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Search results for: Classical MD
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Food Bioactive Ingredients Processing Using Membrane Distillation
PublicationSeparation processes are an important part of today’s food industries, especially in the case of specific bioactive components due to their health benefits. In general, processing of bioactive food ingredients assumes the introduction of integrated system directed to their separation, fractionation, and recovery. Recently, membrane distillation (MD) has been considered as an alternative membrane-based separation and concentration...
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Exemplaria classica (Formerly: Exemplaria. Revista Int. de Literat. Comparada 1138-1922)
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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Piotr Figura dr inż.
PeoplePiotr Figura is employed as an assistant professor at the Department of Finance at the Faculty of Management and Economics, Gdansk University of Technology. He is a member of Commission for the Verification of Learning Outcomes, as well as an academic reviewer of the Central Exemination Booard. He is the author or co-author of several scientific monographs including: Standard financial indicators for stock enterprises; Classical...
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Teleportation seen from spacetime: on 2-spinor aspects of quantum information processing
PublicationZastosowanie formalizmu 2-spinowego do kwantowego przetwarzania informacji zilustrowane przykładem teleportacji i relatywistycznej korelacji błędu.
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The role of low-energy electrons in the charging process of LISA test masses
PublicationThe estimate of the total electron yield is fundamental for our understanding of the test-mass charging associated with cosmic rays in the Laser Interferometer Space Antenna (LISA) Pathfinder mission and in the forthcoming gravitational wave observatory LISA. To unveil the role of low energy electrons in this process owing to galactic and solar energetic particle events, in this work we study the interaction of keV and sub-keV...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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"Car-Parrinello molecular dynamics" jako kluczowe narzędzie informatyczne w badaniach syntezy cienkich warstw diamentowych metodą PA CVD
PublicationPraca omawia zastosowanie metody Car-Parrinello MD w symulacji procesu wzrostu cienkich warstw diamentowych w metodzie PAC VD.
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Materials Science -- Classical Particle Approach (2022)
e-Learning CoursesThis is the course webpage for Materials Science -- Classical Particle Approach.
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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...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Francesco Fedele M.D.
PeopleFrancesco Fedele is a Medical Resident in Obstetrics and Gynaecology at San Raffaele Hospital in Milan, Italy. Previously, he held the same position at Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico in Milan. He received his surgical training at Azienda Ospedaliera Universitaria Integrata in Verona, Italy from 2022 to 2024.He graduated with honors from the 6-year International MD Program Degree in Medicine and Surgery...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Efficient Recovery of Noble Metal Ions (Pd2+, Ag+, Pt2+, and Au3+) from Aqueous Solutions Using N,N'-Bis(salicylidene)ethylenediamine (Salen) as an Extractant (Classic Solvent Extraction) and Carrier (Polymer Membranes)
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Sensorless Rotor Position Estimation of Doubly-Fed Induction Generator Based on Backstepping Technique
PublicationThis paper proposes a speed observer algorithm for the sensorless control of a doubly-fed induction generator based on classical adaptive backstepping technique. The sensorless control is shown using classic stator field oriented control which is used to active and reactive power control. Performance of the proposed algorithm of a speed observer is validated by simulation and experimental results obtained using a small-rating generator...
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Jarosław Chojnacki prof. dr hab. inż.
PeopleBorn in 1961 in Bydgoszcz, professional education started at the Chemical Technical Highschool (I. Łukasiewicz). He graduated from the Faculty of Chemistry at the Gdańsk University of Technology in 1986, defending the work on ion-selective electrodes. Subsequent studies were related to organic and siliconorganic synthesis and, from 2002 year on, to crystallography. The doctoral thesis concerned the Silanotiolanes of coinage metals...
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Bounds on the cover time of parallel rotor walks
PublicationThe rotor-router mechanism was introduced as a deterministic alternative to the random walk in undirected graphs. In this model, a set of k identical walkers is deployed in parallel, starting from a chosen subset of nodes, and moving around the graph in synchronous steps. During the process, each node successively propagates walkers visiting it along its outgoing arcs in round-robin fashion, according to a fixed ordering. We consider...
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Materials Science - classical particle approach 2023/2024
e-Learning CoursesComputer modeling and design of materials, kierunek: Nanotechnologia, specjalność: Mathematics for new materials design, II stopień, semestr 3
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Bounds on the Cover Time of Parallel Rotor Walks
PublicationThe rotor-router mechanism was introduced as a deterministic alternative to the random walk in undirected graphs. In this model, a set of k identical walkers is deployed in parallel, starting from a chosen subset of nodes, and moving around the graph in synchronous steps. During the process, each node maintains a cyclic ordering of its outgoing arcs, and successively propagates walkers which visit it along its outgoing arcs in...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Database of the estimations of the numbers of simplices of triangulation of some classical Lie groups
Open Research DataIt is know that any smooth manifold can be triangulated. The number of simplices of triangulation of a given manifold depends on its topological and combinatorial structure. The data consists of the lower bounds for the numbers of simplices of each dimension of any triangulation of classical Lie groups U(n), SU(n), Sp(n), and SO(n) for n up to 25. Each...
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Md Khalid
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Characterization of PVDF/Graphene Nanocomposite Membranes for Water Desalination with Enhanced Antifungal Activity
PublicationSeawater desalination is a worldwide concern for the sustainable production of drinking water. In this regard, membrane distillation (MD) has shown the potential for effective brine treatment. However, the lack of appropriate MD membranes limits its industrial expansion since they experience fouling and wetting issues. Therefore, hydrophobic membranes are promising candidates to successfully deal with such phenomena that are typical...
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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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2,6-Bis((benzoyl-R)amino)pyridine (R = H, 4-Me, and 4-NMe2) Derivatives for the Removal of Cu(II), Ni(II), Co(II), and Zn(II) Ions from Aqueous Solutions in Classic Solvent Extraction and a Membrane Extraction
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Jan Kozicki dr hab. inż. arch.
PeopleIn year 2002 after obtaining master's degree in construction was employed on Faculty of Civil and Environmental Engineering. In 2004 obtained master's degree in architecture on Faculty of Architecture focusing on a research outpost on Mars. Defended PhD in year 2007 in the field of numerical modeling. In 2013 obtained Licentiate degree in theoretical physics on University of Gdańsk. In year 2014 obtained habilitation in technical...
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [11010630088555281]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [3300730069453161]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [1101063008855121]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 46 - Tissue image [11010630088559391]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088557301]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [11010630088551441]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088552681]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [11010630088558961]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [11010630088555091]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 46 - Tissue image [11010630088556111]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 46 - Tissue image [11010630088552741]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 46 - Tissue image [1101063008855631]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088556511]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088551701]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [11010630088553711]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 52 - Tissue image [11010630088554471]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 46 - Tissue image [11010630088554301]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088554561]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088552601]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 46 - Tissue image [11010630088554631]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088557861]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Classical Hodgkin lymphoma, lymphocyte-rich - Male, 65 - Tissue image [11010630088555261]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.