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Search results for: modeling
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Instability of 2,2-di(pyridin-2-yl)acetic acid. Tautomerization versus decarboxylation
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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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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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Optimal Distribution of the Nonoverlapping Conducting Disks
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Conductivity of Fibre Composites with Fractures on the Boundary of Inclusions
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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On the origin of surface imposed anisotropic growth of salicylic and acetylsalicylic acids crystals during droplet evaporation
PublicationIn this paper droplet evaporative crystallization of salicylic acid (SA) and acetylsalicylic acid (ASA) crystals on different surfaces, such as glass, polyvinyl alcohol (PVA), and paraffin was studied. The obtained crystals were analyzed using powder X-ray diffraction (PXRD) technique. In order to better understand the effect of the surface on evaporative crystallization, crystals deposited on glass were scraped off. Moreover,...
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Exploring the cocrystallization potential of urea and benzamide
PublicationThe cocrystallization landscape of benzamide and urea interacting with aliphatic and aromatic carboxylic acids was studied both experimentally and theoretically. Ten new cocrystals of benzamide were synthesized using an oriented samples approach via a fast dropped evaporation technique. Information about types of known bi-component cocrystals augmented with knowledge of simple binary eutectic mixtures was used for the analysis...
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R&D in a post centrally-planned economy: The macroeconomic effects in Poland
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Ab initio study of phenyl benzoate: structure, conformational analysis, dipole moment, IR and Raman vibrational spectra
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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A hypothesis for GPCR activation
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Attaching an alkali metal atom to an alkaline earth metal oxide (BeO, MgO, or CaO) yields a triatomic metal oxide with reduced ionization potential and redirected polarity
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Functionalization of the transition metal oxides FeO, CoO, and NiO with alkali metal atoms decreases their ionization potentials by 3–5 eV
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Computational studies of intermolecular interactions in aqueous solutions of poly(vinylmethylether)
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublicationPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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Polymerization of chloro-p-xylylenes, quantum-chemical study
PublicationThe p-xylylene monomers of parylene N, C and D have similar high polymerization reactivity. For effective copolymerization processes this fact is basically a draw- back and for instance the copolymerization with styrene doesn't go at all (Corley et al. J Pol Sc 13(68):137156, 1954). Substitution of terminal hydrogen atoms by chlorine atoms reduces reactivity dramatically. 7,7,8,8-tetrachloro-p- xylylene and 2,5,7,7,8,8-hexachloro-p-xylylene...
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The effective elastic properties of human trabecular bone may be approximated using micro-finite element analyses of embedded volume elements.
PublicationBoundary conditions (BCs) and sample size affect the measured elastic properties of cancellous bone. Samples too small to be representative appear stiffer under kinematic uniform BCs (KUBCs) than under periodicity-compatible mixed uniform BCs (PMUBCs). To avoid those effects, we propose to determine the effective properties of trabecular bone using an embedded configuration. Cubic samples of various sizes (2.63, 5.29, 7.96, 10.58...
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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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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A first-principles study of electronic and magnetic properties of 4d transition metals doped in Wurtzite GaN for spintronics applications
PublicationWe studied the electronic and magnetic properties of wurtzite GaN (w-GaN) doped with different concentrations of the 4d transition metal ions Nb, Mo, and Ru. We incorporated spin-polarized plane-wave density functional theory within an ultrasoft pseudopotential formalism. The 4d transition metals were doped at different geometrical sites to determine the geometry with the lowest total energy and the one that induced the largest...
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Theoretical designing of selenium heterocyclic non-fullerene acceptors with enhanced power conversion efficiency for organic solar cells: a DFT/TD-DFT-based prediction and understanding
PublicationIn this study, we have designed and explored a new series of non-fullerene acceptors for possible applications in organic solar cells. We have designed four molecules named as APH1 to APH4 after end-capped modification of recently synthesized Y6-Se-4Cl molecule. Density functional theory and time dependent-density functional theory have been employed for computing geometric and photovoltaic parameters of the designed molecules....
