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Search results for: PROTEIN-STRUCTURE MODELING, COARSE GRAINING, UNRES MODEL OF POLYPEPTIDE CHAINS, MOLECULAR DYNAMICS, DATA-ASSISTED SIMULATIONS
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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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PTD4 Peptide Increases Neural Viability in an In Vitro Model of Acute Ischemic Stroke
PublicationIschemic stroke is a disturbance in cerebral blood flow caused by brain tissue ischemia and hypoxia. We optimized a multifactorial in vitro model of acute ischemic stroke using rat primary neural cultures. This model was exploited to investigate the pro-viable activity of cell-penetrating peptides: arginine-rich Tat(49–57)-NH2 (R49KKRRQRRR57-amide) and its less basic analogue, PTD4 (Y47ARAAARQARA57-amide). Our model included glucose...
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Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Proceedings of the 9th International Conference on Structural Dynamics, EURODYN 2014
PublicationSince offshore wind turbine supporting structures are subjected to dynamic environments with time-varying loading conditions, it is important to model their dynamic behavior and validate these models by means of vibrational experiments. In this paper assessment of dynamical state of the structure is investigated by means of both: numerical modeling, and experimental modal analysis. In experimental modal analysis, capturing the...
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Experimental analysis of the behaviour of different types of joints in the steel structure model subjected to earthquake loading
PublicationThe present paper reports the results of the experimental study performed to investigate the behaviour of two different types of joints (destroyed and welded ones) in the model of the steel structure under seismic excitations. The structure was subjected to three earthquakes, namely Kobe, Loma Prieta and Northridge, using the shaking table investigation. The results obtained from the study...
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Integration Data Model of the Bathymetric Monitoring System for Shallow Waterbodies Using UAV and USV Platforms
PublicationChanges in the seafloor relief are particularly noticeable in shallow waterbodies (at depths up to several metres), where they are of significance for human safety and environmental protection, as well as for which the highest measurement accuracy is required. The aim of this publication is to present the integration data model of the bathymetric monitoring system for shallow waterbodies using Unmanned Aerial Vehicles (UAV) and...
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Recent improvements in prediction of protein structure by global optimization of a potential energy function
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Crystal and molecular structure of bis(O,O'-diethyldithiophosphato-S,S')nickel(II): A redetermination
PublicationDoniesienie przedstawia ponownie wyznaczoną strukturę tytułowego, centrosymetrycznego kompleksu, [Ni{S2P(OC2H5)2}2]. Centralny rdzeń (S2P)2 jest płaski, co potwierdza wcześniejsze wyniki uzyskane przez McConnell'a i Kastalsky'ego, przy czym odchylenia standardowe są około siedmiokrotnie mniejsze oraz wyznaczono wszystkie pozycje atomów wodoru. W strukturze krystalicznej zaobserwowano róznież parę krótkich kontaktów HH (2.33 Å).
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Triticale extrudates – Changes of macrostructure, mechanical properties and molecular water dynamics during hydration
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Quantum structure in competing lizard communities
PublicationAlmost two decades of research on applications of the mathematical formalism of quantum theory as a modeling tool in domains different from the micro-world has given rise to many successful applications in situations related to human behavior and thought, more specifically in cognitive processes of decision-making and the ways concepts are combined into sentences. In this article, we extend this approach to animal behavior, showing...
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Modeling Parallel Applications in the MERPSYS Environment
PublicationThe chapter presents how to model parallel computational applications for which simulation of execution in a large-scale parallel or distributed environment is performed within the MERPSYS environment. Specifically, it is shown what approaches can be adopted to model key paradigms often used for parallel applications: master-slave, geometric parallelism (single program multiple data), pipelined and divide-and-conquer applications....
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Stability of delay induced oscillations in gene expression of Hes1 protein model
PublicationW pracy prezentowana jest matematyczna analiza modelu ekspresji genu białka Hes1. Rozważamy układ równań z dwoma opóźnieniami - w produkcji białka Hes1 oraz jego mRNA. Dowodzimy istnienia i jednoznaczności oraz nieujemności rozwiązań. Pokazujemy istnienie dokładnie jednego dodatniego stanu stacjonarnego. Wykazujemy, że stabilność stanu stacjonarnego zależy od sumy opóźnień. Podajemy warunek dostateczny na wystąpienie bifurkacji...
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The role of the One-Belt One-Road initiative in China's exports and global value chains
PublicationResearch background: China is regarded as the “world factory” highly involved in international trade and plays an increasingly important role in the global value chains (GVC). Additionally, the “One-Belt One-Road” (OBOR) initiative was proposed by the Chinese government to further promote China in the international market. Purpose of the article: The article explores the role of the OBOR in China’s exports and global value...
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Design-Oriented Constrained Modeling of Antenna Structures
PublicationFast surrogate models are crucially important to reduce the cost of design process of antenna structures. Due to curse of dimensionality, standard (data-driven) modeling methods exhibit serious limitations concerning the number of independent geometry parameters that can be handled but also (and even more importantly) their parameter ranges. In this work, a design-oriented modeling framework is proposed in which the surrogate is...
