Filters
total: 4932
-
Catalog
displaying 1000 best results Help
Search results for: MOLECULAR DYNAMICS SIMULATION
-
Spatiotemporal dynamics of the active perirheic zone in a natural wetland floodplain
PublicationAbstract The ecologically and biogeochemically significant perirheic zone is a part of the floodplain where waters originating from both the river and adjacent floodplain are present. In this study, we investigate the spatiotemporal dynamics of the active perirheic zone, i.e. river and floodplain waters and their transient mixing extent. This is achieved by using the Hydraulic Mixing-Cell method, a complement to a fully integrated...
-
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...
-
Simulation of Signal Propagation Along Fractional-Order Transmission Lines
PublicationIn this paper, the simulation method of signal propagation along fractional-order (FO) transmission lines is presented. Initially, fractional calculus and the model of FO transmission line are introduced. Then, the algorithm allowing for simulation of the nonmonochromatic wave propagation along FO transmission lines is presented. It employs computations in the frequency domain, i.e., an analytical excitation is transformed to the...
-
Fatty acids as molecular carriers in cleavable antifungal conjugates
PublicationConjugates composed of C2-18 fatty acid (FA) residues as a molecular carrier and 5-fluorocytosine (5-FC) as an active agent, released upon the action of intracellular esterases on the ester bond between FA and “trimethyl lock” intramolecular linker, demonstrate good in vitro activity against human pathogenic yeasts of Candida spp. The minimal inhibitory concentrations (MIC) values for the most active conjugates containing caprylic...
-
Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
-
Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
-
Simulation of parallel similarity measure computations for large data sets
PublicationThe paper presents our approach to implementation of similarity measure for big data analysis in a parallel environment. We describe the algorithm for parallelisation of the computations. We provide results from a real MPI application for computations of similarity measures as well as results achieved with our simulation software. The simulation environment allows us to model parallel systems of various sizes with various components...
-
Simulation Environment in Python for Ship Encounter Situations
PublicationTo assess the risk of collision in radar navigation distance-based safety measures such as Distance at the Closest Point of Approach and Time to the Closest Point of Approach are most commonly used. Also Bow Crossing Range and Bow Crossing Time measures are good complement to the picture of the meeting situation. When ship safety domain is considered then Degree of Domain Violation and Time to Domain Violation can be applied. This...
-
Experimental and numerical analysis of the pyrolysis dynamics of a single wood particle: presentation of the radiographic technique
PublicationPyrolysis is an oxygen-free process for the thermal decomposition of raw materials. The heat conduction and flow of pyrolysis products (i.e., the gas fraction and liquid vapour generated during pyrolysis) influence the process and products. In this work, the influence of the orientation of wooden particle fibres with respect to the direction of the heat source on the dynamics of the process was investigated, where there were two...
-
Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams
PublicationThe interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology,...
-
Experimental Verification of Storm Sewer Transient Flow Simulation
PublicationThe paper focuses mainly on laboratory investigations of transient and transcritical flow in a single pipe of a sewer system. The aim of this paper is to present a comparison between pressure values calculated by an improved McCormack scheme and those measured at the hydraulic laboratory of the Gdansk University of Technology, which were observed inside a pipe in an experiment for water flow with pressurization. The analysis proves...
-
Mathematical modelling and computer simulation of activated sludge systems.Second edition
PublicationMathematical Modelling and Computer Simulation of Activated Sludge Systems – Second Edition, provides, from the process engineering perspective, a comprehensive and up-to-date overview regarding various aspects of the mechanistic (“white box”) modelling and simulation of advanced activated sludge systems performing biological nutrient removal. In the new edition of the book, a special focus is given to nitrogen removal and an overview...
-
Computer Simulation in Predicting Biochemical Processes and Energy Balance at WWTPs
PublicationNowadays, the use of mathematical models and computer simulation allow analysis of many different technological solutions as well as testing various scenarios in a short time and at low financial budget in order to simulate the scenario under typical conditions for the real system and help to find the best solution in design or operation process. The aim of the study was to evaluate different concepts of biochemical processes and...
-
Probabilistic sensitivity of limit states of structures : The Monte Carlo simulation
PublicationThe main issue of the paper is the probabilistic sensitivity of the limit states of structures with respect to selected input design variables. Attempt to the problem is done by the dedicated Monte Carlo simulation procedure. Basic design variables are random variables of given probability distributions, presented in the form of random numbers. Uni-parametrical increment of the dominant basic variable (basic variables) is done,...
-
Monitoring of CRT by means of impedance multiple measurements - simulation studies
PublicationCardiac resynchronization therapy (CRT) is a very promising treatment for patients with congestive heart failure. An Impedance Cardiography (ICG) is used for evaluation of heart mechanical activity. A simulation study with the use of a FEM model was performed. The developed realistic model of the thorax, based on CT data obtained from examination of a 68-year-old man, consisted of 212 000 tetrahedral elements. Different configurations...
