scholarly journals Atomistic Study of the Role of Defects on α → ϵ Phase Transformations in Iron under Hydrostatic Compression

Metals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 1040 ◽  
Author(s):  
Hoang-Thien Luu ◽  
Roberto G. A. Veiga ◽  
Nina Gunkelmann
Keyword(s):  
Phase Transformation ◽  
Edge Dislocation ◽  
Transformation Process ◽  
Parent Material ◽  
Hydrostatic Compression ◽  
Initial Structure ◽  
Ε Phase ◽  
Dynamics Simulations ◽  
Cottrell Atmospheres

It has long been known that iron undergoes a phase transformation from body-centered cubic/ α structure to the metastable hexagonal close-packed/ ε phase under high pressure. However, the interplay of line and planar defects in the parent material with the transformation process is still not fully understood. We investigated the role of twins, dislocations, and Cottrell atmospheres in changing the crystalline iron structure during this phase transformation by using Monte Carlo methods and classical molecular dynamics simulations. Our results confirm that embryos of ε -Fe nucleate at twins under hydrostatic compression. The nucleation of the hcp phase is observed for single crystals containing an edge dislocation. We observe that the buckling of the dislocation can help to nucleate the dense phase. The crystal orientations between the initial structure α -Fe and ε -Fe in these simulations are 110 b c c | | 0001 h c p . The presence of Cottrell atmospheres surrounding an edge dislocation in bcc iron retards the development of the hcp phase.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

Exploring secondary interactions and the role of temperature in moisture-contaminated polymer networks through molecular simulations

Soft Matter ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. 2942-2956
Author(s):  
Rishabh D. Guha ◽  
Ogheneovo Idolor ◽  
Katherine Berkowitz ◽  
Melissa Pasquinelli ◽  
Landon R. Grace
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Temperature Variation ◽  
Polymer Networks ◽  
Molecular Simulations ◽  
Effect Of Temperature ◽  
Secondary Interactions ◽  
Dynamics Simulations ◽  
Secondary Bonding

We investigated the effect of temperature variation on the secondary bonding interactions between absorbed moisture and epoxies with different morphologies using molecular dynamics simulations.

scholarly journals Towards designing globular antimicrobial peptide mimics: role of polar functional groups in biomimetic ternary antimicrobial polymers

Soft Matter ◽  
2021 ◽  
Author(s):  
Garima Rani ◽  
Kenichi Kuroda ◽  
Satyavani Vemparala
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Bacterial Membrane ◽  
Simulation Data ◽  
Antimicrobial Polymers ◽  
Polar Groups ◽  
Methacrylate Polymers ◽  
Dynamics Simulations ◽  
Polar Functional Groups

Using atomistic molecular dynamics simulations, we study the interaction of ternary methacrylate polymers, composed of charged cationic, hydrophobic and neutral polar groups, with model bacterial membrane. Our simulation data shows...

scholarly journals Prediction of Functional Consequences of Missense Mutations in ANO4 Gene

2021 ◽  
Vol 22 (5) ◽  
pp. 2732
Author(s):  
Nadine Reichhart ◽  
Vladimir M. Milenkovic ◽  
Christian H. Wetzel ◽  
Olaf Strauß
Keyword(s):  
Transmembrane Protein ◽  
Functional Characterization ◽  
Missense Mutations ◽  
Mutant Proteins ◽  
Functional Consequences ◽  
New Perspective ◽  
The Stability ◽  
Dynamics Simulations ◽  
And Function

The anoctamin (TMEM16) family of transmembrane protein consists of ten members in vertebrates, which act as Ca2+-dependent ion channels and/or Ca2+-dependent scramblases. ANO4 which is primarily expressed in the CNS and certain endocrine glands, has been associated with various neuronal disorders. Therefore, we focused our study on prioritizing missense mutations that are assumed to alter the structure and stability of ANO4 protein. We employed a wide array of evolution and structure based in silico prediction methods to identify potentially deleterious missense mutations in the ANO4 gene. Identified pathogenic mutations were then mapped to the modeled human ANO4 structure and the effects of missense mutations were studied on the atomic level using molecular dynamics simulations. Our data show that the G80A and A500T mutations significantly alter the stability of the mutant proteins, thus providing new perspective on the role of missense mutations in ANO4 gene. Results obtained in this study may help to identify disease associated mutations which affect ANO4 protein structure and function and might facilitate future functional characterization of ANO4.

scholarly journals Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure

2021 ◽  
Vol 23 (10) ◽  
pp. 5984-5991
Author(s):  
Letizia Tavagnacco ◽  
Ester Chiessi ◽  
Emanuela Zaccarelli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Chain ◽  
Linear Polymer ◽  
Dynamics Simulations ◽  
Linear Polymer Chain

By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we unveil the role of pressure in the coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM).

Influence of material parameters on 2D-martensitic transformation based on the phase-field finite-element method

2019 ◽  
Vol 116 (6) ◽  
pp. 614
Author(s):  
Li Chang ◽  
Gao Jingxiang ◽  
Zhang Dacheng ◽  
Chen Zhengwei ◽  
Han Xing
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Phase Transformation ◽  
Martensitic Transformation ◽  
Phase Field ◽  
Martensite Transformation ◽  
Transformation Process ◽  
Martensite Phase ◽  
Phase Field Method ◽  
Element Method

Obtaining an accurate microscopic representation of the martensitic transformation process is key to realizing the best performance of materials and is of great significance in the field of material design. Due to the martensite phase transformation is rapidly, the current experimental is hard to capture all the information in the Martensite phase transformation process. Combining the phase-field method with the finite-element method, a model of martensitic transformation from a metastable state to a steady state is established. The law of a single martensite nucleus during martensitic transformation is accurately described. By changing the key materials that affect martensite transformation and the phase-field parameters, the effects of the parameters on the single martensitic nucleation process are obtained. This study provides an important theoretical basis for effectively revealing the essence of martensite transformation and can determine effective ways to influence martensite transformation, obtain the optimal parameters and improve the mechanical properties of such materials.

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