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Search results for: moleular modelling
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Molecular action of isoflavone genistein in the human epithelial cell line HaCaT
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The molecular mechanism of genistein action in lysosomal storage diseases: A transcriptomic approach
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Molecular Dynamics Study of the Internal Water Molecules in Vasopressin and Oxytocin Receptors
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Molecular Diagnostics of Brain Tumours by Measuring the 5-Methylcytosine Level in Their DNA
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Separation of variables in molecular-dynamics simulations: A criterion to estimate the quality of the approximation
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Molecular Diffusion Simulation on ARUZ – Massively-parallel FPGA-based Machine
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A Model of Thermally Activated Molecular Transport: Implementation in a Massive FPGA Cluster
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Molecular features of thymidine analogues governing the activity of human thymidine kinase
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Molecular self-assembly and optical activity of chiral thionooxalamic acid esters
PublicationZsyntezowano kilka optycznie czynnych estrów dietylowych kwasu bis(tiooksamowego). Związki te, z powodu ich zdolności do tworzenia ze sobą komplementarnych cyklicznych wiązań wodorowych, są potencjalnie użytecznym materiałem budulcowym większych układów supramolekularnych. Odpowiednie układy modelowe otrzymano z optycznie czynnych 1,2-diamin, które poddano acylowaniu chlorooksooctanem etylu, a następnie otrzymane półprodukty tionowano...
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Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study
PublicationW pracy analizowano oddziaływanie dwóch nisko-toksycznych pochodnych amfoterycyny B (związki SAmE i PAmE) z modelami błon lipidowych. Badania wykonane zostały za pomocą dynamiki molekularnej. Modele błon oprócz fosfolipidów DMPC zawierały odpowiednio cholesterol (model błony zwierzęcej) lub ertosterol (model błony grzybowej). Analiza wyników wykazała, że obie pochodne amfoterycyny B zachowują się inaczej w błonie cholesterolowej...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Brain/blood distribution described by a combination of partition coefficient and molecular mass
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Multiplatform metabolomics provides insight into the molecular basis of chronic kidney disease
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Separation of zinc from aqueous samples using a molecular imprinting technique
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Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours
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Molecular and structural characteristics of cod gelatin films modifiedwith EDC and TGase
PublicationCod gelatin films before and after cross-linking of gelatin with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) or transglutaminase (TGase) have been characterized by FT-IR spectroscopy and DSC analysis. For comparison, a film prepared from unmodified pig gelatin has been also analysed. The difference spectra showed that cod gelatin during the film formation involved first of all water-to-amide hydrogen bonds, and the film...
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The FMO analysis of the molecular interaction of fentanyl derivatives with the μ-opioid receptor
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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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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublicationPyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure...
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublicationParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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A Molecular dynamics study of the influence of chemical reduction on the structure of amorphous germania
PublicationPraca poświęcona jest badaniom struktury blisko- i średniozasięgowej redukowanego amorficznego tlenku germanu o składzie 1Ge 1GeO2 za pomocą symulacji dynamiczno-molekularnych. Symulacje MD realizowano w zespole mikrokanonicznym (NVE), z wykorzystaniem dwuciałowego potencjału oddziaływania miedzyatomowego Borna-Mayera-Hugginsa. Wyraźnie widoczna tendencja do aglomeracji neutralnych atomów Ge została porównana z tendencją do aglomeracji...
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The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation
PublicationPraca poświęcona jest badaniom struktury blisko i średniozasięgowej częściowo zredukowanego szkła ołowiowo-krzemianowego o stechiometrii 1Pb1PbO1SiO2 uzyskanego na drodze symulacji dynamiczno-molekularnych. Otrzymane rezultaty porównamy z danymi otrzymanymi dla szkła niemodyfikowanego (2PbO1SiO2) i całkowicie zredukowanego (2Pb1SiO2).
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Ab initio molecular treatment for charge transfer by S3+ ion on hydrogen.
PublicationPoliczono adiabatyczne potencjały oddziaływania między jonem siarki i wodoru. Dokonano obliczeń nieadiabatycznych sprzężeń pomiędzy tymi potencjałami. Obliczenia wykazały, że należy wziąć pod uwagę niezbadany wcześniej poziom energetyczny jonu siarki aby dokładnie wyjaśnić mechanizm przechwytu ładunku.
