Exact distributed kinetic Monte Carlo simulations for on-lattice chemical kinetics: lessons learnt from medium- and large-scale benchmarks.

Kinetic Monte Carlo (KMC) simulations have been instrumental in multiscale catalysis studies, enabling the elucidation of the complex dynamics of heterogeneous catalysts and the prediction of macroscopic performance metrics, such as activity and selectivity. However, the accessible length- and time-scales have been a limiting factor in such simulations. For instance, handling lattices containing millions of sites with 'traditional' sequential KMC implementations is prohibitive owing to large memory requirements and long simulation times. We have recently established an approach for exact, distributed, lattice-based simulations of catalytic kinetics which couples the Time-Warp algorithm with the Graph-Theoretical KMC framework, enabling the handling of complex adsorbate lateral interactions and reaction events within large lattices. In this work, we develop a lattice-based variant of the Brusselator system, a prototype chemical oscillator pioneered by Prigogine and Lefever in the late 60s, to benchmark and demonstrate our approach. This system can form spiral wave patterns, which would be computationally intractable with sequential KMC, while our distributed KMC approach can simulate such patterns 15 and 36 times faster with 625 and 1600 processors, respectively. The medium- and large-scale benchmarks thus conducted, demonstrate the robustness of the approach, and reveal computational bottlenecks that could be targeted in further development efforts. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Large-scale benchmarks of the time-warp/graph-theoretical kinetic Monte Carlo approach for distributed on-lattice simulations of catalytic kinetics.

Motivated by the need to perform large-scale kinetic Monte Carlo (KMC) simulations, in the context of unravelling complex phenomena such as catalyst reconstruction and pattern formation, we extend the work of Ravipati et al. [S. Ravipati, G. D. Savva, I.-A. Christidi, R. Guichard, J. Nielsen, R. Réocreux and M. Stamatakis, Comput. Phys. Commun., 2022, 270, 108148] in benchmarking the performance of a distributed-computing, on-lattice KMC approach. The latter, implemented in our software package Zacros, combines the graph-theoretical KMC framework with the Time-Warp algorithm for parallel discrete event simulations, and entails dividing the lattice into subdomains, each assigned to a processor. The cornerstone of the Time-Warp algorithm is the state queue, to which snapshots of the simulation state are saved regularly, enabling historical KMC information to be corrected when conflicts occur at subdomain boundaries. Focusing on three model systems, we highlight the key Time-Warp parameters that can be tuned to optimise performance. The frequency of state saving, controlled by the state saving interval, δsnap, is shown to have the largest effect on performance, which favours balancing the overhead of re-simulating KMC history with that of writing state snapshots to memory. Also important is the global virtual time (GVT) computation interval, ΔτGVT, which has little direct effect on the progress of the simulation but controls how often the state queue memory can be freed up. We also find that pre-allocating memory for the state queue data structure favours performance. These findings will guide users in maximising the efficiency of Zacros or other distributed KMC software, which is a vital step towards realising accurate, meso-scale simulations of heterogeneous catalysis.

Speeding up the Detection of Adsorbate Lateral Interactions in Graph-Theoretical Kinetic Monte Carlo Simulations.

Kinetic Monte Carlo (KMC) has become an indispensable tool in heterogeneous catalyst discovery, but realistic simulations remain computationally demanding on account of the need to capture complex and long-range lateral interactions between adsorbates. The Zacros software package (https://zacros.org) adopts a graph-theoretical cluster expansion (CE) framework that allows such interactions to be computed with a high degree of generality and fidelity. This involves solving a series of subgraph isomorphism problems in order to identify relevant interaction patterns in the lattice. In an effort to reduce the computational burden, we have adapted two well-known subgraph isomorphism algorithms, namely, VF2 and RI, for use in KMC simulations and implemented them in Zacros. To benchmark their performance, we simulate a previously established model of catalytic NO oxidation, treating the O* lateral interactions with a series of progressively larger CEs. For CEs with long-range interactions, VF2 and RI are found to provide impressive speedups relative to simpler algorithms. RI performs best, giving speedups reaching more than 150× when combined with OpenMP parallelization. We also simulate a recently developed methane cracking model, showing that RI offers significant improvements in performance at high surface coverages.

