Crystal Nucleation Kinetics in Supercooled Germanium: MD Simulations versus Experimental Data

2020 ◽  
Vol 124 (36) ◽  
pp. 7979-7988 ◽  
Author(s):  
Azat O. Tipeev ◽  
Edgar D. Zanotto ◽  
José P. Rino
Keyword(s):  
Experimental Data ◽  
Md Simulations ◽  
Crystal Nucleation ◽  
Nucleation Kinetics

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

scholarly journals Unveiling the self-association and desolvation in crystal nucleation

IUCrJ ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 468-479
Author(s):  
Danning Li ◽  
Yongli Wang ◽  
Shuyi Zong ◽  
Na Wang ◽  
Xin Li ◽  
...  
Keyword(s):  
Density Functional ◽  
Interaction Strength ◽  
Solution Chemistry ◽  
The Self ◽  
Crystal Nucleation ◽  
Nucleation Kinetics ◽  
Molecular Conformations ◽  
Self Association ◽  
Induction Times ◽  
The Relationship

As the first step in the crystallization process, nucleation has been studied by many researchers. In this work, phenacetin (PHEN) was selected as a model compound to investigate the relationship between the solvent and nucleation kinetics. Induction times at different supersaturation in six solvents were measured. FTIR and NMR spectroscopy were employed to explore the solvent–solute interactions and the self-association properties in solution. Density functional theory (DFT) was adopted to evaluate the strength of solute–solvent interactions and the molecular conformations in different solvents. Based on these spectroscopy data, molecular simulation and nucleation kinetic results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics is discussed. Both the solute–solvent interaction strength and the supramolecular structure formed by the self-association of solute molecules affect the nucleation rate. The findings reported here shed new light on the molecular mechanism of nucleation in solution.

scholarly journals A hierarchical Bayesian framework for force field selection in molecular dynamics simulations

2016 ◽  
Vol 374 (2060) ◽  
pp. 20150032 ◽  
Author(s):  
S. Wu ◽  
P. Angelikopoulos ◽  
C. Papadimitriou ◽  
R. Moser ◽  
P. Koumoutsakos
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Force Field ◽  
Computational Cost ◽  
Md Simulations ◽  
Bayesian Framework ◽  
Underlying Structure ◽  
Hierarchical Bayesian ◽  
Wide Range ◽  
Selection Of

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

scholarly journals Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Tobias Schneider ◽  
Andrej Berg ◽  
Zeynel Ulusoy ◽  
Martin Gamerdinger ◽  
Christine Peter ◽  
...  
Keyword(s):  
Experimental Data ◽  
Functional Characterization ◽  
Isotopic Labeling ◽  
Md Simulations ◽  
Conformational Space ◽  
Coarse Grained ◽  
Covalent Attachment ◽  
Binding Studies ◽  
Polyubiquitin Chains ◽  
Polypeptide Chains

AbstractUbiquitylation is an eminent posttranslational modification referring to the covalent attachment of single ubiquitin molecules or polyubiquitin chains to a target protein dictating the fate of such labeled polypeptide chains. Here, we have biochemically produced artificially Lys11-, and Lys27-, and Lys63-linked ubiquitin dimers based on click-chemistry generating milligram quantities in high purity. We show that the artificial linkage used for the conjugation of two ubiquitin moieties represents a fully reliable surrogate of the natural isopeptide bond by acquiring highly resolved nuclear magnetic resonance (NMR) spectroscopic data including ligand binding studies. Extensive coarse grained and atomistic molecular dynamics (MD) simulations allow to extract structures representing the ensemble of domain-domain conformations used to verify the experimental data. Advantageously, this methodology does not require individual isotopic labeling of both ubiquitin moieties as NMR data have been acquired on the isotopically labeled proximal moiety and complementary MD simulations have been used to fully interpret the experimental data in terms of domain-domain conformation. This combined approach intertwining NMR spectroscopy with MD simulations makes it possible to describe the conformational space non-canonically Lys11-, and Lys27-linked ubiquitin dimers occupy in a solution averaged ensemble by taking atomically resolved information representing all residues in ubiquitin dimers into account.

