Empty Sites Research Articles

Elastic coupling power stroke mechanism of the F1-ATPase molecular motor

The angular velocity profile of the 120° F1-ATPase power stroke was resolved as a function of temperature from 16.3 to 44.6 °C using a ΔμATP = -31.25 kBT at a time resolution of 10 μs. Angular velocities during the first 60° of the power stroke (phase 1) varied inversely with temperature, resulting in negative activation energies with a parabolic dependence. This is direct evidence that phase 1 rotation derives from elastic energy (spring constant, κ = 50 kBT·rad-2). Phase 2 of the power stroke had an enthalpic component indicating that additional energy input occurred to enable the γ-subunit to overcome energy stored by the spring after rotating beyond its 34° equilibrium position. The correlation between the probability distribution of ATP binding to the empty catalytic site and the negative Ea values of the power stroke during phase 1 suggests that this additional energy is derived from the binding of ATP to the empty catalytic site. A second torsion spring (κ = 150 kBT·rad-2; equilibrium position, 90°) was also evident that mitigated the enthalpic cost of phase 2 rotation. The maximum ΔGǂ was 22.6 kBT, and maximum efficiency was 72%. An elastic coupling mechanism is proposed that uses the coiled-coil domain of the γ-subunit rotor as a torsion spring during phase 1, and then as a crankshaft driven by ATP-binding-dependent conformational changes during phase 2 to drive the power stroke.

Temperature-programmed desorption of CO2, formed by CO photooxidation on TiO2 surface

Temperature-programmed desorption (TPD) spectra of CO2, remaining on the dehydroxylated powder TiO2 (anatase and rutile) surface after photooxidation of CO at T = 293 K, were analysed. It was shown that the CO2 TPD peak appears at T > 400 K, has a symmetric shape, and its maximum position (Tm) depends on the CO2 coverage: the lower is the CO2 amount, the higher is the Tm value. The CO2 TPD peak is well fitted with the second-order desorption kinetics with Edes = 1.15 ± 0.05 eV and ν = 0.32 ± 0.02 cm2 s−1 for anatase and Edes = 1.24 ± 0.05 eV and ν = 0.16 ± 0.01 cm2 s−1 for rutile. The desorption process can be interpreted as monomolecular desorption of carbonate species with two types of precursor states: 1) “over an empty site” and 2) “over a filled site”. It was supposed that CO2 thermal desorption resulted from migration of strongly bonded carbonate species (CO3) along the surface (via the precursor state “over an empty site”) and interaction of them (desorption from precursor state “over a filled site”).

Random growth lattice filling model of percolation: a crossover from continuous to discontinuous transition

A random growth lattice filling model of percolation with a touch and stop growth rule is developed and studied numerically on a two dimensional square lattice. Nucleation centers are continuously added one at a time to the empty lattice sites and clusters are grown from these nucleation centers with a growth probability g. For a given g (), the system passes through a critical point during the growth process where the transition from a disconnected to a connected phase occurs. The model is found to exhibit second order continuous percolation transitions as ordinary percolation for whereas for it exhibits weak first order discontinuous percolation transitions. The continuous transitions are characterized by estimating the values of the critical exponents associated with the order parameter fluctuation and the fractal dimension of the spanning cluster over the whole range of g. The discontinuous transitions, however, are characterized by a compact spanning cluster, lattice size independent fluctuation of the order parameter per lattice, departure from power law scaling in the cluster size distribution and weak bimodal distribution of the order parameter. The nature of transitions are further confirmed by studying the Binder cumulant. Instead of a sharp tricritical point, a tricritical region is found to occur for 0.5 < g < 0.8 within which the values of the critical exponents change continuously until the crossover from continuous to discontinuous transition is completed.

Ring-through-ring molecular shuttling in a saturated [3]rotaxane.

