Related papers: Two-Domain DNA Strand Displacement
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
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,…
The question of whether DNA is intrinsically conducting or not is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing (inter…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
We study the theoretical problem of synthesizing multiple DNA strands under spatial constraints, motivated by large-scale DNA synthesis technologies. In this setting, strands are arranged in an array and synthesized according to a fixed…
The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
Patchy particles have received great attention due to their ability to develop directional and selective interactions and serve as building units for the self-assembly of innovative colloidal molecules and crystalline structures. Although…
It is shown how to take advantage of the frequent occurrence of double-strand breaks in the genome of prokaryotic cells, in order to reduce their high efficient reproductive capability. The analysis examines the physical status of the free…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
Tensor-valued data arise naturally in neuroimaging, genomics, climate science, and spatiotemporal networks, where multilinear dependencies across modes carry information that is destroyed under vectorization. Existing approaches either…
Localization property in the disordered few-chain DNA systems with a long-range correlation is numerically investigated. We apply the chain system with the correlated disorder in the interchain and/or intrachain hoppings to the simple model…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…