Do theoretical physicists care about the protein-folding problem?

The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.Comment: 27 pages, 4 figures, LaTeX file, aipproc package. To be published in the book: "Meeting on Fundamental Physics 'Alberto Galindo'", Alvarez-Estrada R. F. et al. (Ed.), Madrid: Aula Documental, 200

Lithium Batteries and the Solid Electrolyte Interphase (SEI)—Progress and Outlook

Interfacial dynamics within chemical systems such as electron and ion transport processes have relevance in the rational optimization of electrochemical energy storage materials and devices. Evolving the understanding of fundamental electrochemistry at interfaces would also help in the understanding of relevant phenomena in biological, microbial, pharmaceutical, electronic, and photonic systems. In lithium-ion batteries, the electrochemical instability of the electrolyte and its ensuing reactive decomposition proceeds at the anode surface within the Helmholtz double layer resulting in a buildup of the reductive products, forming the solid electrolyte interphase (SEI). This review summarizes relevant aspects of the SEI including formation, composition, dynamic structure, and reaction mechanisms, focusing primarily on the graphite anode with insights into the lithium metal anode. Furthermore, the influence of the electrolyte and electrode materials on SEI structure and properties is discussed. An update is also presented on state-of-the-art approaches to quantitatively characterize the structure and changing properties of the SEI. Lastly, a framework evaluating the standing problems and future research directions including feasible computational, machine learning, and experimental approaches are outlined

Correction: Resolving nanoscopic structuring and interfacial THz dynamics in setting cements

Correction for ‘Resolving nanoscopic structuring and interfacial THz dynamics in setting cements’ by Fu V. Song et al., Mater. Adv., 2022, 3, 4982–4990, https://doi.org/10.1039/D1MA01002F.Funder: Horizon 2020 Framework Programme; FundRef: https://doi.org/10.13039/10.13039/100010661; Grant(s): ACT, No. 299668 Funder: Engineering and Physical Sciences Research Council; FundRef: https://doi.org/10.13039/10.13039/501100000266; Grant(s): EP/K000128/1, EP/L000202 Funder: Science and Technology Facilities Council; FundRef: https://doi.org/10.13039/10.13039/501100000271; Grant(s): RB1100006, RB1110428 and RB1310334 Funder: Sapienza Università di Roma; FundRef: https://doi.org/10.13039/10.13039/501100004271 Funder: McMaster University; FundRef: https://doi.org/10.13039/10.13039/100009776 Funder: University of British Columbia; FundRef: https://doi.org/10.13039/10.13039/501100005247 Funder: Natural Sciences and Engineering Research Council of Canada; FundRef: https://doi.org/10.13039/10.13039/501100000038; Grant(s): RGPIN 04598, RY

Structure and spectroscopy of CuH prepared via borohydride reduction

Copper(I) hydride (cuprous hydride, CuH) was the first binary metal hydride to be discovered (in 1844) and is singular in that it is synthesized in solution, at ambient temperature. There are several synthetic paths to CuH, one of which involves reduction of an aqueous solution of CuSO(4)·5H(2)O by borohydride ions. The product from this procedure has not been extensively characterized. Using a combination of diffraction methods (X-ray and neutron) and inelastic neutron scattering spectroscopy, we show that the CuH from the borohydride route has the same bulk structure as CuH produced by other routes. Our work shows that the product consists of a core of CuH with a shell of water and that this may be largely replaced by ethanol. This offers the possibility of modifying the properties of CuH produced by aqueous routes

Atomic and vibrational origins of mechanical toughness in bioactive cement during setting

Bioactive glass ionomer cements (GICs) have been in widespread use for ~40 years in dentistry and medicine. However, these composites fall short of the toughness needed for permanent implants. Significant impediment to improvement has been the requisite use of conventional destructive mechanical testing, which is necessarily retrospective. Here we show quantitatively, through the novel use of calorimetry, terahertz (THz) spectroscopy and neutron scattering, how GIC’s developing fracture toughness during setting is related to interfacial THz dynamics, changing atomic cohesion and fluctuating interfacial configurations. Contrary to convention, we find setting is non-monotonic, characterized by abrupt features not previously detected, including a glass–polymer coupling point, an early setting point, where decreasing toughness unexpectedly recovers, followed by stress-induced weakening of interfaces. Subsequently, toughness declines asymptotically to long-term fracture test values. We expect the insight afforded by these in situ non-destructive techniques will assist in raising understanding of the setting mechanisms and associated dynamics of cementitious materials

From Molten Calcium Aluminates through Phase Transitions to Cement Phases

Crystalline calcium aluminates are a critical setting agent in cement. To date, few have explored the microscopic and dynamic mechanism of the transitions from molten aluminate liquids, through the supercooled state to glassy and crystalline phases, during cement clinker production. Herein, the first in situ measurements of viscosity and density are reported across all the principal molten phases, relevant to their eventual crystalline structures. Bulk atomistic computer simulations confirm that thermophysical properties scale with the evolution of network substructures interpenetrating melts on the nanoscale. It is demonstrated that the glass transition temperature (T-g) follows the eutectic profile of the liquidus temperature (T-m), coinciding with the melting zone in cement production. The viscosity has been uniquely charted over 14 decades for each calcium-aluminate phase, projecting and justifying the different temperature zones used in cement manufacture. The fragile-strong phase transitions are revealed across all supercooled phases coinciding with heterogeneous nucleation close to 1.2T(g), where sintering and quenching occur in industrial-scale cement processing

Spectroscopic Evidence for an Oxazolone Structure in Anionic b-Type Peptide Fragments

Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b2 fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800–1800 cm–1 spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b2 fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far