Wyniki wyszukiwania dla: COMPUTATIONAL CHEMISTRY
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JOURNAL OF COMPUTATIONAL CHEMISTRY
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REVIEWS IN COMPUTATIONAL CHEMISTRY
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Theoretical and Computational Chemistry
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The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry
Dane BadawczeThe developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic...
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5-Selenocyanato and 5-trifluoromethanesulfonyl derivatives of 2′-deoxyuridine: synthesis, radiation and computational chemistry as well as cytotoxicity
Publikacja5-Selenocyanato-2′-deoxyuridine (SeCNdU) and 5-trifluoromethanesulfonyl-2′-deoxyuridine (OTfdU) have been synthesized and their structures have been confirmed with NMR and MS methods. Both compounds undergo dissociative electron attachment (DEA) when irradiated with X-rays in an aqueous solution containing a hydroxyl radical scavenger. The DEA yield of SeCNdU significantly exceeds that of 5-bromo-2′-deoxyuridine (BrdU), remaining...
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JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
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Turkish Computational and Theoretical Chemistry
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Journal of Computational Biophysics and Chemistry
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COMPUTATIONAL BIOLOGY AND CHEMISTRY
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Computational and Theoretical Chemistry
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublikacjaGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublikacjaThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublikacjaThe 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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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublikacjaWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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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
PublikacjaA 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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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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An efficient molecular docking using conformational space annealing
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On the joint time-frequency characteristics of chemical oscillations
PublikacjaZaprezentowano rezultaty analizy czasowo-częstotliwościowej rejestrów potencjałowych oscylacyjnej reakcji Biełousowa-Żabotyńskiego (BŻ). Wybraną reprezentację czasowo-częstotliwościową w postaci algorytmu STFT zastosowano do analizy typowych przebiegów reakcji BŻ, prowadzonej w układzie zamkniętym. Zaprezentowano spektrogramy STFT ukazujące czasowo-częstotliwościową strukturę oscylacji regularnych, mieszanych i chaotycznych. Na...
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THE PERFORMANCE OF SELECTED AB INITIO METHODS IN ESTIMATING ELECTRON BINDING ENERGIES OF SUPERHALOGEN ANIONS
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MOLECULAR SIMULATIONS OF NEOCARZINOSTATIN CHROMOPHORE RELEASE MECHANISM
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublikacjaFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Theoretical studies of the dependence of nuclear quadrupole coupling constants on intermolecular forces
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Kinetic flux vector splitting scheme for solving non-reactive multi-component flows
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Ab initio studies of the structure, physicochemical properties and behavior of lead chlorides and chloroplumbate anions in gaseous and aqueous phases
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Journal of Applied and Computational Mechanics
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COMPUTATIONAL MATERIALS SCIENCE
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Journal of Computational Science
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PLoS Computational Biology
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JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
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Computational Economics
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COMPUTATIONAL STATISTICS
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Computational Linguistics
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COMPUTATIONAL COMPLEXITY
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Computational Toxicology
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Computational Methods in Science and Technology
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Journal of Computational and Theoretical Nanoscience
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Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study
PublikacjaThe present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4′-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the...
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Rengel Cane Sia Doctoral Candidate
OsobyI'm Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master's thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master's degree in Chemistry in the Mindanao...
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DISCRETE & COMPUTATIONAL GEOMETRY
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COMPUTATIONAL & APPLIED MATHEMATICS
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Journal of Computational Electronics
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Computational Intelligence and Neuroscience
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Journal of Computational Finance
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Journal of Computational Geometry
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Computational Particle Mechanics
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BIOINFO Computational Mathematics
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Computational Condensed Matter
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Advances in Computational Design
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Computational Management Science
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Advances in Computational Research
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Computational Thermal Sciences
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BIOINFO Computational Optimization
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Journal of Computational Linguistics
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Frontiers in Computational Neuroscience
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npj Computational Materials
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Computational Visual Media
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Computational Social Networks
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Applied and Computational Mechanics
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Journal of Computational Dynamics
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Computational Mathematics and Modeling
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Computational Brain and Behavior
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Computational and Mathematical Methods
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Computational and Mathematical Biophysics
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JOURNAL OF COMPUTATIONAL NEUROSCIENCE
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Mathematical and Computational Applications
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Computational Continuum Mechanics
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JOURNAL OF COMPUTATIONAL MATHEMATICS
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Applied and Computational Mathematics
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Journal of Computational Technologies
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Nature Computational Science
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Journal of Computational Geometry
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Advanced Potential Energy Surfaces for Molecular Simulation
PublikacjaAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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FOUNDATIONS OF COMPUTATIONAL MATHEMATICS
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COMPUTATIONAL MATHEMATICS AND MATHEMATICAL PHYSICS
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COMPUTATIONAL STATISTICS & DATA ANALYSIS
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Computational Methods and Function Theory
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Computational and Mathematical Organization Theory
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Journal of Algorithms & Computational Technology
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Journal of Theoretical and Computational Acoustics
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Computational Methods for Differential Equations
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Bulletin of Computational Applied Mathematics
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Journal of Computational Applied Mechanics
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Biomedical Engineering and Computational Biology
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IEEE Transactions on Computational Imaging
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Journal of Computational Simulation and Modeling
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Journal of Computational Design and Engineering
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European Journal of Computational Mechanics
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International Journal of Computational Biology
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EURO Journal on Computational Optimization
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Journal of Computational and Theoretical Transport
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Journal of Bioinformatics and Computational Biology
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Journal of Computational Multiphase Flows
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IEEE Computational Intelligence Magazine
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ACM Transactions on Computational Logic
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Journal of Computational Social Science
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JOURNAL OF COMPUTATIONAL ANALYSIS AND APPLICATIONS
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Transactions of the Association for Computational Linguistics
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Journal of Computational and Nonlinear Dynamics
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