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 Free energy pathways of a multistable liquid crystal device

Soft Matter ◽  
2015 ◽  
Vol 11 (24) ◽  
pp. 4809-4817 ◽  
Author(s):  
Halim Kusumaatmaja ◽  
Apala Majumdar
Keyword(s):  
Free Energy ◽  
Liquid Crystal ◽  
Energy Landscape ◽  
Minimum Energy ◽  
Transition States ◽  
Minimum Free Energy ◽  
Free Energy Landscape ◽  
Liquid Crystal Device ◽  
Energy Configurations ◽  
Energy Pathways

Understanding the free energy landscape of a multistable liquid crystal device in terms of its minimum free energy configurations, transition states, free energy barriers and minimum energy pathways.

scholarly journals Annealing synchronizes the 70S ribosome into a minimum-energy conformation

2021 ◽  
Author(s):  
Xiaofeng Chu ◽  
Xin Su ◽  
Mingdong Liu ◽  
Li Li ◽  
Tianhao Li ◽  
...  
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Energy Landscape ◽  
Minimum Energy ◽  
Boltzmann Distribution ◽  
Minimum Free Energy ◽  
Biological Macromolecules ◽  
Single Molecule Level ◽  
30S Subunit ◽  
70S Ribosome

Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven inter-subunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes, and exhibits a minimum energy in the free energy landscape. One can readily crystallize these minimum-energy ribosomes, which have great potential for synchronizing proteins on a single-molecule level. Our experimental results are consistent with theoretical analysis on the temperature-dependent Boltzmann distribution, and offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing can be extended to study protein folding and explore conformational and energy landscape.

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 Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

2021 ◽  
Vol 11 (9) ◽  
pp. 4052
Author(s):  
Alice Romeo ◽  
Mattia Falconi ◽  
Alessandro Desideri ◽  
Federico Iacovelli
Keyword(s):  
Free Energy ◽  
Double Helix ◽  
Minimum Energy ◽  
Switching Mechanism ◽  
Linker Length ◽  
Energy Profiles ◽  
Functional Dna ◽  
Triplex Forming Oligonucleotide ◽  
Dynamics Simulations ◽  
Free Energy Profiles

The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices.

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 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
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