Wyniki wyszukiwania - Biblioteka Nauki

1

Probing of Cu2+ ions binding to A β (5−16) peptide using ITC measurements and MD simulations

100%

Makowska J. , Żmudzińska W. , Wyrzykowski D. , Brzozowski K. , Zblewska H. , Chmurzyński L.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2016

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tom Vol. 20, No 4

409--416

EN

It is shown that probably three residues: His6, His14 and His16 in the original sequence A β (1−42) serve as metal-binding sites for Cu2+ions. On the other hand, there is a possibility that only one of them plays a crucial role in the formation of the{A β (1-42)-Cu2+} complex. The isothermal titration calorimetry (ITC) measurements supported by molecular dynamic simulation (MD) with the NMR-derived restrains were used to investigate the interactions of Cu2+ with A β(5-16), a fragment of the A β(1-42) protein, with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, termed HZ1. The conditional thermodynamic parameters suggest that the formation of the Cu2+-HZ1 complex is both an enthalpy and entropy driven process under the experimental conditions. The studies presented here (after comparison with our previous results) show that the affinity of peptides to copper metal ions depends on two factors: the primary structure (amino acid composition) and the shape of the peptide conformation adopted.

2

Molecular dynamics simulation of manipulation of metallic nanoclusters on stepped surfaces

100%

Mahboobi S. , Meghdari A. , Jalili N. , Amiri F.

Open Physics

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2011

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tom 9

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nr 2

454-465

EN

Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on stepped surfaces. Five surface forms are considered in the simulations. The system parts are made of pure transition metals and Sutton-Chen many-body potential is used as interatomic potential. The conditions which are subjected to change in the tests include: materials used for particles and substrate, and surface step conditions. In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Simulation results show the effect of the aforementioned working conditions on the particle behavior as well as changes in the pushing forces. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines which guarantee better success in the manipulation process.

3

The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation

88%

Rybicki J. , Witkowska A. , Bergmański G. , Mancini G. , Feliziani S.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2003

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tom Vol. 7, No 2

243-256

EN

The paper is dedicated to a molecular dynamics (MD) study of the structure of partially reduced lead-silicate glass of composition 1Pb 1PbO 1SiO2. The simulations have been performed in the constant volume regime, using a two-body potential (Born-Mayer repulsive forces, and Coulomb forces due to full ionic charges). The system was initially prepared as a well equilibrated hot melt, and then slowly cooled down to 300K. The information on short-range correlations were obtained in a conventional way (from pair and angular distribution functions), while the medium-range order was studied via cation-anion ring analysis. In the paper, the short- and medium-range order in the simulated system is discussed and compared with the structure of a glassy completely reduced system, i.e. 2Pb 1SiO2 and unreduced one, i.e. 2PbO 1SiO2 glass.

4

Preferential solvation of amides by methanol - a comparison of molecular dynamics calculations with the experimental data

88%

Zielkiewicz J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2001

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tom Vol. 5, No 3

317-329

EN

Using the Kirkwood-Buff theory of solutions, the preferential solvation of the N-methylacet-amide (NMA), N-methylformamide, (NMF), and N,N-dimethylformamide, (DMF), molecule has been investigated in the binary {amide+methanol} mixtures at 313.15 K. Moreover, for the {amide+methanol} mixtures, where amide = NMF, DMF, and NMA, the molecular dynamics calculations at xamide=0.518 were performed. From the obtained molecule-molecule radial distribution functions, (rdf), and atom-atom rdf, it was possible to estimate the local mole fractions around the amide molecule, the orientation effects of molecules within the solvation shell, and a possibility of the formation of complexes. The general picture obtained from analysis of the molecular dynamics results is consistent with the deductions derived from thermodynamic data.

5

Limitations of Applicability of the Green-Kubo Approach for Calculating the Thermal Conductivity of a Confined Liquid in Computer Simulations

88%

Hyżorek K. , Tretiakov K. V.

Computational Methods in Science and Technology

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2016

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tom Vol. 22, No. 4

197--200

EN

: Thermal conductivity (λ) of the Lennard-Jones liquid in cylindrical nanochannels has been determined using the Green-Kubo (GK) approach in equilibrium Molecular Dynamics simulations. Good convergence of λ(τ ) has been observed along the nanochannel’s axis where the periodic boundary conditions are applied. However, it has been found that the estimation of limiting value of λ(τ ) in the transverse direction, where walls confine the liquid, is ambiguous.

6

Synergistic mechanism of dodecylamine/octanol mixtures enhancing lepidolite flotation from the self-aggregation behaviors at the air/liquid interface

75%

Bai Y. , Xu M. , Wen W. , Zhu S. , Mo W. , Yan P.

