Filtry
wszystkich: 389
wybranych: 376
Wyniki wyszukiwania dla: SHELTERIN COMPLEX · MOLECULAR DYNAMICS · TRF1 · TRF2 · TIN2 · APOLLO
-
Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublikacjaInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
-
Structure of partially reduced xPbO (1-x)SiO2 glasses: combined EXAFS and MD study
PublikacjaWykorzystując połączenie metody EXAFS (extended X-ray absorption finestructure) i symulacji MD (molecular dynamics) zbadano strukturęczęściowo zredukowanych szkieł ołowiowo-krzemianowych o różnejstechiometrii wyjściowej. W wyniku analizy uzyskano szczegółowyopis struktury lokalnej wokół atomów ołowiu i jej zmiany w funkcjiskładu szkła i poziomu redukcji. Określono również jaką tendencjędo aglomeracji w metaliczne klastry wykazują...
-
Visualizing spatially decomposed intermolecular correlations in the infrared spectra of aprotic liquids
PublikacjaInfrared (IR) spectroscopy is commonly used to study intermolecular interactions in the liquid phase, including solvation phenomena. On the other hand, ab initio molecular dynamics (AIMD) simulations offer the possibility to obtain IR spectra from first principles. Surpassing the experiment, AIMD simulations can deliver additional information on the spatial intermolecular correlations underlying the IR spectrum of the liquid. Although...
-
The complete stereochemistry of the antibiotic candicidin A3 (syn. ascosin A3, levorin A3)
PublikacjaHerein, the stereostructure of the aromatic heptaene macrolide (AHM) antifungal antibiotic candicidin A3 (syn. ascosin A3, levorin A3) has been established upon the 2D NMR studies, consisting of DQF-COSY, TOCSY, ROESY, HSQC and HMBC experiments, as well as upon extensive molecular dynamics simulations. The geometry of the heptaenic chromophore was defined as: (22E, 24E, 26Z, 28Z, 30E, 32E, 34E). The previously unreported absolute...
-
Water Behavior Near the Lipid Bilayer
PublikacjaIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
-
Model of aeration system at biological wastewater treatment plant for control design purposes
PublikacjaThe wastewater treatment plant (WWTP) is a dynamic, very complex system, in which the most important control parameter is the dissolved oxygen (DO) con-centration. The air is supplied to biological WWTP by the aeration system. Aera-tion is an important and expensive activity in WWTP. The aeration of sewage ful-fils a twofold role. Firstly, oxygen is provided as the main component for biolog-ical processes. Secondly, it supports...
-
FPGA Based Real Time Simulations of the Face Milling Process
PublikacjaThe article presents a successful implementation of the milling process simulation at the Field-Programmable Gate Array (FPGA). By using FPGA, very rigorous Real-Time (RT) simulation requirements can be met. The response time of the FPGA simulations is significantly reduced, and the time synchronization is better than in a typical RT system implemented in software. The FPGA-based approach is characterized by enormous flexibility...
-
Two-Level Multivariable Control System of Dissolved Oxygen Tracking and Aeration System for Activated Sludge Processes
PublikacjaThe problem of tracking dissolved oxygen is one of the most complex and fundamental issues related to biological processes. The dissolved oxygen level in aerobic tanks has significant influence on behaviour and activity of microorganism inhabiting the plant. Aerated tanks are supplied with air from an aeration system (blowers, pipes, throttling valves, diffusers). It is a complex dynamic system governed by nonlinear hybrid dynamics....
-
Hopf bifurcation in time‐delayed gene expression model with dimers
PublikacjaWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the formation of dimers (i.e., complex formed by two protein monomers), the way in which dimers bind to DNA and time delay in translation process. For the model consisting of three ordinary differential equations with time delay, we derive conditions for stability of the positive...
-
A new approach to active noise and vibration control - [Part I: the known frequency case]
PublikacjaThis paper presents a new approach to rejection of complex-valued sinusoidal disturbances acting at the output of a discrete-time stable linear plant with unknown dynamics. It is assumed that the frequency of the sinusoidal disturbance is known, and that the output signal is contaminated with wideband measurement noise. The disturbance rejection control rule is first derived and analyzed for a nominal plant model, different from...
