Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Shape-morphing systems can be found in many areas, including smart textiles, autonomous robotics, biomedical devices, drug delivery and tissue engineering. The natural analogues of such systems are exemplified by nastic plant motions, where a variety of organs such as tendrils, bracts, leaves and flowers respond to environmental stimuli (such as humidity, light or touch) by varying internal turgor, which leads to dynamic conformations governed by the tissue composition and microstructural anisotropy of cell walls. Inspired by these botanical systems, we printed composite hydrogel architectures that are encoded with localized, anisotropic swelling behaviour controlled by the alignment of cellulose fibrils along prescribed four-dimensional printing pathways. When combined with a minimal theoretical framework that allows us to solve the inverse problem of designing the alignment patterns for prescribed target shapes, we can programmably fabricate plant-inspired architectures that change shape on immersion in water, yielding complex three-dimensional morphologies.

/pdf/biomimetic-4d-printing-27deareeqd.pdf

Biomimetic 4D printing

Chemical methods developed over the past two decades enable preparation of colloidal nanocrystals with uniform size and shape. These Brownian objects readily order into superlattices. Recently, the range of accessible inorganic cores and tunable surface chemistries dramatically increased, expanding the set of nanocrystal arrangements experimentally attainable. In this review, we discuss efforts to create next-generation materials via bottom-up organization of nanocrystals with preprogrammed functionality and self-assembly instructions. This process is often driven by both interparticle interactions and the influence of the assembly environment. The introduction provides the reader with a practical overview of nanocrystal synthesis, self-assembly, and superlattice characterization. We then summarize the theory of nanocrystal interactions and examine fundamental principles governing nanocrystal self-assembly from hard and soft particle perspectives borrowed from the comparatively established fields of micro...

Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials

Journal of Physics Condensed Matter: Preface

Journal of Physics A - Mathematical and General, Special Issue. SI Aug 11 2006 ?? Preface

We studied the mechanical process of seed pods opening in Bauhinia variegate and found a chirality-creating mechanism, which turns an initially flat pod valve into a helix. We studied conﬁgurations of strips cut from pod valve tissue and from composite elastic materials that mimic its structure. The experiments reveal various helical conﬁgurations with sharp morphological transitions between them. Using the mathematical framework of “incompatible elasticity,” we modeled the pod as a thin strip with a flat intrinsic metric and a saddle-like intrinsic curvature. Our theoretical analysis quantitatively predicts all observed conﬁgurations, thus linking the pod’s microscopic structure and macroscopic conformation. We suggest that this type of incompatible strip is likely to play a role in the self-assembly of chiral macromolecules and could be used for the engineering of synthetic self-shaping devices.

/pdf/geometry-and-mechanics-in-the-opening-of-chiral-seed-pods-1lmekfwc0t.pdf

Geometry and Mechanics in the Opening of Chiral Seed Pods

The connection between a surface's metric and its Gaussian curvature (Gauss theorem) provides the base for a shaping principle of locally growing or shrinking elastic sheets. We constructed thin gel sheets that undergo laterally nonuniform shrinkage. This differential shrinkage prescribes non-Euclidean metrics on the sheets. To minimize their elastic energy, the free sheets form three-dimensional structures that follow the imposed metric. We show how both large-scale buckling and multiscale wrinkling structures appeared, depending on the nature of possible embeddings of the prescribed metrics. We further suggest guidelines for how to generate each type of feature.

http://science.sciencemag.org/content/sci/315/5815/1116.full.pdf

Shaping of Elastic Sheets by Prescription of Non-Euclidean Metrics

Non-Euclidean plates are a subset of the class of elastic bodies having no stress-free configuration. Such bodies exhibit residual stress when relaxed from all external constraints, and may assume complicated equilibrium shapes even in the absence of external forces. In this work we present a mathematical framework for such bodies in terms of a covariant theory of linear elasticity, valid for large displacements. We propose the concept of non-Euclidean plates to approximate many naturally formed thin elastic structures. We derive a thin plate theory, which is a generalization of existing linear plate theories, valid for large displacements but small strains, and arbitrary intrinsic geometry. We study a particular example of a hemispherical plate. We show the occurrence of a spontaneous buckling transition from a stretching dominated configuration to bending dominated configurations, under variation of the plate thickness.

http://www.ma.huji.ac.il/~razk/Publications/PDF/ESK08.pdf

Elastic theory of unconstrained non-Euclidean plates

Non-Euclidean plates are plates (“stacks” of identical surfaces) whose two-dimensional intrinsic geometry is not Euclidean, i.e. cannot be realized in a flat configuration. They can be generated via different mechanisms, such as plastic deformation, natural growth or differential swelling. In recent years there has been a concurrent theoretical and experimental progress in describing and fabricating non-Euclidean plates (NEP). In particular, an effective plate theory was derived and experimental methods for a controlled fabrication of responsive NEP were developed. In this paper we review theoretical and experimental works that focus on shape selection in NEP and provide an overview of this new field. We made an effort to focus on the governing principles, rather than on details and to relate the main observations to known mechanical behavior of ordinary plates. We also point out to open questions in the field and to its applicative potential.

The mechanics of non-Euclidean plates

This review compares the conceptualization and practice of early real-space renormalization group methods with the conceptualization of more recent real-space transformations based on tensor networks. For specificity, it focuses upon two basic methods: the ``potential-moving'' approach most used in the period 1975--1980 and the ``rewiring method'' as it has been developed in the last five years. The newer method, part of a development called the tensor renormalization group, was originally based on principles of quantum entanglement. It is specialized for computing approximations for tensor products constituting, for example, the free energy or the ground state energy of a large system. It can attack a wide variety of problems, including quantum problems, which would otherwise be intractable. The older method is formulated in terms of spin variables and permits a straightforward construction and analysis of fixed points in rather transparent terms. However, in the form described here it is unsystematic, offers no path for improvement, and of unknown reliability. The new method is formulated in terms of index variables which may be considered as linear combinations of the statistical variables. Free energies emerge naturally, but fixed points are more subtle. Further, physical interpretations of the index variables are often elusive due to a gauge symmetry which allows only selected combinations of tensor entries to have physical significance. In applications, both methods employ analyses with varying degrees of complexity. The complexity is parametrized by an integer called $\ensuremath{\chi}$ (or $D$ in the recent literature). Both methods are examined in action by using them to compute fixed points related to Ising models for small values of the complexity parameter. They behave quite differently. The old method gives a reasonably good picture of the fixed point, as measured, for example, by the accuracy of the measured critical indices. This happens at low values of $\ensuremath{\chi}$, but there is no known systematic way of getting more accurate results within the old method. In contrast, the rewiring method seems to work poorly in fixed point calculations at low $\ensuremath{\chi}$. This stands in contrast to the known excellent performance of these newer methods in calculations of free energy, but not fixed points, at large values of $\ensuremath{\chi}$. Speculations are offered with a particular eye to seeing the reasons why the results of these two approaches are so different.

https://jfi.uchicago.edu/~efrati/articles/EWKK14.pdf

Efi Efrati

Papers

Geometry and Mechanics in the Opening of Chiral Seed Pods

Shaping of Elastic Sheets by Prescription of Non-Euclidean Metrics

Elastic theory of unconstrained non-Euclidean plates

The mechanics of non-Euclidean plates

Real Space Renormalization in Statistical Mechanics