From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape.

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins.

Sudden Deaths Among Oil and Gas Extraction Workers Resulting from Oxygen Deficiency and Inhalation of Hydrocarbon Gases and Vapors - United States, January 2010-March 2015.

In 2013, an occupational medicine physician from the University of California, San Francisco, contacted CDC's National Institute for Occupational Safety and Health (NIOSH), and the Occupational Safety and Health Administration (OSHA) about two oil and gas extraction worker deaths in the western United States. The suspected cause of these deaths was exposure to hydrocarbon gases and vapors (HGVs) and oxygen (O2)-deficient atmospheres after opening the hatches of hydrocarbon storage tanks. The physician and experts from NIOSH and OSHA reviewed available fatality reports from January 2010 to March 2015, and identified seven additional deaths with similar characteristics (nine total deaths). Recommendations were made to industry and regulators regarding the hazards associated with opening hatches of tanks, and controls to reduce or eliminate the potential for HGV exposure were proposed. Health care professionals who treat or evaluate oil and gas workers need to be aware that workers might report symptoms of exposure to high concentrations of HGVs and possible O2 deficiency; employers and workers need to be aware of this hazard and know how to limit exposure. Medical examiners investigating the death of oil and gas workers who open tank hatches should consider the contribution of O2 deficiency and HGV exposure.

Occupational HIV Transmission Among Male Adult Film Performers - Multiple States, 2014.

In 2014, the California Department of Public Health was notified by a local health department of a diagnosis of acute human immunodeficiency virus (HIV) infection* and rectal gonorrhea in a male adult film industry performer, aged 25 years (patient A). Patient A had a 6-day history of rash, fever, and sore throat suggestive of acute retroviral syndrome at the time of examination. He was informed of his positive HIV and gonorrhea test results 6 days after his examination. Patient A had a negative HIV-1 RNA qualitative nucleic acid amplification test (NAAT)(†) 10 days before symptom onset. This investigation found that during the 22 days between the negative NAAT and being informed of his positive HIV test results, two different production companies directed patient A to have condomless sex with a total of 12 male performers. Patient A also provided contact information for five male non-work-related sexual partners during the month before and after his symptom onset. Patient A had additional partners during this time period for which no locating information was provided. Neither patient A nor any of his interviewed sexual partners reported taking HIV preexposure prophylaxis (PrEP). Contact tracing and phylogenetic analysis of HIV sequences amplified from pretreatment plasma revealed that a non-work-related partner likely infected patient A, and that patient A likely subsequently infected both a coworker during the second film production and a non-work-related partner during the interval between his negative test and receipt of his positive HIV results. Adult film performers and production companies, medical providers, and all persons at risk for HIV should be aware that testing alone is not sufficient to prevent HIV transmission. Condom use provides additional protection from HIV and sexually transmitted infections (STIs). Performers and all persons at risk for HIV infection in their professional and personal lives should discuss the use of PrEP with their medical providers.

Multiresolution quantum chemistry in multiwavelet bases: excited states from time-dependent Hartree-Fock and density functional theory via linear response.

A fully numerical method for the time-dependent Hartree-Fock and density functional theory (TD-HF/DFT) with the Tamm-Dancoff (TD) approximation is presented in a multiresolution analysis (MRA) approach. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. The integral equation is efficiently and adaptively solved using a numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H2, Be, N2, H2O, and C2H4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. We introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.

Isocyanates and work-related asthma: Findings from California, Massachusetts, Michigan, and New Jersey, 1993-2008.

BACKGROUND: Isocyanates remain a leading cause of work-related asthma (WRA). METHODS: Two independent data systems were analyzed for the period 1993-2008: (1) State-based WRA case surveillance data on persons with isocyanate-induced WRA from four states, and (2) Occupational Safety and Health Administration (OSHA) Integrated Management Information System (IMIS) isocyanate air sampling results. RESULTS: We identified 368 cases of isocyanate-induced WRA from 32 industries and 678 OSHA isocyanate air samples with detectable levels from 31 industries. Seventeen industries were unique to one or the other dataset. CONCLUSION: Isocyanate-induced WRA continues to occur in a wide variety of industries. Two data systems uncovered industries with isocyanate exposures and/or illness. Improved control measures and standards, including medical surveillance, are needed. More emphasis is needed on task-specific guidance, spill clean-up procedures, skin and respiratory protection, and targeted medical monitoring to mitigate the hazards of isocyanate use.

