Related papers: Parallel DNA Synthesis : Two PCR product from one …

Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…

We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…

We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…

DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables…

DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…

Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard…

Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…

The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…

Retrosynthesis consists of breaking down a chemical compound recursively step-by-step into molecular precursors until a set of commercially available molecules is found with the goal to provide a synthesis route. Its two primary research…

This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…

We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching processes, we show the existance of a new…

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process…

Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which…

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…

This paper focuses on automated synthesis of divide-and-conquer parallelism, which is a common parallel programming skeleton supported by many cross-platform multithreaded libraries. The challenges of producing (manually or automatically) a…

We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…

Radiogenomic map linking image features and gene expression profiles is useful for noninvasively identifying molecular properties of a particular type of disease. Conventionally, such map is produced in three separate steps: 1)…

Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…

Two forms of G4-DNA, with parallel and pairwise anti-parallel strands, are studied using atomic force microscopy. The directionality of the strands affects the molecules' structural properties (different height and length) and their…

Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA…