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Search results for: molecular dynamic simulation
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Dynamic soil improvement by hybrid technologies
PublicationHybrid method of subsoil improvement for road embankment foundation is described. This method is composed of two wellknown methods: dynamic replacement (DR) and microblasting (DDC) one (Deep Dynamic Compaction). The method was used for both the strengthening of the fully saturated organic subsoil as well as for acceleration of the consolidation of the organic layers. The practice ensures the expected results. A proper example on...
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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Adaptive dynamic control allocation for dynamic positioning of marine vessel based on backstepping method and sequential quadratic programming
PublicationIt is generally assumed in dynamic positioning of over-actuated marine vessels that the control effectiveness matrix (input matrix) is known and constant, or, in case of fault information, it is estimated by the fault detection and diagnosis system. The purpose of the study is to develop the adaptive dynamic positioning control system for an over-actuated marine vessel in the presence of uncertainties and with emphasis on limited...
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Dynamic unattended measurement based routing algorithm for diffServ architecture
PublicationDynamic routing is very important in terms of assuring QoS in today's packet networks especially for streaming and elastic services. Existing solutions dedicated to dynamic routing are often too complicated and seem to be not usable in real time traffic scenarios where transferred traffic may vary significantly. This was the main reason for research and new routing mechanism proposal which should apply to today's packet networks....
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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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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...
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Journal of Simulation
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SIMULATION & GAMING
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Simulation in Healthcare
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublicationIn this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects...
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Dynamic model of nuclear power plant turbine
PublicationThe paper presents the dynamic multivariable model of Nuclear Power Plant steam turbine. Nature of the processes occurring in a steam turbine causes a task of modeling it very difficult, especially when this model is intended to be used for on-line optimal process control (model based) over wide range of operating conditions caused by changing power demand. Particular property of developed model is that it enables calculations...
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Ship Dynamic Positioning Based on Nonlinear Model Predictive Control
PublicationThe presented work explores the simulation test results of using nonlinear model predictive control algorithm for ship dynamic positioning. In the optimization task, a goal function with a penalty was proposed with a variable prediction step. The results of the proposed control algorithm were compared with backstepping and PID. The effect of estimation accuracy on the control quality with the implemented algorithms was investigated....
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Antimicrobial molecular nanocarrier–drug conjugates
PublicationMany antimicrobial drugs are poorly active against pathogenic microbes causing intracellular infections, such as Mycobacterium tuberculosis or Plasmodium falciparum. On the other hand, several known antimicrobial agents are not effective enough because of their limited cellular penetration. A common feature of both challenges is the inability of an active agent to cross the biological membrane(s). One of the possible approaches...
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Simulation model for evaluation of QoS routing algorithm in large packet networks
PublicationThe variety of traffic transferred via current telecommunication networks includes also voice, which should meet quality requirements. One of mechanisms, which can support QoS in current packet networks, is routing. There exist many routing proposals which should introduce the QoS into the network but practically they don't. Following paper presents the realization of simulation model for evaluation of a new routing algorithm DUMBRA...
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Measurements of Subnanometer Molecular Layers
PublicationSelected methods of formation and detection of nanometer and subnanometer molecular layers were shown. Additionally, a new method of detection and measurement with subnanometer resolution of layers adsorbed or bonded to the gate dielectric of the ion selective field effect transistor (ISFET) was presented.
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Molecular Umbrella as A Nanocarrier for Antifungals
PublicationA molecular umbrella composed of two O‐sulfated cholic acid residues was applied for the construction of conjugates with cispentacin, containing a “trimethyl lock” (TML) or o‐dithiobenzylcarbamoyl moiety as a cleavable linker. Three out of five conjugates demonstrated antifungal in vitro activity against C. albicans and C. glabrata but not against C. krusei, with MIC90 values in the 0.22–0.99 mM range and were not hemolytic. Antifungal...
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Simulation Game BiM 2022/2023
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Dynamic charging of electric buses
PublicationDespite the continuous development of electrochemical battery technology and the multitude of electric buses on offer, it is still not possible to exploit electric buses in urban transport on an all-day basis without the necessity of charging them. It is therefore necessary to build point-to-point contact charging stations or induction charging stations at the terminals. This results in substantial financial outlays connected with...
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Solving the Problem of Dynamic Adaptability of Artificial Intelligence Systems that Control Dynamic Technical Objects
PublicationThis paper investigates the increase in the response speed and stability of artificial intelligence systems that control dynamic technical objects. The problem of calculating the optimal time of switching an artificial intelligence system between software classes by the criterion of the rigidity degree of the model of a control object is considered. The solution of this problem is proposed for the general case of the control object...
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Estimating and Forecasting GDP in Poland with Dynamic Factor Model
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Control System Design for Dynamic Positioning using Vectorial Backstepping
PublicationThe problem of synthesis a dynamic positioning system for low frequency model of surface vessel was considered in this paper. The recursive vectorial backstepping control design was used to keep a fixed position and heading in presence of wave disturbances. The passive observer was introduced to smooth the measurements and to estimate the velocities needed for the control algorithm. The computer simulation results were given to...
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An Evaluation Engine for Dynamic Ranking of Cloud Providers
PublicationThe paper focuses on creation of an effective dynamic ranking service for IaaS, PaaS and SaaS cloud providers. It considers building a quality model for this purpose along with definition of quality measure- ment procedures. The paper discusses several techniques known from already existing price comparison engines that could be modified and adopted for comparison of cloud providers. A technique for filtering measured data is proposed,...
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Designing Particle Kalman Filter for Dynamic Positioning
PublicationThe article presents a comparative analysis of two variants of the Particle Kalman Filter designed by using two different ship motion models. The first filter bases only on the kinematic model of the ship and can be used in many types of vehicles, regardless of the vehicle dynamics model. The input value to the filter is the noisy position of the ship. The second filter makes use of the kinematic and dynamic models of the moving...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Performance evaluation of unified memory and dynamic parallelism for selected parallel CUDA applications
PublicationThe aim of this paper is to evaluate performance of new CUDA mechanisms—unified memory and dynamic parallelism for real parallel applications compared to standard CUDA API versions. In order to gain insight into performance of these mechanisms, we decided to implement three applications with control and data flow typical of SPMD, geometric SPMD and divide-and-conquer schemes, which were then used for tests and experiments. Specifically,...
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Simulation of the IT Service and Project Management Environment
PublicationThe authors of this paper present a simulation of the socio-technical system in which teams of students – regarded as low-maturity organizations – were given a task to utilize the (relatively) mature technologies that support IT project and service management. The experiment consisted of the following phases: teams formation, introduction to technologies used during the simulation, performing a set of reactive and proactive service...
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Rengel Cane Sia Doctoral Candidate
PeopleI’m Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master’s thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master’s degree in Chemistry in the Mindanao...
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Molecular level interpretation of excess infrared spectroscopy
PublicationInfrared (IR) spectroscopy is an invaluable tool in studying intermolecular interactions in solvent mixtures. The deviation of the IR spectrum of a mixture from the spectra of its pure components is a sensitive measure of the non-ideality of solutions and the modulation of intermolecular interactions introduced by mutual influence of the components. Excess IR spectroscopy, based on the established notion of excess thermodynamic...
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DYNAMIC ANALYSIS OF HISTORIC RAILWAY BRIDGES IN POLAND IN THE CONTEXT OF ADJUSTING THEM TO PENDOLINO TRAINS
PublicationThe article presents the dynamic analysis of the historic railway bridge in Tczew as an example of the usefulness of such type of bridge for high-speed trains. The model of the bridge and the simulation of rolling stock passage was performed in SOFISTIK program. The scope of work includes experimental studies, the solution of the problem concerning the correct solution features dynamic model takes into account the dependencies...
