Swarm Learning for decentralized and confidential clinical machine learning.

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning-a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine.

Social evolution of shared biofilm matrix components.

Biofilm formation is an important and ubiquitous mode of growth among bacteria. Central to the evolutionary advantage of biofilm formation is cell-cell and cell-surface adhesion achieved by a variety of factors, some of which are diffusible compounds that may operate as classical public goods-factors that are costly to produce but may benefit other cells. An outstanding question is how diffusible matrix production, in general, can be stable over evolutionary timescales. In this work, using Vibrio cholerae as a model, we show that shared diffusible biofilm matrix proteins are indeed susceptible to cheater exploitation and that the evolutionary stability of producing these matrix components fundamentally depends on biofilm spatial structure, intrinsic sharing mechanisms of these components, and flow conditions in the environment. We further show that exploitation of diffusible adhesion proteins is localized within a well-defined spatial range around cell clusters that produce them. Based on this exploitation range and the spatial distribution of cell clusters, we constructed a model of costly diffusible matrix production and related these length scales to the relatedness coefficient in social evolution theory. Our results show that production of diffusible biofilm matrix components is evolutionarily stable under conditions consistent with natural biofilm habitats and host environments. We expect the mechanisms revealed in this study to be relevant to other secreted factors that operate as cooperative public goods in bacterial communities and the concept of exploitation range and the associated analysis tools to be generally applicable.

Prediction Challenge: Simulating Rydberg photoexcited cyclobutanone with surface hopping dynamics based on different electronic structure methods.

This research examines the nonadiabatic dynamics of cyclobutanone after excitation into the n → 3s Rydberg S2 state. It stems from our contribution to the Special Topic of the Journal of Chemical Physics to test the predictive capability of computational chemistry against unseen experimental data. Decoherence-corrected fewest-switches surface hopping was used to simulate nonadiabatic dynamics with full and approximated nonadiabatic couplings. Several simulation sets were computed with different electronic structure methods, including a multiconfigurational wavefunction [multiconfigurational self-consistent field (MCSCF)] specially built to describe dissociative channels, multireference semiempirical approach, time-dependent density functional theory, algebraic diagrammatic construction, and coupled cluster. MCSCF dynamics predicts a slow deactivation of the S2 state (10 ps), followed by an ultrafast population transfer from S1 to S0 (<100 fs). CO elimination (C3 channel) dominates over C2H4 formation (C2 channel). These findings radically differ from the other methods, which predicted S2 lifetimes 10-250 times shorter and C2 channel predominance. These results suggest that routine electronic structure methods may hold low predictive power for the outcome of nonadiabatic dynamics.

Temperature effects on the internal conversion of excited adenine and adenosine.

This work aims to elucidate the dependence of the excited-state lifetime of adenine and adenosine on temperature. So far, it has been experimentally shown that while adenine's lifetime is unaffected by temperature, adenosine's lifetime strongly depends on it. However, the non-Arrhenius temperature dependence has posed a challenge in explaining this phenomenon. We used surface hopping to simulate the dynamics of adenine and adenosine in the gas phase at 0 and 400 K. The temperature effects were observed under the initial conditions via Wigner sampling with thermal corrections. Our results confirm that adenine's excited-state lifetime does not depend on temperature, while adenosine's lifetime does. Adenosine's dependency is due to intramolecular vibrational energy transfer from adenine to the ribose group. At 0 K, this transfer reduced the mean kinetic energy of adenine's moiety so much that internal conversion is inhibited, and the lifetime elongated by a factor of 2.3 compared to that at 400 K. The modeling also definitively ruled out the influence of viscosity, which was proposed as an alternative explanation previously.

Clinical significance of differential serum-signatures for early prediction of severe dengue among Eastern Indian patients.

