DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science.

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.

Faraday cage screening reveals intrinsic aspects of the van der Waals attraction.

General properties of the recently observed screening of the van der Waals (vdW) attraction between a silica substrate and silica tip by insertion of graphene are predicted using basic theory and first-principles calculations. Results are then focused on possible practical applications, as well as an understanding of the nature of vdW attraction, considering recent discoveries showing it competing against covalent and ionic bonding. The traditional view of the vdW attraction as arising from pairwise-additive London dispersion forces is considered using Grimme's "D3" method, comparing results to those from Tkatchenko's more general many-body dispersion (MBD) approach, all interpreted in terms of Dobson's general dispersion framework. Encompassing the experimental results, MBD screening of the vdW force between two silica bilayers is shown to scale up to medium separations as 1.25 de/d, where d is the bilayer separation and de is its equilibrium value, depicting antiscreening approaching and inside de Means of unifying this correlation effect with those included in modern density functionals are urgently required.

Inducing protein aggregation by extensional flow.

Relative to other extrinsic factors, the effects of hydrodynamic flow fields on protein stability and conformation remain poorly understood. Flow-induced protein remodeling and/or aggregation is observed both in Nature and during the large-scale industrial manufacture of proteins. Despite its ubiquity, the relationships between the type and magnitude of hydrodynamic flow, a protein's structure and stability, and the resultant aggregation propensity are unclear. Here, we assess the effects of a defined and quantified flow field dominated by extensional flow on the aggregation of BSA, ß2-microglobulin (ß2m), granulocyte colony stimulating factor (G-CSF), and three monoclonal antibodies (mAbs). We show that the device induces protein aggregation after exposure to an extensional flow field for 0.36-1.8 ms, at concentrations as low as 0.5 mg mL-1 In addition, we reveal that the extent of aggregation depends on the applied strain rate and the concentration, structural scaffold, and sequence of the protein. Finally we demonstrate the in situ labeling of a buried cysteine residue in BSA during extensional stress. Together, these data indicate that an extensional flow readily unfolds thermodynamically and kinetically stable proteins, exposing previously sequestered sequences whose aggregation propensity determines the probability and extent of aggregation.

Selected Cardiovascular and Psychological Changes Throughout a Competitive Season in Collegiate Female Swimmers.

Dobson, J, Harris, B, Claytor, A, Stroud, L, Berg, L, and Chrysosferidis, P. Selected cardiovascular and psychological changes throughout a competitive season in collegiate female swimmers. J Strength Cond Res 34(11): 3062-3069, 2020-Measures that reflect the balance between training-induced fatigue and recovery can provide valuable feedback to help revise training plans. The aim of this study was to use multidimensional measures of the vagal control of the heart rate (HR), psychological stress, and burnout to investigate the impact of overload training and tapering in female swimmers. Thirteen female Division-1 swimmers completed the HR and psychological measures 3 times during a competitive season: (a) at the beginning of the season (BL), (b) eleven weeks later during a period of overload training (OL), and (c) eleven more weeks later and after a taper (TP). Cardiovascular measures included the resting logarithm of the root mean square of successive R-R intervals (lnRMSSD), HR responses to forced breathing (HRdiff), and HR responses to sustained handgrip exercise (HRhg). Psychological measures consisted of the Athlete Burnout Questionnaire and the Recovery-Stress Questionnaire. Repeated measures analyses of variance revealed that sport devaluation, reduced accomplishment, general stress, and emotional exhaustion all increased throughout the season (all were p < 0.05). Also, lnRMSSDrest decreased (p < 0.01) and HRhg increased (p < 0.05) during OL, both of which then returned to BL levels during TP (p < 0.05 and p < 0.01, respectively); whereas HRdiff values fell progressively during the season (p < 0.05). The results indicate that OL impaired cardiac vagal stimulation, and the bulk of evidence indicated that it was fully restored during a TP. In conclusion, lnRMSSD and HRhg were particularly sensitive to changes in workload throughout the season, and so those measures may be especially useful for preventing an excessive accumulation of training-induced fatigue.

Retrieval practice and judgements of learning enhance transfer of physiology information.

