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Search results for: QM/MM FREE ENERGY SIMULATIONS
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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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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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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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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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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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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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The assessment of metrological properties of segmental orifice based on simulations and experiments
PublicationSegmental orifices are often used to measure flows of heterogeneous mixtures, especially in flow meters in the power industry, for example. The orifice (with module m= 0.25) was installed in a stainless-steel pipe with internal diameter of 50 mm, placed in a hydraulic water system. The research was performed for Reynolds numbers ranging from 9,000 to 17,000. The flow characteristics of this orifice obtained based on simulation...
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The reductivity of the transition metals - calculations
Open Research DataThe dataset includes the reduction enthalpy and Gibbs energy simulated for Co, Cu, Fe, La, Mo, Ni, Sr, Ti, and W from oxide form into metallic form in hydrogen. Simulations were performed using HSC Chemistry software.
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced 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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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Simulations of wave propagation and attenuation in fields of colliding ice floes
Open Research DataThis dataset contains results of numerical smulations of sea ice-wave interactions, corresponding to laboratory experiments conducted at the Large Ice Model Basin (LIMB) at the Hamburg Ship Model Basin (HSVA) as part of the LS-WICE ("Loads on Structure and Waves in Ice"; https://zenodo.org/record/1067170#.XrLt_dhpxhE) project. THe simulations were conducted...
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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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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Ocean mixed layer dynamics: high-resolution simulations of wind, wave and convective effects
Open Research DataThis dataset contains results of high-resolution numerical simulations of the ocean mixed layer (OML) forced by wind, waves and cooling from the atmosphere, i.e., under strongly turbulent, convective conditions. The goal is to provide detailed, three-dimensional information about OML circulation, turbulent kinetic energy, and temperature and salinity...
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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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Simulations of flows in the coastal zone of the Baltic Sea
Open Research DataThe study area is located in the Southern Baltic, within Polish Marine Areas, adjacent to the coastline in the vicinity of Lubiatowo village, where The Coastal Research Station (CRS) – a field laboratory of the Institute of Hydro-Engineering of the Polish Academy of Sciences (IBW PAN) –is situated. The numerical reconstruction of the coastal flow was...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublicationThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Garnizon district in Gdansk, Poland
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma analysis / BedZED, London
Open Research DataThe data presents the results of work on the analysis of contemporary neighbourhoods. The aim of this part of the research was to analysis housing estates already existed in various cities in Europe. The analyses ware done in real time with AI and powered for key factors such as sun hours, daylight potential, noise, wind, and microclimate. These data...
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Seestadt Aspern, Vienna, Austria
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma (formerly Spacemaker) / Battersea Power Station Development, London
Open Research DataThe data presents the results of work on the analysis of contemporary neighbourhoods. The aim of this part of the research was to analysis housing estates already existed in various cities in Europe. The analyses ware done in real time with AI and powered for key factors such as sun hours, daylight potential, noise, wind, and microclimate. These data...
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Case Study NEB Atlas / part II - Autodesk Forma analysis / ZAC de Bonne, Grenoble, France
Open Research DataThe data presents the results of work on the analysis of contemporary neighbourhoods. The aim of this part of the research was to analysis housing estates already existed in various cities in Europe. The analyses ware done in real time with AI and powered for key factors such as sun hours, daylight potential, noise, wind, and microclimate. These data...
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Brunnshög district in Lund, Sweden
Open Research DataThe data presents the results of work on the analysis of contemporary neighbourhoods. The aim of this part of the research was to analysis housing estates already existed in various cities in Europe. The analyses ware done in real time with AI and powered for key factors such as sun hours, daylight potential, noise, wind, and microclimate. These data...
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Västra Hamnen, Malmö, Sweden.
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Hammarby-Sjöstad, Stockholm, Sweden.
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Pilestredet Park, Oslo, Norway.
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma analysis / King’s Cross, London, UK.
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma analysis / Oceanhamnen, Helsingborg, Sweden
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Case Study NEB Atlas / part II - Autodesk Forma analysis / La Courrouze district in Rennes, France
Open Research DataThe data present the results of the work on the analysis of modern settlements. The goal of this part of the research was to analyze housing estates already in place in various European cities. Analyses were performed in real time using artificial intelligence, and responses were searched for sun hours, daylight potential, noise, wind, and microclimate....
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Towards improved energy efficiency of future smart ships by application of advanced CFD simulations – case study
PublicationThe international trade plays crucial role in today’s globally developed world’s economy. Many people are unaware of the unimaginable volume of cargo being transported every year by oceans and seas. For most of the time invisible from land the shipping industry preserves its strong position of the most cost-efficient and environmental friendly mean of transport. However during last years the shipping industry is under great pressure...
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The laws of thermodynamics: entropy, free energy, information and complexity
PublicationW rozdziale przedstawiono podstawowe Zasady Termodynamiki. Omówiono zagadnienia związane z pojęciem entropii, energii Gibbsa, egzergii oraz systemami złożonymi.