-
Generalised heart rate statistics reveal neurally mediated homeostasis transients
PublikacjaDistributions of accelerations and decelerations, obtained from increments of heart rate recorded during a head-up tilt table (HUTT) test provide short-term characterization of the complex cardiovascular response to a rapid controlled dysregulation of homeostasis. A generalised statistic is proposed for evaluating the neural reflexes responsible for restoring the homeostatic dynamics. An evaluation of the effects on heart rate...
-
Spectral Finite Element Method in Condition Monitoring and Damage Detection
PublikacjaIt is well known that the dynamic behaviour of engineering structures may carry very important and crucial information that can be further used for the assessment of their condition as well as detection of any damage induced. The current interest in monitoring techniques based on the propagation of guided elastic waves requires that numerical techniques used for modelling the phenomena associated must shift into the realm of high...
-
Central-force decomposition of spline-based modified embedded atom method potential
PublikacjaCentral-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in...
-
Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublikacjaF1-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...
-
Redundantly Actuated 3RRR Parallel Planar Manipulator - Numerical Analyses of its Dynamics Sensitivity on Modifications of its Platform’s Inertia Parameters
PublikacjaIn the paper, numerical analyses, as well as dynamics of a complex mechanism, are presented. Two objectives are crucial for the paper: inverse dynamic model is needed (dedicated to be use in the model predictive controller); an identification method is searched (some trajectory parameters are controlled, when specific trajectory is tracked under an open-loop model-based control), as selected parameters must be identified for the...
-
Antioxidant Interactions between Major Phenolic Compounds Found in 'Ataulfo' Mango Pulp: Chlorogenic, Gallic, Protocatechuic and Vanillic Acids
PublikacjaPhenolic compounds are known to have antioxidant capacity; however, there is little information about molecular interactions between particular phenolics found in fruits at different developmental stages. Therefore, the total antioxidant capacity of the phenolic compounds of a fruit may not correspond to the sum of individual antioxidant capacity given by antioxidants from that tissue. In this study, individual antioxidant capacity...
-
Hyaluronan-Chondroitin Sulfate Anomalous Crosslinking Due to Temperature Changes
PublikacjaGlycosaminoglycans are a wide class of biopolymers showing great lubricating properties due to their structure and high affinity to water. Two of them, hyaluronic acid and chondroitin sulfate, play an important role in articular cartilage lubrication. In this work, we present results of the all-atom molecular dynamics simulations of both molecules placed in water-based solution. To mimic changes of the physiological conditions,...
-
A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublikacjaThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
-
Comparative molecular modelling of biologically active sterols
PublikacjaMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
-
Entropy of water calculated from harmonic approximation: estimation of the accuracy of method
PublikacjaSome molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm(3)) and within the temperature range of 5-90 degrees C. By using harmonic approximation, both the entropy of water S-H and the specific heat c(v) were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (similar...
-
Effect of Acetylation and Beta‐Amylase Treatment on Complexation of Debranched Starch with Naringenin
PublikacjaStarch inclusion complexation has been shown to improve solubility of water insoluble molecules. Potato starch and Hylon VII are acetylated at two levels and then debranched alone or combined with β‐amylase hydrolysis, and its complexes with naringenin are prepared in aqueous conditions and characterized in this study. Both soluble and insoluble complexes are formed with the soluble complex present in the supernatant and the insoluble...
-
Optimum Control of Gyroscopic Systems
PublikacjaThe problem of optimum control of transverse rotor vibrations with gyroscopic interactions has been described and solved in the paper. An integral performance index has been defined for such system in order to minimize vibration level of a chosen rotor point. For this reason, an efficient way of finding the weight coefficients of integral performance index for multi-degrees-of-freedom system with gyroscopic interactions has been...
-
A Comprehensive Review: Applications of the Kozeny–Carman Model in Engineering with Permeability Dynamics
PublikacjaIn this review article, we investigate the dynamic nature of the Kozeny–Carman Model concerning permeability and its application in engineering contexts. Providing insights into the changing dynamics of permeability within mining, petroleum, and geotechnical engineering, among other engineering applications. While some are complex and require additional modifcations to be applicable, others are simple and still function in specifc...
-
How to choose drive’s rated power in electrified urban transport?