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Journal of Dynamic Behavior of Materials
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Dynamic Relationships Management Journal
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SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL
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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...
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Web-based real-time simulation system
PublicationThe paper presents the development of a simulation system composed of a real-time plant simulator with real-time controller included in the software-in-the-loop structure using web-based communication. The client-server architecture build in a TCP/IP network environment was introduced, where the server is a computing unit for real-time high temporal resolution plant simulation (and optionally also as controllers' platform) and...
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Systems Analysis Modelling Simulation
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Molecular Imaging and Nanotechnology—Emerging Tools in Diagnostics and Therapy
PublicationPersonalized medicine is emerging as a new goal in the diagnosis and treatment of diseases. This approach aims to establish differences between patients suffering from the same disease, which allows to choose the most effective treatment. Molecular imaging (MI) enables advanced insight into molecule interactions and disease pathology, improving the process of diagnosis and therapy and, for that reason, plays a crucial role in personalized...
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Contribution of dynamic vehicle loads to pavement failure
PublicationPavement surfaces are not ideally even, which causes dynamic loads of vehicle axles. Distribution of dynamic loads of a given axle is similar to normal distribution and can be described by static load and dynamic load coefficient. The dynamic load coefficient depends on road profile, vehicle speed, properties of suspensions and static load of axle. While for a given road section road profile remains constant, vehicle speed and...
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Grzegorz Zieliński dr inż.
PeopleAuthor of over 100 scientific publications (both in Polish and English) in the field of service management, entity improvement, including medical entities. Scientific and research interests include areas related to the maturity and excellence of enterprises in various aspects of their activities. He participated in research projects of the National Science Center and projects implemented by international consortia under the European...
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SIMULATION MODEL OF ASON/GMPLS ARCHITECTURE
PublicationGrowing demands of information society concerned with sophisticated applications could be satisfied by ASON/GMPLS architecture comprehended as Automatically Switched Optical Network (ASON) with Generalized Multi-Protocol Label Switching (GMPLS). The ASON/GMPLS proposition represents the future direction of Next Generation Network (NGN) architecture. Therefore considerable work has to be done to examine this solution. In this aspect...
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Dynamic Content Internationalization in Web Applications
PublicationThis paper shows a concept for providing dynamic internationalization to web applications. Presented work is based on the Java Web Platform but described concepts can be successfully implemented on other platforms. It shows how textual data being part of web pages static and dynamic content can be localized dynamically during application runtime. All concepts presented were or are still being developed in an existing conference...
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Dynamic Research of Masonry Vault in a Technical Scale
PublicationThe paper presents preliminary results of dynamic tests of the masonry barrel vault in a technical scale. Experimental studies are intended to identify material properties of homogenized masonry vaults under dynamic loads. The aim of the work is to create numerical models to analyse vault’s dynamic response to dynamic loads in a simplest and accurate way. The process of building the vault in a technical scale is presented in the...
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SIMULATION OF PROCEED® SURGICAL MESH APPLIED TO VENTRAL HERNIA REPAIR
PublicationIn the present research, Proceed® implant is considered. The system is subjected to short-time dynamic pressure load, similar to post-operative cough naturally occurring in human abdomen. The model refers to a clinical case of 5cm of hernia operated by Proceed implant fixed by 15 joints every 3cm around the orifice. The simulations of the implanted mesh are performed by means of the Finite Element Method. The implant is modelled...
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Three-dimensional conceptual model for service-oriented simulation
Publicationn this letter, we propose a novel three-dimensional conceptual model for an emerging service-oriented simulation paradigm. The model can be used as a guideline or an analytic means to find the potential and possible future directions of the current simulation frameworks. In particular, the model inspects the crossover between the disciplines of modeling and simulation, service-orientation, and software/systems engineering. Finally,...
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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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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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Communications in Nonlinear Science and Numerical Simulation
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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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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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Molecular Physics Reports
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