNs (Recurrent Neural Networks), scheduled sampling, BiLSTM (Bidirectional Long Short-Term Memory) and a modified attention model. BiLSTM was...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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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...
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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...
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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
PublicationBackground 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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Knowledge Risks in the COVID-19 Pandemic
PublicationThis conceptual paper aims to identify, present, and analyse potential knowledge risks organizations face in external and dynamic crises such as the COVID-19 pandemic. Until only recently, many researchers and practitioners have perceived knowledge primarily as something positive. This view has changed recently with a growing number of studies highlighting risks related to knowledge. The on-going COVID-19 pandemic can be seen as an...
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Conformation-family Monte Carlo: A new method for crystal structure prediction
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Plasma Amino Acids May Improve Prediction Accuracy of Cerebral Vasospasm after Aneurysmal Subarachnoid Haemorrhage
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Synthesis, structure characterization and thermal propertiesof [Zr<sub>6</sub>(μ<sub>3</sub>-O)<sub>4</sub>(μ<sub>3</sub>-OH)<sub>4</sub>(OOCCH<sub>2</sub><sup>t</sup>Bu)<sub>9</sub>(μ<sub>2</sub>-OH)<sub>3</sub>]<sub>2</sub>
PublicationTytułowy związek otrzymano w reakcji Zr(OiPr)4 z nadmiarem kwasu 3,3-dimetylobutyrowego. Rentgenowska analiza strukturalna została wykonana w temperaturze 103 i 153K. Struktury zawierają dimery podjednostek o wzorze: [Zr6(μ3-O)4(μ3-OH)4-(OOCCH2tBu)9] połączonych 6 mostkującymi grupami μ2-OH. Analiza zmiennotemperaturowych...
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Update a simple hypoplastic constitutive model
PublicationW artykule omówiono uproszczona formę hipoplastycznego konstytutywnego prawa materiałowego do opisu zachowania się materiałów granulowanych. Wykonano symulacje testów elementów i porównano wyniki z doświadczeniami.
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[Chapter] 2. Thermostable enzymes in food processing
PublicationW rozdziale przedstawiono charakterystykę termostabilnych hydrolaz glikozydów, izomeraz, transferaz,lipaz i enzymów proteolitycznych w przetwórstwie rozmaitych surowców źywnościowych. Podano przyczyny termostabilności tych enzymów oraz wymieniono korzyści wynikające z ich stosowania.
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Thickness accuracy of sash gang sawing
PublicationThin lamellae, corresponding to the layer components of structural glued members, i.e. 2-ply or 3-ply glued parquet, can be manufactured in re-sawing operations of kiln-dried wood blocks. These must be prepared with high dimensional accuracy and adequate surface quality following specific technical requirements for lamellae thickness variations, especially in the upper layers of the glued composite parquet. The accuracy of oak...
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Crystal structure and electronic structure of CePt2In7
PublicationWe report a corrected crystal structure for the CePt2In7 superconductor, refined from single crystal x-ray diffraction data. The corrected crystal structure shows a different Pt–In stacking along the c-direction in this layered material than was previously reported. In addition, all of the atomic sites are fully occupied with no evidence of atom site mixing, resolving a discrepancy between the observed high resistivity ratio of...
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NUMERICAL ESTIMATION OF HULL HYDRODYNAMIC DERIVATIVES IN SHIP MANOUVERING PREDICTION
PublicationOperating in crowded waterways pose a risk of accidents and disasters due to maneuvering limitations of the ship. In order to predict ship’s maneuvering characteristics at the design stage, model tests are often executed as the most accurate prediction tool. Two approaches can be distinguished here: free running model tests and numerical simulations based on planar motion model with the use of hydrodynamic derivatives obtained...
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Application of a hybrid mechanistic/machine learning model for prediction of nitrous oxide (N2O) production in a nitrifying sequencing batch reactor
PublicationNitrous oxide (N2O) is a key parameter for evaluating the greenhouse gas emissions from wastewater treatment plants. In this study, a new method for predicting liquid N2O production during nitrification was developed based on a mechanistic model and machine learning (ML) algorithm. The mechanistic model was first used for simulation of two 15-day experimental trials in a nitrifying sequencing batch reactor. Then, model predictions...