PublikacjaSelection of drive's rated power influences not only vehicle's dynamics, but also its energy efficiency. Mentioned above approach requires a multiphysical model, which covers both mechanical and electrical phenomena. This paper discusses how selection of traction drive's rated power influences vehicle energy consumption on example of a trolleybus. A complex mathematical model was developed in Matlab/Simulink to describe the multiphisical...
-
Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublikacjaSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
-
Contribution to the mechanism of liquid membrane oscillators involving cationic surfactant.
PublikacjaIt is shown that liquid membrane oscillators with cationic surfactants havemore complex oscillation patterns than observed previously. The actual details of the oscillations depend strongly on the nature of the membrane material, dislosing even the presence of parallel molecular events. It appearsthat sampling topology also has a great influence on the observed oscillato-ry behaviour. Variation of oscillation patterns with...
-
Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublikacjaInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
-
Power System Dynamics. Stability and Control. 3rd edition
PublikacjaComprehensive, state-of-the-art review of information on the electric power system dynamics and stability. It places the emphasis first on understanding the underlying physical principles before proceeding to more complex models and algorithms. The book explores the influence of classical sources of energy, wind farms and virtual power plants, power plants inertia and control strategy on power system stability. The book cover...
-
Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublikacjaSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
-
Direct human contact with siloxanes (silicones): safety or risk. Part 1: characteristics of siloxanes (silicones
PublikacjaSiloxanes are commonly known as silicones. They belong to the organosiliconcompounds and are exclusively obtained by synthesis. Their chemical structuredetermines a range of physicochemical properties which were recognized as unique.Due to the susceptibility to chemical modifications, ability to create short, long orcomplex polymer particles, siloxanes found an application in many areas of human life.
-
Wind resource assessment and energy yield prediction for the small wind turbine on the Szubieniczne Hill
PublikacjaThe goal of this study is to preliminary assess the wind resources on the Szubieniczne Hill in order to predict the annual energy production for planned small wind turbine. The analyzed site is located close to the Gdańsk University of Technology campus, in complex urban environment additionally surrendered by forested hills. The assessment is based on Computational Fluid Dynamics simulations which allow to evaluate the wind energy potential...
-
Folding‐upon‐repair DNA nanoswitches for monitoring DNA repair enzymes activity
PublikacjaWe demonstrate here a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containing O6‐methyl‐guanine (O6‐MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation...
-
Water-mediated long-range interactions between the internal vibrations of remote proteins
PublikacjaIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
-
The Reactivity of Phosphanylphosphinidene Complexes of Transition Metals Toward Terminal Dihaloalkanes
PublikacjaThe reactivities of phosphanylphosphinidene complexes [(DippN)2W(Cl)(η2-P−PtBu2)]− (1), [(pTol3P)2Pt(η2- P=PtBu2)] (2), and [(dppe)Pt(η2-P=PtBu2)] (3) toward dihaloalkanes and methyl iodide were investigated. The reactions of the anionic tungsten complex (1) with stochiometric Br(CH2)nBr (n = 3, 4, 6) led to the formation of neutral complexes with a tBu2PP(CH2)3Br ligand or neutral dinuclear complexes with unusual tetradentate...
-
Cadmium complex possessing simultaneously silanethiolato- and dithiocarbamato-ligands. A novel single-source precursor of cadmium sulfide
PublikacjaThermal decomposition of suitable coordination compounds may be used as efficient route for fabrication of semiconducting layers. A new potential CdS precursor—a cadmium complex with all-sulfur Cd-coordination sphere [Cd{l-SSi(OBut)3}(S2CNC4H8)]2 (1) —has been prepared and its properties are investigated. The complex was obtained in the reaction between dimeric bis(tri-tert-butoxysilanethiolato) cadmium(II) [Cd{SSi(OBut)3}2]2 and...
-
Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublikacjaCysteine–water cluster cations Cys(H2O)3,6 + and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collisioninduced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies...
-
Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublikacjaUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
-
Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated 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...
-
Swarm Algorithms in Modern Engineering Optimization Problems
PublikacjaComplexity of today engineering problems is constantly increasing. Scientists no longer are facing issues, for which simple, mathematical programming methods are sufficient. Issues like autonomic vehicle navigation or classification are considered to be challenging, and although there exist valid means to solve them, in some cases there still is some place for improvement. With emergence of a new type of optimization techniques...
