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Full-scale CFD simulations for the determination of ship resistance as a rational, alternative method to towing tank experiments
PublicationResults of ship resistance predictions obtained from towing tank experiments are affected by the method used to extrapolate from a model scale to a ship scale. Selection of method to determine a form factor is subjective and the extrapolation method is accurate for typical hull forms. For innovative hull forms the proper method for calculating the form factor is questionable. Moreover, the influence of the extrapolation method...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Finite element method simulations of various cases of crash tests with N2/W4/A steel road barrier
PublicationThe subject of this study is performance of N2/W4/A steel road safety barrier investigated in numerical simulations. System was checked under several types of initial conditions, which were assumed basing on the TB11 and TB32 normative crash tests. The main goal of present study is to investigate the relationship between initial conditions (angle and velocity) of the impact and the severity indices (associated to the vehicle occupant) during...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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3D DEM simulations of monotonic interface behaviour between cohesionless sand and rigid wall of different roughness
PublicationArtykuł omawia wyniki metodą elementów dyskretnych (DEM) dotyczace zachowania się strefy kontaktu między bezkohezyjnym piaskiem a sztywną scianą o różnej szorstkości. Obliczenia wykonano dla dla różnej wysokości, nachylenia i rozstawu rowków wzdłuż sciany, które symulowały jej szorstkość. W symulacjach zmieniano dodatkowo ciśnienie pionowe i początkowy wskaźnik porowatosci piasku. Nacisk położono na wpływ szorstkości na mobilizowany...
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Low-Cost Design Optimization of Microwave Passives Using Multi-Fidelity EM Simulations and Selective Broyden Updates
PublicationGeometry parameters of contemporary microwave passives have to be carefully tuned in the final stages of their design process to ensure the best possible performance. For reliability reasons, the tuning has to be to be carried out at the level of full-wave electromagnetic (EM) simulations. This is because traditional modeling methods are incapable of quantifying certain phenomena that may affect operation and performance of these...
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The dataset of simulations for optimal and non-optimal rotating receiver angles of multicoil dynamic wireless power transfer system
Open Research DataThe provided dataset is part of the simulation results shown in related journal paper "Optimal Rotating Receiver Angles Estimation for Multicoil Dynamic Wireless Power Transfer".
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Innovations in Wastewater Treatment: Harnessing Mathematical Modeling and Computer Simulations with Cutting-Edge Technologies and Advanced Control Systems
PublicationThe wastewater treatment landscape in Central Europe, particularly in Poland, has undergone a profound transformation due to European Union (EU) integration. Fueled by EU funding and rapid technological advancements, wastewater treatment plants (WWTPs) have adopted cutting-edge control methods to adhere to EU Water Framework Directive mandates. WWTPs contend with complexities such as variable flow rates, temperature fluctuations,...
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NUMERICAL SIMULATIONS OF HONING PROCESS OF THIN WALL CYLINDER LINERS, WITH CONSTANT AND WITH VARIABLE THICKNESS OF WALL OF HONED PARTS
PublicationNumerical simulations of honing process of thin-wall cylinder liners, with constant and with variable thickness of the wall of honed workpieces can improve and can help to conduct the experimental research of honing process and can improve the honing process. A very valuable research assumption, before performing the numerical analysis of computer simulation of honing process, is the measurement of the real geometry of the honing...
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Machine Learning Algorithm-Based Tool and Digital Framework for Substituting Daylight Simulations In Early- Stage Architectural Design Evaluation
PublicationThe aim of this paper is to examine the new method of obtaining the simulation-based results using backpropagation of errors artificial neural networks. The primary motivation to conduct the research was to determine an alternative, more efficient and less timeconsuming method which would serve to achieve the results of daylight simulations. Three daylight metrics: Daylight Factor, Daylight Autonomy and Daylight Glare Probability have...
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Application of the discrete Green's function-based antenna simulations for excitation of the total-field/scattered-field interface in the FDTD method
PublicationIn this article, the discrete Green's function formulation of the finite-difference time-domain (DGF-FDTD) method is proposed for simulation of wire antennas irradiating inhomogeneous dielectric scatterers. Surface equivalence theorem in the discrete domain is used to separate the problem into an inhomogeneous domain and a wire antenna that are simulated with the use of FDTD and DGF-FDTD, respectively. Then, the excitation of the...
