Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

2016 ◽  
Vol 145 (3) ◽  
pp. 034109 ◽  
Author(s):  
Tanmoy Sanyal ◽  
M. Scott Shell
Keyword(s):  
Relative Entropy ◽  
Local Density ◽  
Coarse Grained ◽  
Implicit Solvation

Transferability of Local Density-Assisted Implicit Solvation Models for Homogeneous Fluid Mixtures

2019 ◽  
Vol 15 (5) ◽  
pp. 2881-2895 ◽  
Author(s):  
David Rosenberger ◽  
Tanmoy Sanyal ◽  
M. Scott Shell ◽  
Nico F. A. van der Vegt
Keyword(s):  
Local Density ◽  
Implicit Solvation ◽  
Homogeneous Fluid ◽  
Fluid Mixtures ◽  
Solvation Models

scholarly journals Partial structure factors derived from coarse-grained phase-separation dynamics on a disordered lattice with density fluctuations

2021 ◽  
Author(s):  
Puwadet Sutipanya ◽  
Takashi Arai
Keyword(s):  
Phase Separation ◽  
Structure Factor ◽  
Lattice Point ◽  
Local Density ◽  
Lattice Points ◽  
Concentration Fluctuations ◽  
Coarse Grained ◽  
Partial Structure ◽  
Disordered Lattice ◽  
Structure Factors

Abstract The simplest and most time-efficient phase-separation dynamics simulations are carried out on a disordered lattice to calculate the partial structure factors of coarse-grained A-B binary mixtures. The typical coarse-grained phase-separation models use regular lattices and can describe the local concentrations but cannot describe both local density and concentration fluctuations. To introduce fluctuation for local density in the model, the particle positions from a hard sphere fluid model are determined as disordered lattice points for the model. Then we place the local order parameter as the difference of the concentrations of A and B components on each lattice point. The concentration at each lattice point is time-evolved by discrete equations derived from the Cahn-Hilliard equation. From both fluctuations, Bhatia and Thornton’s structure factor can be accurately calculated. The structure factor for concentration fluctuations at the large wavenumber region gives us the correct mean concentrations of the components. Using the mean concentrations, partial structure factors can be converted from three of Bhatia and Thornton’s structure factors. The present model and procedures can provide a means of analysing the structural properties of many materials that exhibit complex morphological changes.

scholarly journals Inferring functional units in ion channel pores via relative entropy

2021 ◽  
Vol 50 (1) ◽  
pp. 37-57
Author(s):  
Michael Schmidt ◽  
Indra Schroeder ◽  
Daniel Bauer ◽  
Gerhard Thiel ◽  
Kay Hamacher
Keyword(s):  
Relative Entropy ◽  
Network Models ◽  
Coarse Grained ◽  
Model Parameters ◽  
First Principle ◽  
Structure And Dynamics ◽  
Entropy Minimization ◽  
Minimization Procedure ◽  
Anisotropic Network ◽  
Protein Models

AbstractCoarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.

The Alteration of the Pore Spaces in Sandstones

1973 ◽  
Vol 31 ◽  
pp. 210-211
Author(s):  
R. E. Ferrell ◽  
G. G. Paulson
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
The Other ◽  
Coarse Grained ◽  
Depositional Fabric ◽  
Soluble Components ◽  
Scanning Electron ◽  
Shape And Size

The pore spaces in sandstones are the result of the original depositional fabric and the degree of post-depositional alteration that the rock has experienced. The largest pore volumes are present in coarse-grained, well-sorted materials with high sphericity. The chief mechanisms which alter the shape and size of the pores are precipitation of cementing agents and the dissolution of soluble components. Each process may operate alone or in combination with the other, or there may be several generations of cementation and solution.The scanning electron microscope has ‘been used in this study to reveal the morphology of the pore spaces in a variety of moderate porosity, orthoquartzites.