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On the possibility of molecular recognition of taste substances studied by Gabor analysis of oscillations
PublicationBadano wpływ substancji odpowiedzialnych za wrażenia smakowe należące do czterech klas smaku (słodki, słony, gorzki i kwaśny) na charakterystyki oscylacyjne w nitrometanowym oscylatorze zawierającym kationowy surfaktant: chlorek benzylodimetylotetradecyloamoniowy. Zapropnowano nowe podejście oparte o transformację Gabora za pomocą której otrzymano widma mocy dla posczególnych układów. Wykazano, że dwuwymiarowa forma tych widm może...
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The structure of porous and spontaneously densified amorphous PbSiO3: a Molecular Dynamics study.
PublicationW pracy zaproponowano nową metodę numerycznego otrzymywania strukturporowatych metodą dynamiki molekularnej. Metoda polega na rozpoczęciu symulacji z ładunkami ekranowanymi i stopniowym zwiększaniu ich do pełnych ładunków jonowych. Metodę zastosowano do układu PbSiO3.
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Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublicationAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
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Determinants of the Internationalization of Family Firms - a Structural Eqquation Modeling Analysis
PublicationCurrently, international behaviors of family businesses (FBs) attract a growing interest of researchers. In an increasingly competitive environment, numerous FBs are forced to expand into foreign markets in search for ways to survive or grow. The article is both theoretical and empirical. In the theoretical part it presents theoretical concepts of FBs internationalization, especially determinants for their going international....
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Modeling of truss with cold-formed section and positive eccentricity in the node
PublicationThis work is dedicated to establishing the load carrying capacity of tensed and compressed truss’ nodes made of cold-formed open cross sections. The occurrence of bending in the truss’ nodes is the result of a specific production technology for system lattice girders assumed by the designer and the producer. The aim of this research is to present the methodology of conduct for creation of computational models that best depict the...
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Design and modeling of the piezoelectric motor based on three resonance actuators
PublicationThis paper describes a piezoelectric motor which combines advantages from two existing piezoelectric motors topologies. The research work presents the design, simulations and measurements of the piezoelectric motor with three rotation-mode actuators. The aim of the project was to obtain the high speed piezoelectric motor. Other advantages of this conception are blocking torque, short response times, the ability to work in a hostile...
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Modeling of multi-cavity Fabry-Perot optical fiber sensors
PublicationReflectance characteristics of a two-cavity extrinsic Fabry-Perot optical fiber sensor were investigated using computer modeling. Calculations were performed using a plane wave-based approach, selected for clarity of results. Based on the modeling results, it can be concluded that the two-cavity Fabry-Perot interferometer can be used to measure two different quantities, such as refractive index and temperature, independently. It...
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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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Improving performance of large thrust bearings through modeling and experimentation
PublicationLarge thrust bearings are highly loaded machine elements and their failures cause serious losses. Start ups and stoppages of the bearing under load are specially critical regimes of operation. Load carrying capacity depends on the profile of the oil gap. In transient states this profile is also changing. In the design of large thrust bearings minimizing thermo-elastic deformations is an important goal, which can be accomplished...
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Accurate modeling of quasi-resonant inverter fed IM drive
PublicationIn this paper wide-band modeling methodology of a parallel quasi-resonant dc link inverter (PQRDCLI) fed induction machine (IM) is presented. The modeling objective is early-design stage prediction of conductive electromagnetic interference (EMI) emissions of the considered converter fed IM drive system. Operation principles of the selected topology of PQRDCLI feeding IM drive are given. Modeling of the converter drive system is...
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Modeling of lapping plate wear and conditioning in single-sided lapping
PublicationIn order to achieve higher quality on worked surfaces with lower roughness, very high accuracy of shape and dimensions it is crucial to improve conventional finishing technologies and to develop new working principles. Single-sided lapping is one of the most effective planarization technologies and it is determined by a number of factors and boundary conditions. The most significant influence over a dimensional and profile accuracy,...
