Related papers: DNA Circuits Based on Isothermal Constrained Loop …

In order to demonstrate acceleration of electrons to relativistic scales by an on chipdielectric laser accelerator (DLA), a ponderomotive focusing scheme capable of capturingand transporting electrons through nanometer-scale apertures over…

Counterfactual data augmentation (CDA) is a method for controlling information or biases in training datasets by generating a complementary dataset with typically opposing biases. Prior work often either relies on hand-crafted rules or…

In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…

DNA looping has been observed to enhance and suppress transcriptional noise but it is uncertain which of these two opposite effects is to be expected for given conditions. Here, we derive analytical expressions for the main quantifiers of…

DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…

Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…

Many unsupervised domain adaptation (UDA) methods have been proposed to bridge the domain gap by utilizing domain invariant information. Most approaches have chosen depth as such information and achieved remarkable success. Despite their…

We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…

We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…

Because of the limitations of classical silicon based computational technology, several alternatives to traditional method in form of unconventional computing have been proposed. In this paper we will focus on DNA computing which is showing…

Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…

For many decades, advances in static verification have focused on linear integer arithmetic (LIA) programs. Many real-world programs are, however, written with non-linear integer arithmetic (NLA) expressions, such as programs that model…

Existing large language models (LLMs) that mainly focus on Standard American English (SAE) often lead to significantly worse performance when being applied to other English dialects. While existing mitigations tackle discrepancies for…

Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…

A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…

Constrained Horn Clauses (CHCs) are often used in automated program verification. Thus, techniques for (dis-)proving satisfiability of CHCs are a very active field of research. On the other hand, acceleration techniques for computing…

We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…

Formal transformations somehow resembling the usual derivative are surprisingly common in computer science, with two notable examples being derivatives of regular expressions and derivatives of types. A newcomer to this list is the…

Many unsupervised domain adaptation (UDA) methods exploit domain adversarial training to align the features to reduce domain gap, where a feature extractor is trained to fool a domain discriminator in order to have aligned feature…