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Search results for: molecular dynamic simulation
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Dynamic ranking of cloud providers
PublicationThe paper focuses on how to create an effective dynamic ranking service for IaaS,PaaS and SaaS cloud providers. It considers building of a quality model for thispurpose along with definition of quality measurement procedures. The paper discussesseveral techniques known from already existing price comparison engines that couldbe modified and adopted for comparison of cloud providers. Furthermore, a tech-nique for filtering measured...
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A Perspective on Fast-SPICE Simulation Technology
PublicationThis chapter presents an introduction to the area of accelerated transistor-level (‘fast-SPICE’) simulation for automated verification and characterization of integrated circuits (ICs) from technologist’s perspective. It starts with outlining goals, expectations and typical usage models for fast-SPICE simulators, stressing how they differ from regular SPICE tools. It continues with presenting and classifying core technologies typically...
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Degradation of a nano-cutting tool: an MD simulation
PublicationW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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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...
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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublicationInteraction between 2, 3, 5 and 7 atomic layers of gold and a (111) silicon surface was investigated with the molecular dynamics simulation method. The simulation of the diffusion interaction between gold and silicon in the temperature range 425-925 K has been carried out. The peculiarities of the concentration changes of the interacting components and the atomic density at the boundary...
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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...
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Grand Challenges on the Theory of Modeling and Simulation
PublicationModeling & Simulation (M&S) is used in many different fields and has made many significant contributions. As a field in its own right, there have been many advances in methodologies and technologies. In 2002 a workshop was held in Dagstuhl, Germany, to reflect on the grand challenges facing M&S. Ten years on, a series of M& S Grand Challenge activities are marking a decade of progress and are providing an opportunity to reflect...
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Real-time simulation in non real-time environment
PublicationSimulation in real-time is a very useful tool because of didactical and practical benefits. Very important benefit of real-time simulation is a fact that operator’s decision can be taken into account in the same time scale as the real system would work. This enables construction of simulators, and opportunity to test control algorithms in Hardware in The Loop scheme using target industrial equipment. Professional real-time environments...
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Boundary value problems for dynamic equations with advanced arguments on time scales
PublicationPraca dotyczy równań i nierówności dynamicznych z wyprzedzonym argumentami. Przedmiotem badań były problemy istnienia rozwiązań równań dynamicznych. Sformułowano warunki dostatczne na istnienie jedynego rozwiązania w odpowiednim obszarze ograniczonym przez górne i dolne rozwiązanie.
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Dynamic Semantic Visual Information Management
PublicationDominant Internet search engines use keywords and therefore are not suited for exploration of new domains of knowledge, when the user does not know specific vocabulary. Browsing through articles in a large encyclopedia, each presenting a small fragment of knowledge, it is hard to map the whole domain, see relevant concepts and their relations. In Wikipedia for example some highly relevant articles are not linked with each other....
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Selected Features of Dynamic Voting
PublicationIn multi-agent systems composed of autonomous agents with local knowledge, it is often desirable to aggregate their knowledge in order to make an educated decision. One of the methods of agreeing to a common decision is voting. A new history-based dynamic weight protocol allows for identification of the agents which contribute to the correct system decision. The main advantage of this approach, compared to static weighted system...
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublicationPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
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The consideration to the dynamic systems parameter identification
PublicationIn this paper, a concept for continuous-time dynamic systems parameter identification using modulating function approach is presented. It refers to linear as well as selected non-linear systems. It shows the possibility of direct application without converting differential equation. In particular cases direct application can decrease the amount of computation in non-linear system identification, which generally requires Fourier...
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Dynamic mechanical properties and flexing fatigue resistance of tire sidewall rubber as function of waste tire rubber reclaiming degree
PublicationA stepwise downsizing method of gel particles in reclaimed rubber to a micro-nano scale and its excellent dynamic performance in tire sidewall were introduced by this work. The results showed that the size of gel particles decreased from several micrometers to micro-nanometers with the increase of reclaiming degree, accompanied by reduced molecular weight and widened molecular weight distribution of sol fraction. The addition of...