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals Sugar Industry: Effect of Dextran Concentrations on the Sucrose Crystallization in Aqueous Solutions

2019 ◽  
Vol 2019 ◽  
pp. 1-6 ◽  
Author(s):  
Abdelali Borji ◽  
Fatima-Ezzahra Borji ◽  
Abdelaziz Jourani
Keyword(s):  
Experimental Data ◽  
Aqueous Solutions ◽  
Growth Process ◽  
Sugar Industry ◽  
Nucleation Kinetics ◽  
Metastable Zone Width ◽  
Zone Width ◽  
Industry Effect ◽  
Instantaneous Nucleation ◽  
Metastable Zone

Using the spectrophotometric method, as a new method, the influence of dextran on the sucrose solubility and metastable zone width has been studied. In agreement with the literature the experimental data show that the dextran has a negligible effect on the sucrose solubility. The results also show that this impurity decreases the sucrose metastable zone width. The study of the nucleation kinetics performed, using Nyvlt’s approach, shows that the dextran accelerates the nucleation and that the nuclei are formed in the solution by instantaneous nucleation. The presence of dextran in the system causes a decrease in the growth rate of sucrose. The growth process of sucrose is governed by a Birth and Spread mechanism. The kinetic parameters of sucrose growth in aqueous solutions without and with dextran were estimated.

Nucleation and Glass Formation

1985 ◽  
Vol 57 ◽  
Author(s):  
D. R. Uhlmann ◽  
M. C. Weinberg
Keyword(s):  
Glass Formation ◽  
Nucleation Theory ◽  
Crystal Nucleation ◽  
Oxide Glass ◽  
Classical Nucleation Theory ◽  
Nucleation Kinetics ◽  
Formation Behavior ◽  
Homogeneous Crystal ◽  
Exponential Factors

AbstractThe role of nucleation kinetics in affecting glass formation behavior is discussed. Also considered are measurements of homogeneous crystal nucleation in a variety of liquids. For a number of oxide glass-forming liquids, available data indicate pre-exponential factors which are larger than those predicted from classical nucleation theory by factors of 1017 to 1049. Possible sources of this discrepancy are discussed.

Kinetic Study Of Crystallisation In Amorphous Thin Lpcvd Si Films

1993 ◽  
Vol 321 ◽  
Author(s):  
B. Pieraggi ◽  
J. P. Guillemet ◽  
B. de Mauduit
Keyword(s):  
Experimental Data ◽  
Steady State ◽  
Isothermal Annealing ◽  
Nucleation Kinetics ◽  
Crystallisation Kinetics ◽  
Crystallisation Behaviour ◽  
Steady State Rate ◽  
State Rate ◽  
Si Films

ABSTRACTThe crystallisation behaviour of LPCVD silicon films has been investigated by TEM from in situ isothermal annealing of undoped a-Si films deposited from disilane (Si2H6) at temperatures 450,465 and 480 °C and at gas pressure of 200 MTorr. Nucleation kinetics, grain growth rates and crystallisation kinetics were determined for temperatures ranging from 600 to 675 °C. Nucleation kinetics have been experimentally determined in the early first stages of annealing : they do not show any steady-state rate and are fitted according to a power law. Experimental data for crystallisation kinetics are fitted by an Avrami law without introducing any incubation time.

scholarly journals Analytical solutions of mushy layer equations describing directional solidification in the presence of nucleation

2018 ◽  
Vol 376 (2113) ◽  
pp. 20170217 ◽  
Author(s):  
Dmitri V. Alexandrov ◽  
Alexander A. Ivanov ◽  
Irina V. Alexandrova
Keyword(s):  
Phase Transition ◽  
Supercooled Liquid ◽  
Crystal Nucleation ◽  
Supersaturated Solution ◽  
Pure Liquid ◽  
Particle Nucleation ◽  
Nucleation Kinetics ◽  
Differential Model ◽  
Phase Transition Interface ◽  
Phase Transition Boundary

The processes of particle nucleation and their evolution in a moving metastable layer of phase transition (supercooled liquid or supersaturated solution) are studied analytically. The transient integro-differential model for the density distribution function and metastability level is solved for the kinetic and diffusionally controlled regimes of crystal growth. The Weber–Volmer–Frenkel–Zel’dovich and Meirs mechanisms for nucleation kinetics are used. We demonstrate that the phase transition boundary lying between the mushy and pure liquid layers evolves with time according to the following power dynamic law: , where Z 1 ( t )= βt 7/2 and Z 1 ( t )= βt 2 in cases of kinetic and diffusionally controlled scenarios. The growth rate parameters α , β and ε are determined analytically. We show that the phase transition interface in the presence of crystal nucleation and evolution propagates slower than in the absence of their nucleation. This article is part of the theme issue ‘From atomistic interfaces to dendritic patterns’.

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