Search results for: STRUCTURAL DYNAMICS
-
Structural Dynamics
Journals -
Structural Dynamics and Stability of Composite Structures
Publication -
Structural Dynamics and Stability of Composite Structures
PublicationThis an editorial for a special Issue devoted to the application of dynamic and stability analysis of composite structures. In structural applications, past few decades have seen outstanding advances in the use of composite materials including Functionally Graded Materials (FGM). Most structures, whether they are used in civil, marine, or aerospace engineering, are subjected to dynamic loads during their operation.Therefore, dynamic...
-
Structural Change and Economic Dynamics
Journals -
Proceedings of the 9th International Conference on Structural Dynamics, EURODYN 2014
PublicationSince offshore wind turbine supporting structures are subjected to dynamic environments with time-varying loading conditions, it is important to model their dynamic behavior and validate these models by means of vibrational experiments. In this paper assessment of dynamical state of the structure is investigated by means of both: numerical modeling, and experimental modal analysis. In experimental modal analysis, capturing the...
-
Uncertainty Quantification in Experimental Structural Dynamics Identification of Composite Material Structures
PublicationComposite materials are widely used in manufacture of aerospace and wind energy structural components. These load carrying structures are subjected to dynamic time-varying loading conditions. Robust structural dynamics identification procedure impose tight constraints on the quality of modal models estimates obtained from vibration experiments. Modal testing results are influenced by numerous factors introducing uncertainty to...
-
An adaptive-noise Augmented Kalman Filter approach for input-state estimation in structural dynamics
PublicationThe establishment of a Digital Twin of an operating engineered system can increase the potency of Structural Health Monitoring (SHM) tools, which are then bestowed with enhanced predictive capabilities. This is particularly relevant for wind energy infrastructures, where the definition of remaining useful life is a main driver for assessing the efficacy of these systems. In order to ensure a proper representation of the physical...
-
Structural Dynamics - 2022/2023
e-Learning Coursesprzedmiot na II semestrze studiów drugiego stopnia kierunku Civil Engineering
-
Structural Dynamics 2023/2024
e-Learning Coursesprzedmiot na II semestrze studiów drugiego stopnia kierunku Civil Engineering
-
Lattice Dynamics and Structural Phase Transitions in Eu2O3
Publication -
EARTHQUAKE ENGINEERING & STRUCTURAL DYNAMICS
Journals -
Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublicationThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
-
Historic bridge modelling using laser scanning, ground penetrating radar and finite element methods in the context of structural dynamics
PublicationPraca dotyczy modelowania MES zabytkowej konstrukcji mostowej przy użyciu danych geometrycznych pochodzących ze skanowania laserowego oraz georadaru. Z uwagi na brak badań materiału budujcego most, przeprowadza się analize wrażliwości konstrukcji na zmiany modułu sprężystości granitu.
-
Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
-
Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
-
Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
-
Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
Publication -
International Journal of Structural Stability and Dynamics
Journals -
Experimental study on earthquake-induced pounding between structural elements made of different building materials
PublicationCelem artykułu jest pokazanie wyników dwóch eksperymentów dotyczących zderzeń pomiędzy elementami wykonanymi z różnych materiałów budowlanych, takich jak: stal, beton, drewno i ceramika. Pierwszy z nich polegał na zrzucaniu kul na płaską powierzchnię, drugi dotyczył zderzeń modeli konstrukcji poddanych wymuszeniom sejsmicznym na stole wstrząsowym. Wyniki testów pokazują, iż wpływ materiału elementów kolidujących ze sobą na zachowanie...
-
Analytical expression between the impact damping ratio and the coefficient of restitution in the non-linear viscoelastic model of structural pounding
PublicationWyniki wcześniejszych badań pokazują, iż nieliniowy model lepko-sprężysty zderzeń konstrukcji budowlanych podczas trzęsień ziemi najdokładniej symuluje siłę zderzenia w czasie kontaktu oraz odpowiedź konstrukcji. Celem niniejszego artykułu jest wyprowadzenie wzoru na zależność pomiędzy liczbą tłumienia zderzenia (parametr wspomnianego modelu) a współczynnikiem odbicia, który jest parametrem często stosowanym i analizowanym w literaturze....