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Robust Parameter Estimation and Output Prediction for Reactive Carrier-Load Nonlinear Dynamic Networks
PublicationIn this paper an extension of on-line model simplification technique for a class of networked systems, namely reactive carrier-load nonlinear dynamic networked system (RCLNDNS), kept within point-parametric model (PPM) framework is addressed. The PPM is utilised to acquire a piece wise constant time-varying parameter linear structure for the RCLNDNS suitable for the on-line one step ahead prediction that may be applied to monitoring...
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Electricity demand prediction by multi-agent system with history-based weighting
PublicationEnergy and load demand forecasting in short-horizons, over an interval ranging from one hour to one week, is crucial for on-line scheduling and security functions of power system. Many load forecasting methods have been developed in recent years which are usually complex solutions with many adjustable parameters. Best-matching models and their relevant parameters have to be determined in a search procedure. We propose a hybrid...
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Application of MARKAL model to optimisation of electricity generation structure in Poland in the long-term time horizon. Part II. Model and forecasts assumptions
PublicationIn this paper, the next in a series of publications on the subject, assumptions are presented of a power system development model in terms of electricity generation technology infrastructure in Poland, in the long term perspective until 2060. The model is based on the mathematical structure of the MARKAL optimization package. Among other things developed are a forecast of the final demand for electricity and heat, the current...
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Monosaccharides as internal probes for the determination of the absolute configuration of 2-butanol
PublicationD-dlukoza, D-mannoza i L-ramnoza zostały poddane reakcji z mieszaniną racemiczną 2-butanolu. Otrzymane w ten sposób glikozydy były analizowane za pomocą spektroskopii NMR, z wykorzystaniem eksperymentów COSY i NOESY. Analiza konformacyjna wiązania glikozydowego (dokonana w oparciu o modelowanie molekularne i heteronuklearne stałe sprzężenia) wraz z analizą sprzężeń dipolowych obserwowanych w widmie NOESY umożliwiła określenie konfiguracji...
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The model of photovoltaic phenomenon in thin inhomogeneously organic film
PublicationW pracy przedstawiono model zjawiska fotowoltaicznego w obecności gradientu pułapek nośników ładunku. Zakładając, że długość dyfuzji ekscytonów związana jest z koncentracją pułapek, wykazano, że napięcie fotowoltaiczne silnie zależy od gradientu koncentracji pułapek.
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Teleportation seen from spacetime: on 2-spinor aspects of quantum information processing
PublicationZastosowanie formalizmu 2-spinowego do kwantowego przetwarzania informacji zilustrowane przykładem teleportacji i relatywistycznej korelacji błędu.
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Revisiting properties of CaCoSinO2n+2. Crystal and electronic structure
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Model of distributed learning objects repository for a heterogenic internet environment
PublicationW artykule wprowadzono pojęcie komponentu edukacyjnego jako rozszerzenie obiektu edukacyjnego o elementy zachowania (metody). Zaproponowane podejście jest zgodne z paradygmatem obiektowym. W oparciu o komponent edukacyjny zaprojektowano model budowy repozytorium materiałów edukacyjnych. Model ten jest oparty o usługi sieciowe i rejestry UDDI. Komponent edukacyjny oraz model repozytorium mogą znaleźć zastosowanie w konstrukcji zbiorów...
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Ship Resistance Prediction with Artificial Neural Networks
PublicationThe paper is dedicated to a new method of ship’s resistance prediction using Artificial Neural Network (ANN). In the initial stage selected ships parameters are prepared to be used as a training and validation sets. Next step is to verify several network structures and to determine parameters with the highest influence on the result resistance. Finally, other parameters expected to impact the resistance are proposed. The research utilizes...
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Damaged plasticity model - seismic analysis of structure of the Petronas Twin Towers (Kuala Lumpur) in Malaysia
PublicationThe 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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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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