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Optimization of Hydrogen - Evolving Photochemical Molecular Devices
PublicationA molecular photocatalyst consisting of a RuII photocenter, a tetrapyridophenazine bridging ligand, and a PtX2 (X=Cl or I) moiety as the catalytic center functions as a stable system for light-driven hydrogen production. The catalytic activity of this photochemical molecular device (PMD) is significantly enhanced by exchanging the terminal chlorides at the Pt center for iodide ligands. Ultrafast transient absorption spectroscopy...
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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...
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Analysis of data fusion algorithms for the vessel with the dynamic positioning system
PublicationThe dynamic positioning (DP) system on the vessel is operated to control the position and heading of the vessel with the use of propellers and thrusters installed on the board. On DP vessels redundant measurement systems of position, heading and the magnitude and direction of environmental forces are required for safety at sea. In this case, a fusion of data is needed from individual measurement devices. The article proposes a...
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Influence of addition of carbon nanotubes on rheological properties of selected liquid lubricants - a computer simulation study
PublicationThis work is motivated by the improvement of anti-friction properties of lubricants by addition of CNTs proved experimentally in literature. In particular, a methodology is developed to compute the shear viscosity of liquid lubricants (Propylene Glycol) based on Molecular Dynamics simulation. Non-Equilibrium molecular dynamics (NEMD) approach is used with a reactive force field ReaxFF implemented in LAMMPS. The simulations are...
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Simulation of the switched reluctance drive system
PublicationSwitched reluctance motors (SRM), unlike other types of motors, for their application require a control system and the supply from a power electronic converter. A method of modelling and mathematical model of an SRM in a switched reluctance drive (SRD) system is presented in the paper. Modelling is based on Lagrange's energy method. Coefficients of the Lagrange's equation have been calculated using the finite element method (FEM)....
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Molecular Targets for Anticandidal Chemotherapy
PublicationA relatively small number of anticandidal chemotherapeutics used in clinical practice is at least in part consequence of a limited number of their molecular targets: ergosterol in the membrane, lanosterol demethylase, b(1!3) glucan synthase, and DNA/RNA biosynthesis. Much more potential novel targets have been revealed by the comparative genomic studies identifying essential genes unique for Candida albicans or resulted from recognition...
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublicationThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublicationIn the paper we present a modern efficient parallel OpenMP+CUDA implementation of crowd simulation for hybrid CPU+GPU systems and demonstrate its higher performance over CPU-only and GPU-only implementations for several problem sizes including 10 000, 50 000, 100 000, 500 000 and 1 000 000 agents. We show how performance varies for various tile sizes and what CPU–GPU load balancing settings shall be preferred for various domain...
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The surface photoconductivity in molecular layers
PublicationW pracy przedstawiono rezultaty analizy fotoprądów powierzchniowych w cienkich warstwach tetracenu i pentacenu. W szczególności badano wpływ obecności defektów strukturalnych w warstwach na charakterystyki fotoprądów i transport nośników ładunku.
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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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GENERAL DYNAMIC PROJECTING OF MAXWELL EQUATIONS
PublicationA complete – system of Maxwell equations is splitting into independent subsystems by means of a special dynamic projecting technique. The technique relies upon a direct link between field components that determine correspondent subspaces. The explicit form of links and corresponding subspace evolution equations are obtained in conditions of certain symmetry, it is illustrated by examples of spherical and quasi-one-dimensional waves.
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Transmission protocol simulation framework for the resource-constrained sensor network
PublicationIn this paper the simulation framework for simulation of the sensor network protocol is presented. The framework enables the simultaneous development of the sensor network software and the protocol for the wireless data transmission. The advantage of using the framework is the convergence of the simulation with the real software, because the same software is used in real sensor network nodes and in the simulation framework. The...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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Neural modelling of dynamic systems with time delays based on an adjusted NEAT algorithm
PublicationA problem related to the development of an algorithm designed to find an architecture of artificial neural network used for black-box modelling of dynamic systems with time delays has been addressed in this paper. The proposed algorithm is based on a well-known NeuroEvolution of Augmenting Topologies (NEAT) algorithm. The NEAT algorithm has been adjusted by allowing additional connections within an artificial neural network and...
