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Search results for: DAMPING, DYNAMICS, DIFFERENTIAL EQUATIONS, LOWERING A LIFEBOAT, NUMERICAL SIMULATIONS
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Self-Organization in Multi-Agent Systems Based on Examples of Modeling Economic Relationships between Agents
PublicationThe goal of the research was to observe and analyze self-organization patterns in Multi-Agent Systems (MAS) by modeling basic economic relationships between agents forming a closed loop of relations necessary for their survival. The paper describes a worked-out MAS including an example of a production cycle and used economic rules. A special focus is put on behavior rules and decision systems of an individual agent such as: product...
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Study on the Influence of an Axial Distance Between Rotors on a Performance of a Small Counter-Rotating Wind Turbine
PublicationIn this paper, results of the investigation on the performance of a small counter-rotating wind turbinehas been presented. Computational Fluid Dynamics methodshave been used forwind turbine simulations. Rotors representation were introduced into computational domain by means of Actuator Line Model. Influence of an axial distance of CRWTrotorshas been investigated. In all studied configurations rotors were counter-rotating...
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Weakly Hydrated Solute of Mixed Hydrophobic–Hydrophilic Nature
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane...
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Cable-stayed cantilever structures as an expat of unique application in the construction of a building located in seismic area – an author’s project of multifunctional building in Lisbon, Portugal
PublicationThe article presents numerical simulations for the modelling of seismic impact on the structure of unique cantilever cablestayed structure with application of two methods. The Response Spectrum method, in which a spectrum of the structure's responses to an earthquake's impact is generated and the Accelerogram method, in which we generate dynamic load in the form of a diagram of the connection between acceleration and time for...
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3-D finite-difference time-domain modelling of ground penetrating radar for identification of rebars in complex reinforced concrete structures
PublicationThis paper presents numerical and experimental investigations to identify reinforcing bars using the ground penetrating radar (GPR) method. A novel element of the paper is the inspection of different arrangements of reinforcement bars. Two particular problems, i.e. detection of few adjacent transverse bars and detection of a longitudinal bar located over or under transverse reinforcement, have been raised. An attention was also...
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FEM and experimental investigations of concrete temperature field in the massive stemwall of the bridge abutment
PublicationThe paper deals with the prediction of early-age concrete temperature of cast-in-place stemwall of the bridge abutment. The considered object is an arch bridge located in Gda´nsk. In the case of massive structures, it is particularly important to not exceed the temperature difference between the core and the concrete surface. Too high temperature gradient generates an increase in thermal stresses, what could be the reason of exceeding...
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Modelling of shear zones during quasi-static granular silo flow using material point method (MPM)
PublicationThe paper focuses on confined silo flow of cohesionless sand. The problem considered is a quasi-static flow in a plane strain model silo with parallel walls simulated with the material point method (MPM). The simulation used a non-local hypoplastic constitutive model. Initially, the paper validated the implemented numerical approach with basic element tests and a plane strain compression test. The subsequent MPM calculations for...
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Mathemathical model of radial passive magnetic bearing
PublicationIn the article mathematical radial model of passive magnetic bearings to ocean engineering units has been presented. The units application in underwater thrusters should increase propulsion systems durability and gives lower maintenance costs. The rotor of electric motor is hanging in magnetic field taken from radial passive magnetic bearings. However axial direction maintenance must be controlled with electromagnets and their...
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Analysis of Floodplain Inundation Using 2D Nonlinear Diffusive Wave Equation Solved with Splitting Technique
PublicationIn the paper a solution of two-dimensional (2D) nonlinear diffusive wave equation in a partially dry and wet domain is considered. The splitting technique which allows to reduce 2D problem into the sequence of one-dimensional (1D) problems is applied. The obtained 1D equations with regard to x and y are spatially discretized using the modified finite element method with the linear shape functions. The applied modification referring...
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On the non-linear dynamics of torus-shaped and cylindrical shell structures
PublicationIn this study, the non-linear dynamic analysis of torus-shaped and cylindrical shell-like structures has been studied. The applied material is assumed as the functionally graded material (FGM). The structures are considered to be used for important machines such as wind turbines. The effects of some environmental factors on the analysis like temperature and humidity have been considered. The strain field has been calculated in...
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Impact of thermal backfill parameters on current-carrying capacity of power cables installed in the ground
PublicationProper design of power installations with the participation of power cables buried in homogeneous and thermally well-conductive ground does not constitute a major problem. The situation changes when the ground is non-homogeneous and thermally low-conductive. In such a situation, a thermal backfill near the cables is commonly used. The optimization of thermal backfill parameters to achieve the highest possible current-carrying capacity...
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CFD analysis of fluid flow through the labyrinth seal
PublicationSteam and gas turbines are some of the fundamental means of power generation. The energy efficiency of the turbines, however, is not satisfactory. Ever since the start-up of the first turbine in the world, engineers have been striving for their increased efficiency. Multiple solutions to the problem of steam loss in an operating turbine are available. The use of seals is one of them. Empirical methods or numerical calculations...
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GPR simulations for diagnostics of a reinforced concrete beam
PublicationThe most popular technique for modelling of an electromagnetic field, the finite difference time domain (FDTD) method, has recently become a popular technique as an interpretation tool for ground penetrating radar (GPR) measurements. The aim of this study is to detect the size and the position of damage in a reinforced concrete beam using GPR maps. Numerical simulations were carried out using the finite differ-ence time domain...
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Antenna Modeling Using Variable-Fidelity EM Simulations and Constrained Co-Kriging
PublicationUtilization of fast surrogate models has become a viable alternative to direct handling of fullwave electromagnetic (EM) simulations in EM-driven design. Their purpose is to alleviate the difficulties related to high computational cost of multiple simulations required by the common numerical procedures such as parametric optimization or uncertainty quantification. Yet, conventional data-driven (or approximation) modeling techniques...
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Design and computational fluid dynamics analysis of the last stage of innovative gas-steam turbine
PublicationResearch regarding blade design and analysis of flow has been attracting interest for over a century. Meanwhile new concepts and design approaches were created and improved. Advancements in information technologies allowed to introduce computational fluid dynamics and computational flow mechanics. Currently a combination of mentioned methods is used for the design of turbine blades. These methods enabled us to improve flow efficiency...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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A Comparison of Simplified Two-dimensional Flow Models Exemplified by Water Flow in a Cavern
PublicationThe paper shows the results of a comparison of simplified models describing a two-dimensional water flow in the example of a water flow through a straight channel sector with a cavern. The following models were tested: the two-dimensional potential flow model, the Stokes model and the Navier-Stokes model. In order to solve the first two, the boundary element method was employed, whereas to solve the Navier-Stokes equations, the...
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AN OVERVIEW OF HEAT TRANSFER ENHANCEMENT BASED UPON NANOPARTICLES INFLUENCED BY INDUCED MAGNETIC FIELD WITH SLIP CONDITION VIA FINITE ELEMENT STRATEGY
PublicationThe mathematical model of heat generation and dissipation during thermal energy transmission employing nanoparticles in a Newtonian medium is investigated. Dimensionless boundary layer equations with correlations for titanium dioxide, copper oxide, and aluminium oxide are solved by the finite element method. Parameters are varied to analyze their impact on the flow fields. Various numerical experiments are performed consecutively...
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On Wrinkling in Sandwich Panels with an Orthotropic Core
PublicationThis paper deals with the local loss of stability (wrinkling) problem of a thin facing of a sandwich panel. Classical solutions to the problem of facing instability resting on a homogeneous and isotropic substructure (a core) are compared. The relations between strain energy components associated with different forms of core deformations are discussed. Next, a new solution for the orthotropic core is presented in detail, which...
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Three dimensional simulations of FRC beams and panels with explicit definition of fibres-concrete interaction
PublicationHigh performance concrete (HPC) is a quite novel material which has been rapidly developed in the last few decades. It exhibits superior mechanical properties and durability comparing to normal concrete. HPC can achieve also superior tensile performance if strong fibres (steel or carbon) are implemented in the matrix. Thus, there exist the unabated interest in studying how the addition of different types of fibres modifies the...
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At the Limits of Criticality-Based Quantum Metrology: Apparent Super-Heisenberg Scaling Revisited
PublicationWe address the question of whether the super-Heisenberg scaling for quantum estimation is indeed realizable. We unify the results of two approaches. In the first one, the original system is compared with its copy rotated by the parameter-dependent dynamics. If the parameter is coupled to the one-body part of the Hamiltonian, the precision of its estimation is known to scale at most as N−1 (Heisenberg scaling) in terms of the number...
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An algorithm to generate high dense packing of particles with various shapes
PublicationDiscrete Element Method (DEM) is one of available numerical methods to compute movement of particles in large scale simulations. The method has been frequently applied to simulate the cases of grain or bulk material as the major research issue. The paper describes a new method of generating high dense packing with mixed material of two different shape used in DEM simulation. The initial packing is an important parameter to control,...
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Simulations of air and water flow in a model dike during overflow experiments
PublicationFlow in flood dikes, earth dams, and embankments occurs in variably saturated conditions, with pores of the earth material filled partly with water and partly with air. In routine engineering analysis, the influence of pore air is neglected and the air pressure is assumed equal to atmospheric. In some circumstances, for example, during overtopping of the dike by water, the effect of pore air on water flow and stability of the structure...
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Turning maneuver as a potential cause of the next stability failure mode for a ship in operation
PublicationThe only formal stability-related requirement referring to a turning maneuver of a ship results from the IS Codeand its application is limited to passenger ships only. The goal of the adopted criterion is to prevent an excessiveangle of heel in turn. Likewise, the remaining prescriptive criteria, this one is simply based on the concept ofa threshold that must not be exceeded. In this case, the angle of heel...
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Experimental and computational study on mechanical behaviour of carpentry corner log joints
PublicationThis work concerns experimental and numerical research on carpentry joints used in historic wooden buildings in southeastern Poland and western Ukraine. These structures are mainly sacred buildings, and the types of corner log joints characteristic of this region are primarily saddle-notch and dovetail joints; thus, these two types of joints were analysed in this study. The modelling of historic timber structures is a complex...
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About Unusual Diffraction and Thermal Self-Action of Magnetosonic Beam
PublicationThe dynamics of slightly diverging two-dimensional beams whose direction forms a constant angle θ with the equilibrium straight magnetic strength is considered. The approximate dispersion relations and corresponding links which specify hydrodynamic perturbations in confined beams are derived. The study is dedicated to the diffraction of a magnetosonic beam and nonlinear thermal self-action of a beam in a thermoconducting gaseous plasma....
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A Compact Basis for Reliable Fast Frequency Sweep via the Reduced-Basis Method
PublicationA reliable reduced-order model (ROM) for fast frequency sweep in time-harmonic Maxwell’s equations by means of the reduced-basis method is detailed. Taking frequency as a parameter, the electromagnetic field in microwave circuits does not arbitrarily vary as frequency changes, but evolves on a very low-dimensional manifold. Approximating this low-dimensional manifold by a low dimension subspace, namely, reduced-basis space, gives...
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Finite-element analysis of a base-isolated multi-storey steel building under seismic motions
PublicationNumerical simulation of the seismic behaviour of a multi-storey steel building, both fixed-base and base-isolated, under the 1940 El Centro earthquake was performed in this paper. The analyzed 4-storey building was decoupled from the shaking ground with the Polymeric Bearings, which can be considered a proposal of a new seismic isolation system. It consists of rectangular-shaped blocks made of a specially prepared flexible polymeric...
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Simulations of wave propagation and attenuation in fields of colliding ice floes
Open Research DataThis dataset contains results of numerical smulations of sea ice-wave interactions, corresponding to laboratory experiments conducted at the Large Ice Model Basin (LIMB) at the Hamburg Ship Model Basin (HSVA) as part of the LS-WICE ("Loads on Structure and Waves in Ice"; https://zenodo.org/record/1067170#.XrLt_dhpxhE) project. THe simulations were conducted...
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A two dimensional approach for modelling of pennate muscle behaviour
PublicationThe purpose of this study was to elaborate a two-dimensional approach for unipennate and bipennate striated skeletal muscle modelling. Behavior of chosen flat pennate muscle is modelled as a rheological system composed of serially linked passive and active fragments having different mechanical properties. Each fragment is composed of three elements: mass element, elastic element and viscous element. Each active fragment furthermore...
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DETECTION OF DEBONDING IN STEEL BARS EMBEDDED IN CONCRETE USING GUIDED WAVE PROPAGATION
PublicationThe paper presents a non-destructive diagnostic technique based on guided wave propagation phenomenon used to assess the adhesive bonding between a steel bar and a concrete cover. Double-layered cylindrical specimens with different levels of debonding and its location were investigated. The influence of bonding length on the excitation of multiple modes of longitudinal guided waves was analysed. Numerical simulations of guided...
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Damaged plasticity model - seismic analysis of structure of the Petronas Twin Towers (Kuala Lumpur) in Malaysia
PublicationThe article presents numerical simulations for the modelling of seismic impact on the structure of Petronas Twin Towers (Kuala Lumpur) in Malaysia with application of two methods. The Response Spectrum method, in which a spectrum of the structure's responses to an earthquake's impact is generated and the Acceletogram (BETA) method, in which we generate dynamic load in the form of a diagram of the connection between acceleration...
