Ab initio calculation of the shock Hugoniot of bulk silicon

We describe how ab initio molecular dynamics can be used to determine the Hugoniot locus (states accessible by a shock wave) for materials with a number of stable phases, and with an approximate treatment of plasticity and yield, without having to simulate these phenomena directly. We consider the case of bulk silicon, with forces from density-functional theory, up to 70 GPa. The fact that shock waves can split into multiple waves due to phase transitions or yielding is taken into account here by specifying the strength of any preceding waves explicitly based on their yield strain. Points corresponding to uniaxial elastic compression along three crystal axes and a number of postshock phases are given, including a plastically yielded state, approximated by an isotropic stress configuration following an elastic wave of predetermined strength. The results compare well to existing experimental data for shocked silicon.We thank Alan Minchinton, Richard Needs, Nikos Nikiforakis, Stephen Walley and David Williamson for useful input and discussions.This research was supported with funding from Orica Ltd. and the following grants: MINECO-Spain’s Plan Nacional Grant No. FIS2012-37549-C05-01, Basque Government Grant No. PI2014-105 CIC07 2014-2016, and EU Grant “ElectronStopping” in the Marie Curie CIG Program. Part of this work was performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service [41], provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and funding from the Science and Technology Facilities Council

Dimethyl fumarate blocks pro-inflammatory cytokine production via inhibition of TLR induced M1 and K63 ubiquitin chain formation

Dimethyl fumarate (DMF) possesses anti-inflammatory properties and is approved for the treatment of psoriasis and multiple sclerosis. While clinically effective, its molecular target has remained elusive - although it is known to activate anti-oxidant pathways. We find that DMF inhibits pro-inflammatory cytokine production in response to TLR agonists independently of the Nrf2-Keap1 anti-oxidant pathway. Instead we show that DMF can inhibit the E2 conjugating enzymes involved in K63 and M1 polyubiquitin chain formation both in vitro and in cells. The formation of K63 and M1 chains is required to link TLR activation to downstream signaling, and consistent with the block in K63 and/or M1 chain formation, DMF inhibits NFκB and ERK1/2 activation, resulting in a loss of pro-inflammatory cytokine production. Together these results reveal a new molecular target for DMF and show that a clinically approved drug inhibits M1 and K63 chain formation in TLR induced signaling complexes. Selective targeting of E2s may therefore be a viable strategy for autoimmunity

Phase Transition Lowering in Dynamically Compressed Silicon

Silicon, being one of the most abundant elements in nature, attracts wide-ranging scientific and technological interest. Specifically, in its elemental form, crystals of remarkable purity can be produced. One may assume that this would lead to silicon being well understood, and indeed, this is the case for many ambient properties, as well as for higher-pressure behaviour under quasi-static loading. However, despite many decades of study, a detailed understanding of the response of silicon to rapid compression—such as that experienced under shock impact—remains elusive. Here, we combine a novel free-electron laser-based X-ray diffraction geometry with laser-driven compression to elucidate the importance of shear generated during shock compression on the occurrence of phase transitions. We observe lowering of the hydrostatic phase boundary in elemental silicon, an ideal model system for investigating high-strength materials, analogous to planetary constituents. Moreover, we unambiguously determine the onset of melting above 14 GPa, previously ascribed to a solid–solid phase transition, undetectable in the now conventional shocked diffraction geometry; transitions to the liquid state are expected to be ubiquitous in all systems at sufficiently high pressures and temperatures

Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting

Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both inhibit Ubc13 by covalent adduct formation through a Michael addition at the Ubc13 active site cysteine. The resulting adducts of both compounds exploit a binding groove unique to Ubc13. We developed a Ubc13 mutant which resists NSC697923 inhibition and, using this mutant, we show that the inhibition of cellular DNA damage and NF-κB signaling by NSC697923 is largely due to specific Ubc13 inhibition. We propose that unique structural features near the Ubc13 active site could provide a basis for the rational development and design of specific Ubc13 inhibitors

Ubiquitin, SUMO, and Nedd8 as Therapeutic Targets in Cancer

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