It is well-documented that retrieval practice enhances the recall of simple and complex information (Karpicke and Aue in Educ Psychol Rev 27(2):317-326, 2015). Evidence is also accumulating that retrieval practice can enhance other cognitive processes such as the ability to critically evaluate research articles (Dobson et al. in Med Educ 52(5):513-525, 2018) and transfer of learning (Butler in J Exp Psychol Learn Mem Cogn 36(5):1118, 2010). One aim of this investigation was to explore the effects of retrieval practice on transfer of learning with physiology information. A second aim was to compare recall and transfer of physiology information following retrieval practice versus a judgment of learning task (JOL) that is potentially less time consuming for students to use. Participants were randomly assigned to learn three physiology texts using each of the following strategies: (1) studying a text four times (S-S-S-S), (2) studying and then retrieving a text two times (S-R-S-R), and (3) studying a text four times while completing multiple JOL during the second and fourth repetitions (S-S/J-S-S/J). Recall and accuracy on transfer questions were assessed 1 week after the learning phase, and the results were analyzed using repeated measures ANOVAs. The S-R-S-R strategy (21.35 ± 1.08%) produced significantly greater recall than the S-S-S-S strategy (17.35 ± 0.86%), and both the S-R-S-R (44.60 ± 2.55%) and S-S/J-S-S/J (41.79 ± 2.63%) strategies lead to significantly greater transfer than the S-S-S-S strategy (36.07 ± 2.40%). These results provide evidence that retrieval practice enhances recall and transfer of physiology information and that a JOL task can also prove to be beneficial but to a lesser degree.

Using extensional flow to reveal diverse aggregation landscapes for three IgG1 molecules.

Monoclonal antibodies (mAbs) currently dominate the biopharmaceutical sector due to their potency and efficacy against a range of disease targets. These proteinaceous therapeutics are, however, susceptible to unfolding, mis-folding, and aggregation by environmental perturbations. Aggregation thus poses an enormous challenge to biopharmaceutical development, production, formulation, and storage. Hydrodynamic forces have also been linked to aggregation, but the ability of different flow fields (e.g., shear and extensional flow) to trigger aggregation has remained unclear. To address this question, we previously developed a device that allows the degree of extensional flow to be controlled. Using this device we demonstrated that mAbs are particularly sensitive to the force exerted as a result of this flow-field. Here, to investigate the utility of this device to bio-process/biopharmaceutical development, we quantify the effects of the flow field and protein concentration on the aggregation of three mAbs. We show that the response surface of mAbs is distinct from that of bovine serum albumin (BSA) and also that mAbs of similar sequence display diverse sensitivity to hydrodynamic flow. Finally, we show that flow-induced aggregation of each mAb is ameliorated by different buffers, opening up the possibility of using the device as a formulation tool. Perturbation of the native state by extensional flow may thus allow identification of aggregation-resistant mAb candidates, their bio-process parameters and formulation to be optimized earlier in the drug-discovery pipeline using sub-milligram quantities of material.

Retrieval practice enhances the ability to evaluate complex physiology information.

OBJECTIVE: Many investigations have shown that retrieval practice enhances the recall of different types of information, including both medical and physiological, but the effects of the strategy on higher-order thinking, such as evaluation, are less clear. The primary aim of this study was to compare how effectively retrieval practice and repeated studying (i.e. reading) strategies facilitated the evaluation of two research articles that advocated dissimilar conclusions. A secondary aim was to determine if that comparison was affected by using those same strategies to first learn important contextual information about the articles. METHODS: Participants were randomly assigned to learn three texts that provided background information about the research articles either by studying them four consecutive times (Text-S) or by studying and then retrieving them two consecutive times (Text-R). Half of both the Text-S and Text-R groups were then randomly assigned to learn two physiology research articles by studying them four consecutive times (Article-S) and the other half learned them by studying and then retrieving them two consecutive times (Article-R). Participants then completed two assessments: the first tested their ability to critique the research articles and the second tested their recall of the background texts. RESULTS: On the article critique assessment, the Article-R groups' mean scores of 33.7 ± 4.7% and 35.4 ± 4.5% (Text-R then Article-R group and Text-S then Article-R group, respectively) were both significantly (p < 0.05) higher than the two Article-S mean scores of 19.5 ± 4.4% and 21.7 ± 2.9% (Text-S then Article-S group and Text-R then Article-S group, respectively). There was no difference between the two Article-R groups on the article critique assessment, indicating those scores weren't affected by the different contextual learning strategies. CONCLUSION: Retrieval practice promoted superior critical evaluation of the research articles, and the results also indicated the strategy enhanced the recall of background information.

