Wyniki wyszukiwania dla: Molecular docking and simulation study
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 100 mm stroke subjected only to a mass load of 1100 g
Dane BadawczeThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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Dynamics of a linear pneumatic actuator with 80 mm piston diameter and 100 mm stroke subjected only to a mass load of 2570 g
Dane BadawczeThe aim of the study was to determine the dynamics of a linear pneumatic cylinder subjected only to mass load. An actuator of one of the well known European manufacturers was tested.The experiment were to measure pressure changes in both chambers of the actuator and the position of the piston during stroke and retracting. The test was repeated 11 times....
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The effect of chitosan concentration and molecular weight on endotoxin content
Dane BadawczeThe dataset includes results to determine the effect of chitosan concentration and molecular weight on endotoxin content as well as the effect of purification methods. The endotoxin concentration was determined using the PyroGene Recombinant Factor C Endpoint Fluorescent Assay. Chitosan 0.6% in 0.1M glycolic acid from Chemat LMW, MMW, and HMW were used...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublikacjaOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Wiktoria Wojnicz dr hab. inż.
OsobyDSc in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2019 PhD in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2009 (with distinction) Publikacje z listy MNiSW (2009 - ) Wojnicz W., Wittbrodt E., Analysis of muscles' behaviour. Part I. The computational model of muscle. Acta of Bioengineering and Biomechanics, Vol. 11, No.4, 2009, p. 15-21 Wojnicz W., Wittbrodt E., Analysis...
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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublikacjaInteraction between 2, 3, 5 and 7 atomic layers of gold and a (111) silicon surface was investigated with the molecular dynamics simulation method. The simulation of the diffusion interaction between gold and silicon in the temperature range 425-925 K has been carried out. The peculiarities of the concentration changes of the interacting components and the atomic density at the boundary...
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Analytical predictions for the buckling of a nanoplate subjected to non-uniform compression based on the four-variable plate theory
PublikacjaIn the present study, the buckling analysis of the rectangular nanoplate under biaxial non-uniform compression using the modified couple stress continuum theory with various boundary conditions has been considered. The simplified first order shear deformation theory (S-FSDT) has been employed and the governing differential equations have been obtained using the Hamilton’s principle. An analytical approach has been applied to obtain...
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Transdermal transport of collagen and hyaluronic acid using water in oil microemulsion
PublikacjaCollagen and hyaluronic acid (HA) are biopolymers that affect the appearance and condition of the skin. Delivery of these compounds into the skin is highly challenging since have a number of disadvantageous properties, such as high molecular weight and hydrophilicity. Here, we evaluated the transdermal penetration of low and high molecular weight collagen and HA from microemulsions. A number of microemulsion formulations, differing...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublikacjaIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pACYCpBAD to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pACYCpBAD to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pCC90 to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pACYCpBAD to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pCC90 to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pACYCpBAD to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pCC90 to glass in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: AAEC191A/pCC90 to polystyrene in a dynamic system
Dane BadawczeThe attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this...
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Electrical characteristics simulation of top-gated graphene field-effect transistor (GFET) with 10 μm x 10 μm graphene channel
Dane BadawczeThe presented data set is part of the research on graphene field-effect transistor (GFET) modelling. The calculations were performed with the use of GFET Tool program (https://nanohub.org/resources/gfettool DOI: 10.4231/D3QF8JK5T), which enabled simulation of the drain current (Id) vs. drain voltage (Vd) characteristics for different gate voltages (Vg)...
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Electrical characteristics simulation of top-gated graphene field-effect transistor (GFET) with 10 μm x 3 μm graphene channel
Dane BadawczeThe presented data set is part of the research on graphene field-effect transistor (GFET) modelling. The calculations were performed with the use of GFET Tool program (https://nanohub.org/resources/gfettool DOI: 10.4231/D3QF8JK5T), which enabled simulation of the drain current (Id) vs. drain voltage (Vd) characteristics for different gate voltages (Vg)...
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Dagmara Lisman PhD
OsobyScientist, biologist, forensic geneticist. She completed her master's studies at the West Pomeranian University of Technology in Szczecin, at the Faculty of Biology, and obtained a doctoral degree in forensic genetics at the Pomeranian Medical University in Szczecin. Currently, he works as an assistant at the Department of Forensic Medicine of the same university. Her research, conducted at the Department of Forensic Genetics at...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublikacjaUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Overproduction of CaMet15p native and His-tag versions.
Dane BadawczeEnzyme of fungal L-methionine biosynthetic pathway: O-acetylhomoserine sulfhydrylase (Met15p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of CaStr2p native and His-tag versions.
Dane BadawczeEnzyme of fungal L-methionine biosynthetic pathway: cystathionine-γ-synthase (CaStr2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of homoserine O-acetyltransferase (CaMet2p) native and His-tag versions.
Dane BadawczeEnzyme of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublikacjaHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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Design of battery charging system update for glider launcher
PublikacjaThis paper presents an innovative solution for increasing life of lead-acid batteries used in a glider launcher. The study is focused on upgrading a charging system instead of a costly full replacement of it. Based on literature review, the advanced three-stage charging profile was indicated. The new topology of the power converter was proposed and a simulation model was developed. A simulation study was performed which leads to...
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Application of the neural networks for developing new parametrization of the Tersoff potential for carbon
PublikacjaPenta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3-bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the...
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Model-based testing for execution algorithms in the simulation of cyber-physical systems
PublikacjaThe understanding of simulation semantics of a hybrid system is a challenge for computational engineers as it requires expertise in computer science, engineering, numerical methods, and mathematics at once. The testing methods for the execution of a simulation are being researched but not yet applied on the industrial level. Consequently, the semantics of the simulation becomes a critical artifact in the system development process....
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Simulation of perovskite-based CuI/CH3NH3PbI3/TiO2 solar cell performance
Dane BadawczeThe presented data set is part of the theoretical research on novel thin-layer lead-halide perovskite solar cells with different inorganic transparent conductive oxides used as charge transport layers. In this study CuI/CH3NH3PbI3/TiO2 model structure (Model 1) was investigated by the use of the SCAPS-1D simulation method (https://scaps.elis.ugent.be/).
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Simulation of perovskite-based CuI/CH3NH3PbI3/SnO2 solar cell performance
Dane BadawczeThe presented data set is part of the theoretical research on novel thin-layer lead-halide perovskite solar cells with different inorganic transparent conductive oxides used as charge transport layers. In this study CuI/CH3NH3PbI3/SnO2 model structure (Model 2) was investigated by the use of the SCAPS-1D simulation method (https://scaps.elis.ugent.be/).
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Simulation of perovskite-based CuI/CH3NH3PbI3/ZnO solar cell performance
Dane BadawczeThe presented data set is part of the theoretical research on novel thin-layer lead-halide perovskite solar cells with different inorganic transparent conductive oxides used as charge transport layers. In this study CuI/CH3NH3PbI3/ZnO model structure (Model 3) was investigated by the use of the SCAPS-1D simulation method (https://scaps.elis.ugent.be/).
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Identification and cloning of C. albicans SC5314 genes encoding L-methionine biosynthetic pathway enzymes.
Dane BadawczeEnzymes of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p), O-acetylhomoserine sulfhydrylase (Met15p) and cystathionine-γ-synthase (Str2p) could be exploited as molecular targets for antifungal chemotherapy. The goal of the study was to identify and clone genes encoding mentioned above enzymes. MET2, MET15 and STR2 genes...
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublikacjaMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublikacjaThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
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Electromagnetic interference frequencies prediction model of flyback converter for snubber design
PublikacjaSnubber design for flyback converters usually requires experimental prototype measurements or simulation based on accurate and complex models. In this study simplified circuit modelling of a flyback converter has been described to dimension snubbers in early stage of design process. Simulation based prediction of the transistor and diode ringing frequencies has been validated by measurements in a prototype setup. In that way obtained...
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Survival time prognosis under a Markov model of cancer development
PublikacjaIn this study we look at a breast cancer data set of women from Pomerania region collected in year 1987-1992 in the Medical University of Gdańsk. We analyze the clinical risk factors in conjunction with Markov model of cancer development. We evaluate Artificial Neural Network (ANN) survival time prediction via a simulation study.
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Potential diagnostic utility of recombinant Toxoplasma gondii proteins for detecting anti-Toxoplasma gondii IgG antibodies in horses serum samples
Dane BadawczeToxoplasmosis is caused by an intracellular protozoan, Toxoplasma gondii, and is a parasitic disease that occurs in all warm-blooded animals, including humans. Toxoplasmosis is one of the most common parasitic diseases of animals and results in reproductive losses. Diagnosis of toxoplasmosis is currently based on serological assays using native antigens...
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Potential diagnostic utility of recombinant Toxoplasma gondii proteins for detecting anti-Toxoplasma gondii IgG antibodies in goat serum samples
Dane BadawczeToxoplasmosis is caused by an intracellular protozoan, Toxoplasma gondii, and is a parasitic disease that occurs in all warm-blooded animals, including humans. Toxoplasmosis is one of the most common parasitic diseases of animals and results in reproductive losses. Diagnosis of toxoplasmosis is currently based on serological assays using native antigens...
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Potential diagnostic utility of recombinant Toxoplasma gondii proteins for detecting anti-Toxoplasma gondii IgG antibodies in feline serum samples
Dane BadawczeToxoplasmosis is caused by an intracellular protozoan, Toxoplasma gondii, and is a parasitic disease that occurs in all warm-blooded animals, including humans. Toxoplasmosis is one of the most common parasitic diseases of animals and results in reproductive losses. Diagnosis of toxoplasmosis is currently based on serological assays using native antigens...
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Comparative Analysis of Numerical and Experimental Studies of the Airflow Around the Sample of Urban Development
PublikacjaIn this paper, on the background of a short overview of the recent advances in the field of Environmental Wind Engineering (EWE), a comparison of wind tunnel experiment and numerical simulation for some cases of airflow around an urban layout have been reported. The purpose of the study is quantitative and qualitative comparison of measurements in the wind tunnel as well as numerical simulation using Ansys Fluent software. The...
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Damian Rosiak dr inż.
OsobyWykształcenie Studia I stopnia - inżynierskie, kierunek BIOTECHNOLOGIATytuł pracy inżynierskiej: "Reakcja halogenków rtęci(II) z wybranymi N-benzoilotiomocznikami i charakterystyka strukturalna jej produktów"Promotor: prof. dr hab. inż. Barbara Becker, prof. zw. PG Studia II stopnia - magisterskie, kierunek BIOTECHNOLOGIATytuł pracy magisterskiej: "Reakcje halogenków rtęci(II) z wybranymi tiomocznikami i charakterystyka produktów"Praca...
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublikacjaPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
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Anomalous Behavior of Hyaluronan Crosslinking Due to the Presence of Excess Phospholipids in the Articular Cartilage System of Osteoarthritis
PublikacjaLubrication of articular cartilage is a complex multiscale phenomenon in synovial joint organ systems. In these systems, synovial fluid properties result from synergistic interactions between a variety of molecular constituent. Two molecular classes in particular are of importance in understanding lubrication mechanisms: hyaluronic acid and phospholipids. The purpose of this study is to evaluate interactions between hyaluronic acid...
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Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies
PublikacjaOsmolytes, the small organic molecules accumulated in cells under environmental stress, can modulate the stability of biopolymers such as proteins and DNA. In spite of many years of research, there is no established molecular mechanism of the influence of osmolytes on DNA structure. Here, we used two model osmolytes that denature (urea) or stabilize (trimethylglycine, TMG) proteins to study their effect on DNA in aqueous solutions...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublikacjaChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublikacjaWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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Milena Marycz dr inż.
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Niebezpieczeństwo ukryte w żywności-aminy biogenne. Cz. II. Metody oznaczania i wyzwania.
PublikacjaZe względu na aktywność biologiczną amin biogennych ich oznaczanie zarówno jakościowe, jak i ilościowe w żywności ma istotne znaczenie w celu zapewnienia ochrony zdrowia i życia ludzkiego. Obecnie do monitoringu amin biogennych w żywności najczęściej wykorzystuje się: wysokosprawną chromatografię cieczową (HPLC), chromatografię cienkowarstwową (TLC) oraz absorpcyjną spektrofotometrię cząsteczkową. Są to jednak techniki czasochłonne,...
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Linear and branched polyester resins based on dimethyl-2,5-furandicarboxylate for coating applications
PublikacjaIn this study, novel bio-based hydroxyl-functional (co)polyesters from dimethyl-2, 5-furandicarboxylate (DMF), 2,3-butanediol, and a variety of comonomers viz. glycerol, pentaerythritol or trimethylolpropane are prepared using a solvent-free, bulk polycondensation technique. Extensive molecular and thermal characterization was performed to elucidate the properties of these materials. The materials showed suitable properties for solvent-borne...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublikacjaThe 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...