Dimer Arrangements Research Articles

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

Molecular mechanism of ligand gating and opening of NMDA receptor.

Glutamate transmission and activation of ionotropic glutamate receptors are the fundamental means by which neurons control their excitability and neuroplasticity1. The N-methyl-D-aspartate receptor (NMDAR) is unique among all ligand-gated channels, requiring two ligands-glutamate and glycine-for activation. These receptors function as heterotetrameric ion channels, with the channel opening dependent on the simultaneous binding of glycine and glutamate to the extracellular ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, respectively2,3. The exact molecular mechanism for channel gating by the two ligands has been unclear, particularly without structures representing the open channel and apo states. Here we show that the channel gate opening requires tension in the linker connecting the LBD and transmembrane domain (TMD) and rotation of the extracellular domain relative to the TMD. Using electron cryomicroscopy, we captured the structure of theGluN1-GluN2B(GluN1-2B) NMDAR in its open state bound to a positive allosteric modulator. This process rotates and bends the pore-forming helices in GluN1 and GluN2B, altering the symmetry of the TMD channel from pseudofourfold to twofold. Structures of GluN1-2B NMDAR in apo and single-liganded states showed that binding of either glycine or glutamate alone leads to distinct GluN1-2B dimer arrangements but insufficient tension in the LBD-TMD linker for channel opening. This mechanistic framework identifies a key determinant for channel gating and a potential pharmacological strategy for modulating NMDAR activity.

Assembly of Copper Alkynyl Clusters into Dimensionally Diverse Coordinated Polymers Mediated by Pyridine Ligands.

Surface ligands play crucial roles in modifying the properties of metal nanoclusters and stabilizing atomically precise structures, and also serve as vital linkers for constructing cluster-based coordination polymers. In this study, we present the results of the solvothermal synthesis of eight novel copper alkynyl clusters incorporating pyridine ligands using a one-pot method. The resulting compounds underwent characterization through elemental analysis, Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (PXRD), and single-crystal X-ray diffraction (SCXRD). Our observations revealed that distinct pyridine ligands with varying lengths and coordination sites exert significant influence on the structure and dimensionality of the clusters. The structural diversity of these clusters led to the formation of one-dimensional (1D), two-dimensional (2D), or dimer arrangements linked by seven pyridine bridging ligands. Remarkably, these complexes exhibited unique UV-vis absorption and photoluminescence properties, which were influenced by the specific bridging ligand and structural framework. Furthermore, density functional theory (DFT) calculations demonstrated the capability of the conjugated system in the pyridine ligand to impact the band gap of clusters. This study not only unveils the inherent structural diversity in coordination polymers based on copper alkynyl clusters but also offers valuable insights into harnessing ligand engineering for structural and property modulation.

Alternate conformational states of the HIV-1 capsid protein: Atomistic structures and dynamics of interconversion.

The HIV-1 capsid protein assembles into a conical shell that encases the viral RNA genome. The capsid protein is a two-domain protein, with the C-terminal domain (CTD) forming a dimer. Depending on being in a solution environment or the crystalline state, different dimer arrangements have been observed for the full capsid protein, as well as a truncated construct consisting of only the CTD. To characterize the structures and dynamics of these alternate quaternary arrangements, we carried out atomistic simulations using the weighted ensemble enhanced sampling strategy. Our simulations generated continuous pathways for interconversion between the two states with rate constants that agree with those measured by 19F NMR exchange spectroscopy. Our results demonstrate the advantages of pairing atomistic simulations with 19F NMR and have implications for the structural polymorphism of the HIV-1 viral capsid assembly process.

Understanding Quantum Plasmonic Enhancement in Nanorod Dimers from Time-Dependent Orbital-Free Density Functional Theory

Localized surface plasmon resonances could yield extreme enhancement of local electric fields at surfaces of plasmonic nanostructures. Herein, we have performed quantum mechanical simulations to systematically study plasmonic resonances in sodium (Na) nanorod dimers based on time-dependent orbital-free density functional theory. Several representative geometries, including end-to-end, side-to-side, and right-angle T- and L-shaped dimer arrangements are explored in detail. The optical spectra, tunneling electric current, and electric field enhancement (hot spots) are examined as a function of the size of the nanorods, their relative arrangement, and their gap distance (≤2 nm). Two plasmon resonant modes are identified to be responsible for the observed electric field enhancement. One of them is of quantum nature, arising from quantum tunneling across the gap of the two nanorods. The other mode is of electrostatic nature, originating from the dipolar interaction between the plasmonic oscillations of each nanorod. Among the examined geometries, the end-to-end dimer exhibits the strongest field enhancement, which increases with the aspect ratio and the gap distance. The interplay between electron tunneling across the gap and the spill-out of electrons at the nanorod surfaces is revealed to dominate the modulation of plasmonic resonances and field enhancement in the nanorod dimers.