On the "Matsubara heating" of overtone intensities and Fermi splittings.

Classical molecular dynamics (MD) and imaginary-time path-integral dynamics methods underestimate the infrared absorption intensities of overtone and combination bands by typically an order of magnitude. Plé et al. [J. Chem. Phys. 155, 2863 (2021)] have shown that this is because such methods fail to describe the coupling of the centroid to the Matsubara dynamics of the fluctuation modes; classical first-order perturbation theory (PT) applied to the Matsubara dynamics is sufficient to recover most of the lost intensity in simple models and gives identical results to quantum (Rayleigh-Schrödinger) PT. Here, we show numerically that the results of this analysis can be used as post-processing correction factors, which can be applied to realistic (classical MD or path-integral dynamics) simulations of infrared spectra. We find that the correction factors recover most of the lost intensity in the overtone and combination bands of gas-phase water and ammonia and much of it for liquid water. We then re-derive and confirm the earlier PT analysis by applying canonical PT to Matsubara dynamics, which has the advantage of avoiding secular terms and gives a simple picture of the perturbed Matsubara dynamics in terms of action-angle variables. Collectively, these variables "Matsubara heat" the amplitudes of the overtone and combination vibrations of the centroid to what they would be in a classical system with the oscillators (of frequency Ωi) held at their quantum effective temperatures [of ℏΩi coth(ßℏΩi/2)/2kB]. Numerical calculations show that a similar neglect of "Matsubara heating" causes path-integral methods to underestimate Fermi resonance splittings.

Which quantum statistics-classical dynamics method is best for water?

There are a variety of methods for including nuclear quantum effects in dynamics simulations by combining quantum Boltzmann statistics with classical dynamics. Among them are thermostatted ring-polymer molecular dynamics (TRPMD), centroid molecular dynamics (CMD), quasi-centroid molecular dynamics (QCMD), and the linearised semi-classical initial value representation (LSC-IVR). Here we make a systematic comparison of these methods by calculating the infrared spectrum of water in the gas phase, and in the liquid and ice phases (using the q-TIP4P/F model potential). Some of these results are taken from previous work, and some of them are new (including the LSC-IVR calculations for ice, and extensions of all the spectra into the near-infrared region dominated by overtone and combination bands). Our results suggest that QCMD is the best method for reproducing fundamental transitions in the spectrum, and that LSC-IVR gives the best overall description of the spectrum (albeit with large errors in the bend fundamental band caused by zero-point-energy leakage). The TRPMD method gives damped spectra that line up with the QCMD spectra, and is by far the cheapest method.

Differential effects of hormone therapy on serotonin, vascular function and mood in the KEEPS.

BACKGROUND: Serotonin (5-hydroxytryptamine, 5-HT) is modulated by sex steroid hormones and affects vascular function and mood. In the Kronos Early Estrogen Prevention Cognitive and Affective Ancillary Study (KEEPS-Cog), women randomized to oral conjugated equine estrogens (oCEE) showed greater benefit on affective mood states than women randomized to transdermal 17ß-estradiol (tE2) or placebo (PL). This study examined the effect of these treatments on the platelet content of 5-HT as a surrogate measure of 5-HT synthesis and uptake in the brain. METHODS: The following were measured in a subset (n = 79) of women enrolled in KEEPS-Cog: 5-HT by ELISA, carotid intima-medial thickness (CIMT) by ultrasound, endothelial function by reactive hyperemic index (RHI), and self-reported symptoms of affective mood states by the Profile of Mood States (POMS) questionnaire. RESULTS: Mean platelet content of 5-HT increased by 107.0%, 84.5% and 39.8%, in tE2, oCEE and PL groups, respectively. Platelet 5-HT positively correlated with estrone in the oCEE group and with 17ß- estradiol in the tE2 group. Platelet 5-HT showed a positive association with RHI, but not CIMT, in the PL and oCEE groups. Reduction in mood scores for depression-dejection and anger-hostility was associated with elevations in platelet 5-HT only in the oCEE group (r = -0.5, p = 0.02). CONCLUSIONS: Effects of oCEE compared to tE2 on RHI and mood may be related to mechanisms involving platelet, and perhaps neuronal, uptake and release of 5-HT and reflect conversion of estrone to bioavailable 17ß-estradiol in platelets and the brain.