-
Probabilistic sensitivity of limit states of structures. The Monte Carlo simulation
PublicationDesign sensitivity deals with the variation of structural response, implicitly dependent on the design variables of the problem. An attempt is made to implement probabilistic notation in engineering sensitivity analysis. The procedure to implement the sensitivity of a structural limit state to a given basic variable is described in the paper - its main idea, depicted by a flowchart and numerical examples of engineering analysis....
-
Simulation Model of IMS/NGN with Transport Stratum Based on MPLS Technology
PublicationIn the paper we continue our research on traffic modelling in the Next Generation Network (NGN) architecture, which includes the IP Multimedia Subsystem (IMS) elements. A simulation model of a single NGN domain with transport stratum based on the Multiprotocol Label Switching (MPLS) technology is proposed, which allows evaluation of mean response time of this stratum. The simulation model is applied to verify the results obtained...
-
Numerical simulation of screw displacement pile interaction with non-cohesive soil
PublicationA trial numerical simulation of screw displacement pile interaction with non-cohesive subsoil during the transfer of compression load. The simulation was carried out in an axisymmetric system. The technological phases of pile installation in the ground were numerically modelled using equivalent processes which provided similar effects to real technical actions. The results of the numerical calculations were verified by comparing...
-
Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublicationResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
-
Analysis of Agricultural and Engineering Systems using Simulation Decomposition
PublicationThis paper focuses on the analysis of agricultural and engineering processes using simulation decomposition (SD). SD is a technique that utilizes Monte Carlo simulations and distribution decomposition to visually evaluate the source and the outcome of different portions of data. Here, SD is applied to three distinct processes: a model problem, a nondestructive evaluation testing system, and an agricultural food-water energy system....
-
Simulation of electric hearing - influence of simulation parameters on quality of output signal
PublicationW środowisku programistycznym Matlab stworzono symulację słuchu elektrycznego pacjenta implantowanego. W symulacji zastosowano algorytm przetwarzania wykorzystywany w komercyjnych systemach implantów ślimakowych - CIS (Continuous Interleaved Sampling). W pracy zbadano wpływ ilości kanałów, jak i innych parametrów sygnałów wyjściowych przy zastosowaniu sygału mowy jako sygnału wejściowego symulacji.
-
Synthetic strategies in construction of organic low molecular-weight carrier-drug conjugates
PublicationInefficient transportation of polar metabolic inhibitors through cell membranes of eukaryotic and prokaryotic cells precludes their direct use as drug candidates in chemotherapy. One of the possible solutions to this problem is application of the ‘Trojan horse’ strategy, i.e. conjugation of an active substance with a molecular carrier of organic or inorganic nature, facilitating membrane penetration. In this work, the synthetic...
-
Bio‐polyols synthesized by liquefaction of cellulose: Influence of liquefaction solvent molecular weight
PublicationCurrently, the plastics industry including polyurethanes is based on the use of petrochemicals. For this reason, scientists are looking for new types of renewable resources for the substitution of petrochemical substances. This work aims to evaluate the effect of polyethylene glycols (PEG) with different molecular mass impact on properties of bio-based polyols synthesized via biomass liquefaction of cellulose. To date, research...
-
Molecular Biology of Meniscal Healing: A Narrative Review
Publication -
FEM simulation of laminate failure in the three point bending
PublicationThe paper presents a FEM simulation of failure of laminate subjected to the three point bending. The numeri-cal model is based on the equivalent single layer approach with 6-paramater non-linear shell theory kinematics. It is implemented in the non-commercial FEM code. The failure initiation is detected with the use of Tsai-Wu criterion. After the failure onset the progressive failure process is modelled through the appropriate...
-
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...
-
Simulation of Wave Propagation in Media Described by Fractional-Order Models
PublicationIn this paper, algorithms for simulation of the wave propagation in electromagnetic media described by fractional-order (FO) models (FOMs) are presented. Initially, fractional calculus and FO Maxwell's equations are introduced. The problem of the wave propagation is formulated for media described by FOMs. Then, algorithms for simulation of the non-monochromatic wave propagation are presented which employ computations in the time...
-
OCEAN DYNAMICS
Journals -
Beyond the helium buffer: 12C−2 rotational cooling in cold traps with H2 as a partner gas: interaction forces and quantum dynamics
Publicationabstract = { The scattering cross-sections and corresponding rate coefficients for rotationally inelastic collisions of $^{12}$C$_2$^-$ ($^2 \Sigma_g^+$) with H$_2$ ($^1 \Sigma_g^+$) are presented over a broad range of cold-trap temperatures. They have been calculated using quantum scattering theory that employs a new ab initio potential energy surface. The rate coefficients for the inelastic processes in the anionic partner are...
-
Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
-
Simulation of stroboscopic effects
PublicationOmówiono zasadę pomiaru prędkości obrotowej za pomocą stroboskopu. Przedstawiono przyrządy wirtualne do symulacji efektu stroboskopowego przy pomiarze prędkości obrotowej i analizy działania częstościomierza rezonansowego.
-
Log signals simulation.
