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Gioldasis, Christos (author), Gkamas, Apostolos (author), Moultos, O. (author), Vlahos, Costas Hristos (author)The chemical feedback between building blocks in templated polymerization of diblock copolymers and their consecutive micellization was studied for the first time by means of coarse-grained molecular dynamics simulations. Using a stochastic polymerization model, we were able to reproduce the experimental findings on the effect of chemical...journal article 2023
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Moultos, O. (author), Tsimpanogiannis, Ioannis N. (author)Available data from experiments and molecular simulations for the intra-diffusivities of H (Formula presented.) and O (Formula presented.) in H (Formula presented.) O, and for the self-diffusivity of pure H (Formula presented.) O (at pressure and temperature conditions in which the solvent is in the vapour phase) are compared against...journal article 2023
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Hu, D. (author), Li, Z. (author), Fan, J. (author), Zhang, Kouchi (author)As a critical part of speeding up industrial electrification, power electronics, and its packaging technology are undergoing rapid development. Cu nanoparticle sintering technology has therefore received extensive attention for its excellent performance in the die-attachment layer, where the mechanical properties are essential to be known for...conference paper 2023
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Liang, Peijie (author), Pan, Zhiliang (author), Tang, Liang (author), Zhang, Kouchi (author), Yang, Daoguo (author), He, Siliang (author), Yan, Haidong (author)Based on molecular dynamics (MD), in this study, a model was established to simulate the initial coating morphology of silver paste by using a random algorithm, and the effects of different sizes of particles on sintering porosity were also analyzed. The MD result reveals that compared with the sintering process using large-scale silver...journal article 2022
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Chen, Wei (author), Chen, Ye (author), Cao, Yixing (author), Cui, Z. (author), Fan, Xuejun (author), Zhang, Kouchi (author), Fan, J. (author)In a light-emitting diode (LED) package, silicone encapsulant serves as a chip protector and enables the light to transmit, since it exhibits the advantages of high light transmittance, high refractive index, and high thermal stability. However, its reliability is still challenged under harsh operation conditions. In this study, the optical...journal article 2022
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Vlugt, T.J.H. (author)In this manuscript, we show how to compute partial molar properties (e.g. partial molar volumes, energies, and enthalpies) of fluid mixtures from single Molecular Dynamics simulations in the microcanonical or canonical ensemble, using only relatively simple post-processing of trajectories. The method uses least squares linear regression of...journal article 2022
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Chen, Y. (author), Dolado, Jorge S. (author), Li, Z. (author), Yin, Suhong (author), Yu, Qijun (author), Kostiuchenko, A. (author), Ye, G. (author)In this paper, the atomic structures of sodium aluminosilicate hydrate (N–A–S–H) gels with different Si/Al ratios are studied by molecular dynamics simulation. An N–A–S–H gel model was obtained from the polymerization of Si(OH)<sub>4</sub> and Al(OH)<sub>3</sub> monomers with the use of a reactive force field (ReaxFF). The simulated atomic...journal article 2022
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Fragasso, A. (author), de Vries, Hendrik W. (author), Andersson, John (author), van der Sluis, E.O. (author), van der Giessen, Erik (author), Onck, Patrick R. (author), Dekker, C. (author)Nuclear pore complexes (NPCs) regulate all molecular transport between the nucleus and the cytoplasm in eukaryotic cells. Intrinsically disordered Phe-Gly nucleoporins (FG-Nups) line the central conduit of NPCs to impart a selective barrier where large proteins are excluded unless bound to a transport receptor (karyopherin; Kap). Here, we...journal article 2022
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Gonzalez Nelson, A.M. (author)Metal–organic frameworks (MOFs) are ordered arrays of polytopic organic ligands, commonly called linkers, which interconnect metal-based inorganic building units via coordination bonds. The highly precise assembly of well defined building blocks into extended 3-D networks, known as reticular chemistry, has allowed researchers in this field to...doctoral thesis 2021
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Chen, Yun (author), Dolado, Jorge S. (author), Yin, Suhong (author), Yu, Qijun (author), Kostiuchenko, Albina (author), Li, Zhenming (author), Ye, Guang (author)The understanding of sodium aluminosilicate hydrate (N-A-S-H) gel is still limited due to its complex and amorphous structure. Recently, molecular dynamics simulation has provided a unique opportunity to better understand the structure of N-A-S-H gel from nanoscale. In this work, the N-A-S-H gel structure was obtained by simulating the...conference paper 2021
