scholarly journals Minimum free-energy path of homogenous nucleation from the phase-field equation

2009 ◽  
Vol 130 (24) ◽  
pp. 244507 ◽  
Author(s):  
Masao Iwamatsu
Author(s):  
Luis Espath ◽  
Victor Calo

AbstractWe propose a phase-field theory for enriched continua. To generalize classical phase-field models, we derive the phase-field gradient theory based on balances of microforces, microtorques, and mass. We focus on materials where second gradients of the phase field describe long-range interactions. By considering a nontrivial interaction inside the body, described by a boundary-edge microtraction, we characterize the existence of a hypermicrotraction field, a central aspect of this theory. On surfaces, we define the surface microtraction and the surface-couple microtraction emerging from internal surface interactions. We explicitly account for the lack of smoothness along a curve on surfaces enclosing arbitrary parts of the domain. In these rough areas, internal-edge microtractions appear. We begin our theory by characterizing these tractions. Next, in balancing microforces and microtorques, we arrive at the field equations. Subject to thermodynamic constraints, we develop a general set of constitutive relations for a phase-field model where its free-energy density depends on second gradients of the phase field. A priori, the balance equations are general and independent of constitutive equations, where the thermodynamics constrain the constitutive relations through the free-energy imbalance. To exemplify the usefulness of our theory, we generalize two commonly used phase-field equations. We propose a ‘generalized Swift–Hohenberg equation’—a second-grade phase-field equation—and its conserved version, the ‘generalized phase-field crystal equation’—a conserved second-grade phase-field equation. Furthermore, we derive the configurational fields arising in this theory. We conclude with the presentation of a comprehensive, thermodynamically consistent set of boundary conditions.


2019 ◽  
Vol 19 (2) ◽  
pp. 285
Author(s):  
Jaka Fajar Fatriansyah ◽  
Hanindito Haidar Satrio ◽  
Muhammad Joshua Yuriansyah Barmaki ◽  
Arbi Irsyad Fikri ◽  
Mochamad Chalid

Phase field model has been successfully derived from ordinary metal phase field equation to simulate the behavior of semi-crystalline polymer solidification phenomenon. To obtain the polymer phase field model, a non-conserved phase field equation can be expanded to include the unique polymer parameters, which do not exist in metals, for example, polymer melt viscosity and diffusion coefficient. In order to expand this model, we include free energy density and non-local free energy density based on Harrowel-Oxtoby and Ginzburg-Landau theorem for polymers. The expansion principle for a higher order of binary phase field parameter was employed to obtain fully modified phase field equation. To optimize the final properties of the products, the solidification phenomenon in polymers is very important. Here, we use our modified equation to investigate the effect of melt viscosity on the rate of solidification by employing ordinary differential equation numerical methods. It was found that the rate of solidification is related to the melting temperature and the kinetic coefficient.


Author(s):  
Ben Cao ◽  
Xiaokang Zhang ◽  
Jieqiong Wu ◽  
Bin Wang ◽  
Qiang Zhang ◽  
...  

Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.


2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Junwei Wang ◽  
Chrameh Fru Mbah ◽  
Thomas Przybilla ◽  
Benjamin Apeleo Zubiri ◽  
Erdmann Spiecker ◽  
...  

2017 ◽  
Vol 147 (15) ◽  
pp. 152718 ◽  
Author(s):  
Clark Templeton ◽  
Szu-Hua Chen ◽  
Arman Fathizadeh ◽  
Ron Elber

Author(s):  
Markus Schmuck ◽  
Marc Pradas ◽  
Grigorios A. Pavliotis ◽  
Serafim Kalliadasis

We derive a new, effective macroscopic Cahn–Hilliard equation whose homogeneous free energy is represented by fourth-order polynomials, which form the frequently applied double-well potential. This upscaling is done for perforated/strongly heterogeneous domains. To the best knowledge of the authors, this seems to be the first attempt of upscaling the Cahn–Hilliard equation in such domains. The new homogenized equation should have a broad range of applicability owing to the well-known versatility of phase-field models. The additionally introduced feature of systematically and reliably accounting for confined geometries by homogenization allows for new modelling and numerical perspectives in both science and engineering. Our results are applied to wetting dynamics in porous media and to a single channel with strongly heterogeneous walls.


2017 ◽  
Vol 114 (21) ◽  
pp. E4158-E4167 ◽  
Author(s):  
Bogdan Lev ◽  
Samuel Murail ◽  
Frédéric Poitevin ◽  
Brett A. Cromer ◽  
Marc Baaden ◽  
...  

Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.


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