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See detailQuantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions
Stoehr, Martin UL; Tkatchenko, Alexandre UL

in Science Advances (2019), 5(12), 0024

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in ... [more ▼]

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems. [less ▲]

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See detailImpact of nuclear vibrations on van der Waals and Casimir interactions at zero and finite temperature
Venkataram, Prashanth; Hermann, Jan; Vongkovit, Teerit et al

in Science Advances (2019), 5(1), 0456

Recent advances in measuring van der Waals (vdW) interactions have probed forces on molecules at nanometric separations from metal surfaces and demonstrated the importance of infrared nonlocal ... [more ▼]

Recent advances in measuring van der Waals (vdW) interactions have probed forces on molecules at nanometric separations from metal surfaces and demonstrated the importance of infrared nonlocal polarization response and temperature effects, yet predictive theories for these systems remain lacking. We present a theoretical framework for computing vdW interactions among molecular structures, accounting for geometry, short-range electronic delocalization, dissipation, and collective nuclear vibrations (phonons) at atomic scales, along with long-range electromagnetic interactions in arbitrary macroscopic environments. We primarily consider experimentally relevant low-dimensional carbon allotropes, including fullerenes, carbyne, and graphene, and find that phonons couple strongly with long-range electromagnetic fields depending on molecular dimensionality and dissipation, especially at nanometric scales, creating delocalized phonon polaritons that substantially modify infrared molecular response. These polaritons, in turn, alter vdW interaction energies between molecular and macroscopic structures, producing nonmonotonic power laws and nontrivial temperature variations at nanometric separations feasible in current experiments. [less ▲]

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See detailLiquid crystal elastomer shell actuators with negative order parameter
Jampani, Venkata UL; Reguengo De Sousa, Kevin; Ferreira Machado, Joana et al

in Science Advances (2019), 5(4), 1

Liquid crystals (LCs) are nonsolids with long-range orientational order, described by a scalar order parameter ⟨P2⟩=1/2⟨3cos2β−1⟩. Despite the vast set of existing LC materials, one-third of the order ... [more ▼]

Liquid crystals (LCs) are nonsolids with long-range orientational order, described by a scalar order parameter ⟨P2⟩=1/2⟨3cos2β−1⟩. Despite the vast set of existing LC materials, one-third of the order parameter value range, −1/2< 〈P2〉 < 0, has until now been inaccessible. Here, we present the first material with negative LC order parameter in its ground state, in the form of elastomeric shells. The optical and actuation characteristics are opposite to those of conventional LC elastomers (LCEs). This novel class of anti-ordered elastomers gives access to the previously secluded range of liquid crystallinity with 〈P2〉 < 0, providing new challenges for soft matter physics and adding a complementary type of LCE actuator that is attractive for applications in, e.g., soft robotics [less ▲]

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See detailTheoretical guidelines to create and tune electric skyrmion bubbles
Pereira Goncalves, M. A.; Escorihuela-Sayalero, Carlos; Garca-Fernandez, Pablo et al

in SCIENCE ADVANCES (2019), 5(2),

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See detailReliable and practical computational description of molecular crystal polymorphs
Hoja, Johannes; Ko, Hsin-Yu; Neumann, Marcus A. et al

in Science Advances (2019), 5

Reliable prediction of the polymorphic energy landscape of a molecular crystal would yield profound insight into drug development in terms of the existence and likelihood of late-appearing polymorphs ... [more ▼]

Reliable prediction of the polymorphic energy landscape of a molecular crystal would yield profound insight into drug development in terms of the existence and likelihood of late-appearing polymorphs. However, the computational prediction of molecular crystal polymorphs is highly challenging due to the high dimensionality of conformational and crystallographic space accompanied by the need for relative free energies to within 1 kJ/mol per molecule. In this study, we combine the most successful crystal structure sampling strategy with the most successful first-principles energy ranking strategy of the latest blind test of organic crystal structure prediction methods. Specifically, we present a hierarchical energy ranking approach intended for the refinement of relative stabilities in the final stage of a crystal structure prediction procedure. Such a combined approach provides excellent stability rankings for all studied systems and can be applied to molecular crystals of pharmaceutical importance. [less ▲]

