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Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions…
High-resolution quasi-elastic neutron scattering spectroscopy was used to measure H2O and D2O hydrated RNA samples. The contribution of scattering from RNA was subtracted out by taking the difference of the signals between the two samples.…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
Random organizing hyperuniform fluid induced by reciprocal activation is a non-equilibrium fluid with vanishing density fluctuations at large length scales like crystals. Here we extend this new state of matter to a closed manifold, namely…
A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture…
Despite very high temperatures accompanying lunar origin, indigenous water in the form of OH has been unambiguously observed in Apollo samples in recent years. Such observations have prompted questions about the abundance and distribution…
Amorphous phase-change materials enable fast and reversible switching in optical and electronic devices, yet crystallization kinetics are still controlled primarily through empirical thermal protocols. Here we identify a microscopic picture…
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
A biochemical oscillator model, describing developmental stage of myxobacteria, is analyzed mathematically. Observations from numerical simulations show that in a certain range of parameters, the corresponding system of ordinary…
A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life such as sugars, nucleotides, amino acids, and lipids to "molecular food sources" that have likely…
Solid-state synthesis from powder precursors is the primary processing route to advanced multicomponent ceramic materials. Designing ceramic synthesis routes is usually a laborious, trial-and-error process, as heterogeneous mixtures of…