Loss of Molecular Roughness upon Coarse-Graining Predicts the Artificially Accelerated Mobility of Coarse-Grained Molecular Simulation Models

2020 ◽  
Vol 16 (3) ◽  
pp. 1411-1419 ◽  
Author(s):  
Melissa K. Meinel ◽  
Florian Müller-Plathe
Keyword(s):  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Graining ◽  
Coarse Grained

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

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.

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.

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study

Soft Matter ◽  
2017 ◽  
Vol 13 (38) ◽  
pp. 6770-6783 ◽  
Author(s):  
Joshua E. Condon ◽  
Arthi Jayaraman
Keyword(s):  
Molecular Simulation ◽  
Simulation Study ◽  
Coarse Grained ◽  
Star Polymer ◽  
Backbone Flexibility ◽  
Polymer Architecture ◽  
Polymer Conjugates ◽  
Coarse Grained Simulations

Using coarse-grained simulations, we study the effect of varying oligonucleic acid (ONA) backbone flexibility, ONA charge and star polymer architecture on structure and thermodynamics of ONA–star polymer conjugates assembly.

A new spectral coarse-graining algorithm based on K-means clustering in complex networks

2019 ◽  
Vol 33 (01) ◽  
pp. 1850421 ◽  
Author(s):  
Lang Zeng ◽  
Zhen Jia ◽  
Yingying Wang
Keyword(s):  
Complex Networks ◽  
Large Scale ◽  
Dynamic Properties ◽  
Coarse Graining ◽  
Kuramoto Model ◽  
Coarse Grained ◽  
Original Network ◽  
Topological Information ◽  
Real World Applications ◽  
Large Scale Networks

Coarse-graining of complex networks is one of the important algorithms to study large-scale networks, which is committed to reducing the size of networks while preserving some topological information or dynamic properties of the original networks. Spectral coarse-graining (SCG) is one of the typical coarse-graining algorithms, which can keep the synchronization ability of the original network well. However, the calculation of SCG is large, which limits its real-world applications. And it is difficult to accurately control the scale of the coarse-grained network. In this paper, a new SCG algorithm based on K-means clustering (KCSCG) is proposed, which cannot only reduce the amount of calculation, but also accurately control the size of coarse-grained network. At the same time, KCSCG algorithm has better effect in keeping the network synchronization ability than SCG algorithm. A large number of numerical simulations and Kuramoto-model example on several typical networks verify the feasibility and effectiveness of the proposed algorithm.

scholarly journals Trivial low energy states for commuting Hamiltonians, and the quantum PCP conjecture

2013 ◽  
Vol 13 (5&6) ◽  
pp. 393-429
Author(s):  
Matthew Hastings
Keyword(s):  
Ground State ◽  
Coding Theory ◽  
Energy State ◽  
Ground States ◽  
Coarse Graining ◽  
Quantum Circuit ◽  
Technical Condition ◽  
Two Dimensions ◽  
Low Energy ◽  
Coarse Grained

We consider the entanglement properties of ground states of Hamiltonians which are sums of commuting projectors (we call these commuting projector Hamiltonians), in particular whether or not they have ``trivial" ground states, where a state is trivial if it is constructed by a local quantum circuit of bounded depth and range acting on a product state. It is known that Hamiltonians such as the toric code only have nontrivial ground states in two dimensions. Conversely, commuting projector Hamiltonians which are sums of two-body interactions have trivial ground states\cite{bv}. Using a coarse-graining procedure, this implies that any such Hamiltonian with bounded range interactions in one dimension has a trivial ground state. In this paper, we further explore the question of which Hamiltonians have trivial ground states. We define an ``interaction complex" for a Hamiltonian, which generalizes the notion of interaction graph and we show that if the interaction complex can be continuously mapped to a $1$-complex using a map with bounded diameter of pre-images then the Hamiltonian has a trivial ground state assuming one technical condition on the Hamiltonians holds (this condition holds for all stabilizer Hamiltonians, and we additionally prove the result for all Hamiltonians under one assumption on the $1$-complex). While this includes the cases considered by Ref.~\onlinecite{bv}, we show that it also includes a larger class of Hamiltonians whose interaction complexes cannot be coarse-grained into the case of Ref.~\onlinecite{bv} but still can be mapped continuously to a $1$-complex. One motivation for this study is an approach to the quantum PCP conjecture. We note that many commonly studied interaction complexes can be mapped to a $1$-complex after removing a small fraction of sites. For commuting projector Hamiltonians on such complexes, in order to find low energy trivial states for the original Hamiltonian, it would suffice to find trivial ground states for the Hamiltonian with those sites removed. Such trivial states can act as a classical witness to the existence of a low energy state. While this result applies for commuting Hamiltonians and does not necessarily apply to other Hamiltonians, it suggests that to prove a quantum PCP conjecture for commuting Hamiltonians, it is worth investigating interaction complexes which cannot be mapped to $1$-complexes after removing a small fraction of points. We define this more precisely below; in some sense this generalizes the notion of an expander graph. Surprisingly, such complexes do exist as will be shown elsewhere\cite{fh}, and have useful properties in quantum coding theory.

scholarly journals A scaled MP-PIC method for bubbling fluidization

2021 ◽  
Author(s):  
Xing Zhao ◽  
Yong Jiang ◽  
Fei Li ◽  
Wei Wang
Keyword(s):  
Fluidized Beds ◽  
Volume Fraction ◽  
Phase Particle ◽  
Scaling Law ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Particle In Cell ◽  
Wide Range ◽  
Pic Method ◽  
Multi Phase

Coarse-grained methods have been widely used in simulations of gas-solid fluidization. However, as a key parameter, the coarse-graining ratio, and its relevant scaling law is still far from reaching a consensus. In this work, a scaling law is developed based on a similarity analysis, and then it is used to scale the multi-phase particle-in-cell (MP-PIC) method, and validated in the simulation of two bubbling fluidized beds. The simulation result shows this scaled MP-PIC can reduce the errors of solids volume fraction and velocity distributions over a wide range of coarse-graining ratios. In future, we expect that a scaling law with consideration of the heterogeneity inside a parcel or numerical particle will further improve the performance of coarse-grained modeling in simulation of fluidized beds.

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