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Search results for: Molecular dynamics simulations
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublicationTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublicationUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...
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A novel one-variable first-order shear deformation theory for biaxial buckling of a size-dependent plate based on Eringen’s nonlocal differential law
PublicationPurpose – This paper aims to present a new one-variable first-order shear deformation theory (OVFSDT) using nonlocal elasticity concepts for buckling of graphene sheets. Design/methodology/approach – The FSDT had errors in its assumptions owing to the assumption of constant shear stress distribution along the thickness of the plate, even though by using the shear correction factor (SCF), it has been slightly corrected, the errors...
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Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response
PublicationSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublicationAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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A new open-source software developed for numerical simulations usingdiscrete modeling methods
PublicationThe purpose of this work is to present the development of an open-source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [F. Donzé, S.A. Magnier, Formulation of a three-dimensional numerical model of brittle behavior, Geophys....
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublicationRadiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This...
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Triplet–Triplet Annihilation Upconverting Liposomes: Mechanistic Insights into the Role of Membranes in Two-Dimensional TTA-UC
PublicationTriplet−triplet annihilation upconversion (TTA-UC) implemented in nanoparticle assemblies is of emerging interest in biomedical applications, including in drug delivery and imaging. As it is a bimolecular process, ensuring sufficient mobility of the sensitizer and annihilator to facilitate effective collision in the nanoparticle is key. Liposomes can provide the benefits of two-dimensional confinement and condensed concentration...
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Mixed, quantum-classical description of electron density transfer in the collision process
PublicationIn this work, we investigate an ion-atom model describing the time-dependent evolution of electron density during the collision. For a S3+- H system, numerical simulations are based on classical trajectory calculations, and the electron density behaviour is described with the time-dependent Schrödinger equation. We apply the finite difference method to obtain quantitative insights into the charge transfer dynamics, providing detailed...
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Executing Multiple Simulations in the MERPSYS Environment
PublicationThe chapter investigates the steps necessary to perform a simulation instance in the MERPSYS environment and discusses potential limitations in case when vast numbers of simulations are required. An extended architecture is proposed which includes a JMS-based simulation queue and multiple distributed simulators, overcoming the potential bottlenecks. The chapter introduces also methods for preparing suites of multiple simulations...
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Comparative molecular modelling of biologically active sterols
PublicationMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
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Dynamics of quantum entanglement
PublicationA model of discrete dynamics of entanglement of a bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied by an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of subsystems. For some mixed states...
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Adsorption onto zeolites: molecular perspective
Publication2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent...
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Dissociative ionization dynamics of dielectric gas C3F7CN
PublicationFluoronitrile C3F7CN is a promising candidate for the replacement of SF6 dielectric gas in high-voltage insulation. We present a combined experimental and theoretical study on its ionization dynamics probed in the 0-100 eV energy range. We exploited the total ion collection technique to determine the absolute ionization cross section, mass spectrometry to determine the fragment branching ratios and ab initio nonadiabatic molecular...
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Directed pulse dynamics
PublicationIntroducing a projection method into a one-dimensional model of a pulse propagation in isotropic media, we derive and investigate a system of equation describing dynamics ultrashort pulses of opposite directions ofpropagation and ones with interaction of directed pulses with different polarization.
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Oddziaływania taboru na mosty kolejowe przy zmiennych parametrach ruchu
PublicationW pracy poruszono zagadnienia związane z identyfikacją oraz modelowaniem układu dynamicznego most-pojazd ruchomy. Za element szczególnie istotny uznano czynnik obciążający. Opracowano i wdrożono metodykę identyfikacji cech dynamicznych rzeczywistego pojazdu szynowego. Eksperyment badawczy przeprowadzono dla jednostki trakcyjnej EN57, jednak nie ma żadnych ograniczeń w stosowaniu metody dla innego, konwencjonalnego taboru szynowego....
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FPGA Based Real Time Simulations of the Face Milling Process
PublicationThe article presents a successful implementation of the milling process simulation at the Field-Programmable Gate Array (FPGA). By using FPGA, very rigorous Real-Time (RT) simulation requirements can be met. The response time of the FPGA simulations is significantly reduced, and the time synchronization is better than in a typical RT system implemented in software. The FPGA-based approach is characterized by enormous flexibility...
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Intelligent monitoring the vertical dynamics of wheeled inspection vehicles
PublicationThe problem of intelligent monitoring of the vertical dynamics of wheeled inspection vehicles is addressed. With the independent MacPherson suspension system installed, the basic analysis focuses on the evaluation of the parameters of the so-called quarter car model. To identify a physically motivated continuous description, in practice, dedicated integral-horizontal filters are used. The obtained discrete model, which retains...
