scholarly journals Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation

RNA ◽  
2009 ◽  
Vol 15 (12) ◽  
pp. 2248-2263 ◽  
Author(s):  
J. Zhang ◽  
J. Dundas ◽  
M. Lin ◽  
R. Chen ◽  
W. Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Three Dimensional ◽  
Energy Estimation

scholarly journals On the Kirchhoff-Love Hypothesis (Revised and Vindicated)

2021 ◽  
Author(s):  
Olivier Ozenda ◽  
Epifanio G. Virga
Keyword(s):  
Free Energy ◽  
Dimension Reduction ◽  
Three Dimensional ◽  
Energy Functional ◽  
The Other ◽  
Variational Model ◽  
Two Dimensional ◽  
Elastic Plates ◽  
Kinematic Constraint ◽  
Free Energy Functional

AbstractThe Kirchhoff-Love hypothesis expresses a kinematic constraint that is assumed to be valid for the deformations of a three-dimensional body when one of its dimensions is much smaller than the other two, as is the case for plates. This hypothesis has a long history checkered with the vicissitudes of life: even its paternity has been questioned, and recent rigorous dimension-reduction tools (based on standard $\varGamma $ Γ -convergence) have proven to be incompatible with it. We find that an appropriately revised version of the Kirchhoff-Love hypothesis is a valuable means to derive a two-dimensional variational model for elastic plates from a three-dimensional nonlinear free-energy functional. The bending energies thus obtained for a number of materials also show to contain measures of stretching of the plate’s mid surface (alongside the expected measures of bending). The incompatibility with standard $\varGamma $ Γ -convergence also appears to be removed in the cases where contact with that method and ours can be made.

scholarly journals Boundary conditions in topological AdS4/CFT3

2021 ◽  
Vol 2021 (2) ◽  
Author(s):  
Pietro Benetti Genolini ◽  
Matan Grinberg ◽  
Paul Richmond
Keyword(s):  
Field Theory ◽  
Free Energy ◽  
Boundary Conditions ◽  
Smooth Solution ◽  
Three Dimensional ◽  
Field Theories ◽  
Legendre Transformation ◽  
Generating Functional ◽  
Holographic Duals

Abstract We revisit the construction in four-dimensional gauged Spin(4) supergravity of the holographic duals to topologically twisted three-dimensional $$ \mathcal{N} $$ N = 4 field theories. Our focus in this paper is to highlight some subtleties related to preserving supersymmetry in AdS/CFT, namely the inclusion of finite counterterms and the necessity of a Legendre transformation to find the dual to the field theory generating functional. Studying the geometry of these supergravity solutions, we conclude that the gravitational free energy is indeed independent from the metric of the boundary, and it vanishes for any smooth solution.

scholarly journals Skewed thermodynamic geometry and optimal free energy estimation

2020 ◽  
Vol 153 (24) ◽  
pp. 244119
Author(s):  
Steven Blaber ◽  
David A. Sivak
Keyword(s):  
Free Energy ◽  
Energy Estimation ◽  
Thermodynamic Geometry

scholarly journals Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD

2017 ◽  
Author(s):  
Nathan A. Bernhardt ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Free Energy ◽  
Transcription Factor ◽  
Biological Function ◽  
Double Helix ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Conversion Process ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Helix Bundle

AbstractProteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.TOC Image

Extended high temperature low field expansions for the Ising model

1979 ◽  
Vol 57 (8) ◽  
pp. 1239-1245 ◽  
Author(s):  
S. McKenzie
Keyword(s):  
Free Energy ◽  
High Temperature ◽  
Ising Model ◽  
Three Dimensional ◽  
Low Field ◽  
Hypercubic Lattice

High temperature low field expansions are derived from the free energy of the Ising model for several two- and three-dimensional lattices. These represent a considerable advance on earlier work. Expansions for the four-dimensional hypercubic lattice are also presented.

Generalized Born implicit solvent models for small molecule hydration free energies

2017 ◽  
Vol 19 (2) ◽  
pp. 1677-1685 ◽  
Author(s):  
Martin Brieg ◽  
Julia Setzler ◽  
Steffen Albert ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Small Molecules ◽  
Implicit Solvent ◽  
Free Energies ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Generalized Born ◽  
Solvent Models ◽  
Molecular Force ◽  
Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

Docking, Binding Free Energy Estimation, and MD Simulation of Newly Designed CQ and HCQ Analogues Against the Spike-ACE2 Complex of SARS-CoV-2

2021 ◽  
Vol 6 (4) ◽  
pp. 77-89
Author(s):  
Anjoomaara H. Patel ◽  
Riya B. Patel ◽  
MahammadHussain J. Memon ◽  
Samiya S. Patel ◽  
Sharav A. Desai ◽  
...  
Keyword(s):  
Free Energy ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Docking Studies ◽  
Radius Of Gyration ◽  
Ligand Interaction ◽  
Energy Estimation ◽  
Efficacious Treatment ◽  
Protein Ligand Interaction ◽  
Derivatives Of

The coronavirus disease 2019 (COVID-19) virus has been spreading rapidly, and scientists are endeavouring to discover drugs for its efficacious treatment. Chloroquine phosphate, an old drug for treatment of malaria, has shown to have apparent efficacy and acceptable safety against COVID-19. As a part of Drug Discovery Hackathon-2020, in this study, the authors have tried making the derivatives of CQ and HCQ using MarvinSketch by ChemAxon. Molecular docking studies of these ligands were performed using Glide by Schrodinger, and ADME profiles were obtained by using QikProp. The obtained results after data analysis demonstrated that ligands HCQ_imidazoll, choloroquine_3c, HCQ_pyrrolC had good binding affinity and complied with all the ADME parameters. The molecular dynamic simulation of these ligands in complex with the 2019-nCoV RBD/ACE-2-B0AT1 complex PDB ID: 6M17 were carried out, and the parameters like RMSD, RMSF, and radius of gyration were observed to understand the fluctuations and protein-ligand interaction.

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