scholarly journals Metadynamics studies of crystal nucleation

IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 256-266 ◽  
Author(s):  
Federico Giberti ◽  
Matteo Salvalaglio ◽  
Michele Parrinello
Keyword(s):  
Molecular Dynamics ◽  
Phase Transitions ◽  
State Of The Art ◽  
Sampling Technique ◽  
Short Review ◽  
Crystal Nucleation ◽  
Crystalline Solid ◽  
Enhanced Sampling ◽  
Long Timescales ◽  
Direct Investigation

Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation.

scholarly journals Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

2020 ◽  
Author(s):  
Vojtěch Mlýnský ◽  
Petra Kührová ◽  
Tomáš Kühr ◽  
Michal Otyepka ◽  
Giovanni Bussi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
State Of The Art ◽  
Dynamic Properties ◽  
Md Simulations ◽  
Experimental Methods ◽  
Fine Tuning ◽  
Enhanced Sampling ◽  
Structural Dynamic ◽  
Nmr Data

ABSTRACTDetermination of RNA structural-dynamic properties is challenging for experimental methods. Thus atomistic molecular dynamics (MD) simulations represent a helpful technique complementary to experiments. However, contemporary MD methods still suffer from limitations of force fields (ffs), including imbalances in the non-bonded ff terms. We have recently demonstrated that some improvement of state-of-the-art AMBER RNA ff can be achieved by adding a new term for H-bonding called gHBfix, which increases tuning flexibility and reduces the risk of side-effects. Still, the first gHBfix version did not fully correct simulations of short RNA tetranucleotides (TNs). TNs are key benchmark systems due to availability of unique NMR data, although giving too much weight on improving TN simulations can easily lead to over-fitting to A-form RNA. Here we combine the gHBfix version with another term called tHBfix, which separately treats H-bond interactions formed by terminal nucleotides. This allows to refine simulations of RNA TNs without affecting simulations of other RNAs. The approach is in line with adopted strategy of current RNA ffs, where the terminal nucleotides possess different parameters for the terminal atoms than the internal nucleotides. The combination of gHBfix with tHBfix significantly improves the behavior of RNA TNs during well-converged enhanced-sampling simulations. TNs mostly populate canonical A-form like states while spurious intercalated structures are largely suppressed. Still, simulations of r(AAAA) and r(UUUU) TNs show some residual discrepancies with the primary NMR data which suggests that future tuning of some other ff terms might be useful.

Phase field theory of crystal nucleation and polycrystalline growth: A review

2006 ◽  
Vol 21 (2) ◽  
pp. 309-319 ◽  
Author(s):  
L. Gránásy ◽  
T. Pusztai ◽  
T. Börzsönyi ◽  
G. Tóth ◽  
G. Tegze ◽  
...  
Keyword(s):  
Field Theory ◽  
Molecular Dynamics ◽  
Phase Field ◽  
Growth Front ◽  
Growth Patterns ◽  
Crystal Nucleation ◽  
Model Parameters ◽  
Nucleation Barrier ◽  
Broad Variety ◽  
Long Timescales

We briefly review our recent modeling of crystal nucleation and polycrystalline growth using a phase field theory. First, we consider the applicability of phase field theory for describing crystal nucleation in a model hard sphere fluid. It is shown that the phase field theory accurately predicts the nucleation barrier height for this liquid when the model parameters are fixed by independent molecular dynamics calculations. We then address various aspects of polycrystalline solidification and associated crystal pattern formation at relatively long timescales. This late stage growth regime, which is not accessible by molecular dynamics, involves nucleation at the growth front to create new crystal grains in addition to the effects of primary nucleation. Finally, we consider the limit of extreme polycrystalline growth, where the disordering effect due to prolific grain formation leads to isotropic growth patterns at long times, i.e., spherulite formation. Our model of spherulite growth exhibits branching at fixed grain misorientations, induced by the inclusion of a metastable minimum in the orientational free energy. It is demonstrated that a broad variety of spherulitic patterns can be recovered by changing only a few model parameters.

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.

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins

2015 ◽  
Vol 119 (46) ◽  
pp. 14594-14603 ◽  
Author(s):  
Ole Juul Andersen ◽  
Julie Grouleff ◽  
Perri Needham ◽  
Ross C. Walker ◽  
Frank Jensen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Molecular Dynamics Method ◽  
Enhanced Sampling ◽  
Dynamics Method

Structure, phase transitions and molecular dynamics in ferroelastic crystal pyrrolidinium hexachloroantimonate(V), [C4H8NH2][SbCl6]

2005 ◽  
Vol 7 (4) ◽  
pp. 381-390 ◽  
Author(s):  
Ryszard Jakubas ◽  
Beata Bednarska-Bolek ◽  
Jacek Zaleski ◽  
Wojciech Medycki ◽  
Krystyna Hołderna-Natkaniec ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Phase Transitions ◽  
Structure Phase

scholarly journals Cholinium amino acid-based ionic liquids

2021 ◽  
Author(s):  
Andrea Le Donne ◽  
Enrico Bodo
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Computational Chemistry ◽  
Special Class ◽  
State Of The Art ◽  
Short Review ◽  
Research Activity ◽  
Intensive Research ◽  
Low Toxicity ◽  
Molecular Components

AbstractBoosted by the simplicity of their synthesis and low toxicity, cholinium and amino acid-based ionic liquids have attracted the attention of researchers in many different fields ranging from computational chemistry to electrochemistry and medicine. Among the uncountable IL variations, these substances occupy a space on their own due to their exceptional biocompatibility that stems from being entirely made by metabolic molecular components. These substances have undergone a rather intensive research activity because of the possibility of using them as greener replacements for traditional ionic liquids. We present here a short review in the attempt to provide a compendium of the state-of-the-art scientific research about this special class of ionic liquids based on the combination of amino acid anions and cholinium cations.

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