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Search results for: MOLECULAR DYNAMICS METHOD
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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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...
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Water Behavior Near the Lipid Bilayer
PublicationIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
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Entropy of water calculated from harmonic approximation: estimation of the accuracy of method
PublicationSome molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm(3)) and within the temperature range of 5-90 degrees C. By using harmonic approximation, both the entropy of water S-H and the specific heat c(v) were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (similar...
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Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublicationCysteine–water cluster cations Cys(H2O)3,6 + and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collisioninduced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies...
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A novel hierarchically-porous diamondized polyacrylonitrile sponge-like electrodes for acetaminophen electrochemical detection
PublicationA novel composite electrode material consisting of tangled fibrous polyacrylonitrile-based hierarchically-struc- tured nanocomposites has been produced by wet-spinning, carbonized and decorated with a carbon nano- architecture by microwave plasma-enhanced chemical vapor deposition and investigated as a metal-free electrode for the enhanced electrochemical detection of acetaminophen. Surprisingly, the hierarchical fiber ar- chitecture...
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Why is TASK Quarterly a Significant Journal to Publish Your Article? —A Bibliometric Analysis of a Scientific and Technical Journal
PublicationA bibliometric analysis of TASK Quarterly in the years 1997-2021 in terms of various bibliometric indicators was performed to celebrate the 25th anniversary of the publication of the first issue of the journal. The number of publications and citations increased over the mentioned span of years. The leading countries in terms of the greatest number of papers published in TASK Quarterly are Poland, Italy, Germany, Ukraine, USA and...
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Refined theoretical study of radiative association: Cross sections and rate constants for the formation of SiN
PublicationRadiative association of silicon mononitride (SiN) in its two lowest molecular electronic states is studied through quantum and classical dynamics. Special attention is paid to the behavior of the cross section at high collision energies. A modified expression for the semiclassical cross section is presented which excludes transitions to continuum states. This gives improved agreement with quantum mechanical perturbation theory...
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublicationThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....
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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublicationThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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A BODIPY‐Based Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐Resolved Emission and Transient Absorption Spectroscopy
PublicationBODIPY and BODIPY-derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization-resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY-cholesterol derivative in homogeneous...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublicationAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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A new open-source software developed for numerical simulations usingdiscrete modeling methods
PublicationThe purpose of this work is to present the development of an open-source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [F. Donzé, S.A. Magnier, Formulation of a three-dimensional numerical model of brittle behavior, Geophys....
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Nonlocal Models of Plates and Shells with Applications in Micro- and Nanomechanics
PublicationNowadays, the use of small-scale structures in micro/nanomachines has become more and more widespread. The most important applications of such small-sized parts are in micro-electro-mechanical systems (MEMS) as well as nano-electro-mechanical systems (NEMS) as actuators, sensors, energy harvesters. For example, nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and...
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Genotyping Techniques for Determining the Diversity of Microorganisms
PublicationTyping of microbial pathogens, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. The part...
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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Mixed, quantum-classical description of electron density transfer in the collision process
PublicationIn this work, we investigate an ion-atom model describing the time-dependent evolution of electron density during the collision. For a S3+- H system, numerical simulations are based on classical trajectory calculations, and the electron density behaviour is described with the time-dependent Schrödinger equation. We apply the finite difference method to obtain quantitative insights into the charge transfer dynamics, providing detailed...
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Wybrane elementy nieliniowej dynamiki struktur kratowych
PublicationW pracy jest dyskutowany problem nieliniowej dynamiki struktur kratowych. Zastosowano stacjonarny opis Lagrange'a (ang. Total Lagrange), pokazano silne i słabe sformułowanie dla pręta kratowego, jego aplikację do MES. W zakresie całkowania równań ruchu przedstawiono metodę Newmarka i metodę-a dla problemów liniowych i nieliniowych. Załączony przykład numeryczny ilustruje cechy przedstawionych metod.
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Niebezpieczeństwo ukryte w żywności-aminy biogenne. Cz. II. Metody oznaczania i wyzwania.
PublicationZe względu na aktywność biologiczną amin biogennych ich oznaczanie zarówno jakościowe, jak i ilościowe w żywności ma istotne znaczenie w celu zapewnienia ochrony zdrowia i życia ludzkiego. Obecnie do monitoringu amin biogennych w żywności najczęściej wykorzystuje się: wysokosprawną chromatografię cieczową (HPLC), chromatografię cienkowarstwową (TLC) oraz absorpcyjną spektrofotometrię cząsteczkową. Są to jednak techniki czasochłonne,...
