On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics

2013 ◽  
Vol 34 (16) ◽  
pp. 1375-1384 ◽  
Author(s):  
Tetsuya Morishita ◽  
Satoru G. Itoh ◽  
Hisashi Okumura ◽  
Masuhiro Mikami
Keyword(s):  
Free Energy ◽  
Logarithmic Mean ◽  
Force Dynamics ◽  
Energy Profiles ◽  
Free Energy Profiles

scholarly journals Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

2021 ◽  
Author(s):  
Amanuel Wolde-Kidan ◽  
Anna Herrmann ◽  
Albert Prause ◽  
Michael Gradzielski ◽  
Rainer Haag ◽  
...  
Keyword(s):  
Free Energy ◽  
Time Resolved ◽  
Energy Profiles ◽  
Penetration Data ◽  
Free Energy Profiles

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

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.

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles

2002 ◽  
Vol 116 (11) ◽  
pp. 4389-4402 ◽  
Author(s):  
Lula Rosso ◽  
Peter Mináry ◽  
Zhongwei Zhu ◽  
Mark E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Profiles ◽  
Free Energy Profiles

scholarly journals Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

2018 ◽  
Vol 14 (3) ◽  
pp. e1006024 ◽  
Author(s):  
Hidetoshi Kono ◽  
Shun Sakuraba ◽  
Hisashi Ishida
Keyword(s):  
Free Energy ◽  
Energy Profiles ◽  
Nucleosomal Dna ◽  
Superhelical Turn ◽  
Free Energy Profiles
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