On Multi-scale Computational Design of Structural Materials Using the Topological Derivative

2017 ◽  
pp. 289-308
Author(s):  
J. Oliver ◽  
A. Ferrer ◽  
J. C. Cante ◽  
S. M. Giusti ◽  
O. Lloberas-Valls
Keyword(s):  
Computational Design ◽  
Structural Materials ◽  
Topological Derivative ◽  
Multi Scale

scholarly journals Computational Design and Analysis of a Magic Snake

2020 ◽  
Vol 12 (5) ◽  
Author(s):  
Zilong Li ◽  
Songming Hou ◽  
Thomas C. Bishop
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Computational Design ◽  
Space Curve ◽  
One Dimensional ◽  
3D Structures ◽  
Multi Scale ◽  
3D Space ◽  
Slender Bodies ◽  
Self Similar

Abstract The Magic Snake (Rubik’s Snake) is a toy that was invented decades ago. It draws much less attention than Rubik’s Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of “embedding” to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.

Topological derivative for multi-scale linear elasticity models applied to the synthesis of microstructures

2010 ◽  
Vol 84 (6) ◽  
pp. 733-756 ◽  
Author(s):  
S. Amstutz ◽  
S. M. Giusti ◽  
A. A. Novotny ◽  
E. A. de Souza Neto
Keyword(s):  
Linear Elasticity ◽  
Topological Derivative ◽  
Multi Scale

scholarly journals Mesoscale computational protocols for the design of highly cooperative bivalent macromolecules

2019 ◽  
Author(s):  
S. Saurabh ◽  
F. Piazza
Keyword(s):  
Large Scale ◽  
Real Life ◽  
Computational Design ◽  
Md Simulations ◽  
Coarse Grained ◽  
Immune Synapse ◽  
Multi Scale ◽  
Therapeutic Molecules ◽  
Potentials Of Mean Force ◽  
Design Protocol

ABSTRACTThe last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while it is widely accepted that large-scale flexibility (10 − 100 nm) and free/constrained dynamics (100 ns −µs) control the activity of such novel molecules, computational strategies at the mesoscale still lag behind experiments in optimizing the design of crucial features, such as the binding cooperativity (a.k.a. avidity).In this study, we introduced different coarse-grained models of a polymer-linked, two-nanobody composite molecule, with the aim of laying down the physical bases of a thorough computational drug design protocol at the mesoscale. We show that the calculation of suitable potentials of mean force allows one to apprehend the nature, range and strength of the thermodynamic forces that govern the motion of free and wall-tethered molecules. Furthermore, we develop a simple computational strategy to quantify the encounter/dissociation dynamics between the free end of a wall-tethered molecule and the surface, at the roots of binding cooperativity. This procedure allows one to pinpoint the role of internal flexibility and weak non-specific interactions on the kinetic constants of the NB-wall encounter and dissociation. Finally, we quantify the role and weight of rare events, which are expected to play a major role in real-life situations, such as in the immune synapse, where the binding kinetics is likely dominated by fluctuations.SIGNIFICANCEMultivalent and multispecific molecules composed of polymer-linked nanobodies have gained interest as engineered alternatives to conventional antibodies. These therapeutic molecules have a larger reach due to their smaller size and promise substantial and tunable gains in avidity. This paper studies a model diabody to lay the bases of a multi-scale computational design of the structural and dynamical determinants of binding cooperativity, rooted in a blend of atomistic and coarse-grained MD simulations and concepts from statistical mechanics.

Multi-scale Analysis of the Crystallization of Amorphous Germanium Telluride

2014 ◽  
Vol 1697 ◽  
Author(s):  
Jie Liu ◽  
Xu Xu ◽  
Lucien Brush ◽  
M. P. Anantram
Keyword(s):  
Nucleation Rate ◽  
Elastic Energy ◽  
Annealing Temperature ◽  
Scaling Limit ◽  
Computational Design ◽  
Growth Speed ◽  
Design And Optimization ◽  
Germanium Telluride ◽  
Multi Scale ◽  
Crystallization Properties

ABSTRACTThe crystallization properties of the phase change material (PCM) germanium telluride (GeTe) are investigated. It is shown that the critical nucleus radius of a crystalline cluster is smaller than 1.4nm when the annealing temperature is lower than 600K, indicating an extremely promising scaling scenario. It is revealed that the elastic energy, which is largely ignored in existing PCM crystallization studies, plays an important role in determining various crystallization properties and the ultimate scaling limit of the PCM. By omitting the influence of elastic energy, the critical formation energy (critical nuclei radius) will be underestimated by 41.7% (22.4%), and the nucleation rate will be overestimated by 74.2% when the annealing temperature is 600 K. The methodology proposed here is capable of quantitatively calculating the nucleation rate and growth speed of amorphous PCM from first principle calculations, which is relevant to computational design and optimization of PCM.

Sensitivity of the macroscopic response of elastic microstructures to the insertion of inclusions

2010 ◽  
Vol 466 (2118) ◽  
pp. 1703-1723 ◽  
Author(s):  
Sebastián M. Giusti ◽  
Antonio A. Novotny ◽  
Eduardo A. de Souza Neto
Keyword(s):  
Elastic Inclusion ◽  
Contrast Ratio ◽  
Analytical Formula ◽  
Elasticity Tensor ◽  
Topological Derivative ◽  
Multi Scale ◽  
Topological Asymptotic Analysis ◽  
Potential Applicability ◽  
Circular Elastic Inclusion ◽  
Macroscopic Response

This paper proposes an exact analytical formula for the topological sensitivity of the macroscopic response of elastic microstructures to the insertion of circular inclusions. The macroscopic response is assumed to be predicted by a well-established multi-scale constitutive theory where the macroscopic strain and stress tensors are defined as volume averages of their microscopic counterpart fields over a representative volume element (RVE) of material. The proposed formula—a symmetric fourth-order tensor field over the RVE domain—is a topological derivative which measures how the macroscopic elasticity tensor changes when an infinitesimal circular elastic inclusion is introduced within the RVE. In the limits, when the inclusion/matrix phase contrast ratio tends to zero and infinity, the sensitivities to the insertion of a hole and a rigid inclusion, respectively, are rigorously obtained. The derivation relies on the topological asymptotic analysis of the predicted macroscopic elasticity and is presented in detail. The derived fundamental formula is of interest to many areas of applied and computational mechanics. To illustrate its potential applicability, a simple finite element-based example is presented where the topological derivative information is used to automatically generate a bi-material microstructure to meet pre-specified macroscopic properties.

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