Rearrangement Of Clusters Research Articles

Results of 13c nmr and ftir spectroscopy of kerogen of the upper devonian domanik of the Timan-Pechorian basin

A kerogen samples set from organic carbon rich rocks of the Middle Frasnian Early Famennian age (Domanikites) of the Timan-Pechora basin, was characterized by the Rock-Eval pyrolysis data, solid-state 13C NMR spectroscopy and Fourier transform IR spectroscopy. Additionally, the spectral characteristics of kerogen isolated from rocks artificially maturated in an autoclave in the presence of water were investigated. In general, the direction of transformation of the kerogen structure with a natural or artificial maturation coincides. For kerogen, subjected to artificial maturation, is characterized by an increase in the concentration of terminal methyl groups in relation to the methylene units. Artificial maturation of kerogen leads to a more rapid rearrangement of aromatic clusters with the accumulation of bridgehead and protonated carbon as compared with natural maturation.

Correlation Between Plasticity and Atomic Structure Evolution of a Rejuvenated Bulk Metallic Glass

This article aims to establish a relation between the excitation of atomic structure, namely rejuvenation, and plasticity behavior of a Zr-based bulk metallic glass (BMG). The synchrotron X-ray diffraction (XRD) results showed that the cryothermal treatment leads to rejuvenation of the material, which is manifested by the structural disordering and the rearrangement of atomic clusters. It was also revealed that the rejuvenated structure provides more potential sites for shear-banding events during compressive loading. Hence, the homogeneous plasticity improves in the rejuvenated samples, which is recognized by a self-organized critical state of serrations in the stress–strain curves and high population of shear bands on the lateral surface of samples. On the other hand, a high energy barrier for shear transitions in as-cast specimens led to a semi-brittle failure with low plastic deformation. In general, with the increase in the number of cryothermal cycles, the rejuvenation as well as the non-localized deformation enhances in the BMG.

Size, orientation, and strength of Na-montmorillonite flocs flowing in a laminar shear flow

The flowing behavior of montmorillonite flocs coagulated in NaCl solution was visualized using a device called Couette chamber which was designed to analyze the strength of floc against breakup in a laminar shear flow generated in the gap between two concentric cylinders. The rotation ax of cylinders was oriented horizontally to avoid the effect of sedimentation during measurement. Observation of the morphology of flowing flocs was performed with a high-speed camera under sufficiently high salt concentration to induce rapid coagulation of montmorillonite as a function of shear rate. The recorded image of flocs demonstrated that the average flowing flocs is approximated by an ellipsoid of equivalent inertial moment with a length ratio of two principal axes being around 2. The most probable orientation of the major axis was found to be the flow direction. Assuming flocs are ellipsoids and will be disrupted by the effect of extensional component of the flow field, the cohesive strength supporting the disintegrating clusters was calculated on the basis of the simple model of floc strength proposed previously for the breakup of a floc under turbulent flow. The tendency of structural enforcement by the rearrangement of internal clusters was recorded with an increase in size of floc irrespective of ionic strength. In addition, the enforcement of cohesive strength by the effect of dehydration of proximately adsorbed sodium ions at extremely high ionic strength was confirmed.

Abstract LB-210: An enhanced tumor evolution model for colorectal cancer evolution

Abstract The classical genetic model of colorectal cancer presents somatic APC mutations as the earliest genomic alterations, followed by KRAS and TP53 mutations. However, the timing and relative order of clonal expansion and other types of somatic genome alterations such as genomic rearrangements are still unclear. Here, we performed detailed analysis of somatic genetic alterations, including point mutations, copy number alterations and genomic rearrangements, in 63 whole-genome sequenced colorectal cancers from the Cancer Genome Atlas Research Network. The relative order of these alterations occurring during tumorigenesis was inferred from variant allele fractions. We found that driver point mutations, gene fusions, and arm level copy losses typically arise early. Copy-neutral loss of heterozygosity is often a two-step event: a deletion followed by a duplication. Different mechanisms act in different genomic regions to optimize the DNA dosage. Chromothripsis, clustered genomic rearrangements previously thought to occur as a single catastrophic event, is frequent and may occur multiple times independently in the same tumor through different mechanisms. In contrast to recent studies reporting neutral growth of tumors, selection is often present on subclones. Our results suggest that different evolutionary models can operate in a single tumor at different stages. Combining these results, we present a refined tumor progression model for human colorectal cancer. Our enhanced genetic model significantly expands our understanding of tumorigenesis process. Citation Format: Lixing Yang. An enhanced tumor evolution model for colorectal cancer evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-210.

