freud: A software suite for high throughput analysis of particle simulation data
TL;DR: The freud Python package provides the core tools for finding particle neighbors in periodic systems, and offers a uniform API to a wide variety of methods implemented using these tools, enabling analysis of a broader class of data ranging from biomolecular simulations to colloidal experiments.
About: This article is published in Computer Physics Communications.The article was published on 2020-09-01 and is currently open access. It has received 114 citations till now. The article focuses on the topics: NumPy & Python (programming language).
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TL;DR: A two-layer model is developed, representing the grafted polymer around an NP by spherical dry and interpenetration layers, that quantitatively predicts that the thicknesses of the two layers depend on one universal parameter, x, the degree of overcrowding of grafted chains relative to chains in the melt.
Abstract: The structure of neat melts of polymer-grafted nanoparticles (GNPs) is studied via coarse-grained molecular dynamics simulations. We systematically vary the degree of polymerization and grafting density at fixed nanoparticle (NP) radius and study in detail the shape and size of the GNP coronas. For sufficiently high grafting density, chain sections close to the NP core are extended and form a dry layer. Further away from the NP, there is an interpenetration layer, where the polymer coronas of neighboring GNPs overlap and the chain sections have almost unperturbed conformations. To better understand this partitioning, we develop a two-layer model, representing the grafted polymer around an NP by spherical dry and interpenetration layers. This model quantitatively predicts that the thicknesses of the two layers depend on one universal parameter, x, the degree of overcrowding of grafted chains relative to chains in the melt. Both simulations and theory show that the chain extension free energy is nonmonotonic with increasing chain length at a fixed grafting density, with a well-defined maximum. This maximum is indicative of the crossover from the dry layer-dominated to interpenetration layer-dominated regime, and it could have profound consequences on our understanding of a variety of anomalous transport properties of these GNPs. Our theoretical approach therefore provides a facile means for understanding and designing solvent-free GNP-based materials.
51 citations
TL;DR: In this article, the authors used coarse-grained molecular dynamics simulations of soft disks to determine the skyrmion interaction potentials and found that the simulations are able to reproduce the full two-dimensional phase behavior.
Abstract: Phases of matter are ubiquitous with everyday examples including solids and liquids. In reduced dimensions, particular phases, such as the two-dimensional (2D) hexatic phase and corresponding phase transitions occur. A particularly exciting example of 2D ordered systems are skyrmion lattices, where in contrast to previously studied 2D colloid systems, the skyrmion size and density can be tuned by temperature and magnetic field. This allows us to drive the system from a liquid phase to a hexatic phase as deduced from the analysis of the hexagonal order. Using coarse-grained molecular dynamics simulations of soft disks, we determine the skyrmion interaction potentials and we find that the simulations are able to reproduce the full two-dimensional phase behavior. This shows that not only the static behavior of skyrmions is qualitatively well described in terms of a simple two-dimensional model system but skyrmion lattices are versatile and tunable two-dimensional model systems that allow for studying phases and phase transitions in reduced dimensions.
38 citations
23 Feb 2021
TL;DR: In this article, the dot markers are replaced with a novel random color pattern as the sensor's tracking target and a dense optical flow algorithm is used to track the deformation of its elastic contact interface.
Abstract: Recent studies on vision-based tactile sensing have shown promising results on the perception of contact information, which could improve the performance of dexterous manipulations. However, 3-dimensional contact deformation tracking at a higher resolution is desired and remains a challenge for vision-based tactile sensors with monocular configurations. In this work, a similar hardware structure to our previous FingerVision sensor is adopted. The dot markers are replaced with a novel random color pattern as the sensor's tracking target and a dense optical flow algorithm is used to track the deformation of its elastic contact interface. This results in a more accurate 2-dimensional deformation field estimation at a higher resolution in comparison with that obtained using sparse dot markers. Additionally, the denser and more accurate deformation field enables depth estimation with better fidelity. To achieve depth estimation purely from the optical flow field, Gaussian density feature extraction and processing framework are proposed. The resulting depth map can be used independently as a tactile sensing modality, or jointly with the accurate in-plane displacement field as a more complete deformation tracking of contact interfaces for vision-based tactile sensors.
28 citations
TL;DR: In this paper , the spatial distribution of the electron equivalents breaks the symmetry of isotropic programmable atom equivalents, analogous to the anisotropic distribution of valence electrons or coordination sites around a metal atom, leading to a set of well defined coordination geometries and access to three new low-symmetry crystalline phases.
Abstract: Colloidal crystal engineering of complex, low-symmetry architectures is challenging when isotropic building blocks are assembled. Here we describe an approach to generating such structures based upon programmable atom equivalents (nanoparticles functionalized with many DNA strands) and mobile electron equivalents (small particles functionalized with a low number of DNA strands complementary to the programmable atom equivalents). Under appropriate conditions, the spatial distribution of the electron equivalents breaks the symmetry of isotropic programmable atom equivalents, akin to the anisotropic distribution of valence electrons or coordination sites around a metal atom, leading to a set of well-defined coordination geometries and access to three new low-symmetry crystalline phases. All three phases represent the first examples of colloidal crystals, with two of them having elemental analogues (body-centred tetragonal and high-pressure gallium), while the third (triple double-gyroid structure) has no known natural equivalent. This approach enables the creation of complex, low-symmetry colloidal crystals that might find use in various technologies.
27 citations
TL;DR: In this article , the authors apply machine learning techniques to predict the rate of formation of ice nuclei in supercooled water and to study other quantities relevant to nucleation without relying on empirical force fields, albeit invoking the organizing framework of classical nucleation theory.
Abstract: Significance Until recently, simulating ice nucleation with quantum accuracy was deemed impossible due to the prohibitive computational cost of quantum-mechanical calculations. Recent progress enabled by machine learning has made these calculations tractable and thus greatly extended the field of application of molecular dynamics based on ab initio quantum-mechanical theory. We apply these advances to predict the rate of formation of ice nuclei in supercooled water and to study other quantities relevant to nucleation without relying on empirical force fields, albeit invoking the organizing framework of classical nucleation theory. This work is a step toward modeling nucleation processes in more realistic environments and at conditions in which chemical reactions play an important role.
22 citations
References
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TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
46,130 citations
TL;DR: In this article, three parallel algorithms for classical molecular dynamics are presented, which can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors.
32,670 citations
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
Abstract: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting,and publication-quality image generation across user interfaces and operating systems
23,312 citations
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11 Feb 1988TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Abstract: Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.
21,073 citations
"freud: A software suite for high th..." refers methods in this paper
...A second approach is implemented in the LinkCell subclass [34], which uses linked cell lists to find particle neighbors....
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...There are two subclasses of NeighborQuery in freud that each implement different neighbor search algorithms: one implements a bounding volume hierarchy (BVH) [37], while the other implements a cell list [34]....
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