We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

Abstract. Winter has the worst air pollution of the year in the megacity of Beijing. Despite extensive winter studies in recent years, our knowledge of the sources, formation mechanisms and evolution of aerosol particles is not complete. Here we have a comprehensive characterization of the sources, variations and processes of submicron aerosols that were measured by an Aerodyne high-resolution aerosol mass spectrometer from 17 December 2013 to 17 January 2014 along with offline filter analysis by gas chromatography/mass spectrometry. Our results suggest that submicron aerosols composition was generally similar across the winter of different years and was mainly composed of organics (60 %), sulfate (15 %) and nitrate (11 %). Positive matrix factorization of high- and unit-mass resolution spectra identified four primary organic aerosol (POA) factors from traffic, cooking, biomass burning (BBOA) and coal combustion (CCOA) emissions as well as two secondary OA (SOA) factors. POA dominated OA, on average accounting for 56 %, with CCOA being the largest contributor (20 %). Both CCOA and BBOA showed distinct polycyclic aromatic hydrocarbons (PAHs) spectral signatures, indicating that PAHs in winter were mainly from coal combustion (66 %) and biomass burning emissions (18 %). BBOA was highly correlated with levoglucosan, a tracer compound for biomass burning (r2 = 0.93), and made a considerable contribution to OA in winter (9 %). An aqueous-phase-processed SOA (aq-OOA) that was strongly correlated with particle liquid water content, sulfate and S-containing ions (e.g. CH2SO2+) was identified. On average aq-OOA contributed 12 % to the total OA and played a dominant role in increasing oxidation degrees of OA at high RH levels (> 50 %). Our results illustrate that aqueous-phase processing can enhance SOA production and oxidation states of OA as well in winter. Further episode analyses highlighted the significant impacts of meteorological parameters on aerosol composition, size distributions, oxidation states of OA and evolutionary processes of secondary aerosols.

Despite the fact that both electrochemical experiments and density functional theory calculations have testified to the superior electrocatalytic activity and CO-poisoning tolerance of platinum-ruthenium (PtRu) alloy nanoparticles toward the methanol oxidation reaction (MOR), the facet-dependent electrocatalytic properties of PtRu nanoparticles are scarcely revealed because it is extremely difficult to synthesize well-defined facets-enclosed PtRu nanocrystals. Herein, we for the first time report a general synthesis of ultrathin PtRu nanocrystals with tunable morphologies (nanowires, nanorods, and nanocubes) through a one-step solvothermal approach and a systematic investigation of the structure-directing effects of different surfactants and the formation mechanism by control experiments and time-dependent studies. In addition, we utilize these {100} and {111} facets-enclosed PtRu nanocrystals as model catalysts to evaluate the electrocatalytic characteristics of the MOR on different facets. Remarkably, {111}-terminated PtRu nanowires exhibit much higher stability and electrocatalytic mass activity toward MOR, which are 2.28 and 4.32 times higher than those of {100}-terminated PtRu nanocubes and commercial Pt/C, respectively, indicating that PtRu {111} facets possess superior methanol oxidation activity and CO-poisoning resistance relative to {100} facets. Our present work provides a series of well-defined PtRu nanocrystals with tunable facets which would be ideal model electrocatalysts for fundamental research in fuel cell electrocatalysis.

Summary Alternative splicing is a vast source of biological regulation and diversity that is misregulated in cancer and other diseases. To investigate global control of alternative splicing in human cells, we analyzed splicing of mRNAs encoding Bcl2-family apoptosis factors in a genome-wide siRNA screen. The screen identified many novel regulators of Bcl-x and Mcl1 splicing, notably an extensive network of cell cycle factors linked to aurora kinase A. Drugs or siRNAs that induce mitotic arrest promoted pro-apoptotic splicing of Bcl-x, Mcl1, and caspase-9, and altered splicing of other apoptotic transcripts. This response preceded mitotic arrest, indicating coordinated upregulation of pro-death splice variants that promotes apoptosis in arrested cells. These shifts corresponded to post-translational turnover of splicing regulator ASF/SF2, which directly binds and regulates these target mRNAs and globally regulates apoptosis. Broadly, our results reveal an alternative splicing network linking cell cycle control to apoptosis.