Assessing the Impact of Adlayer Description Fidelity on Theoretical Predictions of Coking on Ni(111) at Steam Reforming Conditions.

Methane steam reforming is an important industrial process for hydrogen production, employing Ni as a low-cost, highly active catalyst, which, however, suffers from coking due to methane cracking. Coking is the accumulation of a stable poison over time, occurring at high temperatures; thus, to a first approximation, it can be treated as a thermodynamic problem. In this work, we developed an Ab initio kinetic Monte Carlo (KMC) model for methane cracking on Ni(111) at steam reforming conditions. The model captures C-H activation kinetics in detail, while graphene sheet formation is described at the level of thermodynamics, to obtain insights into the "terminal (poisoned) state" of graphene/coke within reasonable computational times. We used cluster expansions (CEs) of progressively higher fidelity to systematically assess the influence of effective cluster interactions between adsorbed or covalently bonded C and CH species on the "terminal state" morphology. Moreover, we compared the predictions of KMC models incorporating these CEs into mean-field microkinetic models in a consistent manner. The models show that the "terminal state" changes significantly with the level of fidelity of the CEs. Furthermore, high-fidelity simulations predict C-CH island/rings that are largely disconnected at low temperatures but completely encapsulate the Ni(111) surface at high temperatures.

Comparative effects of dried plum and dried apple on bone in postmenopausal women.

Aside from existing drug therapies, certain lifestyle and nutritional factors are known to reduce the risk of osteoporosis. Among the nutritional factors, dried plum or prunes (Prunus domestica L.) is the most effective fruit in both preventing and reversing bone loss. The objective of the present study was to examine the extent to which dried plum reverses bone loss in osteopenic postmenopausal women. We recruited 236 women, 1-10 years postmenopausal, not on hormone replacement therapy or any other prescribed medication known to influence bone metabolism. Qualified participants (n 160) were randomly assigned to one of the two treatment groups: dried plum (100 g/d) or dried apple (comparative control). Participants received 500 mg Ca plus 400 IU (10 µg) vitamin D daily. Bone mineral density (BMD) of lumbar spine, forearm, hip and whole body was assessed at baseline and at the end of the study using dual-energy X-ray absorptiometry. Blood samples were collected at baseline, 3, 6 and 12 months to assess bone biomarkers. Physical activity recall and 1-week FFQ were obtained at baseline, 3, 6 and 12 months to examine physical activity and dietary confounders as potential covariates. Dried plum significantly increased BMD of ulna and spine in comparison with dried apple. In comparison with corresponding baseline values, only dried plum significantly decreased serum levels of bone turnover markers including bone-specific alkaline phosphatase and tartrate-resistant acid phosphatase-5b. The findings of the present study confirmed the ability of dried plum in improving BMD in postmenopausal women in part due to suppressing the rate of bone turnover.

Modeling Electron Transfers Using Quasidiabatic Hartree-Fock States.

