New Polarizable Atomic Force Fields for Calculation of Non-bonded Interactions in Explicit and Implicit Aqueous Surrounding

2010 ◽  
Vol 5 (2) ◽  
pp. 138-149 ◽  
Author(s):  
А.В. Финкельштейн ◽  
A.V. Finkelstein
Keyword(s):  
Force Fields ◽  
Atomic Force

scholarly journals Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions

2011 ◽  
Vol 32 (8) ◽  
pp. 1680-1686 ◽  
Author(s):  
Shide Liang ◽  
Yaoqi Zhou ◽  
Nick Grishin ◽  
Daron M. Standley
Keyword(s):  
Force Fields ◽  
Side Chain ◽  
Series Expansions ◽  
Atomic Force

A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (21) ◽  
pp. 13629-13639 ◽  
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Force Fields ◽  
Coarse Grained ◽  
Unfolded Proteins ◽  
Critical Comparison ◽  
Atomic Models ◽  
Atomic Force

The predicted dimension of unfolded proteins is quite different using native-centric Gō-like models and transferrable (non-structure-based) models based on current atomic force fields.

Atomic Force Fields*

1924 ◽  
Vol 9 (3) ◽  
pp. 237
Author(s):  
F. S. Brackett
Keyword(s):  
Force Fields ◽  
Atomic Force

scholarly journals Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials

2019 ◽  
Vol 2 (11) ◽  
pp. 1900135 ◽  
Author(s):  
David Dubbeldam ◽  
Krista S. Walton ◽  
Thijs J. H. Vlugt ◽  
Sofia Calero
Keyword(s):  
Force Fields ◽  
Nanoporous Materials ◽  
Atomic Force ◽  
Design Parameterization

scholarly journals Exploiting a Mechanical Perturbation of Titin Domain to Identify How Force Field Parameterization Affects Protein Refolding Pathways

2019 ◽  
Author(s):  
David Wang ◽  
Piotr E. Marszalek
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Direct Transition ◽  
Mechanical Perturbation ◽  
Atomic Force ◽  
Force Field Parameterization ◽  
Helical Peptide ◽  
Perturbed Model ◽  
Simulation Time ◽  
Insight Into

AbstractMolecular mechanics force fields have been shown to differ in their predictions of processes such as protein folding. To test how force field differences affect predicted protein behavior, we created a mechanically perturbed model of the beta-stranded I91 titin domain based on atomic force spectroscopy data and examined its refolding behavior using six different force fields. To examine the transferability of the force field discrepancies identified by this model, we compared the results to equilibrium simulations of the weakly helical peptide Ac-(AAQAA)3-NH2. The total simulation time was 80 µs. From these simulations we found significant differences in I91 perturbation refolding ability between force fields. Concurrently, Ac-(AAQAA)3-NH2 equilibration experiments indicated that although force fields have similar overall helical frequencies, they can differ in helical lifetimes. The combination of these results suggests that differences in force field parameterization may allow a more direct transition between the beta and alpha regions of the Ramachandran plot thereby affecting both beta-strand refolding ability and helical lifetimes. Furthermore, the combination of results suggests that using mechanically perturbed models can provide a controlled method to gain more insight into how force fields affect protein behavior.

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

2009 ◽  
Vol 130 (19) ◽  
pp. 195103 ◽  
Author(s):  
Marcos R. Betancourt ◽  
Sheyore J. Omovie
Keyword(s):  
Force Fields ◽  
Coarse Grained ◽  
Atomic Force

Cryogenic atomic force microscopy

1991 ◽  
Vol 49 ◽  
pp. 54-55
Author(s):  
K. A. Fisher ◽  
M. G. L. Gustafsson ◽  
M. B. Shattuck ◽  
J. Clarke
Keyword(s):  
Room Temperature ◽  
Rapid Freezing ◽  
Cryogenic Temperatures ◽  
Soft Or ◽  
Electrically Conductive ◽  
Force Microscopy ◽  
Flexible Molecules ◽  
Advantages And Disadvantages ◽  
Atomic Force ◽  
Chemical Perturbation

The atomic force microscope (AFM) is capable of imaging electrically conductive and non-conductive surfaces at atomic resolution. When used to image biological samples, however, lateral resolution is often limited to nanometer levels, due primarily to AFM tip/sample interactions. Several approaches to immobilize and stabilize soft or flexible molecules for AFM have been examined, notably, tethering coating, and freezing. Although each approach has its advantages and disadvantages, rapid freezing techniques have the special advantage of avoiding chemical perturbation, and minimizing physical disruption of the sample. Scanning with an AFM at cryogenic temperatures has the potential to image frozen biomolecules at high resolution. We have constructed a force microscope capable of operating immersed in liquid n-pentane and have tested its performance at room temperature with carbon and metal-coated samples, and at 143° K with uncoated ferritin and purple membrane (PM).

Use of the Magnetostatic Analogue In Electromagnetic Lens Engineering

1970 ◽  
Vol 28 ◽  
pp. 360-361
Author(s):  
John W. Coleman
Keyword(s):  
Boundary Conditions ◽  
High Performance ◽  
Force Fields ◽  
Optical Design ◽  
Direct Conversion ◽  
Design Engineering ◽  
Design Data ◽  
Scalar Potentials ◽  
Geometric Elements ◽  
At Will

In the design engineering of high performance electromagnetic lenses, the direct conversion of electron optical design data into drawings for reliable hardware is oftentimes difficult, especially in terms of how to mount parts to each other, how to tolerance dimensions, and how to specify finishes. An answer to this is in the use of magnetostatic analytics, corresponding to boundary conditions for the optical design. With such models, the magnetostatic force on a test pole along the axis may be examined, and in this way one may obtain priority listings for holding dimensions, relieving stresses, etc..The development of magnetostatic models most easily proceeds from the derivation of scalar potentials of separate geometric elements. These potentials can then be conbined at will because of the superposition characteristic of conservative force fields.

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