Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Models

Machine learning has recently entered into the mainstream of coarse-grained (CG) molecular modeling and simulation. While a variety of methods for incorporating deep learning into these models exist, many of them involve training neural networks to act directly as the CG force field. This has several benefits, the most significant of which is accuracy. Neural networks can inherently incorporate multi-body effects during the calculation of CG forces, and a well-trained neural network force field outperforms pairwise basis sets generated from essentially any methodology. However, this comes at a significant cost. First, these models are typically slower than pairwise force fields even when accounting for specialized hardware which accelerates the training and integration of such networks. The second, and the focus of this paper, is the need for the considerable amount of data needed to train such force fields. It is common to use tens of microseconds of molecular dynamics data to train a single CG model, which approaches the point of eliminating the CG models usefulness in the first place. As we investigate in this work, it is apparent that this data-hunger trap from neural networks for predicting molecular energies and forces is caused in large part by the difficulty in learning force equivariance, i.e., the fact that force vectors should rotate while maintaining their magnitude in response to an equivalent rotation of the system. We demonstrate that for CG water, networks that inherently incorporate this equivariance into their embedding can produce functional models using datasets as small as a single frame of reference data, which networks without inherent symmetry equivariance cannot

Ionic liquids as tribological performance improving additive for in-service and used fully-formulated diesel engine lubricants

In recent years, several papers have been published that investigate the potential use of ionic liquids (ILs) as additives in lubricants. However, corrosive attack of ILs on lubricated metal surfaces and low miscibility of ILs in the non-polar oils are major obstacles to maintaining an optimum lubrication performance level. High miscibility and no corrosive behaviour of Trihexyltetradecyl phosphonium bis(2,4,4-tri-methylpentyl) phosphinate and Trihexyltetradecyl phosphonium bis(2-ethylhexyl) phosphate, as lubricating oil additives have recently been described in literature. This article presents work on using these phosphonium based ILs as an additive in the fully formulated diesel engine lubricants. This approach could allow the used lubricants to recover their tribological performance for further use at the end of service life. This extension of service life has the potential to generate significant economic and environmental benefits. Also it will add to the much needed knowledge about the effect of interaction between ILs and existing additives in engine-aged lubricants on the tribological performance of ring-liner tribo-system of diesel engines. Results revealed an improvement in friction and antiwear performance of used lubricant by addition of both ILs. However an increase in wear was noted for new (fresh) and in-service lubricant samples. An interesting interference between existing lubricant additives and added ILs in a boundary film formation process has been observed

Motorcycle Helmet Effectiveness in Reducing Head, Face and Brain Injuries by State and Helmet Law

Background: Despite evidence that motorcycle helmets reduce morbidity and mortality, helmet laws and rates of helmet use vary by state in the U.S. Methods: We pooled data from eleven states: five with universal laws requiring all motorcyclists to wear a helmet, and six with partial laws requiring only a subset of motorcyclists to wear a helmet. Data were combined in the Crash Outcome Data Evaluation System\u27s General Use Model and included motorcycle crash records probabilistically linked to emergency department and inpatient discharges for years 2005-2008. Medical outcomes were compared between partial and universal helmet law settings. We estimated adjusted relative risks (RR) and 95 % confidence intervals (CIs) for head, facial, traumatic brain, and moderate to severe head/facial injuries associated with helmet use within each helmet law setting using generalized log-binomial regression. Results: Reported helmet use was higher in universal law states (88 % vs. 42 %). Median charges, adjusted for inflation and differences in state-incomes, were higher in partial law states (emergency department $1987 vs.$1443; inpatient $31,506 vs.$25,949). Injuries to the head and face, including traumatic brain injuries, were more common in partial law states. Effectiveness estimates of helmet use were higher in partial law states (adjusted-RR (CI) of head injury: 2.1 (1.9-2.2) partial law single vehicle; 1.4 (1.2, 1.6) universal law single vehicle; 1.8 (1.6-2.0) partial law multi-vehicle; 1.2 (1.1-1.4) universal law multi-vehicle). Conclusions: Medical charges and rates of head, facial, and brain injuries among motorcyclists were lower in universal law states. Helmets were effective in reducing injury in both helmet law settings; lower effectiveness estimates were observed in universal law states

Long term aging of Selenide glasses: Evidence of sub-Tg endotherms and pre-Tg exotherms

Long term aging is studied on several families of chalcogenide glasses including the Ge-Se, As-Se, Ge-P-Se and Ge-As-Se systems. Special attention is given to the As-Se binary, a system that displays a rich variety of aging behavior intimately tied to sample synthesis conditions and the ambient environment in which samples are aged. Calorimetric (Modulated DSC) and Raman scattering experiments are undertaken. Our results show all samples display a sub-Tg endotherm below Tg in glassy networks possessing a mean coordination number r in the 2.25 < r < 2.45 range. Two sets of AsxSe1-x samples aged for 8 years were compared, set A consisted of slow cooled samples aged in the dark, and set B consisted of melt quenched samples aged at laboratory environment. Samples of set B in the As concentration range, 35% < x < 60%, display a pre-Tg exotherm, but the feature is not observed in samples of set A. The aging behavior of set A presumably represents intrinsic aging in these glasses, while that of set B is extrinsic due to presence of light. The reversibility window persists in both sets of samples but is less well defined in set B. These findings contrast with a recent study by Golovchak et al., which finds the onset of the reversibility window moved up to the stoichiometric composition (x = 40%). Here we show that the upshifted window is better understood as resulting due to demixing of As4Se4 and As4Se3 molecules from the backbone, i.e., Nanoscale phase separation (NSPS). We attribute sub-Tg endotherms to compaction of the flexible part of networks upon long term aging, while the pre-Tg exotherm to NSPS. Finally, the narrowing and sharpening of the reversibility window upon aging is interpreted as the slow 'self-organizing' stress relaxation of the phases just outside the Intermediate phase.Comment: In press - J. of Physics: Condensed Matte

Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells

TET2 is a dioxygenase that catalyses multiple steps of 5-methylcytosine oxidation. Although TET2 mutations frequently occur in various types of haematological malignancies, the mechanism by which they increase risk for these cancers remains poorly understood. Here we show that Tet2?/? mice develop spontaneous myeloid, T- and B-cell malignancies after long latencies. Exome sequencing of Tet2?/? tumours reveals accumulation of numerous mutations, including Apc, Nf1, Flt3, Cbl, Notch1 and Mll2, which are recurrently deleted/mutated in human haematological malignancies. Single-cell-targeted sequencing of wild-type and premalignant Tet2?/? Lin?c-Kit+ cells shows higher mutation frequencies in Tet2?/? cells. We further show that the increased mutational burden is particularly high at genomic sites that gained 5-hydroxymethylcytosine, where TET2 normally binds. Furthermore, TET2-mutated myeloid malignancy patients have significantly more mutational events than patients with wild-type TET2. Thus, Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells, suggesting a novel TET2 loss-mediated mechanism of haematological malignancy pathogenesis

ϕ\phi meson production in dd++Au collisions at sNN=200\sqrt{s_{_{NN}}}=200 GeV

The PHENIX experiment has measured $\phi$ meson production in $d$$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV using the dimuon and dielectron decay channels. The $\phi$ meson is measured in the forward (backward) $d$-going (Au-going) direction, $1.2<y<2.2$ ($-2.2<y<-1.2$) in the transverse-momentum ($p_T$) range from 1--7 GeV/$c$, and at midrapidity $|y|<0.35$ in the $p_T$ range below 7 GeV/$c$. The $\phi$ meson invariant yields and nuclear-modification factors as a function of $p_T$, rapidity, and centrality are reported. An enhancement of $\phi$ meson production is observed in the Au-going direction, while suppression is seen in the $d$-going direction, and no modification is observed at midrapidity relative to the yield in $p$$+$$p$ collisions scaled by the number of binary collisions. Similar behavior was previously observed for inclusive charged hadrons and open heavy flavor indicating similar cold-nuclear-matter effects.Comment: 484 authors, 16 pages, 12 figures, 6 tables. v1 is the version accepted for publication in Phys. Rev. C. Data tables for the points plotted in the figures are given in the paper itsel

Transverse energy production and charged-particle multiplicity at midrapidity in various systems from sNN=7.7\sqrt{s_{NN}}=7.7 to 200 GeV

Measurements of midrapidity charged particle multiplicity distributions, $dN_{\rm ch}/d\eta$, and midrapidity transverse-energy distributions, $dE_T/d\eta$, are presented for a variety of collision systems and energies. Included are distributions for Au$+$Au collisions at $\sqrt{s_{_{NN}}}=200$, 130, 62.4, 39, 27, 19.6, 14.5, and 7.7 GeV, Cu$+$Cu collisions at $\sqrt{s_{_{NN}}}=200$ and 62.4 GeV, Cu$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV, U$+$U collisions at $\sqrt{s_{_{NN}}}=193$ GeV, $d$$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV, $^{3}$He$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV, and $p$$+$$p$ collisions at $\sqrt{s_{_{NN}}}=200$ GeV. Centrality-dependent distributions at midrapidity are presented in terms of the number of nucleon participants, $N_{\rm part}$, and the number of constituent quark participants, $N_{q{\rm p}}$. For all $A$$+$$A$ collisions down to $\sqrt{s_{_{NN}}}=7.7$ GeV, it is observed that the midrapidity data are better described by scaling with $N_{q{\rm p}}$ than scaling with $N_{\rm part}$. Also presented are estimates of the Bjorken energy density, $\varepsilon_{\rm BJ}$, and the ratio of $dE_T/d\eta$ to $dN_{\rm ch}/d\eta$, the latter of which is seen to be constant as a function of centrality for all systems.Comment: 706 authors, 32 pages, 20 figures, 34 tables, 2004, 2005, 2008, 2010, 2011, and 2012 data. v2 is version accepted for publication in Phys. Rev.

Cross Section and Transverse Single-Spin Asymmetry of η\eta Mesons in p↑+pp^{\uparrow}+p Collisions at s=200\sqrt{s}=200 GeV at Forward Rapidity

We present a measurement of the cross section and transverse single-spin asymmetry ($A_N$) for $\eta$ mesons at large pseudorapidity from $\sqrt{s}=200$~GeV $p^{\uparrow}+p$ collisions. The measured cross section for $0.5<p_T<5.0$~GeV/$c$ and $3.0<|\eta|<3.8$ is well described by a next-to-leading-order perturbative-quantum-chromodynamics calculation. The asymmetries $A_N$ have been measured as a function of Feynman-$x$ ($x_F$) from $0.2<|x_{F}|<0.7$, as well as transverse momentum ($p_T$) from $1.0<p_T<4.5$~GeV/$c$. The asymmetry averaged over positive $x_F$ is $\langle{A_{N}}\rangle=0.061{\pm}0.014$. The results are consistent with prior transverse single-spin measurements of forward $\eta$ and $\pi^{0}$ mesons at various energies in overlapping $x_F$ ranges. Comparison of different particle species can help to determine the origin of the large observed asymmetries in $p^{\uparrow}+p$ collisions.Comment: 484 authors, 13 pages, 11 figures, 4 tables, 2008 data. v2 is version accepted by Phys. Rev. D. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be)publicly available at http://www.phenix.bnl.gov/papers.htm