Gender differences in work-related asthma: surveillance data from California, Massachusetts, Michigan, and New Jersey, 1993-2008.

OBJECTIVE: To characterize work-related asthma by gender. METHODS: We analyzed state-based sentinel surveillance data on confirmed work-related asthma cases collected from California, Massachusetts, Michigan, and New Jersey during 1993-2008. We used Chi-square and Fisher's Exact Test statistics to compare select characteristics between females and males. RESULTS: Of the 8239 confirmed work-related asthma cases, 60% were female. When compared to males with work-related asthma, females with work-related asthma were more likely to be identified through workers' compensation (14.8% versus 10.6%) and less likely to be identified through hospital data (14.2% versus 16.9%). Moreover, when compared to males, females were more likely to have work-aggravated asthma (24.4% versus 13.5%) and less likely to have new-onset asthma (48.0% versus 56.5%). Females were also more likely than males with work-related asthma to work in healthcare and social assistance (28.7% versus 5.2%), educational services (11.8% versus 4.2%), and retail trade (5.0% versus 3.9%) industries and in office and administrative support (20.0% versus 4.0%), healthcare practitioners and technical (13.4% versus 1.6%), and education training and library (6.2% versus 1.3%) occupations. Agent groups most frequently associated with work-related asthma were miscellaneous chemicals (20.3%), cleaning materials (15.3%), and indoor air pollutants (14.9%) in females and miscellaneous chemicals (15.7%), mineral and inorganic dusts (13.2%), and pyrolysis products (12.7%) in males. CONCLUSIONS: Among adults with work-related asthma, males and females differ in terms of workplace exposures, occupations, and industries. Physicians should consider these gender differences when diagnosing and treating asthma in working adults.

Response to "Comment on 'Rethinking first-principles electron transport theories with projection operators: the problems caused by partitioning the basis set'" [J. Chem. Phys. 140, 177103 (2014)].

The thesis of Brandbyge's comment [J. Chem. Phys. 140, 177103 (2014)] is that our operator decoupling condition is immaterial to transport theories, and it appeals to discussions of nonorthogonal basis sets in transport calculations in its arguments. We maintain that the operator condition is to be preferred over the usual matrix conditions and subsequently detail problems in the existing approaches. From this operator perspective, we conclude that nonorthogonal projectors cannot be used and that the projectors must be selected to satisfy the operator decoupling condition. Because these conclusions pertain to operators, the choice of basis set is not germane.

Benchmarking Correlation-Consistent Basis Sets for Frequency-Dependent Polarizabilities with Multiresolution Analysis.

This paper presents the first converged frequency-dependent HF polarizability results for general molecules, on a set of 89 closed-shell atoms and molecules. The solver employs multiresolution analysis (MRA) in a multiwavelet basis to compute both ground and response states to a guaranteed precision, which are validated against independent numerical grid calculations on atoms and linear molecules. The MRA ground-state energies and response properties are used to evaluate results in correlation-consistent basis sets up to 5Z augmented with either single or double diffuse functions and core-polarization functions. Systematic trends are revealed through consideration of chemical composition as well as the use of machine learning to cluster convergence trends, the latter suggesting the possibility of learning and correcting basis-set error.

Rethinking first-principles electron transport theories with projection operators: the problems caused by partitioning the basis set.

We revisit the derivation of electron transport theories with a focus on the projection operators chosen to partition the system. The prevailing choice of assigning each computational basis function to a region causes two problems. First, this choice generally results in oblique projection operators, which are non-Hermitian and violate implicit assumptions in the derivation. Second, these operators are defined with the physically insignificant basis set and, as such, preclude a well-defined basis set limit. We thus advocate for the selection of physically motivated, orthogonal projection operators (which are Hermitian) and present an operator-based derivation of electron transport theories. Unlike the conventional, matrix-based approaches, this derivation requires no knowledge of the computational basis set. In this process, we also find that common transport formalisms for nonorthogonal basis sets improperly decouple the exterior regions, leading to a short circuit through the system. We finally discuss the implications of these results for first-principles calculations of electron transport.

Direct Determination of Optimal Real-Space Orbitals for Correlated Electronic Structure of Molecules.

