Molecular Dynamics Simulation of the Effect of Interfaces in Melting and Solid-State Amorphization

1991 ◽  
Vol 230 ◽  
Author(s):  
Dieter Wolf ◽  
Sidney Yip
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Dynamics Simulation ◽  
Elastic Behavior ◽  
Melting Transition ◽  
Extended Defects ◽  
Free Standing ◽  
Extended Phase ◽  
Characteristic Features ◽  
State Amorphization

AbstractA newly developed molecular dynamics code was used to study the effect of free surfaces, grain boundaries and voids in the process of melting. It was found that conventional “thermodynamic melting” occurs via nucleation of the liquid at the extended defects with subsequent growth into the crystal. In the absence of interfaces, or when this transition is kinetically hindered, however, a second type of melting transition can be triggered by an elastic instability first described by Born (“mechanical melting”). It is suggested that the distinct characteristic features associated with the two types of melting are actually observed in solid-state amorphization experiments. A unified thermodynamics-based description, in the form of an extended phase diagram, of melting and solid-state amorphization is proposed which brings out the parallels between these two phenomena and suggests that their underlying causes are apparently the same. By investigating the effect of surface stresses on the structure and elastic behavior of free-standing thin films, we discuss how these concepts need to be modified in thin-film and small-grained materials.

Thermodynamic parallels between solid-state amorphization and melting

1990 ◽  
Vol 5 (2) ◽  
pp. 286-301 ◽  
Author(s):  
D. Wolf ◽  
P. R. Okamoto ◽  
S. Yip ◽  
J. F. Lutsko ◽  
M. Kluge
Keyword(s):  
Solid State ◽  
Amorphous Phase ◽  
Mechanical Instability ◽  
Extended Phase ◽  
Thermally Activated ◽  
Underlying Causes ◽  
Characteristic Features ◽  
Dynamics Simulations ◽  
Solid Liquid ◽  
State Amorphization

A thermodynamics-based description, in the form of an extended phase diagram, of melting and solid-state amorphization is proposed which brings out the parallels between these two phenomena and suggests that their underlying causes are apparently the same. Through molecular dynamics simulations we demonstrate that every crystal, in principle, can undergo two different types of melting transitions with characteristic features that are also observed in radiation- and hydrogenation-induced amorphization experiments on ordered alloys. The first type, defined in terms of free energies, is shown to involve the heterogeneous nucleation of the liquid or amorphous phase at extended lattice defects (such as grain boundaries, free surfaces, voids, or dislocations) and subsequent thermally-activated propagation of solid-liquid/amorphous interfaces through the crystal. The second type, arising from a mechanical instability limit described by Born, is homogeneous and does not require thermally-activated atom mobility. It is suggested that the role of chemical and structural disordering, a prerequisite for irradiation- but not hydrogenation-induced solid-state amorphization, is merely to drive the crystal lattice to a critical combination of volume and temperature at which the amorphous phase can form either heterogeneously or homogeneously.

scholarly journals The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5489
Author(s):  
Alexander Vogel ◽  
Mathias Bosse ◽  
Marcel Gauglitz ◽  
Sarah Wistuba ◽  
Peter Schmidt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Neuropeptide Y ◽  
Solid State Nmr ◽  
Bound State ◽  
Receptor Activation ◽  
Order Parameters ◽  
Dynamics Simulation ◽  
15N Nmr

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.

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