scholarly journals Molecular dynamics simulations of liquid silica crystallization

2018 ◽  
Vol 115 (21) ◽  
pp. 5348-5352 ◽  
Author(s):  
Haiyang Niu ◽  
Pablo M. Piaggi ◽  
Michele Invernizzi ◽  
Michele Parrinello
Keyword(s):  
Free Energy ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Free Energy Surface ◽  
X Ray Diffraction ◽  
Collective Variables ◽  
Atomic Simulations ◽  
The Difference ◽  
Dynamics Simulations ◽  
Good Agreement

Silica is one of the most abundant minerals on Earth and is widely used in many fields. Investigating the crystallization of liquid silica by atomic simulations is of great importance to understand the crystallization mechanism; however, the high crystallization barrier and the tendency of silica to form glasses make such simulations very challenging. Here we have studied liquid silica crystallization to β-cristobalite with metadynamics, using X-ray diffraction (XRD) peak intensities as collective variables. The frequent transitions between solid and liquid of the biased runs demonstrate the highly successful use of the XRD peak intensities as collective variables, which leads to the convergence of the free-energy surface. By calculating the difference in free energy, we have estimated the melting temperature of β-cristobalite, which is in good agreement with the literature. The nucleation mechanism during the crystallization of liquid silica can be described by classical nucleation theory.

scholarly journals Molecular-dynamics simulations of urea nucleation from aqueous solution

2014 ◽  
Vol 112 (1) ◽  
pp. E6-E14 ◽  
Author(s):  
Matteo Salvalaglio ◽  
Claudio Perego ◽  
Federico Giberti ◽  
Marco Mazzotti ◽  
Michele Parrinello
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Molecular Simulations ◽  
Finite Size ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Science And Engineering ◽  
Finite Size Effects ◽  
Dynamics Simulations ◽  
Insight Into

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

Local atomic structure in tetragonal pure ZrO2nanopowders

2010 ◽  
Vol 43 (2) ◽  
pp. 227-236 ◽  
Author(s):  
Leandro M. Acuña ◽  
Diego G. Lamas ◽  
Rodolfo O. Fuentes ◽  
Ismael O. Fábregas ◽  
Márcia C. A. Fantini ◽  
...  
Keyword(s):  
Tetragonal Phase ◽  
Local Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Crystallite Sizes ◽  
Exafs Study ◽  
The Difference ◽  
X Ray Absorption ◽  
Good Agreement

The local atomic structures around the Zr atom of pure (undoped) ZrO2nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr—O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye–Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to thezdirection; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.

scholarly journals Efficiency of immersion mode ice nucleation on surrogates of mineral dust

2007 ◽  
Vol 7 (19) ◽  
pp. 5081-5091 ◽  
Author(s):  
C. Marcolli ◽  
S. Gedamke ◽  
T. Peter ◽  
B. Zobrist
Keyword(s):  
Contact Angle ◽  
Active Sites ◽  
Quantitative Agreement ◽  
Ice Nucleation ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Aqueous Suspensions ◽  
Freezing Temperatures ◽  
Good Agreement ◽  
Heterogeneous Ice Nucleation

Abstract. A differential scanning calorimeter (DSC) was used to explore heterogeneous ice nucleation of emulsified aqueous suspensions of two Arizona test dust (ATD) samples with particle diameters of nominally 0–3 and 0–7 μm, respectively. Aqueous suspensions with ATD concentrations of 0.01–20 wt% have been investigated. The DSC thermograms exhibit a homogeneous and a heterogeneous freezing peak whose intensity ratios vary with the ATD concentration in the aqueous suspensions. Homogeneous freezing temperatures are in good agreement with recent measurements by other techniques. Depending on ATD concentration, heterogeneous ice nucleation occurred at temperatures as high as 256 K or down to the onset of homogeneous ice nucleation (237 K). For ATD-induced ice formation Classical Nucleation Theory (CNT) offers a suitable framework to parameterize nucleation rates as a function of temperature, experimentally determined ATD size, and emulsion droplet volume distributions. The latter two quantities serve to estimate the total heterogeneous surface area present in a droplet, whereas the suitability of an individual heterogeneous site to trigger nucleation is described by the compatibility function (or contact angle) in CNT. The intensity ratio of homogeneous to heterogeneous freezing peaks is in good agreement with the assumption that the ATD particles are randomly distributed amongst the emulsion droplets. The observed dependence of the heterogeneous freezing temperatures on ATD concentrations cannot be described by assuming a constant contact angle for all ATD particles, but requires the ice nucleation efficiency of ATD particles to be (log)normally distributed amongst the particles. Best quantitative agreement is reached when explicitly assuming that high-compatibility sites are rare and that therefore larger particles have on average more and better active sites than smaller ones. This analysis suggests that a particle has to have a diameter of at least 0.1 μm to exhibit on average one active site.

