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Search results for: Molecular dynamics simulations
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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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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublicationACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
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Degradation of a nano-cutting tool: an MD simulation
PublicationW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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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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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Laser-Induced Graphitization of Polydopamine on Titania Nanotubes
PublicationSince the discovery of laser-induced graphite/graphene, there has been a notable surge of scientific interest in advancing diverse methodologies for their synthesis and applications. This study focuses on the utilization of a pulsed Nd:YAG laser to achieve graphitization of polydopamine (PDA) deposited on the surface of titania nanotubes. The partial graphitization is corroborated through Raman and XPS spectroscopies and supported...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublicationTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublicationUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...
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A novel one-variable first-order shear deformation theory for biaxial buckling of a size-dependent plate based on Eringen’s nonlocal differential law
PublicationPurpose – This paper aims to present a new one-variable first-order shear deformation theory (OVFSDT) using nonlocal elasticity concepts for buckling of graphene sheets. Design/methodology/approach – The FSDT had errors in its assumptions owing to the assumption of constant shear stress distribution along the thickness of the plate, even though by using the shear correction factor (SCF), it has been slightly corrected, the errors...
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Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response
PublicationSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and...
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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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Energy landscape and structural transformations of C38 penta-fullerene: The stabilizing role of octagons and insights into penta-octa-penta-fullerene
PublicationTheoretical investigations were conducted to study the stability and energy landscape of C38 penta-fullerene, a structure comprising six penta-graphene unit cells. Vibrational analysis at the B3LYP/def2SVP level revealed 18 negative frequencies, indicating the dynamic instability of penta-fullerene. Analyzing the energy profiles for these vibrational modes led to the identification of six energetically favourable isomers, featuring...
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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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Optimization of the femtosecond laser impulse for excitation and the spin-orbit-mediated dissociation in the NaRb molecule
Open Research DataHigh accuracy ab initio potential energy curves (1tSigma+, 2sSigma+, 1tPi), electronic transition dipole moment function (1tSigma+ - 1tPi), and spin-orbit coupling (2sSigma+ - 1tPi) have been calculated for the NaRb molecule. The time-dependent excitation and dissociation processes in the polar alkali diatomic NaRb molecule and the quantum properties...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublicationRadiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This...
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Triplet–Triplet Annihilation Upconverting Liposomes: Mechanistic Insights into the Role of Membranes in Two-Dimensional TTA-UC
PublicationTriplet−triplet annihilation upconversion (TTA-UC) implemented in nanoparticle assemblies is of emerging interest in biomedical applications, including in drug delivery and imaging. As it is a bimolecular process, ensuring sufficient mobility of the sensitizer and annihilator to facilitate effective collision in the nanoparticle is key. Liposomes can provide the benefits of two-dimensional confinement and condensed concentration...
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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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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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[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....
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Monte Carlo simulations
e-Learning CoursesVirtual platform for the project "Monte Carlo simulations of energetic electrons and positrons in condensed matter".
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WRF-METEOPG: numerical weather forecast data for Poland - Days 218-224, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 239-245, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 225-231, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 267-273, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 281-287, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 295-301, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 211-217, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 302-308, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 253-259, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 274-280, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 246-252, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 288-294, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 260-266, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 232-238, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 204-210, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 1-7, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 71-77, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 36-42, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 57-63, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 78-84, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 85-91, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...
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WRF-METEOPG: numerical weather forecast data for Poland - Days 8-14, Year 2021
Open Research DataWRF-METEOPG is a numerical weather forecast system developed at the Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Poland. The system was built on the basis of the Weather Research and Forecast model version 4.2 and implemented at Centre of Informatics Tricity Academic Supercomputer & Network. Physics parametrization...