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"Chain mobility"
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Highly stretchable polymer semiconductor films through the nanoconfinement effect
by
Wang, Yanming
,
Murmann, Boris
,
Rondeau-Gagné, Simon
in
Amorphous silicon
,
Chain dynamics
,
Chain mobility
2017
Soft and conformable wearable electronics require stretchable semiconductors, but existing ones typically sacrifice charge transport mobility to achieve stretchability. We explore a concept based on the nanoconfinement of polymers to substantially improve the stretchability of polymer semiconductors, without affecting charge transport mobility. The increased polymer chain dynamics under nanoconfinement significantly reduces the modulus of the conjugated polymer and largely delays the onset of crack formation under strain. As a result, our fabricated semiconducting film can be stretched up to 100% strain without affecting mobility, retaining values comparable to that of amorphous silicon. The fully stretchable transistors exhibit high biaxial stretchability with minimal change in on current even when poked with a sharp object. We demonstrate a skinlike finger-wearable driver for a light-emitting diode.
Journal Article
An engineered PET depolymerase to break down and recycle plastic bottles
2020
Present estimates suggest that of the 359 million tons of plastics produced annually worldwide
1
, 150–200 million tons accumulate in landfill or in the natural environment
2
. Poly(ethylene terephthalate) (PET) is the most abundant polyester plastic, with almost 70 million tons manufactured annually worldwide for use in textiles and packaging
3
. The main recycling process for PET, via thermomechanical means, results in a loss of mechanical properties
4
. Consequently, de novo synthesis is preferred and PET waste continues to accumulate. With a high ratio of aromatic terephthalate units—which reduce chain mobility—PET is a polyester that is extremely difficult to hydrolyse
5
. Several PET hydrolase enzymes have been reported, but show limited productivity
6
,
7
. Here we describe an improved PET hydrolase that ultimately achieves, over 10 hours, a minimum of 90 per cent PET depolymerization into monomers, with a productivity of 16.7 grams of terephthalate per litre per hour (200 grams per kilogram of PET suspension, with an enzyme concentration of 3 milligrams per gram of PET). This highly efficient, optimized enzyme outperforms all PET hydrolases reported so far, including an enzyme
8
,
9
from the bacterium
Ideonella sakaiensis
strain 201-F6 (even assisted by a secondary enzyme
10
) and related improved variants
11
–
14
that have attracted recent interest. We also show that biologically recycled PET exhibiting the same properties as petrochemical PET can be produced from enzymatically depolymerized PET waste, before being processed into bottles, thereby contributing towards the concept of a circular PET economy.
Computer-aided engineering produces improvements to an enzyme that breaks down poly(ethylene terephthalate) (PET) into its constituent monomers, which are used to synthesize PET of near-petrochemical grade that can be further processed into bottles.
Journal Article
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees
2014
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
Journal Article
Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography
by
James, Daniel
,
Brünle, Steffen
,
Furrer, Antonia
in
Aspartic acid
,
Aspartic Acid - chemistry
,
Bacteriorhodopsin
2019
Conformational dynamics are essential for proteins to function. We adapted time-resolved serial crystallography developed at x-ray lasers to visualize proteinmotions using synchrotrons. We recorded the structural changes in the light-driven proton-pump bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release at a quality comparable to that of previous x-ray laser experiments. From 10 to 15 milliseconds onwards, we observe large additional structural rearrangements up to 9 angstroms on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid–96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle.
Journal Article
Unblocking the chain – findings from an executive workshop on blockchain in the supply chain
2020
Purpose
There is a lot of interest in blockchain in the supply chain and several papers call it a disruptive technology. Existing research, however, is mostly conceptual and focused on use-case development and early pilots. This paper aims to report the findings from a workshop with managers aimed at empirically exploring what adoption rates and focus areas are for blockchain in the supply chain, what drives blockchain in the supply chain applications and what barriers are to the implementation of blockchain in the supply chain.
Design/methodology/approach
A workshop with managers was organized to empirically explore blockchain adoption levels and focus areas in the supply chain, as well as drivers and barriers of implementation.
Findings
Workshop participants reported that adoption of blockchain in the supply chain today is very limited but actively considered by many. Drivers for this consideration include achieving greater transparency and visibility, as well as, improving processes and reducing costs. Participants identify many barriers, including a lack of understanding of costs and benefits of blockchain in the supply chain. Interestingly, participants report less concern about the feasibility of the technology implying managerial consideration if progressing beyond the technology and into the potential adoption of it. As a result, participants may be moving beyond the hype surrounding blockchain and giving consideration to the many remaining questions. A working technology does not yet mean that there is a feasible supply chain adoption. As a result, it may be too early to tell whether blockchain will be a disruptive technology. This paper identifies several fruitful areas for further consideration by management and in research.
Originality/value
As there is little empirical research on blockchain in the supply chain, this paper moves beyond use-case development and the exploration of pilot cases and studies how companies may consider supply chain adoption beyond the pilot and the early development of blockchain. Although only offering an initial exploration, this paper uncovers progress being reported in industry and many areas where further consideration and research can help advance thinking and practice.
Journal Article
Structural flexibility and protein adaptation to temperature
by
Meng, Xian-liang
,
Dong, Yun-wei
,
Liao, Ming-ling
in
Adaptation
,
Amino acid sequence
,
Amino acids
2018
Orthologous proteins of species adapted to different temperatures exhibit differences in stability and function that are interpreted to reflect adaptive variation in structural “flexibility.” However, quantifying flexibility and comparing flexibility across proteins has remained a challenge. To address this issue, we examined temperature effects on cytosolic malate dehydrogenase (cMDH) orthologs from differently thermally adapted congeners of five genera of marine molluscs whose field body temperatures span a range of ∼60 °C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on K
M of cofactor (NADH)] and structural stability (rate of heat denaturation of activity). To determine how these differences depend on flexibilities of overall structure and of regions known to be important in binding and catalysis, we performed molecular dynamics simulation (MDS) analyses. MDS analyses revealed a significant negative correlation between adaptation temperature and heat-induced increase of backbone atom movements [root mean square deviation (rmsd) of main-chain atoms]. Root mean square fluctuations (RMSFs) of movement by individual amino acid residues varied across the sequence in a qualitatively similar pattern among orthologs. Regions of sequence involved in ligand binding and catalysis—termed mobile regions 1 and 2 (MR1 and MR2), respectively—showed the largest values for RMSF. Heat-induced changes in RMSF values across the sequence and, importantly, in MR1 and MR2 were greatest in cold-adapted species. MDS methods are shown to provide powerful tools for examining adaptation of enzymes by providing a quantitative index of protein flexibility and identifying sequence regions where adaptive change in flexibility occurs.
Journal Article
Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics
by
Hori, Naoto
,
Thirumalai, D.
,
Nguyen, Hung T.
in
639/638
,
639/638/563/982
,
Analytical Chemistry
2022
Although it is known that RNA undergoes liquid–liquid phase separation, the interplay between the molecular driving forces and the emergent features of the condensates, such as their morphologies and dynamic properties, is not well understood. We introduce a coarse-grained model to simulate phase separation of trinucleotide repeat RNAs, which are implicated in neurological disorders. After establishing that the simulations reproduce key experimental findings, we show that once recruited inside the liquid droplets, the monomers transition from hairpin-like structures to extended states. Interactions between the monomers in the condensates result in the formation of an intricate and dense intermolecular network, which severely restrains the fluctuations and mobilities of the RNAs inside large droplets. In the largest densely packed high-viscosity droplets, the mobility of RNA chains is best characterized by reptation, reminiscent of the dynamics in polymer melts. Our work provides a microscopic framework for understanding liquid–liquid phase separation in RNA, which is not easily discernible in current experiments.
The molecular driving forces underlying the liquid–liquid phase separation (LLPS) of RNA are not well understood. Now simulations show that low-complexity RNA sequences undergo LLPS at high RNA concentrations, driven by the formation of Watson–Crick base pairs between distinct RNA polymers. LLPS occurs by merger of small droplets into larger ones and RNA chains in the large droplets exhibit reptation dynamics.
Journal Article
Towards the circular economy in the fashion industry: the second-hand market as a best practice of sustainable responsibility for businesses and consumers
by
Morone, Piergiuseppe
,
Settembre-Blundo, Davide
,
Lupi, Gianluca
in
Analytic hierarchy process
,
Aquatic Pollution
,
Best practice
2022
The transition to a circular economy is a key concern for the fashion industry. The emerging second-hand market is a practice that could enable the circular economy in the fashion industry. As this is an emerging trend, the literature has not yet sufficiently explored how it is possible to simultaneously meet consumer and industry expectations in the management of second-hand garments within the value chain. This article aimed to fill that gap with the analytic hierarchy process, which demonstrated that garment collection and recycling are not necessarily best practices for the circular economy. For this to happen, close collaboration between manufacturers and retailers in the value chain is needed to move the industry towards responsibly sustainable production and consumption models. The results emphasise that harvesting management and internal competition on low-cost collection are critical business drivers, while responsible consumption and benefits are opportunities for consumers.
Journal Article
Solution-processable polytriazoles from spirocyclic monomers for membrane-based hydrocarbon separations
by
Mathias, Ronita
,
Bechis, Irene
,
McCool, Benjamin A
in
Alkynes
,
Boiling points
,
Chain mobility
2023
The thermal distillation of crude oil mixtures is an energy-intensive process, accounting for nearly 1% of global energy consumption. Membrane-based separations are an appealing alternative or tandem process to distillation due to intrinsic energy efficiency advantages. We developed a family of spirocyclic polytriazoles from structurally diverse monomers for membrane applications. The resulting polymers were prepared by a convenient step-growth method using copper-catalysed azide–alkyne cycloaddition, providing very fast reaction rates, high molecular weights and solubilities in common organic solvents and non-interconnected microporosity. Fractionation of whole Arabian light crude oil and atmospheric tower bottom feeds using these materials enriched the low-boiling-point components and removed trace heteroatom and metal impurities (comparable performance with the lighter feed as the commercial polyimide, Matrimid), demonstrating opportunities to reduce the energy cost of crude oil distillation with tandem membrane processes. Membrane-based molecular separation under these demanding conditions is made possible by high thermal stability and a moderate level of dynamic chain mobility, leading to transient interconnections between micropores, as revealed by the calculations of static and swollen pore structures.Thermal fractionation of petroleum consumes large amounts of energy. Here stable microporous polymers are synthesized using click chemistry, which have similar performance to commercial polyimides for the fractionation of light crude oils and successful application to heavy feeds under realistic conditions.
Journal Article
Exploring the structural origins of cryptic sites on proteins
by
Luo, Lingqi
,
Beglov, Dmitri
,
Whitty, Adrian
in
Binding sites
,
Biological Sciences
,
Biophysics and Computational Biology
2018
Molecular dynamics (MD) simulations of proteins reveal the existence of many transient surface pockets; however, the factors determining what small subset of these represent druggable or functionally relevant ligand binding sites, called “cryptic sites,” are not understood. Here, we examine multiple X-ray structures for a set of proteins with validated cryptic sites, using the computational hot spot identification tool FTMap. The results show that cryptic sites in ligand-free structures generally have a strong binding energy hot spot very close by. As expected, regions around cryptic sites exhibit above-average flexibility, and close to 50% of the proteins studied here have unbound structures that could accommodate the ligand without clashes. Nevertheless, the strong hot spot neighboring each cryptic site is almost always exploited by the bound ligand, suggesting that binding may frequently involve an induced fit component. We additionally evaluated the structural basis for cryptic site formation, by comparing unbound to bound structures. Cryptic sites are most frequently occluded in the unbound structure by intrusion of loops (22.5%), side chains (19.4%), or in some cases entire helices (5.4%), but motions that create sites that are too open can also eliminate pockets (19.4%). The flexibility of cryptic sites frequently leads to missing side chains or loops (12%) that are particularly evident in low resolution crystal structures. An interesting observation is that cryptic sites formed solely by the movement of side chains, or of backbone segments with fewer than five residues, result only in low affinity binding sites with limited use for drug discovery.
Journal Article