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Search results for: EMRE,MOLECULAR DYNAMICS, TPP+, METPP+, MBTPP+
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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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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublicationAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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Arginine-, d-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies
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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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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
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Toward mechanosynthesis of diamondoid sructures: viii. quantum-chemical molecular dynamics simulations of hexagonal silicon-iv structure synthesis with stm
Publicationw tej publikacji badano metodami kwantowo-chemicznymi różne strategie mechanosyntezy heksagonalnego krzemu iv. określono przybliżone warunki mechanosyntezy krzemu w formie lonsdaleitu za pomocą uhv-spm.
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Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublicationW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
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Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors—molecular dynamics study of the activated receptor–vasopressin–Gα systems
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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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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Preferential solvation in (amide+alcohol) binary mixtures. Part 2. The N-methylpyrrolidinone+methanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez metanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 1. The N- methylpyrrolidinone+ethanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez etanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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Study of New Oxytocin Antagonist Barusiban (Fe200 440) Affinity Toward Human Oxytocin Receptor Versus Vasopressin V1a and V2 Receptors - Molecular Dynamics Simulation in POPC Bilayer
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Toward Mechanosynthesis of Diamondoid Structures: VI. Quantum-Chemical Molecular Dynamics Comparison of Conditions for the STM Tip Driven Mechanosynthesis on Hydrogenated Si(111), Si(110) and Si(100) Surfaces.
Publicationmożliwość prototypowania przejściowych generacji nano-urządzeń otrzymanych drogą pozycjonowanej mechanosyntezy za pomocą stm wyposażonego w ostrze typu swcnt są analizowane metodą kwantowo-chemicznej dynamiki molekularnej. proponowana strategia syntezy polega na insercji atomów si oraz cząsteczek sih2 we wiązania si-h na uwodornionej powierzchni si(111), si(110) oraz si(100) kryształu krzemu. rezultaty modelowania sugerują, że...
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Katarzyna Merkel dr hab.
PeopleOver the past 15 years, my work has mainly been related to the study of liquid crystal compounds with a diverse structure (discotic, dendrimeric, banana, bimedogenic, uniaxial and biaxial nematics and smectics) as well as polymeric materials (biopolymers, nano-composites) and biological materials. My work concerned mainly the issues of organization, observation of orientation effects, studying the dynamics of molecular processes...
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Kazi Amirul Hossain
PeopleI am a PhD graduate from Gdańsk University of Technology and currently a postdoctoral researcher at IRB Barcelona (Prof. Modesto Orozco lab). My academic focus is on computational biophysics, particularly Molecular Dynamics (MD) and statistical mechanics. I also have expertise in molecular modeling techniques like Molecular Docking, Homology Modeling, and QSAR. I hold an M.S. (Pharm) from NIPER, Kolkata, where I was awarded the...
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Kamil Andrzej Rybacki mgr inż.
PeopleBorn on 23 October 1993 in Gdańsk. In 2017, I have received the M.Sc. Degree at the Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Poland. My main fields of interest include computer simulations of molecular systems, parallel computing in application to computational physics methods and development of various simulation software. Currently, my research is focused on the development of hybrid Molecular...
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The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry
Open Research DataThe 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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DYNAMICOL Ultrafast Charge Transfer in ion atom collision investigated by Molecular Quantum Dynamics Methods
ProjectsProject realized in Faculty of Applied Physics and Mathematics according to PERG08-GA-2010-277201 agreement from 2011-02-22
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On various modelling approaches to real-time visualisation of blood flow
PublicationThis paper reviews various modelling approaches to real-time visualisation of blood flow. These include classic, macroscale approach based on the momentum conservation equation together with a proper constitutive equation. Moreover, modern micro- and mesoscale approaches, such as molecular dynamics and dissipative particle dynamics, are discussed. Advantages and disadvantages of the discussed methods are highlighted with particular...
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Understanding the formation of metastable furan dication in collisions with ions
PublicationThis work relies on complementary theoretical and experimental studies of the processes induced by ion-furan collisions. Results of the Molecular Dynamics simulations and exploration of the energy profiles combined with coincidence mass spectrometry provide complete picture of the fragmentation of furan dication.