Diversity Among Cyanobacterial Photosystem I Oligomers.

Unraveling the oligomeric states of the photosystem I complex is essential to understanding the evolution and native mechanisms of photosynthesis. The molecular composition and functions of this complex are highly conserved among cyanobacteria, algae, and plants; however, its structure varies considerably between species. In cyanobacteria, the photosystem I complex is a trimer in most species, but monomer, dimer and tetramer arrangements with full physiological function have recently been characterized. Higher order oligomers have also been identified in some heterocyst-forming cyanobacteria and their close unicellular relatives. Given technological progress in cryo-electron microscope single particle technology, structures of PSI dimers, tetramers and some heterogeneous supercomplexes have been resolved into near atomic resolution. Recent developments in photosystem I oligomer studies have largely enriched theories on the structure and function of these photosystems.

Simulation and characterization of the bulk refractive index sensitivity of coupled plasmonic nanostructures with the enhancement factor

The bulk refractive index (RI) sensitivity of coupled plasmonic nanostructures, namely gold and silver nanospheres and nanocubes in two-particle (dimer) arrangements, were simulated with the MNPBEM Matlab toolbox. The size of the nanoparticles (10–90 nm) and their separation distance were the running parameters. The enhancement factor (which characterizes the increased RI sensitivity of multi-particle arrangements compared to single particles) was introduced and used to evaluate the effect of particle coupling on the bulk RI sensitivity of the dimer arrangements. The enhancement factor is an exponential function of (D/D0), where D is the separation between the particles and D0 is the diameter of the spheres or the edge length of the cubes, and it was found that significant plasmonic coupling effects (e.g. EF > 1.5) starts below 0.5-0.3 D/D0 for the investigated dimers, depending on their size. It was also found for the four investigated dimer arrangements (gold/silver nanospheres/nanocubes) that the absolute peak shift and the enhancement factor values are inversely proportional: the dimers which have a larger absolute extinction peak shift (at the same particle separation) have smaller relative enhancement compared to single particles.

Monomer–dimer problem on some networks

Abstract Zhang et al. (2012) obtained the exact formula for the number of all possible monomer–dimer arrangements and the asymptotic growth constant on a scale-free small-world network. In this note, we generalize this result and obtain the exact solution on the monomer–dimer model on many networks. Particularly, we prove that these networks have the same asymptotic growth constant of the number of monomer–dimer arrangements.

Superdiffusive transport and energy localization in disordered granular crystals.

We study the spreading of initially localized excitations in one-dimensional disordered granular crystals. We thereby investigate localization phenomena in strongly nonlinear systems, which we demonstrate to differ fundamentally from localization in linear and weakly nonlinear systems. We conduct a thorough comparison of wave dynamics in chains with three different types of disorder-an uncorrelated (Anderson-like) disorder and two types of correlated disorders (which are produced by random dimer arrangements)-and for two types of initial conditions (displacement excitations and velocity excitations). We find for strongly precompressed (i.e., weakly nonlinear) chains that the dynamics depend strongly on the type of initial condition. In particular, for displacement excitations, the long-time asymptotic behavior of the second moment m̃(2) of the energy has oscillations that depend on the type of disorder, with a complex trend that differs markedly from a power law and which is particularly evident for an Anderson-like disorder. By contrast, for velocity excitations, we find that a standard scaling m̃(2)∼t(γ) (for some constant γ) applies for all three types of disorder. For weakly precompressed (i.e., strongly nonlinear) chains, m̃(2) and the inverse participation ratio P(-1) satisfy scaling relations m̃(2)∼t(γ) and P(-1)∼t(-η), and the dynamics is superdiffusive for all of the cases that we consider. Additionally, when precompression is strong, the inverse participation ratio decreases slowly (with η<0.1) for all three types of disorder, and the dynamics leads to a partial localization around the core and the leading edge of a propagating wave packet. For an Anderson-like disorder, displacement perturbations lead to localization of energy primarily in the core, and velocity perturbations cause the energy to be divided between the core and the leading edge. This localization phenomenon does not occur in the sonic-vacuum regime, which yields the surprising result that the energy is no longer contained in strongly nonlinear waves but instead is spread across many sites. In this regime, the exponents are very similar (roughly γ≈1.7 and η≈1) for all three types of disorder and for both types of initial conditions.