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Verification of geotechnical numerical simulations by model tests using PIV technique
PublicationPrzedstawiono metodykę i wyniki badań modelowych stateczności fundamentów bezpośrednich posadowionych w sąsiedztwie kątowych ścian oporowych. Dla takiego złożonego układu fundament - obciążenie - podłoże gruntowe wykonano badania modelowe w płaskim stanie odkształcenia na gruncie naturalnym i analogowym. Trajektorie i izopola przemieszczeń oraz progresywny rozwój kształtu i zasięgu powierzchni poślizgu określono techniką PIV.
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Effect of the template-assisted electrodeposition parameters on the structure and magnetic properties of Co nanowire arrays
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2D Mathematical Model of the Commutator Sliding Contact of an Electrical Machine
PublicationW artykule przedstawiono model matematyczny 2D komutatorowego zestyku ślizgowego z wieloma stopniami swobody. W modelu uwzględniono zmienne wymuszenia działające na szczotkę. Wymuszenia te są wynikiem falistości wirującego komutatora. Szczotka została zamodelowana jako system wielu mas, elementów sprężystych i tłumików rozłożonych w kierunku stycznym i promieniowym. Zamodelowano wszystkie oddziaływania lepkosprężyste pomiędzy komutatorem...
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A model, design, and implementation of an efficient multithreaded workflow execution engine with data streaming, caching, and storage constraints
PublicationThe paper proposes a model, design, and implementation of an efficient multithreaded engine for execution of distributed service-based workflows with data streaming defined on a per task basis. The implementation takes into account capacity constraints of the servers on which services are installed and the workflow data footprint if needed. Furthermore, it also considers storage space of the workflow execution engine and its cost....
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Modeling sequencing batch reactor operational conditions depending on oxygen concentration
PublicationSequencing batch reactors (SBR) can be used as a fill-and draw activated sludge system for wastewater treatment with considerable operating flexibility and the possibility to conduct experiments under standard conditions and extreme case scenarios. Mathematical modeling and computer simulations provide an opportunity to implement existing wastewater processes in modeling software and evaluate different modifications at low costs...
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Coarse-grained model of the native cellulose $$\hbox {I}\alpha$$ and the transformation pathways to the $$\hbox {I}\beta$$ allomorph
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Interaction of amphotericin B and its selected derivatives with membranes: molecular modeling studies
PublicationJest to praca przeglądowa obejmująca krytyczną analizę danych dotyczących oddziaływania amfoterycyny B (AmB) i jej wybranych, mniej toksycznych pochodnych, z błonami lipidowymi. Amfoterycyna B jest antybiotykiem przeciwgrzybowym ale ze względu na jej toksyczność trwają prace nad modyfikacjami chemicznymi tego związku. Celem molekularnym dla tego antybiotyku jest błona lipidowa i dlatego różnicowe powinowactwo AmB i jej pochodnych...
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Data-driven, probabilistic model for attainable speed for ships approaching Gdańsk harbour
PublicationThe growing demand for maritime transportation leads to increased traffic in ports. From this arises the need to observe the consequences of the specific speed ships reach when approaching seaports. However, usually the analyzed cases refer only to the statistical evaluation of the studied phenomenon or to the empirical modelling, ignoring the mutual influence of variables such as ship type, length or weather conditions. In this...
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General Active-RC filter model for computer-aided design
PublicationW pracy przedstawiono ogólną topologię filtru aktywnego RC czasu ciągłego. Proponowany model umożliwia zunifikowaną analizę wszystkich możliwych realizacji układowych filtrów aktywnych RC jako szczególnych przypadków danej struktury ogólnej. Poprawność modelu teoretycznego została zweryfikowana poprzez symulacje w programie SPICE.
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Analysis of molecular structure of starch citrate obtained by a well-stablished method
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Analysis of Isocratic-Chromatographic-Retention Data using Bayesian Multilevel Modeling
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Applicability of an effective conductivity approach in modeling thoracic impedance changes
PublicationThis paper describes numerical simulations of the influence of conductivity changes inside a volume conductor on impedance changes measured on its surface. A simple model based on the finite element method has been developed to estimate an applicability of the effective conductivity theory in human chest modeling. The model consisted of a cylinder with two concentric spheres inside. Simulations were performed for two cases: first...
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Characteristics of Polypeptide/Phospholipid Monolayers on Water and the Plasma‐Activated Polyetheretherketone Support
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Global value chains and labour markets – simultaneous analysis of wages and employment
PublicationThis study examines the overall effect of global value chains (GVCs) on wages and labour demand. It exploits the World Input–Output Database to measure GVC involvement via recently developed participation indices (using both backward and forward linkages) and the relative GVC position using three-stage least squares regression. We find that the relative GVC position is negatively correlated with wages and employment and that the...
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Bio‐polyols synthesized by liquefaction of cellulose: Influence of liquefaction solvent molecular weight
PublicationCurrently, the plastics industry including polyurethanes is based on the use of petrochemicals. For this reason, scientists are looking for new types of renewable resources for the substitution of petrochemical substances. This work aims to evaluate the effect of polyethylene glycols (PEG) with different molecular mass impact on properties of bio-based polyols synthesized via biomass liquefaction of cellulose. To date, research...