Electron transfer processes are ubiquitous in chemistry and of great importance in many systems of biological and commercial interest. The ab initio description of these processes remains a challenge in theoretical chemistry, partly due to the high scaling of many post-Hartree-Fock computational methods. This poses a problem for systems of interest that are not easily investigated experimentally. We show that readily available Hartree-Fock solutions can be used as a quasidiabatic basis to understand electron transfer reactions in a Marcus framework. Nonorthogonal configuration interaction calculations can be used to quantify interactions between the resulting electronic states, and to investigate the adiabatic electron transfer process. When applied to a titanium-alizarin complex used as a model of a Grätzel-type solar cell, this approach yields a correct description of the electron transfer and provides information about the electronic states involved in the process.

Sensory and cognitive factors in the processing of visual velocity.

A symmetrical 6 x 6 factorial design of distances and durations served to produce either 36 different moving stimuli (real movement condition) or 36 static displays separately containing the respective stimulus components (cognitive movement condition). Different metric rules underlay the two types of velocity judgments: Perceptual estimations of real movement obeyed a ratio model, whereas conscious estimations of implied movement obeyed an additive model. Valuation operations differed, too; the scales underlying real velocity were nonlinearly related to the even more compressive scales that underlay cognitive velocity. Implications of these results for velocity research are discussed.

Visual velocity input-output functions: the integration of distance and duration onto subjective velocity.

Subjects made magnitude estimations of moving stimuli produced by a 10 X 10 factorial design of distances and durations. Both group and individual data obeyed the bilinear interaction prediction of a simple ratio model. The relation between perceived and actual velocity, as well as the psychophysical contingencies constructed from the marginal means of the design, could be described by a power function with an exponent of about 0.63 as a representative figure. Plotting subjective velocity against physical velocity with either duration or distance as the parameter resulted, respectively, in families of converging psychophysical power functions. Some implications of the results for velocity research, especially the usefulness of specifying the correct metric structure, are discussed.

Integration of noxious stimulation across separate somatosensory communications systems: a functional theory of pain.

Functional measurement analyses and psychophysical techniques were used to assess how separate, cross-modal, aversive events are integrated in judgements of pain. Subjects made magnitude estimations of noxious stimuli produced by a 6 X 6 factorial design of electric shocks and loud tones. Group data and most of the individual results were consistent with a model of linear pain summation: The estimates of pain approximated the linear sum of the pain estimates of the individual electrocutaneous and auditory components. The relation between painful sensation and current intensity could be described by a mildly expansive power function with an exponent of about 1.1. Auditorily produced painful sensation related to sound pressure level by a mildly compressive power function with an exponent of about 0.90 as a representative figure. Results are interpreted in terms of a functional theory of pain. Noxious events are first transformed to psychological scale values via stimulus-specific psychophysical transfer functions. The outputs of these functions are then combined with other pain-related internal representations of either sensory or cognitive origin, according to simple algebraic models.

Pain combines additively across different sensory systems: a further support for the functional theory of pain.

Subjects made magnitude estimations of noxious stimuli produced by a 6 X 6 factorial design of electric shocks (pulse trains) and loud tones. Group data and all individual results conformed to a linear additive model of pain. The estimates of pain approximated the linear sum of the pain estimates of the individual electrocutaneous and auditory components. Pain related differently to the two inducing stimuli. It grew as a mildly expansive power function of current intensity (with an exponent of about 1.2) but as a mildly compressive power function of sound-pressure level (with an exponent of about 0.8). These results replicate recent findings by the same authors in 1986 using a more aversive type of electric stimulation. They are interpreted as supportive of a new functional approach to understand pain and pain-related phenomena.

Flaxseed reverses atherosclerotic lesion formation and lowers lipoprotein(a) in ovarian hormone deficiency.