PublicationSymulatory logów (urządzeń mierzących prędkość w nawigacji morskiej), które używane są do testowania oraz szkolenia operatorów radarów i systemów antykolizyjnych, powinny posiadać również wyjście impulsowe, które w logu rzeczywistym pochodzi z licznika przebytej drogi, w postaci zadanej liczby impulsów na milę morską. Urządzenie takie to przetwornik cyfrowo-częstotliwościowy w formie programowanego cyfrowo dzielnika częstotliwości....
-
Dynamics of Topology-dependent Water Purification by Siliceous Zeolite Membranes
Publication -
Simulation studies into quayside transport and storage yard operations in container terminals
PublicationThe focus of the paper is on quayside transport and storage yard operations in the sea container terminals. Developed algorithms for solving the issues of load handling and storage space allocation have been applied in the frame of adopted simulation model. The criteria chosen for decision making involved the total makespan of vessel unloading and the utilisation levels of the transportation trucks. Recommendations for unloading...
-
Simulation analysis of a production process with selected six sigma ratios
PublicationComputer technologies allow more and more to model as well as to perform simulation experiments of various processes. The simulation analysis provides a better understanding of the interdependencies between various stages of production processes.The results of simulation studies were presented, the aim of them was to show the opportunities of the analysis of the process according to the scenarios and variants developed in connection...
-
Dynamics of S-unimodal maps used in population modeling.
Open Research DataS-unimodal maps are maps of the interval with negative Schwarzian derivative and having only one turning point (such that the map is increasing to the left of the turning point and decreasing to the right of it). Theory of S-unimodal maps is now a well-developed branch of discrete dynamical systems, including famous Singer theorem which implies existence...
-
Quantum corrections to 4 model solutions and applications to Heisenberg chain dynamics
PublicationThe Heisenberg spin chain is considered in φ^4 model approximation. Quantum corrections to classical solutions of the one-dimensional φ^4 model within the correspondent physics are valuated with account of rest d − 1 dimensions of a d-dimensional theory. A quantization of the model is considered in terms of space- time functional integral. The generalized zeta-function formalism is used to renormalize and evaluate the functional...
-
Modular power converter with superconducting magnetic energy storage for electric power distribution system — Analysis and simulation
PublicationThis paper describes selected issues concerning realization of energy storage system (ESS) designed to operate in power distribution system. This paper presents a modular approach of 300 kVA power converter operating with superconducting magnetic energy storage (SMES), which gives high dynamics together with high power and suitable capability for instantaneous energy storage. Analysis and simulation studies of selected power converter...
-
Quadratic stochastic operators as a tool in modelling the dynamics of a distribution of a population trait
PublicationQuadratic stochastic operators can exhibit a wide variety of asymptotic behaviours and these have been introduced and studied recently. In the present work we discuss biological interpretations that can be attributed to them. We also propose a computer simulation method to illustrate the behaviour of iterates of quadratic stochastic operators.
-
Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
-
Multi-objective optimization of expensive electromagnetic simulation models
PublicationVast majority of practical engineering design problems require simultaneous handling of several criteria. For the sake of simplicity and through a priori preference articulation one can turn many design tasks into single-objective problems that can be handled using conventional numerical optimization routines. However, in some situations, acquiring comprehensive knowledge about the system at hand, in particular, about possible...
-
BIOGAS PRODUCTION FROM BAKERY WASTES -DYNAMICS, RETENTION TIME AND BIOGAS POTENTIAL
PublicationThis paper presents results of bakery-waste methane-fermentation. The scope of the study covers the determination of basic physicochemical parameters, process dynamics and retention time as well as biogas composition and biogas efficiency. Methane fermentation process was carried out in accordance with German Standard DIN 38414 S8 and under condition of 38°C. Conclusion: bakery wastes have big potential for biogas production.
-
Paweł Możejko dr hab.
People -
Periodic Properties of 1D FE Discrete Models in High Frequency Dynamics
PublicationFinite element discrete models of various engineering 1D structures may be considered as structures of certain periodic characteristics. The source of this periodicity comes from the discontinuity of stress/strain field between the elements. This behaviour remains unnoticeable, when low frequency dynamics of these structures is investigated. At high frequency regimes, however, its influence may be strong enough to dominate calculated...
-
On geometry parameterization for simulation-driven design closure of antenna structures
PublicationFull-wave electromagnetic (EM) simulation tools have become ubiquitous in antenna design, especially final tuning of geometry parameters. From the reliability standpoint, the recommended realization of EM-driven design is through rigorous numerical optimization. It is a challenging endeavor with the major issues related to the high computational cost of the process, but also the necessity of handling several objectives and constraints...
-
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...
-
Vibration Diagnostics of Rolling Mills Based on Nonlinear Effects in Dynamics
Publication -
A Comprehensive Review: Applications of the Kozeny–Carman Model in Engineering with Permeability Dynamics
PublicationIn this review article, we investigate the dynamic nature of the Kozeny–Carman Model concerning permeability and its application in engineering contexts. Providing insights into the changing dynamics of permeability within mining, petroleum, and geotechnical engineering, among other engineering applications. While some are complex and require additional modifcations to be applicable, others are simple and still function in specifc...
-
Analysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
PublicationAnalysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
-
Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...