Abstract 3496: Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors

Abstract Chromothripsis and chromoanasynthesis are catastrophic events leading to clustered genomic rearrangements. Whole-genome sequencing revealed frequent complex genomic rearrangements (n= 16/26) in brain tumors developing in mice deficient for factors involved in homologous recombination repair or non-homologous end-joining. Catastrophic events were tightly linked to Myc/Mycn amplification, with increased DNA damage and inefficient apoptotic response already observable at early postnatal stages. Inhibition of repair processes and comparison of the mouse tumors with human medulloblastomas (n=68) and glioblastomas (n=32) identified chromothripsis as associated with MYC/MYCN gains and with DNA repair deficiencies, pointing towards therapeutic opportunities to target DNA repair defects in tumors with complex genomic rearrangements. Citation Format: Manasi Ratnaparkhe, John K. Wong, Pei-Chi Wei, Mario Hlevnjak, Thorsten Kolb, Milena Simovic, Daniel Haag, Yashna Paul, Frauke Devens, Paul Northcott, David T. Jones, Marcel Kool, Anna Jauch, Agata Pastorczak, Wojciech Mlynarski, Andrey Korshunov, Rajiv Kumar, Susanna M. Downing, Stefan M. Pfister, Marc Zapatka, Peter J. McKinnon, Frederick W. Alt, Peter Lichter, Aurelie Ernst. Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3496.

(Invited) Ionic Liquid Electrolytes and Ionogel Composites That Enable High Capacity Anodes for Lithium and Sodium Batteries

Traditional electrolytes currently used for Li-ion and Na-ion devices are not compatible with higher energy-density anodes required for next generation devices, such as Li metal and Na metal anodes. In addition, there is now a recognition that operation at elevated temperatures is desirable for some applications. Therefore, new electrolyte materials are currently actively being investigated for beyond Li-ion technologies. It has recently been shown that, by using an ultra-high concentration of lithium or sodium salt in an ionic liquid (or indeed some organic solvents),it is possible to achieve stable cycling of Li metal and Na metal anodes, often at high rates and current densities, and even in the presence of water. These electrolytes indicate a decoupling of the alkali metal ion dynamics from the bulk with tLi+ or tNa + transport numbers approaching or even exceeding 0.5. We will discuss the structure and transport in these superconcentrated IL systems and the importance of clustering and structural rearrangement in the transport mechanism of the alkali metal cation. It has also been demonstrated that polymerized ionic liquids, such as poly(diallyldimethylammonium) (PDADMA), with either TFSI or FSI counterions, are capable of dissolving even higher concentrations of lithium salt leading to highly conductive solid electrolytes. These materials have high tLi+ and improved mechanical properties and also enable stable Li metal cycling, thus offering exciting opportunities for all solid state lithium batteries. These materials will also be discussed in terms of their phase behavior, conductivity and electrochemical behavior.

Pressure-Controlled Migration of Paramagnetic Centers in a Heterospin Crystal.

A study of the single-crystal-to-single-crystal transformation induced by temperature variation for the chain polymer Cu(II) complex with nitronyl nitroxide showed that an increase in the hydrostatic pressure of up to ∼0.07 GPa completely changes the intracrystalline displacements of molecules relative to one another. This, in turn, significantly affects the interaction energy of the unpaired electrons of the paramagnetic centers and hence the form of the temperature dependence of the magnetic susceptibility χT. The cooling of crystals under normal conditions causes a rearrangement of the intrachain exchange clusters {>N-•O-Cu(II)-O•-N<} accompanied by a shortening of the distances between the paramagnetic centers. This changes the character of exchange interactions and generates multistage spin transitions. An increase in the hydrostatic pressure leads to a drastic change in the O···O distances between the nitroxyl fragments of adjacent chains, an increase in the antiferromagnetic exchange between them, and complete suppression of spin transitions.

Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers.

BackgroundWhole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer.Patients and methodsWe carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 (n = 26) or BRCA2 (n = 22) or from non-carriers (non-BRCA1/2; n = 30).ResultsMatched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes (BRCA1/BRCA2; BRCA1/MUTYH). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non-BRCA1/2 tumours also had somatic signatures indicative of BRCA-deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non-BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53, ATM and CHEK2.ConclusionsOur study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non-BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.

Research Subjects and Research Trends in Medical Informatics.

To identify major research subjects and trends in medical informatics research based on the current set of core medical informatics journals. Analyzing journals in the Web of Science (WoS) medical informatics category together with related categories from the years 2013 to 2017 by using a smart local moving algorithm as a clustering method for identifying the core set of journals. Text mining analysis with binary counting of abstracts from these journals published in the years 2006 to 2017 for identifying major research subjects. Building clusters based on these terms for the complete time period as well as for the periods 2006-2008, 2009-2011, 2012-2014, and 2015-2017 for identifying trends. The identified cluster includes 17 core medical informatics journals. By text mining of these journals, 224,992 different terms in 14,414 articles were identified covering 550 specific key terms. Based on these key terms five clusters were identified: "Biomedical Data Analysis," "Clinical Informatics," "EHR and Knowledge Representation," "Mobile Health," and "Organizational Aspects of Health Information Systems." No shifts in the clusters were observed between the first two 3-year periods. In the third period, some terms like "mobile phone," "mobile apps," and "message" appear. Also, in the third period, a "Clinical Informatics" cluster appears and persists in the fourth period. In the fourth period, a rearrangement of clusters was observed. Beside classical subjects of medical informatics on organizing, representing, and analyzing data, we observed new developments in the context of mobile health and clinical informatics. These subjects tended to grow over the past years, and we can expect this trend to continue.

Physico-Chemical Insights into Gas-Phase and Oxide-Supported Sub-Nanometre AuCu Clusters

Abstract Catalysis by AuCu nanoclusters is a promising scientific field. However, our fundamental understanding of the underlying mechanisms of mixing in AuCu clusters at the sub-nanometre scale and their physico-chemical properties in both the gas-phase and on oxide supports is limited. We have identified the global minima of gas-phase and MgO(100)-supported AuCu clusters with 3–10 atoms using the Mexican Enhanced Genetic Algorithm coupled with density functional theory. Au and Cu adatoms and supported dimers have been also simulated at the same level of theory. The most stable composition, as calculated from mixing and binding energies, is obtained when the Cu proportion is close to 50%. The structures of the most stable free AuCu clusters exhibit Cu-core/Au-shell segregation. On the MgO surface however, there is a preference for Cu atoms to lie at the cluster-substrate interface. Due to the interplay between the number of interfacial Cu atoms and surface-induced cluster rearrangement, on the MgO surface 3D structures become more stable than 2D structures. The O-site of MgO surface is found to be the most favourable adsorption site for both metals. All dimers favour vertical (V) configurations on the surface and their adsorption energies are in the order: AuCu &lt; CuCu &lt; AuAu &lt; AuCu (where the underlined atom is bound to the O-site). For both adatoms and AuCu dimers, adsorption via Cu is more favourable than Au-adsorbed configurations, but, this disagrees with the ordering for the pure dimers due to a combination of electron transfer and the metal-on-top effect. Binding energy (and second difference) and HOMO-LUMO gap calculations show that even-atom (even-electron) clusters are more stable than the neighbouring odd-atom (odd- electron) clusters, which is expected for closed- and open-shell systems. Supporting AuCu clusters on the MgO(100) surface decreases the charge transfer between Au and Cu atoms calculated in free clusters. The results of this study may serve as a foundation for designing better AuCu catalysts.

Intensity Fluctuations in Single-Molecule Surface-Enhanced Raman Scattering.