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A dipole-driven path for electron and positron attachments to gas-phase uracil and pyrimidine molecules: a quantum scattering analysis
PublicationElectron and positron scattering processes in the gas-phase are analysed for uracil and pyrimidine molecules using a multichannel quantum approach at energies close to threshold. The special effects on the scattering dynamics induced by the large dipole moments in both molecules on the spatial features of the continuum leptonic wavefunctions are here linked to the possible bound states of the Rydberg-like molecular anions or ‘positroned’...
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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
PublicationFat 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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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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A first-principles study of electron attachment to the fully hydrated bromonucleobases
PublicationDegradation mechanism of four brominated nucleobases (BrX), potential DNA radiosensitizers, is studied in explicit water solution, using ab initio molecular dynamics. Several fs long dynamics is needed to localize an electron on the nucleobase. Produced by electron attachment BrX anion radical degrades through the bromide anion abstraction, barrier-free (purines) or with low barrier (pyrimidines), to a reactive nucleobase radical....
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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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Surface diffusion and cluster formation of gold on the silicon (111)
PublicationPurpose: Investigation of the gold atoms behaviour on the surface of silicon by molecular dynamics simulation method. The studies were performed for the case of one, two and four atoms, as well as incomplete and complete filling of gold atoms on the silicon surface. Design/methodology/approach: Investigations were performed by the method of molecular dynamics simulation using the Large-scale Atomic/Molecular Massively Parallel...
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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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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublicationAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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Studies of the Interaction Dynamics in Albumin-Chondroitin Sulfate Systems by Recurrence Method
PublicationThe physicochemical basis of lubrication of articular cartilage is still not fully understood. However, the synergy between components of the synovial fluid can be a crucial factor that could explain this phenomenon. This work presents a nonlinear data analysis technique named the recurrence method, applied to the system involving two components of synovial fluid: albumin and chondroitin sulfate (CS) immersed in a water environment....
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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublicationThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye
PublicationThe functioning of the human eye in the extreme range of light intensity requires a combination of the high sensitivity of photoreceptors with their photostability. Here, we identify a regulatory mechanism based on dynamic modulation of light absorption by xanthophylls in the retina, realized by reorientation of pigment molecules induced by trans–cis photoisomerization. We explore this photochemically switchable system using chromatographic...
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Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales
PublicationCoarse-grained models are nowadays extensively used in biomolecular simulations owing to the tremendous extension of size- and time-scale of simulations. The physics-based UNRES (UNited RESidue) model of proteins developed in our laboratory has only two interaction sites per amino-acid residue (united peptide groups and united side chains) and implicit solvent. However, owing to rigorous physics-based derivation, which enabled...
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Influence of addition of carbon nanotubes on rheological properties of selected liquid lubricants - a computer simulation study
PublicationThis work is motivated by the improvement of anti-friction properties of lubricants by addition of CNTs proved experimentally in literature. In particular, a methodology is developed to compute the shear viscosity of liquid lubricants (Propylene Glycol) based on Molecular Dynamics simulation. Non-Equilibrium molecular dynamics (NEMD) approach is used with a reactive force field ReaxFF implemented in LAMMPS. The simulations are...
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Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide – volumetric and compressibility studies
PublicationThe density and sound velocity of the solutions of ionic liquids based on N-alkyl-N-methyl-morpholinium cations, N-ethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-methyl-N-octyl-morpholinium bis(trifluoromethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide in dimethylsulfoxide were measured at T = (298.15 to 318.15)...
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Weakly Hydrated Solute of Mixed Hydrophobic–Hydrophilic Nature
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane...
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Correlated Particle Motion and THz Spectral Response of Supercritical Water
PublicationMolecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translationaland rotational freedom of individual molecules. These changes give rise to substantially different infrared spectra and...
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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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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Why Are Left-Handed G-Quadruplexes Scarce?
PublicationG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....