Computational Design of Knit Templates

We present an interactive design system for knitting that allows users to create template patterns that can be fabricated using an industrial knitting machine. Our interactive design tool is novel in that it allows direct control of key knitting design axes we have identified in our formative study and does so consistently across the variations of an input parametric template geometry. This is achieved with two key technical advances. First, we present an interactive meshing tool that lets users build a coarse quadrilateral mesh that adheres to their knit design guidelines. This solution ensures consistency across the parameter space for further customization over shape variations and avoids helices, promoting knittability. Second, we lift and formalize low-level machine knitting constraints to the level of this coarse quad mesh. This enables us to not only guarantee hand- and machine-knittability, but also provides automatic design assistance through auto-completion and suggestions. We show the capabilities through a set of fabricated examples that illustrate the effectiveness of our approach in creating a wide variety of objects and interactively exploring the space of design variations.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein–protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors

A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a −1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.

Modelling of Mechanisms as a Methodological Tool (the Case of Designing a Cycloidal Pin Transmission)

The suggested modern approach to modelling of objects and systems allows not only to create models but also to use them to study the main properties of the object (system) with a high degree of clarity and adequacy, as well as to develop most important skills of young engineers in creating and implementing digital models of engineering objects.The objective of the study is to analyse capacity of one of the modern automated computational design systems as a methodological tool.The functionality of an automated computational design system is considered for the case of constructing a model of a planetary cycloidal pinion transmission. The resulting model allows visualising the kinematics of the designed mechanism in the form of static or moving graphic images. The model built based on the described approach contains digital images of mechanism parts, which can be transferred without modification to specialised software systems for analysing strength characteristics or manufacturing material models of a product using rapid prototyping methods.The proposed approach allows to perfect actions referring to the analysis of properties and synthesis of new structures using tools that correspond to the modern level of technology development and to get a visual idea of the process of developing a machine from a mathematical model to its material objectification.The research methods are based on the fundamental principles of mathematical and simulation modelling, data analysis and processing using powerful automated computational design tools.The tools used for modelling can be used for different forms of learning, i.e., without reference to specific premises and equipment.

Computational Design for Digitally Fabricated 3D Inductive Power Transfer Coils

The geometric shapes and the relative position of coils influence the performance of a three-dimensional (3D) inductive power transfer system. In this paper, we propose a coil design method for specifying the positions and the shapes of a pair of coils to transmit the desired power in 3D. Given region of interests (ROIs) for designing the transmitter and the receiver coils on two surfaces, the transmitter coil is generated around the center of its ROI first. The center of the receiver coil is estimated as a random seed position in the corresponding 3D surface. At this position, we use the heatmap method with electromagnetic constraints to iteratively extend the coil until the desired power can be transferred via the set of coils. In each step, the shape of the extension, i.e. a new turn of the receiver coil, is found as a spiral curve based on the convex hulls of adjacent turns in the 2D projection plane along their normal direction. Then, the optimal position of the receiver coil is found by maximizing the efficiency of the system. In the next step, the position and the shape of the transmitter coil are optimized based on the fixed receiver coil using the same method. This zig-zag optimization process iterates until an optimum is reached. Simulations and experiments with digitally fabricated prototypes were conducted and the effectiveness of the proposed 3D coil design method was verified. Possible future research directions are highlighted well.

Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing

Red fluorescent proteins (RFPs) have found widespread application in chemical and biological research due to their longer emission wavelengths. Here, we use computational protein design to increase the quantum yield...