Dengue infection can result in simple dengue fever or life-threatening severe dengue. Early identification of severe patients is needed for proper disease management. Dengue infection was screened among 168 symptomatic patients by qRT-PCR, anti-dengue IgM, and IgG ELISA. Dengue patients were categorized according to WHO classification. Viral load and dengue serotypes were determined by qRT-PCR. Levels of acute-phase-proteins (SAP, SAA2; CRP and ApoA1), endothelial (Ang2, VEGF), coagulation (fibrinogen) markers were determined by sandwich ELISA/immunoturbidimetry/western-blotting. Hepatic (ALT, AST, ALP) and other blood biochemical parameters were studied by autoanalyzer and haematology cell counter. Statistical analysis and protein-protein-interaction network were performed by GraphPad-Prism and STRINGS database, respectively. Among 87 dengue patients, significantly higher levels of Ang2, VEGF, CRP, SAA2, ApoA1, AST, ALT, and AST/ALT ratio and low level of fibrinogen were detected in severe-dengue cases compared to dengue without warning-signs, with seven of them severely altered during febrile-phase. Higher fold-change of Ang2 and VEGF as well as decreased fibrinogen were observed among patients with haemorrhagic-manifestation, clinical-fluid accumulation and thrombocytopenia. Functional network analysis predicted Ang2, VEGF, and CRP to be functionally and physically connected and SAA2 and ApoA1 to be functioning together. Correlation analyses also validated this connectivity by a strong positive correlation between Ang2, VEGF, and CRP. PCA analysis followed by hierarchical clustering heatmap analysis segregated severe-dengue patients from the rest, with VEGF, Ang2, ApoA1, AST, and ALT clearly distinguishing the severe-dengue group. Thus, serum levels of VEGF, Ang2, ApoA1, AST, and ALT might act as potential biomarkers for predicting dengue severity during the early stage.

IL-6 dependent expansion of inflammatory MDSCs (CD11b+ Gr-1+) promote Th-17 mediated immune response during experimental cerebral malaria.

Myeloid derived suppressor cells (MDSCs) are a group of heterogeneous cell populations that can suppress T cell responses. Various aspects of MDSCs in regulating immune responses in several cancer and infectious diseases have been reported till date. But the role and regulation of MDSCs have not been systematically studied in the context of malaria. This study depicts the phenotypic and functional characteristics of splenic MDSCs and how they regulate Th-17 mediated immune response during Experimental Cerebral Malaria (ECM). Flow cytometric analysis reveals that MDSCs in the spleen and bone marrow expand at 8 dpi during ECM. Among subtypes of MDSCs, PMN-MDSCs show significant expansion in the spleen but M-MDSCs remain unaltered. Functional analysis of sorted MDSCs from spleens of Plasmodium berghei ANKA (PbA) infected mice shows suppressive nature of these cells and high production of Nitric oxide (NO). Besides, MDSCs were also found to express various inflammatory markers during ECM suggesting the M1 type phenotype of these cells. In-vivo depletion of MDSCs by the use of Anti Gr-1 increases mice survival but doesn't significantly alter the parasitemia. Previously, it has been reported that Treg/Th-17 balance in the spleen is skewed towards Th-17 during ECM. Depletion of MDSCs was found to regulate Th-17 percentages to homeostatic levels and subvert various inflammatory changes in the spleen. Among different factors, IL-6 was found to play an important role in the expansion of MDSCs and expression of inflammatory markers on MDSCs in a STAT3-dependent manner. These findings provide a unique insight into the role of IL-6 in the expansion of the MDSC population which causes inflammatory changes and increased Th-17 responses during ECM.

Importance of NFκß, IL-10 serum levels and DC-SIGN polymorphic haplotypes in determining dengue disease severity among eastern Indian patients.

OBJECTIVES: Dengue viral (DENV) infection is most prevalent arboviral infection in India resulting in wide-range of symptomatic manifestation from simple (DF) to severe dengue (SD). DENV is internalized by dendritic cell receptor, DC-SIGN, which in turn activates inflammatory cytokines: NFκß, IL-10 as adaptive immune response. Present study focused on role of DC-SIGN polymorphisms and these cytokines in SD development among eastern Indian patients. METHOD: DC-SIGN polymorphisms (rs735239, rs4804803, rs2287886) and NFκß, IL-10 concentrations were analysed among 179 dengue patients and 123 healthy individuals by PCR-RFLP and sandwich ELISA, respectively. DENV copies/ml and serotype in patient-sera were measured by quantitative and qualitative real time PCR, respectively. Statistical and haplotype analysis were performed by GraphPad-Prism and SNPStat, respectively. RESULT: Prevalence of DENV serotypes among infected patients: DENV2>DENV4>DENV3>DENV1; those with DENV3 infection reported significantly increased IL-10 level. NFκß and IL-10 concentrations were significantly elevated among SD patients. ROC curve analysis predicted cut-off values of NFκß>13.46 ng/ml and IL-10 > 490.5 pg/ml to detect SD among infected patients with a good sensitivity and specificity. Patients with rs735239-GG, rs2287886-GG genotypes and GGG, GAG haplotypes were significantly associated with SD development, whereas, those with rs4804803-AG exhibited high DENVcopies/ml. Patients with these haplotypes also demonstrated increased NFκß and IL-10. CONCLUSION: This study emphasised importance of DC-SIGN GGG and GAG haplotypes, NFκß and IL-10 concentrations in WHO-defined severe dengue development among infected patients.

