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CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES
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Modeling Methodologies for the Environment EE Msc sem. II r.a. 23/24
Kursy OnlineZrozumienie procesów które mają wpływ na migrację i przemiany zanieczyszczeń w środowisku (ze szczególnym uwzględnieniem wód powierzchniowych). Zajęcia dotyczą podstaw i zasad budowy modeli jakości wody oraz służą pokazaniu jak te modele mogą być wykorzystywane do rozwiązywania problemów w inżynierii środowiska.
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Molecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19
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Modelowanie procesów oscylacyjnych w układach z membraną ciekłą i kationowym surfaktanetm = Modeling of oscillation processes in systems with liquid membrane and cationic surfactant
PublikacjaBadano mechanizm oscylacji róznicy potencjału elektrycznego między fazami wodnymi trójfazowego układu z membraną ciekłą zawierającą kwas pikrynowy rozpuszcony w nitrobenzenie. Wodna faza donorowa zawierała kationowy surfaktant (bromek heksadecylotrimetyloamoniowy) i etanol. Faza akceptorowa składała się z wodnego roztworu sacharozy. Mechanizm sugeruje, że gwałtowna adsorpcja i desorpcja surfaktantu na granicy fazy akceptorowej...
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Exploiting the S4–S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis
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Adsorption of lead (Pb-II) using CaO-NPs synthesized by solgel process from hen eggshell: Response surface methodology for modeling, optimization and kinetic studies
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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
PublikacjaIn 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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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublikacjaA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Bond graph modeling of the new generation engine cooling systems = Zastosowanie metody grafów wiązań do modelowania nowej generacji układów chłodzenia silników spalinowych
PublikacjaW referacie szczegółowo opisano modele wymiany ciepła i przepływów w układzie chłodzenia. Metoda grafów wiązań okazała się szczególnie użyteczną dla modelowania skomplikowanych systemów energetycznych o różnych postaciach energii. Jako przykładu użyto obiegu chłodzenia silnika badawczego na hamowni silnikowej.
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Ionic liquid-assisted sol-gel synthesis of Fe2O3-TiO2 for enhanced photocatalytic degradation of bisphenol a under UV illumination: Modeling and optimization using response surface methodology
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International Journal of Computational Bioinformatics and In Silico Modeling
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Modeling and optimizing the removal of cadmium by Sinapis alba L. from contaminated soil via Response Surface Methodology and Artificial Neural Networks during assisted phytoremediation with sewage sludge
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Measurement and Modeling of Computer Systems (ACM SIG on Computer and Communications Metrics and Performance)
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Modeling of the alcohol dehydrogenase active site. Two different modes of alcohol binding in crystals of zinc and cadmium tri-tert-butoxysilanethiolates evidenced by X-ray diffraction and solid state vibrational spectroscopy
PublikacjaOpisano syntezę, struktury cząsteczkowe oraz widma FT-IR, 1H. 13C, 29Si, 113Cd NMR dziesięciu nowych, mieszanoligandowych kompleksów cynku i kadmu z ligandem tri-tert-butoksysilanotiolanowym i pochodnymi imidazolu. Za pomocą rentgenowskiej analizy strukturalnej i spektroskopii w podczerwieni udokumentowano dwa różne sposoby wiązania etanolu i metanolu w kryształach tych związków. Opisane kompleksy stanowią modele miejsca aktywnego...
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Optimization and Modeling of Cr (VI) Removal from Tannery Wastewater onto Activated Carbon Prepared from Coffee Husk and Sulfuric Acid (H2SO4) as Activating Agent by Using Central Composite Design (CCD)
PublikacjaThe primary goal of this research is to lower the hexavalent chromium (Cr (VI)) concentration that has occurred from the growth of the tannery industry. As a result, the potential for heavy metal concentration is increasing day by day. Industrial effluent containing Cr (VI) contributes significantly to water pollution. Chromium hexavalent ion (Cr (VI)) in wastewater is extremely hazardous to the environment. It is critical to address...
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Numerical modelings of ultrashort pulse propagation and conical emission in multimode optical fibers
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublikacjaA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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On the origin of surface imposed anisotropic growth of salicylic and acetylsalicylic acids crystals during droplet evaporation
PublikacjaIn 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
PublikacjaThe 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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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublikacjaParylene 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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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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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublikacjaGlucosamine-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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R&D in a post centrally-planned economy: The macroeconomic effects in Poland
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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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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublikacjaPraca 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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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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The effective elastic properties of human trabecular bone may be approximated using micro-finite element analyses of embedded volume elements.
PublikacjaBoundary 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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Polymerization of chloro-p-xylylenes, quantum-chemical study
PublikacjaThe 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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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
PublikacjaIn 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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Molecular dynamics of fentanyl bound to μ-opioid receptor
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A first-principles study of electronic and magnetic properties of 4d transition metals doped in Wurtzite GaN for spintronics applications
PublikacjaWe 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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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.
PublikacjaPodczas 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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Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach
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Isomerization and Decomposition of 2-Methylfuran with External Forces
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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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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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