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Chen, Y. (author), Dolado, Jorge S. (author), Yin, Suhong (author), Yu, Qijun (author), Kostiuchenko, A. (author), Li, Z. (author), Ye, G. (author)The understanding of sodium aluminosilicate hydrate (N-A-S-H) gel is still limited due to its complex and amorphous structure. Recently, molecular dynamics simulation has provided a unique opportunity to better understand the structure of N-A-S-H gel from nanoscale. In this work, the N-A-S-H gel structure was obtained by simulating the...conference paper 2021
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Solovev, Yaroslav V. (author), Igolkina, Anna A. (author), Kuliaev, Pavel O. (author), Sulima, Anton S. (author), Zhukov, Vladimir A. (author), Porozov, Yuri B. (author), Pidko, E.A. (author), Andronov, Evgeny E. (author)The difference in symbiotic specificity between peas of Afghanistan and European phenotypes was investigated using molecular modeling. Considering segregating amino acid polymorphism, we examined interactions of pea LykX-Sym10 receptor heterodimers with four forms of Nodulation factor (NF) that varied in natural decorations (acetylation and...journal article 2021
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Jamali, S.H. (author)Knowledge on transport properties of fluids is of great interest for process<br/>and product design development in the chemical, food, pharmaceutical, and<br/>biotechnological industry. In the past few decades, molecular simulation has<br/>become a powerful tool to calculate these properties. In this context, Molecular<br/>Dynamics (MD) is...doctoral thesis 2020
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Srinivasan, P. (author)Shape-memory Alloys (SMAs) exhibit tremendous mechanical properties owing to their reversible phase transformation between the austenitic and the martensitic phase. Out of these, equi-atomic nickel-titanium (NiTi) alloys are the most widely used SMAs for various applications since the transformation occurs close to room temperature. Advances in...doctoral thesis 2020
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Celebi, A.T. (author), Jamali, S.H. (author), Bardow, André (author), Vlugt, T.J.H. (author), Moultos, O. (author)The number of molecules used in a typical Molecular Dynamics (MD) simulations is orders of magnitude lower than in the thermodynamic limit. It is therefore essential to correct diffusivities computed from Molecular Dynamics simulations for finite-size effects. We present a comprehensive review on finite-size effects of diffusion coefficients...journal article 2020
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Tsimpanogiannis, Ioannis N. (author), Jamali, S.H. (author), Economou, Ioannis G. (author), Vlugt, T.J.H. (author), Moultos, O. (author)The translational self-diffusion coefficient and the shear viscosity of water are related by the fractional Stokes–Einstein relation. We report extensive novel molecular dynamics simulations for the self-diffusion coefficient and the shear viscosity of water. The SPC/E and TIP4P/2005 water models are used in the temperature range 220–560 K...journal article 2020
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Zhao, Shidi (author), Restrepo Perez, L. (author), Soskine, Misha (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author), Aksimentiev, A. (author)Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations....journal article 2019
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Verners, O. (author), Lyulin, Alexey V. (author), Simone, A. (author)This reactive molecular dynamics study explores the salt concentration dependence of the viscoelastic and mechanical failure properties of a poly(propylene glycol)/LiPF<sub>6</sub>-based solid polymer electrolyte (SPE) at a graphitic carbon electrode interface. To account for the finite-size effect of interface-confined SPE films, the...journal article 2018
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Dawass, N. (author), Krüger, Peter (author), Schnell, S. K. (author), Bedeaux, D. (author), Kjelstrup, S (author), Simon, J. M. (author), Vlugt, T.J.H. (author)The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood–Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and...journal article 2018
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de Klerk, N.J.J. (author), van der Maas, E.L. (author), Wagemaker, M. (author)Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte andelectrode materials. From molecular dynamics simulations, manyproperties relevant to diffusion can be obtained, including the<br/>diffusion path, amplitude of vibrations, jump rates, radial distribution functions, and collective diffusion...journal article 2018
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