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Speed estimation of a car at impact with a W-beam guardrail using numerical simulations and machine learning
PublikacjaThis paper aimed at developing a new method of estimating the impact speed of a passenger car at the moment of a crash into a W-beam road safety barrier. The determination of such a speed based on the accident outcomes is demanding, because often there is no access to full accident data. However, accurate determination of the impact speed is one of the key elements in the reconstruction of road accidents. A machine learning algorithm...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublikacjaThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Communication and Load Balancing Optimization for Finite Element Electromagnetic Simulations Using Multi-GPU Workstation
PublikacjaThis paper considers a method for accelerating finite-element simulations of electromagnetic problems on a workstation using graphics processing units (GPUs). The focus is on finite-element formulations using higher order elements and tetrahedral meshes that lead to sparse matrices too large to be dealt with on a typical workstation using direct methods. We discuss the problem of rapid matrix generation and assembly, as well as...
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P-666 Detecting gene variants correlated with MII oocytes developed during ovarian stimulation
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublikacjaAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Experimental tests and numerical simulations of full scale composite sandwich segment of a foot- and cycle- bridge
PublikacjaIn the paper experimental tests and numerical simulations of a full cross-section segment of ultimately designed foot-and cycle-bridge are presented. The experimental tests were conducted on element with length reduced to 3 m and unchanged (target) cross-section dimensions. The external skin of structure is GFRP laminate while internal core is PET foam. Several quasi-static tests were performed using hydraulic cylinder to generate...
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublikacjaIn 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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FEM simulations applied to the failure analysis of RC structure under the influence of municipal sewage pressure
PublikacjaThe paper discusses a failure mechanism of reinforced concrete (RC) structure with steel cover that failed under the influence of municipal sewage pressure. To explain the reasons of failure, in-situ measurements, laboratory experiments and comprehensive Finite Element Method (FEM) computations were performed. Non-destructive in-situ scanning tests were carried out to determine quantity and cover thickness of embedded reinforcement...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Simulations of freshwater lens recharge and salt/freshwater interfaces using the HYDRUS and SWI2 packages for MODFLOW
PublikacjaThe paper presents an evaluation of the combined use of the HYDRUS and SWI2 packages for MODFLOW as a potential tool for modeling recharge in coastal aquife rs subject to saltwater intrusion. The HYDRUS package for MODFLOW solves numerically the one-dimensional form of the Richards equation describing water flow in variably- saturated media. The code computes groundwater recharge to or...
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Rapid Yield Optimization of Miniaturized Microwave Passives by Response Features and Variable-Fidelity EM Simulations
PublikacjaThe operation of high-frequency devices, including microwave passive components, can be impaired by fabrication tolerances but also incomplete knowledge concerning operating conditions (temperature, input power levels) and material parameters (e.g., substrate permittivity). Although the accuracy of manufacturing processes is always limited, the effects of parameter deviations can be accounted for in advance at the design phase...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublikacjaThe 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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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublikacjaHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublikacjaExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Improved-Efficacy EM-Based Antenna Miniaturization by Multi-Fidelity Simulations and Objective Function Adaptation
PublikacjaThe growing demands for integration of surface mount design (SMD) antennas into miniatur-ized electronic devices have been continuously imposing limitations on the structure dimen-sions. Examples include embedded antennas in applications such as on-board devices, picosatel-lites, 5G communications, or implantable and wearable devices. The demands for size reduction while ensuring a satisfactory level of the electrical and field...
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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublikacjaThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations
PublikacjaIn this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas–liquid...
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FE-simulations of dynamic shear localization in granular bodies using an Arbitrary Lagrangian-Eulerian formulation.
PublikacjaW artykule przedstawiono wyniki symulacji lokalizacji odkształceń w materiałach granulowanych. Obliczenia wykonano przy zastosowaniu nielokalnego modelu hipoplastycznego dla 2 różnych problemów: sciskania dwuosiowego i przepływu silosowego. W obliczeniach wykorzystano sformułowanie ALE.
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Gradient-based optimization of filters using FD-TD software
PublikacjaW artykule opisane jest nowe podejście do zagadnienia optymalizacji filtrów mikrofalowych pasmowo-przepustowych. Optymalizacja prowadzona jest z wykorzystaniem metody gradientowej poszukiwania minimum wartości funkcji celu oraz przy założeniu pełnofalowej symulacji obwodów metodą różnic skończonych w dziedzinie czasu. W artykule pokazane jest, że stosując zaawansowane techniki cyfrowego przetwarzania sygnałów możliwa jest optymalizacja...
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Low-order models from FD-TD time samples
PublikacjaNiniejszy artykuł zawiera opis szeregu kryteriów pozwalających na automatyczne tworzenie wysokiej jakości modeli sygnałów czasowych uzyskanych w drodze symulacji obwodów wysokiej częstotliwości metodą różnic skończonych w dziedzinie czasu. Podany jest szczegółowy opis selekcji kluczowych parametrów modeli takich jak wybór długości ciągu użytego do konstrukcji modeli, współczynnika decymacji silnie nadpróbkowanego przebiegu w dziedzinie...