Around 20 years ago, the first reports of single-molecule surface-enhanced Raman scattering (SM-SERS) caused a revolution in nanotechnology. Several researchers were quick to recognize the importance of a technique that can provide molecular vibrational fingerprinting at the SM level. Since then, a large amount of work has been devoted to the development of nanostructures capable of SM-SERS detection. A great effort has also been geared toward elucidating the different mechanisms that contribute to the effect. The understanding of the concept of plasmonic SERS hotspots, the role of chemical effects, and the dynamics of atomic and cluster rearrangements in nanometric domains has significantly advanced, driven by new computational and experimental methods used to study SM-SERS. In particular, SERS intensity fluctuations (SIFs) are now recognized as a hallmark of SM-SERS. Interpretation of SM-SERS data must take into consideration temporal and spatial variations as a natural consequence of the extreme localization inherent to surface plasmon resonances. Further analysis of variations in spectral signature, due to either molecular reorientation or photo (or thermal) processes, pointed to a new area that combines the power of SERS fingerprinting at the SM level to modern concepts of catalysis, such as hot-electrons-driven chemistry. This large body of work on the fundamental characteristics of the SM-SERS effect paved the way to the interpretation of other related phenomena, such as tip-enhanced Raman scattering (TERS). Despite all the fundamental progress, there are still very few examples of real applications of SM-SERS. In recent years, our research group has been studying SIFs, focused on different ways to use SM-SERS. The obvious application of SM-SERS is in analytical chemistry, particularly for quantification at ultralow concentrations (below 1 nM). However, quantification using SM-SERS faces a fundamental sampling problem: the analytes (adsorbed in very small amounts, i.e., low surface coverage) must find rare SERS hotspots (areas with intense electric field localization that yields SERS). This limitation leads to strong temporal and spatial variations in SERS intensities, which translates into very large error bars in an experimental calibration curve. We tackled this problem by introducing the concept of "digital SERS". This approach provided a roadmap for SERS quantification at ultralow concentrations and a potential pathway for a better understanding of the "reproducibility problem" associated with SERS. In this Account, we discuss not only the analytical applications but also other implementations of SM-SERS demonstrated by our group. These include the use of SM-SERS as a tool to probe colloidal aggregation, to evaluate the efficiency of SERS substrates, and to characterize the energy of localized resonances. SERS involves a series of random processes: hotspots are rare; surfaces/clusters constantly reconstruct; and molecules diffuse, adsorb, and desorb. All these pathways contribute to strong fluctuations in SERS intensities. Our work indicates that a statistical view of the effect can lead to interesting insights and the potential to fulfill the promise of this SM technique for real-world applications.

Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

In the Methods section of this Article, 'greater than' should have been 'less than' in the sentence 'Putative regions of clustered rearrangements were identified as having an average inter-rearrangement distance that was at least 10 times greater than the whole-genome average for the individual sample. '. The Article has not been corrected.

Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors

Chromothripsis and chromoanasynthesis are catastrophic events leading to clustered genomic rearrangements. Whole-genome sequencing revealed frequent complex genomic rearrangements (n = 16/26) in brain tumors developing in mice deficient for factors involved in homologous-recombination-repair or non-homologous-end-joining. Catastrophic events were tightly linked to Myc/Mycn amplification, with increased DNA damage and inefficient apoptotic response already observable at early postnatal stages. Inhibition of repair processes and comparison of the mouse tumors with human medulloblastomas (n = 68) and glioblastomas (n = 32) identified chromothripsis as associated with MYC/MYCN gains and with DNA repair deficiencies, pointing towards therapeutic opportunities to target DNA repair defects in tumors with complex genomic rearrangements.

Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers

BackgroundComplex clusters of rearrangements are a challenge in interpretation of cancer genomes. Some clusters of rearrangements demarcate clear amplifications of driver oncogenes but others are less well understood. A detailed analysis of rearrangements within these complex clusters could reveal new insights into selection and underlying mutational mechanisms. Patients and methodsHere, we systematically investigate rearrangements that are densely clustered in individual tumours in a cohort of 560 breast cancers. Applying an agnostic approach, we identify 21 hotspots where clustered rearrangements recur across cancers.ResultsSome hotspots coincide with known oncogene loci including CCND1, ERBB2, ZNF217, chr8:ZNF703/FGFR1, IGF1R, and MYC. Others contain cancer genes not typically associated with breast cancer: MCL1, PTP4A1, and MYB. Intriguingly, we identify clustered rearrangements that physically connect distant hotspots. In particular, we observe simultaneous amplification of chr8:ZNF703/FGFR1 and chr11:CCND1 where deep analysis reveals that a chr8–chr11 translocation is likely to be an early, critical, initiating event.ConclusionsWe present an overview of complex rearrangements in breast cancer, highlighting a potential new way for detecting drivers and revealing novel mechanistic insights into the formation of two common amplicons.

High-resolution architecture and partner genes of MYC rearrangements in lymphoma with DLBCL morphology

AbstractGenomic rearrangements in the MYC locus occur in ∼12% of lymphomas with diffuse large B-cell lymphoma (DLBCL) morphology and are associated with inferior outcome. Previous studies exploring MYC rearrangements have primarily used fluorescence in situ hybridization (FISH) assays to characterize break-apart status but have rarely examined breakpoint location, and in some cases have not examined partner identity. We performed targeted sequencing of MYC, BCL2, BCL6, and the immunoglobulin (IG) loci in 112 tumors with DLBCL morphology harboring MYC rearrangement. We characterized the location of the MYC rearrangement at base pair resolution and identified the partner in 88 cases. We observed a cluster of breakpoints upstream of the MYC coding region and in intron 1 (the “genic cluster”). Genic cluster rearrangements were enriched for translocations involving IGH (80%), whereas nongenic rearrangements occurred mostly downstream of the MYC gene with a variety of partners, including IGL and IGK. Other recurrent partners included BCL6, ZCCHC7, and RFTN1, which has not previously been described as a MYC partner. We compared 2 commercially available FISH break-apart assays for the MYC locus and observed discordant results in 32% of cases examined, including some with MYC-IGL and MYC-IGK rearrangements. In cases of high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangement (HGBL-DH), so-called “double-hit” lymphomas, the majority of MYC rearrangements had non-IG partners (65%), with breakpoints outside the genic cluster (72%). In patients with de novo HGBL-DH of DLBCL morphology, MYC-IG rearrangements showed a trend toward inferior time to progression and overall survival compared with MYC–non-IG rearrangements. Our data reveal clinically relevant architecture of MYC rearrangements in lymphomas with DLBCL morphology.

(Keynote) Ionic Liquid Electrolytes and Ionogel Composites that Enable High Capacity Anodes for Lithium and Sodium Batteries

With accelerating growth in demand for longer lasting, more durable and safer rechargeable energy storage technologies, it has become clear that we must find solutions to deliver these features while also using higher energy-density electrodes. As an anode material, graphite is limited in achieving high capacities due to its relatively low specific capacity of 372mAh/g. Li metal presents as an attractive alternative due to a ten-fold increase in specific capacity (3862mAh/g), while Na metal is nearly four times greater at 1166mAh/g. Electrolytes currently used for Li-ion and Na-ion devices are not compatible with these higher energy-density anodes. Instead we show that by using an ultra-high concentration of lithium or sodium salt in an ionic liquid we can facilitate stable cycling of Li metal and Na metal anodes, often at high rates and current densities, and even in the presence of water. These electrolytes indicate a decoupling of the alkali metal ion dynamics from the bulk with tLi+ or tNa+ transport numbers approaching 0.5. We will discuss the structure and transport in these superconcentrated IL systems and the importance of clustering and structural rearrangement in the transport mechanism of the alkali metal cation. Polymerized ionic liquids, such as poly(diallyldimethylammonium) (PDADMA), with either TFSI or FSI counterions, are capable of dissolving even higher concentrations of lithium salt leading to highly conductive solid electrolytes. These materials have high tLi+ and improved mechanical properties and also enable stable Li metal cycling, thus offering exciting opportunities for all solid state lithium batteries. Interestingly, the nature of the counterion associated with the PIL has a significant impact on the compatibility with the IL electrolytes and on the resultant conductivity and mechanical properties. These materials will be discussed in terms of their phase behavior, conductivity and electrochemical behavior.

