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We investigate the use of a Genetic Algorithm (GA) to design a set of photonic crystals (PCs) in one and two dimensions. Our flexible design methodology allows us to optimize PC structures which are optimized for specific objectives. In…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
In the last two decades, DNA self-assembly has grown into a major area of research attracting people from diverse background. It has numerous potential applications such as targeted drug delivery, artificial photosynthesis etc. In the last…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early-stage drug discovery is de novo…
The potential benefit of migrating software design from Structured to Object Oriented Paradigm is manifolded including modularity, manageability and extendability. This design migration should be automated as it will reduce the time…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
There are a number of ways to procedurally generate interesting three-dimensional shapes, and a method where a cellular neural network is combined with a mesh growth algorithm is presented here. The aim is to create a shape from a genetic…
Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their…
Elastic sheets with macroscopic dimensions are easy to deform by bending and stretching. Yet shaping nanometric sheets by mechanical manipulation is hard. Here we show that nanoparticle self-assembly could be used to this end. We…
DNA origami is a novel self-assembly technique allowing one to form various 2D shapes and position matter with nanometer accuracy. It has been used to coordinate placement of nanoscale objects, both organic and inorganic; to make molecular…
When designing new molecules with particular properties, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple…
While machine learning models are typically trained to solve prediction problems, we might often want to use them for optimization problems. For example, given a dataset of proteins and their corresponding fluorescence levels, we might want…
Autonomous materials discovery with desired properties is one of the ultimate goals for materials science, and the current studies have been focusing mostly on high-throughput screening based on density functional theory calculations and…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…