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Molecular structures of two E-azobenzocrown ethers
PublicationRentgenowska analiza strukturalna monokryształów posłużyła do scharakteryzowania struktury izomerów E dwóch azobenzokoron: 13- i 16-członowej. Oba związki krystalizują w układzie jednoskośnym. W komórce elementarnej, w każdym przypadku znajdują się dwie niezależne cząsteczki, różniące się konformacją, szczególnie łańcucha eterowego. Porównując konformacje ''wolnych'' makrocykli z konformacjami ich kompleksów z jonami metali wskazano,...
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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Fatty acids as molecular carriers in cleavable antifungal conjugates
PublicationConjugates composed of C2-18 fatty acid (FA) residues as a molecular carrier and 5-fluorocytosine (5-FC) as an active agent, released upon the action of intracellular esterases on the ester bond between FA and “trimethyl lock” intramolecular linker, demonstrate good in vitro activity against human pathogenic yeasts of Candida spp. The minimal inhibitory concentrations (MIC) values for the most active conjugates containing caprylic...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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Mono- and bi-metallic plasmonic photocatalysts for degradation of organic compounds under UV and visible light irradiation
PublicationTitania powders were surface modified with gold and/or silver nanoparticles (NPs) by photodeposition method. Gold modified titania exhibited much higher photocatalytic activity during methanol dehydrogenation under UV irradiation than titania modified with monometallic silver and bimetallic Au–Ag NPs. Bimetallic photocatalysts exhibited either enhanced or reduced visible light activity, depending on properties of noble metal NPs,...
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Homoleptic mono-, di-, and tetra-iron complexes featuring phosphido ligands: a synthetic, structural, and spectroscopic study
PublicationWe report the first series of homoleptic phosphido iron complexes synthesized by treating either the β-diketiminato complex [(Dippnacnac)FeCl2Li(dme)2] (Dippnacnac = HC[(CMe)N(C6H3-2,6-iPr2)]2) or [FeBr2(thf )2] with an excess of phosphides R2PLi (R = tBu, tBuPh, Cy, iPr). Reaction outcomes depend strongly on the bulkiness of the phosphido ligands. The use of tBu2PLi precursor led to an anionic diiron complex 1 encompassing a planar...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Pressure field in a plane layer
PublicationPraca prezentuje wyniki badań teoretycznych i numerycznych zagadnienia przejścia fal płaskich przez warstwę. Omówiono zagadnienie tworzenia i rozchodzenia się fal w poszczególnych warstwach. Zaproponowano model matematyczny opisujący zmiany ciśnienia wewnątrz warstwy. Analizowano ciśnienie wewnątrz warstwy, fale bieżące i odbite wewnątrz warstwy oraz w ośrodku otaczającym. Przedstawiono wyniki badań numerycznych.
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Hydrothermal synthesis of vanadium ammonium compounds – the crucial role of the pressure
PublicationDue to the structural diversity and chemical activity, vanadium oxides and their derivatives are continuingly in the great interest of scientist. In a large family of vanadium compounds, one of the most interesting are ammonium vanadates (with the general formula (NH4)xVyOz). They have received much attention because of their promising application as cathode material in mono- and multivalent-ion batteries [1]. Hydrothermal synthesis...
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1,4,7,10-Tetraazacyclododecane incorporating salicyli acid moieties. Synthesis and properties
PublicationPochodne 1,4,7,10-tetraazacyklododekanu są związkami które znalazły szerokie zastosowanie w wielu dziedzinach: medycynie, chemii, farmacji, ochronie środowiska itd. Właściwości fizykochemiczne poszczególnych związków determinowane są przez pierścień makrocykliczny i podstawniki. Kwas salicylowy i salicylamid tworzą kompleksy chelatowe z kationami II grupy jak również z metalami przejściowymi. W reakcji acylowania cyklenu pochodnymi...
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Synteza i właściwości nowych pochodnych 1,4,7,10-tetraazacyklododekanu
PublicationCelem pracy była synteza i zbadanie właściwości pochodych 1,4,7,10-tetraazacyklododekanu (cyklenu). Otrzymano trzy grupy związków: alkilowe pochodne cyklenu, acylowe pochodne cyklenu i pochodne posiadające w swojej budowie ugrupowanie azowe. Acylowe pochodne zostały zsyntezowane w reakcji z wykorzystaniem p-nitrofenylowych estrów aktywnych, co nie było do tej pory stosowane w chemii cyklenu. Jest to jednoetapowa reakcja w wyniku...
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Zastosowanie techniki GC-FPD do oznaczania związków cynoorganicznych w próbkach osadów dennych pobranych w morskim porcie Gdańsk oraz w morskim porcie Gdynia
PublicationObecność tributylocyny (TBT-tributyltin) w osadach morskich, a w szczególności w osadach portowych wynika głównie z zastosowania tego związku w farbach do zabezpieczania kadłubów statków przed porastaniem przez florę i faunę morską. Związek ten uwolniony do środowiska wodnego ulega kumulacji głównie w osadach dennych. Wydobywanie lub przemieszczanie tych osadów w trakcie prac pogłębieniowych może prowadzić do poważnych zagrożeń...
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Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams
PublicationThe interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology,...
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The Influence of the Depth of Cut in Single-Pass Grinding on the Microstructure and Properties of the C45 Steel Surface Layer
PublicationThe paper contains the results of a metallographic examination and nanoindentation test conducted for the medium carbon structural steel with low content of Mn, Si, Cu, Cr, and Ni after its grinding to a depth ranging from 2 μm to 20 μm, at constant cutting speed (peripheral speed) of vs = 25 ms−1 and constant feed rate of vft = 1 m/min. Applied grinding parameters did not cause the surface layer hardening, which could generate...
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Monte Carlo simulations of the fracture resistance of an asphalt pavement layer
PublicationThe purpose of the proposed numerical model is to analyze the cracking of the wearing course in a pavement overlay, assuming a pre-existing crack that passes through the binding layer and base. The computations employed the author's simulation-based Monte Carlo material model, which describes the failure process of a Semi-Circular Bend (SCB) specimen during standard laboratory testing of asphalt concrete. A key feature of this...
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Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublicationResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
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Application of boron-doped diamond film and ZnO layer in the Fabry-Pérot interferometer
PublicationIn this article there have been presented the use of boron-doped diamond films for sensor applications. The low-finesse Fabry-Pérot interferometer working in the reflective mode has been implemented. Two kinds of reflective layers have been elaborated: boron-doped diamond thin films and zinc-oxide (ZnO) layer. Thin ZnO layers were deposited by Atomic Layer Deposition (ALD) on the face of a standard telecommunication single-mode...
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Mechanical Behavior of Bi-Layer and Dispersion Coatings Composed of Several Nanostructures on Ti13Nb13Zr Alloy
PublicationTitanium implants are commonly used because of several advantages, but their surface modification is necessary to enhance bioactivity. Recently, their surface coatings were developed to induce local antibacterial properties. The aim of this research was to investigate and compare me-chanical properties of three coatings: multi-wall carbon nanotubes (MWCNTs), bi-layer composed of an inner MWCNTs layer and an outer TiO2 layer, and...
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Synthetic strategies in construction of organic low molecular-weight carrier-drug conjugates
PublicationInefficient transportation of polar metabolic inhibitors through cell membranes of eukaryotic and prokaryotic cells precludes their direct use as drug candidates in chemotherapy. One of the possible solutions to this problem is application of the ‘Trojan horse’ strategy, i.e. conjugation of an active substance with a molecular carrier of organic or inorganic nature, facilitating membrane penetration. In this work, the synthetic...
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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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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Molecular Biology of Meniscal Healing: A Narrative Review
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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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CMGNet: Context-aware middle-layer guidance network for salient object detection
PublicationSalient object detection (SOD) is a critical task in computer vision that involves accurately identifying and segmenting visually significant objects in an image. To address the challenges of gridding issues and feature...
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Performance of a single layer fuel cell based on a mixed proton-electron conducting composite
PublicationMany of the challenges in solid oxide fuel cell technology stem from chemical and mechanical incompatibilities between the anode, cathode and electrolyte materials. Numerous attempts have been made to identify compatible materials. Here, these challenges are circumvented by the introduction of a working single layer fuel cell, fabricated from a composite of proton conducting BaCe0.6Zr0.2Y0.2O3-δ and a mixture of semiconducting...
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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
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Application of gas chromatographic data and 2D molecular descriptors for accurate global mobility potential prediction
PublicationMobility is a key feature affecting the environmental fate, which is of particular importance in the case of persistent organic pollutants (POPs) and emerging pollutants (EPs). In this study, the global mobility classification artificial neural networks-based models employing GC retention times (RT) and 2D molecular descriptors were constructed and validated. The high usability of RT was confirmed based on the feature selection...
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Hydrogen Embrittlement and Oxide Layer E ect in the Cathodically Charged Zircaloy-2
PublicationThe present paper is aimed at determining the less investigated effects of hydrogen uptake on the microstructure and the mechanical behavior of the oxidized Zircaloy-2 alloy. The specimens were oxidized and charged with hydrogen. The different oxidation temperatures and cathodic current densities were applied. The scanning electron microscopy, X-ray electron diffraction spectroscopy, hydrogen absorption assessment, tensile, and...