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CD NIWA jako platforma współpracy biznesu i nauki
PublikacjaArtykuł prezentuje koncepcję Centrum Doskonałości Naukowej Infrastruktury Wytwarzania Aplikacji: CD NIWA, które jest środowiskiem przetwarzania w chmurze obliczeniowej, źródłem stale doskonalonych aplikacji i usług oraz platformą współpracy użytkowników. Interaktywność współdziałania nauki i biznesu jest głównym założeniem i celem Centrum Doskonałości NIWA, które ma też służyć budowaniu społeczności współpracującej w zakresie realizacji...
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THE POTENTIAL OF DIFFERENT VARIETIES OF WHITE CABBAGE IN PHYTOREMEDIATION OF ZN AND CD
PublikacjaThe species belong to the botanical family Brassi- caceae are considered to be useful for phytoremediation of soil contaminated with heavy metals. Problems with use the plants recognized as hyperacumulators is that, the plants need to be harvested shortly after the plants become mature, which causes problems of disposal of obtained biomass. When these plants are dried, they easily crumble and flake off, greatly reducing the yield obtained,...
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Effects of FSW Tool Plunge Depth on Properties of an Al-Mg-Si Alloy T-Joint: Thermomechanical Modeling and Experimental Evaluation
PublikacjaOne of the main challenging issues in friction stir welding (FSW) of stiffened structures is maximizing skin and flange mixing. Among the various parameters in FSW that can affect the quality of mixing between skin and flange is tool plunge depth (TPD). In this research, the effects of TPD during FSW of an Al-Mg-Si alloy T-joint are investigated. The computational fluid dynamics (CFD) method can help understand TPD effects on FSW...
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus - expression and purification
PublikacjaBiałka SSB są niezbędne do życia każdemu organizmowi. W tej pracy prezentujemy wyniki otrzymania i oczyszczania białek SSB Thermus thermophilus i T. aquaticus. Dotąd były znane białka SSB jedynie o budowie homotetrameru lub heterotrimeru. Białka SSB Thermus thermophilus i T. aquaticus stanowią nową klasę białek SSB - białek homodimerycznych. Ponadto dowiedziono, iż białka te są użyteczne w reakcji PCR.
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A surface-exposed DraD protein of uropathogenic Escherichia coli bearing Dr fimbriae may be expressed and secreted independently from DraC usher and DraE adhesin
PublikacjaOperon dra uropatogennych szczepów Escherichia coli Dr+ odpowiedzialny jest za proces bakteryjnej adhezji i inwazji. Operon dra kodujący fimbrie Dr zawiera sześć otwartych ramek odczytu - draA, draB, draC, draD, draP oraz draE. Fimbrie Dr zlokalizowane na powierzchni komórki bakteryjnej, zbudowane są z podjednostek białka DraE. Niewiele wiadomo na temat powierzchniowej ekspresji białka DraD oraz jego roli w procesie biogenezy fimbrii...
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Molecular aspects of biogenesis of Escherichia coli Dr Fimbriae: characterization of DraB-DraE complexes
PublikacjaHemaglutynina Dr uropatogennych szczepów Escherichia coli jest fimbrialnym homopolimerem zbudowanym z podjednostek białkowych DraE kodowanych przez operon dra. Operon dra zawiera geny draB i draC, kodujące białka homologiczne do białek (białko opiekuńcze-białko kanałotwórcze) zaangażowanych w procesie biogenezy struktur polimerycznych eksprymowanych powierzchniowo. Białko DraB jest jednym z białek periplazmatycznych, należącym...
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The chaperone-usher pathway of bacterial adhesin biogenesis - from molecular mechanism to strategies of anti-bacterial prevention and modern vaccine design
PublikacjaSystem chaperone-usher (białko opiekuńcze-białko kanałotwórcze) warunkuje biogenezę powierzchniowych struktur adhezyjnych, odpowiedzialnych za wirulencję wielu bakterii gram-ujemnych. Powyższy mechanizm został zbadany na poziomie strukturalnym w przypadku różnych gatunków bakterii patogennych. Celem powyższej pracy było przedstawienie molekularnego mechanizmu biogenezy struktur adhezyjnych na bazie systemu chaperone-usher. Otrzymane...
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Application of SSB-like protein from Thermus aquaticus in multiplex PCR of human Y-STR markers identification
PublikacjaW tej publikacji prezentujemy zastosowanie białka SSB-podobnego Thermus aquaticus (TaqSSB) w reakcji multiplex PCR w celu identyfikacji markerów ludzkiego Y-STR. Wykorzystanie termostabilnego białka TaqSSB chroni lub redukuje tworzenie przez startery struktur dimerycznych, które powodują hamowanie hybrydyzacji starterów do badanego DNA i redukują ilość starterów dostępnych w reakcji PCR.
