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Search results for: MOLECULAR DYNAMICS
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Two-state dynamics for replicating two-strand systems
PublicationDynamika dwustanowa została zastosowana do opisów układów dwuniciowych, analogicznych do DNA.
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On thermal stability of topological qubit in Kitaev's 4D model
PublicationWe analyse stability of the four-dimensional Kitaev model-a candidate for scalable quantum memory - in finite temperature within the weak coupling Markovian limit. It is shown that, below a critical temperature, certain topological qubit observables X and Z possess relaxation times exponentially long in the size of the system. Their construction involves polynomial in system size algorithm which uses as an input the results of...
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Seismic pounding between adjacent buildings: Identification of parameters, soil interaction issues and mitigation measures
PublicationStructural pounding has been observed in many previous earthquakes due to insufficient gap commonly provided between adjacent structures. The collisions usually generate large impact forces and short duration acceleration pulses which may result in significant damage to the colliding buildings. Because of that, earthquake induced structural pounding has been intensively studied and investigated for the last three decades. Results...
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Analysis of pounding between adjacent buildings founded on different soil types
PublicationEarthquake-induced pounding was experienced in many previous earthquakes and it was found to be a critical issue. This study investigates the effect of pounding between buildings founded on the same and different soil types. Three 3-D buildings with 4, 6 and 8 storeys were considered in this study. Three pounding scenarios were taken into account, i.e. pounding between 4-storey and 6-storey buildings, between 4-storey and 8-storey...
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Influence of stabilizing osmolytes on hen egg white lysozyme fibrillation
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Machine learning-based seismic fragility and seismic vulnerability assessment of reinforced concrete structures
PublicationMany studies have been performed to put quantifying uncertainties into the seismic risk assessment of reinforced concrete (RC) buildings. This paper provides a risk-assessment support tool for purpose of retrofitting and potential design strategies of RC buildings. Machine Learning (ML) algorithms were developed in Python software by innovative methods of hyperparameter optimization, such as halving search, grid search, random...
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What drives sustainable investing? Adoption determinants of sustainable investing exchange-traded funds in Europe
PublicationDespite the growing interest in various topics related to sustainable (ESG) investing, some issues remain understudied, such as the determinants of their utilization at the macro level. This paper contributes to the state of knowledge two-directionally. First, it shows the development of sustainable investing exchange-traded funds (ETFs) in European countries. Second, it traces the significant determinants of adopting sustainable...
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Enhancing seismic performance of steel buildings having semi-rigid connection with infill masonry walls considering soil type effects
PublicationUnpreventable constructional defects are the main issues in the case of steel Moment-Resisting Frames (MRFs) that mostly occur in the rigidities of beam-to-column connections. The present article aims to investigate the effects of different rigidities of structures and to propose Infill Masonry Walls (IMWs) as retrofitting strategy for the steel damaged buildings. A fault or failure to meet a certain consideration of the soil type...
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GVC involvement and the gender wage gap: Micro -evidence on European countries
PublicationWe examine linkages between involvement in global value chains (GVCs) and gender wage inequalities. We use merged data from Structure of Earnings Survey and the World Input Output Database covering 18 European countries. We employ information on employees’ personal and company characteristics and a sectoral involvement in GVCs. In general, the wages of workers from sectors more involved in GVCs are lower. However, the relationship...
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Linkages between services and manufacturing as a new channel for GVC development: Evidence from CEE countries
PublicationThe goal of the paper is to verify a causal relationship between forward linkages from domestic services to manufacturing and the participation/position of a country in global value chains (GVCs) in selected Central and Eastern European economies. We observed a strong polarisation pattern: the Baltic countries along with the Czech Republic strengthen their positions and participation in GVCs by having a strong relationship between...
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The Opening of Central and Eastern European Countries to Free Trade: A Critical Assessment
PublicationThree decades after the fall of the Berlin wall and one and a half decades after the Big Bang enlargement of the European Union (2004-2007), we revisit contrasting narratives about the benefit of both free trade and the EU enlargement for Central and Eastern European (CEE) countries. We distinguish old, pre-2004 EU countries from CEE countries that joined the EU in 2004-2007, as well as from the CEE countries that have not become...
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On the Existence of Homoclinic Type Solutions of a Class of Inhomogenous Second Order Hamiltonian Systems
PublicationWe show the existence of homoclinic type solutions of a class of inhomogenous second order Hamiltonian systems, where a C1-smooth potential satisfies a relaxed superquadratic growth condition, its gradient is bounded in the time variable, and a forcing term is sufficiently small in the space of square integrable functions. The idea of our proof is to approximate the original system by time-periodic ones, with larger and larger...