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Knowledge-Based Expedited Parameter Tuning of Microwave Passives by Means of Design Requirement Management and Variable-Resolution EM Simulations
PublicationThe importance of numerical optimization techniques has been continually growing in the design of microwave components over the recent years. Although reasonable initial designs can be obtained using circuit theory tools, precise parameter tuning is still necessary to account for effects such as electromagnetic (EM) cross coupling or radiation losses. EM-driven design closure is most often realized using gradient-based procedures,...
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Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublicationThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
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Accelerated Gradient-Based Optimization of Antenna Structures Using Multi-Fidelity Simulations and Convergence-Based Model Management Scheme
PublicationThe importance of numerical optimization has been steadily growing in the design of contemporary antenna structures. The primary reason is the increasing complexity of antenna topologies, [ a typically large number of adjustable parameters that have to be simultaneously tuned. Design closure is no longer possible using traditional methods, including theoretical models or supervised parameter sweeping. To ensure reliability, optimization...
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
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<title>Cavity control system advanced modeling and simulations for TESLA linear accelerator and free electron laser</title>
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Molecular Simulations Using Boltzmann’s Thermally Activated Diffusion - Implementation on ARUZ – Massively-parallel FPGA-based Machine
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Quantitative assessment of the influence of tensile softening of concrete in beams under bending by numerical simulations with XFEM and cohesive cracks
PublicationResults of the numerical simulations of the size effect phenomenon for concrete in comparison with experimental data are presented. In-plane geometrically similar notched and unnotched beams under three-point bending are analyzed. EXtended Finite Element Method (XFEM) with a cohesive softening law is used. Comprehensive parametric study with the respect to the tensile strength and the initial fracture energy is performed. Sensitivity...
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Expedited Globalized Antenna Optimization by Principal Components and Variable-Fidelity EM Simulations: Application to Microstrip Antenna Design
PublicationParameter optimization, also referred to as design closure, is imperative in the development of modern antennas. Theoretical considerations along with rough dimension adjustment through supervised parameter sweeping can only yield initial designs that need to be further tuned to boost the antenna performance. The major challenges include handling of multi-dimensional parameter spaces while accounting for several objectives and...
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A Subspace-Splitting Moment-Matching Model-Order Reduction Technique for Fast Wideband FEM Simulations of Microwave Structures
PublicationThis article describes a novel model-order reduction (MOR) approach for efficient wide frequency band finite-element method (FEM) simulations of microwave components. It relies on the splitting of the system transfer function into two components: a singular one that accounts for the in-band system poles and a regular part that has no in-band poles. In order to perform this splitting during the reduction process, the projection...
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An MOR Algorithm Based on the Immittance Zero and Pole Eigenvectors for Fast FEM Simulations of Two-Port Microwave Structures
PublicationThe aim of this article is to present a novel model-order reduction (MOR) algorithm for fast finite-element frequency-domain simulations of microwave two-port structures. The projection basis used to construct the reduced-order model (ROM) comprises two sets: singular vectors and regular vectors. The first set is composed of the eigenvectors associated with the poles of the finite-element method (FEM) state-space system, while...
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Light‐Driven Multi‐Charge Separation in a Push‐Pull Ruthenium‐Based Photosensitizer – Assessed by RASSCF and TDDFT Simulations
PublicationThe performance of photosensitizers in the field of, for example, solar energy conversion, relies on their light-harvesting efficiency in the visible region, population of long-lived charge separated intermediates, as well as their charge-accumulation capacity amongst other properties. In this computational study, we investigate the photophysical properties of a bis(bipyridyl)ruthenium(II)-based black dye (Ru) incorporating a chromophoric...
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Multi-fidelity EM simulations and constrained surrogate modelling for low-cost multi-objective design optimisation of antennas
PublicationIn this study, a technique for low-cost multi-objective design optimisation of antenna structures has been proposed. The proposed approach is an enhancement of a recently reported surrogate-assisted technique exploiting variable-fidelity electromagnetic (EM) simulations and auxiliary kriging interpolation surrogate, the latter utilised to produce the initial approximation of the Pareto set. A bottleneck of the procedure for higher-dimensional...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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The Role of Molecular Structure in Monte Carlo Simulations of the Secondary Electron Yield and Backscattering Coefficient from Methacrylic Acid
PublicationIn this paper, we show the influence of the chemical structure of four different conformers on the secondary electron emission and backscattering of an electron beam from a gel of methacrylic acid. The conformers have different permanent dipole moments, which determines the cross sections for elastic collisions with electrons. The cross sections are used in Monte Carlo simulations of an electron beam, which enters the gel of methacrylic...
