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An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
We explain how hierarchical organization of biological systems emerges naturally during evolution, through a transition in the units of individuality. We will show how these transitions are the result of competing selective forces operating…
Quantum repeaters with multiple quantum memories provide high throughput, low latency, and high fidelity quantum state (qubit) transfer over long distances. However, conventional quantum repeater protocols require full connections among the…
Molecular-scale diodes made from self-assembled monolayers (SAMs) could complement silicon-based technologies with smaller, cheaper, and more versatile devices. However, advancement of this emerging technology is limited by insufficient…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Energy transfer through quantum coherences plays an essential role in diverse natural phenomena and technological applications, such as human vision, light-harvesting complexes, quantum heat engines, and quantum information and computing.…
Retrosynthesis is a problem to infer reactant compounds to synthesize a given product compound through chemical reactions. Recent studies on retrosynthesis focus on proposing more sophisticated prediction models, but the dataset to feed the…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
The fields of Origin of Life and Artificial Life both question what life is and how it emerges from a distinct set of "pre-life" dynamics. One common feature of most substrates where life emerges is a marked shift in dynamics when…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Bacterial quorum sensing can be engineered with a view to the design of biotechnological applications based on their intrinsic role as a means of communication. We propose the creation of a positive feedback loop that will promote the…
RNA can be used as a high-density medium for data storage and transmission; however, an important RNA process -- replication -- is noisy. This paper presents an error analysis for RNA as a data transmission medium, analyzing how deletion…
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…