Physicochemical Problems of Mineral Processing

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2023

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tom Vol. 59, iss. 6

art. no. 176510

EN

Surface tension measurements and molecular dynamics (MD) simulations were used to explore the flotation foam properties and self-aggregation behaviors of dodecylamine (DDA)/octanol (OCT) mixtures formed with different mole ratios at the air/liquid interface. Based on the surface and thermodynamic parameters, the DDA/OCT mixtures exhibited greater interfacial activities and adsorption capacities than their individual components. The MD simulations showed that DDA and OCT were aggregated through hydrogen bonding, coulombic forces and hydrophobic association. OCT was inserted into the DDA adsorption layer, causing the alkyl chains of both DDA and OCT to extend from water to air at varying heights and angles. The addition of OCT improved the hydration of the amino groups and reduced the overall number of hydrogen bonds. The stability of the flotation foam decreased, and the high viscosity and difficult defoaming of the DDA flotation foam were significantly improved. When the DDA/OCT mole ratio was 2:1, the included angle formed between the alkyl chains and the interface was maximized, leading to enhanced compatibility among the alkyl chains, and the hydrogen bond energy was relatively large, which showed a strong synergistic effect. The MD simulation findings were consistent with the results obtained from the lepidolite flotation and surface tension experiments conducted in this study; our results could provide a theoretical foundation for the selection of superior mixed collectors and frothers.

7

Molecular dynamics study of Cu-Pd ordered alloys

75%

Özdemir Kart S. , Erbay A. , Kiliç H. , Cagin T. , Tomak M.

Journal of Achievements in Materials and Manufacturing Engineering

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2008

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tom Vol. 31, nr 1

41-46

EN

Purpose: The goal of the paper is to study the molecular dynamics of Cu-Pd ordered alloys. Design/methodology/approach: The thermal and mechanical properties of Cu, Pd pure metals and their ordered intermetallic alloys of Cu3Pd(L12) and CuPd3(L12) are studied by using the molecular dynamics simulation. The melting behavior of the metals considered in this work is studied by utilizing quantum Sutton-Chen (Q-SC) many-body potential. The effects of temperature and concentration on the physical properties of Cu-Pd system are analyzed. Findings: A wide range of properties of Cu, Pd pure metals and their Cu3Pd and CuPd3 ordered intermetallics is presented. It was found that this potential is suitable to give the general characteristics of the melting process in these systems. Practical implications: The simulation results such as cohesive energy, density, elastic constants, bulk modulus, heat capacity, thermal expansion and melting points are in good agreement with the available experimental data and other theoretical calculations. Originality/value: To the best our knowledge this work presents, for the first time, a wide range of physical properties of alloys focusing on Cu-Pd ordered compounds.

8

Growth of intermetallic compound between indium-based thermal interface material and copper substrate: molecular dynamics simulations

75%

Fałat T. , Płatek B.

Materials Science Poland

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2015

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tom Vol. 33, No. 2

445--450

EN

The diffusion phenomenon occurring between copper and indium was investigated by molecular dynamics simulations. The calculations were carried out in various temperatures in aging domain with the use of the commercially available Materials Studio v.6. software. The results showed that the intermetallic compound (IMC) growth followed the parabolic law, which indicated this growth to be mainly controlled by volume diffusion. The growth activation energy was estimated at 7.48 kJ.mol(-1).

9

Molecular dynamics simulations of potassium channels

75%

Domene C.

Open Chemistry

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2007

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tom 5

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nr 3

635-671

EN

Despite the complexity of ion-channels, MD simulations based on realistic all-atom models have become a powerful technique for providing accurate descriptions of the structure and dynamics of these systems, complementing and reinforcing experimental work. Successful multidisciplinary collaborations, progress in the experimental determination of three-dimensional structures of membrane proteins together with new algorithms for molecular simulations and the increasing speed and availability of supercomputers, have made possible a considerable progress in this area of biophysics. This review aims at highlighting some of the work in the area of potassium channels and molecular dynamics simulations where numerous fundamental questions about the structure, function, folding and dynamics of these systems remain as yet unresolved challenges. [...]

10

Flows in microchannels

75%

Kucaba-Piętal A. , Walenta Z. , Peradzyński Z.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2001

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tom Vol. 5, No 2

179-189

EN

The aim of this paper is to present a survey of the results for the flows of simple gases and liquids with substructure through narrow channels, obtained with the Direct Monte-Carlo and Molecular Dynamics Simulation methods.