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Effect of the integration into Global Value Chains on the employment contract in Central and Eastern European countries
PublicationResearch background: In the era of globalization, there is a need to address decent work deficits in Global Value Chains (GVCs). The forms of working conditions reveal a broad dispersion of contents. The literature review exposes hardly any Europe-focused research assessing the socioeconomic impact of global production links and going beyond their pure economic effects assessed in terms of employment, productivity or wages. Purpose...
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Modeling and control of a redundantly actuated variable mass 3RRR planar manipulator controlled by a model-based feedforward and a model-based-proportional-derivative feedforward–feedback controller
PublicationIn the paper, dynamics of a complex mechatronics system is considered. A redundantly actuated planar manipulator is the base of the mechanical part of it. It is a 3RRR 1 platform based parallel manipulator. To control its trajectory, a model-based feedforward controller is employed. Three aspects are fundamental in the presented investigations. The first focus is on development of an accurate numerical model used to solve the inverse...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublicationABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...
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Smart modeling support for managing complexities and dynamics of knowledge-based systems - part 2
PublicationPrzedstawiono i poddano analizie najnowsze trendy w zakresie kierunków badań dotyczących inteligentnego wspomagania zarządzania dynamiką i kompleksowością systemów opartych na wiedzy.
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Recognizing emotions on the basis of keystroke dynamics
PublicationThe article describes a research on recognizing emotional states on the basis of keystroke dynamics. An overview of various studies and applications of emotion recognition based on data coming from keyboard is presented. Then, the idea of an experiment is presented, i.e. the way of collecting and labeling training data, extracting features and finally training classifiers. Different classification approaches are proposed to be...
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Upgrading low value-added activities in global value chains: a functional specialisation approach
PublicationThis paper aims to identify patterns of functional specialisation (FS) in global value chains (GVCs) and determinants of upgrading them for selected Central Eastern European (CEE) economies. By combing the World Input-Output Database with data on occupations, we reveal a new FS pattern among subgroups of CEEs. Poland and Slovakia have an unfavourable GVC position and specialise in low value-added fabrication function. In contrast,...
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Quantum-correlation breaking channels, broadcasting scenarios, and finite Markov chains
PublicationOne of the classical results concerning quantum channels is the characterization of entanglementbreakingchannels [M. Horodecki et al., Rev. Math. Phys 15, 629 (2003)]. We address the questionwhether there exists a similar characterization on the level of quantum correlations which may gobeyond entanglement. The answer is fully affirmative in the case of breaking quantum correlationsdown to the, so called, QC (Quantum-Classical)...
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Ontological Modeling for Contextual Data Describing Signals Obtained from Electrodermal Activity for Emotion Recognition and Analysis
PublicationMost of the research in the field of emotion recognition is based on datasets that contain data obtained during affective computing experiments. However, each dataset is described by different metadata, stored in various structures and formats. This research can be counted among those whose aim is to provide a structural and semantic pattern for affective computing datasets, which is an important step to solve the problem of data...
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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Systematic Management of Simulation State for Multi-Branch Simulations in Simulink
PublicationSystematic simulation is a technique related and motivated by the formal analysis of hybrid dynamic systems. It combines the exhaustive and conservative nature of traditional model checking with numerical simulation for providing efficient algorithms to manage simulations. Multi-branch simulation is the concept advancing simulation efficiency by reducing the number of state transitions. This paper introduces an approach to implement...
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Silo music: Experimental investigations and a mechanical model
PublicationW artykule opisano zagadnienie zjawisk akustycznych oraz drgań występujących w silosach podczas przepływu materiałów granulowanych.
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Reliability model of two-shaft turbine combustion engine with heat regenerator
PublicationW artykule przedstawiono możliwość zastosowania teorii procesów semimarkowskich do opisu niezawodności turbinowego silnika spalinowego. Opracowano model niezawodnościowy w formie siedmiostanowego procesu semimarkowskiego, umożliwiający określenie prawdopodobieństw przebywania silnika w stanie zdatności oraz wyróżnionych stanach niezdatności.
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Variable‐fidelity modeling of antenna input characteristics using domain confinement and two‐stage Gaussian process regression surrogates
PublicationThe major bottleneck of electromagnetic (EM)-driven antenna design is the high CPU cost of massive simulations required by parametric optimization, uncertainty quantification, or robust design procedures. Fast surrogate models may be employed to mitigate this issue to a certain extent. Unfortunately, the curse of dimensionality is a serious limiting factor, hindering the construction of conventional data-driven models valid over...
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Knowledge-based performance-driven modeling of antenna structures
PublicationThe importance of surrogate modeling techniques in the design of modern antenna systems has been continuously growing over the recent years. This phenomenon is a matter of practical necessity rather than simply a fashion. On the one hand, antenna design procedures rely on full-wave electromagnetic (EM) simulation tools. On the other hand, the computational costs incurred by repetitive EM analyses involved in solving common tasks...