OBJECTIVE: The incidence of cardiovascular disease dramatically increases during menopause, and postmenopausal women seek natural alternatives to hormone therapy. Flaxseed can slow the progression of atherosclerotic lesion formation; however, it is not known whether it can reverse formation that has already occurred. METHODS: Seventy-two female Golden Syrian hamsters were randomly divided into six groups (n = 12), sham-operated (sham) or ovariectomized (ovx), and kept on the same diet for 120 days to allow for atherosclerotic lesion development. After this 120-day period, whole flaxseed was introduced to the diets of hamsters in three of the groups: group 1 (sham + casein); group 2 (ovx + casein); group 3 (ovx + 7.5% flaxseed); group 4 (ovx + 15% flaxseed); group 5 (ovx + 22.5% flaxseed); and group 6 (ovx + 17ß-estradiol). This diet was maintained for an additional 120 days. Lesion regression was examined histologically, and serum was analyzed for total cholesterol, triglyceride, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, Apo A, Apo B, and lipoprotein(a). RESULTS: Results showed that 15% and 22.5% flaxseed, compared with ovx animals, significantly reduced lipoprotein(a) (4.4 mg/dL [ovx] vs 2.15 mg/dL [15% flaxseed] and 0.3 mg/dL [22.5% flaxseed]; P < 0.05) and Apo B (2.8 mg/dL [ovx] vs 2.4 mg/dL [15% flaxseed] and 2.5 mg/dL [22.5% flaxseed]). Flax reduced by 67% the number of animals with aortic arch lesions. CONCLUSIONS: All three doses of flax reduce the severity of lesion formation compared with ovx controls. These results support the efficacy of flaxseed in reducing cardiovascular disease risk.

Oestrogen signalling and neuroprotection in cerebral ischaemia.

17ß-Oestradiol (E(2)) is an important hormone signal that regulates multiple tissues and functions in the body. This review focuses on the neuroprotective actions of E(2) in the brain against cerebral ischaemia and the potential underlying mechanisms. A particular focus of the review will be on the role of E(2) to attenuate NADPH oxidase activation, superoxide and reactive oxygen species generation and reduce oxidative stress in the ischaemic brain as a potentially key neuroprotective mechanism. Evidence of a potential novel role of extranuclear oestrogen receptors in mediating E(2) signalling and neuroprotective actions is also discussed. An additional subject is the growing evidence indicating that periods of long-term oestrogen deprivation, such as those occurring after menopause or surgical menopause, may lead to loss or attenuation of E(2) signalling and neuroprotective actions in the brain, as well as enhanced sensitivity of the hippocampus to ischaemic stress damage. These findings have important implications with respect to the 'critical period hypothesis', which proposes that oestrogen replacement must be initiated at peri-menopause in humans to exert its beneficial cardiovascular and neural effects. The insights gained from these various studies will prove valuable for guiding future directions in the field.

Daily apple versus dried plum: impact on cardiovascular disease risk factors in postmenopausal women.

BACKGROUND: Evidence suggests that consumption of apple or its bioactive components modulate lipid metabolism and reduce the production of proinflammatory molecules. However, there is a paucity of such research in human beings. OBJECTIVE: Women experience a lower rate of cardiovascular disease before menopause compared with men. However, after the onset of menopause, the risk of cardiovascular disease increases drastically due to ovarian hormone deficiency. Hence, we conducted a 1-year clinical trial to evaluate the effect of dried apple vs dried plum consumption in reducing cardiovascular disease risk factors in postmenopausal women. DESIGN: One-hundred sixty qualified postmenopausal women were recruited from the greater Tallahassee, FL, area during 2007-2009 and were randomly assigned to one of two groups: dried apple (75 g/day) or dried plum (comparative control). Fasting blood samples were collected at baseline, 3, 6, and 12 months to measure various parameters. Physical activity recall and 7-day dietary recall were also obtained. RESULTS: Neither of the dried fruit regimens significantly affected the participants' reported total energy intake throughout the study period. On the contrary, women who consumed dried apple lost 1.5 kg body weight by the end of the study, albeit not significantly different from the dried plum group. In terms of cholesterol, serum total cholesterol levels were significantly lower in the dried apple group compared with the dried plum group only at 6 months. Although dried plum consumption did not significantly reduce serum total cholesterol and low-density lipoprotein cholesterol levels, it lowered their levels numerically by 3.5% and 8%, respectively, at 12 months compared with baseline. This may explain the lack of significance observed between the groups. However, within the group, women who consumed dried apple had significantly lower serum levels of total cholesterol and low-density lipoprotein cholesterol by 9% and 16%, respectively, at 3 months compared with baseline. These serum values were further decreased to 13% and 24%, respectively, after 6 months but stayed constant thereafter. The within-group analysis also reported that daily apple consumption profoundly improved atherogenic risk ratios, whereas there were no significant changes in lipid profile or atherogenic risk ratios as a result of dried plum consumption. Both dried fruits were able to lower serum levels of lipid hydroperoxide and C-reactive protein. However, serum C-reactive protein levels were significantly lower in the dried plum group compared with the dried apple group at 3 months. CONCLUSIONS: There were no significant differences between the dried apple and dried plum groups in altering serum levels of atherogenic cholesterols except total cholesterol at 6 months. However, when within treatment group comparisons are made, consumption of 75 g dried apple (about two medium-sized apples) can significantly lower atherogenic cholesterol levels as early as 3 months. Furthermore, consumption of dried apple and dried plum are beneficial to human health in terms of anti-inflammatory and antioxidative properties.

