Filters
total: 461
Search results for: coarse graining, molecular dynamics, openmp, parallel algorithms, unres
-
Generalized adaptive comb filter with improved accuracy and robustness properties
PublicationGeneralized adaptive comb lters can be used to identify/track parameters of quasi-periodically varying systems.In a special, signal case they reduce down to adaptive comblters, applied to elimination or extraction of nonstationarymulti-harmonic signals buried in noise. We proposea new algorithm which combines, in an adaptive way, resultsyielded by several, simultaneously working generalizedadaptive comb lters. Due to its highly...
-
Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
-
Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye
PublicationThe functioning of the human eye in the extreme range of light intensity requires a combination of the high sensitivity of photoreceptors with their photostability. Here, we identify a regulatory mechanism based on dynamic modulation of light absorption by xanthophylls in the retina, realized by reorientation of pigment molecules induced by trans–cis photoisomerization. We explore this photochemically switchable system using chromatographic...
-
The Quick Measure of a Nurbs Surface Curvature for Accurate Triangular Meshing
PublicationNURBS surfaces are the most widely used surfaces for three-dimensional models in CAD/CAE programs. As a model for FEM calculation is prepared with a CAD program it is inevitable to mesh it finally. There are many algorithms for meshing planar regions. Some of them may be used for meshing surfaces but it is necessary to take the curvature of the surface under consideration to avoid poor quality mesh. The mesh must be denser in the...
-
KernelHive: a new workflow-based framework for multilevel high performance computing using clusters and workstations with CPUs and GPUs
PublicationThe paper presents a new open-source framework called KernelHive for multilevel parallelization of computations among various clusters, cluster nodes, and finally, among both CPUs and GPUs for a particular application. An application is modeled as an acyclic directed graph with a possibility to run nodes in parallel and automatic expansion of nodes (called node unrolling) depending on the number of computation units available....
-
Frequency and time domain characteristics of digital control of electric vehicle in-wheel drives
PublicationIn-wheel electric drives are promising as actuators in active safety systems of electric and hybrid vehicles. This new function requires dedicated control algorithms, making it essential to deliver models that reflect better the wheel-torque control dynamics of electric drives. The timing of digital control events, whose importance is stressed in current research, still lacks an analytical description allowing for modeling its...
-
Machine learning-based prediction of preplaced aggregate concrete characteristics
PublicationPreplaced-Aggregate Concrete (PAC) is a type of preplaced concrete where coarse aggregate is placed in the mold and a Portland cement-sand grout with admixtures is injected to fill the voids. Due to the complex nature of PAC, many studies were conducted to determine the effects of admixtures and the compressive and tensile strengths of PAC. Considering that a prediction tool is needed to estimate the compressive and tensile strengths...
-
Machine learning-based prediction of preplaced aggregate concrete characteristics
PublicationPreplaced-Aggregate Concrete (PAC) is a type of preplaced concrete where coarse aggregate is placed in the mold and a Portland cement-sand grout with admixtures is injected to fill the voids. Due to the complex nature of PAC, many studies were conducted to determine the effects of admixtures and the compressive and tensile strengths of PAC. Considering that a prediction tool is needed to estimate the compressive and tensile...
-
Variable-fidelity shape optimization of dual-rotor wind turbines
PublicationPurpose Dual-rotor wind turbines (DRWTs) are a novel type of wind turbines that can capture more power than their single-rotor counterparts. Because their surrounding flow fields are complex, evaluating a DRWT design requires accurate predictive simulations, which incur high computational costs. Currently, there does not exist a design optimization framework for DRWTs. Since the design optimization of DRWTs requires numerous model...
-
Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
-
Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide – volumetric and compressibility studies
PublicationThe density and sound velocity of the solutions of ionic liquids based on N-alkyl-N-methyl-morpholinium cations, N-ethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-methyl-N-octyl-morpholinium bis(trifluoromethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide in dimethylsulfoxide were measured at T = (298.15 to 318.15)...
-
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...
-
Adaptive system for recognition of sounds indicating threats to security of people and property employing parallel processing of audio data streams
PublicationA system for recognition of threatening acoustic events employing parallel processing on a supercomputing cluster is featured. The methods for detection, parameterization and classication of acoustic events are introduced. The recognition engine is based onthreshold-based detection with adaptive threshold and Support Vector Machine classifcation. Spectral, temporal and mel-frequency descriptors are used as signal features. The...
-
Correlated Particle Motion and THz Spectral Response of Supercritical Water
PublicationMolecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translationaland rotational freedom of individual molecules. These changes give rise to substantially different infrared spectra and...
-
[IMe] Advanced numerical methods in mechanics
e-Learning Courses{mlang pl} Dyscyplina: inżynieria mechaniczna Zajęcia obowiązkowe dla doktorantów I i II roku Prowadzący: dr hab. inż. Krzysztof Tesch, prof. PG, dr hab. inż. Arkadiusz Żak, prof. PG Liczba godzin: 45 Forma zajęć: wykład {mlang} {mlang en} Discipline: mechanical engineering Obligatory course for 1st and 2nd-year PhD students Academic teachers: dr hab. inż. Krzysztof Tesch, prof. PG, dr hab. inż. Arkadiusz Żak, prof....
