Related papers: 3DNA: A Tool for DNA Sculpting
We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and…
Image-guided object assembly represents a burgeoning research topic in computer vision. This paper introduces a novel task: translating multi-view images of a structural 3D model (for example, one constructed with building blocks drawn from…
Current nanostructure fabrication by etching is usually limited to planar structures as they are defined by a planar mask. The realisation of three-dimensional (3D) nanostructures by etching requires technologies beyond planar masks. We…
3D fragment reassembly aims to recover the rigid poses of unordered fragment point clouds or meshes in a common object coordinate system to reconstruct the complete shape. The problem becomes particularly challenging as the number of…
DNA Self-Assembly has emerged as an interdisciplinary field with many intriguing applications such DNA bio-sensor, DNA circuits, DNA storage, drug delivery etc. Tile assembly model of DNA has been studied for various computational…
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on…
Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we…
We show how to convert models of complex systems such as 2D cellular automata into a 3D printed object. Our method takes into account the limitations inherent to 3D printing processes and materials. Our approach automates the greater part…
Generic 3D reconstruction from a single image is a difficult problem. A lot of data loss occurs in the projection. A domain based approach to reconstruction where we solve a smaller set of problems for a particular use case lead to greater…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
With the growing model size, deep neural networks (DNN) are increasingly trained over massive GPU accelerators, which demands a proper parallelization plan that transforms a DNN model into fine-grained tasks and then schedules them to GPUs…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
Deep Neural Networks (DNNs) are intensively used to solve a wide variety of complex problems. Although powerful, such systems require manual configuration and tuning. To this end, we view DNNs as configurable systems and propose an…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
We propose an approach to 3D reconstruction via inverse procedural modeling and investigate two variants of this approach. The first option consists in the fitting set of input parameters using a genetic algorithm. We demonstrate the…
Structure-based drug design aims at generating high affinity ligands with prior knowledge of 3D target structures. Existing methods either use conditional generative model to learn the distribution of 3D ligands given target binding sites,…
Coordinating functional parts to operate in concert is essential for machinery. In gear trains, meshed gears are compactly interlocked, working together to impose rotation or translation. In photosynthetic systems, a variety of biological…
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains…
Tile assembly systems in the abstract Tile Assembly Model (aTAM) are computationally universal and capable of building complex shapes, but DNA-based implementations encounter formidable error rates that stifle this theoretical potential.…
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions…