scholarly journals Free Energy Along Transition Pathways from Structure Refinement Simulations

2021 ◽  
Vol 120 (3) ◽  
pp. 97a
Author(s):  
Emmi Pohjolainen ◽  
Andrea C. Vaiana ◽  
Maxim Igaev ◽  
Helmut Grubmuller
2020 ◽  
Author(s):  
Xiaoyong Cao ◽  
Pu Tian

AbstractFree energy is arguably the most important property of molecular systems. Despite great progress in both its efficient estimation by scoring functions/potentials and more rigorous computation based on extensive sampling, we remain far from accurately predicting and manipulating biomolecular structures and their interactions. There are fundamental limitations, including accuracy of interaction description and difficulty of sampling in high dimensional space, to be tackled. Computational graph underlies major artificial intelligence platforms and is proven to facilitate training, optimization and learning. Combining autodifferentiation, coordinates transformation and generalized solvation free energy theory, we construct a computational graph infrastructure to realize seamless integration of fully trainable local free energy landscape with end to end differentiable iterative free energy optimization. This new framework greatly improves efficiency by replacing local sampling with differentiation. Its specific implementation in protein structure refinement achieves superb efficiency and competitive accuracy when compared with state of the art all-atom mainstream methods.


2021 ◽  
Vol 118 (49) ◽  
pp. e2106230118
Author(s):  
Jianyuan Yin ◽  
Kai Jiang ◽  
An-Chang Shi ◽  
Pingwen Zhang ◽  
Lei Zhang

Due to structural incommensurability, the emergence of a quasicrystal from a crystalline phase represents a challenge to computational physics. Here, the nucleation of quasicrystals is investigated by using an efficient computational method applied to a Landau free-energy functional. Specifically, transition pathways connecting different local minima of the Lifshitz–Petrich model are obtained by using the high-index saddle dynamics. Saddle points on these paths are identified as the critical nuclei of the 6-fold crystals and 12-fold quasicrystals. The results reveal that phase transitions between the crystalline and quasicrystalline phases could follow two possible pathways, corresponding to a one-stage phase transition and a two-stage phase transition involving a metastable lamellar quasicrystalline state, respectively.


2020 ◽  
Vol 43 ◽  
Author(s):  
Robert Mirski ◽  
Mark H. Bickhard ◽  
David Eck ◽  
Arkadiusz Gut

Abstract There are serious theoretical problems with the free-energy principle model, which are shown in the current article. We discuss the proposed model's inability to account for culturally emergent normativities, and point out the foundational issues that we claim this inability stems from.


Author(s):  
S. J. Pennycook ◽  
P. D. Nellist ◽  
N. D. Browning ◽  
P. A. Langjahr ◽  
M. Rühle

The simultaneous use of Z-contrast imaging with parallel detection EELS in the STEM provides a powerful means for determining the atomic structure of grain boundaries. The incoherent Z-contrast image of the high atomic number columns can be directly inverted to their real space arrangement, without the use of preconceived structure models. Positions and intensities may be accurately quantified through a maximum entropy analysis. Light elements that are not visible in the Z-contrast image can be studied through EELS; their coordination polyhedra determined from the spectral fine structure. It even appears feasible to contemplate 3D structure refinement through multiple scattering calculations.The power of this approach is illustrated by the recent study of a series of SrTiC>3 bicrystals, which has provided significant insight into some of the basic issues of grain boundaries in ceramics. Figure 1 shows the structural units deduced from a set of 24°, 36° and 65° symmetric boundaries, and 24° and 45° asymmetric boundaries. It can be seen that apart from unit cells and fragments from the perfect crystal, only three units are needed to construct any arbitrary tilt boundary. For symmetric boundaries, only two units are required, each having the same Burgers, vector of a<100>. Both units are pentagons, on either the Sr or Ti sublattice, and both contain two columns of the other sublattice, imaging in positions too close for the atoms in each column to be coplanar. Each column was therefore assumed to be half full, with the pair forming a single zig-zag column. For asymmetric boundaries, crystal geometry requires two types of dislocations; the additional unit was found to have a Burgers’ vector of a<110>. Such a unit is a larger source of strain, and is especially important to the transport characteristics of cuprate superconductors. These zig-zag columns avoid the problem of like-ion repulsion; they have also been seen in TiO2 and YBa2Cu3O7-x and may be a general feature of ionic materials.


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