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Developing competences of IT project managers using simulation games
PublicationProject Management is a domain in which methodological approach is developing very rapidly. Project managers are required to present knowledge of the various methods of project management and apply them to the management of specific projects. It means that project managers must constantly develop their competence, mainly based on good practices from different formal methods of project management. The purpose of this article is...
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Molecular Design Using Selected Concentration Effects in Optically Activated Fluorescent Matrices
PublicationMolecular physics plays a pivotal role in various fields, including medicine, pharmaceuticals, and broader industrial applications. This study aims to enhance the methods for producing specific optically active materials with distinct spectroscopic properties at the molecular level, which are crucial for these sectors, while prioritizing human safety in both production and application. Forensic science, a significant socio-economic...
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Dynamic F-free Coloring of Graphs
PublicationA problem of graph F-free coloring consists in partitioning the vertex set of a graph such that none of the resulting sets induces a graph containing a fixed graph F as an induced subgraph. In this paper we consider dynamic F-free coloring in which, similarly as in online coloring, the graph to be colored is not known in advance; it is gradually revealed to the coloring algorithm that has to color each vertex upon request as well...
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Numerical simulation of laminate composite specimens failure
PublicationThis work presents some numerical results concerning simulation of failure of laminate composite specimens. In the article two tests to determine ultimate strength in an orthotropic layer, are considered: tension (TT1) and compression (TC1) test. The outcome is compared with experimental data provided by [9,10].
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Image simulation and annotation for color blinded
PublicationIn this paper methods for image simulation as seen by a color blinded and a method for constructing images of perceived color difference are presented. The work is also focused on the interactive color description of an image contents. As a result, the individuals having problems with color discrimination can identify colors in an image.W artykule prezentowane są metody symulacji kolorów w obrazach postrzeganych przez osoby ze...
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Towards Scalable Simulation of Federated Learning
PublicationFederated learning (FL) allows to train models on decentralized data while maintaining data privacy, which unlocks the availability of large and diverse datasets for many practical applications. The ongoing development of aggregation algorithms, distribution architectures and software implementations aims for enabling federated setups employing thousands of distributed devices, selected from millions. Since the availability of...
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Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublicationAmphotericin B (AmB) is a lifesaving antibiotic used to treat deep-seated mycotic infections. Both the pharmaceutical activity and highly toxic side effects of the drug rely on its interaction with biomembranes, which is governed by the molecular organization of AmB. In the present work we present detailed analysis of self-assembly of AmB molecules in different environments, interesting from the physiological standpoint, based...
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Simulation model of IPMSM drive with rotor position estimator
PublicationThe paper presents a simulation model of electric drive consisting of: IPMSM motor, inverter and digital controller. The model was designed in Mathlab/Simulink. By modelling of the controller its discrete operation was taken into account in order to simulate precisely a specific sensorless control algorithm. A method for estimation of angular rotor position was proposed. Its mathematical algorithm was explained and errors were...
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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....
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Visual perception of vowels from static and dynamic cues
PublicationThe purpose of the study was to analyse human identification of Polish vowels from static and dynamic durationally slowed visual cues. A total of 152 participants identified 6 Polish vowels produced by 4 speakers from static (still images) and dynamic (videos) cues. The results show that 59% of static vowels and 63% of dynamic vowels were successfully identified. There was a strong confusion between vowels within front, central,...
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublicationThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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Analysis of the dynamic influences on the Lowland Gate in Gdańsk
PublicationThe Lowland Gate has been built in 1626. It is one of the best-preserved historical buildings in Gdansk. The structure is still of the city's infrastructural importance as through it goes a road connecting two districts. The Gate is now so neglected that it is hard to appreciate its value. The main purpose of the investigation carried out was to determine the harmfulness of the traffic on the structure as well as the reasons of...