Modeling Spin-Crossover Dynamics.

In this article, we review nonadiabatic molecular dynamics (NAMD) methods for modeling spin-crossover transitions. First, we discuss different representations of electronic states employed in the grid-based and direct NAMD simulations. The nature of interstate couplings in different representations is highlighted, with the main focus on nonadiabatic and spin-orbit couplings. Second, we describe three NAMD methods that have been used to simulate spin-crossover dynamics, including trajectory surface hopping, ab initio multiple spawning, and multiconfiguration time-dependent Hartree. Some aspects of employing different electronic structure methods to obtain information about potential energy surfaces and interstate couplings for NAMD simulations are also discussed. Third, representative applications of NAMD to spin crossovers in molecular systems of different sizes and complexities are highlighted. Finally, we pose several fundamental questions related to spin-dependent processes. These questions should be possible to address with future methodological developments in NAMD.

Fungal disease suppression and growth promotion potential of endophytic bacteria from ethnomedicinal plants.

103 bacterial isolates obtained from 8 ethnomedicinal plants in Manipur, India were studied for antifungal and plant growth promoting (PGP) activities. Forty-six (46), out of 62 antifungal isolates, showed potent activities against R. solani. Since R. solani (RS), a sheath blight pathogen, threatens rice yields worldwide, the present study was aimed at discovering promising bioinoculants with anti-RS and PGP potential on rice. Twenty-nine (29) endophytic isolates exhibiting promising anti-RS and PGP activities were subjected to seed vigor assays on rice (var. Jatra) and 16 were found to enhance rice seedling vigour by 70% or more over the control. Four (4) strains, Streptomyces sp. (AcRz21), Alkalihalobacillus sp. (PtL11), Bacillus sp. (TgIb5), and Priestia sp. (TgIb12) with the highest vigor indices were studied for growth promotion of rice in field conditions under pathogen-challenged and pathogen-free conditions. These bioactive strains were able to significantly enhance root and shoot biomass and reduce lesion heights caused by R. solani.

Simulations of molecular photodynamics in long timescales.

Nonadiabatic dynamics simulations in the long timescale (much longer than 10 ps) are the next challenge in computational photochemistry. This paper delimits the scope of what we expect from methods to run such simulations: they should work in full nuclear dimensionality, be general enough to tackle any type of molecule and not require unrealistic computational resources. We examine the main methodological challenges we should venture to advance the field, including the computational costs of the electronic structure calculations, stability of the integration methods, accuracy of the nonadiabatic dynamics algorithms and software optimization. Based on simulations designed to shed light on each of these issues, we show how machine learning may be a crucial element for long time-scale dynamics, either as a surrogate for electronic structure calculations or aiding the parameterization of model Hamiltonians. We show that conventional methods for integrating classical equations should be adequate to extended simulations up to 1 ns and that surface hopping agrees semiquantitatively with wave packet propagation in the weak-coupling regime. We also describe our optimization of the Newton-X program to reduce computational overheads in data processing and storage. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.

Pre-Dewar structure modulates protonated azaindole photodynamics.

Recent experimental work revealed that the lifetime of the S3 state of protonated 7-azaindole is about ten times longer than that of protonated 6-azaindole. We simulated the nonradiative decay pathways of these molecules using trajectory surface hopping dynamics after photoexcitation into S3 to elucidate the reason for this difference. Both isomers mainly follow a common ππ* relaxation pathway involving multiple state crossings while coming down from S3 to S1 in the subpicosecond time scale. However, the simulations reveal that the excited-state topographies are such that while the 6-isomer can easily access the region of nonadiabatic transitions, the internal conversion of the 7-isomer is delayed by a pre-Dewar bond formation with a boat conformation.

Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium between excited states.

Pyrene fluorescence after a high-energy electronic excitation exhibits a prominent band shoulder not present after excitation at low energies. The standard assignment of this shoulder as a non-Kasha emission from the second-excited state (S2) has been recently questioned. To elucidate this issue, we simulated the fluorescence of pyrene using two different theoretical approaches based on vertical convolution and nonadiabatic dynamics with nuclear ensembles. To conduct the necessary nonadiabatic dynamics simulations with high-lying electronic states and deal with fluorescence timescales of about 100 ns of this large molecule, we developed new computational protocols. The results from both approaches confirm that the band shoulder is, in fact, due to S2 emission. We show that the non-Kasha behavior is a dynamic-equilibrium effect not caused by a metastable S2 minimum. However, it requires considerable vibrational energy, which can only be achieved in collisionless regimes after transitions into highly excited states. This strict condition explains why the S2 emission was not observed in some experiments.

Bifurcations and hydra effects in Bazykin's predator-prey model.

We consider Bazykin's model to address harvesting induced stability exchanges through bifurcation analysis. We examine the existence of hydra effects and analyze the stock pattern under predator harvesting. Prey harvesting cannot produce hydra effects in our model, whereas predator harvesting may cause multiple hydra effects. Our study reveals that type II response function and mutual interference among predators jointly induce multiple hydra effects and bistability. Bifurcations such as single Hopf-bifurcation, multiple Hopf-bifurcations and multiple saddle-node bifurcations appear for increasing harvesting rate on the predators. However, over-exploitation of the predators cannot generate any such bifurcation in our study. In simulations, the maximum sustainable yield (MSY) exists at a globally stable state. When predator is culled under increasing effort, basin of attraction of the equilibrium corresponding to the higher predator stock gets expanded, which alternatively is in favor of stock benefit for predators. The ecological theory developed in this study might be useful to understand conservation policy and fishery management.

Differential genotypic signatures of Toll-like receptor polymorphisms among dengue-chikungunya mono- and co-infected Eastern Indian patients.

Dengue (DENV) and chikungunya (CHIKV) viral infections trigger high patient morbidity and mortality. Mono-/co-infection of these viruses activates innate immune response, triggering Toll-like receptor (TLR) pathways. The present study investigated the differential role of TLR3, 7 and 8 single-nucleotide polymorphisms (SNPs) between mono- and co-infected Eastern Indian patients. Interaction of TLR polymorphic variants with signal peptidase complex (SPC18) was explored which might affect immune signalling against DENV/CHIKV infections. Out of 550 febrile symptomatic patients, 128 DENV-CHIKV co-infected samples were genotyped for eight SNPs of TLR3 (rs3775290-chr4:186083063), TLR7 (rs179008-chrX:12885540, rs5741880-chrX:12869297, rs179010-chrX:12884766, rs3853839-chrX:12889539) and TLR8 (rs5744080-chrX:12919685, rs3764879-chrX:12906578, rs3764880-chrX:12906707) by PCR-RFLP along with 157 healthy individuals. Statistical analysis established genotypic association of TLR SNPs with DENV-CHIKV co-infection, and difference between mono- and co-infected patients and their role in determining high viral load (HVL) during competitive viral replication among co-infected patients. In silico protein-protein docking evaluated interactive effect of TLR variants with SPC18. The findings revealed patients with CC genotypes of TLR7 and 8 SNPs were significantly susceptible towards co-infection, whereas specific genotypes of TLR7 and 8 imparted protection against co-infection. Differential analysis between mono-/co-infected patients revealed distinct genotypic distribution of TLR3, 7 and 8 SNPs. Co-infected patients with TT-rs179010 exhibited DENV-HVL, whereas CHIKV-HVL was detected among patients with other genotypes. Molecular docking of TLR7-rs179008 Q variant and TLR8-rs3764880 V variant with SPC18 generated better free binding energy. This study underlined the importance of TLR7 and 8 SNPs towards mono-/co-infection of DENV/CHIKV, with certain genotypes associated with co-infection susceptibility. Moreover, it suggested a probable role of specific genotypes of TLR7 and 8 polymorphisms imparting high dengue/chikungunya viral load among co-infected patients.

Intersystem crossing and internal conversion dynamics with GAIMS-TeraChem: Excited state relaxation in 2-cyclopentenone.

Excited states relaxation in complex molecules often involves two types of nonradiative transitions, internal conversion (IC) and intersystem crossing (ISC). In the situations when the timescales of IC and ISC are comparable, an interplay between these two types of transitions can lead to complex nonadiabatic dynamics on multiple electronic states of different characters and spin multiplicities. We demonstrate that the generalized ab initio multiple spawning (GAIMS) method interfaced with the fast graphics processing unit-based TeraChem electronic structure code can be used to model such nonadiabatic dynamics involving both the IC and ISC transitions in molecules of moderate size. We carried out 1500 fs GAIMS simulations leading to the creation of up to 2500 trajectory basis functions to study the excited states relaxation in 2-cyclopentenone. After a vertical excitation from the ground state to the bright S2 state, the molecule quickly relaxes to the S1 state via conical intersection. The following relaxation proceeds along two competing pathways: one involves IC to the ground state, and the other is dominated by ISC to the low-lying triplet states. The time constants describing the population transfer between the six lowest singlet and triplet states predicted by the GAIMS dynamics are in good agreement with the characteristic times of IC and ISC obtained from the analysis of the time-resolved photoelectron spectrum.

Partial impairment of late-stage autophagic flux in murine splenocytes leads to sqstm1/p62 mediated nrf2-keap1 antioxidant pathway activation and induced proteasome-mediated degradation in malaria.

Splenomegaly, a major symptom in Plasmodium infection, is extensively studied for its immunopathological role in mice malaria model infected with Plasmodium berghei ANKA. The status of autophagic regulation in hosts in malaria pathogenesis remains unreported till date. This study demonstrated the autophagy, proteasomal degradation and NRF2-KEAP1 antioxidant pathway status in the host during Plasmodium infection taking murine spleen as our organ of interest. Initial staining and autophagic gene expression indicate a possibility of autophagic pathway activation. Although the conversion of LC3A to LC3B and lysosome-autophagosome fusion increases, the final degradation step remains incomplete. Resultant upregulation of p62 and its altered phosphorylated status enhances its binding to keap1 causing NRF2 translocation to the nucleus. NRF2 act as transcription factor upregulating p62 level itself leading to an autoinduction loop of p62 expression. Interestingly, enhancement of P62 interaction with proteasome subunit RPT1 indicates a possible role in transporting ubiquitinated cargo to proteasome complex. Ubiquitination level increased with subsequent upregulation of all three modes of proteasomal degradation i.e trypsin-like, caspase-like and especially chymotrypsin-like. Sqstm1/p62 plays a critical central role in regulating autophagy, proteasomal degradation, and NRF2-KEAP1 pathway. The incomplete autophagic flux in the final step may be a key therapeutic target, as autophagic degradation and subsequent pathogenic peptide presentation is of utmost necessity for downstream immune response.

Association of serum C-reactive protein level and polymorphisms with susceptibility to dengue infection and severe clinical outcome among eastern Indian patients.

Dengue virus (DENV) infection is a major public health concern in India ranging from simple febrile illness to severe outcome. This study aimed to investigate association of serum CRP level and CRP gene polymorphisms towards development of dengue disease susceptibility and severity among eastern Indian patients. Blood was collected from 348 symptomatic patients. Sera was subjected to serological diagnosis for the presence of anti-dengue IgM, anti-dengue IgG antibodies and dengue NS1 antigen by ELISA. Viral RNA was extracted and the presence of DENV genome, viral load, serotypes was determined by qRT-PCR. CRP level and polymorphisms were determined by immunoturbidimetry and polymerase chain reaction-restriction fragment length polymorphism, respectively. Statistical analysis was performed by GraphPad-Prism. Among 206 dengue patients, CRP level increased significantly among patients within acute phase, and patients with qRT-PCR/NS1 antigen positivity, high viral load (HVL), secondary infection, and DENV4 and DENV2 infections. rs3091244, TT genotype positively associated with dengue susceptibility (p = 0.03). CT genotype of rs3093059 and TT genotype of rs3091244 were found to correlate with elevated CRP level and development of WHO-defined warning signs. TT genotype of rs3091244 was more prevalent among HVL patients. Thus, these CRP polymorphic variants and CRP concentration might act as potential prognostic biomarkers for predicting disease severity among acute-stage dengue patients.

"Dial-In" Emission from a Unique Flexible Material with Polarization Tuneable Spectral Intensity.

The development of organic photoluminescent materials, which show promising roles as catalysts, sensors, organic light-emitting diodes, logic gates, etc., is a major demand and challenge for the global scientific community. In this context, a photoclick polymerization method is adopted for the growth of a unique photoluminescent three-dimensional (3D) polymer film, E, as a model system that shows emission tunability over the range 350-650 nm against the excitation range 295-425 nm. The DFT analysis of energy calculations and π-stacking supports the spectroscopic observations for the material exhibiting a broad range of emission owing to newly formed chromophoric units within the film. Full polarization spectroscopic Mueller matrix studies were employed to extract and quantify the molecular orientational order of both the ground (excitation) and excited (emission) state anisotropies through a set of newly defined parameters, namely the fluorescence diattenuation and fluorescence polarizance. The information contained in the recorded fluorescence Mueller matrix of the organic polymer material provided a useful way to control the spectral intensity of emission by using pre- and post-selection of polarization states. The observation was based on the assumption that the longer lifetime of the excited dipolar orientation is attributed to the compactness of the film.

Feather degradation by keratinolytic bacteria and biofertilizing potential for sustainable agricultural production.

Feathers account for 5-7% of the total weight of chicken have become one of the major pollutants due to their recalcitrant nature. Feather which is constituted of 90% keratin can be a good source of peptides, amino acids, and minerals for use as organic fertilizer. Traditional feather degradation methods consume large amount of energy and reduces the overall quality of the proteins. However, degradation of keratin by keratinolytic bacteria may represent as an alternative for the development of cheap, cost effective, eco-friendly, and easily available nitrogen (N) and minerals rich source as potential organic fertilizers. Keratinase enzymes from bacteria are serine-type proteases showing optimal activity at pH 6 to 9 and 30 to 50 °C. Mechanism of degradation includes, sulfitolysis, proteolysis, followed by deamination. Keratinolytic bacteria showing antagonism against important plant pathogens may act as biocontrol agent. Feather hydrolyzate can also be employed as nitrogenous fertilizers for plant growth. Tryptophan release from the feather degradation can act as precursor for plant phytohormone, indole-3-acetic acid (IAA). Solubilization of inorganic phosphate (P) by keratinolytic bacteria may further elevate the growth of plant. Application of hydrolyzate increases the water holding capacity, N, carbon (C) and mineral content of the soil. It elevates protein, amino acids, and chlorophyll content of plant. Feather hydrolyzate enhances seed germination and growth of plant. Soil application further increases the population of beneficial bacteria. The use of keratinolytic bacteria having antagonistic and plant growth promoting activities, and feather hydrolyzate can emerge as sustainable and alternative tools to promote and improve organic farming, agro-ecosystem, environment, human health, and soil biological activities.

Beyond Born-Oppenheimer theory for ab initio constructed diabatic potential energy surfaces of singlet H3+ to study reaction dynamics using coupled 3D time-dependent wave-packet approach.

The workability of beyond Born-Oppenheimer theory to construct diabatic potential energy surfaces (PESs) of a charge transfer atom-diatom collision process has been explored by performing scattering calculations to extract accurate integral cross sections (ICSs) and rate constants for comparison with most recent experimental quantities. We calculate non-adiabatic coupling terms among the lowest three singlet states of H3+ system (11A', 21A', and 31A') using MRCI level of calculation and solve the adiabatic-diabatic transformation equation to formulate the diabatic Hamiltonian matrix of the same process [S. Mukherjee et al., J. Chem. Phys. 141, 204306 (2014)] for the entire region of nuclear configuration space. The nonadiabatic effects in the D+ + H2 reaction has been studied by implementing the coupled 3D time-dependent wave packet formalism in hyperspherical coordinates [S. Adhikari and A. J. C. Varandas, Comput. Phys. Commun. 184, 270 (2013)] with zero and non-zero total angular momentum (J) on such newly constructed accurate (ab initio) diabatic PESs of H3+. We have depicted the convergence profiles of reaction probabilities for the reactive non-charge transfer, non-reactive charge transfer, and reactive charge transfer processes for different collisional energies with respect to the helicity (K) and total angular momentum (J) quantum numbers. Finally, total and state-to-state ICSs are calculated as a function of collision energy for the initial rovibrational state (v = 0, j = 0) of the H2 molecule, and consequently, those quantities are compared with previous theoretical and experimental results.