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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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Application of PL-Grid Platform for Modeling of the Selected Acoustic Phenomena
PublicationDomain grids are specific computational environments, developed within the PLGrid Plus project. For the Acoustic domain grid two supercomputer grid based services were prepared. Dedicated software consists of the outdoor sound propagation module and psychoacoustical noise dosimeter. The results are presented in a form of maps of sound level and Temporary Threshold Shift (TTS) values, therefore the services may play an informative...
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Analytical modeling of electric drives for vehicle traction control systems
PublicationWheel-torque control bandwidth in vehicle dynamics model is crucial in evaluating optimal tracking ability of tire slip and in analysis of control system stability. Electric drives’ control dynamics are influenced by timing of digital control events, e.g. by sampling instant of motor currents. Reflecting this timing in drive analytical models is therefore important for analysis of vehicle traction systems. The paper considers five...
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Modeling the global atmospheric transport and deposition of mercury to the Great Lakes
PublicationMercury contamination in the Great Lakes continues to have important public health and wildlife ecotoxicology impacts, and atmospheric deposition is a significant ongoing loading pathway. The objective of this study was to estimate the amount and source-attribution for atmospheric mercury deposition to each lake, information needed to prioritize amelioration efforts. A new global, Eulerian version of the HYSPLIT-Hg model was used...
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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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Modeling the Influence of Salts on the Critical Micelle Concentration of Ionic Surfactants
PublicationWe show for the first time that a phenomenological, augmented volume-based thermodynamics (aVBT) model is capable to predict the critical micelle concentrations of ionic surfactants, including ionic liquids, with added salts. The model also adjusts for the type of salt added by including its molecular volume, which might form a connection to the Hofmeister effect. The other physico-chemically relevant quantities included in the...
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GROUP COMPOSER - System for Modeling Agents’ Team Building for Tasks
PublicationMulti-agent systems consist of many autonomous units, called agents, that can interact when trying to achieve their goals. The selection of interaction partners is called team formation. Three basic approaches can be considered to match multi-agent system resources to the problem at hand. To research the properties of different approaches, a software for modeling team formation in multi-agent systems has been created and is presented...
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Modeling the impact of surface currents in a harbor using graph theory
PublicationEnsuring security in a harbor requires research into its infrastructure using spatial environmental data. This paper presents a methodology that defines the design of a graph for modeling the interactions between surface currents and moving objects. Combining this graph with port charts that integrate electronic navigation charts with coastal orthophotographs allows us to perform a multidimensional analysis. In addition, the complete...
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Computational Approaches to Modeling Artificial Emotion – An Overview of the Proposed Solutions
PublicationCybernetic approach to modeling artificial emotion through the use of different theories of psychology is considered in this paper, presenting a review of twelve proposed solutions: ActAffAct, FLAME, EMA, ParleE, FearNot!, FAtiMA, WASABI, Cathexis, KARO, MAMID, FCM, and xEmotion. The main motivation for this study is founded on the hypothesis that emotions can play a definite utility role of scheduling variables in the construction...
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublicationIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
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Performance and Power-Aware Modeling of MPI Applications for Cluster Computing
PublicationThe paper presents modeling of performance and power consumption when running parallel applications on modern cluster-based systems. The model includes basic so-called blocks representing either computations or communication. The latter includes both point-to-point and collective communication. Real measurements were performed using MPI applications and routines run on three different clusters with both Infiniband and Gigabit Ethernet...
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Numerical modeling of force and contact networks in fragmented sea ice
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Modeling of Ozonation of Reactive Black 5 Through a Kinetic Approach
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Modeling of generator performance of BLDC machine using mathematica software
PublicationW artykule porównano trzy modele maszyny bezszczotkowej prądu stałego z magnesami trwałymi(BLDC) w przypadku pracy prądnicowej. Najprostszy model qd0 sprowadzono do dwóch osi prostopadłychzwiązanych z wirnikiem [3]. Zakłada on sinusoidalny rozkład pola w szczelinie. Model opisany wosiach naturalnych wyprowadzono w oparciu o formalizm Lagrnage'a [4] i moŜe uwzględniać dowolnyrozkład pola wzbudzonego przez magnesy trwałe. Model pośredni...
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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