Binaural summation and lateralization of transients: a combined analysis.

Subjects judged the loudness and the lateral position of dichotic transient signals, which were presented at equal and unequal levels, synchronously and asynchronously, to the two ears. Binaural loudness summation of clicks does not obey a law of linear addition: It is partial at low level and superadditive at high level. Supersummation is greater for interaurally delayed clicks than for coincidental ones. The relation between click loudness and sound pressure (over moderate SLs) can be described as a power function with a greater exponent for the binaural function. Lateral positions spread over a greater range for interaural level differences than for interaural time differences. The time-intensity trading ratio was greater than is typically reported for tones. When sound lateralization was induced by interaural time difference, but not by intensity difference, a virtually perfect negative correlation between loudness and extent of off-center displacement existed.

Dichotic, diotic, and monaural summation of loudness: a comprehensive analysis of composition and psychophysical functions.

In a series of six experiments, the method of magnitude estimation, constrained by a multivariate model, was used to assess the rules that govern the summation of the loudness of two-tone complexes. This methodology enabled us to specify the amounts of summation and simultaneously to construct the corresponding loudness scales. The components had different frequency separations and in the different experiments were presented (1) dichotically, a different frequency to each ear; (2) diotically, to both ears; and (3) monaurally. Results replicated and in some conditions extended known features of multiple signal processing by the auditory system. Thus, qualitatively different rules of loudness integration appeared. For monaural and diotic modes of stimulation, overall loudness depended on total sound energy within the critical band, but on the simple sum of component loudnesses beyond the critical band. For dichotic presentations, a fully additive rule of loudness summation appeared, regardless of frequency spacing. For the latter (but not the former), loudness summation was perfect, with the underlying loudness scales closely approximating Stevens's sone scale.

Binaural and temporal integration of the loudness of tones and noises.

Subjects judged the loudness of tones (Experiment 1) and of bursts of noise (Experiment 2) that varied in intensity and duration as well as in mode of presentation (monaural vs. binaural). Both monaural and binaural loudness, for both types of signals, obeyed the bilinear-interaction prediction of the classic temporal integration model. The loudness of short tones grows as a power function of both intensity and duration with different exponents for the two factors (.2 and .3, respectively). The loudness of wide-band noises grows as a power function of duration (with an exponent of approximately .6) but not of sound pressure. For tones, binaural summation was constant but fell short of full additivity. For noises, summation changed across level and duration. Temporal summation followed the same course for monaural and binaural tonal stimuli but not for noise stimuli. Notwithstanding these differences between tone and noise, we concluded that binaural and temporal summation are independently operating integrative networks within the auditory system. The usefulness of establishing the underlying metric structure for temporal summation is emphasized.