-
What drives sustainable investing? Adoption determinants of sustainable investing exchange-traded funds in Europe
PublicationDespite the growing interest in various topics related to sustainable (ESG) investing, some issues remain understudied, such as the determinants of their utilization at the macro level. This paper contributes to the state of knowledge two-directionally. First, it shows the development of sustainable investing exchange-traded funds (ETFs) in European countries. Second, it traces the significant determinants of adopting sustainable...
-
Global value chains, wages, employment and labour production in China: A regional approach
PublicationIn this study we analyse the relationship of trade and global value chains (GVCs) to the labour market in 31 Chinese provinces for 25 sectors, by means of a system of structural equations. We firstly distinguish between provincial value chains (PVCs) and interprovincial value chains (PRVCs) in order to outline their distribution and evolution over time. Then, we investigate to what extent participation in GVCs, PVCs and PRVCs –...
-
GVC involvement and the gender wage gap: Micro -evidence on European countries
PublicationWe examine linkages between involvement in global value chains (GVCs) and gender wage inequalities. We use merged data from Structure of Earnings Survey and the World Input Output Database covering 18 European countries. We employ information on employees’ personal and company characteristics and a sectoral involvement in GVCs. In general, the wages of workers from sectors more involved in GVCs are lower. However, the relationship...
-
Relative Productivity, Country Size and Export Diversification
PublicationThis paper analyses the effects of productivity and country size on the extent of trade structure diversification. Using a testable version of the Ricardian model, we show that relative export variety is an outcome of two forces: a relative productivity change (technological progress) and a relative country size change (labour force growth). The model predictions are validated empirically using product-level trade data for a sample...
-
Linkages between services and manufacturing as a new channel for GVC development: Evidence from CEE countries
PublicationThe goal of the paper is to verify a causal relationship between forward linkages from domestic services to manufacturing and the participation/position of a country in global value chains (GVCs) in selected Central and Eastern European economies. We observed a strong polarisation pattern: the Baltic countries along with the Czech Republic strengthen their positions and participation in GVCs by having a strong relationship between...
-
The Opening of Central and Eastern European Countries to Free Trade: A Critical Assessment
PublicationThree decades after the fall of the Berlin wall and one and a half decades after the Big Bang enlargement of the European Union (2004-2007), we revisit contrasting narratives about the benefit of both free trade and the EU enlargement for Central and Eastern European (CEE) countries. We distinguish old, pre-2004 EU countries from CEE countries that joined the EU in 2004-2007, as well as from the CEE countries that have not become...
-
Equivalent Single Layer Models in Free Vibration Analysis of Laminated Multi-Layered Plates
PublicationThe performance of selected equivalent single-layer (ESL) models is evaluated within several classical benchmark tests for small amplitude free vibration analysis of multi-layered plates. The authors elaborated their own Finite Element software based on the first-order shear deformation (FOSD) theory with some modifications incorporated including a correction of the transverse shear stiffness and an application of zigzag type functions....
-
Periodic Properties of 1D FE Discrete Models in High Frequency Dynamics
PublicationFinite element discrete models of various engineering 1D structures may be considered as structures of certain periodic characteristics. The source of this periodicity comes from the discontinuity of stress/strain field between the elements. This behaviour remains unnoticeable, when low frequency dynamics of these structures is investigated. At high frequency regimes, however, its influence may be strong enough to dominate calculated...
-
Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
-
Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
-
Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
-
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...
-
Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
-
Economic growth, structural change and quality upgrading in New Member States
PublicationThe purpose of this research is to present the recent developments concerning structural change and productivity growth in New Member States and the role played in such process by country specific factors. We focus on ten countries (NMS-10) which joined the EU in 2004 and analyze productivity dynamics of their labor structures between the years 1995 and 2005 in a comparative setting versus EU-15 economies. NMS-10 have gone through...