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Modeling of flow phenomena on the mould plastic interface associated withpolymer injection. Trends Production Technol.**2002 Bd 3 s. 122-137, 11 rys Proceedings of the International Colloquium on Production Science. Gdańsk, April 15th 2002. Ed. D. Spaht. Modelowanie zjawisk zachodzących podczas wtrysku w strefie tworzywo-forma.
PublicationPodczas wtrysku występują w warstwie tworzywa przy ściance formy zjawiska,które są źródłem wad. Opisano powyższe zjawiska oraz zaprezentowano model zachowania się tworzywa w strefie przyściennej z wykorzystaniem symulacji komputerowej procesu wtrysku. Symulację wykonano na komputerach CI TASK przyuzyciu programu FIDAP. Ponadto przedstawiono wyniki badań doświadczalnych w postaci fotografii i profilogramów powierzchni, które...
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Isomerization and Decomposition of 2-Methylfuran with External Forces
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Evaluation of Eucalyptus leaves as an adsorbent for decolorization of Methyl Violet (2B) dye in contaminated waters: Thermodynamic and Kinetics model
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Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
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A Maximum-Likelihood Approach to Force-Field Calibration
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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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Chirality Measures of α-Amino Acids
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Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Multi-Objective Genetic Algorithm (MOGA) As a Feature Selecting Strategy in the Development of Ionic Liquids’ Quantitative Toxicity–Toxicity Relationship Models
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Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach
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Temperature influences on shear stability of a nanosize plate with piezoelectricity effect
PublicationPurpose The purpose of this paper is to predict the mechanical behavior of a piezoelectric nanoplate under shear stability by taking electric voltage into account in thermal environment. Design/methodology/approach Simplified first-order shear deformation theory has been used as a displacement field. Modified couple stress theory has been applied for considering small-size effects. An analytical solution has been taken into account...
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Electro-thermal buckling of elastically supported double-layered piezoelectric nanoplates affected by an external electric voltage
PublicationPurpose Thermal buckling of double-layered piezoelectric nanoplates has been analyzed by applying an external electric voltage on the nanoplates. The paper aims to discuss this issue. Design/methodology/approach Double-layered nanoplates are connected to each other by considering linear van der Waals forces. Nanoplates are placed on a polymer matrix. A comprehensive thermal stress function is used for investigating thermal buckling....
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublicationPartition coefficients define how a solute is distributed between two immiscible phases at equilibrium. The experimental estimation of partition coefficients in a complex system can be an expensive, difficult, and time-consuming process. Here a computational strategy to predict the distributions of a set of solutes in two relevant phase equilibria is presented. The octanol/water and octanol/air partition coefficients are predicted...
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3D Computer Model of the Hip Joint Cartilage
PublicationThis paper presents 3D computer model of the hip joint cartilage in the ANSYS program. Model is made on the basis of anatomy and collected data on the material constants of bone and cartilage components. Analysis and comparison of biochemical model, viscoelastic and molecular mixed - aggregation serves to facilitate the creation of the next model of reality, which could be used in the design of joint prostheses. The correctness...
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[Chapter] 22. Application of physical modeling to study combustion process-es and flow patterns in large-scale boilers and furmaces. W: Optical me- thods and data processing in heat and fluid flow. Ed. C. Greated, J. Cos-grove, J.M. Buick. Bury St. Edmunds. London: Profess. Eng. Publ.**2002 s. 267-277, 4 rys. bibliogr. 6 poz. Zastosowanie modelowania fizycznego do badania procesów spalania pola prze- pływu w przemysłowych kotłach i piecach.
PublicationRozdział zawiera wyniki badań modelowania fizycznego dwuwymiarowego i trój-wymiarowego pola przepływu i procesów spalania w wybranych urządzeniachprzemysłowych.