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Discrete element method simulations of fracture in concrete under uniaxial compression based on its real internal structure
PublicationThe paper describes experimental and numerical results of concrete fracture under quasi-static uniaxial compression. Experimental uniaxial compression tests were performed on concrete cubic specimens. Fracture in concrete was detected at the aggregate level by means of three non-destructive methods: three-dimensional X-ray microcomputed tomography, two-dimensional scanning electron microscope and manual two-dimensional digital...
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Two-dimensional simulations of concrete fracture at aggregate level with cohesive elements based on X-ray lCT images
PublicationThe paper presents results of two-dimensional meso-scale simulations of fracture in notched concrete beams subjected to three-point bending test. Concrete was assumed as a 4-phase material composed of aggregate grains placed in the cement matrix, interfacial transitional zones (ITZs) and macro-voids. The particle distribution was taken from real concrete beams on the basis of X-ray lCT images. Comprehensive numerical analyses were carried...
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Comparative 3D DEM simulations of sand–structure interfaces with similarly shaped clumps versus spheres with contact moments.
PublicationThree-dimensional simulations of a monotonic quasi-static interface behaviour between initially dense cohesionless sand and a rigid wall of different roughness during tests in a parallelly guided direct shear test under constant normal stress are presented. Numerical modelling was carried out by the discrete element method (DEM) using clumps in the form of convex non-symmetric irregularly shaped grains. The clumps had an aspect...
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Examples of numerical simulations of two-dimensional unsaturated flow with VS2DI code using different interblock conductivity averaging schemes
PublicationFlow in unsaturated porous media is commonly described by the Richards equation. This equation is strongly nonlinear due to interrelationships between water pressure head (negative in unsaturated conditions), water content and hydraulic conductivity. The accuracy of numerical solution of the Richards equation often depends on the method used to estimate average hydraulic conductivity between neighboring nodes or cells of the numerical...
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Mitigation effect of face shield to reduce SARS-CoV-2 airborne transmission risk: Preliminary simulations based on computed tomography
PublicationWe aimed to develop a model to quantitatively assess the potential effectiveness of face shield (visor) in reducing airborne transmission risk of the novel coronavirus SARS-CoV-2 during the current COVID-19 pandemic using the computational fluid dynamics (CFD) method. The studies with and without face shield in both an infected and healthy person have been considered in indoor environment simulation. In addition to the influence...
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Mitigation effect of face shield to reduce SARS-CoV-2 airborne transmission risk: Preliminary simulations based on computed tomography
PublicationWe aimed to develop a model to quantitatively assess the potential effectiveness of face shield (visor) in reducing airborne transmission risk of the novel coronavirus SARS-CoV-2 during the current COVID-19 pandemic using the computational fluid dynamics (CFD) method. The studies with and without face shield in both an infected and healthy person have been considered in indoor environment simulation. In addition to the influence...
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Selection of material for X-ray tomography analysis and DEM simulations: comparison between granular materials of biological and non-biological origins
PublicationPhysical properties and X-ray tomography images of five different granular materials: glass bead, glass grit, short grain white rice, sorghum and clay granules (Seramis) are investigated to select the most promising materials for numerical simulations and time-lapse X-ray tomography imaging. The examined materials represent granular materials of non-biological origin (glass bead, glass grit and Seramis) and granular plant materials...
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Simulations of spacing of localized zones in reinforced concrete beams using elasto-plasticity and damage mechanics with non-local softening
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Computational simulations of concrete behaviour under dynamic conditions using elasto-visco-plastic model with non-local softening
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Large eddy simulations of wall-bounded flows using a simplified immersed boundary method and high-order compact schemes
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New model simulations of the global atmospheric electric circuit driven by thunderstorms and electrified shower clouds: The roles of lightning and sprites
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Cost‐efficient performance‐driven modelling of multi‐band antennas by variable‐fidelity electromagnetic simulations and customized space mapping
PublicationElectromagnetic (EM) simulations have become an indispensable tool in the design of contemporary antennas. EM‐driven tasks, for example, parametric optimization, entail considerable computational efforts, which may be reduced by employing surrogate models. Yet, data‐driven modelling of antenna characteristics is largely hindered by the curse of dimensionality. This may be addressed using the recently reported domain‐confinement...
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Simulations of spacing of localized zones in reinforced concrete beams using elastic-plasticity and damage mechanics with non-local softening
PublicationArtykuł omawia obliczanie belek żelbetowych z uwzględnieniem lokalizacji odkształceń. Obliczenia wykonano przy zastosowaniu MES na bazie sprężysto-plastycznego prawa konstytutywnego i modelu zniszczeniowego uwzględniającego degradację sztywności rozszerzonego o długość charakterystyczną mikrostruktury za pomocą teorii nielokalnej.
