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Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA World, self-replicating RNAs have yet to be identified in a natural context, leaving a key…
Due to the asymmetric nature of the nucleotides, the extant informational biomolecule, DNA, is constrained to replicate unidirectionally on a template. As a product of molecular evolution that sought to maximize replicative potential, DNA's…
The origin of life can be understood mathematically to be the origin of information that can replicate. The likelihood that entropy spontaneously becomes information can be calculated from first principles, and depends exponentially on the…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
Program errors can occur in any type of programming, and can manifest in a variety of ways, such as unexpected output, crashes, or performance issues. And program error diagnosis can often be too abstract or technical for developers to…
Experimental mechanisms that yield the growth of homochiral copolymers over their heterochiral counterparts have been advocated by Lahav and co-workers. These chiral amplification mechanisms proceed through racemic {\beta}-sheet-controlled…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
Reinforcement learning has become the dominant paradigm for eliciting reasoning and self-correction capabilities in large language models, but its computational expense motivates exploration of alternatives. Inspired by techniques from…
Bidirectional typechecking, in which terms either synthesize a type or are checked against a known type, has become popular for its scalability (unlike Damas-Milner type inference, bidirectional typing remains decidable even for very…
To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively-studied KPR circuits, DNA…
Self-closing assembly is prone to polymorphism due to thermally-excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
Large-scale pre-trained language models have demonstrated strong capabilities of generating realistic text. However, it remains challenging to control the generation results. Previous approaches such as prompting are far from sufficient,…
As synthetic data becomes higher quality and proliferates on the internet, machine learning models are increasingly trained on a mix of human- and machine-generated data. Despite the successful stories of using synthetic data for…
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant…
Personalized tutoring, teacher training, and education research need access to \emph{targeted} synthetic misconceptions, but privacy and IRB constraints make labelled corpora of real student errors scarce. LLMs could in principle generate…
DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\it polymerase} catalyzing the elongation of a new DNA molecule by adding a…
We discuss temporal efficiency of template-directed polymer synthesis, such as DNA replication and transcription, under a given template string. To weigh the synthesis speed and accuracy on the same scale, we propose a template-directed…
Catastrophic failures of marine engines imply severe loss of functionality and destroy or damage the systems irreversibly. Being sudden and often unpredictable events, they pose a severe threat to navigation, crew, and passengers. The…