Sport-related concussion induces transient cardiovascular autonomic dysfunction.

Recent evidence suggests that concussions may disrupt autonomic cardiovascular control. This study investigated the initial effects of concussion on cardiovascular function using three autonomic reflex tests. Twenty-three recreational athletes (12 women, 11 men) were divided into concussed (n = 12) and control (n = 11) groups. Concussed participants performed forced breathing, standing, and Valsalva autonomic tests four times: 1) within 48 h of injury; 2) 24 h later; 3) 1 wk after injury; and 4) 2 wk after injury. The controls performed the same tests on the same schedule. Differences in heart rate (HR), systolic blood pressure (SBP), and diastolic blood pressure (DBP) responses to the tests were continuously measured using finger photoplethysmography and were analyzed using repeated-measures multivariate ANOVAs and ANOVAs. Within 48 h of injury, the concussed group had significantly greater resting SBP (t21 = 2.44, P = 0.02, d = 1.03), HR (t21 = 2.33, P = 0.03, d = 1.01), and SBP responses to standing (t21 = 2.98, P = 0.01, d = 1.24), and 90% SBP normalization times (t21 = 2.64, P = 0.02, d = 1.10) after the Valsalva, but those group differences subsided 24 h later. There was also a significant interaction with the HR responses to forced breathing (F3,60 = 4.13, P = 0.01, ηp2 = 0.17), indicating the concussed responses declined relative to the control's over time. The results demonstrate that concussion disrupted autonomic cardiovascular control, and that autonomic reflex tests are practical means by which to evaluate that dysfunction.

Identifying Dosage Effect of Light-Emitting Diode Therapy on Muscular Fatigue in Quadriceps.

Hemmings, TJ, Kendall, KL, and Dobson, JL. Identifying dosage effect of light-emitting diode therapy on muscular fatigue in quadriceps. J Strength Cond Res 31(2): 395-402, 2017-The purpose of this study was to compare the effects of various dosages of light-emitting diode therapy (LEDT) on muscle fatigue while performing a single-leg extension to exhaustion. A total of 34 recreationally resistance-trained athletes between the ages of 18 and 26 participated in 4 trials. Each trial included pre-exercise/postexercise blood lactate measurements and 2 sets of 3 maximal voluntary isometric contractions (MVICs), followed by LEDT on 6 points across the superficial quadriceps. Each randomized trial consisted of a placebo, 30, 60, or 120 seconds on each point on the quadriceps. Three minutes after LEDT, the participants performed an eccentric leg extension with 120% of MVIC until fatigue. There was significant increase in the number of repetitions performed between the placebo treatment and 60 seconds (p = 0.023), as well as placebo and 120 seconds (p = 0.004) of irradiation on each point. There were no significant differences in blood lactate levels between any of the 4 trials. In conclusion, LEDT had a positive effect on performance when irradiating 6 points on the superficial quadriceps for 60 and 120 seconds before an eccentric leg extension.

Spooky correlations and unusual van der Waals forces between gapless and near-gapless molecules.

We consider the zero-temperature van der Waals (vdW) interaction between two molecules, each of which has a zero or near-zero electronic gap between a ground state and the first excited state, using a toy model molecule (equilateral H3) as an example. We show that the van der Waals energy between two ground state molecules falls off as D-3 instead of the usual D-6 dependence, when the molecules are separated by distance D. We show that this is caused by a perfect "spooky" correlation between the two fluctuating electric dipoles. The phenomenon is related to, but not the same as, the "resonant" interaction between an electronically excited and a ground state molecule introduced by Eisenschitz and London in 1930. It is also an example of "type C van der Waals non-additivity" recently introduced by one of us [J. F. Dobson, Int. J. Quantum Chem. 114, 1157 (2014)]. Our toy molecule H3 is not stable, but symmetry considerations suggest that a similar vdW phenomenon may be observable, despite Jahn-Teller effects, in molecules with a discrete rotational symmetry and broken inversion symmetry, such as certain metal atom clusters. The motion of the nuclei will need to be included for a definitive analysis of such cases, however.