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Investigation of the Few‐Layer Black Phosphorus Degradation by the Photonic Measurements
PublicationFew-layer black phosphorus (FLBP) is a 2D material that gains worldwide interest for its possible applications, mainly in electronics and optoelec-tronics. However, as FLBP is prone to a degradation process under envi-ronmental conditions, there is a need for a monitoring method allowing investigation of its surface quality. Among many techniques, optoelectronic ones have unique advantages of fast response, non-contact, and non-invasive...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Paweł Możejko dr hab.
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Equivalent single-layer models in deformation analysis of laminated multilayered plates
PublicationThe performance of selected Equivalent Single-Layer (ESL) models is evaluated within several classical benchmark tests for linear static analysis of multi-layered plates. The authors elaborated their own Finite Element software based on the first-order shear deformation theory (FOSD) with some modifications incorporated including a correction of the transverse shear stiffness and an application of zig-zag type functions. Seven...
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Modelling of elastic wave propagation in a bolted joint using a thin layer of shell elements
PublicationThere are many mathematical models describing the propagation of elastic waves through the imperfect boundary of two media. They were successfully applied to modelling of high frequency bulk waves and their interaction with local defects. On the other hand, the existing literature models of bolted connections ignore the aspect of imperfect connection between elements. Therefore, this paper presents the concept of application of...
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Determination of the refractive index and wavelength‐dependent optical properties of few‐layer CrCl3 within the Fresnel formalism
PublicationBased on previous reports on the optical microscopy contrast of mechanically exfoliated few layer CrCl3 transferred on 285 nmand 270 nmSiO2 on Si(100), we focus on the experimental determination of an effective mean complex refractive index via a fitting analysis based on the Fresnel equations formalism. Accordingly, the layer and wavelength-dependent absorbance and reflectance are calculated. Layer and wavelength-dependent optical...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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Mechanical Behavior of Bi-Layer and Dispersion Coatings Composed of Several Nanostructures on Ti Substrate
PublicationThree coatings suitable for biomedical applications, including the dispersion coating composed of multi-wall carbon nanotubes (MWCNTs), MWCNTs/TiO2 bi-layer coating, and MWCNTs-Cu dispersion coating, were fabricated by electrophoretic deposition (EPD) on Ti Grade II substrate. Optical microscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and nanoindentation were applied to study topography, chemical, and...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Systematic Study of Hydration Patterns of Phosphoric(V) Acid and Its Mono-, Di-, and Tripotassium Salts in Aqueous Solution
PublicationSpektroskopia oscylacyjna FTIR w zakresie drgania OD cząsteczki HDO została zastosowana do zbadania różnych form fosforanów w kolejności malejącego stopnia protonacji: H3PO4, KH2PO4, K2HPO4, K3PO4. HDO rozcieńczona izotopowo w H2O została otrzymana przez dodanie odpowiednich ilości wody ciężkiej (D2O) do roztworów w wodzie zwykłej. Do wyizolowania widm HDO zaburzonej przez substancję rozpuszczoną zastosowano metodę widm różnicowych....
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The accretion of the new ice layer on the surface of hexagonal ice crystal and the influence of the local electric field on this process
PublicationThe process of creation of a new layer of ice on the basal plane and on the prism plane of a hexagonal ice crystal is analyzed. It is demonstrated that the ordering of water molecules in the already existing crystal affects the freezing. On the basal plane, when the orientations of water molecules in the ice block are random, the arrangement of the new layer in a cubic manner is observed more frequently — approximately 1.7 times...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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Chitosan-Based Membranes as Gentamicin Carriers for Biomedical Applications — Influence of Chitosan Molecular Weight
PublicationOver the past decade, much attention has been paid to chitosan as a potential drug carrier because of its non-toxicity, biocompatibility, biodegradability and antibacterial properties. The effect of various chitosan characteristics on its ability to carry different antibiotics is discussed in the literature. In this work, we evaluated the influence of the different molecular weights of this polymer on its potential as an antibacterial...
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Thermal and hydraulic phenomena in boundary layer of minijets impingement on curved surfaces
PublicationPresented work considers flow and thermal phenomena occurring during the single minijet impingement on curved surfaces, heated with a constant heat flux, as well as the array of minijets. Numerical analyses, based on the mass, momentum and energy conservation laws, were conducted, regarding single phase and two-phase simulations. Focus was placed on the proper model construction, in which turbulence and boundary layer modeling...
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Microporous Polyurethane Thin Layer as a Promising Scaffold for Tissue Engineering
PublicationThe literature describes that the most efficient cell penetration takes place at 200–500 µm depth of the scaffold. Many different scaffold fabrication techniques were described to reach these guidelines. One such technique is solvent casting particulate leaching (SC/PL). The main advantage of this technique is its simplicity and cost efficiency, while its main disadvantage is the scaffold thickness, which is usually not less than...
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Molecular Oncology
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MOLECULAR PHARMACOLOGY
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