Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates

2010 ◽  
Vol 6 (10) ◽  
pp. 3212-3222 ◽  
Author(s):  
A. Ghoufi ◽  
D. Morineau ◽  
R. Lefort ◽  
P. Malfreyt
Keyword(s):  
Force Field ◽  
Coarse Graining ◽  
Optimization Method ◽  
Mesoporous Silicates ◽  
Multiscale Optimization ◽  
Mcm 41

PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK II: COMPARISONS OF FORCE FIELDS BY FOLDING SIMULATIONS OF SHORT PEPTIDES

2004 ◽  
Vol 03 (03) ◽  
pp. 359-378 ◽  
Author(s):  
YOSHITAKE SAKAE ◽  
YUKO OKAMOTO
Keyword(s):  
Force Field ◽  
Protein Data Bank ◽  
Force Fields ◽  
Data Bank ◽  
Optimization Method ◽  
Short Peptides ◽  
Force Field Parameters ◽  
Hairpin Structures ◽  
Hairpin Peptides ◽  
Folding Simulations

In Paper I of this series, the formulations of the optimization method of existing force-field parameters for protein systems have been presented. We then applied it to five sets of force-field parameters, namely, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM version 22, and OPLS-AA. In order to test the validity of these force fields, the folding simulations of α-helical and β-hairpin peptides have been performed with each of the original and optimized force-field parameters. We found that all five modified force-field parameters gave both α-helical and β-hairpin structures more consistent with the experimental implications than the original force fields.

ChemInform Abstract: Acidity of Substituted MCM-41-Type Mesoporous Silicates Probed by Ammonia.

ChemInform ◽  
2010 ◽  
Vol 28 (31) ◽  
pp. no-no
Author(s):  
H. KOSSLICK ◽  
H. LANDMESSER ◽  
R. FRICKE
Keyword(s):  
Mesoporous Silicates ◽  
Mcm 41

Shaping inductor geometry for casting functionally graded composites

2016 ◽  
Vol 35 (1) ◽  
pp. 16-26 ◽  
Author(s):  
Slawomir Golak ◽  
Mirosław Kordos
Keyword(s):  
Force Field ◽  
Electromagnetic Force ◽  
Low Frequency ◽  
Casting Process ◽  
Optimization Methods ◽  
Optimization Method ◽  
Functionally Graded ◽  
Matrix Composites ◽  
Content Type ◽  
Functionally Graded Composites

Purpose – The attractiveness of functionally graded composites lies in the possibility of a gradual spatial change of their properties such as hardness, strength and wear resistance. The purpose of this paper is to discuss the use of electromagnetic buoyancy to separate the reinforcement particles during the casting process of such a composite. Design/methodology/approach – The basic problem encountered in the process of casting composites is to obtain electromagnetic buoyancy and simultaneously to avoid a flow of the liquid metal which destroys the desired composite structure. In this paper the authors present the methodology of numerical optimization of inductor geometry in order to homogenize the electromagnetic force field distribution. Findings – The optimization method based on searching the solution subspace created by applying knowledge of the modelled process physics proved better than the universal local optimization methods. These results were probably caused by the complex shape of the criterion function hypersurface characterized by the presence of local minima. Practical implications – Due to their characteristics, functionally graded composites are of great interest to the automotive, aerospace and defense industries. In the case of metal matrix composites casting techniques (as the presented one) are the most effective methods of producing functionally graded materials. Originality/value – The paper presents the optimization of a new process of casting functionally graded composites in a low-frequency alternating electromagnetic field. The process involves problems that did not occur previously in the area of electromagnetic processing of materials. The paper proposes the use of special design of inductors to homogenize the electromagnetic force field.

scholarly journals A novel force field parameter optimization method based on LSSVR for ECEPP

FEBS Letters ◽  
2011 ◽  
Vol 585 (6) ◽  
pp. 888-892 ◽  
Author(s):  
Yunling Liu ◽  
Lan Tao ◽  
Jianjun Lu ◽  
Shuo Xu ◽  
Qin Ma ◽  
...  
Keyword(s):  
Force Field ◽  
Parameter Optimization ◽  
Optimization Method ◽  
Field Parameter ◽  
Force Field Parameter

scholarly journals Semi-Automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

2020 ◽  
Author(s):  
Yalun Yu ◽  
Andreas Kramer ◽  
Andrew Simmonett ◽  
Rick Venable ◽  
Alex MacKerell ◽  
...  
Keyword(s):  
Force Field ◽  
Lipid Bilayers ◽  
Long Range ◽  
Liquid Crystalline ◽  
Pair Correlation ◽  
Optimization Method ◽  
Free Energy Calculations ◽  
Fine Tuning ◽  
Compression Isotherm ◽  
High Level

The development of the CHARMM lipid force field (FF) can be traced back to the early 1990s with its current version denoted CHARMM36 (C36). The parametrization of C36 utilized high-level quantum mechanical data and free energy calculations of model compounds before parameters were manually adjusted to yield agreement with experimental properties of lipid bilayers. While such manual fine-tuning of FF parameters is based on intuition and trial-and-error, automated methods can identify beneficial modifications of the parameters via their sensitivities and thereby guide the optimization process. This paper introduces a semi-automated approach to reparametrize the CHARMM lipid FF with consistent inclusion of long-range dispersion through the LennardJones particle-mesh Ewald (LJ-PME) approach. The optimization method is based on thermodynamic reweighting with regularization with respect to the C36 set. Two independent optimizations with different topology restrictions are presented. Targets of the optimizations are primarily liquid crystalline phase properties of lipid bilayers and the compression isotherm of monolayers. Pair correlation functions between water and lipid functional groups in aqueous solution are also included to address headgroup hydration. While the physics of the reweighting strategy itself is well understood, applying it to heterogeneous, complex anisotropic systems poses additional challenges. These were overcome through careful selection of target properties and reweighting settings allowing for the successful incorporation of the explicit treatment of long-range dispersion, and we denote the newly optimized lipid force field as C36/LJ-PME. The current implementation of the optimization protocol will facilitate the future development of the CHARMM and related lipid force fields.<br>

Chromium and titanium/chromium-containing MCM-41 mesoporous silicates as promising catalysts for the photobleaching of azo dyes in aqueous suspensions. A multitechnique investigation

2012 ◽  
Vol 163 ◽  
pp. 85-95 ◽  
Author(s):  
Verónica R. Elías ◽  
Ema V. Sabre ◽  
Elin L. Winkler ◽  
María L. Satuf ◽  
Enrique Rodriguez-Castellón ◽  
...  
Keyword(s):  
Azo Dyes ◽  
Mesoporous Silicates ◽  
Aqueous Suspensions ◽  
Mcm 41
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