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Efektywna metoda wyznaczania trasy statków żaglowych
PublicationZaproponowano metodę wyznaczania suboptymalnej trasy statków żaglowych poruszających się w ograniczonym akwenie morskim. Uwzględniono przy tym dynamikę tego środowiska w tym warunki pogodowe oraz charakterystyki prędkościowe statków żaglowych. Jako kryterium optymalizacji przyjęto czas żeglugi T oraz liczbę wykonanych manewrów ω. Zaprojektowano heurystyczny algorytm oraz odpowiednią aplikację wyznaczania trasy dla ustalonych punktów...
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ANALIZA CECH HYDRO-AERODYNAMICZNYCH BEZZAŁOGOWEGO POJAZDU NAWODNO-POWIETRZNEGO Z WYKORZYSTANIEM EFEKTU PRZYPOWIERZCHNIOWEGO
PublicationW artykule przedstawiono problematykę badań dotyczących opracowania demonstratora technologii bezzałogowego pojazdu nawodno-powietrznego z wykorzystaniem efektu przypowierzchniowego. Opisano podstawowe problemy badawcze związane z analizą cech hydro-aerodynamicznych pojazdu. Opisano przedmiot badań, bezzałogowy pojazd nawodno-powietrzny typu USV-UAV-WIG. Opisano metodę badań. Przeprowadzono wstępną analizę osiągów i zachowania...
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Wykorzystanie algorytmów ewolucyjnych do doboru wzmocnień rozszerzonego obserwatora prędkości maszyny indukcyjnej
PublicationW pracy opisano sposób doboru wzmocnień rozszerzonego obserwatora prędkości maszyny indukcyjnej przy wykorzystaniu algorytmów ewolucyjnych. Zaproponowano funkcję celu opartą na rozkładzie biegunów obserwatora. Ze względu na wpływ prędkości maszyny na dynamikę obserwatora zaproponowano dobór wzmocnień obserwatora dla różnych przedziałów prędkości. Dla poszczególnych przedziałów zaprezentowano wyniki doboru wzmocnień w postaci tabel...
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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Analiza drgań kładki kompozytowej wywołanych działaniem wiatru
PublicationW pracy omówiono sposób przeprowadzenia uproszczonej, numerycznej analizy drgań kładki kompozytowej wywołanych działaniem wiatru. Rozważaniom poddano swobodnie podpartą konstrukcję o rozpiętości 16 m i przekroju w kształcie litery U. W pierwszej kolejności przeprowadzono dwuwymiarową analizę opływu niepodatnego kształtu przekroju kładki w poziomym strumieniu wiatru o prędkości 10 m/s. Obliczenia numeryczne przeprowadzono programem...
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Directed pulse dynamics
PublicationIntroducing a projection method into a one-dimensional model of a pulse propagation in isotropic media, we derive and investigate a system of equation describing dynamics ultrashort pulses of opposite directions ofpropagation and ones with interaction of directed pulses with different polarization.
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Biowodór, „paliwo przyszłości”, dotychczasowe metody otrzymywania , porównanie metod otrzymywania
PublicationWodór jest ważnym pierwiastkiem w przemyśle chemicznym. Biowodór wydaje się być użytecznym odnawialnym nośnikiem energii, który mógłby zastąpić paliwa kopalne. Największym problemem wodoru jest jego rzadkie występowanie w czystej formie molekularnej H 2 . Dlatego otrzymanie biowodoru w objętościach opłacalnych ja ko surowiec czy biopaliwo wiedzie przez bioodpady „przesycone” wodorem. Każdy związek...
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Synteza, struktura chemiczna i właściwości bezizocyjanianowych poliuretanów otrzymywanych z wykorzystaniem CO2 oraz surowców pochodzenia naturalnego.
PublicationZ uwagi na wciąż rosnącą świadomość proekologiczną, politykę zrównoważonego rozwoju, a także nurt zielonej chemii wiodącym trendem w przemyśle tworzyw sztucznych jest poszukiwanie alternatywnych metod otrzymywania materiałów polimerowych. Komercyjnie poliuretany otrzymywane są w wyniku reakcji poliaddycji di- lub poliizocyjanianów z poliolami i małocząsteczkowymi przedłużaczami łańcucha. Z uwagi na niekorzystne właściwości diizocyjanianów,...
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Możliwości zastosowań, potencjalne źródła oraz ewolucja technologiczna sposobu otrzymywania trehalozy ze szczególnym uwzględnieniem enzymu syntazy trehalozy [EC 5.4.99.16]
PublicationJedna z wiodących gałęzi współczesnej biotechnologii opiera się na produkcji białek – przede wszystkim enzymów. Są one powszechnie wykorzystywane: od przemysłu chemicznego poprzez przemysł spożywczy aż po medycynę i życie codzienne (czy ktoś wyobraża sobie w dzisiejszych czasach proszek do prania „bez enzymu”). Przed rozwojem nowoczesnych metod biologii molekularnej i inżynierii genetycznej pozyskiwano interesujące substancje z...