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Computational simulations of concrete behaviour under dynamic conditions using elasto-visco-plastic model with non-local softening.
PublicationW artykule przedstawiono wyniki obliczeniowych symulacji zachowania betonu w warunkach dynamicznych stosując sprężysto-lepko-plastyczny model z nielokalnym osłabieniem. Wykonano obliczenia dla ściskania jednoosiowego, rozciągania jednoosiowego i zginania. Dla dużych prędkości obciążenia uwzględniono fragmentację materiału. Wyniki porównano z doswiadczeniami.
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Mesoscopic simulations of a fracture process in reinforced concrete beam in bending using a 2D coupled DEM/micro-CT approach
PublicationW tej pracy zbadano numerycznie w warunkach 2D złożony proces pękania w krótkiej prostokątnej belce betonowej wzmocnionej jednym prętem podłużnym (bez zbrojenia pionowego) i poddanej quasi-statycznemu zginaniu w trzech punktach. Krytyczne pęknięcie poprzeczne w belce spowodowało jej uszkodzenie podczas doświadczenia. Symulacje numeryczne przeprowadzono klasyczną metodą elementów dyskretnych (DEM). Przyjęto trójfazowy opis betonu:...
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Fast tolerance-aware design optimization of miniaturized microstrip couplers using variable-fidelity EM simulations and re-sponse features
PublicationManufacturing tolerances and other types of uncertainties may considerably affect operation and performance of microwave components and systems. Quantification of these effects is therefore an important part of the design process. It is even more important to obtain designs whose sensitivity to parameter deviations is reduced as much as possible. All of these require statistical analysis carried out at the level of electromagnetic...
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Trees as a Shading System for Streets on the East–West Axis: Computer Simulations for the Selected Geometrical Proportions of Building Developments in Humid Continental Climate
PublicationThe study is aimed at investigating the possibilities for solar protection provided to the street canyon located on the E–W axis and with the following profiles: shallow (height/width (H/W) = 0.2, 0.6, and 1) and deep (H/W = 2) by two rows of trees located at a distance of 3 m away from southern and northern façades. The research was based on numerical simulation analyses conducted in the Rhinoceros® program, with the application...
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Toward mechanosynthesis of diamondoid sructures: viii. quantum-chemical molecular dynamics simulations of hexagonal silicon-iv structure synthesis with stm
Publicationw tej publikacji badano metodami kwantowo-chemicznymi różne strategie mechanosyntezy heksagonalnego krzemu iv. określono przybliżone warunki mechanosyntezy krzemu w formie lonsdaleitu za pomocą uhv-spm.
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Hybrid Monte-Carlo simulations of fluorescence anisotropy decay in disordered two-component systems in the presence of forward and back energy transfer
PublicationW pracy przedstawiono hybrydowy algorytm symulacji Monte Carlo zaniku anizotropii emisji fluorescencji w układach dwuskładnikowych z uwzględnieniem prostego i powrotnego transferu energii. Poprawność nowego algorytmu symulacji Monte Carlo zweryfikowano poprzez porównanie z wynikami obliczeń teoretycznych otrzymanymi w ramach modelu SCDM i z wynikami standardowej symulacji Monte Carlo (algorytm 'step by step').
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Hybrid Monte-Carlo simulations of fluorescence anisotropy decayin three-component donor-mediator-acceptor systems in the presenceof energy transfer
PublicationW pracy przedstawiono nowy hybrydowy algorytm symulacji Monte-Carlo układu trójskładnikowego donor-mediator-akceptor. Działanie algorytmu zilustrowano na przykładzie zaników anizotropii emisji fluorescencji powyższego układu. Porównano wyniki hybrydowej symulacji Monte-Carlo z wynikami klasycznej metody ''step by step''. Stwierdzono bardzo dobrą zgodność wyników obu symulacji, przy czym algorytm hybrydowy wymaga znacznie krótszego...
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Reduced-cost optimization-based miniaturization of microwave passives by multi-resolution EM simulations for internet of things and space-limited applications
PublicationStringent performance specifications along with constraints imposed on physical dimensions, make the design of contemporary microwave components a truly onerous task. In recent years, the latter demand has been growing in importance, with the innovative application areas such as Internet of Things coming into play. The need to employ full-wave electromagnetic (EM) simu-lations for response evaluation, reliable yet CPU heavy, only...
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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...