Jonathan P. K. Doye

Supplementary Material

Akie Kowaguchi, Savan Mehta, Jonathan P. K. Doye, Eva Noya

(pdf file)

Supplementary Material

Akie Kowaguchi, Savan Mehta, Jonathan P. K. Doye, Eva Noya

(pdf file)

A patchy-particle three-dimensional octagonal quasicrystal

Akie Kowaguchi, Savan Mehta, Jonathan P. K. Doye, Eva González Noya

We devise an ideal three-dimensional octagonal quasicrystal that is based upon the two-dimensional Ammann-Beenker tiling and that is potentially suitable for realization with patchy particles. Based on an analysis of its local environments, we design a binary system of five- and eight-patch …

jp, gb, es (code pays fourni par la source)

Chirality transfer in lyotropic twist–bend nematics

Anna Ashkinazi, Hemani Chhabra, Anouar El Moumane, Maxime M. C. Tortora et autres

Using molecular simulations and classical density functional theory, we study the liquid-crystalline phase behavior of a series of bent rod-like mesogens with a controlled degree of chirality introduced through a twist at the center of the particle. In the achiral limit, isotropic, …

gb, us, fr (code pays fourni par la source)

Controlling DNA–RNA strand displacement kinetics with base distribution

Eryk J. Ratajczyk, Jonathan Bath, Petr Šulc, Jonathan P. K. Doye et autres

DNA-RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting DNA-RNA strand displacement reactions is necessary to enable control of processes such as CRISPR-Cas9 gene editing. By combining multiscale modeling with strand displacement experiments, …

us, gb, in, de (code pays fourni par la source)

A One-Component Patchy-Particle Icosahedral Quasicrystal

Eva González Noya, Jonathan P. K. Doye

Designing particles that are able to form icosahedral quasicrystals (IQCs) and that are as simple as possible is not only of fundamental interest but is also important to the potential realization of IQCs in materials other than metallic alloys. Here we introduce …

es, gb (code pays fourni par la source)

A patchy-particle 3-dimensional octagonal quasicrystal

Eva Noya, Akie Kowaguchi, Savan Mehta, Jonathan P. K. Doye

We devise an ideal 3-dimensional octagonal quasicrystal that is based upon the 2-dimensional Ammann-Beenker tiling and that is potentially suitable for realization with patchy particles. Based on an analysis of its local environments we design a binary system of 5- and 8-patch …

Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels

Minh Tri Luu, Jonathan F. Berengut, Jiahe Li, Jasleen Kaur Daljit Singh et autres

In cells, proteins rapidly self-assemble into sophisticated nanomachines. Bioinspired self-assembly approaches, such as DNA origami, have been used to achieve complex three-dimensional (3D) nanostructures and devices. However, current synthetic systems are limited by low yields in hierarchical assembly and challenges in rapid …

au, gb (code pays fourni par la source)

Pipelined information flow in molecular mechanical circuits leads to increased error and irreversibility

Ian Seet, Thomas E. Ouldridge, Jonathan P. K. Doye

Pipelining is a design technique for logical circuits that allows for higher throughput than circuits in which multiple computations are fed through the system one after the other. It allows for much faster computation than architectures in which inputs must pass through …

gb (code pays fourni par la source)

Controlling DNA-RNA strand displacement kinetics with base distribution

Eryk J. Ratajczyk, Jonathan Bath, Petr Šulc, Jonathan P. K. Doye et autres

DNA-RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting DNA-RNA strand displacement reactions is necessary to enable control of processes such as CRISPR-Cas9 gene editing. By combining multi-scale modelling with strand displacement experiments …

pl, gb, us, de (code pays fourni par la source)

Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life

Ed Johnston, Buse Isbilir, Vikram Alva, Tanmay A. M. Bharat et autres

Abstract Surface layers (S-layers) are two-dimensional (2D) crystalline lattices that frequently coat prokaryotic cells, playing a crucial role in protection, maintaining cellular integrity, and mediating environmental interactions. However, the molecular landscape of these abundant proteins has remained underexplored due to a lack …

gb, de (code pays fourni par la source)

Coarse-grained modeling of DNA–RNA hybrids

Eryk J. Ratajczyk, Petr Šulc, Andrew J. Turberfield, Jonathan P. K. Doye et autres

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By …

gb, us, de (code pays fourni par la source)