Structural Characterization of the Self-Association of the Death Domain of p75NTR

The neurotrophin receptor p75NTR conveys multiple signals via its intracellular death domain. However, how the death domain is activated and interacts with downstream adaptors remains unclear. Here, we report two crystal structures of the p75NTR death domain in the form of a non-covalent asymmetric dimer and a Cys379-Cys379 disulfide bond linked symmetric dimer, respectively. These two dimer arrangements have not previously been observed in other death domain-containing proteins. Further analysis shows that both the Cys379-Cys379 disulfide linked and non-covalent full-length p75NTR dimers are present on the cell surface. These observations suggest that various oligomers may exist simultaneously on the cell surface, and that p75NTR activation and signalling may be modulated by neurotrophins or other factors via inducing a shift of the equilibrium between different oligomeric states.

Broad-bandwidth and ultrafast electromagnetic response of coupled bimetal nanoantennas in few-cycle laser applications

We explore the field enhancement and temporal response of coupled bi-metal Ag/Au core-shell nanoparticle antennas. The bimetal antennas exhibit ultra-broadband resonances and allow exploiting the local field enhancement for few-cycle laser applications such as elements with an ultrafast response in nanoplasmonic device. We study dimer, trimer and heptamer arrangements and find that the Ag/Au core-shell trimer shows that a very high enhancement factor with an amplitude exceeds 120, but still facilitates an ultrafast response. Such systems may be ideal for the generation of attosecond light pulses based on high harmonic generation by employing nanoplasmonic field enhancement.

Monomer–dimer model on a scale-free small-world network

The explicit determination of the number of monomer–dimer arrangements on a network is a theoretical challenge, and exact solutions to monomer–dimer problem are available only for few limiting graphs with a single monomer on the boundary, e.g., rectangular lattice and quartic lattice; however, analytical research (even numerical result) for monomer–dimer problem on scale-free small-world networks is still missing despite the fact that a vast variety of real systems display simultaneously scale-free and small-world structures. In this paper, we address the monomer–dimer problem defined on a scale-free small-world network and obtain the exact formula for the number of all possible monomer–dimer arrangements on the network, based on which we also determine the asymptotic growth constant of the number of monomer–dimer arrangements in the network. We show that the obtained asymptotic growth constant is much less than its counterparts corresponding to two-dimensional lattice and Sierpinski fractal having the same average degree as the studied network, which indicates from another aspect that scale-free networks have a fundamentally distinct architecture as opposed to regular lattices and fractals without power-law behavior.

Enumeration of Perfect Matchings of a Type of Quadratic Lattice on the Torus

A quadrilateral cylinder of length $m$ and breadth $n$ is the Cartesian product of a $m$-cycle(with $m$ vertices) and a $n$-path(with $n$ vertices). Write the vertices of the two cycles on the boundary of the quadrilateral cylinder as $x_1,x_2,\cdots,x_m$ and $y_1,y_2,\cdots ,y_m$, respectively, where $x_i$ corresponds to $y_i(i=1,2,\dots, m)$. We denote by $Q_{m,n,r}$, the graph obtained from quadrilateral cylinder of length $m$ and breadth $n$ by adding edges $x_iy_{i+r}$ ($r$ is a integer, $0\leq r &lt; m$ and $i+r$ is modulo $m$). Kasteleyn had derived explicit expressions of the number of perfect matchings for $Q_{m,n,0}$ [P.W. Kasteleyn, The statistics of dimers on a lattice I: The number of dimer arrangements on a quadratic lattice, Physica 27(1961), 1209–1225]. In this paper, we generalize the result of Kasteleyn, and obtain expressions of the number of perfect matchings for $Q_{m,n,r}$ by enumerating Pfaffians.

Toward Verdazyl Radical-Based Materials: Ab Initio Inspection of Potential Organic Candidates for Spin-Crossover Phenomenon

