| 1. |
- Breznau, Nate, et al.
(författare)
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Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44
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Tidskriftsartikel (refereegranskat)abstract
- This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
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| 2. |
- Aho, Noora, et al.
(författare)
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Scalable Constant pH Molecular Dynamics in GROMACS
- 2022
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:10, s. 6148-6160
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.
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| 3. |
- Bauer, C., et al.
(författare)
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Electron injection and recombination in Ru(dcbpy)(2)(NCS)(2) sensitized nanostructured ZnO
- 2001
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1089-5647 .- 1520-6106 .- 1520-5207. ; 105:24, s. 5585-5588
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Tidskriftsartikel (refereegranskat)abstract
- The dynamics of electron-transfer processes between bis(tetrabutylammonium) cis-bis(thiocyanato)bis(2,2'-bypiridine-4,4'-dicarboxylato)ruthenium(II) (called N719) and nanostructured ZnO films have been investigated by femtosecond and nanosecond spectroscopy. The incident photon to current conversion efficiency (IPCE) for these dye-sensitized electrodes was 36% in the maximum of 530 nm, corresponding to a quantum efficiency of 80%. The highest: IPCE values were obtained when the electrodes were prepared under conditions where formation of dye aggregates in the pores of the nanostructured films is avoided. For such films, the electron injection time was in the subpicosecond regime (< 300 fs), which is comparable to the N719-TiO2 system. The back electron-transfer kinetics between conduction band electrons and oxidized dye molecules were biexponential with time constants of 300 mus and 2.6 us. Variation of the light intensity did not affect the time constants, but only their relative weights. The kinetics of back electron transfer in the N719-ZnO and N719-TiO2 systems were found to be identical.
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| 4. |
- Bauer, Christophe, et al.
(författare)
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Electron injection and recombination in Ru(dcbpy)(2)(NCS)(2) sensitized nanostructured ZnO
- 2001
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Ingår i: JOURNAL OF PHYSICAL CHEMISTRY B. - : AMER CHEMICAL SOC. - 1089-5647. ; 105:24, s. 5585-5588
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Tidskriftsartikel (refereegranskat)abstract
- The dynamics of electron-transfer processes between bis(tetrabutylammonium) cis-bis(thiocyanato)bis(2,2'-bypiridine-4,4'-dicarboxylato)ruthenium(II) (called N719) and nanostructured ZnO films have been investigated by femtosecond and nanosecond spectrosco
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| 5. |
- Bauer, C., et al.
(författare)
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Interfacial electron-transfer dynamics in Ru(tcterpy)(NCS)(3)-sensitized TiO2 nanocrystalline solar cells
- 2002
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 106:49, s. 12693-12704
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Tidskriftsartikel (refereegranskat)abstract
- The anchoring of the ruthenium dye {(C4H9)(4)N}[Ru(Htcterpy)(NCS)(3)] (with tcterpy = 4,4',4-tricarboxy2,2':6',2-terpyridine), the so-called black dye, onto nanocrystalline TiO2 films has been characterized by UV-vis and FT-IR spectroscopies. FT-IR spectroscopy data suggest that dye molecules are bound to the surface by a bidentate binuclear coordination mode. The interfacial electron-transfer (ET) dynamics has been investigated by femtosecond pump-probe transient absorption spectroscopy and nanosecond laser flash photolysis. The electron-injection process from the dye excited state into the TiO2 conduction band is biexponential with a fast component (200 +/- 50 fs) and a slow component (20 ps). These two components can be attributed to the electron injection from the initially formed and the relaxed dye excited states, respectively. Nanosecond kinetic data suggest the existence of two distinguishable regimes (I and II) for the rates of reactions between injected electrons and oxidized dye molecules or oxidized redox species (D+ or I-2(.-)). The frontier between these two regimes is defined by the number of injected electrons per particle (Ne), which was determined to be about 1. The present kinetic study was undertaken within regime I (N-e > 1). Under these conditions, the back-electron-transfer kinetics is comparable to that in systems with other ruthenium complexes adsorbed onto TiO2. The reduction of oxidized dye molecules by iodide results in the formation of I-2(.-) on a very fast time scale (<20 ns). Within regime 1, the decay of I-2(.-) occurs in similar to100 ns via reaction with injected electrons (I-2(.-) + e(-) --> 2I(-)). In regime II (N-e less than or equal to 1), which corresponds to the normal operating conditions of dye-sensitized solar cells, the decay of I-2(.-) is very slow and likely occurs via the dismutation reaction (2I(2)(.-) --> I- + I-3(-)). Our results predict that, under high light intensity (N-e > 1), the quantum efficiency losses in dye-sensitized solar cells will be important because of the dramatic acceleration of the reaction between I-2(.-) and injected electrons. Mechanisms for the ET reactions involving injected electrons are proposed. The relevance of the present kinetic studies for dye-sensitized nanocrystalline solar cells is discussed.
