scholarly journals Systematic Coarse-Grained Models for Molecular Systems Using Entropy

Proceedings ◽  
2020 ◽  
Vol 46 (1) ◽  
pp. 27
Author(s):  
Evangelia Kalligiannaki ◽  
Vagelis Harmandaris ◽  
Markos Katsoulakis
Keyword(s):  
Bootstrap Method ◽  
Coarse Graining ◽  
Research Area ◽  
Potential Of Mean Force ◽  
Coarse Grained ◽  
Molecular Systems ◽  
Matching Methods ◽  
Force Matching ◽  
Mesoscopic Models ◽  
Body Potential

The development of systematic coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of different methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. We focus on methods based on information theory, such as relative entropy, showing that they provide parameterizations of coarse-grained models at equilibrium by minimizing a fitting functional over a parameter space. We also connect them with structural-based (inverse Boltzmann) and force matching methods. All the methods mentioned in principle are employed to approximate a many-body potential, the (n-body) potential of mean force, describing the equilibrium distribution of coarse-grained sites observed in simulations of atomically detailed models. We also present in a mathematically consistent way the entropy and force matching methods and their equivalence, which we derive for general nonlinear coarse-graining maps. We apply, and compare, the above-described methodologies in several molecular systems: A simple fluid (methane), water and a polymer (polyethylene) bulk system. Finally, for the latter we also provide reliable confidence intervals using a statistical analysis resampling technique, the bootstrap method.

scholarly journals Bottom-Up Coarse-Grained Modeling of DNA

2021 ◽  
Vol 8 ◽  
Author(s):  
Tiedong Sun ◽  
Vishal Minhas ◽  
Nikolay Korolev ◽  
Alexander Mirzoev ◽  
Alexander P. Lyubartsev ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Deoxyribonucleic Acid ◽  
Persistence Length ◽  
Coarse Graining ◽  
Potential Of Mean Force ◽  
Coarse Grained ◽  
Bottom Up ◽  
Slow Dynamic ◽  
Molecular Systems ◽  
Fine Grained

Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, “melting,” and DNA condensation.

scholarly journals Path space force matching and relative entropy methods for coarse-graining molecular systems at transient regimes

2018 ◽  
Vol 136 ◽  
pp. 331-340 ◽  
Author(s):  
Evangelia Kalligiannaki ◽  
Markos Katsoulakis ◽  
Petr Plechac ◽  
Vagelis Harmandaris
Keyword(s):  
Relative Entropy ◽  
Coarse Graining ◽  
Path Space ◽  
Entropy Methods ◽  
Molecular Systems ◽  
Force Matching ◽  
Transient Regimes

scholarly journals Systematic Bottom-Up Molecular Coarse-Graining via Force Matching using Anisotropic Particles

2022 ◽  
Author(s):  
David Huang ◽  
Huong Nguyen
Keyword(s):  
Organic Semiconductors ◽  
Condensed Phase ◽  
Simulation Models ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Anisotropic Particles ◽  
Fine Grained ◽  
Force Matching ◽  
Anisotropic Force ◽  
Dynamics Simulations

We derive a systematic and general method for parametrizing coarse-grained molecular models consisting of anisotropic particles from fine-grained (e.g. all-atom) models for condensed-phase molecular dynamics simulations. The method, which we call anisotropic force-matching coarse-graining (AFM-CG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarse-grained and fine-grained phase-space distributions to derive equations for the coarse-grained forces, masses, and moments of inertia in terms of properties of a condensed-phase fine-grained system. We verify the accuracy and efficiency of the method by coarse-graining liquid-state systems of two different anisotropic organic molecules, benzene and perylene, and show that the parametrized coarse-grained models more accurately describe properties of these systems than previous anisotropic coarse-grained models parametrized using other methods that do not account for finite-temperature and many-body effects on the condensed-phase coarse-grained interactions. The AFM-CG method will be useful for developing accurate and efficient dynamical simulation models of condensed-phase systems of molecules consisting of large, rigid, anisotropic fragments, such as nucleic acids, liquid crystals, and organic semiconductors.