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Mixed electromagnetic - circuits modeling and parallelization for rigorouscharacterization of cosite interference in wireless communication channels. W: UGC 2002 Homepage [online]. Department of Defense High Performance Com- puting Modernization Program. Users Group Conference 2002. Austin, Texas, USA. June 10-14, 2002. [Dostęp: 15 grudnia**2002]. Dostępny w World Wide Web: http://www.hpcmo.hpc.mil/Htdocs/UGC/UGC02/paper/[45 slajdów]. Modelowanie układów elektromagnetycznych i zrównoleglanie w celu określenia wzajemnych oddziaływań w bezprzewodowych kanałach komunikacyjnych.
PublicationRównoległe działanie sąsiadujące modułów nadawczo-odbiorczych typowo prowa-dzi do efektów ubocznych z powodu wzajemnych oddziaływań, które obniżają pa-rametry sieci. W celu scharakteryzowania takich efektów, zaprezentowano roz-wiązanie równań Maxwella w dziedzinie czasu z modelowaniem efektów nielinio-wych.
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Sławomir Jerzy Ambroziak dr hab. inż.
PeopleSławomir J. Ambroziak was born in Poland, in 1982. He received the M.Sc., Ph.D. and D.Sc. degrees in radio communication from Gdańsk University of Technology (Gdańsk Tech), Poland, in 2008, 2013, and 2020 respectively. Since 2008 he is with the Department of Radiocommunication Systems and Networks of the Gdańsk Tech: 2008-2013 as Research Assistant, 2013-2020 as Assistant Professor, and since 2020 as Associate Professor. He is...
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Łukasz Skarżyński dr hab. inż.
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Wojciech Kustra dr inż.
PeopleI am a Faculty member (Assistant Professor, Highway and Transportation Engineering Department) at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland). My main research interests include: road safety, accident analysis, traffic modeling, transportation planning, traffic engineering, transport management, gis analysis.
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Nicole Nawrot dr inż.
PeopleDr. Eng. Nicole Nawrot has been employed at the Department of Sanitary Engineering since 2016. In 2021, she obtained a PhD in the field of engineering and technical sciences in the discipline of environmental engineering, mining and energy. Doctoral thesis entitled "Heavy metals in urban retention tanks bottom sediments: distribution, source tracking, and evaluation of phytostabilization adaptability and performance of P. australis...
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Michał Michna dr hab. inż.
PeopleMichal Michna received the M.Sc. and Ph.D. degrees in electrical engineering from the Gdansk University of Technology (GUT), Gdansk, Poland, in 1998 and 2005, respectively. Since 2004, he was employed at the Department of Power Electronics and Electrical Machines of the Gdańsk University of Technology (assistant, assistant professor, senior lecturer). In 2010-2015 he was a deputy of head of the Department of Power Electronics and...
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Magdalena Brzozowska-Woś dr hab. inż.
PeopleMagdalena Brzozowska-Woś is a graduate of the Faculty of Management and Economics of the Gdańsk University of Technology (specialization: management systems). She is also a graduate of Postgraduate Studies in Advertising (Faculty of Management and Economics, GUT) and Postgraduate Studies in Public Relations (SWPS University of Humanities and Social Sciences). In the years 2000-2003, she cooperated with Panorama Internet sp. z o....
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Krzysztof Cwalina dr inż.
PeopleKrzysztof Kamil Cwalina w 2013 r. uzyskał tytuł inżyniera na Wydziale Elektroniki, Telekomunikacji i Informatyki Politechniki Gdańskiej; w 2014 r. uzyskał tytuł magistra inżyniera, a w 2017 r. otrzymał stopień doktora nauk technicznych w dyscyplinie: telekomunikacja, także na WETI PG. Aktualnie pracuje na stanowisku adiunkta w Katedrze Systemów i Sieci Radiokomunikacyjnych Wydziału Elektroniki, Telekomunikacji i Informatyki Politechniki...
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Bohdan Pakhaliuk PhD student
PeopleBohdan Pakhaliuk received the B.Sc. and M.Sc. degrees in industrial electonics from Chernihiv National University of Technology, Chernihiv, Ukraine, in 2016 and 2018 respectively. He is PhD student of double postgraduate study, in Gdansk University of Technology and Chernihiv National University of Technology. He is junior researcher of the Department of Biomedical Radioelectronics Apparatus and Systems, Chernihiv National University...