Filters
total: 128
filtered: 114
Search results for: STRUCTURAL DYNAMICS
-
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...
-
NONSTRUCTURAL STIFFNESS ASSESSMENT IN INSTRUMENTED STEEL BUILDINGS
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...
-
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...
-
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....
-
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...
-
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...
-
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...
-
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...
-
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,...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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...
-
Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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....
-
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)...
-
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...
-
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,...
-
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...
-
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,...
-
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...
-
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...
-
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...
-
Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
Publication -
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...
-
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...
-
Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
-
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...
-
Forced vibrations in a dynamic system that is damped by a mechanism that trans-pass through its singular position
PublicationIn the paper, vibrations of a hybrid multibody-continuous system are investigated. For all the mechanical devices, effective damping methods are crucial in the design process. To obtain it, installation of viscous dampers or elasto-viscous elements is dominant. In the paper, an alternative method is investigated. It is based on modal disparity. To describe the method briefly, when structural damping is present in continuous systems,...