-
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...
-
Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
-
Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
-
Structural response of existing spatial truss roof construction based on Cosserat rod theory
PublicationPaper presents the application of the Cosserat rod theory and newly developed associated finite elements code as the tools that support in the expert-designing engineering practice. Mechanical principles of the 3D spatially curved rods, dynamics (statics) laws, principle of virtual work are discussed. Corresponding FEM approach with interpolation and accumulation techniques of state variables are shown that enable the formulation...
-
Dynamic Response of the Suspended on a Single Cable Footbridge
PublicationThe article presents numerical simulations, dynamic in situ load tests and a structural health monitoring (SHM) system installed in a suspended on a single cable footbridge. Numerical simulations performed prior to construction indicated the possibility of structural dynamics problems, finally confirmed in the course of dynamic test loading. In the dynamic load course the bridge deck developed vibrations displaying accelerations...
-
In-depth characterization of icosahedral ordering in liquid copper
PublicationThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...
-
Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
-
Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
-
Dynamic effect of the vehicle passing under lightweight footbridge.
PublicationThe paper describes a numerical study of dynamic response of cable-stayed steel footbridge for a big lorry passing underneath. The footbridge is an existing object crossing Wolska street in Warsaw. The structural model of footbridge was verified by dynamic test loading. A numerical study of a vehicle passing under footbridge is presented. 2D and 3D incompressible flow fields are modeled using sliding mesh in transient CFD computation....
-
Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
-
Krzysztof Jan Kaliński prof. dr hab. inż.
PeopleKrzysztof J. Kaliński completed his MSc study at Gdańsk University of Technology (GUT) Faculty of Production Engineering (1980, result – get a first). He obtained PhD at GUT Faculty of Machine Building (1988, result – get a first), DSc at GUT Faculty of Mechanical Engineering (ME) (2002, result – get a first), and professor’s title – w 2013 r. In 2015 r. he became full professor.His research area includes: theoretical and applied...
-
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...
-
Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan 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...
-
High frequency dynamics of an isotropic Timoshenko periodic beam by the use of the Time-domain Spectral Finite Element Method
PublicationIn this work results of numerical simulations and experimental measurements related to the high frequency dynamics of an aluminium Timoshenko periodic beam are presented. It was assumed by the authors that the source of beam structural periodicity comes from periodical alterations to its geometry due to the presence of appropriately arranged drill-holes. As a consequence of these alterations dynamic characteristics of the beam...
-
Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
-
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...
-
Application of the finite element methods in long-term simulation of the multi-physics systems with large transient response differences
PublicationApplication of the Finite Element Method (FEM) and the Multibody Dynamics Method allows analyzing of complex physical systems. Complexity of the system could be related both to the geometry and the physical description of phenomenon. The metod is the excellent tool for analyzing statics or dynamics of the mechanical systems, and permits tracking of Multi Body System (MBS) transient response for the long-term simulations and application...
-
Modal Adjustment of Rayleigh Based Structural Damping and Coordinate-Partitioning Algorithm Dedicated to Frictionless Contact Constraints between Multibody System and Structure Modelled with Finite Elements
PublicationThe paper presents a dedicated numerical algorithm. The algorithm is advantageous during investigations of the dynamics of a hybrid multibody / finite-elements system. We focus our attention on interactions resulting from mechanical contact. Pointwise contact connects a vertex of the multibody structure and a surface of the elastic reference body. Instead of a positive value of the relative penetration factor, constraint equations...
-
Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
-
Marta Kuc-Czarnecka dr
PeopleMarta Kuc-Czarnecka is the deputy head of the Department of Statistics and Economics at the Faculty of Management and Economics of the Gdańsk University of Technology. She also serves as the Dean's proxy for AMBA accreditation. She is a co-founder of Rethinking Economics Gdańsk and a member of the Foundation Edward Lipiński for the promotion of pluralism in economic sciences. In 2018-2022, she was Eurofound’s quality of life and...