Mechanically interlocked molecules such as rotaxanes and catenanes comprise two or more components whose motion relative to each other can be controlled. A [2]rotaxane molecular shuttle, for example, consists of an axle bearing two recognition sites and a single macrocyclic wheel that can undergo a to-and-fro motion along the axle-shuttling between the recognition sites. The ability of mechanically interlocked molecules to undergo this type of large-amplitude change is the core mechanism behind almost every interlocked molecular switch or machine, including sophisticated mechanical systems such as a molecular elevator and a peptide synthesizer. Here, as a way to expand the scope of dynamics possible at the molecular level, we have developed a molecular shuttling mechanism involving the exchange of rings between two recognition sites in a saturated [3]rotaxane (one with no empty recognition sites). This was accomplished by passing a smaller ring through a larger one, thus achieving ring-through-ring molecular shuttling.

Effect of self-deflection on a totally asymmetric simple exclusion process with functions of site assignments

This study proposes a model of a totally asymmetric simple exclusion process on a single-channel lane with functions of site assignments along the pit lane. The system model attempts to insert a new particle to the leftmost site at a certain probability by randomly selecting one of the empty sites in the pit lane, and reserving it for the particle. Thereafter, the particle is directed to stop at the site only once during its travel. Recently, the system was determined to show a self-deflection effect, in which the site usage distribution biases spontaneously toward the leftmost site, and the throughput becomes maximum when the site usage distribution is slightly biased to the rightmost site. Our exact analysis describes this deflection effect and show a good agreement with simulations.

Elucidating the Role of the Boronic Esters in the Suzuki-Miyaura Reaction: Structural, Kinetic, and Computational Investigations.

The Suzuki-Miyaura reaction is the most practiced palladium-catalyzed, cross-coupling reaction because of its broad applicability, low toxicity of the metal (B), and the wide variety of commercially available boron substrates. A wide variety of boronic acids and esters, each with different properties, have been developed for this process. Despite the popularity of the Suzuki-Miyaura reaction, the precise manner in which the organic fragment is transferred from boron to palladium has remained elusive for these reagents. Herein, we report the observation and characterization of pretransmetalation intermediates generated from a variety of commonly employed boronic esters. The ability to confirm the intermediacy of pretransmetalation intermediates provided the opportunity to clarify mechanistic aspects of the transfer of the organic moiety from boron to palladium in the key transmetalation step. A series of structural, kinetic, and computational investigations revealed that boronic esters can transmetalate directly without prior hydrolysis. Furthermore, depending on the boronic ester employed, significant rate enhancements for the transfer of the B-aryl groups were observed. Overall, two critical features were identified that enable the transfer of the organic fragment from boron to palladium: (1) the ability to create an empty coordination site on the palladium atom and (2) the nucleophilic character of the ipso carbon bound to boron. Both of these features ultimately relate to the electron density of the oxygen atoms in the boronic ester.

Microvascular Decompression for Classical Trigeminal Neuralgia Caused by Venous Compression: Novel Anatomic Classifications and Surgical Strategy

Microvascular decompression of the trigeminal nerve is the most effective treatment for trigeminal neuralgia. However, when encountering classical trigeminal neuralgia caused by venous compression, the procedure becomes much more difficult, and failure or recurrence because of incomplete decompression may become frequent. This study aimed to investigate the anatomic variation of the culprit veins and discuss the surgical strategy for different types. We performed a retrospective analysis of 64 consecutive cases in whom veins were considered as responsible vessels alone or combined with other adjacent arteries. The study classified culprit veins according to operative anatomy and designed personalized approaches and decompression management according to different forms of compressive veins. Curative effects were assessed by the Barrow Neurological Institute (BNI) pain intensity score and BNI facial numbness score. The most commonly encountered veins were the superior petrosal venous complex (SPVC), which was artificially divided into 4 types according to both venous tributary distribution and empty point site. We synthetically considered these factors and selected an approach to expose the trigeminal root entry zone, including the suprafloccular transhorizontal fissure approach and infratentorial supracerebellar approach. The methods of decompression consist of interposing and transposing by using Teflon, and sometimes with the aid of medical adhesive. Nerve combing (NC) of the trigeminal root was conducted in situations of extremely difficult neurovascular compression, instead of sacrificing veins. Pain completely disappeared in 51 patients, and the excellent outcome rate was 79.7%. There were 13 patients with pain relief treated with reoperation. Postoperative complications included 10 cases of facial numbness, 1 case of intracranial infection, and 1 case of high-frequency hearing loss. The accuracy recognition of anatomic variation of the SPVC is crucial for the management of classical trigeminal neuralgia caused by venous compression. Selecting an appropriate approach and using reasonable decompression methods can bring complete postoperative pain relief for most cases. NC can be an alternative choice for extremely difficult cases, but it could lead to facial numbness more frequently.