-
Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublikacjaHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
-
Modeling an Industrial Revolution: How to Manage Large-Scale, Complex IoT Ecosystems?
PublikacjaAdvancements around the modern digital industry gave birth to a number of closely interrelated concepts: in the age of the Internet of Things (IoT), System of Systems (SoS), Cyber-Physical Systems (CPS), Digital Twins and the fourth industrial revolution, everything revolves around the issue of designing well-understood, sound and secure complex systems while providing maximum flexibility, autonomy and dynamics. The aim of the...
-
Antifungal Activity of Homoaconitate and Homoisocitrate Analogs
PublikacjaThirteen structural analogs of two initial intermediates of the L-alpha-aminoadipate pathway of L-lysine biosynthesis in fungi have been designed and synthesized, including fluoro- and epoxy-derivatives of homoaconitate and homoisocitrate. Some of the obtainedcompounds exhibited at milimolar range moderate enzyme inhibitory properties against homoaconitase and/or homoisocitrate dehydrogenase of Candida albicans. The structural...
-
An analysis of observability and detectability for different sets of measured outputs - CSTR case study
PublikacjaA problem of proving the observability/detectability at a given measured output for non-linear biochemical systems has been addressed in this paper. A theory of indistinguishable state trajectories has been used to prove the properties of the observability or detectability of this system. It is related to taking system dynamics into consideration depending on initial conditions and the impact of inputs taking into account a given...
-
SONIC - Self-optimizing narrowband interference canceler: comparison of two frequency tracking strategies
PublikacjaThis paper presents a new approach to rejection of complex-valued sinusoidal disturbances acting at the output of a discrete-time linear stable plant with unknown and possibly time-varying dynamics. It is assumed that both the instantaneous frequency of the sinusoidal disturbance and its amplitude may be slowly varying with time and that the output signal is contaminated with wideband measurement noise. The proposed disturbance...
-
Intermolecular Hydrogen Bonding Directed by Aryl–Perfluoroaryl π–π Stacking Interactions
PublikacjaThe crystal structures of five compounds capable of forming self-complementary hydrogen bonds but crystallizing as catemers or creating more complex crystal structures were compared with their complexes prepared by cocrystallization with perfluoroaryl compounds. The results of X-ray diffraction revealed that in all the cases the π–π stacking interactions caused reorganization of hydrogen bonds and induced creation of the expected...
-
Oznaczanie śladowych ilości związków organicznych w próbkach o złożonych matrycach zgodne z regułami ''zielonej chemii analitycznej''. Krótkołańcuchowe kwasy karboksylowe = Increasingly green approaches to the determination of selected trace organic in complex matrices. Short chain carboxylic acids
PublikacjaNowadays the great stress is put on environment protection and the activities to minimize the effect of chemical analyses on the environment are discussed. When environmentally friendly methodologies of analytes determination are applied the term "green analytical chemistry" is used. In general, the determination of organic compounds in complex matrices, which is a frequent analytical task, requires separation of sample components...
-
Establishing the allosteric mechanism in CRISPR‐Cas9
PublikacjaAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
-
Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublikacjaSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
-
Acid–Base Equilibrium and Self-Association in Relation to High Antitumor Activity of Selected Unsymmetrical Bisacridines Established by Extensive Chemometric Analysis
PublikacjaUnsymmetrical bisacridines (UAs) represent a novel class of anticancer agents previously synthesized by our group. Our recent studies have demonstrated their high antitumor potential against multiple cancer cell lines and human tumor xenografts in nude mice. At the cellular level, these compounds affected 3D cancer spheroid growth and their cellular uptake was selectively modulated by quantum dots. UAs were shown to undergo metabolic...
-
The Role of Electron Transfer in the Fragmentation of Phenyl and Cyclohexyl Boronic Acids
PublikacjaIn this study, novel measurements of negative ion formation in neutral potassium-neutral boronic acid collisions are reported in electron transfer experiments. The fragmentation pattern of phenylboronic acid is comprehensively investigated for a wide range of collision energies, i.e., from 10 to 1000 eV in the laboratory frame, allowing some of the most relevant dissociation channels to be probed. These studies were performed in...