The benefit of self-testing and interleaving for synthesizing concepts across multiple physiology texts.

A testing-based learning strategy is one that relies on the act of recalling (i.e., testing) information after exposure, and interleaving is a strategy in which the learning materials are presented in a serial order (e.g., texts 1, 2, 3, 1, 2, 3, 1, 2, 3) versus a blocked order (e.g., texts 1, 1, 1, 2, 2, 2, 3, 3, 3). Although both learning strategies have been thoroughly investigated, few studies have examined their additive effect with higher-order cognitive tasks such as the ability to identify themes across multiple texts, and none of those did so using physiology information. The purpose of the present study was to compare recall and thematic processing across five different physiology texts. Participants were randomly assigned to learn the texts using one of the following four learning strategies: 1) study-study-study (S-S-S) using a blocked order, 2) S-S-S using an interleaved order, 3) study-test-study (S-T-S) using a blocked order, and 4) S-T-S using an interleaved order. Over the course of the following week, the S-T-S groups had more stable recall of key text ideas compared with the S-S-S groups, and the S-T-S group had more stable recall of thematic information than the S-S-S group when interleaving was used as the presentation order.

Self-testing promotes superior retention of anatomy and physiology information.

The testing effect shows that learning is enhanced by the act of recalling information after exposure. Although the testing effect is among the most robust findings in cognitive science, much of its empirical support is from laboratory studies and it has been applied as a strategy for enhancing learning in the classroom in a limited fashion. The purpose of this investigation was to replicate the testing effect in a university anatomy and physiology course and to extend the applicability of it to independent student study. Students repeatedly studied three sets of passages that described structures and concepts pertaining to (1) cardiac electrophysiology, (2) ventilation and (3) endocrinology. Each student was randomly assigned to study one of those three passage sets by reading it three consecutive times (R-R-R), another by reading and then rereading it while taking notes (R-R + N) and the third by reading it, recalling as much as possible (i.e., self-testing) and then rereading it (R-T-R). Retention assessed after 1 week was significantly greater following R-T-R (53.95 ± 1.72) compared to R-R-R (48.04 ± 1.83) and R-R + N (48.31 ± 1.78). Evidence is also presented that suggests students benefited from instructions to self-test when preparing for exams on their own. The testing effect, then, can be generalized to real-life settings such as university anatomy and physiology courses and to independent study situations.

Self-testing produces superior recall of both familiar and unfamiliar muscle information.

Dozens of studies have found learning strategies based on the "testing effect" promote greater recall than those that rely solely on reading; however, the advantages of testing are often only observed after a delay (e.g., 2-7 days later). In contrast, our research, which has focused on kinesiology students learning kinesiology information that is generally familiar to them, has consistently demonstrated that testing-based strategies produce greater recall both immediately and after a delay. In an attempt to understand the discrepancies in the literature, the purpose of the present study was to determine if the time-related advantages of a testing-based learning strategy vary with one's familiarity with the to-be-learned information. Participants used both read-only and testing-based strategies to repeatedly study three different sets of information: 1) previously studied human muscle information (familiar information), 2) a mix of previously studied and previously unstudied human muscle information (mixed information), and 3) previously unstudied muscle information that is unique to sharks (unfamiliar information). Learning was evaluated via free recall assessments administered immediately after studying and again after a 1-wk delay and a 3-wk delay. Across those three assessments, the read-only strategy resulted in mean scores of 29.26 ± 1.43, 15.17 ± 1.29, and 5.33 ± 0.77 for the familiar, mixed, and unfamiliar information, respectively, whereas the testing-based strategy produced scores of 34.57 ± 1.58, 16.90 ± 1.31, and 8.33 ± 0.95, respectively. The results indicate that the testing-based strategy produced greater recall immediately and up through the 3-wk delay regardless of the participants' level of familiarity with the muscle information.

Density functional theory analysis of structural and electronic properties of orthorhombic perovskite CH3NH3PbI3.