We demonstrate how to determine numerically nearly exact orthonormal orbitals that are optimal for the evaluation of the energy of arbitrary (correlated) states of atoms and molecules by minimization of the energy Lagrangian. Orbitals are expressed in real space using a multiresolution spectral element basis that is refined adaptively to achieve the user-specified target precision while avoiding the ill-conditioning issues that plague AO basis set expansions traditionally used for correlated models of molecular electronic structure. For light atoms, the orbital solver, in conjunction with a variational electronic structure model [selected Configuration Interaction (CI)] provides energies of comparable precision to a state-of-the-art atomic CI solver. The computed electronic energies of atoms and molecules are significantly more accurate than the counterparts obtained with the orbital sets of the same rank expanded in Gaussian AO bases, and can be determined even when linear dependence issues preclude the use of the AO bases. It is feasible to optimize more than 100 fully correlated numerical orbitals on a single computer node, and significant room exists for additional improvement. These findings suggest that real-space orbital representations might be the preferred alternative to AO representations for high-end models of correlated electronic states of molecules and materials.

Silicosis Among Immigrant Engineered Stone (Quartz) Countertop Fabrication Workers in California.

Importance: Silicosis associated with inhalation of respirable crystalline silica among engineered stone countertop fabrication workers is an emerging health concern. Objective: To describe clinical, socioeconomic, and occupational characteristics of patients diagnosed with silicosis associated with engineered stone in California. Design, Setting, and Participants: This case series included reported cases of silicosis associated with fabrication of engineered stone countertops, as identified by statewide surveillance by the California Department of Public Health (2019-2022). Data analysis was performed from October 2022 to March 2023. Exposures: Patient interviews and medical record abstractions were used to assess occupational exposure to respirable crystalline silica, including duration of work tenure and preventive measures undertaken. Main Outcomes and Measures: Demographics, clinical characteristics, health care utilization, and clinical outcomes were obtained, including vital status, hypoxia, and lung transplant. Results: This case series identified 52 male patients meeting inclusion criteria; median (IQR) age was 45 (40-49) years, and 51 were Latino immigrants. Ten (19%) were uninsured, and 20 (39%) had restricted-scope Medi-Cal; 25 (48%) presented initially to an emergency department. A delay in diagnosis occurred in 30 (58%) patients, most commonly due to alternative initial diagnoses of bacterial pneumonia (9 [30%]) or tuberculosis (8 [27%]). At diagnosis, 20 (38%) patients had advanced disease (progressive massive fibrosis) with severely or very severely reduced forced expiratory volume in 1 second in 8 (18%) and 5 (11%), respectively. Of the cases, 10 (19%) were fatal; median (IQR) age at death was 46 (38-51) years, and 6 patients (12%) were alive with chronic resting hypoxia. Eleven were referred for lung transplant: 3 underwent transplant with 1 fatality; 7 were declined transplant, with 6 fatalities; and 1 died prior to listing. Median (IQR) work tenure was 15 (10-20) years; 23 (45%) reported use of water suppression for dust mitigation, and 25 (48%) continued to fabricate stone after being diagnosed with silicosis. Conclusions and Relevance: In this case series performed in California, silicosis associated with occupational exposure to dust from engineered stone primarily occurred among young Latino immigrant men. Many patients presented with severe disease, and some cases were fatal.

Active Surveillance of Engineered Stone Workers Facilitates Early Identification of Silicosis: A Discussion of Surveillance of Occupational Lung Diseases.

Silicosis in workers exposed to respirable crystalline silica while fabricating engineered stone products is an emerging respiratory health issue. We describe silicosis in engineered stone workers in California and examine clinical features by the source of identification. Cases were identified passively using hospital-based patient discharge data or actively through outreach and medical testing following enforcement investigation. Outcomes were examined based on the source of case identification. We identified 18 cases diagnosed between 2006 and 2020. Cases identified passively compared to other identification methods were associated with lower percent predicted forced vital capacity (FVC) (P ≤ .01), forced expiratory volume in 1 s (FEV1) (P ≤ .01), and diffusing capacity of the lungs for carbon monoxide (DLCO) (P < .01) at the time of diagnosis and were more likely to be identified following death or lung transplant (P = .01). Our experience demonstrates delays in diagnosis and case identification when relying on passive surveillance methods. Enhanced public health surveillance systems can improve the early detection of occupational lung disease and inform future prevention policies.

