Related papers: Computational complexity and pragmatic solutions f…
We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
Bottom-up fabrication of inorganic nanostructures is emerging as an alternative to classical top-down approaches, offering precise nanometer-scale control at relatively low cost and effort. In particular, DNA nanostructures provide…
The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of…
This technical report deals with the concept of an artificial DNA which contains a blueprint of the structure and organization of an embedded system. This blueprint can be used to build up the embedded system in a self-organizing manner at…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
Inverse design of short single-stranded RNA and DNA sequences (aptamers) is the task of finding sequences that satisfy a set of desired criteria. Relevant criteria may be, for example, the presence of specific folding motifs, binding to…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized…
Winfree (1998) showed that discrete Sierpinski triangles can self-assemble in the Tile Assembly Model. A striking molecular realization of this self-assembly, using DNA tiles a few nanometers long and verifying the results by atomic-force…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Computational methods for designing interactions between colloidal particles that induce self-assembly have received much attention for their promise to discover tailored materials. However, it often remains a challenge to translate…
We provide a framework for the design and analysis of dynamic programming algorithms for surface-embedded graphs on n vertices and branchwidth at most k. Our technique applies to general families of problems where standard dynamic…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
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…
The branching algorithm is a fundamental technique for designing fast exponential-time algorithms to solve combinatorial optimization problems exactly. It divides the entire solution space into independent search branches using…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…