The organic-inorganic hybrid perovskite CH3NH3PbI3 is a novel light harvester, which can greatly improve the solar-conversion efficiency of dye-sensitized solar cells. In this article, a first-principle theoretical study is performed using local, semi-local and non-local exchange-correlation approximations to find a suitable method for this material. Our results, using the non-local optB86b + vdWDF functional, excellently agree with the experimental data. Thus, consideration of weak van der Waals interactions is demonstrated to be important for the accurate description of the properties of this type of organic-inorganic hybrid materials. Further analysis of the electronic properties reveals that I 5p electrons can be photo-excited to Pb 6p empty states. The main interaction between the organic cations and the inorganic framework is through the ionic bonding between CH3 and I ions. Furthermore, I atoms in the Pb-I framework are found to be chemically inequivalent because of their different chemical environments.

The flexible nature of exchange, correlation, and Hartree physics: resolving "delocalization" errors in a "correlation free" density functional.

By exploiting freedoms in the definitions of "correlation," "exchange," and "Hartree" physics in ensemble systems, we better generalise the notion of "exact exchange" (EXX) to systems with fractional occupations of the frontier orbitals, arising in the dissociation limit of some molecules. We introduce the linear EXX ("LEXX") theory whose pair distribution and energy are explicitly piecewise linear in the occupations f(i)(σ). We provide explicit expressions for these functions for frontier s and p shells. Used in an optimised effective potential (OEP) approach the LEXX yields energies bounded by the piecewise linear "ensemble EXX" (EEXX) energy and standard fractional optimised EXX energy: E(EEXX) ≤ E(LEXX) ≤ E(EXX). Analysis of the LEXX explains the success of standard OEP methods for diatoms at large spacing, and why they can fail when both spins are allowed to be non-integer so that "ghost" Hartree interactions appear between opposite spin electrons in the usual formula. The energy E(LEXX) contains a cancellation term for the spin ghost case. It is evaluated for H, Li, and Na fractional ions with clear derivative discontinuities for all cases. The p-shell form reproduces accurate correlation-free energies of B-F and Al-Cl. We further test LEXX plus correlation energy calculations on fractional ions of C and F and again we find both derivative discontinuities and good agreement with exact results.

Electron affinities and ionisation potentials for atoms via "benchmark" tdDFT calculations with and without exchange kernels.

One of the known weaknesses of the adiabatic connection fluctuation dissipation (ACFD) correlation energy functional under the direct random-phase approximation (RPA) is its failure to accurately predict energy differences between dissimilar systems. In this work we evaluate ionisation potentials I and electron affinities A for atoms and ions with one to eighteen electrons using the ACFD functional under the RPA, and with the "PGG (Petersilka-Gossmann-Gross)" and "RXH (radial exchange hole)" model exchange kernels. All calculations are carried out using a real-space, all electron method with an exact exchange groundstate to minimise errors. As expected, the RPA is less accurate even than some regular density functional theory approaches, while the introduction of a dynamical exchange kernel improves results. In contrast to the case of atomic groundstate energies, the PGG kernel outperforms the RXH kernel for I and A. Mean absolute errors for I/A are found to be 3.27/2.38 kcal/mol, 4.38/5.43 kcal/mol, and 9.24/ 8.94 kcal/mol for the PGG, RXH, and RPA, respectively. We thus show that the inclusion of even the simple "RXH" kernel improves both quantities when compared to the RPA.

Binding and interlayer force in the near-contact region of two graphite slabs: experiment and theory.

Via a novel experiment, Liu et al. [Phys. Rev. B 85, 205418 (2012)] estimated the graphite binding energy, specifically the cleavage energy, an important physical property of bulk graphite. We re-examine the data analysis and note that within the standard Lennard-Jones model employed, there are difficulties in achieving internal consistency in the reproduction of the graphite elastic properties. By employing similar models which guarantee consistency with the elastic constant, we find a wide range of model dependent binding energy values from the same experimental data. We attribute some of the difficulties in the determination of the binding energy to: (i) limited theoretical understanding of the van der Waals dispersion of graphite cleavage, (ii) the mis-match between the strong bending stiffness of the graphite-SiO2 cantilever and the weak asymptotic inter-layer forces that are integrated over to produce the binding energy. We find, however, that the data do support determination of a maximum inter-layer force that is relatively model independent. We conclude that the peak force per unit area is 1.1 ± 0.15 GPa for cleavage, and occurs at an inter-layer spacing of 0.377 ± 0.013 nm.

Assessment of range-separated time-dependent density-functional theory for calculating C6 dispersion coefficients.

We assess a variant of linear-response range-separated time-dependent density-functional theory (TDDFT), combining a long-range Hartree-Fock (HF) exchange kernel with a short-range adiabatic exchange-correlation kernel in the local-density approximation (LDA) for calculating isotropic C6 dispersion coefficients of homodimers of a number of closed-shell atoms and small molecules. This range-separated TDDFT tends to give underestimated C6 coefficients of small molecules with a mean absolute percentage error of about 5%, a slight improvement over standard TDDFT in the adiabatic LDA which tends to overestimate them with a mean absolute percentage error of 8%, but close to time-dependent Hartree-Fock which has a mean absolute percentage error of about 6%. These results thus show that introduction of long-range HF exchange in TDDFT has a small but beneficial impact on the values of C6 coefficients. It also confirms that the present variant of range-separated TDDFT is a reasonably accurate method even using only a LDA-type density functional and without adding an explicit treatment of long-range correlation.

Retrieval practice is an efficient method of enhancing the retention of anatomy and physiology information.

Although a great deal of empirical evidence has indicated that retrieval practice is an effective means of promoting learning and memory, very few studies have investigated the strategy in the context of an actual class. The primary purpose of this study was to determine if a series of very brief retrieval quizzes could significantly improve the retention of previously tested information throughout an anatomy and physiology course. A second purpose was to determine if there were any significant differences between expanding and uniform patterns of retrieval that followed a standardized initial retrieval delay. Anatomy and physiology students were assigned to either a control group or groups that were repeatedly prompted to retrieve a subset of previously tested course information via a series of quizzes that were administered on either an expanding or a uniform schedule. Each retrieval group completed a total of 10 retrieval quizzes, and the series of quizzes required (only) a total of 2 h to complete. Final retention of the exam subset material was assessed during the last week of the semester. There were no significant differences between the expanding and uniform retrieval groups, but both retained an average of 41% more of the subset material than did the control group (ANOVA, F = 129.8, P = 0.00, ηp(2) = 0.36). In conclusion, retrieval practice is a highly efficient and effective strategy for enhancing the retention of anatomy and physiology material.

MBD + C: How to Incorporate Metallic Character into Atom-Based Dispersion Energy Schemes.

The dispersion component of the van der Waals interaction in low-dimensional metals is known to exhibit anomalous "Type-C non-additivity" [Int. J. Quantum Chem. 2014, 114, 1157]. This causes dispersion energy behavior at asymptotically large separations that is missed by popular atom-based schemes for dispersion energy calculations. For example, the dispersion interaction energy between parallel metallic nanotubes at separation D falls off asymptotically as approximately D-2, whereas current atom-based schemes predict D-5 asymptotically. To date, it has not been clear whether current atom-based theories also give the dispersion interaction inaccurately at smaller separations for low-dimensional metals. Here, we introduce a new theory that we term "MBD + C". It permits inclusion of Type C effects efficiently within atom-based dispersion energy schemes such as many body dispersion (MBD) and universal MBD (uMBD). This allows us to investigate asymptotic, intermediate, and near-contact regimes with equal accuracy. (The large contact energy of intimate metallic bonding is not primarily governed by dispersion energy and is described well by the semi-local density functional theory.) Here, we apply a simplified version, "nn-MBD + C", of our new theory to calculate the dispersion interaction for three low-dimensional metallic systems: parallel metallic chains of gold atoms, parallel Li-doped graphene sheets, and parallel (4,4) armchair carbon nanotubes. In addition to giving the correct asymptotic behavior, the new theory seamlessly gives the dispersion energy down to near-contact geometry, where it is similar to MBD but can give up to 15% more dispersion energy than current MBD schemes, in the systems studied so far. This percentage increases with separation until nn-MBD + C dominates MBD at asymptotic separations.