Abstract LB-378: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Abstract Chromothripsis is a newly discovered mutational phenomenon involving massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in cancer suggest that chromothripsis may be far more common than initially inferred from low resolution DNA copy number data. Here, we analyze the patterns of chromothripsis across 2,658 tumors spanning 39 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of &amp;gt;50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy number states, a considerable fraction of the events involves multiple chromosomes as well as additional structural alterations. In addition to non-homologous end-joining, we detect signatures of replicative processes and templated insertions. Chromothripsis contributes to oncogene amplification as well as to inactivation of genes such as mismatch-repair related genes. These findings show that chromothripsis is a major process driving genome evolution in human cancer. Citation Format: Isidro Cortés-Ciriano, June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung, Lixing Yang, Dmitry Gordenin, Leszek J. Klimczak, Cheng-Zhong Zhang, David S. Pellman, Peter J. Park. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-378.

A multiscale shear-transformation-zone (STZ) model and simulation of plasticity in amorphous solids

In this work, we have developed a multiscale shear-transformation-zone (STZ) model to simulate inelastic deformations in amorphous materials at macroscale without using phenomenological constitutive modeling. The main novelties of the multiscale method are two: (1) the multiscale method employs an atomistic-based representative sampling cell (RS-cell) that is embedded in every quadrature points of macroscale finite elements, and it generically contains potential shear-transformation-zones. Thus the evolution of RS-cells can naturally allow molecular clusters having irreversible microstructure rearrangements at microscale in response to applied loads, and subsequently translate the effects of the irreversible rearrangements of molecular clusters in each RS-cell to inelastic responses at the continuum scale, i.e. delineating the defect-mediated amorphous plasticity, and (2) the method uses a Parrinello-Rahman molecular mechanics based the Cauchy-Born rule to construct an atomistically-informed constitutive model at continuum level, which is able to quantitatively measure amorphous plasticity behaviors, including plastic flow stress, inelastic hysteresis loops under cyclic loading, and strain localizations at macroscale. By doing so, we have successfully simulated plastic deformation in the Lennard-Jones binary glass (LJBG) at macroscale level. Moreover, we have shown that the multiscale shear-transformation-zone can capture cyclic plasticity and the shear band formations in LJBG material.

The Interplay Between Hydrogen Bonding and Coulombic Forces in Determining the Structure of Sulfuric Acid-Amine Clusters.

Acid-base cluster chemistry drives atmospheric new particle formation (NPF), but the details of the growth mechanisms are difficult to experimentally probe. Clusters of ammonia, alkylamines, and sulfuric acid, species fundamental to NPF, are probed by infrared spectroscopy. These spectra show that substitution of amines for ammonia, which is linked to accelerated growth, induces profound structural rearrangement in clusters with initial compositions (NH4+) n+1(HSO4-) n (1 ≤ n ≤ 3). This rearrangement is driven by the loss of N-H hydrogen bond donors, yielding direct bisulfate-bisulfate hydrogen bonds, and its onset with respect to cluster composition indicates that more substituted amines induce rearrangement at smaller sizes. A simple model counting hydrogen bond donors and acceptors explains these observations. The presence of direct hydrogen bonds between formal anions shows that hydrogen bonding can compete with Coulombic forces in determining cluster structure. These results suggest that NPF mechanisms may be highly dependent on amine identity.

Application and Limitations of Nanocasting in Metal-Organic Frameworks.

Nanocasting can be a useful strategy to transfer the catalytic metal clusters in metal-organic frameworks (MOFs) to an all-inorganic support such as silica. The incorporation of silica in the MOF pores as a secondary support has the potential to extend the application of the highly tunable metal-based active sites in MOFs to high temperature catalysis. Here, we demonstrate the applicability of the nanocasting method to a range of MOFs that incorporate catalytically attractive hexazirconium, hexacerium, or pentanickel oxide-based clusters (UiO-66, (Ce)UiO-66, (Ce)UiO-67, (Ce)MOF-808, DUT-9, and In- and Ni-postmetalated NU-1000). We describe, in tutorial form, the challenges associated with nanocasting of MOFs that are related to their small pore size and to considerations of chemical and mechanical stability, and we provide approaches to overcome some of these challenges. Some of these nanocast materials feature the site-isolated clusters in a porous, thermally stable silica matrix, suitable for catalysis at high temperatures; in others, structural rearrangement of clusters or partial cluster aggregation occurs, but extensive aggregation can be mitigated by the silica skeleton introduced during nanocasting.