Soft condensed matter physics of foods and macronutrients

S Assenza, R Mezzenga - Nature Reviews Physics, 2019 - nature.com
Understanding food properties is paramount for enhancing features such as appearance,
taste and texture, for improving health-related factors such as minimizing the onset of …

Computational design of transmembrane pores

C Xu, P Lu, TM Gamal El-Din, XY Pei, MC Johnson… - Nature, 2020 - nature.com
Transmembrane channels and pores have key roles in fundamental biological processes
and in biotechnological applications such as DNA nanopore sequencing,–, resulting in …

Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers

F Kriegel, N Ermann, J Lipfert - Journal of structural biology, 2017 - Elsevier
Nucleic acids are central to the storage and transmission of genetic information. Mechanical
properties, along with their sequence, both enable and fundamentally constrain the …

Martini coarse-grained force field: extension to DNA

JJ Uusitalo, HI Ingólfsson, P Akhshi… - Journal of chemical …, 2015 - ACS Publications
We systematically parameterized a coarse-grained (CG) model for DNA that is compatible
with the Martini force field. The model maps each nucleotide into six to seven CG beads and …

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

BEK Snodin, F Randisi, M Mosayebi, P Šulc… - The Journal of …, 2015 - pubs.aip.org
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

F Grünewald, R Alessandri, PC Kroon… - Nature …, 2022 - nature.com
Molecular dynamics simulations play an increasingly important role in the rational design of
(nano)-materials and in the study of biomacromolecules. However, generating input files …

Biomimetic potassium-selective nanopores

ET Acar, SF Buchsbaum, C Combs, F Fornasiero… - Science …, 2019 - science.org
Reproducing the exquisite ion selectivity displayed by biological ion channels in artificial
nanopore systems has proven to be one of the most challenging tasks undertaken by the …

Detecting DNA and RNA and differentiating single-nucleotide variations via field-effect transistors

KM Cheung, JM Abendroth, N Nakatsuka, B Zhu… - Nano …, 2020 - ACS Publications
We detect short oligonucleotides and distinguish between sequences that differ by a single
base, using label-free, electronic field-effect transistors (FETs). Our sensing platform utilizes …

DNA sequence and length dictate the assembly of nucleic acid block copolymers

FJ Rizzuto, MD Dore, MG Rafique, X Luo… - Journal of the …, 2022 - ACS Publications
The self-assembly of block copolymers is often rationalized by structure and microphase
separation; pathways that diverge from this parameter space may provide new mechanisms …

[HTML][HTML] DNA local-flexibility-dependent assembly of phase-separated liquid droplets

A Shakya, JT King - Biophysical journal, 2018 - cell.com
Phase separation of intracellular components has been recently realized as a mechanism
by which cells achieve membraneless organization. Here, we study the associative liquid …