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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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Dynamics of quantum entanglement
PublicationA model of discrete dynamics of entanglement of a bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied by an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of subsystems. For some mixed states...
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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...
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Investigation of the laser generated ablation plasma plume dynamics and plasma plume sound wave dynamics
PublicationWe investigated the dynamics of laser generated ablation plasma plume expanding in ambient air and dynamics of the sound wave generated by the expanding plasma. The ablation plasma plume was generated during nanosecond laser micromachining of the thin metal foil. The time-resolved images of the expanding plasma plume and sound wave were captured at several nanosecond intervals. Using captured images the expansion rate of the plasma...
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Dynamics of Ice Jam Formation and Release
PublicationThe numerical model DynaRICE and its application to ice jam formation and release is presented. The model is a two-dimensional coupled flow and ice dynamic model. The ice dynamic component, which includes both the internal ice resistance and boundary friction on ice motion, uses a Lagrangian SPH method. The hydrodynamic component of the model uses a streamline upwind finite element method, which is capable of simulating trans-critical...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Analiza właściwości rozszerzonego obserwatora prędkości maszyny indukcyjnej
PublicationRozszerzony obserwator prędkości został zaproponowany przez prof. Krzemińskiego i jest oparty na rozszerzonym modelu maszyny indukcyjnej, gdzie wprowadzona został nowa zmienna ζ. Jest to nowe podejście do estymacji zmiennych stanu maszyny indukcyjnej i nie wszystkie problemy zostały do tej pory rozwiązane. Zaproponowano wykorzystanie algorytmów ewolucyjnych do doboru wzmocnień obserwatora. W celu redukcji nakładów obliczeniowych...
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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...
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Ocena wpływu dawki DME na wybrane wskaźniki procesu spalania w dwupaliwowym silniku o zapłonie samoczynnym
PublicationPrzedmiotem rozprawy jest analiza wpływu różnej ilości odparowanego DME wprowadzonego do kolektora dolotowego na wybrane wskaźniki spalania DME/ON dla wielu punktów pracy, turbodoładowanego silnika o zapłonie samoczynnym. Jako punkty pracy silnika, wybrano punkty najbardziej reprezentujące cykl jazdy WLTP dla samochodu Volkswagen Golf IV. Analizę procesu współspalania przeprowadzono z wykorzystaniem danych pomiarowych, uzyskanych...
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Numerical solution of threshold problems in epidemics and population dynamics
PublicationA new algorithm is proposed for the numerical solution of threshold problems in epidemics and population dynamics. These problems are modeled by the delay-differential equations, where the delay function is unknown and has to be determined from the threshold conditions. The new algorithm is based on embedded pair of continuous Runge–Kutta method of order p = 4 and discrete Runge–Kutta method of order q = 3 which is used for the...
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Modelling of planar movement dynamics of upper limb
PublicationThe original model describing planar movement dynamics of upper limb is presented. The upper limb is modelled as two-joints system loaded by external forces and internal forces of striated skeletal muscles. A behaviour of each muscle is modelled as a system composed of serially linked rheologic fragments that have different mechanical properties. These muscle models allow us to simulate a behaviour of short fusiform muscle (3DOF...
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Lattice dynamics of Mg2SiO4
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On dynamics of origami-inspired rod
PublicationWe discuss the dynamics of a relatively simple origami-inspired structure considering discrete and continuum models. The latter was derived as a certain limit of the discrete model. Here we analyze small in-plane deformations and related equations of infinitesimal motions. For both models, dispersion relations were derived and compared. The comparison of the dispersion relations showed that the continuum model can capture the behavior...
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Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp: Phosphorus dynamics
PublicationThis is the third paper of the series about “Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp”. In this paper, phosphorus dynamics were investigated under the condition of culturing bighead carp and common carp with added fish food (nitrogen dynamics is discussed in the second paper because their behaviors are so different from each other). Nearly fifty days’ observation results...
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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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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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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Roadmap on dynamics of molecules and clusters in the gas phase
PublicationThis roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty orders of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity...
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Periodic and chaotic dynamics in a map‐based neuron model
PublicationMap-based neuron models are an important tool in modeling neural dynamics and sometimes can be considered as an alternative to usually computationally costlier models based on continuous or hybrid dynamical systems. However, due to their discrete nature, rigorous mathematical analysis might be challenging. We study a discrete model of neuronal dynamics introduced by Chialvo in 1995. In particular, we show that its reduced one-dimensional...