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See detailIncreasing bulk photovoltaic current by strain tuning
Nadupalli, Shankari; Kreisel, Jens UL; Granzow, Torsten

in SCIENCE ADVANCES (2019), 5(3),

Photovoltaic phenomena are widely exploited not only for primary energy generation but also in photocatalytic, photoelectrochemistry, or optoelectronic applications. In contrast to the interface-based ... [more ▼]

Photovoltaic phenomena are widely exploited not only for primary energy generation but also in photocatalytic, photoelectrochemistry, or optoelectronic applications. In contrast to the interface-based photovoltaic effect of semiconductors, the anomalous or bulk photovoltaic effect in ferroelectrics is not bound by the Shockley-Queisser limit and, thus, can potentially reach high efficiencies. Here, we observe in the example of an Fe-doped LiNbO3 bulk single crystal the existence of a purely intrinsic ``piezophotovoltaic'' effect that leads to a linear increase in photovoltaic current density. The increase reaches 75 under a low uniaxial compressive stress of 10 MPa, corresponding to a strain of only 0.005\%. The physical origin and symmetry properties of the effect are investigated, and its potential for strain-tuned efficiency increase in nonconventional photovoltaic materials is presented. [less ▲]

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See detailMultiple-q noncollinear magnetism in an itinerant hexagonal magnet
Takagi, R.; White, J. S.; Hayami, S. et al

in SCIENCE ADVANCES (2018), 4(11),

rticle Figures & Data Info & Metrics eLetters PDF Abstract Multiple-q spin order, i.e., a spin texture characterized by a multiple number of coexisting magnetic modulation vectors q, has recently ... [more ▼]

rticle Figures & Data Info & Metrics eLetters PDF Abstract Multiple-q spin order, i.e., a spin texture characterized by a multiple number of coexisting magnetic modulation vectors q, has recently attracted attention as a source of nontrivial magnetic topology and associated emergent phenomena. One typical example is the triple-q skyrmion lattice state stabilized by Dzyaloshinskii-Moriya interactions in noncentrosymmetric magnets, while the emergence of various multiple-q states of different origins is expected according to the latest theories. Here, we investigated the magnetic structure of the itinerant polar hexagonal magnet Y3Co8Sn4, in which several distinctive mechanisms favoring multiple-q states are allowed to become active. Small-angle neutron-scattering experiments suggest the formation of incommensurate triple-q magnetic order with an in-plane vortex-like spin texture, which can be most consistently explained in terms of the novel four-spin interaction mechanism inherent to itinerant magnets. The present results suggest a new route to realizing exotic multiple-q orders and that itinerant hexagonal magnets, including the R3M8Sn4 family with wide chemical tunability, can be a unique material platform to explore their rich phase diagrams. [less ▲]

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See detailFlagellar number governs bacterial spreading and transport efficiency
Najafi, Javad; Shaebani, Mohammad Reza; John, Thomas et al

in SCIENCE ADVANCES (2018), 4(9),

Peritrichous bacteria synchronize and bundle their flagella to actively swim, while disruption of the bundle leads to a slow motility phase with a weak propulsion. It is still not known whether the number ... [more ▼]

Peritrichous bacteria synchronize and bundle their flagella to actively swim, while disruption of the bundle leads to a slow motility phase with a weak propulsion. It is still not known whether the number of flagella represents an evolutionary adaptation toward optimizing bacterial navigation. We study the swimming dynamics of differentially flagellated Bacillus subtilis strains in a quasi-two-dimensional system. We find that decreasing the number of flagella N-f reduces the average turning angle between two successive run phases and enhances the run time and the directional persistence of the run phase. As a result, having fewer flagella is beneficial for long-distance transport and fast spreading while having a lot of flagella is advantageous for the processes that require a slower spreading, such as biofilm formation. We develop a two-state random walk model that incorporates spontaneous switchings between the states and yields exact analytical expressions for transport properties, in remarkable agreement with experiments. The results of numerical simulations based on our two-state model suggest that the efficiency of searching and exploring the environment is optimized at intermediate values of N-f. The optimal choice of N-f, for which the search time is minimized, decreases with increasing the size of the environment in which the bacteria swim. [less ▲]