11

Molecular dynamics study on axial elastic modulus of carbon nanoropes

75%

Mehralian F. , Firouz-Abadi R. D. , Norouzi M.

Archives of Civil and Mechanical Engineering

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2019

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tom Vol. 19, no. 4

1127--1134

EN

Carbon nanoropes (CNRs) are of interest for a wide variety of nanotechnological applica-tions. Since little attention has been paid to mechanical properties of CNRs, their axial elasticmodulus is explored herein. Molecular dynamics (MDs) simulations are adopted for analysisof Young's modulus of CNRs. It is also shown that increase in the initial helical angledecreases Young's modulus; however, by increase in the number of CNTs and strands,different influence on Young's modulus emerges. Therefore, the highest value of Young'smodulus obtained at the lower value of initial helical angle and consequently, Young'smodulus of bundle of straight CNTs is higher than CNRs with hierarchical helical structure. Itis further observed that Young's modulus experiences a non-monotonic variation withrespect to the number of CNTs (n) and strands (N) such that the increasing procedure ofYoung's modulus with respect to the number of CNTs and strands switches to decrease onesat n = 4 and N = 3. Therefore, the results obtained in the present study assist to control theelastic property of CNR by suitable design of number of CNTs, strands and initial helicalangle of CNT and strand and can lead to inspire optimal design of advanced nanostructures.

12

The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.

75%

Mazerski J. , Muchewicz K.

Acta Biochimica Polonica

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2000

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tom 47

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nr 1

65-78

EN

Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.

13

Gel–glass transition in silica and nitrided silica aerogels – experiment and computer modelling

63%

Szaniawska K. , Murawski L. , Rybicki J. , Witkowska A. , Walewski M.

Optica Applicata

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2003

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tom Vol. 33, nr 1

75-81

EN

Nitrided silica aerogel was sintered at 1600 °C in vacuum or nitrogen atmosphere and the effect of densification was compared with that observed in silica aerogel. It has been shown that homogeneous oxynitride glasses containing 8.4–13 wt% can be obtained by densification of nitrided aerogels. The densification process of nitrided aerogels was simulated by computer modeling using classical molecular dynamics (MD) simulations. MD simulations have shown that densification process proceeds in a similar way as in the experiment. In addition, the simulations indicate that oxynitride glasses can be obtained by densification of Si–O–N system.

14

Dopant ions size impact on structural properties of ordered poly(3,4-ethylenedioxythiophene) systems

63%

Śniechowski M. , Kozik T. A. , Łużny W.

Polimery

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2020

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tom T. 65, nr 9

639--643

EN

The purpose of this work was to determine whether the structures of ordered part of novel poly(3,4-ethylenedioxythiophene) PEDOT : OTf (doped with trifluoromethanesulfonate anions) and PEDOT : HSulf (doped with hydrogensulfate anions) systems could really be simply the layered structure of PEDOT : Tos (doped with tosylate anions) with the counter ion changed to the appropriate one. Insight into this problem could be provided by molecular dynamics simulations but also by swarm intelligence optimization, developed earlier for the purpose of investigating the other structures.

PL

Zbadano zdolność struktury uporządkowanej części nowych układów domieszkowanych poli(3,4-etylenodioksytiofenu) (PEDOT) [PEDOT : OTf (domieszkowane anionami trifluorometanosulfonianowymi) i PEDOT : HSulf (domieszkowane anionami wodorosiarczanowymi)] do powielania znanej z literatury warstwowej struktury PEDOT : Tos (domieszkowane anionami tosylanowymi) z jonem domieszki zmienionym na odpowiedni. Poszukiwania nowych struktur wspomagano symulacjami dynamiki molekularnej, a także z zastosowaniem optymalizacji opartej na algorytmach inteligencji stadnej.

15

Metal atom clustering in reduced lead-, bismuth- and antimony-silicate glasses: a comparative molecular dynamics study.

51%

Witkowska A. , Rybicki J. , Bośko J. , Feliziani S.

Optica Applicata

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2000

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tom Vol. 30, nr 4

685-689

EN

We report on the results of molecular dynamics (MD) simulations of the formation of metallic granules in totally reduced lead-, bismuth- and antimony-silicate glasses of composition xMe(1-x)SiO/sub 2/, Me=Pb, Pi Sb, x=0.25, 0.5. The simulations were performed in the NVE ensemble, with two-body Born-Mayer-Huggins interaction potential. For all the glasses considered a strong tendency of heavy metal atoms to agglomerate was observed. In this contribution we compare the distributions of the sizes of Pb, Bi and Sb granules and their packing.