Computing many-body wave functions with guaranteed precision: the first-order Møller-Plesset wave function for the ground state of helium atom.

We present an approach to compute accurate correlation energies for atoms and molecules using an adaptive discontinuous spectral-element multiresolution representation for the two-electron wave function. Because of the exponential storage complexity of the spectral-element representation with the number of dimensions, a brute-force computation of two-electron (six-dimensional) wave functions with high precision was not practical. To overcome the key storage bottlenecks we utilized (1) a low-rank tensor approximation (specifically, the singular value decomposition) to compress the wave function, and (2) explicitly correlated R12-type terms in the wave function to regularize the Coulomb electron-electron singularities of the Hamiltonian. All operations necessary to solve the Schrödinger equation were expressed so that the reconstruction of the full-rank form of the wave function is never necessary. Numerical performance of the method was highlighted by computing the first-order Møller-Plesset wave function of a helium atom. The computed second-order Møller-Plesset energy is precise to ~2 microhartrees, which is at the precision limit of the existing general atomic-orbital-based approaches. Our approach does not assume special geometric symmetries, hence application to molecules is straightforward.

Rare case of occupational pulmonary hemorrhage in a firefighter.

Alveolar hemorrhage associated with physical exertion, known as exercise-induced pulmonary hemorrhage (EIPH), is a rare condition linked to strenuous exertion. This can be an unusual form of respiratory and occupational illness. We present the case of a healthy firefighter who developed fatal pulmonary hemorrhage after participating in a strenuous physical training exercise regimen. This case represents a severe presentation of EIPH, which results from the disruption of the pulmonary blood-gas barrier as a result of strenuous exertion. Clinicians caring for those in vocations and recreation involving extremely vigorous exercise should be aware that such activities can cause EIPH.

Follow-up of neck and shoulder pain among sewing machine operators: The Los Angeles garment study.

BACKGROUND: The aim of the present study is to explore factors affecting or modifying self-reported neck/shoulder pain in sewing machine operators. METHODS: We investigated self-report neck/shoulder pain in 247 workers who participated in a 4-month prospective intervention study for musculoskeletal disorders. All participants were immigrants. We examine the influence of individual and work-related factors on changes in neck/shoulder pain during follow-up employing linear mixed models with time-spline functions. RESULTS: We observed a dramatic decline (72%) in self-reported pain intensity in the first month of follow-up, followed by a small increase from the first to fourth month (4% per month). Workers who perceived and reported their physical workload as high or worked overtime experienced less overall pain reduction. Higher baseline pain intensity, being of Hispanic ethnicity (vs. Asian), and taking cumulative daily rest time during work of 35 min or more allowing for muscles to rest were associated with a larger pain reduction in the first month, but not thereafter. CONCLUSION: Our findings indicate that some work-related factors may be of clinical relevance for reducing neck/shoulder pain. Having lower physical workloads and less overtime work should be considered when treating patients or planning workplace interventions for managing work-related musculoskeletal disorders in this underserved immigrant population.

Computational prediction of alpha/beta selectivities in the pyrolysis of oxygen-substituted phenethyl phenyl ethers.

Phenethyl phenyl ether (PPE; PhCH 2CH 2OPh) is the simplest model for the most common beta-O-4 linkage in lignin. Previously, we developed a computational scheme to calculate the alpha/beta product selectivity in the pyrolysis of PPE by systematically exploiting error cancellation in the computation of relative rate constants. The alpha/beta selectivity is defined as the selectivity between the competitive hydrogen abstraction reaction paths on the alpha- and beta-carbons of PPE. We use density functional theory and employ transition state theory where we include diagonal anharmonic correction in the vibrational partition functions for low frequency modes for which a semiclassical expression is used. In this work we investigate the effect of oxygen substituents (hydroxy, methoxy) in the para position on the phenethyl ring of PPE on the alpha/beta selectivities. The total alpha/beta selectivity increases when substituents are introduced and is larger for the methoxy than the hydroxy substituent. The strongest effect of the substituents is observed for the alpha-pathway of the hydrogen abstraction by the phenoxyl chain carrying radical for which the rate increases. For the beta pathway and the abstraction by the R-benzyl radical (R = OH,OCH 3) the rate decreases with the introduction of the substituents. These findings are compared with results from recent experimental studies.