Related papers: Dynamics and Control of DNA Sequence Amplification
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
In this work, a nonlinear model predictive controller is developed for a batch polymerization process. The physical model of the process is parameterized along a desired trajectory resulting in a trajectory linearized piecewise model (a…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
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…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…
Designing DNA and protein sequences with improved function has the potential to greatly accelerate synthetic biology. Machine learning models that accurately predict biological fitness from sequence are becoming a powerful tool for…
Eukaryotic cells are often exposed to fluctuations in growth conditions as well as endogenous and exogenous stress-related agents. In addition, during development global patterns of gene transcription change dramatically, and these changes…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
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 this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a new variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
DNA replication is a process which is common to all domains of life yet different replication mechanisms are seen among different organisms. The mechanism of replication on such a structure is not yet understood. With this bigger picture in…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…