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Moving out of CF3‐Land: Synthesis, Receptor Affinity, and in silico Studies of NK1 Receptor Ligands Containing a Pentafluorosulfanyl (SF5) Group
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Electrochemically assisted deposition of hydroxyapatite on Ti6Al4V substrates covered by CVD diamond films — Coating characterization and first cell biological results
PublikacjaAlthough titaniumand its alloys are widely used as implant material for orthopedic and dental applications they show only limited corrosion stability and osseointegration in different cases. The aim of the presented research was to develop and characterize a novel surface modification system from a thin diamond base layer and a hydroxyapatite (HAp) top coating deposited on the alloy Ti6Al4V widely used for implants in contact with bone....
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FEM Analysis of Multi Storied RC Structure using (E-TAB simulation ) and Need of High rise structures in Developing Countries
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Non-linear circuit model of a single doubly-fed induction machine formulated in natural axes for drive systems simulation purposes
PublikacjaMathematical modelling and a circuit model formulated in natural axes of a single doubly-fed induction machine, with the account of magnetic circuit nonlinearity are presented in the paper. Derivation of the model differential equations was based on Lagrange's energy method. State functions of magnetic elements in the model are non-linear and depend on all currents flowing in the machine windings and on the angle of rotor position....
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Conducted emi identification in power electronic converters : modeling of EMI generation and propagation using circuit simulation and wiener filtering methods.
PublikacjaThis work presents the circuit simulations and the conventional signal processing technique (Wiener filtering) in order to reconstruct conducted ElectroMagnetic Interferences (EMI), generated and propagated in power electronics converters. In the simulation study, the most accurate presently available models of components of circuit have been used and improved. The proposed Wiener filtering method allows to identifying the transfer...
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Tackling Air Pollution in Cities with Modelling and Simulation: Remote Group Model Building as an Educational Tool Supporting System Dynamics Modelling
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Cementless controlled low-strength material (CLSM) based on waste glass powder and hydrated lime: Synthesis, characterization and thermodynamic simulation
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A Dynamic Forecast Demand Scenario Analysis to Design an Automated Parcel Lockers Network in Pamplona (Spain) Using a Simulation-Optimization Model
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Comparison of Macintosh and Intubrite laryngoscopes for orotracheal intubation by nurses during resuscitation: preliminary data of a randomized crossover simulation-based study
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Influence of gas turbine controller adjustment on ship propulsion system behaviour in rough sea conditions. Part 2. The simulation investigations.
PublikacjaPrzedstawiono model dynamiki układu napędowego okrętowego, wykorzystując metodę elementów skończonych. Układ napędowy składa się z dwóch turbin gazowych napędzających poprzez przekładnię mechaniczną zębatą pędnik o nastawnym skoku. W symulacji układu napędowego zadawano wymuszenia wartością zadaną nastaw prędkości na regulatorze oraz wymuszenia od falowania morza w zależności od stanu morza. Przedstawiono wyniki takich symulacji.
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Nonlinear harmonic amplitudes in air coils above and below a metal plate as a function of tensile strength via finite element simulation.
PublikacjaOpisano wyniki obliczeń numerycznych (symulacja metodą MES) wpływu naprężeń na amplitudy nieliniowych harmonicznych napięcia indukowanego w cewkach powietrznych umieszczonych nad i pod płytą.
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Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublikacjaW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
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Fast EM-Driven Nature-Inspired Optimization of Antenna Input Characteristics Using Response Features and Variable-Resolution Simulation Models
PublikacjaUtilization of optimization technique is a must in the design of contemporary antenna systems. Often, global search methods are necessary, which are associated with high computational costs when conducted at the level of full-wave electromagnetic (EM) models. In this study, we introduce an innovative method for globally optimizing reflection responses of multi-band antennas. Our approach uses surrogates constructed based on response...
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Integrating modelling, simulation and data management tools to create a planning support system for the improvement of air quality by urban planning solutions
PublikacjaThe urbanization pressure requires urban planners, designers, and policy makers to be more responsive to the challenges related to improving the quality of the urban environment and the living conditions of the inhabitants. One of the many environmental issues that need to be taken into account is urban air pollution. As the process of urban ventilation and air pollution dis-persion is significantly affected by the urban layout,...
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublikacjaThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Innovativeness and Competitiveness of the New European Union States in Variable Economic Situation between 2006 and 2013
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublikacjaThe experimental analysis of the wood chip removing system during its redesigning in the existing sliding table circular saw and computational fluid dynamic (CFD) numerical simulations of the air flow process is presented in the paper. The attention was focused on the extraction hood and the bottom shelter of the actual existing system. The main aim was to perform experimental research on the pressure distribution inside the...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough 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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Prediction of cast-in-place concrete strength of the extradosed bridge deck based on temperature monitoring and numerical simulations
PublikacjaThe work is devoted to the implementation of a monitoring system for high performance concrete embedded in the span of an extradosed bridge deck using a modified maturity method augmented by numerical simulations conducted by the authors’ FEM code. The paper presents all research stages of bridge construction and considers the conclusions drawn from the results of laboratory tests, field measurements, and numerical calculations....
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Use of Innovative and Advanced Computer Simulations of Chemical Speciation of Heavy Metals in Soils and Other Environmental Samples
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublikacjaBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Finite element method simulations of various cases of crash tests with N2/W4/A steel road barrier
PublikacjaThe 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...