Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanism Insight into the Constitutional Phase Change Selection of Dynameric Framework Libraries.

ABSTRACT: We show that the use of reversibly connected trialdehyde cores and diamine hydrophilic/hydrophobic connectors may generate libraries of dynameric frameworks of variable composition. The dynamic reversible imine- and trans-imination reactions induce the progressive segregation of libraries consisting of homo- and heterodynameric frameworks through the constitutional selection and successive precipitation of low-soluble hydrophobic films and hydrophilic/hydrophobic core-shell particles. This "precipitation-driven segregation" results in the formation of membrane with unique asymmetric morpholgy. Systematic compositional changes of dynamers, segregating solvents, and casting surfaces were correlated with the emerged membrane structure, and NMR/transmission electron microscopy-energy-dispersive X-ray characterizations mostly supported their hypothesis.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC6641219 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Mechanism Insight into the Constitutional Phase Change Selection of Dynameric Framework Libraries.

Zhang Yan Y Barboiu Mihail M

ACS omega 20180111 1

We show that the use of reversibly connected trialdehyde cores and diamine hydrophilic/hydrophobic connectors may generate libraries of dynameric frameworks of variable composition. The dynamic reversible imine- and trans-imination reactions induce the progressive segregation of libraries consisting of homo- and heterodynameric frameworks through the constitutional selection and successive precipitation of low-soluble hydrophobic films and hydrophilic/hydrophobic core-shell particles. This "prec ...[more]

PMID: 31457895

Similar Datasets

Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.

Project description:The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k(cat) values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified (447)GGLPQK(452) as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment.

| S-EPMC3240725 | biostudies-literature

Direct atomic insight into the role of dopants in phase-change materials.

Project description:Doping is indispensable to tailor phase-change materials (PCM) in optical and electronic data storage. Very few experimental studies, however, have provided quantitative information on the distribution of dopants on the atomic-scale. Here, we present atom-resolved images of Ag and In dopants in Sb2Te-based (AIST) PCM using electron microscopy and atom-probe tomography. Combing these with DFT calculations and chemical-bonding analysis, we unambiguously determine the dopants' role upon recrystallization. Composition profiles corroborate the substitution of Sb by In and Ag, and the segregation of excessive Ag into grain boundaries. While In is bonded covalently to neighboring Te, Ag binds ionically. Moreover, In doping accelerates the crystallization and hence operation while Ag doping limits the random diffusion of In atoms and enhances the thermal stability of the amorphous phase.

| S-EPMC6684653 | biostudies-literature

ζ-Glycine: insight into the mechanism of a polymorphic phase transition.

Project description:Glycine is the simplest and most polymorphic amino acid, with five phases having been structurally characterized at atmospheric or high pressure. A sixth form, the elusive ζ phase, was discovered over a decade ago as a short-lived intermediate which formed as the high-pressure ∊ phase transformed to the γ form on decompression. However, its structure has remained unsolved. We now report the structure of the ζ phase, which was trapped at 100 K enabling neutron powder diffraction data to be obtained. The structure was solved using the results of a crystal structure prediction procedure based on fully ab initio energy calculations combined with a genetic algorithm for searching phase space. We show that the fate of ζ-glycine depends on its thermal history: although at room temperature it transforms back to the γ phase, warming the sample from 100 K to room temperature yielded β-glycine, the least stable of the known ambient-pressure polymorphs.

| S-EPMC5619850 | biostudies-literature

Libraries against libraries for combinatorial selection of replicating antigen-antibody pairs.

Project description:Antibodies are among the most highly selective tight-binding ligands for proteins. Because the human genome project has deciphered the proteome, there is an opportunity to use combinatorial antibody libraries to select high-affinity antibodies to every protein encoded by the genome. However, this is a large task because the selection formats used today for combinatorial antibody libraries are geared toward generating antibodies to one antigen at a time. Here, we describe a method that accelerates the identification of antibodies to a multitude of antigens simultaneously by matching combinatorial antibody libraries against eukaryotic antigen libraries so that replication-competent cognate antigen-antibody pairs can be directly selected. Phage and yeast display systems are used because they each link genotype to phenotype and can be replicated individually. When combined with cell sorting, the two libraries can be selected against each other for recovery of cognate antigen-antibody clones in a single experiment.

| S-EPMC2621251 | biostudies-literature

Functional Constitutional Dynamic Networks Revealing Evolutionary Reproduction/Variation/Selection Principles.

Project description:Within the broad research efforts to engineer chemical pathways to yield high-throughput evolutionary synthesis of genes and their screening for dictated functionalities, we introduce the evolution of nucleic-acid-based constitutional dynamic networks (CDNs) that follow reproduction/variation/selection principles. These fundamental principles are demonstrated by assembling a library of nucleic-acid strands and hairpins as functional modules for evolving networks. Primary T1-initiated selection of components from the library assembles a parent CDN X, where the evolved constituents exhibit catalytic properties to cleave the hairpins in the library. Cleavage of the hairpins yields fragments, which reproduces T1 to replicate CDN X, whereas the other fragments T2 and T3 select other components to evolve two other CDNs, Y and Z (variation). By applying appropriate counter triggers, we demonstrate the guided selection of networks from the evolved CDNs. By integrating additional hairpin substrates into the system, CDN-dictated emergent catalytic transformations are accomplished. The study provides pathways to construct evolutionary dynamic networks revealing enhanced gated and cascaded functions.

| S-EPMC7498142 | biostudies-literature

Metal-Formate Framework Stiffening and Its Relevance to Phase Transition Mechanism.