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The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublicationPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublicationAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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Förster Resonance Energy Transfer and Trapping in Selected Systems: Analysis by Monte-Carlo Simulations
PublicationMetoda symulacji Monte Carlo została opisana i zastosowana jako efektywne narzędzie do analizy wyników pomiarów transferu energii w wybranych układach, dla których zastosowanie podejścia analitycznego jest ograniczone lub nawet niemożliwe. Pokazano, że symulacja Monte Carlo pozwala obliczyć tzw. czynnik orientacyjny dla układów częściowo uporządkowanych oraz szereg innych wielkości ważnych do opisu zjawiska transferu energii, które...
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<title>Cavity control system advanced modeling and simulations for TESLA linear accelerator and free electron laser</title>
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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins
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Evaluation the environmental fate of pharmaceuticals using a level III model based on poly-parameter linear free energy relationships
PublicationOpisano możliwości zastosowania modelu ''Level III Model'' do opisu losu środowiskowego pozostałości farmaceutyków w środowisku. Zastosowany model umożliwia oszacowanie trwałości, stężeń oraz transportu poszczególnych zanieczyszczeń pomiędzy poszczególnymi elementami składowymi środowiska (powietrze, woda, gleba i osady denne).
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Hybrid Monte-Carlo simulations of fluorescence anisotropy decay in disordered two-component systems in the presence of forward and back energy transfer
PublicationW pracy przedstawiono hybrydowy algorytm symulacji Monte Carlo zaniku anizotropii emisji fluorescencji w układach dwuskładnikowych z uwzględnieniem prostego i powrotnego transferu energii. Poprawność nowego algorytmu symulacji Monte Carlo zweryfikowano poprzez porównanie z wynikami obliczeń teoretycznych otrzymanymi w ramach modelu SCDM i z wynikami standardowej symulacji Monte Carlo (algorytm 'step by step').
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Hybrid Monte-Carlo simulations of fluorescence anisotropy decayin three-component donor-mediator-acceptor systems in the presenceof energy transfer
PublicationW pracy przedstawiono nowy hybrydowy algorytm symulacji Monte-Carlo układu trójskładnikowego donor-mediator-akceptor. Działanie algorytmu zilustrowano na przykładzie zaników anizotropii emisji fluorescencji powyższego układu. Porównano wyniki hybrydowej symulacji Monte-Carlo z wynikami klasycznej metody ''step by step''. Stwierdzono bardzo dobrą zgodność wyników obu symulacji, przy czym algorytm hybrydowy wymaga znacznie krótszego...
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Maximum transportation growth in energy and solute particles in Prandtl martial across a vertical 3D-heated surface: Simulations achieved using by finite element approach
PublicationThe goal of this study is to determine the maximum energy and solute particles' transportation growth in a 3D-heated region of Prandtl martial through a dynamic magnetic field. The effects of this field on the properties of solvent molecules and heat conduction are studied. A correctly stated functional method and a finite element approach are comparable to a certain type of differential equations. In order demonstrate the effects...
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Ewa Klugmann-Radziemska prof. dr hab.
PeopleEwa Klugmann-Radziemska graduated from the University of Gdansk with a degree in physics, and since 1996 has been associated with the Gdansk University of Technology, when she began PhD studies. Currently, he is a professor at the Faculty of Chemistry at the Gdansk University of Technology, since 2006 head of the Department of Chemical Apparatus and Machinery. In the years 2008–2016 she was the Vice-Dean for cooperation and development,...
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Michał Ryms dr hab. inż.
PeopleMichał Ryms, PhD, DSc, Eng. is the physicist, graduate of the Gdańsk University of Technology. PhD thesis defended at the Chemical Faculty. Since 2011 an employee at the Department of Energy Conversion and Storage, Chemical Faculty, Gdansk University of Technology, POLAND – now as an associate professor. His research interests includes: improvement of energy efficiency and possibilities of new application of phase change materials...
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Robert Bogdanowicz dr hab. inż.
PeopleRobert Bogdanowicz received his Ph.D. degree with honours in Electronics from the Gdansk University of Technology. He worked as a post-doc researcher in Ernst-Moritz-Arndt-Universität Greifswald Institut für Physik. He has initiated optical emission imaging of muti-magnetron pulsed plasma and contributed to the development of antibacterial implant coatings deposited by high-power impulse magnetron sputtering. He moved back to...
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Stability and phase transition investigation of olanzapine polymorphs
PublicationWe use electrical embedded-fragment QM method with both DFT/ωB97XD/6-31G* and MP2/6-31G* to investigate the phase transformations of olanzapine. Gibbs free energy calculations predict that form I is always the most stable structure and form II is the least stable one, while form IV is more stable than form III below about 200 K but less stable above this temperature, implying a polymorphic phase transformation. This may account...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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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....