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Modelling of planar movement dynamics of upper limb
PublicationThe original model describing planar movement dynamics of upper limb is presented. The upper limb is modelled as two-joints system loaded by external forces and internal forces of striated skeletal muscles. A behaviour of each muscle is modelled as a system composed of serially linked rheologic fragments that have different mechanical properties. These muscle models allow us to simulate a behaviour of short fusiform muscle (3DOF...
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Lattice dynamics of Mg2SiO4
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Investigation of the laser generated ablation plasma plume dynamics and plasma plume sound wave dynamics
PublicationWe investigated the dynamics of laser generated ablation plasma plume expanding in ambient air and dynamics of the sound wave generated by the expanding plasma. The ablation plasma plume was generated during nanosecond laser micromachining of the thin metal foil. The time-resolved images of the expanding plasma plume and sound wave were captured at several nanosecond intervals. Using captured images the expansion rate of the plasma...
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Bias-Dependent Dynamics of Degradation and Recovery in Perovskite Solar Cells
PublicationDegradation of perovskite solar cells (PSCs) is often found to be partially or fully reversible when the cells are allowed to recover in the dark. Unlike the dynamics of degradation, knowledge about the dynamics of PSC cell recovery is very limited. Here, we demonstrate that the PSC recovery strongly depends on the electrical bias conditions during the light-induced degradation and that it can be manipulated by applying an external...
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On dynamics of origami-inspired rod
PublicationWe discuss the dynamics of a relatively simple origami-inspired structure considering discrete and continuum models. The latter was derived as a certain limit of the discrete model. Here we analyze small in-plane deformations and related equations of infinitesimal motions. For both models, dispersion relations were derived and compared. The comparison of the dispersion relations showed that the continuum model can capture the behavior...
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Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp: Phosphorus dynamics
PublicationThis is the third paper of the series about “Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp”. In this paper, phosphorus dynamics were investigated under the condition of culturing bighead carp and common carp with added fish food (nitrogen dynamics is discussed in the second paper because their behaviors are so different from each other). Nearly fifty days’ observation results...
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Antimicrobial molecular nanocarrier–drug conjugates
PublicationMany antimicrobial drugs are poorly active against pathogenic microbes causing intracellular infections, such as Mycobacterium tuberculosis or Plasmodium falciparum. On the other hand, several known antimicrobial agents are not effective enough because of their limited cellular penetration. A common feature of both challenges is the inability of an active agent to cross the biological membrane(s). One of the possible approaches...
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Measurements of Subnanometer Molecular Layers
PublicationSelected methods of formation and detection of nanometer and subnanometer molecular layers were shown. Additionally, a new method of detection and measurement with subnanometer resolution of layers adsorbed or bonded to the gate dielectric of the ion selective field effect transistor (ISFET) was presented.
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Molecular Umbrella as A Nanocarrier for Antifungals
PublicationA molecular umbrella composed of two O‐sulfated cholic acid residues was applied for the construction of conjugates with cispentacin, containing a “trimethyl lock” (TML) or o‐dithiobenzylcarbamoyl moiety as a cleavable linker. Three out of five conjugates demonstrated antifungal in vitro activity against C. albicans and C. glabrata but not against C. krusei, with MIC90 values in the 0.22–0.99 mM range and were not hemolytic. Antifungal...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Roadmap on dynamics of molecules and clusters in the gas phase
PublicationThis roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty orders of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity...
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Periodic and chaotic dynamics in a map‐based neuron model
PublicationMap-based neuron models are an important tool in modeling neural dynamics and sometimes can be considered as an alternative to usually computationally costlier models based on continuous or hybrid dynamical systems. However, due to their discrete nature, rigorous mathematical analysis might be challenging. We study a discrete model of neuronal dynamics introduced by Chialvo in 1995. In particular, we show that its reduced one-dimensional...
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Numerical Simulations for Transonic Flow in Control Valve
PublicationResults of numerical simulations for transonic flow in control valve are presented. The valve is the main part of an adaptive pneumatic shock absorber. Flow structure in the valve domain and the influence of the flow non-uniformity in the valve on a mass flow rate is investigated. Numerical simulation results are compared with experimental data.
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Application of advanced CFD simulations in seakeeping analysis of ships (case study)
PublicationThe novel design process of many types of ships needs estimation of seakeeping properties. Especially ships like Offshore Supply Vessels, Wind Farm Support Vessels, Research Vessels, ferries, military vessels, rescue vessels require extended analysis of ship behavior on rough sea. The main reason for improving ships operability in different sea conditions is need of rising efficiency of propulsion system, reducing hull added resistance,...
