scholarly journals A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules

2021 ◽  
Vol 94 (10) ◽  
Author(s):  
Roberto Menichetti ◽  
Marco Giulini ◽  
Raffaello Potestio
Keyword(s):  
Lattice Gas ◽  
Coarse Grained ◽  
Enhanced Sampling ◽  
Mapping Space ◽  
Metric Properties ◽  
Specific Choice ◽  
Quantitative Manner ◽  
Discontinuous Phase ◽  
Reduced Representations ◽  
Discontinuous Phase Transitions

Abstract A mapping of a macromolecule is a prescription to construct a simplified representation of the system in which only a subset of its constituent atoms is retained. As the specific choice of the mapping affects the analysis of all-atom simulations as well as the construction of coarse-grained models, the characterisation of the mapping space has recently attracted increasing attention. We here introduce a notion of scalar product and distance between reduced representations, which allows the study of the metric and topological properties of their space in a quantitative manner. Making use of a Wang–Landau enhanced sampling algorithm, we exhaustively explore such space, and examine the qualitative features of mappings in terms of their squared norm. A one-to-one correspondence with an interacting lattice gas on a finite volume leads to the emergence of discontinuous phase transitions in mapping space, which mark the boundaries between qualitatively different reduced representations of the same molecule. Graphicabstract

scholarly journals Fundamental ingredients for discontinuous phase transitions in the inertial majority vote model

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Jesus M. Encinas ◽  
Pedro E. Harunari ◽  
M. M. de Oliveira ◽  
Carlos E. Fiore
Keyword(s):  
Phase Transitions ◽  
Majority Vote ◽  
Vote Model ◽  
Discontinuous Phase ◽  
Discontinuous Phase Transitions

scholarly journals Coarse Graining, Nonmaximal Entropy, and Power Laws

Entropy ◽  
2018 ◽  
Vol 20 (10) ◽  
pp. 737
Author(s):  
Fernando Pérez-Cárdenas ◽  
Lorenzo Resca ◽  
Ian Pegg
Keyword(s):  
Maximum Entropy ◽  
Power Law ◽  
Lattice Gas ◽  
Maximum Entropy Principle ◽  
Coarse Graining ◽  
Power Laws ◽  
Density Fluctuations ◽  
Coarse Grained ◽  
Dimensional Lattice ◽  
Entropy Principle

We show that coarse graining produces significant and predictable effects on the entropy of states of equilibrium when the scale of coarse graining becomes comparable to that of density fluctuations. We demonstrate that a coarse-grained entropy typically evolves toward a state of effective equilibrium with a lower value than that of the state of maximum entropy theoretically possible. The finer the coarse graining, the greater the drop in effective entropy, and the more relevant the fluctuations around that. Fundamental considerations allow us to derive a remarkable power law that relates coarse graining to the effective entropy gap. Another power law is found that precisely relates the noise range of effective entropy fluctuations to coarse graining. We test both power laws with numerical simulations based on a well-studied two-dimensional lattice gas model. As expected, the effects of these power laws diminish as our description approaches a macroscopic level, eventually disappearing in the thermodynamic limit, where the maximum entropy principle is reasserted.

scholarly journals Current fluctuations in nonequilibrium discontinuous phase transitions

2021 ◽  
Vol 104 (6) ◽  
Author(s):  
C. E. Fiore ◽  
Pedro E. Harunari ◽  
C. E. Fernández Noa ◽  
Gabriel T. Landi
Keyword(s):  
Phase Transitions ◽  
Current Fluctuations ◽  
Discontinuous Phase ◽  
Discontinuous Phase Transitions

Local instability aboveTcin ABO3perovskites with discontinuous phase transitions

2011 ◽  
Vol 67 (a1) ◽  
pp. C334-C334
Author(s):  
K. Roleder ◽  
K. Szot ◽  
M. Górny ◽  
Z. Ujma ◽  
D. Kajewski ◽  
...  
Keyword(s):  
Phase Transitions ◽  
Local Instability ◽  
Discontinuous Phase ◽  
Discontinuous Phase Transitions

Multiscale enhanced sampling driven by multiple coarse-grained models

2014 ◽  
Vol 616-617 ◽  
pp. 20-24 ◽  
Author(s):  
Kei Moritsugu ◽  
Tohru Terada ◽  
Akinori Kidera
Keyword(s):  
Coarse Grained ◽  
Enhanced Sampling

Atomistic and Coarse-Grained Modeling Strategies for Thin Film Nucleation and Growth on Quasicrystalline Surfaces

2013 ◽  
Vol 1517 ◽  
Author(s):  
James W. Evans ◽  
Patricia A. Thiel ◽  
Bariş Ünal
Keyword(s):  
Lattice Gas ◽  
Film Growth ◽  
Kinetic Monte Carlo ◽  
Coarse Grained ◽  
Dynamics Modeling ◽  
Strain Effects ◽  
Adsorption Sites ◽  
Quantum Size ◽  
Step Dynamics ◽  
Key Aspects

ABSTRACTStrategies are described for modeling the kinetics of non-equilibrium film growth during deposition of metals on quasicrystalline substrates. We review previous atomistic-level lattice-gas modeling and Kinetic Monte Carlo simulation for pseudomorphic (or commensurate) submonolayer growth based on a “disordered or irregular bond-network” (DBN) of neighboring adsorption sites. We describe extensions to treat strain effects and multilayer growth, and discuss a type of commensurate-incommensurate transition expected around 2-3 layers. We also describe a coarse-grained “step dynamics” modeling which tracks the dynamics of island edges in each layer rather than individual atoms. Step dynamics models can also include key aspects of the physics such as layer-dependent energetics, including quantum size effects, and strain effects.

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