Disruption of the ndhF1 gene affects Chl fluorescence through state transition in the Cyanobacterium Synechocystis sp. PCC 6803, resulting in apparent high efficiency of photosynthesis.

PubMed

Ogawa, Takako; Harada, Tetsuyuki; Ozaki, Hiroshi; Sonoike, Kintake

2013-07-01

In Synechocystis sp. PCC 6803, the disruption of the ndhF1 gene (slr0844), which encodes a subunit of one of the NDH-1 complexes (NDH-1L complex) serving for respiratory electron transfer, causes the largest change in Chl fluorescence induction kinetics among the kinetics of 750 disruptants searched in the Fluorome, the cyanobacterial Chl fluorescence database. The cause of the explicit phenotype of the ndhF1 disruptant was examined by measurements of the photosynthetic rate, Chl fluorescence and state transition. The results demonstrate that the defects in respiratory electron transfer obviously have great impact on Chl fluorescence in cyanobacteria. The inactivation of NDH-1L complexes involving electron transfer from NDH-1 to plastoquinone (PQ) would result in the oxidation of the PQ pool, leading to the transition to State 1, where the yield of Chl fluorescence is high. Apparently, respiration, although its rate is far lower than that of photosynthesis, could affect Chl fluorescence through the state transition as leverage. The disruption of the ndhF1 gene caused lower oxygen-evolving activity but the estimated electron transport rate from Chl fluorescence measurements was faster in the mutant than in the wild-type cells. The discrepancy could be ascribed to the decreased level of non-photochemical quenching due to state transition. One must be cautious when using the Chl fluorescence parameter to estimate photosynthesis in mutants defective in state transition.

Radiationless Transitions and Excited-State Absorption of Low-Field Chromium Complexes in Solids

DTIC Science & Technology

1989-07-20

host-lattice modes and, in the case of the scandium compound with 5 % chromium concentration, of the a and tIg 2g localized modes. The local-mode...Radiationless transitions and excited-state Final report I/I/86-5/31/89 absorption of low-field chromium complexes 6. PERFORMING ORG. REPORT NUMBER ( 1 in...complexes, chromium ; tunable lasers, high pressure,-photoluminescence 4. 26, AMTVrAC? (Cbm e @CAP N Igemem’ a IdoMit’ by block nambew) The continuation of a

Theoretical studies for the rates and kinetic isotope effects of the excited-state double proton transfer in the 1:1 7-azaindole:H2O complex using variational transition state theory including multidimensional tunneling.

PubMed

Duong, My Phu Thi; Kim, Yongho

2010-03-18

Variational transition state theory calculations including multidimensional tunneling (VTST/MT) for excited-state tautomerization in the 1:1 7-azaindole:H(2)O complex were performed. Electronic structures and energies for reactant, product, transition state, and potential energy curves along the reaction coordinate were computed at the CASSCF(10,9)/6-31G(d,p) level of theory. The potential energies were corrected by second-order multireference perturbation theory to take the dynamic electron correlation into consideration. The final potential energy curves along the reaction coordinate were generated at the MRPT2//CASSCF(10,9)/6-31G(d,p) level. Two protons in the excited-state tautomerization are transferred concertedly, albeit asynchronously. The position of the variational transition state is very different from the conventional transition state, and is highly dependent on isotopic substitution. Rate constants were calculated using VTST/MT, and were on the order of 10(-6) s(-1) at room temperature. The HH/DD kinetic isotope effects are consistent with experimental observations; consideration of both tunneling and variational effects was essential to predict the experimental values correctly.

Quantifying Complexity in Quantum Phase Transitions via Mutual Information Complex Networks

NASA Astrophysics Data System (ADS)

Valdez, Marc Andrew; Jaschke, Daniel; Vargas, David L.; Carr, Lincoln D.

2017-12-01

We quantify the emergent complexity of quantum states near quantum critical points on regular 1D lattices, via complex network measures based on quantum mutual information as the adjacency matrix, in direct analogy to quantifying the complexity of electroencephalogram or functional magnetic resonance imaging measurements of the brain. Using matrix product state methods, we show that network density, clustering, disparity, and Pearson's correlation obtain the critical point for both quantum Ising and Bose-Hubbard models to a high degree of accuracy in finite-size scaling for three classes of quantum phase transitions, Z2, mean field superfluid to Mott insulator, and a Berzinskii-Kosterlitz-Thouless crossover.

Experimental and theoretical study of the electronic spectrum of the BAr2 complex: Transition to the excited valence B(2s2p2 2D) state

NASA Astrophysics Data System (ADS)

Krumrine, Jennifer R.; Alexander, Millard H.; Yang, Xin; Dagdigian, Paul J.

2000-03-01

The 2s2p22D←2s22p 2P valence transition in the BAr2 cluster is investigated in a collaborative experimental and theoretical study. Laser fluorescence excitation spectra of a supersonic expansion of B atoms entrained in Ar at high source backing pressures display several features not assignable to the BAr complex. Resonance fluorescence is not observed, but instead emission from the lower 3s state. Size-selected fluorescence depletion spectra show that these features in the excitation spectrum are primarily due to the BAr2 complex. This electronic transition within BAr2 is modeled theoretically, similarly to our earlier study of the 3s←2p transition [M. H. Alexander et al., J. Chem. Phys. 106, 6320 (1997)]. The excited potential energy surfaces of the fivefold degenerate B(2s2p22D) state within the ternary complex are computed in a pairwise-additive model employing diatomic BAr potential energy curves which reproduce our previous experimental observations on the electronic states emanating from the B(2D)+Ar asymptote. The simulated absorption spectrum reproduces reasonably well the observed fluorescence depletion spectrum. The theoretical model lends insight into the energetics of the approach of B to multiple Ar atoms, and how the orientation of B p-orbitals governs the stability of the complex.

Vibrational energy transfer dynamics in ruthenium polypyridine transition metal complexes.

PubMed

Fedoseeva, Marina; Delor, Milan; Parker, Simon C; Sazanovich, Igor V; Towrie, Michael; Parker, Anthony W; Weinstein, Julia A

2015-01-21

Understanding the dynamics of the initial stages of vibrational energy transfer in transition metal complexes is a challenging fundamental question which is also of crucial importance for many applications, such as improving the performance of solar devices or photocatalysis. The present study investigates vibrational energy transport in the ground and the electronic excited state of Ru(4,4'-(COOEt)2-2,2-bpy)2(NCS)2, a close relative of the efficient "N3" dye used in dye-sensitized solar cells. Using the emerging technique of ultrafast two-dimensional infrared spectroscopy, we show that, similarly to other transition-metal complexes, the central Ru heavy atom acts as a "bottleneck" making the energy transfer from small ligands with high energy vibrational stretching frequencies less favorable and thereby affecting the efficiency of vibrational energy flow in the complex. Comparison of the vibrational relaxation times in the electronic ground and excited state of Ru(4,4'-(COOEt)2-2,2-bpy)2(NCS)2 shows that it is dramatically faster in the latter. We propose to explain this observation by the intramolecular electrostatic interactions between the thiocyanate group and partially oxidised Ru metal center, which increase the degree of vibrational coupling between CN and Ru-N modes in the excited state thus reducing structural and thermodynamic barriers that slow down vibrational relaxation and energy transport in the electronic ground state. As a very similar behavior was earlier observed in another transition-metal complex, Re(4,4'-(COOEt)2-2,2'-bpy)(CO)3Cl, we suggest that this effect in vibrational energy dynamics might be common for transition-metal complexes with heavy central atoms.

Complexity and multifractality of neuronal noise in mouse and human hippocampal epileptiform dynamics.

PubMed

Serletis, Demitre; Bardakjian, Berj L; Valiante, Taufik A; Carlen, Peter L

2012-10-01

Fractal methods offer an invaluable means of investigating turbulent nonlinearity in non-stationary biomedical recordings from the brain. Here, we investigate properties of complexity (i.e. the correlation dimension, maximum Lyapunov exponent, 1/f(γ) noise and approximate entropy) and multifractality in background neuronal noise-like activity underlying epileptiform transitions recorded at the intracellular and local network scales from two in vitro models: the whole-intact mouse hippocampus and lesional human hippocampal slices. Our results show evidence for reduced dynamical complexity and multifractal signal features following transition to the ictal epileptiform state. These findings suggest that pathological breakdown in multifractal complexity coincides with loss of signal variability or heterogeneity, consistent with an unhealthy ictal state that is far from the equilibrium of turbulent yet healthy fractal dynamics in the brain. Thus, it appears that background noise-like activity successfully captures complex and multifractal signal features that may, at least in part, be used to classify and identify brain state transitions in the healthy and epileptic brain, offering potential promise for therapeutic neuromodulatory strategies for afflicted patients suffering from epilepsy and other related neurological disorders.

Complex transitions between spike, burst or chaos synchronization states in coupled neurons with coexisting bursting patterns

NASA Astrophysics Data System (ADS)

Gu, Hua-Guang; Chen, Sheng-Gen; Li, Yu-Ye

2015-05-01

We investigated the synchronization dynamics of a coupled neuronal system composed of two identical Chay model neurons. The Chay model showed coexisting period-1 and period-2 bursting patterns as a parameter and initial values are varied. We simulated multiple periodic and chaotic bursting patterns with non-(NS), burst phase (BS), spike phase (SS), complete (CS), and lag synchronization states. When the coexisting behavior is near period-2 bursting, the transitions of synchronization states of the coupled system follows very complex transitions that begins with transitions between BS and SS, moves to transitions between CS and SS, and to CS. Most initial values lead to the CS state of period-2 bursting while only a few lead to the CS state of period-1 bursting. When the coexisting behavior is near period-1 bursting, the transitions begin with NS, move to transitions between SS and BS, to transitions between SS and CS, and then to CS. Most initial values lead to the CS state of period-1 bursting but a few lead to the CS state of period-2 bursting. The BS was identified as chaos synchronization. The patterns for NS and transitions between BS and SS are insensitive to initial values. The patterns for transitions between CS and SS and the CS state are sensitive to them. The number of spikes per burst of non-CS bursting increases with increasing coupling strength. These results not only reveal the initial value- and parameter-dependent synchronization transitions of coupled systems with coexisting behaviors, but also facilitate interpretation of various bursting patterns and synchronization transitions generated in the nervous system with weak coupling strength. Project supported by the National Natural Science Foundation of China (Grant Nos. 11372224 and 11402039) and the Fundamental Research Funds for Central Universities designated to Tongji University (Grant No. 1330219127).

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

PubMed Central

Duchi, Diego; Gryte, Kristofer; Robb, Nicole C; Morichaud, Zakia; Sheppard, Carol; Wigneshweraraj, Sivaramesh

2018-01-01

Abstract Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation. PMID:29177430

Land management in the American southwest: a state-and-transition approach to ecosystem complexity.

PubMed

Bestelmeyer, Brandon T; Herrick, Jeffrey E; Brown, Joel R; Trujillo, David A; Havstad, Kris M

2004-07-01

State-and-transition models are increasingly being used to guide rangeland management. These models provide a relatively simple, management-oriented way to classify land condition (state) and to describe the factors that might cause a shift to another state (a transition). There are many formulations of state-and-transition models in the literature. The version we endorse does not adhere to any particular generalities about ecosystem dynamics, but it includes consideration of several kinds of dynamics and management response to them. In contrast to previous uses of state-and-transition models, we propose that models can, at present, be most effectively used to specify and qualitatively compare the relative benefits and potential risks of different management actions (e.g., fire and grazing) and other factors (e.g., invasive species and climate change) on specified areas of land. High spatial and temporal variability and complex interactions preclude the meaningful use of general quantitative models. Forecasts can be made on a case-by-case basis by interpreting qualitative and quantitative indicators, historical data, and spatially structured monitoring data based on conceptual models. We illustrate how science- based conceptual models are created using several rangeland examples that vary in complexity. In doing so, we illustrate the implications of designating plant communities and states in models, accounting for varying scales of pattern in vegetation and soils, interpreting the presence of plant communities on different soils and dealing with our uncertainty about how those communities were assembled and how they will change in the future. We conclude with observations about how models have helped to improve management decision-making.

State transition storyboards: A tool for designing the Goldstone solar system radar data acquisition system user interface software

NASA Technical Reports Server (NTRS)

Howard, S. D.

1987-01-01

Effective user interface design in software systems is a complex task that takes place without adequate modeling tools. By combining state transition diagrams and the storyboard technique of filmmakers, State Transition Storyboards were developed to provide a detailed modeling technique for the Goldstone Solar System Radar Data Acquisition System human-machine interface. Illustrations are included with a description of the modeling technique.

DFT Analysis of Spin Crossover in Mn(III) Complexes: Is a Two-Electron S = 2 to S = 0 Spin Transition Feasible?

PubMed

Amabilino, Silvia; Deeth, Robert J

2017-03-06

Six-coordinate, rigorously octahedral d 4 Mn(III) spin crossover (SCO) complexes are limited by symmetry to an S = 1 (intermediate spin, IS) to S = 2 (high spin, HS) transition. In order to realize the potential S = 0 to S = 2 transition, a lower symmetry and/or change in coordination number is needed, which we explore here computationally. First, a number of complexes are analyzed to develop a reliable and relatively fast DFT protocol for reproducing known Mn(III) spin state energetics. The hybrid meta-GGA functional TPSSh with a modest split valence plus polarization basis set and an empirical dispersion correction is found to predict correctly the ground spin state of Mn(III) complexes, including true low-spin (LS) S = 0 systems, with a range of donor sets including the hexadentate [N 4 O 2 ] Schiff base ligands. The electronic structure design criteria necessary for realizing a ΔS = 2 SCO transition are described, and a number of model complexes are screened for potential SCO behavior. Five-coordinate trigonal-bipyramidal symmetry fails to yield any suitable systems. Seven-coordinate, approximately pentagonal bipyramidal symmetry is more favorable, and when a known pentadentate macrocyclic donor is combined with π-acceptor axial ligands, a novel Mn(III) complex, [Mn(PABODP)(PF 3 ) 2 ] 3+ (PABODP = 2,13-dimethyl-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18),2,12,14,16-pentaene), is predicted to have the right spin state energetics for an S = 0 to S = 2 transition. Successful synthesis of such a complex could provide the first example of a ΔS = 2 SCO transition for d 4 Mn(III). However, the combination of a rigid macrocycle and a high coordination number dilutes the stereochemical activity of the d electrons, leading to relatively small structural changes between HS and LS systems. It may therefore remain a challenge to realize strong cooperative effects in Mn(III) systems.

Cyclotron transitions of bound ions

NASA Astrophysics Data System (ADS)

Bezchastnov, Victor G.; Pavlov, George G.

2017-06-01

A charged particle in a magnetic field possesses discrete energy levels associated with particle rotation around the field lines. The radiative transitions between these levels are the well-known cyclotron transitions. We show that a bound complex of particles with a nonzero net charge displays analogous transitions between the states of confined motion of the entire complex in the field. The latter bound-ion cyclotron transitions are affected by a coupling between the collective and internal motions of the complex and, as a result, differ from the transitions of a "reference" bare ion with the same mass and charge. We analyze the cyclotron transitions for complex ions by including the coupling within a rigorous quantum approach. Particular attention is paid to comparison of the transition energies and oscillator strengths to those of the bare ion. Selection rules based on integrals of collective motion are derived for the bound-ion cyclotron transitions analytically, and the perturbation and coupled-channel approaches are developed to study the transitions quantitatively. Representative examples are considered and discussed for positive and negative atomic and cluster ions.

Complex band structures of transition metal dichalcogenide monolayers with spin-orbit coupling effects

NASA Astrophysics Data System (ADS)

Szczęśniak, Dominik; Ennaoui, Ahmed; Ahzi, Saïd

2016-09-01

Recently, the transition metal dichalcogenides have attracted renewed attention due to the potential use of their low-dimensional forms in both nano- and opto-electronics. In such applications, the electronic and transport properties of monolayer transition metal dichalcogenides play a pivotal role. The present paper provides a new insight into these essential properties by studying the complex band structures of popular transition metal dichalcogenide monolayers (MX 2, where M  =  Mo, W; X  =  S, Se, Te) while including spin-orbit coupling effects. The conducted symmetry-based tight-binding calculations show that the analytical continuation from the real band structures to the complex momentum space leads to nonlinear generalized eigenvalue problems. Herein an efficient method for solving such a class of nonlinear problems is presented and yields a complete set of physically relevant eigenvalues. Solutions obtained by this method are characterized and classified into propagating and evanescent states, where the latter states manifest not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gap of MX 2 monolayers, where electrons can directly tunnel between the band gap edges. To describe these tunneling currents, decay behavior of electronic states in the forbidden energy region is elucidated and their importance within the ballistic transport regime is briefly discussed.

Magnetic properties of the Fe{sup II} spin crossover complex in emulsion polymerization of trifluoroethylmethacrylate using poly(vinyl alcohol)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuki, Atsushi, E-mail: suzuki@mat.usp.ac.j; Iguchi, Motoi; Oku, Takeo

2010-04-15

Influence of chemical substitution in the Fe{sup II} spin crossover complex on magnetic properties in emulsion polymerization of trifluoroethylmethacrylate using poly(vinyl alcohol) as a protective colloid was investigated near its high spin/low spin (HS/LS) phase transition. The obvious bi-stability of the HS/LS phase transition was considered by the identification of multiple spin states between the quintet (S=2) states to single state (S=0) across the excited triplet state (S=1). Magnetic parameters of gradual shifts of anisotropy g-tensor supported by the molecular distortion of the spin crossover complex would arise from a Jahn-Teller effect regarding ligand field theory on the basis ofmore » a B3LYP density functional theory using electron spin resonance (ESR) spectrum and X-ray powder diffraction. - Graphical abstract: AFM surface image of the emulsion particles with the spin crossover complex.« less

H theorem for generalized entropic forms within a master-equation framework

NASA Astrophysics Data System (ADS)

Casas, Gabriela A.; Nobre, Fernando D.; Curado, Evaldo M. F.

2016-03-01

The H theorem is proven for generalized entropic forms, in the case of a discrete set of states. The associated probability distributions evolve in time according to a master equation, for which the corresponding transition rates depend on these entropic forms. An important equation describing the time evolution of the transition rates and probabilities in such a way as to drive the system towards an equilibrium state is found. In the particular case of Boltzmann-Gibbs entropy, it is shown that this equation is satisfied in the microcanonical ensemble only for symmetric probability transition rates, characterizing a single path to the equilibrium state. This equation fulfils the proof of the H theorem for generalized entropic forms, associated with systems characterized by complex dynamics, e.g., presenting nonsymmetric probability transition rates and more than one path towards the same equilibrium state. Some examples considering generalized entropies of the literature are discussed, showing that they should be applicable to a wide range of natural phenomena, mainly those within the realm of complex systems.

Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Meng-Chiao; Sturm, Matthew B.; Almo, Steven C.

2010-01-12

Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple {pi}-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the {pi}-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common featuresmore » of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H{sub 2}O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.« less

Zn vacancy-donor impurity complexes in ZnO

NASA Astrophysics Data System (ADS)

Frodason, Y. K.; Johansen, K. M.; Bjørheim, T. S.; Svensson, B. G.; Alkauskas, A.

2018-03-01

Results from hybrid density functional theory calculations on the thermodynamic stability and optical properties of the Zn vacancy (VZn) complexed with common donor impurities in ZnO are reported. Complexing VZn with donors successively removes its charge-state transition levels in the band gap, starting from the most negative one. Interestingly, the presence of a donor leads only to modest shifts in the positions of the VZn charge-state transition levels, the sign and magnitude of which can be interpreted from a polaron energetics model by taking hole-donor repulsion into account. By employing a one-dimensional configuration coordinate model, luminescence lineshapes and positions were calculated. Due to the aforementioned effects, the isolated VZn gradually changes from a mainly nonradiative defect with transitions in the infrared region in n -type material, to a radiative one with broad emission in the visible range when complexed with shallow donors.

Ab initio investigation of electric and magnetic dipole electronic transitions in the complex of oxygen with benzene.

PubMed

Valiev, R R; Minaev, B F

2016-09-01

The electric dipole transitions between pure spin and mixed spin electronic states are calculated at the XMC-QDPT2 and MCSCF levels of theory, respectively, for different intermolecular distances of the C6H6 and O2 collisional complex. The magnetic dipole transition moment between the mixed-spin ground ("triplet") and the first excited ("singlet") states is calculated by quadratic response at MCSCF level of theory. The obtained results confirm the theory of intensity borrowing and increasing the intensity of electronic transitions in the C6H6 + O2 collision. The calculation of magnetically induced current density is performed for benzene molecule being in contact with O2 at the distances from 3.5 to 4.5 Å. The calculation shows that the aromaticity of benzene is rising due to the conjugation of π-MOs of both molecules. The C6H6 + O2 complex becomes nonaromatic at the short distances (r < 3.5 Å). The computation of static polarizability in the excited electronic states of the C6H6 + O2 collisional complex at various distances supports the theory of red solvatochromic shift of the a → X band. Graphical abstract The C6H6+ O2 collisional complex.

High Pressure Optical Studies of the Thallous Halides and of Charge-Transfer Complexes

NASA Astrophysics Data System (ADS)

Jurgensen, Charles Willard

High pressure was used to study the insulator -to-metal transition in sulfur and the thallous halides and to study the intermolecular interactions in charge -transfer complexes. The approach to the band overlap insulator -to-metal transition was studied in three thallous halides and sulfur by optical absorption measurements of the band gap as a function of pressure. The band gap of sulfur continuously decreases with pressure up to the insulator -to-metal transition which occurs between 450 and 485 kbars. The results on the thallous halides indicate that the indirect gap decreases more rapidly than the direct gap; the closing of the indirect gap is responsible for the observed insulator -to-metal transitions. High pressure electronic and vibrational spectroscopic measurements on the solid-state complexes of HMB-TCNE were used to study the intermolecular interactions of charge -transfer complexes. The vibrational frequency shifts indicate that the degree of charge transfer increases with pressure which is independently confirmed by an increase in the molar absorptivity of the electronic charge-transfer peak. Induction and dispersion forces contribute towards a red shift of the charge-transfer peak; however, charge-transfer resonance contributes toward a blue shift and this effect is dominant for the HMB-TCNE complexes. High pressure electronic spectra were used to study the effect of intermolecular interactions on the electronic states of TCNQ and its complexes. The red shifts with pressure of the electronic spectra of TCNQ and (TCNQ)(' -) in polymer media and of crystalline TCNQ can be understood in terms of Van der Waals interactions. None of the calculations which considered intradimer distance obtained the proper behavior for either the charge-transfer of the locally excited states of the complexes. The qualitative behavior of both states can be interpreted as the effect of increased mixing of the locally excited and charge transfer states.

Synthesis and spectroscopic characterization of gallic acid and some of its azo complexes

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; Hagagg, Sawsan S.; Ali, Alaa E.; Nasr, Nessma M.

2012-04-01

A series of gallic acid and azo gallic acid complexes were prepared and characterized by elemental analysis, IR, electronic spectra and magnetic susceptibility. The complexes were of different geometries: Octahedral, Tetrahedral and Square Planar. ESR was studied for copper complexes. All of the prepared complexes were of isotropic nature. The thermal analyses of the complexes were studied by DTA and DSC techniques. The thermodynamic parameters and the thermal transitions, such as glass transitions, crystallization and melting temperatures for some ligands and their complexes were evaluated and discussed. The entropy change values, ΔS#, showed that the transition states are more ordered than the reacting complexes. The biological activities of some ligands and their complexes are tested against Gram positive and Gram negative bacteria. The results showed that some complexes have a well considerable activity against different organisms.

Speeding Up Sigmatropic Shifts-To Halve or to Hold.

PubMed

Tantillo, Dean J

2016-04-19

Catalysis is common. Rational catalyst design, however, is at the frontier of chemical science. Although the histories of physical organic and synthetic organic chemistry boast key chapters involving [3s,3s] sigmatropic shifts, catalysis of these reactions is much less common than catalysis of ostensibly more complex processes. The comparative dearth of catalysts for sigmatropic shifts is perhaps a result of the perception that transition state structures for these reactions, like their reactants, are nonpolar and therefore not amenable to selective stabilization and its associated barrier lowering. However, as demonstrated in this Account, transition state structures for [3s,3s] sigmatropic shifts can in fact have charge distributions that differ significantly from those of reactants, even for hydrocarbon substrates, allowing for barriers to be decreased and rates increased. In some cases, differences in charge distribution result from the inclusion of heteroatoms at specific positions in reactants, but in other cases differences are actually induced by catalysts. Perhaps surprisingly, strategies for complexation of transition state structures that remain nonpolar are also possible. In general, the strategies for catalysis employed can be characterized as involving either mechanistic intervention, where a catalyst induces a change from the concerted mechanism expected for a [3s,3s] sigmatropic shift to a multistep process (cutting the transformation into halves or smaller pieces) whose overall barrier is decreased relative to the concerted process, or transition state complexation, where a catalyst simply binds (holds) more tightly to the transition state structure for a [3s,3s] sigmatropic shift than to the reactant, leading to a lower barrier in the presence of the catalyst. Both of these strategies can be considered to be biomimetic in that enzymes frequently induce multistep processes and utilize selective transition state stabilization for the steps involved. In addition, transition state complexation was the principle around which catalytic antibodies were originally designed. The field of catalysis of sigmatropic shifts is now ready for rational design. The studies described here all provide evidence for the origins of rate acceleration, derived in large part from the results of quantum chemical calculations, that can now be applied to the design of new catalysts for [3s,3s] and other sigmatropic shifts.

Order-disorder phase transition in the peroxidovanadium complex NH4[VO(O2)2(NH3)].

PubMed

Schwendt, Peter; Gyepes, Róbert; Chrappová, Jana; Němec, Ivan; Vaněk, Přemysl

2018-07-05

Complex NH 4 [VO(O 2 ) 2 (NH 3 )] (1) undergoes an order-disorder phase transition at T c ~258K. This transition is accompanied by change in the space group of the orthorhombic lattice and also by significant structural rearrangements of the constituent molecules, which are pertinent mostly to their NH 4 + ions and their ammonia ligands. The low-temperature solid state IR and Raman spectra of 1 were corroborated by solid-state computations that employed Gaussian functions as the basis set. Results of these computations yielded excellent agreement with experimental data. On the curves of temperature dependence of vibrational modes, the phase transition is expressed by an abrupt change of the slope above T c . Copyright © 2018 Elsevier B.V. All rights reserved.

A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

PubMed

Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

2009-07-28

Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

Recurrence-plot-based measures of complexity and their application to heart-rate-variability data.

PubMed

Marwan, Norbert; Wessel, Niels; Meyerfeldt, Udo; Schirdewan, Alexander; Kurths, Jürgen

2002-08-01

The knowledge of transitions between regular, laminar or chaotic behaviors is essential to understand the underlying mechanisms behind complex systems. While several linear approaches are often insufficient to describe such processes, there are several nonlinear methods that, however, require rather long time observations. To overcome these difficulties, we propose measures of complexity based on vertical structures in recurrence plots and apply them to the logistic map as well as to heart-rate-variability data. For the logistic map these measures enable us not only to detect transitions between chaotic and periodic states, but also to identify laminar states, i.e., chaos-chaos transitions. The traditional recurrence quantification analysis fails to detect the latter transitions. Applying our measures to the heart-rate-variability data, we are able to detect and quantify the laminar phases before a life-threatening cardiac arrhythmia occurs thereby facilitating a prediction of such an event. Our findings could be of importance for the therapy of malignant cardiac arrhythmias.

Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics.

PubMed

Gani, Terry Z H; Kulik, Heather J

2017-11-14

Accurate predictions of spin-state ordering, reaction energetics, and barrier heights are critical for the computational discovery of open-shell transition-metal (TM) catalysts. Semilocal approximations in density functional theory, such as the generalized gradient approximation (GGA), suffer from delocalization error that causes them to overstabilize strongly bonded states. Descriptions of energetics and bonding are often improved by introducing a fraction of exact exchange (e.g., erroneous low-spin GGA ground states are instead correctly predicted as high-spin with a hybrid functional). The degree of spin-splitting sensitivity to exchange can be understood based on the chemical composition of the complex, but the effect of exchange on reaction energetics within a single spin state is less well-established. Across a number of model iron complexes, we observe strong exchange sensitivities of reaction barriers and energies that are of the same magnitude as those for spin splitting energies. We rationalize trends in both reaction and spin energetics by introducing a measure of delocalization, the bond valence of the metal-ligand bonds in each complex. The bond valence thus represents a simple-to-compute property that unifies understanding of exchange sensitivity for catalytic properties and spin-state ordering in TM complexes. Close agreement of the resulting per-metal-organic-bond sensitivity estimates, together with failure of alternative descriptors demonstrates the utility of the bond valence as a robust descriptor of how differences in metal-ligand delocalization produce differing relative energetics with exchange tuning. Our unified description explains the overall effect of exact exchange tuning on the paradigmatic two-state FeO + /CH 4 reaction that combines challenges of spin-state and reactivity predictions. This new descriptor-sensitivity relationship provides a path to quantifying how predictions in transition-metal complex screening are sensitive to the method used.

Ultrafast Transient Absorption Spectroscopy of Polymer-Based Organophotoredox Catalysts Mimicking Transition-Metal Complexes

NASA Astrophysics Data System (ADS)

Jamhawi, Abdelqader; Paul, Anam C.; Smith, Justin D.; Handa, Sachin; Liu, Jinjun

2017-06-01

Transition-metal complexes of rare earth metals including ruthenium and iridium are most commonly employed as visible-light photocatalysts. Despite their highly important and broad applications, they have many disadvantages including high cost associated with low abundance in earth crust, potential toxicity, requirement of specialized ligands for desired activity, and difficulty in recycling of metal contents as well as associated ligands. Polymer-based organophotoredox catalysts are promising alternatives and possess unique advantages such as easier synthesis from inexpensive starting material, longer excited state life time, broad range of activity, sustainability, and recyclability. In this research talk, time-resolved photoluminescence and femtosecond transient absorption (TA) spectroscopy measurements of three novel polymer-based organophotoredox catalysts will be presented. By our synthetic team, their catalytic activity has been proven in some highly valuable chemical transformations, that otherwise require transition metal complexes. Time-resolved spectroscopic investigations have demonstrated that photoinduced processes in these catalysts are similar to the transition metal complexes. Especially, intramolecular vibrational relaxation, internal conversion, and intersystem crossing from the S1 state to the T1 state all occur on a sub-picosecond timescale. The long lifetime of the T1 state ( 2-3 microsecond) renders these polymers potent oxidizing and reducing agents. A spectroscopic and kinetic model has been developed for global fitting of TA spectra in both the frequency and time domains. Implication of the current ultrafast spectroscopy studies of these novel molecules to their roles in photocatalysis will be discussed.

Comparative Analysis of Light-Harvesting Antennae and State Transition in chlorina and cpSRP Mutants.

PubMed

Wang, Peng; Grimm, Bernhard

2016-11-01

State transitions in photosynthesis provide for the dynamic allocation of a mobile fraction of light-harvesting complex II (LHCII) to photosystem II (PSII) in state I and to photosystem I (PSI) in state II. In the state I-to-state II transition, LHCII is phosphorylated by STN7 and associates with PSI to favor absorption cross-section of PSI. Here, we used Arabidopsis (Arabidopsis thaliana) mutants with defects in chlorophyll (Chl) b biosynthesis or in the chloroplast signal recognition particle (cpSRP) machinery to study the flexible formation of PS-LHC supercomplexes. Intriguingly, we found that impaired Chl b biosynthesis in chlorina1-2 (ch1-2) led to preferentially stabilized LHCI rather than LHCII, while the contents of both LHCI and LHCII were equally depressed in the cpSRP43-deficient mutant (chaos). In view of recent findings on the modified state transitions in LHCI-deficient mutants (Benson et al., 2015), the ch1-2 and chaos mutants were used to assess the influence of varying LHCI/LHCII antenna size on state transitions. Under state II conditions, LHCII-PSI supercomplexes were not formed in both ch1-2 and chaos plants. LHCII phosphorylation was drastically reduced in ch1-2, and the inactivation of STN7 correlates with the lack of state transitions. In contrast, phosphorylated LHCII in chaos was observed to be exclusively associated with PSII complexes, indicating a lack of mobile LHCII in chaos Thus, the comparative analysis of ch1-2 and chaos mutants provides new evidence for the flexible organization of LHCs and enhances our understanding of the reversible allocation of LHCII to the two photosystems. © 2016 American Society of Plant Biologists. All Rights Reserved.

Comparative Analysis of Light-Harvesting Antennae and State Transition in chlorina and cpSRP Mutants1[OPEN

PubMed Central

Wang, Peng

2016-01-01

State transitions in photosynthesis provide for the dynamic allocation of a mobile fraction of light-harvesting complex II (LHCII) to photosystem II (PSII) in state I and to photosystem I (PSI) in state II. In the state I-to-state II transition, LHCII is phosphorylated by STN7 and associates with PSI to favor absorption cross-section of PSI. Here, we used Arabidopsis (Arabidopsis thaliana) mutants with defects in chlorophyll (Chl) b biosynthesis or in the chloroplast signal recognition particle (cpSRP) machinery to study the flexible formation of PS-LHC supercomplexes. Intriguingly, we found that impaired Chl b biosynthesis in chlorina1-2 (ch1-2) led to preferentially stabilized LHCI rather than LHCII, while the contents of both LHCI and LHCII were equally depressed in the cpSRP43-deficient mutant (chaos). In view of recent findings on the modified state transitions in LHCI-deficient mutants (Benson et al., 2015), the ch1-2 and chaos mutants were used to assess the influence of varying LHCI/LHCII antenna size on state transitions. Under state II conditions, LHCII-PSI supercomplexes were not formed in both ch1-2 and chaos plants. LHCII phosphorylation was drastically reduced in ch1-2, and the inactivation of STN7 correlates with the lack of state transitions. In contrast, phosphorylated LHCII in chaos was observed to be exclusively associated with PSII complexes, indicating a lack of mobile LHCII in chaos. Thus, the comparative analysis of ch1-2 and chaos mutants provides new evidence for the flexible organization of LHCs and enhances our understanding of the reversible allocation of LHCII to the two photosystems. PMID:27663408

Encapsulating model complexity and landscape-scale analyses of state-and-transition simulation models: an application of ecoinformatics and juniper encroachment in sagebrush steppe ecosystems

USGS Publications Warehouse

O'Donnell, Michael

2015-01-01

State-and-transition simulation modeling relies on knowledge of vegetation composition and structure (states) that describe community conditions, mechanistic feedbacks such as fire that can affect vegetation establishment, and ecological processes that drive community conditions as well as the transitions between these states. However, as the need for modeling larger and more complex landscapes increase, a more advanced awareness of computing resources becomes essential. The objectives of this study include identifying challenges of executing state-and-transition simulation models, identifying common bottlenecks of computing resources, developing a workflow and software that enable parallel processing of Monte Carlo simulations, and identifying the advantages and disadvantages of different computing resources. To address these objectives, this study used the ApexRMS® SyncroSim software and embarrassingly parallel tasks of Monte Carlo simulations on a single multicore computer and on distributed computing systems. The results demonstrated that state-and-transition simulation models scale best in distributed computing environments, such as high-throughput and high-performance computing, because these environments disseminate the workloads across many compute nodes, thereby supporting analysis of larger landscapes, higher spatial resolution vegetation products, and more complex models. Using a case study and five different computing environments, the top result (high-throughput computing versus serial computations) indicated an approximate 96.6% decrease of computing time. With a single, multicore compute node (bottom result), the computing time indicated an 81.8% decrease relative to using serial computations. These results provide insight into the tradeoffs of using different computing resources when research necessitates advanced integration of ecoinformatics incorporating large and complicated data inputs and models. - See more at: http://aimspress.com/aimses/ch/reader/view_abstract.aspx?file_no=Environ2015030&flag=1#sthash.p1XKDtF8.dpuf

Epitaxial strain-mediated spin-state transitions: can we switch off magnetism?

NASA Astrophysics Data System (ADS)

Rondinelli, James; Spaldin, Nicola

2008-03-01

We use first-principles density functional theory calculations to explore spin-state transitions in epitaxially strained LaCoO3. While high-spin to low-spin state transitions in minerals are common in geophysics, where pressures can reach over 200 GPa, we explore whether heteroepitaxial strain can achieve similar transitions with moderate strain in thin films. LaCoO3 is known to undergo a low-spin (S=0, t2g^6eg^0) to intermediate-spin (S=1, t2g^5eg^1) or high-spin (S=2, t2g^4eg^2) state transition with increasing temperature, and thus makes it a promising candidate material for strain-mediated spin transitions. Here we discuss the physics of the low-spin transition and changes in the electronic structure of LaCoO3, most notably, the metal-insulator transition that accompanies the spin-state transitions with epitaxial strain. As thin film growth techniques continue to reach atomic-level precision, we suggest this is another approach for controlling magnetism in complex oxide heterostructures.

Widom Lines in Binary Mixtures of Supercritical Fluids.

PubMed

Raju, Muralikrishna; Banuti, Daniel T; Ma, Peter C; Ihme, Matthias

2017-06-08

Recent experiments on pure fluids have identified distinct liquid-like and gas-like regimes even under supercritical conditions. The supercritical liquid-gas transition is marked by maxima in response functions that define a line emanating from the critical point, referred to as Widom line. However, the structure of analogous state transitions in mixtures of supercritical fluids has not been determined, and it is not clear whether a Widom line can be identified for binary mixtures. Here, we present first evidence for the existence of multiple Widom lines in binary mixtures from molecular dynamics simulations. By considering mixtures of noble gases, we show that, depending on the phase behavior, mixtures transition from a liquid-like to a gas-like regime via distinctly different pathways, leading to phase relationships of surprising complexity and variety. Specifically, we show that miscible binary mixtures have behavior analogous to a pure fluid and the supercritical state space is characterized by a single liquid-gas transition. In contrast, immiscible binary mixture undergo a phase separation in which the clusters transition separately at different temperatures, resulting in multiple distinct Widom lines. The presence of this unique transition behavior emphasizes the complexity of the supercritical state to be expected in high-order mixtures of practical relevance.

Defect states of complexes involving a vacancy on the boron site in boronitrene

NASA Astrophysics Data System (ADS)

Ngwenya, T. B.; Ukpong, A. M.; Chetty, N.

2011-12-01

First principles calculations have been performed to investigate the ground state properties of freestanding monolayer hexagonal boronitrene (h-BN). We have considered monolayers that contain native point defects and their complexes, which form when the point defects bind with the boron vacancy on the nearest-neighbor position. The changes in the electronic structure are analyzed to show the extent of localization of the defect-induced midgap states. The variations in formation energies suggest that defective h-BN monolayers that contain carbon substitutional impurities are the most stable structures, irrespective of the changes in growth conditions. The high energies of formation of the boron vacancy complexes suggest that they are less stable, and their creation by ion bombardment would require high-energy ions compared to point defects. Using the relative positions of the derived midgap levels for the double vacancy complex, it is shown that the quasi-donor-acceptor pair interpretation of optical transitions is consistent with stimulated transitions between electron and hole states in boronitrene.

Computing with dynamical systems based on insulator-metal-transition oscillators

NASA Astrophysics Data System (ADS)

Parihar, Abhinav; Shukla, Nikhil; Jerry, Matthew; Datta, Suman; Raychowdhury, Arijit

2017-04-01

In this paper, we review recent work on novel computing paradigms using coupled oscillatory dynamical systems. We explore systems of relaxation oscillators based on linear state transitioning devices, which switch between two discrete states with hysteresis. By harnessing the dynamics of complex, connected systems, we embrace the philosophy of "let physics do the computing" and demonstrate how complex phase and frequency dynamics of such systems can be controlled, programmed, and observed to solve computationally hard problems. Although our discussion in this paper is limited to insulator-to-metallic state transition devices, the general philosophy of such computing paradigms can be translated to other mediums including optical systems. We present the necessary mathematical treatments necessary to understand the time evolution of these systems and demonstrate through recent experimental results the potential of such computational primitives.

Simulation evaluation of two VTOL control/display systems in IMC approach and shipboard landing

NASA Technical Reports Server (NTRS)

Merrick, V. K.

1984-01-01

Two control/display systems, which differed in overall complexity but were both designed for VTOL flight operations to and from small ships in instrument meteorological conditions (IMC), were tested using the Ames Flight Simulator for Advanced Aircraft (FSAA). Both systems have attitude command in transition and horizontal-velocity command in hover; the more complex system also has longitudinal-acceleration and flightpath-angle command in transition, and vertical-velocity command in hover. The most important overall distinction between the two systems for the viewpoint of implementation is that in one - the more complex - engine power and nozzle position are operated indirectly through flight controllers, whereas in the other they are operated directly by the pilot. Simulated landings were made on a moving model of a DD 963 Spruance-class destroyer. Acceptable transitions can be performed in turbulence of 3 m/sec rms using either system. Acceptable landings up to sea state 6 can be performed using the more complex system, and up to sea state 5 using the other system.

Complexity and multifractality of neuronal noise in mouse and human hippocampal epileptiform dynamics

NASA Astrophysics Data System (ADS)

Serletis, Demitre; Bardakjian, Berj L.; Valiante, Taufik A.; Carlen, Peter L.

2012-10-01

Fractal methods offer an invaluable means of investigating turbulent nonlinearity in non-stationary biomedical recordings from the brain. Here, we investigate properties of complexity (i.e. the correlation dimension, maximum Lyapunov exponent, 1/fγ noise and approximate entropy) and multifractality in background neuronal noise-like activity underlying epileptiform transitions recorded at the intracellular and local network scales from two in vitro models: the whole-intact mouse hippocampus and lesional human hippocampal slices. Our results show evidence for reduced dynamical complexity and multifractal signal features following transition to the ictal epileptiform state. These findings suggest that pathological breakdown in multifractal complexity coincides with loss of signal variability or heterogeneity, consistent with an unhealthy ictal state that is far from the equilibrium of turbulent yet healthy fractal dynamics in the brain. Thus, it appears that background noise-like activity successfully captures complex and multifractal signal features that may, at least in part, be used to classify and identify brain state transitions in the healthy and epileptic brain, offering potential promise for therapeutic neuromodulatory strategies for afflicted patients suffering from epilepsy and other related neurological disorders. This paper is based on chapter 5 of Serletis (2010 PhD Dissertation Department of Physiology, Institute of Biomaterials and Biomedical Engineering, University of Toronto).

Assessment of TD-DFT and LF-DFT for study of d − d transitions in first row transition metal hexaaqua complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlahović, Filip; Perić, Marko; Zlatar, Matija, E-mail: matijaz@chem.bg.ac.rs

2015-06-07

Herein, we present the systematic, comparative computational study of the d − d transitions in a series of first row transition metal hexaaqua complexes, [M(H{sub 2}O){sub 6}]{sup n+} (M{sup 2+/3+} = V {sup 2+/3+}, Cr{sup 2+/3+}, Mn{sup 2+/3+}, Fe{sup 2+/3+}, Co{sup 2+/3+}, Ni{sup 2+}) by the means of Time-dependent Density Functional Theory (TD-DFT) and Ligand Field Density Functional Theory (LF-DFT). Influence of various exchange-correlation (XC) approximations have been studied, and results have been compared to the experimental transition energies, as well as, to the previous high-level ab initio calculations. TD-DFT gives satisfactory results in the cases of d{sup 2}, d{supmore » 4}, and low-spin d{sup 6} complexes, but fails in the cases when transitions depend only on the ligand field splitting, and for states with strong character of double excitation. LF-DFT, as a non-empirical approach to the ligand field theory, takes into account in a balanced way both dynamic and non-dynamic correlation effects and hence accurately describes the multiplets of transition metal complexes, even in difficult cases such as sextet-quartet splitting in d{sup 5} complexes. Use of the XC functionals designed for the accurate description of the spin-state splitting, e.g., OPBE, OPBE0, or SSB-D, is found to be crucial for proper prediction of the spin-forbidden excitations by LF-DFT. It is shown that LF-DFT is a valuable alternative to both TD-DFT and ab initio methods.« less

Recognition of human activity characteristics based on state transitions modeling technique

NASA Astrophysics Data System (ADS)

Elangovan, Vinayak; Shirkhodaie, Amir

2012-06-01

Human Activity Discovery & Recognition (HADR) is a complex, diverse and challenging task but yet an active area of ongoing research in the Department of Defense. By detecting, tracking, and characterizing cohesive Human interactional activity patterns, potential threats can be identified which can significantly improve situation awareness, particularly, in Persistent Surveillance Systems (PSS). Understanding the nature of such dynamic activities, inevitably involves interpretation of a collection of spatiotemporally correlated activities with respect to a known context. In this paper, we present a State Transition model for recognizing the characteristics of human activities with a link to a prior contextbased ontology. Modeling the state transitions between successive evidential events determines the activities' temperament. The proposed state transition model poses six categories of state transitions including: Human state transitions of Object handling, Visibility, Entity-entity relation, Human Postures, Human Kinematics and Distance to Target. The proposed state transition model generates semantic annotations describing the human interactional activities via a technique called Casual Event State Inference (CESI). The proposed approach uses a low cost kinect depth camera for indoor and normal optical camera for outdoor monitoring activities. Experimental results are presented here to demonstrate the effectiveness and efficiency of the proposed technique.

77 FR 28421 - Supplemental Draft Environmental Impact Statement for the Central Corridor Light Rail Transit...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-14

... DEPARTMENT OF TRANSPORTATION Federal Transit Administration Supplemental Draft Environmental Impact Statement for the Central Corridor Light Rail Transit Project, Minneapolis and Saint Paul, MN... Minneapolis and Saint Paul downtown areas as well as the University of Minnesota and the State Capitol complex...

Approaches to incorporating climate change effects in state and transition simulation models of vegetation

Treesearch

Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham

2012-01-01

Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...

Chiral diamines. 1. Relative energies of (-)-sparteine conformers, interconversion barriers, and alkyllithium complexes

NASA Astrophysics Data System (ADS)

Wiberg, K. B.; Bailey, W. F.

2000-12-01

The structures of the four lower energy sparteine complexes were examined at several theoretical levels including B3P86/6-31G∗ and B3P86/6-311+G∗. The transition states for interconverting two pairs of conformers were determined using the synchronous transit-guided quasi-Newton procedure. Complexes with lithium hydride and propyllithium also were examined. The bidentate complexes formed from conformer 1b and propyllithium had two conformations with essentially the same energy. This may account for the low enantioselectivity observed in the reaction of alkyllithium-sparteine complexes with carbonyl compounds.

Metastable state en route to traveling-wave synchronization state

NASA Astrophysics Data System (ADS)

Park, Jinha; Kahng, B.

2018-02-01

The Kuramoto model with mixed signs of couplings is known to produce a traveling-wave synchronized state. Here, we consider an abrupt synchronization transition from the incoherent state to the traveling-wave state through a long-lasting metastable state with large fluctuations. Our explanation of the metastability is that the dynamic flow remains within a limited region of phase space and circulates through a few active states bounded by saddle and stable fixed points. This complex flow generates a long-lasting critical behavior, a signature of a hybrid phase transition. We show that the long-lasting period can be controlled by varying the density of inhibitory/excitatory interactions. We discuss a potential application of this transition behavior to the recovery process of human consciousness.

Assessing the density functional theory-based multireference configuration interaction (DFT/MRCI) method for transition metal complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Escudero, Daniel, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de; Thiel, Walter, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de

2014-05-21

We report an assessment of the performance of density functional theory-based multireference configuration interaction (DFT/MRCI) calculations for a set of 3d- and 4d-transition metal (TM) complexes. The DFT/MRCI results are compared to published reference data from reliable high-level multi-configurational ab initio studies. The assessment covers the relative energies of different ground-state minima of the highly correlated CrF{sub 6} complex, the singlet and triplet electronically excited states of seven typical TM complexes (MnO{sub 4}{sup −}, Cr(CO){sub 6}, [Fe(CN){sub 6}]{sup 4−}, four larger Fe and Ru complexes), and the corresponding electronic spectra (vertical excitation energies and oscillator strengths). It includes comparisons withmore » results from different flavors of time-dependent DFT (TD-DFT) calculations using pure, hybrid, and long-range corrected functionals. The DFT/MRCI method is found to be superior to the tested TD-DFT approaches and is thus recommended for exploring the excited-state properties of TM complexes.« less

Control and instanton trajectories for random transitions in turbulent flows

NASA Astrophysics Data System (ADS)

Bouchet, Freddy; Laurie, Jason; Zaboronski, Oleg

2011-12-01

Many turbulent systems exhibit random switches between qualitatively different attractors. The transition between these bistable states is often an extremely rare event, that can not be computed through DNS, due to complexity limitations. We present results for the calculation of instanton trajectories (a control problem) between non-equilibrium stationary states (attractors) in the 2D stochastic Navier-Stokes equations. By representing the transition probability between two states using a path integral formulation, we can compute the most probable trajectory (instanton) joining two non-equilibrium stationary states. Technically, this is equivalent to the minimization of an action, which can be related to a fluid mechanics control problem.

Photodissociation Studies of Metal-Containing Clusters and Complexes

NASA Astrophysics Data System (ADS)

Pilgrim, Jeffrey Scott

1995-01-01

There have been two major areas of investigation for researchers working with laser ablation in molecular beams. The first area is the study of weakly-bound complexes. These complexes are bound by electrostatic interactions. In the present study the weakly bound interactions of the rare gases with the magnesium ion are investigated with electronic spectroscopy. The second major area is the study of metal and metal-containing clusters. Examples of previous investigations are the alkali metal clusters and the fullerenes. The present investigation is on metal -carbon clusters. The so-called metallo-carbohedrenes and metal-carbon nanocrystals are studied. Resonance enhanced photodissociation spectroscopy is used to obtain electronic excitation spectra of the Mg^+-rare gas species in the ultraviolet region. This investigation is facilitated by a reflectron time-of-flight mass spectrometer. The interaction of the rare gas with the metal ion is attributed to a "solvation" of the atomic ion transition. Simple bonding arguments predict that the excited state is more bound than the ground state for these complexes. This will result in a shift of the complex vibronic origin to lower energy from the atomic ion transition. This is exactly what is observed in the experiment with progressively larger shifts for the heavier rare gases. The electronic excitation spectra allow the vibrational frequencies and anharmonicities for these complexes to be obtained for the excited state. In turn, the excited state bond dissociation energies can be determined. Finally, conservation of energy allows calculation of the ground state bond dissociation energies. In the metal-carbon systems the stability of the metallo-carbohedrene, met-car, stoichiometry is shown to extend into the transition period at least to the iron group. Photodissociation with a 532 nm laser causes a loss of metal atoms for met-cars formed with first row transition metals and a loss of metal-carbon units for met-cars formed from second-row transition metal atoms. Larger metal-carbon clusters are found to be face-centered-cubic nanocrystals. Photodissociation of these nanocrystals causes fragmentation into smaller nanocrystals. In addition, nanocrystals also dissociatively rearrange into the met -car structure. Two of the metal-carbon nanocrystals ( rm Ti_{14}C_{13 }^+ and rm V_{14 }C_{13}^+) fragment into the met-car with a trapped carbon atom.

Transitions between multiple equilibria of paleo climate: a glimpse in to the dynamics of abrupt climate change

NASA Astrophysics Data System (ADS)

Ferreira, David; Marshall, John; Ito, Takamitsu; McGee, David; Moreno-Chamarro, Eduardo

2017-04-01

The dynamics regulating large climatic transitions such as glacial-interglacial cycles or DO events remains a puzzle. Forcings behind these transitions are not robustly identified and potential candidates (e.g. Milankovitch cycles, freshwater perturbations) often appear too weak to explain such dramatic transitions. A potential solution to this long-standing puzzle is that Earth's climate is endowed with multiple equilibrium states of global extent. Such states are commonly found in low-order or conceptual climate models, but it is unclear whether a system as complex as Earth's climate can sustain multiple equilibrium states. Here we report that multiple equilibrium states of the climate system are also possible in a complex, fully dynamical coupled ocean-atmosphere-sea ice GCM with idealized Earth-like geometry, resolved weather systems and a hydrological cycle. In our model, two equilibrium states coexist for the same parameters and external forcings: a Warm climate with a small Northern hemisphere sea ice cap and a large southern one and a Cold climate with large ice caps at both poles. The dynamical states of the Warm and Cold solutions exhibit striking similarities with our present-day climate and the climate of the Last Glacial Maximum, respectively. A carbon cycle model driven by the two dynamical states produces an atmospheric pCO2 draw-down of about 110 pm between the Warm and Cold states, close to Glacial-Interglacial differences found in ice cores. Mechanism controlling the existence of the multiple states and changes in the atmospheric CO2 will be briefly presented. Finally we willdescribe transition experiments from the Cold to the Warm state, focusing on the lead-lags in the system, notably between the Northern and Southern Hemispheres climates.

Electronic structure of the [MNH2]+ (M = Sc-Cu) complexes.

PubMed

Hendrickx, Marc F A; Clima, Sergiu

2006-11-23

B3LYP geometry optimizations for the [MNH2]+ complexes of the first-row transition metal cations (Sc+-Cu+) were performed. Without any exception the ground states of these unsaturated amide complexes were calculated to possess planar geometries. CASPT2 binding energies that were corrected for zero-point energies and including relativistic effects show a qualitative trend across the series that closely resembles the experimental observations. The electronic structures for the complexes of the early and middle transition metal cations (Sc+-Co+) differ from the electronic structures derived for the complexes of the late transition metal cations (Ni+ and Cu+). For the former complexes the relative higher position of the 3d orbitals above the singly occupied 2p(pi) HOMO of the uncoordinated NH2 induces an electron transfer from the 3d shell to 2p(pi). The stabilization of the 3d orbitals from the left to the right along the first-row transition metal series causes these orbitals to become situated below the HOMO of the NH2 ligand for Ni+ and Cu+, preventing a transfer from occurring in the [MNH2]+ complexes of these metal cations. Analysis of the low-lying states of the amide complexes revealed a rather unique characteristic of their electronic structures that was found across the entire series. Rather exceptionally for the whole of chemistry, pi-type interactions were calculated to be stronger than the corresponding sigma-type interactions. The origin of this extraordinary behavior can be ascribed to the low-lying sp2 lone pair orbital of the NH2 ligand with respect to the 3d level.

A stromal region of cytochrome b6f subunit IV is involved in the activation of the Stt7 kinase in Chlamydomonas

PubMed Central

Zito, Francesca; Blangy, Stéphanie; Auroy, Pascaline; Johnson, Xenie; Peltier, Gilles

2017-01-01

The cytochrome (cyt) b6f complex and Stt7 kinase regulate the antenna sizes of photosystems I and II through state transitions, which are mediated by a reversible phosphorylation of light harvesting complexes II, depending on the redox state of the plastoquinone pool. When the pool is reduced, the cyt b6f activates the Stt7 kinase through a mechanism that is still poorly understood. After random mutagenesis of the chloroplast petD gene, coding for subunit IV of the cyt b6f complex, and complementation of a ΔpetD host strain by chloroplast transformation, we screened for impaired state transitions in vivo by chlorophyll fluorescence imaging. We show that residues Asn122, Tyr124, and Arg125 in the stromal loop linking helices F and G of cyt b6f subunit IV are crucial for state transitions. In vitro reconstitution experiments with purified cyt b6f and recombinant Stt7 kinase domain show that cyt b6f enhances Stt7 autophosphorylation and that the Arg125 residue is directly involved in this process. The peripheral stromal structure of the cyt b6f complex had, until now, no reported function. Evidence is now provided of a direct interaction with Stt7 on the stromal side of the membrane. PMID:29078388

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

NASA Technical Reports Server (NTRS)

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Radiationless Transitions and Excited-State Absorption in Tunable Laser Materials

DTIC Science & Technology

1992-09-01

chromium - doped halide elpasolites K2 NaGaF 6 , K2 NaScF6 and Cs2NaYCl 6 , and on the laser-active TI0 (l) color center in KCI. Luminescence lifetime...Non-radiative transitions, transition metals, chromium , ¶SLWmER o E tunable lasers, high pressure, luminescence, color centers ൙. SECURITY O...quenching and excited-state absorption are major loss mechanisms. Low-crystal-field chromium complexes in ordered perovskites of cubic elpasolite structure

A code for analysis of the fine structure in near-rigid weakly-bonded open-shell complexes that consist of a diatomic radical in a Σ3 state and a closed-shell molecule

NASA Astrophysics Data System (ADS)

Fawzy, Wafaa M.

2010-10-01

A FORTRAN code is developed for simulation and fitting the fine structure of a planar weakly-bonded open-shell complex that consists of a diatomic radical in a Σ3 electronic state and a diatomic or a polyatomic closed-shell molecule. The program sets up the proper total Hamiltonian matrix for a given J value and takes account of electron-spin-electron-spin, electron-spin rotation interactions, and the quartic and sextic centrifugal distortion terms within the complex. Also, R-dependence of electron-spin-electron-spin and electron-spin rotation couplings are considered. The code does not take account of effects of large-amplitude internal rotation of the diatomic radical within the complex. It is assumed that the complex has a well defined equilibrium geometry so that effects of large amplitude motion are negligible. Therefore, the computer code is suitable for a near-rigid rotor. Numerical diagonalization of the matrix provides the eigenvalues and the eigenfunctions that are necessary for calculating energy levels, frequencies, relative intensities of infrared or microwave transitions, and expectation values of the quantum numbers within the complex. Goodness of all the quantum numbers, with exception of J and parity, depends on relative sizes of the product of the rotational constants and quantum numbers (i.e. BJ, CJ, and AK), electron-spin-electron-spin, and electron-spin rotation couplings, as well as the geometry of the complex. Therefore, expectation values of the quantum numbers are calculated in the eigenfunctions basis of the complex. The computational time for the least squares fits has been significantly reduced by using the Hellman-Feynman theory for calculating the derivatives. The computer code is useful for analysis of high resolution infrared and microwave spectra of a planar near-rigid weakly-bonded open-shell complex that contains a diatomic fragment in a Σ3 electronic state and a closed-shell molecule. The computer program was successfully applied to analysis and fitting the observed high resolution infrared spectra of the O 2sbnd HF/O 2sbnd DF and O 2sbnd N 2O complexes. Test input file for simulation and fitting the high resolution infrared spectrum of the O 2sbnd DF complex is provided. Program summaryProgram title: TSIG_COMP Catalogue identifier: AEGM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 10 030 No. of bytes in distributed program, including test data, etc.: 51 663 Distribution format: tar.gz Programming language: Fortran 90, free format Computer: SGI Origin 3400, workstations and PCs Operating system: Linux, UNIX and Windows (see Restrictions below) RAM: Case dependent Classification: 16.2 Nature of problem: TSIG_COMP calculates frequencies, relative intensities, and expectation values of the various quantum numbers and parities of bound states involved in allowed ro-vibrational transitions in semi-rigid planar weakly-bonded open-shell complexes. The complexes of interest contain a free radical in a Σ3 state and a closed-shell partner, where the electron-spin-electron-spin interaction, electron-spin rotation interaction, and centrifugal forces significantly modify the spectral patterns. To date, ab initio methods are incapable of taking these effects into account to provide accurate predictions for the ro-vibrational energy levels of the complexes of interest. In the TSIG_COMP program, the problem is solved by using the proper effective Hamiltonian and molecular basis set. Solution method: The program uses a Hamiltonian operator that takes into account vibration, end-over-end rotation, electron-spin-electron-spin and electron-spin rotation interactions as well as the various centrifugal distortion terms. The Hamiltonian operator and the molecular basis set are used to set up the Hamiltonian matrix in the inertial axis system of the complex of interest. Diagonalization of the Hamiltonian matrix provides the eigenvalues and the eigenfunctions for the bound ro-vibrational states. These eigenvalues and eigenfunctions are used to calculate frequencies and relative intensities of the allowed infrared or microwave transitions as well as expectation values of all the quantum numbers and parities of states involved in the transitions. The program employs the method of least squares fits to fit the observed frequencies to the calculated frequencies to provide the molecular parameters that determine the geometry of the complex of interest. Restrictions: The number of transitions and parameters included in the fits is limited to 80 parameters and 200 transitions. However, these numbers can be increased by adjusting dimensions of the arrays (not recommended). Running the program under MS windows is recommended for simulations of any number of transitions and for fitting a relatively small number of parameters and transitions (maximum 15 parameters and 82 transitions), for fitting larger number of parameters run time error may occur. Because spectra of weakly bonded complexes are recorded at low temperatures, in most of cases fittings can be performed under MS windows. Running time: Problem-dependent. The provided test input for Linux fits 82 transitions and 21 parameters, the actual run time is 62 minutes. The provided test input file for MS windows fits 82 transitions and 15 parameters; the actual runtime is 5 minutes.

Allylic amination reactivity of Ni, Pd, and Pt heterobimetallic and monometallic complexes.

PubMed

Carlsen, Ryan W; Ess, Daniel H

2016-06-14

Transition metal heterobimetallic complexes with dative metal-metal interactions have the potential for novel fast reactivity. There are few studies that both compare the reactivity of different metal centers in heterobimetallic complexes and compare bimetallic reactivity to monometallic reactivity. Here we report density-functional calculations that show the reactivity of [Cl2Ti(N(t)BuPPh2)2M(II)(η(3)-methallyl)] heterobimetallic complexes for allylic amination follows M = Ni > Pd > Pt. This reactivity trend was not anticipated since the amine addition transition state involves M(II) to M(0) reduction and this could disadvantage Ni. Comparison of heterobimetallic complexes to the corresponding monometallic (CH2)2(N(t)BuPPh2)2M(II)(η(3)-methallyl) complexes reveals that this reactivity trend is due to the bimetallic interaction and that the bimetallic interaction significantly lowers the barrier height for amine addition by >10 kcal mol(-1). The impact of the early transition metal center on the amination addition barrier height depends on the late transition metal center. The lowest barrier heights for this reaction occur when late and early transition metal centers are from the same periodic table row.

Solar chemistry of metal complexes

NASA Astrophysics Data System (ADS)

Gray, H. B.; Maverick, A. W.

1981-12-01

Electronic excited states of certain transition metal complexes undergo oxidation-reduction reactions that store chemical energy. Such reactions have been extensively explored for mononuclear complexes. Two classes of polynuclear species exhibit similar properties, and these complexes are now being studied as possible homogeneous sensitizer-catalysts for hydrogen production from aqueous solutions.

Performance and state-space analyses of systems using Petri nets

NASA Technical Reports Server (NTRS)

Watson, James Francis, III

1992-01-01

The goal of any modeling methodology is to develop a mathematical description of a system that is accurate in its representation and also permits analysis of structural and/or performance properties. Inherently, trade-offs exist between the level detail in the model and the ease with which analysis can be performed. Petri nets (PN's), a highly graphical modeling methodology for Discrete Event Dynamic Systems, permit representation of shared resources, finite capacities, conflict, synchronization, concurrency, and timing between state changes. By restricting the state transition time delays to the family of exponential density functions, Markov chain analysis of performance problems is possible. One major drawback of PN's is the tendency for the state-space to grow rapidly (exponential complexity) compared to increases in the PN constructs. It is the state space, or the Markov chain obtained from it, that is needed in the solution of many problems. The theory of state-space size estimation for PN's is introduced. The problem of state-space size estimation is defined, its complexities are examined, and estimation algorithms are developed. Both top-down and bottom-up approaches are pursued, and the advantages and disadvantages of each are described. Additionally, the author's research in non-exponential transition modeling for PN's is discussed. An algorithm for approximating non-exponential transitions is developed. Since only basic PN constructs are used in the approximation, theory already developed for PN's remains applicable. Comparison to results from entropy theory show the transition performance is close to the theoretic optimum. Inclusion of non-exponential transition approximations improves performance results at the expense of increased state-space size. The state-space size estimation theory provides insight and algorithms for evaluating this trade-off.

Satellite remote sensing of landscape freeze/thaw state dynamics for complex Topography and Fire Disturbance Areas Using multi-sensor radar and SRTM digital elevation models

NASA Technical Reports Server (NTRS)

Podest, Erika; McDonald, Kyle; Kimball, John; Randerson, James

2003-01-01

We characterize differences in radar-derived freeze/thaw state, examining transitions over complex terrain and landscape disturbance regimes. In areas of complex terrain, we explore freezekhaw dynamics related to elevation, slope aspect and varying landcover. In the burned regions, we explore the timing of seasonal freeze/thaw transition as related to the recovering landscape, relative to that of a nearby control site. We apply in situ biophysical measurements, including flux tower measurements to validate and interpret the remotely sensed parameters. A multi-scale analysis is performed relating high-resolution SAR backscatter and moderate resolution scatterometer measurements to assess trade-offs in spatial and temporal resolution in the remotely sensed fields.

A Networks Approach to Modeling Enzymatic Reactions.

PubMed

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

Evaluating transition state structures of vanadium-phosphatase protein complexes using shape analysis.

PubMed

Sánchez-Lombardo, Irma; Alvarez, Santiago; McLauchlan, Craig C; Crans, Debbie C

2015-06-01

Shape analysis of coordination complexes is well-suited to evaluate the subtle distortions in the trigonal bipyramidal (TBPY-5) geometry of vanadium coordinated in the active site of phosphatases and characterized by X-ray crystallography. Recent studies using the tau (τ) analysis support the assertion that vanadium is best described as a trigonal bipyramid, because this geometry is the ideal transition state geometry of the phosphate ester substrate hydrolysis (C.C. McLauchlan, B.J. Peters, G.R. Willsky, D.C. Crans, Coord. Chem. Rev. http://dx.doi.org/10.1016/j.ccr.2014.12.012 ; D.C. Crans, M.L. Tarlton, C.C. McLauchlan, Eur. J. Inorg. Chem. 2014, 4450-4468). Here we use continuous shape measures (CShM) analysis to investigate the structural space of the five-coordinate vanadium-phosphatase complexes associated with mechanistic transformations between the tetrahedral geometry and the five-coordinate high energy TBPY-5 geometry was discussed focusing on the protein tyrosine phosphatase 1B (PTP1B) enzyme. No evidence for square pyramidal geometries was observed in any vanadium-protein complexes. The shape analysis positioned the metal ion and the ligands in the active site reflecting the mechanism of the cleavage of the organic phosphate in a phosphatase. We identified the umbrella distortions to be directly on the reaction path between tetrahedral phosphate and the TBPY-5-types of high-energy species. The umbrella distortions of the trigonal bipyramid are therefore identified as being the most relevant types of transition state structures for the phosphoryl group transfer reactions for phosphatases and this may be related to the possibility that vanadium is an inhibitor for enzymes that support both exploded and five-coordinate transition states. Copyright © 2015 Elsevier Inc. All rights reserved.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

PubMed

Jacobson, Leif D; Bochevarov, Art D; Watson, Mark A; Hughes, Thomas F; Rinaldo, David; Ehrlich, Stephan; Steinbrecher, Thomas B; Vaitheeswaran, S; Philipp, Dean M; Halls, Mathew D; Friesner, Richard A

2017-11-14

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis.

PubMed

Burschowsky, