Browse
Submit Data
Databases
API
Help

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photo-printing of faceted DNA patchy particles.

ABSTRACT: Patchy particles with shape complementarity can serve as building blocks for assembling colloidal superstructures. Alternatively, encoding information on patches using DNA can direct assembly into a variety of crystalline or other preprogrammed structures. Here, we present a tool where DNA is used both to engineer shape and to encode information on colloidal particles. Two reactive oil emulsions with different but complementary DNA (cDNA) brushes are assembled into CsCl-like crystalline lattices. The DNA brushes are recruited to and ultimately localized at the junctions between neighboring droplets, which gives rise to DNA-encoded faceted patches. The emulsions are then solidified by ultraviolet (UV) polymerization, producing faceted patchy particles. The facet size and DNA distribution are determined by the balance between the DNA binding energy and the elastic deformation energy of droplets. This method leads to a variety of new patchy particles with directional interactions in scalable quantities.

SUBMITTER: Diaz A JA

PROVIDER: S-EPMC7245101 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Photo-printing of faceted DNA patchy particles.

Diaz A Jairo A JA Oh Joon Suk JS Yi Gi-Ra GR Pine David J DJ

Proceedings of the National Academy of Sciences of the United States of America 20200508 20

Patchy particles with shape complementarity can serve as building blocks for assembling colloidal superstructures. Alternatively, encoding information on patches using DNA can direct assembly into a variety of crystalline or other preprogrammed structures. Here, we present a tool where DNA is used both to engineer shape and to encode information on colloidal particles. Two reactive oil emulsions with different but complementary DNA (cDNA) brushes are assembled into CsCl-like crystalline lattices ...[more]

PMID: 32385150

Similar Datasets

Predictive supracolloidal helices from patchy particles.

Project description:A priori prediction of supracolloidal architectures from nanoparticle and colloidal assembly is a challenging goal in materials chemistry and physics. Despite intense research in this area, much less has been known about the predictive science of supracolloidal helices from designed building blocks. Therefore, developing conceptually new rules to construct supracolloidal architectures with predictive helicity is becoming an important and urgent task of great scientific interest. Here, inspired by biological helices, we show that the rational design of patchy arrangement and interaction can drive patchy particles to self-assemble into biomolecular mimetic supracolloidal helices. We further derive a facile design rule for encoding the target supracolloidal helices, thus opening the doors to the predictive science of these supracolloidal architectures. It is also found that kinetics and reaction pathway during the formation of supracolloidal helices offer a unique way to study supramolecular polymerization, and that well-controlled supracolloidal helices can exhibit tailorable circular dichroism effects at visible wavelengths.

| S-EPMC4228328 | biostudies-literature

Spatial confinement governs orientational order in patchy particles.

Project description:Orientational order in condensed matter plays a key role in determining material properties such as ferromagnetism, viscoelasticity or birefringence. We studied purely orientational ordering in closely-packed one-patch colloidal particles confined between flat substrates, where the particles can only rotate and are ordered via the sticky interaction between the patches. For the first time, we experimentally realized a rich variety of mesoscopic patterns through orientational ordering of colloids by controlling patch size and confinement thickness. The combination of experiment and numerical simulation reveals the decisive role of confinement: An ordered state(s) is selected from the (meta)stable options in bulk when it is commensurate with the system geometry and boundary conditions; otherwise, frustration induces a unique order. Our study offers a new means of systematic control over mesoscopic structures via orientational ordering in patchy particles. The system would also possess unique functionalities through the rotational response of the particles to external stimuli.

| S-EPMC4893746 | biostudies-literature

Exploiting limited valence patchy particles to understand autocatalytic kinetics.

Project description:Autocatalysis, i.e., the speeding up of a reaction through the very same molecule which is produced, is common in chemistry, biophysics, and material science. Rate-equation-based approaches are often used to model the time dependence of products, but the key physical mechanisms behind the reaction cannot be properly recognized. Here, we develop a patchy particle model inspired by a bicomponent reactive mixture and endowed with adjustable autocatalytic ability. Such a coarse-grained model captures all general features of an autocatalytic aggregation process that takes place under controlled and realistic conditions, including crowded environments. Simulation reveals that a full understanding of the kinetics involves an unexpected effect that eludes the chemistry of the reaction, and which is crucially related to the presence of an activation barrier. The resulting analytical description can be exported to real systems, as confirmed by experimental data on epoxy-amine polymerizations, solving a long-standing issue in their mechanistic description.

| S-EPMC6035234 | biostudies-literature

Rotational diffusion affects the dynamical self-assembly pathways of patchy particles.

Project description:Predicting the self-assembly kinetics of particles with anisotropic interactions, such as colloidal patchy particles or proteins with multiple binding sites, is important for the design of novel high-tech materials, as well as for understanding biological systems, e.g., viruses or regulatory networks. Often stochastic in nature, such self-assembly processes are fundamentally governed by rotational and translational diffusion. Whereas the rotational diffusion constant of particles is usually considered to be coupled to the translational diffusion via the Stokes-Einstein relation, in the past decade it has become clear that they can be independently altered by molecular crowding agents or via external fields. Because virus capsids naturally assemble in crowded environments such as the cell cytoplasm but also in aqueous solution in vitro, it is important to investigate how varying the rotational diffusion with respect to transitional diffusion alters the kinetic pathways of self-assembly. Kinetic trapping in malformed or intermediate structures often impedes a direct simulation approach of a kinetic network by dramatically slowing down the relaxation to the designed ground state. However, using recently developed path-sampling techniques, we can sample and analyze the entire self-assembly kinetic network of simple patchy particle systems. For assembly of a designed cluster of patchy particles we find that changing the rotational diffusion does not change the equilibrium constants, but significantly affects the dynamical pathways, and enhances (suppresses) the overall relaxation process and the yield of the target structure, by avoiding (encountering) frustrated states. Besides insight, this finding provides a design principle for improved control of nanoparticle self-assembly.

| S-EPMC4687537 | biostudies-literature

Surface roughness directed self-assembly of patchy particles into colloidal micelles.

Project description:Colloidal particles with site-specific directional interactions, so called "patchy particles", are promising candidates for bottom-up assembly routes towards complex structures with rationally designed properties. Here we present an experimental realization of patchy colloidal particles based on material independent depletion interaction and surface roughness. Curved, smooth patches on rough colloids are shown to be exclusively attractive due to their different overlap volumes. We discuss in detail the case of colloids with one patch that serves as a model for molecular surfactants both with respect to their geometry and their interactions. These one-patch particles assemble into clusters that resemble surfactant micelles with the smooth and attractive sides of the colloids located at the interior. We term these clusters "colloidal micelles". Direct Monte Carlo simulations starting from a homogeneous state give rise to cluster size distributions that are in good agreement with those found in experiments. Important differences with surfactant micelles originate from the colloidal character of our model system and are investigated by simulations and addressed theoretically. Our new "patchy" model system opens up the possibility for self-assembly studies into finite-sized superstructures as well as crystals with as of yet inaccessible structures.

| S-EPMC3390863 | biostudies-literature

Toward coordinated colloids: site-selective growth of titania on patchy silica particles.

Project description:Rational synthesis of coordinated spherical colloids is reported by site-selective growth of secondary hemispherical patches on primary spherical particles with quasi-defined coordination numbers and positions. We clarify the importance of mass transport phenomena on the site-specific secondary nucleation/growth in nanoparticulate colloidal systems. By comparing ultrasonic and conventional agitation during patch growth, we found that enhanced mass transfer is the key to controlled, homogeneous transport of the molecular precursors in a solvent onto the nanoparticles. With chemically defined nucleation sites, the surfaces of spherical silica particles were modified for use as a new kind of colloid with patches at desired coordination positions. Our observations represent a significant breakthrough in colloidal chemistry and self-assembly.

| S-EPMC4369688 | biostudies-literature

Facile self-assembly of colloidal diamond from tetrahedral patchy particles via ring selection.

