Molecular knots

SDP Fielden, DA Leigh… - Angewandte Chemie …, 2017 - Wiley Online Library
The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in
the last few years that more complex small‐molecule knot topologies have been realized …

Polymers with spatial or topological constraints: Theoretical and computational results

C Micheletti, D Marenduzzo, E Orlandini - Physics Reports, 2011 - Elsevier
In this review, we provide an organized summary of the theoretical and computational
results that are available for polymers subject to spatial or topological constraints. Because …

The mechanical bond in biological systems

SR Beeren, CT McTernan, F Schaufelberger - Chem, 2023 - cell.com
The field of mechanically interlocked molecules (MIMs) has advanced rapidly in recent
years, with much work focused on their use in materials, sensing, and catalysis. However …

Quantum-inspired encoding enhances stochastic sampling of soft matter systems

F Slongo, P Hauke, P Faccioli, C Micheletti - Science Advances, 2023 - science.org
Quantum advantage in solving physical problems is still hard to assess due to hardware
limitations. However, algorithms designed for quantum computers may engender …

Complex DNA knots detected with a nanopore sensor

R Kumar Sharma, I Agrawal, L Dai, PS Doyle… - Nature …, 2019 - nature.com
Equilibrium knots are common in biological polymers—their prevalence, size distribution,
structure, and dynamics have been extensively studied, with implications to fundamental …

Stereoselective synthesis of a composite knot with nine crossings

L Zhang, AJ Stephens, AL Nussbaumer… - Nature Chemistry, 2018 - nature.com
The simultaneous synthesis of a molecular nine-crossing composite knot that contains three
trefoil tangles of the same handedness and a 9 7 3 link (a type of cyclic [3] catenane …

Molecular knots in biology and chemistry

NCH Lim, SE Jackson - Journal of Physics: Condensed Matter, 2015 - iopscience.iop.org
Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating
topological entities can be either useful or cumbersome. In recent decades, the importance …

Topoly: Python package to analyze topology of polymers

P Dabrowski-Tumanski, P Rubach… - Briefings in …, 2021 - academic.oup.com
The increasing role of topology in (bio) physical properties of matter creates a need for an
efficient method of detecting the topology of a (bio) polymer. However, the existing tools …

DNA–DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting

D Marenduzzo, E Orlandini, A Stasiak… - Proceedings of the …, 2009 - National Acad Sciences
Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids
is both highly knotted and neatly structured. What is the physical basis of this organization …

The polymer physics of single DNA confined in nanochannels

L Dai, CB Renner, PS Doyle - Advances in colloid and interface science, 2016 - Elsevier
In recent years, applications and experimental studies of DNA in nanochannels have
stimulated the investigation of the polymer physics of DNA in confinement. Recent advances …