Related papers: Error Catastrophe Can Be Avoided by Proofreading I…
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…
Fault-tolerant distributed algorithms are central for building reliable spatially distributed systems. Unfortunately, the lack of a canonical precise framework for fault-tolerant algorithms is an obstacle for both verification and…
Data-driven generation of molecules with desired properties, also known as inverse molecular design (IMD), has attracted significant attention in recent years. Despite the significant progress in the accuracy and diversity of solutions,…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
One of the main goals of Artificial Life is to research the conditions for the emergence of life, not necessarily as it is, but as it could be. Artificial Chemistries are one of the most important tools for this purpose because they provide…
The wayward quality of continuous prompts stresses the importance of their interpretability as unexpected and unpredictable behaviors appear following training, especially in the context of large language models automating people-sensitive…
Among the biggest challenges in property-based testing (PBT) is the constrained random generation problem: given a predicate on program values, randomly sample from the set of all values satisfying that predicate, and only those values.…
Controller synthesis, including reset controller, feedback controller, and switching logic controller, provides an essential mechanism to guarantee the correctness and reliability of hybrid systems in a correct-by-construction manner.…
Causal machine learning has the potential to revolutionize decision-making by combining the predictive power of machine learning algorithms with the theory of causal inference. However, these methods remain underutilized by the broader…
Under high cylindrical confinement, segments of ring polymers can be localized along the long axis of the cylinder by introducing internal loops within the ring polymer. The emergent organization of the polymer segments occurs because of…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
Nonlinear constrained optimization problems are encountered in many scientific fields. To utilize the huge calculation power of current computers, many mathematic models are also rebuilt as optimization problems. Most of them have…
Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…
Model error estimation remains one of the key challenges in uncertainty quantification and predictive science. For computational models of complex physical systems, model error, also known as structural error or model inadequacy, is often…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
With the increasing importance of distributed systems as a computing paradigm, a systematic approach to their design is needed. Although the area of formal verification has made enormous advances towards this goal, the resulting…
We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing Machines that we introduced in a previous article. The use of Turing Machines allows for very simple mechanisms of code growth and code…
A mystery about the origins of life is which molecular structures $-$ and what spontaneous processes $-$ drove the autocatalytic transition from simple chemistry to biology? Using the HP lattice model of polymer sequence spaces leads to the…
Research on the birth and evolution of life are reviewed with reference to the maximum entropy production principle (MEPP). It has been shown that this principle is essential for consistent understanding of the birth and evolution of life.…