-
Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublicationHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
-
A spline-based FE approach to modelling of high frequency dynamics of 1-D structures
PublicationIn this paper a computational methodology leading to the development of a new class of FEs, based on the application of continuous and smooth approximation polynomials, being splines, has been presented. Application of the splines as appropriately defined piecewise elemental shape functions led the authors to the formulation of a new approach for FEM, named as spFEM, where contrary to the well-known NURBS approach, the boundaries...
-
Numerical Investigation on Dynamic Performance of a Multi-storey Steel Structure Model and Comparison with Experimental Results
PublicationShaking table testing is the most commonly adopted method to simulate earthquake forces. This approach allows us to analyze the dynamic performance and provides a valuable insight into the dynamics of building structures, which helps to improve their future safety and reliability. The present study aims to conduct a numerical evaluation of dynamic response of a multi-storey steel structure model, which was previously examined during...
-
Numerical investigation on dynamic performance of a multi-storey steel structure model and comparison with experimental results
PublicationShaking table testing is the most commonly adopted method to simulate earthquake forces. This approach allows us to analyze the dynamic performance and provides a valuable insight into the dynamics of building structures, which helps to improve their future safety and reliability. The present study aims to conduct a numerical evaluation of dynamic response of a multi-storey steel structure model, which was previously examined during...
-
Processing of point cloud data retrieved from terrestrial laser scanning for structural modeling by Finite Element Method
PublicationFinite Element Method is one most popular contemporary method of strength analysis. The method is an advanced method for solving differential equations, based on discretization, which means that area is divided into finite elements. Each finite element has a solution of the equation approximated by specific functions and performing the actual calculations only for nodes of this division. Finite Element Method is widely used in...
-
Estimation of nonstructural stiffness in instrumented steel frames
PublicationLateral stiffness of nonstructural components may significantly influence the initial stiffness of the entire structure and consequently alter its dynamic characteristics. While methods for simulating structural members are well-established, approaches for modeling nonstructural components that also participate in seismic response are notably less developed. In this paper a simplified, physically-intuitive approach for estimating...
-
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...
-
Tunable Dielectric Switching of (Quinuclidinium)[MnCl4] Hybrid Compounds
PublicationInorganic−organic hybrid QMnCl (Q = quinuclidinium) crystals were synthesized and characterized. The X-ray and variable-temperature IR/Raman analysis demonstrate that the crystals undergo a reversible structural phase transition, which originates from an order−disorder process and is related to the dynamics of the organic Q cation. Dielectric function measurements disclose a switchability between low (“OFF”) and high (“ON”) dielectric...
-
Selected Aspects of 3D Printing for Emergency Replacement of Structural Elements
PublicationThe paper presents a synthetic characterization of modern methods of manufacturing or regenerating machine elements. Considered methods are machining and additive methods, in particular 3D printing in the FDM/FFF technique. For the study, the authors made samples of the holder bracket using selected methods. Samples made by machining operations, 3D printing with various filling were tested. The paper contains a technical and economic...
-
Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublicationThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
-
DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
-
Why Are Left-Handed G-Quadruplexes Scarce?
PublicationG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....
-
Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublicationOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
-
Safety assessment of a concrete viaduct damaged by vehicle impact and an evaluation of the repair
PublicationDamage to lower parts of viaducts caused by impact from under-passing high vehicles is relatively frequent. One such incident, in which a viaduct was damaged by the impact from a truck with an improperly assembled hydraulic crane, is considered in this work. The analysis is based on a detailed object damage evaluation, 3D laser scanning, and numerical simulations. The aim of the study is to accurately model the vehicle impact into...
-
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...
-
An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
-
Tomasz Wąsowicz dr hab.