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Differential analysis of dynamic immittance spectra
PublicationThis work presents a new approach to the analysis of immittance spectrograms of systems characterised by non-stationarity. The possibility of linking the evolution of the immittance response with changes in the parameters describing the system is achieved by introducing a spectrum in differential form. By using the above procedure, it becomes possible to separate elements with a dependence (or lack thereof) from an independent...
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Simulation investigation of perovskite-based solar cells
PublicationThree models of thin-layer lead-halide perovskite solar cells with different electron-transport layers (TiO2,SnO2,ZnO) were investigatedby the simulation method. The perovskite layer thickness was optimized for all the systems. The analysis of the standard photovoltaic cell performanceparameters at various operating temperatures was performed. The best performance was achieved for the system with theSnO2conductive layer.
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Agent-based social network as a simulation of a market behaviour
PublicationRecent years and the outbreak of world's economic crisis in 2008 proved the crucial importance of reliable analysis of market dynamics. However, werarely apply models of proper detail level (the global prosperity forecast of 2007 can be seen as a grim proof). The behaviour of individuals and companies is far from being ideal and rational. Many claims that the economic paradigm of rational expectations (coming from J. Muth and R....
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Optimal Rotating Receiver Angles Estimation for Multicoil Dynamic Wireless Power Transfer
PublicationThis study proposed an approach to dynamic wireless charging that uses a rotating receiver coil. Our simulation study focused on the verification of a novel way of increasing the coupling coefficient and power transfer stability by following the flux of the transmitting coils. To obtain the highest possible coupling by means of the FEM analysis, we studied the optimization of the trajectory of the angular velocity of the rotating...
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Simulation of Parallel Applications on Large-scale Distributed Systems
PublicationThis chapter has a form of a review article in the field of simulating High-Performance Computing systems. We justify the need for a new versatile simulator considering heterogeneity, energy efficiency and reliability of HPC systems. We sketch the problems that need to be solved by such simulator and rationalize using discrete-event simulation for this purpose. Based on a review of existing discrete-event HPC simulation solutions...
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Problems of Active Dynamic Thermography Measurement Standardization in Medicine
PublicationReliability of thermographic diagnostics in medicine is an important practical problem. In the field of static thermography, a great deal of effort has been made to define the conditions for thermographic measurements, which is now the golden standard for such research. In recent years, there are more and more reports on dynamic tests with external stimulation, such as Active Dynamic Thermography, Thermographic Signal Reconstruction...
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Analiza właściwości rozszerzonego obserwatora prędkości maszyny indukcyjnej
PublicationRozszerzony obserwator prędkości został zaproponowany przez prof. Krzemińskiego i jest oparty na rozszerzonym modelu maszyny indukcyjnej, gdzie wprowadzona został nowa zmienna ζ. Jest to nowe podejście do estymacji zmiennych stanu maszyny indukcyjnej i nie wszystkie problemy zostały do tej pory rozwiązane. Zaproponowano wykorzystanie algorytmów ewolucyjnych do doboru wzmocnień obserwatora. W celu redukcji nakładów obliczeniowych...
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Electromagnetic Simulation with 3D FEM for Design Automation in 5G Era
PublicationElectromagnetic simulation and electronic design automation (EDA) play an important role in the design of 5G antennas and radio chips. The simulation challenges include electromagnetic effects and long simulation time and this paper focuses on simulation software based on finite-element method (FEM). The state-of-the-art EDA software using novel computational techniques based on FEM can not only accelerate numerical analysis, but...
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Anisotropic mechanical behavior and auxeticity of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe investigate the mechanical properties of penta-graphene (PG), a recently proposed two-dimensional carbon allotrope using atomistic simulation techniques combined with the empirical description of interatomic interactions. We report on the dependence of its three in-plane mechanical moduli (i.e. Young's modulus, Poisson's ratio and shear modulus) on the deformation direction, strain and temperature. We show that PG displays a...