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Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
PublicationThe thermally induced self-healing mechanisms in metallopolymers based on bisterpyridine complexes of iron(II) sulfate and cadmium(II) bromide, respectively, were studied by means of combined quantum mechanical/molecular mechanical (QM/MM) simulations and Raman spectroscopy. Two possible healing schemes, one based on a decomplexation of the cross-linking complexes and a second one relying on the dissociation of ionic clusters,...
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Spatiotemporal dynamics of the active perirheic zone in a natural wetland floodplain
PublicationAbstract The ecologically and biogeochemically significant perirheic zone is a part of the floodplain where waters originating from both the river and adjacent floodplain are present. In this study, we investigate the spatiotemporal dynamics of the active perirheic zone, i.e. river and floodplain waters and their transient mixing extent. This is achieved by using the Hydraulic Mixing-Cell method, a complement to a fully integrated...
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Recognizing emotions on the basis of keystroke dynamics
PublicationThe article describes a research on recognizing emotional states on the basis of keystroke dynamics. An overview of various studies and applications of emotion recognition based on data coming from keyboard is presented. Then, the idea of an experiment is presented, i.e. the way of collecting and labeling training data, extracting features and finally training classifiers. Different classification approaches are proposed to be...
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Molecular Imaging and Nanotechnology—Emerging Tools in Diagnostics and Therapy
PublicationPersonalized medicine is emerging as a new goal in the diagnosis and treatment of diseases. This approach aims to establish differences between patients suffering from the same disease, which allows to choose the most effective treatment. Molecular imaging (MI) enables advanced insight into molecule interactions and disease pathology, improving the process of diagnosis and therapy and, for that reason, plays a crucial role in personalized...
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Simulation of the number of storm overflows considering changes in precipitation dynamics and the urbanisation of the catchment area: a probabilistic approach
PublicationThis paper presents a probabilistic methodology that allows the study of the interactions between changes in rainfall dynamics and impervious areas in urban catchment on a long- and short-term basis. The proposed probabilistic model predict future storm overflows while taking into account the dynamics of changes in impervious areas and rainfall. In this model, a logistic regression method was used to simulate overflow resulting...
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Fast bubble dynamics and sizing
PublicationSingle bubble sizing is usually performed by measuring the resonant bubble response using the Dual Frequency Ultrasound Method. However, in practice, the use of millisecond-duration chirp-like waves yields nonlinear distortions of the bubble oscillations. In comparison with the resonant curve obtained under harmonic excitation, it was observed that the bubble dynamic response shifted by up to 20 percent of the resonant frequency...
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Dynamics of Ice Jam Formation and Release
PublicationThe numerical model DynaRICE and its application to ice jam formation and release is presented. The model is a two-dimensional coupled flow and ice dynamic model. The ice dynamic component, which includes both the internal ice resistance and boundary friction on ice motion, uses a Lagrangian SPH method. The hydrodynamic component of the model uses a streamline upwind finite element method, which is capable of simulating trans-critical...
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Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublicationExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
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Numerical Simulations of Hydrodynamic Open-Water Characteristics of a Ship Propeller
PublicationThe paper presents the results of numerical simulations of ship propeller operation bearing the name of Propeller Open Water (POW) Tests. The object of tests was a sample ship propeller (PPTC1), the geometrical and kinematic data of which are available, along with the results of model tests, on the official page of the research centre involved in the measurements. The research aimed at verifying the correctness of results of numerical...
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Numerical tests of time-stepping schemes in the context of FEM for 6-field shell dynamics
PublicationThe paper deals with integration of dynamic equations of irregular shells performed with relatively long time steps. Numerical instability appearing often in this kind of analysis motivated the authors to present some studies based on numerical tests referring to convergence problems of finite element analysis as well the applied stability conditions. The analysis is carried out on simulations of shell dynamics with the where the...
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Technological capability dynamics through cluster organizations
PublicationPurpose – The purpose of the paper is to portrait how members of cluster organizations (COs) perceive the role of COs in enabling them to accumulate technological capability (TC) significant for their innovation. Design/methodology/approach – The authors report the findings from their qualitative study based on an analysis of four COs. The organizational inertia and absorptive capacity (AC) theories are the theoretical underpinning...
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Two-state dynamics for replicating two-strand systems
PublicationDynamika dwustanowa została zastosowana do opisów układów dwuniciowych, analogicznych do DNA.