How spatial structure and neighbor uncertainty promote mutualists and weaken black queen effects

The ubiquity of cooperative cross-feeding (a resource-exchange mutualism) raises two related questions: Why is cross-feeding favored over self-sufficiency, and how are cross-feeders protected from non-producing cheaters? The Black Queen Hypothesis suggests that if leaky resources are costly, then there should be selection for either gene loss or self-sufficiency, but selection against mutualistic inter-dependency. Localized interactions have been shown to protect mutualists against cheaters, though their effects in the presence of self-sufficient organisms are not well understood. Here we develop a stochastic spatial model to examine how spatial effects alter the predictions of the Black Queen Hypothesis. Microbes need two essential resources to reproduce, which they can produce themselves (at a cost) or take up from neighbors. Additionally, microbes need empty sites to give birth into. Under well mixed mean-field conditions, the cross-feeders will always be displaced by a non-producer and a self-sufficient microbe. However, localized interactions have two effects that favor production. First, a microbe that interacts with a small number of neighbors will not always receive the essential resources it needs; this effect slightly harms cross-feeders but greatly harms non-producers. Second, microbes tend to displace other microbes that produce resources they need; this effect also slightly harms cross-feeders but greatly harms non-producers. Our work therefore suggests localized interactions produce an accelerating cost of non-production. Thus, the right trade-off between the cost of producing resources and the cost of sometimes being resource-limited can favor mutualistic inter-dependence over both self-sufficiency and non-production.

Ab initio simulation of structure and surface energy of low-index surfaces of stoichiometric α-Fe2O3

The structure and surface energy of a series of low-index surfaces of stoichiometric α-Fe2O3 (hematite) are investigated using the periodic Hartree–Fock approach with an a posteriori correction of the correlation energy. The simulations show that, amongst the modeled facets, (011¯2) and (0001) are the most stable surfaces of hematite, which is consistent with the fact that the latter are the dominant growth faces exposed on natural α-Fe2O3. The Fe-terminated (0001) surface is shown to exhibit a large relaxation of the surface atoms. It is argued that this arises mainly due to the fact that the surface cations are located opposite empty cation sites in the filled-filled-unfilled cation sequence along the c-axis. In contrast, the (011¯2) plane cuts the crystal through a plane of empty cation sites, thus giving rise to relatively small relaxations and surface energies. The small relaxations and concomitant exposure of five-coordinate cation sites may be important for the catalytic activity of hematite. The simulations also show that the relative stability of the investigated surfaces changes after a full lattice relaxation with the (0001) and (112¯6) facets relaxing disproportionately large. Wherever possible, the simulations are compared with previous simulation data and experimental results. A Wulff–Gibbs construction is also presented.

Characterising knotting properties of polymers in nanochannels.

Using a lattice model of polymers in a tube, we define one way to characterise different configurations of a given knot as either "local" or "non-local", based on a standard approach for measuring the "size" of a knot within a knotted polymer chain. The method involves associating knot-types to subarcs of the chain, and then identifying a knotted subarc with minimal arclength; this arclength is then the knot-size. If the resulting knot-size is small relative to the whole length of the chain, then the knot is considered to be localised or "local"; otherwise, it is "non-local". Using this definition, we establish that all but exponentially few sufficiently long self-avoiding polygons (closed chains) in a tubular sublattice of the simple cubic lattice are "non-locally" knotted. This is shown to also hold for the case when the same polygons are subject to an external tensile force, as well as in the extreme case when they are as compact as possible (no empty lattice sites). We also provide numerical evidence for small tube sizes that at equilibrium non-local knotting is more likely than local knotting, regardless of the strength of the stretching or compressing force. The relevance of these results to other models and recent experiments involving DNA knots is also discussed.

