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Search results for: QM/MM
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Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
PublicationThe thermally induced self-healing mechanisms in metallopolymers based on bisterpyridine complexes of iron(II) sulfate and cadmium(II) bromide, respectively, were studied by means of combined quantum mechanical/molecular mechanical (QM/MM) simulations and Raman spectroscopy. Two possible healing schemes, one based on a decomplexation of the cross-linking complexes and a second one relying on the dissociation of ionic clusters,...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Badania składu chemicznego materiału rury 323,90x12,70 mm
PublicationWykonano badania składu chemicznego materiału rury i dokonano oceny zgodności z atestem i normą.
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Raw data for the paper "Mutually polarizable QM/MM model with in situ optimized localized basis functions"
Open Research DataThis dataset contains raw data used to generate plots in the paper Mutually polarizable QM/MM model with in situ optimized localized basis functions. The paper is devoted to a second generation of the TINKTEP model -- an QM/MM approach combining linear-scaling DFT (ONETEP) and a polarizable force field (AMOEBA).
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On the design of planar high directivity proximity couplers in the mm-wave range
PublicationPrzedyskutowano problemy projektowania sprzęgaczy zbliżeniowych wykonywanych w technologii planarnej i przeznaczonych do pracy w zakresie fal milimetrowych. Zasadniczym celem badań było zaprojektowanie, wykonanie i przebadanie układu sprzęgacza o wysokiej kierunkowości i umiarkowanym poziomie sprzężenia pracującego w zakresie 40-50GHz. Przedyskutowano i zamodelowano różne konfiguracje sprzęgaczy. Stwierdzono, że znane zasady projektowania...
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Towards modelling of the environmental fate of pharmaceuticals using the QSPR-MM scheme
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Survivin expression in invasive pituitary gland adenomas with a diameter exceeding 20 mm
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Badania składu chemicznego i własności mechanicznych materiału rury fi 323,85x12,7 mm
PublicationWykonano badania składu chemicznego i właściwości mechanicznych materiału (stal nierdzewna typu 316L)
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Flow boiling of R1233zd(E) in a 3 mm vertical tube at moderate and high reduced pressures
PublicationThe results of flow boiling of R1233zd(E) in a 3 mm vertical stainless steel tube are presented at moderate and high saturation temperatures. Integral flow characteristics in the form of pressure drop and heat transfer coefficient are discussed for saturation temperatures ranging from 115 to 145 °C (corresponding reduced pressures from 0.2 to 0.7), mass velocity of 800 kg/m2s and heat flux of 20 kW/m2. All of the obtained heat...
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublicationPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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Design of mm-wave MIC frequency multiplayers and mixers using simple microstrip high-pass filters
PublicationPrzedyskutowano podstawowe wymagania dotyczące impedancji elementów półprzewodnikowych wykorzystywanych w mieszaczach i powielaczach częstotliwości projektowanych dla zakresu fal milimetrowych. Określono typy układów filtrujących niezbędnych w różnych częściach układów, podkreślając znaczenie filtrów górnoprzepustowych. Mikropaskowy filtr ze zwartym brzegiem został wykonany i zaimplementowany w mieszaczu pracującym w zakresie 20-40GHz.
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Ekspertyza przyczyn korozji złącza spawanego rury ze szwem 129x3,0 mm z instalacji flokulatora
PublicationCelem pracy było ustalenie przyczyn korozji złącza spawanego rury ze szwem 130x3,0 mm z instalacji flokulatora. Instalacja była wykonana ze stali nierdzewnej AISI 316L. Zakres pracy obejmował: wykonanie analizy EDX składu chemicznego spoiny oraz nalotów obecnych na rurociągu, wykonanie badań próbek metalograficznych wraz z określeniem mikrostruktury
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Rozkład naprężeń mechanicznych w łyżce o szerokości 500 mm, przeznaczonej do koparki podsiębiernej
PublicationW artykule zaprezentowano optymalizację kształtu łyżki koparki przedsiębiernej z wykorzystaniem analizy wytrzymałościowej. Analizę oparto na trójwymiarowym modelu konstrukcji łyżki z zastosowaniem metody elementów skończonych (MES). Opracowanie wspomnianej metody pozwoliło na modyfikację konstrukcji łyżki, która dała w efekcie obniżenie naprężeń złożonych w newralgicznych obszarach konstrukcji łyżki. Przedstawiona analiza okazała...
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Investigations on mixture preparation for two phase adiabatic pressure drop of R134a flowing in 5 mm diameter channel
PublicationThe article presents detailed two-phase adiabatic pressure drops data for refrigerant R134a. Study cases have been set for a mass flux varying from 200 to 400 kg/m2 s, at the saturation temperature of 19.4 ◦C. Obtained experimental data was compared with the available correlations from the literature for the frictional pressure drop during adiabatic flow. Influence of mixture preparation on pressure drop was investigated, for...
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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MM Science Journal
Journals -
Maryland medicine : MM : a publication of MEDCHI, the Maryland State Medical Society
Journals -
Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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SU‐GG‐T‐208: 3‐D Dosimetric Comparison of IMRT with 2.5 Mm HD120 MLC Using Optical CT Based Polymer Gel and PRESAGE Dosimeters
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 12 mm piston rod diameter and 25 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 20 mm piston rod diameter and 100 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 14 mm piston rod diameter and 500 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 25 mm piston rod diameter and 50 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 20 mm piston rod diameter and 200 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 25 mm piston rod diameter and 500 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 32 mm piston rod diameter and 25 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 20 mm piston rod diameter and 500 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 20 mm piston rod diameter and 50 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 20 mm piston rod diameter and 25 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 25 mm piston rod diameter and 200 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 25 mm piston rod diameter and 100 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 25 mm piston rod diameter and 200 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 12 mm piston rod diameter and 50 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 14 mm piston rod diameter and 25 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 32 mm piston rod diameter and 100 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 32 mm piston rod diameter and 500 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 14 mm piston rod diameter and 200 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 25 mm piston rod diameter and 25 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 25 mm piston rod diameter and 500 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 25 mm piston rod diameter and 50 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 12 mm piston rod diameter and 100 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 32 mm piston rod diameter and 50 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 14 mm piston rod diameter and 100 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 12 mm piston rod diameter and 500 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 100 mm piston diameter, 32 mm piston rod diameter and 200 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 63 mm piston diameter, 25 mm piston rod diameter and 100 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...
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Simulation of a linear pneumatic actuator with 32 mm piston diameter, 12 mm piston rod diameter and 200 mm stroke
Open Research DataThe aim of the simulation was to determine the dynamics of linear pneumatic actuators with different sizes and flow properties. The simulation used the actuator dynamics model as described in [1] and the St Venant - Wantzel's mass flow rate model. The simulation experiment was to calculate the pressure changes in both chambers of the actuator as well...