On the Origin of the Microscystalline Structure in Rapidly Solidified IN-100 Powder

1977 ◽  
Vol 35 ◽  
pp. 260-261
Author(s):  
J. M. Walsh ◽  
K. P. Gumz ◽  
J. C. Whittles ◽  
B. H. Kear
Keyword(s):  
The Other ◽  
Coarse Grained ◽  
Microcrystalline Structure ◽  
Routine Examination ◽  
Atomization Process ◽  
Centrifugal Atomization ◽  
Splat Quenching ◽  
Powder Particles ◽  
Dendritic Microstructures ◽  
Rapidly Solidified

During a routine examination of the microstructure of rapidly solidified IN-100 powder, produced by a newly-developed centrifugal atomization process1, essentially two distinct types of microstructure were identified. When a high melt superheat is maintained during atomization, the powder particles are predominantly coarse-grained, equiaxed or columnar, with distinctly dendritic microstructures, Figs, la and 4a. On the other hand, when the melt superheat is reduced by increasing the heat flow to the disc of the rotary atomizer, the powder particles are predominantly microcrystalline in character, with typically one dendrite per grain, Figs, lb and 4b. In what follows, evidence is presented that strongly supports the view that the unusual microcrystalline structure has its origin in dendrite erosion occurring in a 'mushy zone' of dynamic solidification on the disc of the rotary atomizer.The critical observations were made on atomized material that had undergone 'splat-quenching' on previously solidified, chilled substrate particles.

Ab initio band theory approach to electron energy loss near edge structures

1988 ◽  
Vol 46 ◽  
pp. 506-507
Author(s):  
Xudong Weng ◽  
O.F. Sankey ◽  
Peter Rez
Keyword(s):  
Ab Initio ◽  
Local Density ◽  
Interpolation Method ◽  
Atomic Orbital ◽  
Plane Waves ◽  
Large Set ◽  
Theory Approach ◽  
Band Theory ◽  
Atomic Orbitals ◽  
Pseudopotential Calculations

Single electron band structure techniques have been applied successfully to the interpretation of the near edge structures of metals and other materials. Among various band theories, the linear combination of atomic orbital (LCAO) method is especially simple and interpretable. The commonly used empirical LCAO method is mainly an interpolation method, where the energies and wave functions of atomic orbitals are adjusted in order to fit experimental or more accurately determined electron states. To achieve better accuracy, the size of calculation has to be expanded, for example, to include excited states and more-distant-neighboring atoms. This tends to sacrifice the simplicity and interpretability of the method.In this paper. we adopt an ab initio scheme which incorporates the conceptual advantage of the LCAO method with the accuracy of ab initio pseudopotential calculations. The so called pscudo-atomic-orbitals (PAO's), computed from a free atom within the local-density approximation and the pseudopotential approximation, are used as the basis of expansion, replacing the usually very large set of plane waves in the conventional pseudopotential method. These PAO's however, do not consist of a rigorously complete set of orthonormal states.

Flux-pinning-related defect structures in melt-processed YBa2Cu3O7-x

1993 ◽  
Vol 51 ◽  
pp. 936-937
Author(s):  
Z. L. Wang ◽  
R. Kontra ◽  
A. Goyal ◽  
D. M. Kroeger ◽  
L.F. Allard
Keyword(s):  
Volume Fraction ◽  
Local Density ◽  
Stacking Faults ◽  
Image Resolution ◽  
Defect Structures ◽  
Atomic Structures ◽  
Transmission Electron ◽  
Point Image ◽  
Related Defect ◽  
Point To Point

Previous studies of Y2BaCuO5/YBa2Cu3O7-δ(Y211/Y123) interfaces in melt-processed and quench-melt-growth processed YBa2Cu3O7-δ using high resolution transmission electron microscopy (HRTEM) and energy dispersive X-ray spectroscopy (EDS) have revealed a high local density of stacking faults in Y123, near the Y211/Y123 interfaces. Calculations made using simple energy considerations suggested that these stacking faults may act as effective flux-pinners and may explain the observations of increased Jc with increasing volume fraction of Y211. The present paper is intended to determine the atomic structures of the observed defects. HRTEM imaging was performed using a Philips CM30 (300 kV) TEM with a point-to-point image resolution of 2.3 Å. Nano-probe EDS analysis was performed using a Philips EM400 TEM/STEM (100 kV) equipped with a field emission gun (FEG), which generated an electron probe of less than 20 Å in diameter.Stacking faults produced by excess single Cu-O layers: Figure 1 shows a HRTEM image of a Y123 film viewed along [100] (or [010]).

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