-
Parameter and delay estimation of linear continuous-time systems
PublicationIn this paper the problem of on-line identification of non-stationary delay systems is considered. Dynamics of supervised industrial processes is described by ordinary differential equations. Discrete-time mechanization of their continuous-time representations is based on dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures implemented in recursive forms are applied for simultaneous identification...
-
Why Are Left-Handed G-Quadruplexes Scarce?
PublicationG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....
-
Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
-
Swarm-Assisted Investment Planning of a Bioethanol Plant
PublicationBioethanol is a liquid fuel for which a significant increase in the share of energy sources has been observed in the economies of many countries. The most significant factor in popularizing bioethanol is the profitability of investments in construction of facilities producing this energy source, as well as the profitability of its supply chain. With the market filled with a large amount of equipment used in the bioethanol production...
-
Rotational state-changing collisions of C2H− and C2N− anions with He under interstellar and cold ion trap conditions: A computational comparison
PublicationWe present an extensive range of quantum calculations for the state-changing rotational dynamics involving two simple molecular anions that are expected to play some role in the evolutionary analysis of chemical networks in the interstellar environments, C2H− (X1Σ+) and C2N− (X3Σ−), but for which inelastic rates are only known for C2H−. The same systems are also of direct interest in modeling selective photo-detachment experiments...
-
Online sound restoration system for digital library applications
PublicationAudio signal processing algorithms were introduced to the new online non-commercial service for audio restoration intended to enhance the content of digitized audio repositories. Missing or distorted audio samples are predicted using neural networks and a specific implementation of the Jannsen interpolation method based on the autoregressive model (AR) combined with the iterative restoring of missing signal samples. Since the distortion...
-
Parameter and delay estimation of linear continuous-time systems
PublicationIn this paper the problem of on-line identification of non-stationary delay systems is considered. Dynamics of supervised industrial processes is usually described by ordinary differential equations. Discrete-time mechanization of their continuous-time representations is based on dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures implemented in recursive forms are applied for simultaneous...
-
On–line Parameter and Delay Estimation of Continuous–Time Dynamic Systems
PublicationThe problem of on-line identification of non-stationary delay systems is considered. The dynamics of supervised industrial processes are usually modeled by ordinary differential equations. Discrete-time mechanizations of continuous-time process models are implemented with the use of dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures mechanized in recursive forms are applied for simultaneous...
-
Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
-
Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas
PublicationSix new 1-benzoyl-3-phenylthiourea and 1-benzoyl-3-(2-methylphenyl)thiourea complexes of mercury( II) were obtained in the reactions of the ligands with HgX2 in methanol (X = Cl, Br, I). Their structures, determined by single-crystal X-ray diffraction analysis, exhibit different stoichiometries and molecular organization. Coordination centers adopt more or less distorted tetrahedral geometry (five structures) or distorted trigonal...
-
Optimization of hybrid parallel application execution in heterogeneous high performance computing systems considering execution time and power consumption
PublicationMany important computational problems require utilization of high performance computing (HPC) systems that consist of multi-level structures combining higher and higher numbers of devices with various characteristics. Utilizing full power of such systems requires programming parallel applications that are hybrid in two meanings: they can utilize parallelism on multiple levels at the same time and combine together programming interfaces...
-
Scheduling with Complete Multipartite Incompatibility Graph on Parallel Machines
PublicationIn this paper we consider a problem of job scheduling on parallel machines with a presence of incompatibilities between jobs. The incompatibility relation can be modeled as a complete multipartite graph in which each edge denotes a pair of jobs that cannot be scheduled on the same machine. Our research stems from the works of Bodlaender, Jansen, and Woeginger (1994) and Bodlaender and Jansen (1993). In particular, we pursue the...
-
On the problem of optimised allocation of water quality sensors and actuators in DWDS
PublicationThe problems of water quality sensors and actuators placement in drinking water distribution systems (DWDSs) are addressed as separate, primarily. However, against the background of control systems theory, the nature of DWDSs dynamics indicates that these both problems are interdependent and impact the design of related water quality monitoring and control structures and algorithms. The research work presented in this paper is...
-
On noncausal weighted least squares identification of nonstationary stochastic systems
PublicationIn this paper, we consider the problem of noncausal identification of nonstationary, linear stochastic systems, i.e., identification based on prerecorded input/output data. We show how several competing weighted (windowed) least squares parameter smoothers, differing in memory settings, can be combined together to yield a better and more reliable smoothing algorithm. The resulting parallel estimation scheme automatically adjusts...
-
The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin 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...
-
Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough 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...
-
Adsorption onto zeolites: molecular perspective
Publication2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent...
-
Contribution to the mechanism of liquid membrane oscillators involving cationic surfactant.