Project description:In the last decade, one of the most widely examined compounds of motal-organic frameworks was undoubtedly ((CH3)2NH2)(Zn(HCOO)3), but the problem of the importance of framework dynamics in the order-disorder phase change of the mechanism has not been fully clarified. In this study, a combination of temperature-dependent dielectric, calorimetric, IR, and Raman measurements was used to study the impact of ((CH3)2NH2)(Zn(DCOO)3) formate deuteration on the phase transition mechanism in this compound. This deuteration led to the stiffening of the metal-formate framework, which in turn caused an increase in the phase transition temperature by about 5 K. Interestingly, the energetic ordering of DMA+ cations remained unchanged compared to the non-deuterated compound.

| S-EPMC8537347 | biostudies-literature

Enzyme-Guided Selection and Cascaded Emergence of Nanostructured Constitutional Dynamic Networks.

Project description:Enzymes (endonucleases) are coupled to constitutional dynamic networks to stimulate the selection of a constituent and cascaded emergence of a new network. This is exemplified with the EcoRI-dictated depletion of a network and selection of a constituent that activates the cascaded emergence of a new network. The new network is further depleted by HindIII to a selected constituent that can be coupled to the cascaded emergence of a dynamic network. In addition, upon subjecting a [3 × 3] constitutional dynamic network to endonucleases EcoRI and HindIII, the programmed hierarchical selection of [2 × 2] constitutional dynamic networks followed by the biocatalytic selection of a constituent for the subsequent emergence of new networks is demonstrated.

| S-EPMC7467759 | biostudies-literature

Insights into the Multiscale Lubrication Mechanism of Edible Phase Change Materials.

Project description:Investigation of a lubrication behavior of phase change materials (PCM) can be challenging in applications involving relative motion, e.g., sport (ice skating), food (chocolates), energy (thermal storage), apparel (textiles with PCM), etc. In oral tribology, a phase change often occurs in a sequence of dynamic interactions between the ingested PCM and oral surfaces from a licking stage to a saliva-mixed stage at contact scales spanning micro- (cellular), meso- (papillae), and macroscales. Often the lubrication performance and correlations across length scales and different stages remain poorly understood due to the lack of testing setups mimicking real human tissues. Herein, we bring new insights into lubrication mechanisms of PCM using dark chocolate as an exemplar at a single-papilla (meso)-scale and a full-tongue (macro) scale covering the solid, molten, and saliva-mixed states, uniting highly sophisticated biomimetic oral surfaces with in situ tribomicroscopy for the first time. Unprecedented results from this study supported by transcending lubrication theories reveal how the tribological mechanism in licking shifted from solid fat-dominated lubrication (saliva-poor regime) to aqueous lubrication (saliva-dominant regime), the latter resulted in increasing the coefficient of friction by at least threefold. At the mesoscale, the governing mechanisms were bridging of cocoa butter in between confined cocoa particles and fat coalescence of emulsion droplets for the molten and saliva-mixed states, respectively. At the macroscale, a distinctive hydrodynamic viscous film formed at the interface governing the speed-dependent lubrication behavior indicates the striking importance of multiscale analyses. New tribological insights across different stages and scales of phase transition from this study will inspire rational design of the next generation of PCM and solid particle-containing materials.

| S-EPMC9880949 | biostudies-literature

PATIENT RECRUITMENT USING ELECTRONIC HEALTH RECORDS UNDER SELECTION BIAS: A TWO-PHASE SAMPLING FRAMEWORK.

Project description:Electronic health records (EHRs) are increasingly recognized as a cost-effective resource for patient recruitment in clinical research. However, how to optimally select a cohort from millions of individuals to answer a scientific question of interest remains unclear. Consider a study to estimate the mean or mean difference of an expensive outcome. Inexpensive auxiliary covariates predictive of the outcome may often be available in patients' health records, presenting an opportunity to recruit patients selectively, which may improve efficiency in downstream analyses. In this paper we propose a two-phase sampling design that leverages available information on auxiliary covariates in EHR data. A key challenge in using EHR data for multiphase sampling is the potential selection bias, because EHR data are not necessarily representative of the target population. Extending existing literature on two-phase sampling design, we derive an optimal two-phase sampling method that improves efficiency over random sampling while accounting for the potential selection bias in EHR data. We demonstrate the efficiency gain from our sampling design via simulation studies and an application evaluating the prevalence of hypertension among U.S. adults leveraging data from the Michigan Genomics Initiative, a longitudinal biorepository in Michigan Medicine.

| S-EPMC11323140 | biostudies-literature

A Phase-Change Mechanism of GST-SL Based Superlattices upon Sb Flipping.

Project description:Reversible phase-change behaviors of Ge-Sb-Te based superlattices (GST-SL) were studied by ab initio molecular dynamics (AIMD) simulations based on three models containing Ge/Sb intermixing, namely the Petrov-mix, Ferro-mix, and Kooi-mix models. The flipping behavior of Sb atoms was found in all the three GST-SL models in the melting process. Among them the Kooi-mix model exhibited the best stability, and the analyses of bond length distribution and electron localization function provided a better explanation on the phase transition of GST-SL. Finally, we proposed a fast switching model for GST-SL based on Sb flipping.

| S-EPMC7828381 | biostudies-literature

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