Neighbor-considered migration facilitates cooperation in prisoner’s dilemma games

Migration (e.g. between cities and nations) has been shown to be an effective mechanism in facilitating the evolution of cooperation in spatial games. In contingent migration (e.g. success-driven migration), individuals choose the relocation place based on their expected payoffs. In other words, success-driven migration assumes that individuals make decisions about where to migrate strategically rather than randomly. Existing behavioral experiments have shown that human have other-regarding preference. In this paper, we study individuals’ cooperation behaviors in the prisoner’s dilemma game on a two-dimensional square lattice, where individuals have other-regarding migration preference. We introduce a neighbor-considered migration strategy, which considers both benefits of individuals and their neighbors. During the migration process, an individual always moves to a reachable empty site with the highest fairness payoff, which takes the benefit of all relevant stakeholders (including the particular individual and the neighbors) into consideration. We explore the effect of the different fairness, while considering the individuals when they weigh their own interests and their neighbors’ interests. Our simulation results indicate that neighbor-considered migration can effectively promote the level of cooperation by helping cooperative clusters evade the invasion of defectors.

Analytical and simulation studies of 2D asymmetric simple exclusion process

Two species of particles driven perpendicularly and interacting through hardcore exclusion on the 2D lattice is studied. Each particle has three moving directions without the back step. Under periodic boundary conditions, an intermediate phase has been found at which some particles could move along the border of jamming stripes. We have performed mean field analysis for the moving and intermediate phase respectively. The analytical results agree with the simulation results well. The empty site moves along the interface of jamming stripes when the system only has one empty site. The average movement of empty site in one Monte Carlo step (MCS) has been analyzed through the master equation. Under open boundary conditions, the system exhibits moving and jamming phases. The critical injection probability αc shows non-monotonically against the forward moving probability q. The analytical results of average velocity, the density and the flow rate against the injection probability in the moving phase also agree with simulation results well.

Cell-size distribution and scaling in a one-dimensional Kolmogorov-Johnson-Mehl-Avrami lattice model with continuous nucleation.

The Kolmogorov-Johnson-Mehl-Avrami (KJMA) growth model is considered on a one-dimensional (1D) lattice. Cells can grow with constant speed and continuously nucleate on the empty sites. We offer an alternative mean-field-like approach for describing theoretically the dynamics and derive an analytical cell-size distribution function. Our method reproduces the same scaling laws as the KJMA theory and has the advantage that it leads to a simple closed form for the cell-size distribution function. It is shown that a Weibull distribution is appropriate for describing the final cell-size distribution. The results are discussed in comparison with Monte Carlo simulation data.

The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology.

Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site. Analysis of these structures suggests that substrate binding induces a domain rotation to close the active site. Such a substrate-induced domain rotation has also been observed in some other GH13 enzymes.

Pop Songs and Solastalgia in a Broken City

Pop Songs and Solastalgia in a Broken City

Chickadees neither win-shift nor win-stay when foraging

The win-shift versus win-stay distinction supposes that foraging animals use one of two movement rules when searching for food: win-stay to return to locations where they previously found food and win-shift to avoid locations where they previously found food. Win-shift and win-stay rules describe, for example, the behaviour of rats foraging in a radial arm maze, the behaviour of animals in delayed matching and nonmatching to sample tasks, and the behaviour of nectarivorous birds feeding on depleting and replenishing nectar sources. The present study investigated whether black-capped chickadees, Poecile atricapillus , searching for food use win-shift and win-stay rules in response to different reward contingencies. Chickadees first searched multiple spatially dispersed sites for food hidden randomly in these sites, then after several minutes returned to find these sites replenished in the win-stay condition, or empty and other sites baited in the win-shift condition. Birds performed no better than chance at returning to baited sites in the win-stay condition or avoiding previously baited sites in the win-shift condition. Instead, chickadees used preferred search patterns regardless of the win-shift or win-stay contingencies they experienced. Search sequences, however, showed greater stereotypy under win-stay than under win-shift conditions even though the locations of baited sites were determined randomly. Chickadees are year-round residents in relatively small home ranges and may forage using well-established movement rules that, in our experiments, led to neither win-stay nor win-shift behaviour. The stereotypy of search does, however, appear to be influenced by win-stay and win-shift foraging outcomes.