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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublicationMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Physical, chemical and biochemical properties of Western Siberia Sphagnum and Carex peat soils
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Equivalent Single Layer Models in Free Vibration Analysis of Laminated Multi-Layered Plates
PublicationThe performance of selected equivalent single-layer (ESL) models is evaluated within several classical benchmark tests for small amplitude free vibration analysis of multi-layered plates. The authors elaborated their own Finite Element software based on the first-order shear deformation (FOSD) theory with some modifications incorporated including a correction of the transverse shear stiffness and an application of zigzag type functions....
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On integro-differential equations with delayed arguments
PublicationPraca dotyczy problemów różniczkowo-całkowych z warunkami początkowymi oraz brzegowymi typu okresowego. Podano warunki na istnienie i jednoznaczność rozwiązania. Badania dotyczyły również nierówności różniczkowo-całkowych z argumentami typu opóżnionego. Podano przykłady, które mogą mieć zastosowanie w problemach inżynierskich.
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Boundary value problems for dynamic equations of Volterra type on time scales
PublicationPraca dotyczy równań i nierówności dla problemów dynamicznych typu Volterry. Podano warunki dostateczne na istnienie ekstremalnych rozwiązań w obszarze ograniczonym przez dolne i górne rozwiązania. Praca zawiera również pewne uwagi dla konkretnych zagadnień różniczkowych i dyskretnych.
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Dynamic inequalities and equations of Volterra type on time scales
PublicationPraca dotyczy całkowo-różniczkowych równań dynamicznych typu Volterry z warunkami początkowymi. Stosując twierdzenie Banacha o punkcie stałym pokazano istnienie jedynego rozwiązania liniowego równania dynamicznego. Stosując metodę iteracji monotonicznych pokazano istnienie rozwiązań ekstremalnych dla problemów nieliniowych. Badano też nierówności dynamiczne. Praca zawiera również uwagi dotyczące zagadnień różniczkowych i różnicowych.
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Positive solutions to boundary value problems for impulsive second-order differential equations
PublicationIn this paper, we discuss four-point boundary value problems for impulsive second-order differential equations. We apply the Krasnoselskii's fixed point theorem to obtain sufficient conditions under which the impulsive second-order differential equations have positive solutions. An example is added to illustrate theoretical results.
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Positive solutions to second order four-point impulsive problems with deviating arguments
PublicationStosując tw. Leggetta-Williamsa, podano warunki dostateczne na istnienie dodatnich rozwiązań dla czteropunktowych problemów brzegowych dla równań różniczkowych rzędu drugiego z odchylonymi argumentami. Dyskutowane były problemy gdy argument odchylony był typu opóźnionego lub wyprzedzonego.
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Vibration Diagnostics of Rolling Mills Based on Nonlinear Effects in Dynamics
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In silico approaches for better understanding cysteine cathepsin-glycosaminoglycan interactions
PublicationCysteine cathepsins constitute the largest cathepsin family, with 11 proteases in human that are present primarily within acidic endosomal and lysosomal compartments. They are involved in the turnover of intracellular and extracellular proteins. They are synthesized as inactive procathepsins that are converted to mature active forms. Cathepsins play important roles in physiological and pathological processes and, therefore, receive...
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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublicationAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublicationThe main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water–water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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Brittle fracture of 100-, 110-, 111-oriented Cu crystals: MD vs. TB/MD approach
PublicationPrzeprowadzono wieloskalowe symulacje nanoindentacji miedzi nieskończenie twardym narzędziem, przy zastosowaniu metody dynamiki molekularnej, z siłami liczonymi na bieżąco w formalizmie ciasnego wiązania (TB). Przedstawiono wyniki dla trzech orientacji krystalicznych podłoża. Badano efekt dołączenia obliczeń TB na siłę normalną odczuwaną przez narzędzie i na przemieszczenia atomów podłoża, przez porównywanie z symulacją czystą...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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A highly-efficient technique for evaluating bond-orientational order parameters
PublicationWe propose a novel, highly-efficient approach for the evaluation of bond-orientational order parameters (BOPs). Our approach exploits the properties of spherical harmonics and Wigner 3jj-symbols to reduce the number of terms in the expressions for BOPs, and employs simultaneous interpolation of normalised associated Legendre polynomials and trigonometric functions to dramatically reduce the total number of arithmetic operations....
