Related papers: A Self-Replicating Peptide Nucleic Acid
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
In the synthesis of metallic nanoparticles in microemulsions, we hypothesized that particle size is mainly controlled by the reaction rate. Thus, the changes observed on the particle sizes as reaction conditions, such as concentrations,…
This paper introduces a method to generate highly selective encodings that can be magnetically "programmed" onto physical modules to enable them to self-assemble in chosen configurations. We generate these encodings based on Hadamard…
We present a minimal motif model for transmembrane cell signaling. The model assumes signaling events taking place in spatially distributed nanoclusters regulated by a birth/death dynamics. The combination of these spatio-temporal aspects…
Recently the first chemical systems which show the amplification of enantiometric excess (ee) was found. Inspired by these experiments, we propose a few chemical reaction models in a closed system. The reactions consist of autocatalytic…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
The kinetic processes in nanoparticle-based catalysis are dominated by large fluctuations and spatiotemporal heterogeneities, in particular for diffusion-influenced reactions which are far from equilibrium. Here, we report results from…
Chemical reaction prediction is pivotal for accelerating drug discovery and synthesis planning. Despite advances in data-driven models, current approaches are hindered by an overemphasis on parameter and dataset scaling. Some methods…
In this work we explore surrogate models to optimize plasma enhanced atomic layer deposition (PEALD) in high aspect ratio features. In plasma-based processes such as PEALD and atomic layer etching, surface recombination can dominate the…
Feedback-rich neural architectures can regenerate earlier representations and inject temporal context, making them a natural setting for strictly local synaptic plasticity. Existing literature raises doubt about whether a minimal,…
The assembly of nanometer-sized building blocks into complex morphologies is not only of fundamental interest but also plays a key role in material science and nanotechnology. We show that the shape of self-assembled superstructures formed…
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties.…
It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication,…
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…
Neural populations exposed to a certain stimulus learn to represent it better. However, the process that leads local, self-organized rules to do so is unclear. We address the question of how can a neural periodic input be learned and use…
The nucleon axial form factors -- axial $G_A$, induced pseudoscalar $\widetilde{G}_P$ and pseudoscalar $G_P$ -- have displayed large systematics in lattice QCD calculations. The major symptoms were the violation of the partially conserved…
RNA in extant biological systems is homochiral; it consists exclusively of D-ribonucleotides rather than L-ribonucleotides. How the homochirality of RNA emerged is not known. Here, we use stochastic simulations to quantitatively explore the…