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See detailCatalysis beyond frontier molecular orbitals: Selectivity in partial hydrogenation of multi-unsaturated hydrocarbons on metal catalysts
Liu, Wei; Jiang, Yingda; Dostert, Karl-Heinz et al

in Science Advances (2017), 3

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the ... [more ▼]

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the microscopic origins of hydrogenation chemoselectivity, we performed a comprehensive theoretical investigation on the reactivity of two a,b-unsaturated carbonyls—isophorone and acrolein—on seven (111) metal surfaces: Pd, Pt, Rh, Ir, Cu, Ag, and Au. In doing so, we uncover a general mechanism that goes beyond the celebrated frontier molecular orbital theory, rationalizing the C--C bond activation in isophorone and acrolein as a result of significant surface-induced broadening of high-energy inner molecular orbitals. By extending our calculations to hydrogen-precovered surface and higher adsorbate surface coverage, we further confirm the validity of the “inner orbital broadening mechanism” under realistic catalytic conditions. The proposed mechanism is fully supported by our experimental reaction studies for isophorone and acrolein over Pd nanoparticles terminated with (111) facets. Although the position of the frontier molecular orbitals in these molecules, which are commonly considered to be responsible for chemical interactions, suggests preferential hydrogenation of the C--O double bond, experiments show that hydrogenation occurs at the C--C bond on Pd catalysts. The extent of broadening of inner molecular orbitals might be used as a guiding principle to predict the chemoselectivity for a wide class of catalytic reactions at metal surfaces. [less ▲]

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See detailMachine learning of accurate energy-conserving molecular force fields
Chmiela, Stefan; Tkatchenko, Alexandre UL; Sauceda, Huziel et al

in Science Advances (2017), 3

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems— we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate ... [more ▼]

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems— we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. [less ▲]

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See detailGeodetic measurements reveal similarities between post–Last Glacial Maximum and present-day mass loss from the Greenland ice sheet
Knudsen, Shfaqat; Bamber, Ingo; Bevis, Michael et al

in Science Advances (2016), 2(9),

Accurate quantification of the millennial-scale mass balance of the Greenland ice sheet (GrIS) and its contribution to global sea-level rise remain challenging because of sparse in situ observations in ... [more ▼]

Accurate quantification of the millennial-scale mass balance of the Greenland ice sheet (GrIS) and its contribution to global sea-level rise remain challenging because of sparse in situ observations in key regions. Glacial isostatic adjustment (GIA) is the ongoing response of the solid Earth to ice and ocean load changes occurring since the Last Glacial Maximum (LGM; ~21 thousand years ago) and may be used to constrain the GrIS deglaciation history. We use data from the Greenland Global Positioning System network to directly measure GIA and estimate basin wide mass changes since the LGM. Unpredicted, large GIA uplift rates of +12 mm/year are found in southeast Greenland. These rates are due to low upper mantle viscosity in the region, from when Greenland passed over the Iceland hot spot about 40 million years ago. This region of concentrated soft rheology has a profound influence on reconstructing the deglaciation history of Greenland. We reevaluate the evolution of the GrIS since LGM and obtain a loss of 1.5-m sea-level equivalent from the northwest and southeast. These same sectors are dominating modern mass loss. We suggest that the present destabilization of these marine-based sectors may increase sea level for centuries to come. Our new deglaciation history and GIA uplift estimates suggest that studies that use the Gravity Recovery and Climate Experiment satellite mission to infer present-day changes in the GrIS may have erroneously corrected for GIA and underestimated the mass loss by about 20 gigatons/year. [less ▲]

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