Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets.

Variant callers typically produce massive numbers of false positives for structural variations, such as cancer-relevant copy-number alterations and fusion genes resulting from genome rearrangements. Here we describe an ultrafast and accurate detector of somatic structural variations that reduces read-mapping costs by filtering out reads matched to pan-genome k-mer sets. The detector, which we named ETCHING (for efficient detection of chromosomal rearrangements and fusion genes), reduces the number of false positives by leveraging machine-learning classifiers trained with six breakend-related features (clipped-read count, split-reads count, supporting paired-end read count, average mapping quality, depth difference and total length of clipped bases). When benchmarked against six callers on reference cell-free DNA, validated biomarkers of structural variants, matched tumour and normal whole genomes, and tumour-only targeted sequencing datasets, ETCHING was 11-fold faster than the second-fastest structural-variant caller at comparable performance and memory use. The speed and accuracy of ETCHING may aid large-scale genome projects and facilitate practical implementations in precision medicine.

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein on the viral envelope mediates human angiotensin-converting enzyme 2 binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein models described in our previous work and performed all-atom molecular dynamics simulations to gain insight into the structural dynamics and interactions between S protein and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes and the influences of antibody on the motion of S protein receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy.

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein on the viral envelope mediates human angiotensin-converting enzyme 2 (ACE2) binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein models described in our previous work, and performed all-atom molecular dynamics simulations to get insight into the structural dynamics and interactions between S protein and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes, and the influences of antibody on the motion of S protein receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy.

Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane.

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2) and is considered the major target for drug and vaccine development. We previously built fully glycosylated full-length SARS-CoV-2 S protein models in a viral membrane including both open and closed conformations of the receptor-binding domain (RBD) and different templates for the stalk region. In this work, multiple µs-long all-atom molecular dynamics simulations were performed to provide deeper insights into the structure and dynamics of S protein and glycan functions. Our simulations reveal that the highly flexible stalk is composed of two independent joints and most probable S protein orientations are competent for ACE2 binding. We identify multiple glycans stabilizing the open and/or closed states of the RBD and demonstrate that the exposure of antibody epitopes can be captured by detailed antibody-glycan clash analysis instead of commonly used accessible surface area analysis that tends to overestimate the impact of glycan shielding and neglect possible detailed interactions between glycan and antibodies. Overall, our observations offer structural and dynamic insights into the SARS-CoV-2 S protein and potentialize for guiding the design of effective antiviral therapeutics.

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane.

This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane.

This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19) so that researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

Aspirin Use Is Not Associated with Lower Thyroid Cancer Risk: A Nationwide Nested Case-Control Study.

Background: While aspirin use is known to be associated with reduced incidence of various cancer types, it is unclear whether this benefit extends to thyroid cancer. We aimed to evaluate the association between aspirin use and thyroid cancer development. Methods: This nested case-control study used nationwide data from the Korean National Health Insurance Service-National Sample Cohort 2002-2015. In total, 4547 individuals with newly developed thyroid cancer were matched with 13,641 controls based on age, sex, and follow-up period. Odds ratios (ORs) and 95% confidence intervals (CIs) for thyroid cancer development according to aspirin use were analyzed using a multivariable conditional logistic regression model. Results: The number of days for which patients with thyroid cancer used aspirin (the proportions of no use, <30 days/year, 30-90 days/year, and ≥90 days/year were 93.03%, 6.51%, 0.31%, and 0.15%, respectively) was comparable with that of the controls (p = 0.371, chi-squared test). The risk of thyroid cancer development was not associated with the duration of aspirin use (ORs [CI] for aspirin use <30 days/year, 30-90 days/year, and ≥90 days/year were 1.11 [0.96-1.28], 1.01 [0.54-1.88], and 1.23 [0.50-3.06], respectively, compared with no use) after adjusting for body mass index, smoking status, hypertension, Charlson comorbidity index, and number of outpatient visits per year. In addition, subgroup analyses stratified by age, sex, and follow-up duration did not reveal any significant association between aspirin use and thyroid cancer. Conclusions: Our findings suggest that even extended aspirin use may not impact the prevention or onset of thyroid cancer.

Formation of arsenic clusters in InAs nanowires with an Al2O3 shell.

An in-depth understanding of thermal behavior and phase evolution is required to apply heterostructured nanowires (NWs) in real devices. The intermediate status during the vaporization process of InAs NWs in an Al2O3 shell was studied by conducting quenching during in situ heating experiments, using a transmission electron microscope. The formation of As clusters in the amorphous Al2O3 shell was confirmed by analyzing the high-angle annular dark field images and energy-dispersive X-ray spectra. The As clusters existed independently in the shell and were also observed at the end of the InAs pieces obtained after quenching. The formation process of the As clusters was demonstrated from a theoretical perspective. Moreover, an ab initio molecular dynamics simulation (AIMD) was conducted to study the atomic and molecular behaviors.

Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers.

Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for quantitative characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ≈ 21.5 Å) to DMPC (hydrophobic thickness ≈ 25.5 Å) bilayers, ΔG(DLPC → DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ∼22 Å. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ∼26 Å. Using this effective hydrophobic length, ΔG(DLPC → DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the quantitative characterization of protein-lipid interactions at all-atom resolution.

Anisotropic atomistic evolution during the sublimation of polar InAs nanowires.

Sublimation is an interesting phenomenon that is frequently observed in nature. The thermal behavior of InAs NWs with As-face polarity and the [1[combining macron]1[combining macron]1[combining macron]] growth direction of the zinc blende structure were studied by using in situ transmission electron microscopy (TEM). In this study, the anisotropic morphological and atomistic evolution of InAs nanowires (NWs) was observed during decomposition. Two specific phenomena were observed during the continuous heating of the NWs as observed using the TEM: the decomposition of the InAs NWs around 380 °C, much lower than the melting temperature, and the formation of particular crystallographic facets during decomposition. The low decomposition temperature is related to vaporization under the vacuum conditions of the TEM. The anisotropic decomposition of the InAs NWs during heating can be explained based on the polarity and the surface energy difference of the zinc blende structure of InAs. For example, the decomposition along the [111] direction (that is, the indium-atom-terminated plane) was continuous, resulting in a few high-index planes, for example, (022), (3[combining macron]1[combining macron]1[combining macron]), and (200), whereas that in the opposite direction (the [1[combining macron]1[combining macron]1[combining macron]] direction) occurred abruptly with the formation of ledges and steps on the (1[combining macron]1[combining macron]1[combining macron]) planes, accompanied by the generation of small grooves on the surface of the NWs. Finally, density functional theory calculations were conducted to understand the sublimation of the InAs NWs from a theoretical point of view. This study is meaningful that it provides an insight into the microstructural evolution of polar nanomaterials during heating by theoretical and experimental approaches.

Polyselenide Anchoring Using Transition-Metal Disulfides for Enhanced Lithium-Selenium Batteries.

While selenium has recently been proposed as a lithium battery cathode as a promising alternative to a lithium-sulfur battery, dissolution of intermediate species should be resolved to improve its cycle stability. Here, we report the promising results of transition-metal disulfides as an anchoring material and the underlying origin for preventing active material loss from the electrode using density functional theory calculations. Group 5 and 4 disulfides (VS2, NbS2, TaS2, TiS2, ZrS2, and HfS2) in particular show anchoring capabilities superior to those of group 6 disulfides (CrS2, MoS2, and WS2). The governing interaction controlling the latter relative anchoring strengths is shown to be charge transfer as understood by crystal-field theory. The current findings and methodologies provide novel chemical insight for the further design of inorganic anchoring materials for both lithium-selenium and lithium-sulfur batteries.

Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature.

Gangliosides are a class of glycosphingolipids (GSLs) with amphiphilic character that are found at the outer leaflet of the cell membranes, where their ability to organize into special domains makes them vital cell membrane components. However, a molecular understanding of GSL-rich membranes in terms of their clustered organization, stability, and dynamics is still elusive. To gain molecular insight into the organization and dynamics of GSL-rich membranes, we performed all-atom molecular-dynamics simulations of bicomponent ganglioside GM1 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers with varying concentrations of GM1 (10%, 20%, and 30%). Overall, the simulations show very good agreement with available experimental data, including x-ray electron density profiles along the membrane normal, NMR carbohydrate proton-proton distances, and x-ray crystal structures. This validates the quality of our model systems for investigating GM1 clustering through an ordered-lipid-cluster analysis. The increase in GM1 concentration induces tighter lipid packing, driven mainly by inter-GM1 carbohydrate-carbohydrate interactions, leading to a greater preference for the positive curvature of GM1-containing membranes and larger cluster sizes of ordered-lipid clusters (with a composite of GM1 and POPC). These clusters tend to segregate and form a large percolated cluster at a 30% GM1 concentration at 293 K. At a higher temperature of 330 K, however, the segregation is not maintained.

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly ß-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein ß-barrel assembly machine (BAM) catalyzes the insertion and folding of the ß-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane ß-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate ß-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane ß-barrel proteins.

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.

The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

E. coli outer membrane and interactions with OmpLA.

The outer membrane of Gram-negative bacteria is a unique asymmetric lipid bilayer composed of phospholipids (PLs) in the inner leaflet and lipopolysaccharides (LPSs) in the outer leaflet. Its function as a selective barrier is crucial for the survival of bacteria in many distinct environments, and it also renders Gram-negative bacteria more resistant to antibiotics than their Gram-positive counterparts. Here, we report the structural properties of a model of the Escherichia coli outer membrane and its interaction with outer membrane phospholipase A (OmpLA) utilizing molecular dynamics simulations. Our results reveal that given the lipid composition used here, the hydrophobic thickness of the outer membrane is ∼3 Šthinner than the corresponding PL bilayer, mainly because of the thinner LPS leaflet. Further thinning in the vicinity of OmpLA is observed due to hydrophobic matching. The particular shape of the OmpLA barrel induces various interactions between LPS and PL leaflets, resulting in asymmetric thinning around the protein. The interaction between OmpLA extracellular loops and LPS (headgroups and core oligosaccharides) stabilizes the loop conformation with reduced dynamics, which leads to secondary structure variation and loop displacement compared to that in a DLPC bilayer. In addition, we demonstrate that the LPS/PL ratios in asymmetric bilayers can be reliably estimated by the per-lipid surface area of each lipid type, and there is no statistical difference in the overall membrane structure for the outer membranes with one more or less LPS in the outer leaflet, although individual lipid properties vary slightly.

ST-analyzer: a web-based user interface for simulation trajectory analysis.

Molecular dynamics (MD) simulation has become one of the key tools to obtain deeper insights into biological systems using various levels of descriptions such as all-atom, united-atom, and coarse-grained models. Recent advances in computing resources and MD programs have significantly accelerated the simulation time and thus increased the amount of trajectory data. Although many laboratories routinely perform MD simulations, analyzing MD trajectories is still time consuming and often a difficult task. ST-analyzer, http://im.bioinformatics.ku.edu/st-analyzer, is a standalone graphical user interface (GUI) toolset to perform various trajectory analyses. ST-analyzer has several outstanding features compared to other existing analysis tools: (i) handling various formats of trajectory files from MD programs, such as CHARMM, NAMD, GROMACS, and Amber, (ii) intuitive web-based GUI environment--minimizing administrative load and reducing burdens on the user from adapting new software environments, (iii) platform independent design--working with any existing operating system, (iv) easy integration into job queuing systems--providing options of batch processing either on the cluster or in an interactive mode, and (v) providing independence between foreground GUI and background modules--making it easier to add personal modules or to recycle/integrate pre-existing scripts utilizing other analysis tools. The current ST-analyzer contains nine main analysis modules that together contain 18 options, including density profile, lipid deuterium order parameters, surface area per lipid, and membrane hydrophobic thickness. This article introduces ST-analyzer with its design, implementation, and features, and also illustrates practical analysis of lipid bilayer simulations.

Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics.

Lipopolysaccharide (LPS), a component of Gram-negative bacterial outer membranes, comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of an Escherichia coli R1 (core) O6 (antigen) LPS molecule. Several all-atom bilayers are built and simulated with lipid A only (LIPA) and varying lengths of 0 (LPS0), 5 (LPS5), and 10 (LPS10) O6 antigen repeating units; a single unit of O6 antigen contains five sugar residues. From (1)H,(1)H-NOESY experiments, cross-relaxation rates are obtained from an O-antigen polysaccharide sample. Although some experimental deviations are due to spin-diffusion, the remaining effective proton-proton distances show generally very good agreement between NMR experiments and molecular dynamics simulations. The simulation results show that increasing the LPS molecular length has an impact on LPS structure and dynamics and also on LPS bilayer properties. Terminal residues in a LPS bilayer are more flexible and extended along the membrane normal. As the core and O-antigen are added, per-lipid area increases and lipid bilayer order decreases. In addition, results from mixed LPS0/5 and LPS0/10 bilayer simulations show that the LPS O-antigen conformations at a higher concentration of LPS5 and LPS10 are more orthogonal to the membrane and less flexible. The O-antigen concentration of mixed LPS bilayers does not have a significant effect on per-lipid area and hydrophobic thickness. Analysis of ion and water penetration shows that water molecules can penetrate inside the inner core region, and hydration is critical to maintain the integrity of the bilayer structure.

New approach to the reduction of recombination in dye-sensitised solar cells via complexation of oxidised species.

Although dye-sensitised solar cells (DSSCs) have received great attention as low-cost and clean energy conversion devices, their conversion efficiency still lags behind that of inorganic solar cells. One of the reasons is due to the recombination of injected electrons with the oxidised species of the redox couple that are present in the electrolyte near the surface of the bare TiO2 particles. While most research has focused on blocking the bare surface of the TiO2 nanoparticles, we have introduced a new approach that can directly reduce the concentration of the oxidised species of the redox couple present in the electrolytes through complex formation. Recombination was reduced by the addition of cyclodextrins (CDs) to a polyethyleneglycol dimethyl ether (PEGDME) electrolyte containing iodide/triiodide redox couples that can form a complex with the triiodide. Experimental and theoretical investigation of the complex formation between triiodide and the CD in PEGDME matrix was performed. Increase in total power conversion efficiency was achieved using the alpha-CD as an additive in a low volatile PEGDME based electrolyte. Electrochemical impedance spectra and intensity modulated photovoltage spectroscopy measurements showed that the increase in the short-circuit current density is due to the suppression of surface recombination by the complex formation between the CDs and the triiodide ions.

Strengthening effect of single-atomic-layer graphene in metal-graphene nanolayered composites.

Graphene is a single-atomic-layer material with excellent mechanical properties and has the potential to enhance the strength of composites. Its two-dimensional geometry, high intrinsic strength and modulus can effectively constrain dislocation motion, resulting in the significant strengthening of metals. Here we demonstrate a new material design in the form of a nanolayered composite consisting of alternating layers of metal (copper or nickel) and monolayer graphene that has ultra-high strengths of 1.5 and 4.0 GPa for copper-graphene with 70-nm repeat layer spacing and nickel-graphene with 100-nm repeat layer spacing, respectively. The ultra-high strengths of these metal-graphene nanolayered structures indicate the effectiveness of graphene in blocking dislocation propagation across the metal-graphene interface. Ex situ and in situ transmission electron microscopy compression tests and molecular dynamics simulations confirm a build-up of dislocations at the graphene interface.