The origin of magnetic interactions in verdazyl-based radical stackings is examined using ab initio wave function and density functional theory (DFT) calculations. Starting from the reported crystal structure of the 1,1'-bis(verdazyl)ferrocene diradical compound, the singlet-triplet energy difference has been evaluated on the basis of multireference difference dedicated configurations interaction calculations and suggested the innocent role of the ferrocene spacer. Using the underlying pi-dimer verdazyl structures, the J variations and potential energy surfaces of parallel and antiparallel face-to-face arrangements have been studied with respect to the verdazyl-verdazyl separation to evaluate the Coulomb repulsion U and bandwidth W. While coupled-cluster CCSD(T) calculations are suggestive of a weak bond formation in both dimer arrangements (approximately 40 kJ mol(-1)), the DFT approach fails to reproduce the bonding character. The intrinsically delocalized character of the magnetic orbitals favors an S = 0 ground state, but importantly, the S = 1 spin state is also bound. A typical 0.4 A increase (i.e., 10%) of the verdazyl-verdazyl equilibrium distance accompanying a 16 kJ mol(-1) adiabatic energy difference is calculated between the S = 0 and S = 1 states. In this distance separation regime, we finally suggest that either a relative 1.2 A slippage or a approximately 42 degrees relative orientation of the verdazyl rings is likely to give rise to a high-spin S = 1 ground state. These features are symptomatic of a bistable system, and an interpretation of the exchange interaction in verdazyl pi-dimer structures in terms of spin transition is proposed.

Diphosphine and Diarsine Complexes of Germanium(II) Halides—Preparation, Spectroscopic, and Structural Studies

The Ge(II) halide complexes [GeX(2)(L-L)] (L-L = o-C(6)H(4)(PPh(2))(2), o-C(6)H(4)(PMe(2))(2), Me(2)P(CH(2))(2)PMe(2); X = Cl, Br, I. L-L = Et(2)P(CH(2))(2)PEt(2); X = Cl or Br. L-L = o-C(6)H(4)(AsMe(2))(2); X = Br or I) and [GeCl(L-L)][GeCl(3)] (L-L = o-C(6)H(4)(AsMe(2))(2)) have been prepared and characterized by IR, (1)H and (31)P{(1)H} NMR spectroscopy, and microanalyses. The crystal structures of [GeX(2){o-C(6)H(4)(PPh(2))(2)}] (X = Cl, Br, I) reveal discrete mononuclear units with a very asymmetric bidentate o-C(6)H(4)(PPh(2))(2) ligand and a bent GeX(2) unit. Those of [GeX(2){o-C(6)H(4)(PMe(2))(2)}] show symmetrically coordinated diphosphine with loosely associated dimer arrangements, formed through long Ge...X bridges between adjacent monomer units. [GeX(2){R(2)P(CH(2))(2)PR(2)}] (R = Me; X = Cl, Br, I. R = Et; X = Cl, Br) all show discrete monomer structures with 2-fold crystallographic symmetry and based upon four-coordinate Ge, with the diphosphine chelating and approximately linear GeX(2) units. [GeI(2){o-C(6)H(4)(AsMe(2))(2)}] involves significant intermolecular Ge...I interactions, giving rise to a zigzag polymer chain. Finally, the structure of [GeCl{o-C(6)H(4)(AsMe(2))(2)}][GeCl(3)] shows pyramidal cations and anions both with crystallographic mirror symmetry, with the diarsine symmetrically chelating, and long Ge...Cl interactions give a loosely associated chain polymer with alternating cations and anions. Comparisons across this series of structurally diverse complexes are discussed.

Estimate of Benzene−Triphenylene and Triphenylene−Triphenylene Interactions: A Topic Relevant to Columnar Discotic Liquid Crystals

The interaction potential energy of several benzene−triphenylene and triphenylene−triphenylene dimer arrangements has been calculated by a Moller−Plesset second order perturbation theory with a suitably modified 6-31G* basis set. This approach, already tested and successfully employed on the benzene dimer, is presently shown to reproduce, with a level of accuracy comparable to other computationally affordable methods, the interaction potential energy of a few representative configurations of naphthalene dimer, for which high-level ab initio reference data exist. Thus, the method has been confidently applied to the interaction energy computation of the above-mentioned more complex dimers, for which high-level ab initio calculations are yet unfeasible. Comparisons have been made with the results obtained with an empirical force field and, as regards the benzene−triphenylene dimer, also with a dispersion corrected DFT method. The computed set of data may contribute to comprehending how aromatic interactions ...

Crystal Structure of Human Lectin-like, Oxidized Low-Density Lipoprotein Receptor 1 Ligand Binding Domain and Its Ligand Recognition Mode to OxLDL

Lectin-like, oxidized low-density lipoprotein (LDL) receptor 1, LOX-1, is the major receptor for oxidized LDL (OxLDL) in endothelial cells. We have determined the crystal structure of the ligand binding domain of LOX-1, with a short stalk region connecting the domain to the membrane-spanning region, as a homodimer linked by an interchain disulfide bond. In vivo assays with LOX-1 mutants revealed that the "basic spine," consisting of linearly aligned arginine residues spanning over the dimer surface, is responsible for ligand binding. Single amino acid substitution in the dimer interface caused a severe reduction in LOX-1 binding activity, suggesting that the correct dimer arrangement is crucial for binding to OxLDL. Based on the LDL model structure, possible binding modes of LOX-1 to OxLDL are proposed.