PeopleTomasz Wąsowicz's research was first related to high-resolution atomic spectroscopy and focused on measurements and analysis of the transition probabilities of the forbidden lines, the hyperfine and isotopic structure of spectral lines of heavy elements, Stark effect in the helium atom. Tomasz Wąsowicz currently studies physicochemical processes occurring during interactions of various forms of radiation with atoms and molecules...
-
Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
-
The saga of a fish: from a survival guide to closing lemmas
PublicationIn the paper by D. Burago, S. Ivanov and A. Novikov, “A survival guide for feeble fish”, it has been shown that a fish with limited velocity can reach any point in the (possibly unbounded) ocean provided that the fluid velocity field is incompressible, bounded and has vanishing mean drift. This result extends some known global controllability theorems though being substantially nonconstructive. We give a fish a different recipe...
-
Footbridges. Dynamic Design – Selected Problems
PublicationModern footbridges create challenge in esthetic and structural design. Breaking the proven canons is a recipe for architectural success. However esthetic form has to be also a functional pedestrian bridge. Therefore a good FEM modeling is a key element in engineering part of design. The paper presents selected problems related to the modeling of the dynamic construction of footbridges. Several basic dynamic problems concerning...
-
Dissolution of Nb-doped hydroxyapatite prepared via low-temperature mechanochemical method: Spectroscopy studies
PublicationCalcium phosphate glass ceramics with nominal hydroxyapatite stoichiometry doped with niobium were synthesized using simple as well as low-temperature mechanochemical method and then in the form of compressed pellet were submitted to the static dissolution process in distilled water for one month. The results of structural analysis, performed mainly on the base of spectroscopic methods such as: infrared absorption spectroscopy,...
-
The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
-
Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne 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...
-
Updating Finite Element Model of a Wind Turbine Blade Section Using Experimental Modal Analysis Results
PublicationThis paper presents selected results and aspects of themultidisciplinary and interdisciplinary research oriented for the experimental and numerical study of the structural dynamics of a bend-twist coupled full scale section of awind turbine blade structure.Themain goal of the conducted research is to validate finite elementmodel of themodified wind turbine blade section mounted in the flexible support structure accordingly to the...
-
Smart acoustic band structures
PublicationSmart acoustic band structures exhibit very interesting and non-standard physical properties due to the periodic nature of their certain characteristic on different scale levels. They manifest mostly in their frequency spectra as socalled frequency band-gaps or stop-bands, what has a great impact on the behaviour of these structures in relation to the propagation of vibro-acoustic signals that can be transmitted through the structures...
-
Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
-
Critical Review on Robust Speed Control Techniques for Permanent Magnet Synchronous Motor (PMSM) Speed Regulation
PublicationThe permanent magnet synchronous motor (PMSM) is a highly efficient energy saving machine. Due to its simple structural characteristics, good heat radiation capability, and high efficiency, PMSMs are gradually replacing AC induction motors in many industrial applications. The PMSM has a nonlinear system and lies on parameters that differ over time with complex high-class dynamics. To achieve the excessive performance operation...
-
Influence of Added Water Mass on Ship Structure Vibration Parameters in Virtual and Real Conditions
PublicationModelling of ship structures in a virtual environment is now standard practice. Unfortunately, many engineers forget to consideri the influence of added water on the frequency values and the amplitude of natural vibrations. The article presents the effect of water damping on the frequency values of the individual natural vibration modes. The tests were carried out in two stages. First, the mentioned values were determined using...
-
Ipertrofan Revisited—The Proposal of the Complete Stereochemistry of Mepartricin A and B
PublicationBeing a methyl ester of partricin, the mepartricin complex is the active substance of a drug called Ipertrofan (Tricandil), which was proven to be useful in treatment of benign prostatic hyperplasia and chronic nonbacterial prostatitis/chronic pelvic pain syndrome. Nevertheless, no direct structural evidence on the stereochemistry of its components has been presented to date. In this contribution, we have conducted detailed, NMR-driven...
-
Closer look into the structures of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water
PublicationIn recent years, deep eutectic solvents (DES) and it’s mixture with water have become more and more attention as green solvents used in chemistry. However, there are only a few theoretical studies on the mechanisms of pure DES and DES-water complex formation. Therefore, the structural properties of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water have been investigated by means of Molecular...
-
Experimental and Numerical Study on Dynamics of Two Footbridges with Different Shapes of Girders
PublicationThe paper presents the experimental and numerical results of the dynamic system identification and verification of the behavior of two footbridges in Poland. The experimental part of the study involved vibration testing under different scenarios of human-induced load, impulse load, and excitations induced by vibration exciter. Based on the results obtained, the identification of dynamic parameters of the footbridges was performed...
-
Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
-
Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
-
Modelling of high frequency dynamic responses of engineering structures
PublicationModelling of high frequency dynamic responses of engineering structures, especially those related to wave propagation, is a real numerical challenge. Nowadays most of numerical models, used for that purpose, are based on the application of various finite element techniques. However, finite element discrete models may also be considered as possessing certain periodic structures, which may manifest themselves in particular scenarios....
-
Deformable model of a butterfly in motion on the example of Attacus atlas
PublicationInsect wings can undergo significant chordwise (camber) as well as spanwise (twist) deformation during flapping flight but the effect of these deformations is not well understood. The shape and size of butterfly wings leads to particularly large wing deformations, making them an ideal test case for investigation of these effects. High-speed videogrammetry was used to capture the wing kinematics and deformations. The movements of...
-
Experimental Study on Dynamics of Wooden House Wall Panels with Different Thermal Isolation
PublicationWood frame buildings are very popular in regions that are exposed to different dynamic excitations including earthquakes. Therefore, their seismic resistance is really important in order to prevent structural damages and human losses. The aim of the present paper is to show the results of experimental tests focused on the dynamic response of wall panels of a wooden frame building with thermal isolation made of mineral wool and...
-
Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublicationAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
-
Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublicationInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
-
Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublicationACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
-
Investigating the disease- modifying properties of sclerotiorin in Alzheimer's therapy using acetylcholinesterase inhibition
PublicationAlzheimer's disease (AD) is a progressive neurodegenerative disorder caused due to the damage and loss of neurons in specific brain regions. It is the most common form of dementia observed in older people. The symptoms start with memory loss and gradually cause the inability to speak and do day-to-day activities. The cost of caring for those affected individuals is huge and is probably beyond most developing countries capability....
-
Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
-
Aerodynamic Shape Optimization for Delaying Dynamic Stall of Airfoils by Regression Kriging
PublicationThe phenomenon of dynamic stall produce adverse aerodynamic loading which can adversely affect the structural strength and life of aerodynamic systems. Aerodynamic shape optimization (ASO) provides an effective approach for delaying and mitigating dynamic stall characteristics without the addition of auxiliary system. ASO, however, requires multiple evaluations time-consuming computational fluid dynamics models. Metamodel-based...
-
Theoretical examination of the fracture behavior of BC3 polycrystalline nanosheets: Effect of crack size and temperature
Publication2D carbon graphene nanostructures are elements of advanced materials and systems. This theoretical survey provides explanation to the mechanical and fracture behavior of mono- and polycrystalline BC3 nanosheets (denoted as MC- and PCBC3NS, respectively) as a function of temperature and the type of crack defects. The mechanical performance of PCBC3NS at elevated temperatures was monitored varying the number of grain boundaries (the...
-
Multi-objective optimization of the cavitation generation unit structure of an advanced rotational hydrodynamic cavitation reactor
PublicationHydrodynamic cavitation (HC) has been widely considered a promising technique for industrial-scale process intensifications. The effectiveness of HC is determined by the performance of hydrodynamic cavitation reactors (HCRs). The advanced rotational HCRs (ARHCRs) proposed recently have shown superior performance in various applications, while the research on the structural optimization is still absent. The present study, for the...
-
Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
Publication -
Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...