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| 6. |
- Bauer, C., et al.
(författare)
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Ultrafast relaxation dynamics of charge carriers relaxation in ZnO nanocrystalline thin films
- 2004
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 387:03-jan, s. 176-181
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast spectroscopy has been used to study the relaxation processes of charge carriers in ZnO nanocrystalline thin films. A broad red-IR absorption band linked to shallowly trapped electrons was observed by spectroelectrochemical measurements. Femtosecond transient absorption data revealed multiexponential decays of the charge carriers with time constants ranging from 1 to 400 ps. The decay profile of the signal shows a probe wavelength dependence. This effect is assigned to the trapping (localisation) of nonequilibrium charge carriers which occurs on a time scale of similar to1 ps. The recombination of shallowly trapped electrons with deeply trapped holes, determined by single-photon counting, mainly occurs in 400 ps.
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| 7. |
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| 8. |
- Bauer, C., et al.
(författare)
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Ultrafast studies of electron injection in Ru dye sensitized SnO2 nanocrystalline thin film
- 2002
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Ingår i: International Journal of Photoenergy (Online). - 1110-662X .- 1687-529X. ; 4:1, s. 17-20
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Tidskriftsartikel (refereegranskat)abstract
- By using two-color femtosecond transient absorption spectroscopy, we have measured the electron injection rate for bis(tetrabutylammonium) cis di(thiocyanato) bis (2,2-bypiridine-4,4 carboxylic acid) Ruthenium (II) dye ( called N719) into SnO2 nanocrystalline thin films. The electron injection rate has been measured by monitoring the formation of the dye oxidized state and the arrival of electrons in the conduction band. Dynamics of electron injection are multiexponential (0.2, 4 and 130 ps) and are therefore slower than the N719-ZnO or N719-TiO2 systems. The photocurrent action spectrum of N719-SnO2 shows a quantum efficiency of 0.65 at 530 nm proving that efficient charge separation can take place despite of the relatively slow electron injection rate.
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| 9. |
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| 10. |
- Buslaev, Pavel, et al.
(författare)
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Best Practices in Constant pH MD Simulations : Accuracy and Sampling
- 2022
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:10, s. 6148-6160
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Tidskriftsartikel (refereegranskat)abstract
- Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the A-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys. 1996, 105, 2414-2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput. 2022, DOI: 10.1021 /acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on how to set up and perform long time scale constant pH MD simulations. We found that barriers associated with the torsions of side chains in the CHARMM36m force field are too high for reaching convergence in constant pH MD simulations on microsecond time scales. To avoid the high computational cost of extending the sampling, we propose small modifications to the force field to selectively reduce the torsional barriers. We demonstrate that with such modifications we obtain converged distributions of both protonation and torsional degrees of freedom and hence consistent pK(a) estimates, while the sampling of the overall configurational space accessible to proteins is unaffected as compared to normal MD simulations. We also show that the results of constant pH MD depend on the accuracy of the correction potentials. While these potentials are typically obtained by fitting a low-order polynomial to calculated free energy profiles, we find that higher order fits are essential to provide accurate and consistent results. By resolving problems in accuracy and sampling, the work described in this and the accompanying paper paves the way to the widespread application of constant pH MD beyond pK(a) prediction.
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