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Towards Understanding of Mechanics of Hernia Managed by Synthetic Mesh in Laparoscopic Operation: A Single Case Study
PublicationIn this paper a research towards understanding of mechanics of ventral hernia operated with the use of Physiomesh Open image in new window implant and SecureStrap Open image in new window staples is described. Experimental and numerical studies are conducted for that purpose. Experimental works cover uni-axial tension tests of the implant samples and of the implant-staples-tissue system. Also experiments on implant-staples-tissue...
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Studying road restraint systems to develop new guidelines
PublicationThe paper will present a proposed approach to such work along with preliminary results of numerical studies for selected problems using road safety devices such as safety barriers on horizontal curves, the effect of kerbs on bridges or the location of obstacles within the barrier’s working width. The paper will discuss assumptions to a methodology of numerical models, calculations and automated processing of data to help with assessing...
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Experimental and theoretical study on high-temperature creep of VT6 titanium alloy under multi-axial loading conditions
PublicationIn the framework of damage mechanics, we discuss a new mathematical model that describes the kinetics of the stress–strain state and damage accumulation during material degradation by the mechanism of long-term strength under complex multiaxial stress state. An experimental and theoretical technique is proposed for determination of material parameters and scalar constitutive functions for damaged media based on specially set experiments...
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Assessment of the impact of jet impingement technique on the energy efficiency of air-cooled BIPV/T roof tile
PublicationThe paper concerns a numerical analysis of cooling of the hybrid photovoltaic (PV) modules dedicated to Building-Integrated Photovoltaic/Thermal (BIPV/T) systems. Attention was focused on the photovoltaic roof tiles, using a jet impingement technique, in which the intensification of heat transfer is ensured by streams of air hitting the heat exchange partition. A series of numerical simulations were carried out to assess an influence...
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Modelling reinforced concrete beams under mixed shear-tension failure with different continuous FE approaches
PublicationThe paper presents quasi-static numerical simulations of the behaviour of short reinforced concrete beams without shear reinforcement under mixed shear-tension failure using the FEM and four various constitutive continuum models for concrete. First, an isotropic elasto-plastic model with a Drucker-Prager criterion defined in compression and with a Rankine criterion defined in tension was used. Next, an anisotropic smeared crack...
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Laplace domain BEM for anisotropic transient elastodynamics
PublicationIn this paper, we describe Laplace domain boundary element method (BEM) for transient dynamic problems of three-dimensional finite homogeneous anisotropic linearly elastic solids. The employed boundary integral equations for displacements are regularized using the static traction fundamental solution. Modified integral expressions for the dynamic parts of anisotropic fundamental solutions and their first derivatives are obtained....
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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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...
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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,...
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Combined numerical and experimental approach to determine numerical model of abdominal scaffold
PublicationA proper junction of the prosthesis and the abdominal wall is important in successful hernia repair. The number of tacks should be balanced to assure appropriate mesh fixation and not to induce post-operative pain. Numerical simulations help to find this balance. The study is aimed at creating a proper numerical model of a knitted surgical mesh subjected to boundary conditions and load occurring in the abdominal cavity. Continuous,...
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Surface diffusion and cluster formation of gold on the silicon (111)
PublicationPurpose: Investigation of the gold atoms behaviour on the surface of silicon by molecular dynamics simulation method. The studies were performed for the case of one, two and four atoms, as well as incomplete and complete filling of gold atoms on the silicon surface. Design/methodology/approach: Investigations were performed by the method of molecular dynamics simulation using the Large-scale Atomic/Molecular Massively Parallel...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Expedited Acquisition of Database Designs for Reduced-Cost Performance-Driven Modeling and Rapid Dimension Scaling of Antenna Structures
PublicationFast replacement models have been playing an increasing role in high-frequency electronics, including the design of antenna structures. Their role is to improve computational efficiency of the procedures that normally entail large numbers of expensive full-wave electromagnetic (EM) simulations, e.g., parametric optimization or uncertainty quantification. Recently introduced performance-driven modeling methods, such as the nested...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Folding‐upon‐repair DNA nanoswitches for monitoring DNA repair enzymes activity
PublicationWe demonstrate here a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containing O6‐methyl‐guanine (O6‐MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation...