Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation

2005 ◽  
Vol 122 (8) ◽  
pp. 084707 ◽  
Author(s):  
Victoria Castells ◽  
Paul R. Van Tassel
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Free Energy ◽  
Lattice Model ◽  
Conformational Transition ◽  
Energy Profiles ◽  
Model Protein ◽  
Free Energy Profiles

Elastic Constants and Pair Potentials for Nematogenic Lattice Models

1998 ◽  
Vol 12 (22) ◽  
pp. 2305-2323 ◽  
Author(s):  
S. Romano
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Free Energy ◽  
Energy Density ◽  
Boundary Conditions ◽  
Elastic Constants ◽  
Lattice Model ◽  
Pair Potential ◽  
Lattice Models ◽  
Free Energy Density

Director configurations in nematic Liquid Crystals can be determined by minimizing their elastic free-energy density, on the basis of elastic constants and of specific boundary conditions; in some published cases, this has been obtained by numerical procedures where the elastic free-energy density plays the same role as the overall potential energy in a standard Monte Carlo simulation. The "potentials" used in these papers are short-ranged but, in general, not pairwise additive, unless the three elastic constants are set to a common value, thus reducing the potential to the well-known Lebwohl–Lasher lattice model.On the other hand, one can construct, possibly in different ways, a lattice model with pairwise additive interactions, approximately reproducing the elastic free-energy density, where parameters defining the pair potential are expressed as linear combinations of elastic constants; a nematogenic pair interaction of this kind, originally proposed by Gruhn and Hess (T. Gruhn and S. Hess, Z. Naturforsch.A51, 1 (1996)), has been investigated here by Monte Carlo simulation with periodic boundary conditions, i.e. aimed at the resulting bulk behavior.

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.

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