The Effects of Si on the Nucleation Kinetics of Ferrite in Dual Phase Steels

2007 ◽  
Vol 26-28 ◽  
pp. 1307-1310 ◽  
Author(s):  
Sang Hwan Lee ◽  
Kyung Jong Lee
Keyword(s):  
Free Energy ◽  
Interfacial Energy ◽  
Free Energy Change ◽  
Nucleation Theory ◽  
Energy Change ◽  
Classical Nucleation Theory ◽  
Nucleation Kinetics ◽  
Kinetics Of ◽  
Volume Free Energy Change ◽  
Thermodynamic Factors

It is generally accepted that Si promotes kinetics of polygonal ferrite due to thermodynamic factors such as Ae3 and maximum amount of ferrite formed. However, in this study, it was found that the difference between the measured rates of ferrite formation in C-Mn steel and Si added steel was much larger than that expected considering only thermodynamic factors. The classical nucleation theory with pillbox model was adopted to figure out what is the most controlling factor in formation of ferrite. The volume free energy change was calculated by use of the dilute solution model. The diffusivity of carbon (DC) was formulated as functions of C, Mn and Si by using experimental data. It was found that the volume free energy change was still predominant but the kinetic factors such as interfacial energy and the diffusivity of carbon by addition of Si were not negligible at lower undercooling. However, with increasing undercooling, the diffusivity of C was the most effective on the ferrite kinetics, though the ambiguity of treating interfacial energy was not yet clear.

Dissolution and Growth Kinetics of Small Crystals in Liquids

1991 ◽  
Vol 238 ◽  
Author(s):  
Michael J. Uttormark ◽  
Michael O. Thompson ◽  
Paulette Clancy
Keyword(s):  
Molecular Dynamics ◽  
Melting Point ◽  
Driving Force ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Equilibrium Melting Point ◽  
Small Crystals ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Nucleation Phenomenon

ABSTRACTMolecular Dynamics simulations of the melting of small crystalline clusters (≃800 atoms) in the liquid have been performed at various temperatures above the equilibrium melting point. The melting rates as functions of size and temperature are derived and compared to that predicted by Classical Nucleation Theory. It is found that the driving force for the melting of clusters does not follow the form assumed in the theory, and that this difference is most apparent for clusters containing less than 300 atoms. The implications of these findings on nucleation phenomenon and possible sources for the discrepancies are discussed.

scholarly journals Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

2021 ◽  
Author(s):  
Christos Lamprakis ◽  
Ioannis Andreadelis ◽  
John Manchester ◽  
Camilo Velez-Vega ◽  
José S. Duca ◽  
...  
Keyword(s):  
Free Energy ◽  
Membrane Proteins ◽  
Force Field ◽  
Biological Activities ◽  
Coarse Grained ◽  
Protein Oligomerization ◽  
Free Energy Surface ◽  
Collective Variables ◽  
Protein Dimerization ◽  
Dimerization Process

<p>Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could ultimately lead to new approaches in designing novel therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we use parallel tempering metadynamics simulations in the well-tempered ensemble to evaluate the performance of Martini 2.2P and Martini open-beta 3 (Martini 3) force fields in reproducing the structure and energetics of the dimerization process of membrane proteins and proteins in an aqueous solution in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association by estimating large barriers in distinct areas, which likely leads to overaggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results in a systematic underestimation of the free energy of association for proteins in solution, while it performs well in describing the association of membrane proteins. In all cases the near-native dimer complexes are identified as minima in the free energy surface albeit not always as the lowest minima. In the case of Martini 3 we find that the spurious supramolecular protein aggregation present in Martini 2.2P multimer simulations is alleviated and thus this force field may be more suitable for the study of protein oligomerization. We propose that the use of enhanced sampling simulations with a refined coarse-grained force field and appropriately defined collective variables is a robust approach for studying the protein dimerization process, although one should be cautious of the ranking of energy minima.</p>

Analytical Investigation on the Homogeneous Nucleation in a Mono-Component and Bi-Component Droplet

2019 ◽  
Author(s):  
Xi Xi ◽  
Hong Liu ◽  
Chang Cai ◽  
Ming Jia ◽  
Weilong Zhang
Keyword(s):  
Nucleation Rate ◽  
Homogeneous Nucleation ◽  
Ambient Pressure ◽  
Analytical Investigation ◽  
Bubble Nucleation ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Liquid Temperature ◽  
Wide Range ◽  
Good Agreement

Abstract The work attempts to analyze the performance of homogeneous nucleation by using the non-equilibrium thermodynamics theory and the classical nucleation theory. A nucleation rate graph was constructed under a wide range of operating temperature conditions. The results indicate that the superheat limit temperature (SLT) estimated by the modified homogeneous nucleation sub-model is in good agreement with the experimental results. The nucleation rate increases exponentially with the liquid temperature rise when the liquid temperature exceeds the SLT under atmospheric pressure. The superheated temperature needed to trigger the bubble nucleation decreases with the elevated ambient pressure.

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