Related papers: Implementing Non-Equilibrium Networks with Active …

DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…

We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical…

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…

DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages…

We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test…

We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…

DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…

Recent work has shown how chemical reaction network theory may be used to design dynamical systems that can be implemented biologically in nucleic acid-based chemistry. While this has allowed the construction of advanced open-loop circuitry…

Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…

Reacting astrophysical flows can be challenging to model because of the difficulty in accurately coupling hydrodynamics and reactions. This can be particularly acute during explosive burning or at high temperatures where nuclear statistical…

Solid-phase synthesis techniques underpin the synthesis of DNA, oligopeptides, oligosaccharides, and combinatorial libraries for drug discovery. State-of-the-art solid-phase synthesizers can produce oligonucleotides up to 200-300…

We report transport properties and particle current rectification operation in a double-stranded tight-binding ladder network within non-equilibrium Green's function (NEGF) formalism that can easily be generalized in multi-stranded systems.…

Over the last years, analyses performed on a stochastic model of catalytic reaction networks have provided some indications about the reasons why wet-lab experiments hardly ever comply with the phase transition typically predicted by…

Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…

Charge exchange (CE) reactions offer a major opportunity to excite nuclear isovector modes, providing clues about the nuclear interaction in the medium. Moreover, double charge exchange (DCE) reactions are proving to be a tempting tool to…

Autocatalytic cores are minimal units in reaction networks (RNs) responsible for the emergence of autocatalysis. In the absence of explicit catalysis, i.e., when an entity appears both as reactant and product in the same reaction, they are…

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…

The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…

Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metabolic regulation. Beyond their well-known role in conferring…

Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…