Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics

Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We employ (1) the simplified TDDFT schemes of Grimme et al. and (2) the Hammes-Schiffer−Tully approach to obtain nonadiabatic couplings from finite-difference calculations. The resulting scheme delivers an accurate physical picture while virtually eliminating the two computationally most demanding steps of the algorithm. Combined with our GPU-based integral routines for SCF, TDDFT, and TDDFT derivative calculations, NAMD simulations of systems of a few hundreds of atoms at a reasonable time scale become accessible on a single compute node. To demonstrate this and to present a first, illustrative example, we perform TDDFT/MM-NAMD simulations of the rhodopsin protein

Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors

Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S1 lifetimes. Although all four rotors show different S1 excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies

Hyaluronic acid levels predict risk of hepatic encephalopathy and liver-related death in HIV/viral hepatitis coinfected patients

Background: Whereas it is well established that various soluble biomarkers can predict level of liver fibrosis, their ability to predict liver-related clinical outcomes is less clearly established, in particular among HIV/viral hepatitis co-infected persons. We investigated plasma hyaluronic acid’s (HA) ability to predict risk of liver-related events (LRE; hepatic coma or liver-related death) in the EuroSIDA study. Methods: Patients included were positive for anti-HCV and/or HBsAg with at least one available plasma sample. The earliest collected plasma sample was tested for HA (normal range 0–75 ng/mL) and levels were associated with risk of LRE. Change in HA per year of follow-up was estimated after measuring HA levels in latest sample before the LRE for those experiencing this outcome (cases) and in a random selection of one sixth of the remaining patients (controls). Results: During a median of 8.2 years of follow-up, 84/1252 (6.7%) patients developed a LRE. Baseline median (IQR) HA in those without and with a LRE was 31.8 (17.2–62.6) and 221.6 ng/mL (74.9–611.3), respectively (p<0.0001). After adjustment, HA levels predicted risk of contracting a LRE; incidence rate ratios for HA levels 75–250 or ≥250 vs. <75 ng/mL were 5.22 (95% CI 2.86–9.26, p<0.0007) and 28.22 (95% CI 14.95–46.00, p<0.0001), respectively. Median HA levels increased substantially prior to developing a LRE (107.6 ng/mL, IQR 0.8 to 251.1), but remained stable for controls (1.0 ng/mL, IQR –5.1 to 8.2), (p<0.0001 comparing cases and controls), and greater increases predicted risk of a LRE in adjusted models (p<0.001). Conclusions: An elevated level of plasma HA, particularly if the level further increases over time, substantially increases the risk of contracting LRE over the next five years. HA is an inexpensive, standardized and non-invasive supplement to other methods aimed at identifying HIV/viral hepatitis co-infected patients at risk of hepatic complications

Search for unbound 15Be states in the 3n+12Be channel

15Be is expected to have low-lying 3/2+ and 5/2+ states. A first search did not observe the 3/2+ [A. Spyrou et al., Phys. Rev. C 84, 044309 (2011)], however, a resonance in 15Be was populated in a second attempt and determined to be unbound with respect to 14Be by 1.8(1) MeV with a tentative spin-parity assignment of 5/2+ [J. Snyder et al., Phys. Rev. C 88, 031303(R) (2013)]. Search for the predicted 15Be 3/2+ state in the three-neutron decay channel. A two-proton removal reaction from a 55 MeV/u 17C beam was used to populate neutron-unbound states in 15Be. The two-, three-, and four-body decay energies of the 12Be + neutron(s) detected in coincidence were reconstructed using invariant mass spectroscopy. Monte Carlo simulations were performed to extract the resonance and decay properties from the observed spectra. The low-energy regions of the decay energy spectra can be described with the first excited unbound state of 14Be (E_x=1.54 MeV, E_r=0.28 MeV). Including a state in 15Be that decays through the first excited 14Be state slightly improves the fit at higher energies though the cross section is small. A 15Be component is not needed to describe the data. If the 3/2+ state in 15Be is populated, the decay by three-neutron emission through 14Be is weak, less than or equal to 11% up to 4 MeV. In the best fit, 15Be is unbound with respect to 12Be by 1.4 MeV (unbound with respect to $14Be by 2.66 MeV) with a strength of 7%.Comment: 6 pages, 5 figures, accepted in Physical Review

First observation of 13^{13}Li ground state

The ground state of neutron-rich unbound $^{13}$Li was observed for the first time in a one-proton removal reaction from $^{14}$Be at a beam energy of 53.6 MeV/u. The $^{13}$Li ground state was reconstructed from $^{11}$Li and two neutrons giving a resonance energy of 120$^{+60}_{-80}$ keV. All events involving single and double neutron interactions in the Modular Neutron Array (MoNA) were analyzed, simulated, and fitted self-consistently. The three-body ($^{11}$Li+$n+n$) correlations within Jacobi coordinates showed strong dineutron characteristics. The decay energy spectrum of the intermediate $^{12}$Li system ($^{11}$Li+$n$) was described with an s-wave scattering length of greater than -4 fm, which is a smaller absolute value than reported in a previous measurement.Comment: Accepted for publication in Phys. Rev. C as a Rapid Communicatio

HIF1 and DROSHA are involved in MMACHC repression in hypoxia

The MMACHC gene encodes for an enzyme involved in intracellular vitamin B12 metabolism, and autosomal recessive defects in MMACHC represent the most common disorder of intracellular vitamin B12 metabolism. Recent studies have identified increased levels of reactive oxygen species in cells and tissues with MMACHC dysfunction, suggesting a role for oxidative stress in disease. To investigate the link between oxidative stress and MMACHC, we exposed mice as well as human and mouse cells to hypoxia, and found significant repression of MMACHC in all investigated tissues (retina, eyecup, liver, kidney) and cell lines (HeLa, ARPE-19, human and mouse fibroblasts, 661W). Furthermore, in HeLa cells, we found transcriptional repression already at 5% oxygen, which was stable during prolonged hypoxia up to 5 days, and a return of MMACHC transcripts to normal levels only 24 h after reoxygenation. This hypoxia-induced downregulation of MMACHC was not due to altered function of the known MMACHC controlling transcription factor complex HCFC1/THAP11/ZNF143. Using in vitro RNA interference against hypoxia-induced transcription factors (HIF1A, HIF2A and REST) as well as the microRNA transcription machinery (DROSHA), we observed release of hypoxia-dependent downregulation of MMACHC expression by HIF1A and DROSHA knockdowns, whose combined effect was additive. Together, these results strongly indicate that MMACHC is a hypoxia-regulated gene whose downregulation appears to be partially mediated through both hypoxia-induced transcription factor and microRNA machinery. These findings suggest that oxidative stress could impair vitamin B12 metabolism by repression of MMACHC in healthy as well as in diseased individuals