Mesoscale methods

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Large Scale ◽  
Equations Of Motion ◽  
Dissipative Particle Dynamics ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Collision Dynamics ◽  
Force Matching ◽  
Multiparticle Collision Dynamics ◽  
Long Time ◽  
Boltzmann Method

Coarse-graining is an increasingly commonplace approach to study, as economically as possible, large-scale, and long-time phenomena. This chapter covers the main methods. Brownian and Langevin dynamics are introduced, with practical details of the solution of the modified equations of motion. Several techniques which aim to bridge the gap to the hydrodynamic regime are described: these include dissipative particle dynamics, multiparticle collision dynamics, and the lattice Boltzmann method. Several examples of program code are provided. In the last part of the chapter, the derivation of a coarse-grained potential from an atomistic one is considered using force-matching and structure-matching, and the limitations of these approaches are discussed.

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

2015 ◽  
Vol 143 (8) ◽  
pp. 084105 ◽  
Author(s):  
Evangelia Kalligiannaki ◽  
Vagelis Harmandaris ◽  
Markos A. Katsoulakis ◽  
Petr Plecháč
Keyword(s):  
Coarse Graining ◽  
Molecular Systems ◽  
Force Matching ◽  
Related Information ◽  
Generalized Force ◽  
Information Metrics

Minimalist models for proteins: a comparative analysis

2010 ◽  
Vol 43 (3) ◽  
pp. 333-371 ◽  
Author(s):  
Valentina Tozzini
Keyword(s):  
Phase Diagram ◽  
Comparative Analysis ◽  
Amino Acid ◽  
Degrees Of Freedom ◽  
Predictive Power ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Molecular Systems ◽  
Modern Molecular Biology ◽  
Functional Forms

AbstractThe last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex.In this paper, the CG models are reviewed and their features, applications and performances compared. This analysis, restricted to proteins, focuses on the minimalist models, namely those reducing at minimum the number of degrees of freedom without losing the possibility of explicitly describing the secondary structures. This class includes models using a single or a few interacting centers (beads) for each amino acid.From this analysis several issues emerge. The difficulty in building these models resides in the need for combining transferability/predictive power with the capability of accurately reproducing the structures. It is shown that these aspects could be optimized by accurately choosing the force field (FF) terms and functional forms, and combining different parameterization procedures. In addition, in spite of the variety of the minimalist models, regularities can be found in the parameters values and in FF terms. These are outlined and schematically presented with the aid of a generic phase diagram of the polypeptide in the parameter space and, hopefully, could serve as guidelines for the development of minimalist models incorporating the maximum possible level of predictive power and structural accuracy.

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems

2012 ◽  
Vol 136 (19) ◽  
pp. 194115 ◽  
Author(s):  
Avisek Das ◽  
Lanyuan Lu ◽  
Hans C. Andersen ◽  
Gregory A. Voth
Keyword(s):  
Coarse Graining ◽  
Coarse Grained ◽  
Molecular Systems

scholarly journals Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids

2021 ◽  
Author(s):  
Wanying Huang ◽  
Xinwen Ou ◽  
JunYan Luo
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Coarse Graining ◽  
Simulation Method ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Multi Scale

Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation, that is, the target distribution function, the PMF potential energy is extracted, and then the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have gone through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.

scholarly journals On the three-dimensional spatial correlations of curved dislocation systems

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Joseph Pierre Anderson ◽  
Anter El-Azab
Keyword(s):  
Correlation Function ◽  
Slip System ◽  
Correlation Functions ◽  
Mean Field ◽  
Coarse Graining ◽  
Dislocation Dynamics ◽  
Coarse Grained ◽  
Spatial Correlation Function ◽  
Line System ◽  
Dislocation Densities

AbstractCoarse-grained descriptions of dislocation motion in crystalline metals inherently represent a loss of information regarding dislocation-dislocation interactions. In the present work, we consider a coarse-graining framework capable of re-capturing these interactions by means of the dislocation-dislocation correlation functions. The framework depends on a convolution length to define slip-system-specific dislocation densities. Following a statistical definition of this coarse-graining process, we define a spatial correlation function which will allow the arrangement of the discrete line system at two points—and thus the strength of their interactions at short range—to be recaptured into a mean field description of dislocation dynamics. Through a statistical homogeneity argument, we present a method of evaluating this correlation function from discrete dislocation dynamics simulations. Finally, results of this evaluation are shown in the form of the correlation of dislocation densities on the same slip-system. These correlation functions are seen to depend weakly on plastic strain, and in turn, the dislocation density, but are seen to depend strongly on the convolution length. Implications of these correlation functions in regard to continuum dislocation dynamics as well as future directions of investigation are also discussed.

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