379. New Zinc Finger Protein Nuclease Architectures for More Efficient Gene Modification Therapies

Top of pageAbstract Recent studies have shown that zinc finger protein nucleases (ZFNs) may be used to introduce precise, therapeutically beneficial changes into the genome. This approach offers considerable promise for the correction of monogenic diseases, and should also allow the ablation of genes whose expression is harmful in particular disease settings. Realizing the full potential of ZFN-mediated gene modification therapy, however, will require the development of methods for routinely engineering ZFNs that cleave with high efficiency at virtually any DNA sequence, since a separation distance of as few as forty bp between the sites of nuclease cleavage and desired sequence change can lead to a significant reduction in gene modification efficiencies. In order to address these issues we have engineered and characterized several improvements to the architecture of our designed ZFNs. In initial studies, we systematically varied the length and composition of the linker connecting the zinc finger and nuclease domains, and determined the impact of these changes on the cleavage efficiency and optimal target arrangement of the resultant ZFN (which functions as a dimer). It was observed both in vitro and in vivo that ZFNs could be efficiently designed to cleave targets separated by 4-8 bps, with maximal activity obtained when monomer sites were separated by 4, 5 or 6 bp. Next, structure-based design was used to engineer asymmetric contacts into the dimer interface in order to create ZFNs that could function only as heterodimers. This was of interest from the standpoint of enhancing both the specificity and efficiency of ZFN performance, since prohibiting formation of the therapeutically irrelevant homodimer would eliminate the possibility of off-target effects. Biochemical and cellular studies revealed that the resultant ZFNs functioned as desired. Finally, we examined whether re-ordering of the zinc finger and nuclease domains within the ZFN polypeptide would enable functional assembly of novel dimer arrangements on the target DNA (|[ldquo]|head to head' and |[ldquo]|head to tail|[rdquo]|, in addition to the natural |[ldquo]|tail to tail|[rdquo]| arrangement). This was of interest because the availability of an increased number of productive arrangements would directly enhance our capacity to design ZFNs to cleave at any chosen base. We have demonstrated that the |[ldquo]|re-ordered|[rdquo]| ZFNs may be combined with each other and with the parental architecture to yield dimers that cut preferentially in all three configurations (|[ldquo]|head to head|[rdquo]|, |[ldquo]|tail to tail|[rdquo]| and |[ldquo]|head to tail|[rdquo]|). Together, these approaches have significantly improved the cleavage efficiency and targeting specificity of the ZFN platform, and have enhanced our capacity to design ZFNs for use in therapeutic gene modification.

Coherent state monitoring in quantum dots

We study the dynamics of excitonic states in dimer and trimer arrangements of colloidal quantum dots using a density-matrix approach. The dots are coupled via a dipole-dipole interaction akin to the F\"orster mechanism. Coherent oscillations of tuned donor dots are shown to appear as plateaus in the acceptor dot, and therefore in its optical response. This behavior provides one with an interesting and unique handle to monitor the quantum state of the dimer, an ``eavesdroping arrangement.'' A trimer cluster in a symmetrical loop shows steady states in a shorter characteristic time than the typical radiative lifetime of the dots. Breaking the symmetry of the loop results again in damping oscillatory states in the donor dots and plateaus in the eavesdropping∕acceptor dot. The use of realistic parameters allows direct comparison with recent experiments and indicates that coherent-state monitoring is possible in real experiments.

Intermolecular Force Fields of Large Molecules by the Fragmentation Reconstruction Method (FRM): Application to a Nematic Liquid Crystal

A new intermolecular force field for the liquid-crystal-forming molecule 5CB (4-cyano, 4‘n-pentyl biphenyl) has been derived from two-body interaction energies, obtained by the fragmentation reconstruction method (FRM). The accuracy of this purely quantum mechanical approach has been verified by comparing FRM and directly ab initio computed interaction energies, obtaining a very satisfactory agreement with a maximum absolute error lower than 0.4 kcal/mol. The comparison was performed for a large number of internal geometries and dimer arrangements of two fragments of 5CB, namely, 4-cyano biphenyl (0CB) and n-pentyl benzene (5B). The potential energy surface of the 5CB dimer has then been used to parametrize a many-site model interaction potential suitable for computer simulations.