A halide-free pyridinium-substituted η3-cycloheptatrienide-Pd complex.

We report the synthesis and characterization of a novel 4-(dimethylamino)pyridinium-substituted η3-cycloheptatrienide-Pd complex which is free of halide ligands. Diacetonitrile{η3-[4-(dimethylamino)pyridinium-1-yl]cycloheptatrienido}palladium(II) bis(tetrafluoroborate), [Pd(C2H3N)2(C14H16N2)](BF4)2, was prepared by the exchange of two bromide ligands for noncoordinating anions, which results in the empty coordination sites being occupied by acetonitrile ligands. As described previously, exchange of only one bromide leads to a dimeric complex, di-μ-bromido-bis({η3-[4-(dimethylamino)pyridinium-1-yl]cycloheptatrienido}palladium(II)) bis(tetrafluoroborate) acetonitrile disolvate, [Pd2Br2(C14H16N2)2](BF4)2·2CH3CN, with bridging bromide ligands, and the crystal structure of this compound is also reported here. The structures of the cycloheptatrienide ligands of both complexes are analogous to the dibromide derivative, showing the allyl bond in the β-position with respect to the pyridinium substituent. This indicates that, unlike a previous interpretation, the main reason for the formation of the β-isomer cannot be internal hydrogen bonding between the cationic substituents and bromide ligands.

Spin-charge separation in atomic chains

Quantum Magnetism Strongly interacting electrons lined up along a string can experience the so-called spin-charge separation, where the electrons “split” into effective carriers of spin and charge, which then move independently. This phenomenon has been observed, somewhat indirectly, in solids. Hilker et al. show spin-charge separation in a direct way by using a one-dimensional (1D) array of cold atoms, playing the role of electrons, whose degrees of freedom of spin and charge can be monitored using a fermionic quantum gas microscope. Empty sites in the 1D lattice moved freely without disturbing the underlying antiferromagnetic order. Science , this issue p. [484][1] [1]: /lookup/doi/10.1126/science.aam8990

Revealing hidden antiferromagnetic correlations in doped Hubbard chains via string correlators.

Topological phases, like the Haldane phase in spin-1 chains, defy characterization through local order parameters. Instead, nonlocal string order parameters can be employed to reveal their hidden order. Similar diluted magnetic correlations appear in doped one-dimensional lattice systems owing to the phenomenon of spin-charge separation. Here we report on the direct observation of such hidden magnetic correlations via quantum gas microscopy of hole-doped ultracold Fermi-Hubbard chains. The measurement of nonlocal spin-density correlation functions reveals a hidden finite-range antiferromagnetic order, a direct consequence of spin-charge separation. Our technique, which measures nonlocal order directly, can be readily extended to higher dimensions to study the complex interplay between magnetic order and density fluctuations.

Coarsening with nontrivial in-domain dynamics: Correlations and interface fluctuations.

Using numerical simulations we investigate the space-time properties of a system in which spirals emerge within coarsening domains, thus giving rise to nontrivial internal dynamics. Initially proposed in the context of population dynamics, the studied six-species model exhibits growing domains composed of three species in a rock-paper-scissors relationship. Through the investigation of different quantities, such as space-time correlations and the derived characteristic length, autocorrelation, density of empty sites, and interface width, we demonstrate that the nontrivial dynamics inside the domains affects the coarsening process as well as the properties of the interfaces separating different domains. Domain growth, aging, and interface fluctuations are shown to be governed by exponents whose values differ from those expected in systems with curvature driven coarsening.