PublicationIt is shown that liquid membrane oscillators with cationic surfactants havemore complex oscillation patterns than observed previously. The actual details of the oscillations depend strongly on the nature of the membrane material, dislosing even the presence of parallel molecular events. It appearsthat sampling topology also has a great influence on the observed oscillato-ry behaviour. Variation of oscillation patterns with...
-
Numerical modeling of quantum dynamical processes
PublicationIn this dissertation I present a high-precision (15, 18 or 33 decimal places) C++ implementation of quantum dynamics time propagation algorithms for both time-independent and time-dependent Hamiltonian with an inhomogeneous source term. Moreover I present an extension of both algorithms for time propagation to handle arbitrary number of coupled electronic levels. I have performed a careful validation of these implementations comparing...
-
Online sound restoration system for digital library applications.
PublicationAudio signal processing algorithms were introduced to the new online non-commercial service for audio restoration intended to enhance the content of digitized audio repositories. Missing or distorted audio samples are predicted using neural networks and a specific implementation of the Jannsen interpolation method based on the autoregressive model (AR) combined with the iterative restoring of missing signal samples. Since the distortion...
-
Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublicationExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
-
Tunable Dielectric Switching of (Quinuclidinium)[MnCl4] Hybrid Compounds
PublicationInorganic−organic hybrid QMnCl (Q = quinuclidinium) crystals were synthesized and characterized. The X-ray and variable-temperature IR/Raman analysis demonstrate that the crystals undergo a reversible structural phase transition, which originates from an order−disorder process and is related to the dynamics of the organic Q cation. Dielectric function measurements disclose a switchability between low (“OFF”) and high (“ON”) dielectric...
-
Improvements to the two-phase sandwich method for calculating the melting points of pure metals
PublicationThe thermophysical properties of metal alloys are often investigated via molecular dynamics (MD) simulations.An exact and reliable estimation of the thermophysical parameters from the MD data requires a properly and carefullyelaborated methodology. In this paper, an improved two-phase sandwich method for the determination of the metal meltingtemperature is proposed, based on the solid-liquid equilibrium theory. The new method was...
-
Massively parallel linear-scaling Hartree–Fock exchange and hybrid exchange–correlation functionals with plane wave basis set accuracy
PublicationWe extend our linear-scaling approach for the calculation of Hartree–Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem. Phys. 139, 214103 (2013)] to leverage massive parallelism. Our approach has been implemented in the ONETEP (Order-N Electronic Total Energy Package) density functional theory framework, which employs a basis of non-orthogonal generalized Wannier functions (NGWFs) to achieve...
-
The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
-
The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
-
Dissociative ionization dynamics of dielectric gas C3F7CN
PublicationFluoronitrile C3F7CN is a promising candidate for the replacement of SF6 dielectric gas in high-voltage insulation. We present a combined experimental and theoretical study on its ionization dynamics probed in the 0-100 eV energy range. We exploited the total ion collection technique to determine the absolute ionization cross section, mass spectrometry to determine the fragment branching ratios and ab initio nonadiabatic molecular...
-
Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublicationXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
-
Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublicationThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
-
Efficient synthesis and antifungal investigation of nucleosides’ quaternary ammonium salt derivatives
PublicationQuaternary ammonium salts are a group of compounds with diverse biological properties, the most important of which are their antiviral, antibacterial, and antifungal activities. The quaternization reactions of 5'-O-tosyl derivatives of uridine and thymidine with triethylamine, trimethylamine, 4-(N ,N -dimethylamino)pyridine, 2-methylpyridine, and pyridine are described in this article. Two of the synthesized compounds are exceptional...
-
DYNWIR S-70 program for modal analysis of multisupported and multimass rotors
PublicationThe article provides a brief description of the program Dynwir-S-70 (currently being developed in the Rotor Dynamics and Slide Bearings Department in the Institute of Fluid-Flow Machinery Polish Academy of Sciences in Gdansk) which is a program for analysis of multi-supported and multi-mass rotors. Used algorithms and the construction of mass and stiffness matrix were presented. Damping matrix structure based on Rayleigh damping...
-
Modeling two phase flow in large scale fractured porous media with an extended multiple interacting continua method
PublicationWe present a two phase flow conceptual model, the corresponding simulator (2pMINC) and a workflow for large-scale fractured reservoirs, based on a continuum fracture approach which uses the multiple interacting continua (MINC) method complemented with an improved upscaling technique. The complex transient behavior of the flow processes in fractured porous media is captured by subgridding the coarse blocks in nested volume elements...
-
In-depth characterization of icosahedral ordering in liquid copper
PublicationThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...
-
About Unusual Diffraction and Thermal Self-Action of Magnetosonic Beam
PublicationThe dynamics of slightly diverging two-dimensional beams whose direction forms a constant angle θ with the equilibrium straight magnetic strength is considered. The approximate dispersion relations and corresponding links which specify hydrodynamic perturbations in confined beams are derived. The study is dedicated to the diffraction of a magnetosonic beam and nonlinear thermal self-action of a beam in a thermoconducting gaseous plasma....
-
Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...