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublicationAmphotericin B (AmB) is a lifesaving antibiotic used to treat deep-seated mycotic infections. Both the pharmaceutical activity and highly toxic side effects of the drug rely on its interaction with biomembranes, which is governed by the molecular organization of AmB. In the present work we present detailed analysis of self-assembly of AmB molecules in different environments, interesting from the physiological standpoint, based...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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Mechanical Properties of Single-Walled Carbon Nanotubes with AIREBO Force-Filed
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Roadmap on dynamics of molecules and clusters in the gas phase
PublicationThis roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty orders of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity...
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Application of the neural networks for developing new parametrization of the Tersoff potential for carbon
PublicationPenta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3-bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the...
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Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid
PublicationOne of the possible applications of ionic liquids is to produce electricity from heat. The iron oxide nanoparticle is a potent electrical particle, which is expected to improve the heat’s efficiency to electricity conversion, however, it is prone to aggregation and sedimentation, which hamper its application. One of the methods to enhance the nanoparticle’s solubility and electrical properties is the use of a stabilizing component...
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Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies
PublicationOsmolytes, the small organic molecules accumulated in cells under environmental stress, can modulate the stability of biopolymers such as proteins and DNA. In spite of many years of research, there is no established molecular mechanism of the influence of osmolytes on DNA structure. Here, we used two model osmolytes that denature (urea) or stabilize (trimethylglycine, TMG) proteins to study their effect on DNA in aqueous solutions...
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Fractional Calculus Evaluation of Hyaluronic Acid Crosslinking in a Nanoscopic Part of Articular Cartilage Model System
PublicationThis work presents a study of the mechanism of physical crosslinking of hyaluronic acid in the presence of common phospholipids in synovial joint organ systems. Molecular dynamic simulations have been executed to understand the formation of hyaluronan networks at various phospholipid concentrations. The results of the simulations suggest that the mechanisms exhibit subdiffusion characteristics. Transportation quantities derive...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Antibiotic-sterol interactions provide insight into the selectivity of natural aromatic analogues of amphotericin B and their photoisomers
PublicationAromatic heptaene macrolides (AHMs) belong to the group of polyene macrolide antifungal antibiotics. Members of this group were the first to be used in the treatment of systemic fungal infections. Amphotericin B (AmB), a non-aromatic representative of heptaene macrolides, is of significant clinical importance in the treatment of internal mycoses. It includes the all-trans heptaene chromophore, whereas the native AHMs contain two...
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Anomalous Behavior of Hyaluronan Crosslinking Due to the Presence of Excess Phospholipids in the Articular Cartilage System of Osteoarthritis
PublicationLubrication of articular cartilage is a complex multiscale phenomenon in synovial joint organ systems. In these systems, synovial fluid properties result from synergistic interactions between a variety of molecular constituent. Two molecular classes in particular are of importance in understanding lubrication mechanisms: hyaluronic acid and phospholipids. The purpose of this study is to evaluate interactions between hyaluronic acid...
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CENTRAL-FORCE DECOMPOSITION OF THE TERSOFF POTENTIAL
PublicationCentral forces play important role in the analysis of results obtained with particle simulation methods, since they allow evaluating stress fields. In this work we derive expressions for a central-force decompositon of the Tersoff potential, which is often used to describe interatomic interactions in covalently bonded materials. We simplify the obtained expressions and discuss their properties.
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Torsional elasticity and energetics of F1-ATPase
PublicationFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
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Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations
PublicationIn this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas–liquid...
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The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublicationMembers of a novel class of anticancer compounds, exhibiting high antitumor activity, i.e. the unsymmetrical bisacridines (UAs), consist of two heteroaromatic ring systems. One of the ring systems is an imidazoacridinone moiety, with the skeleton identical to the structural base of Symadex. The second one is a 1-nitroacridine moiety, hence it may be regarded as Nitracrine’s structural basis. These monoacridine units are connected...
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Solubility of carbon dioxide in water: Some useful results for hydrate nucleation
PublicationIn this paper, the solubility of carbon dioxide (CO2) in water along the isobar of 400 bar is determined by computer simulations using the well-known TIP4P/Ice force field for water and the TraPPE model for CO2. In particular, the solubility of CO2 in water when in contact with the CO2 liquid phase and the solubility of CO2 in water when in contact with the hydrate have been determined. The solubility of CO2 in a liquid–liquid...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...