Related papers: Hydrogen peroxide thermochemical oscillator as dri…
The structure of the self-cleaving hairpin ribozyme is well characterized, and its folding has been examined in bulk and by single-molecule fluorescence, establishing the importance of cations, especially magnesium in the stability of the…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Even the simplest organisms are too complex to have spontaneously arisen fully-formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of…
Hydrogen gas is a promising alternative to fossil fuels due to its high energy output and environmentally safe byproducts. Various morphologies of photocatalytic materials have been explored for high-efficiency H$_2$ production, for…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
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…
A small, bimetallic particle in a hydrogen peroxide solution can propel itself by means of an electrocatalytic reaction. The swimming is driven by a flux of ions around the particle. We model this process for the presence of a monovalent…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
We report on a large scale computer simulation study of crystal nucleation in hard spheres. Through a combined analysis of real and reciprocal space data, a picture of a two-step crystallization process is supported: First dense, amorphous…
The formation of regular precipitate stripes in the wake of moving chemical reaction-diffusion fronts is investigated. Experiments on the $NaOH+CuCl_2$ reaction in PVA hydrogel yield stripes parallel or slightly oblique to the front that…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life, but supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…
The observed single-handedness of biological amino acids and sugars has long been attributed to autocatalysis. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross inhibition of the two chiral…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
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…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
It has been suggested that major transitions in evolution require the emergence of novelties, often associated to the cooperative behaviour of previously existing objects or agents. A key innovation involves the first cooperative…