Project description:Diamond-structured crystals, particularly those with cubic symmetry, have long been attractive targets for the programmed self-assembly of colloidal particles, due to their applications as photonic crystals that can control the flow of visible light. While spherical particles decorated with four patches in a tetrahedral arrangement-tetrahedral patchy particles-should be an ideal building block for this endeavor, their self-assembly into colloidal diamond has proved elusive. The kinetics of self-assembly pose a major challenge, with competition from an amorphous glassy phase, as well as clathrate crystals, leaving a narrow widow of patch widths where tetrahedral patchy particles can self-assemble into diamond crystals. Here we demonstrate that a two-component system of tetrahedral patchy particles, where bonding is allowed only between particles of different types to select even-member rings, undergoes crystallization into diamond crystals over a significantly wider range of patch widths conducive for experimental fabrication. We show that the crystallization in the two-component system is both thermodynamically and kinetically enhanced, as compared to the one-component system. Although our bottom-up route does not lead to the selection of the cubic polytype exclusively, we find that the cubicity of the self-assembled crystals increases with increasing patch width. Our designer system not only promises a scalable bottom-up route for colloidal diamond but also offers fundamental insight into crystallization into open lattices.

| S-EPMC8640719 | biostudies-literature

Mikto-Arm Stars as Soft-Patchy Particles: From Building Blocks to Mesoscopic Structures.

Project description:We present an atomistic molecular dynamics study of self-assembled mikto-arm stars, which resemble patchy-like particles. By increasing the number of stars in the system, we propose a systematic way of examining the mutual orientation of these fully penetrable patchy-like objects. The individual stars maintain their patchy-like morphology when creating a mesoscopic (macromolecular) self-assembled object of more than three stars. The self-assembly of mikto-arm stars does not lead to a deformation of the stars, and their shape remains spherical. We identified characteristic sub-units in the self-assembled structure, differing by the mutual orientation of the nearest neighbor stars. The current work aims to elucidate the possible arrangements of the realistic, fully penetrable patchy particles in polymer matrix and to serve as a model system for further studies of nanostructured materials or all-polymer nanocomposites using the mikto-arm stars as building blocks.

| S-EPMC8037958 | biostudies-literature

The Proof Is in the <i>Pidan</i>: Generalizing Proteins as Patchy Particles.

Project description:The Chinese century egg, or pidan, is a traditional preparation of duck eggs that can be stored for months at room temperature without degradation. Raw eggs are soaked in a strong alkaline and salt solution, and the albumin gradually forms a stable, transparent gel. Here, we show that pidan gels belong to the class of materials formed from "patchy particles". We found that the β-sheet structure of ovalbumin, the major protein constituent of egg white, is preserved during gelation, while α-helical regions undergo a degree of unfolding into unstructured random coils that may form attractive patches. Upon dilution in additional strong base, the phase behavior of pidan gels is consistent with patchy-particle thermodynamics. This protein gel is also physically and structurally similar to the protein gels that form the squid lens. Both systems exhibit patchy thermodynamics, and the constituent proteins share physical features including a structured, charged core, and polar, unstructured "arms" that form attractive patches. Our work provides a path toward rational design of proteins for precisely structured, volume-spanning materials.

| S-EPMC6062823 | biostudies-literature

Whole blood leukocytes gene expression in human subjects exposed to printing shop particles

Project description:This study investigates differential expression in human blood leukocytes, from subjects who work in print shops, exposed to particles over time. The time points range over 2 weeks: 1-Monday, 2-Friday, 3-following Monday (rested), and 4-Friday

2020-08-31 | GSE142351 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data