A Minimum Free Energy Reaction Path for the E2 Reaction between Fluoro Ethane and a Fluoride Ion

2004 ◽  
Vol 126 (31) ◽  
pp. 9492-9493 ◽  
Author(s):  
Bernd Ensing ◽  
Alessandro Laio ◽  
Francesco L. Gervasio ◽  
Michele Parrinello ◽  
Michael L. Klein
Keyword(s):  
Free Energy ◽  
Reaction Path ◽  
Minimum Free Energy ◽  
Fluoride Ion ◽  
Energy Reaction

scholarly journals The Free Energy Reaction Path Theory of Reliable Protein Folding

2009 ◽  
Vol 96 (3) ◽  
pp. 589a-590a
Author(s):  
Gregg Lois ◽  
Jerzy Blawzdziewicz ◽  
Corey O'Hern
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Reaction Path ◽  
Energy Reaction

scholarly journals Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path

2008 ◽  
Vol 95 (6) ◽  
pp. 2692-2701 ◽  
Author(s):  
Gregg Lois ◽  
Jerzy Blawzdziewicz ◽  
Corey S. O’Hern
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Reaction Path ◽  
Energy Landscapes ◽  
Complex Energy ◽  
Energy Reaction

Minimum free energy coding for DNA storage

2021 ◽  
pp. 1-1
Author(s):  
Ben Cao ◽  
Xiaokang Zhang ◽  
Jieqiong Wu ◽  
Bin Wang ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Minimum Free Energy ◽  
Dna Storage ◽  
Energy Coding

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

scholarly journals Magic number colloidal clusters as minimum free energy structures

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Junwei Wang ◽  
Chrameh Fru Mbah ◽  
Thomas Przybilla ◽  
Benjamin Apeleo Zubiri ◽  
Erdmann Spiecker ◽  
...  
Keyword(s):  
Free Energy ◽  
Magic Number ◽  
Minimum Free Energy ◽  
Colloidal Clusters

scholarly journals Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways

2017 ◽  
Vol 147 (15) ◽  
pp. 152718 ◽  
Author(s):  
Clark Templeton ◽  
Szu-Hua Chen ◽  
Arman Fathizadeh ◽  
Ron Elber
Keyword(s):  
Free Energy ◽  
Minimum Energy ◽  
Minimum Free Energy ◽  
Rock Climbing ◽  
Global Algorithm ◽  
Energy Pathways

scholarly journals String method solution of the gating pathways for a pentameric ligand-gated ion channel

2017 ◽  
Vol 114 (21) ◽  
pp. E4158-E4167 ◽  
Author(s):  
Bogdan Lev ◽  
Samuel Murail ◽  
Frédéric Poitevin ◽  
Brett A. Cromer ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Minimum Free Energy ◽  
Agonist Binding ◽  
String Method ◽  
Transition Analysis ◽  
Subunit Interface ◽  
Ion Conducting ◽  
Allosteric Mechanisms

Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.

The Minimum Free Energy for a Continuous-Spectrum Material

2011 ◽  
pp. 307-323
Author(s):  
Giovambattista Amendola ◽  
Mauro Fabrizio ◽  
John Murrough Golden
Keyword(s):  
Free Energy ◽  
Continuous Spectrum ◽  
Minimum Free Energy

Representation of the Minimum Free Energy in the Time Domain

2011 ◽  
pp. 269-276
Author(s):  
Giovambattista Amendola ◽  
Mauro Fabrizio ◽  
John Murrough Golden
Keyword(s):  
Free Energy ◽  
Time Domain ◽  
Minimum Free Energy ◽  
The Time Domain

The Minimum Free Energy

2011 ◽  
pp. 235-267
Author(s):  
Giovambattista Amendola ◽  
Mauro Fabrizio ◽  
John Murrough Golden
Keyword(s):  
Free Energy ◽  
Minimum Free Energy
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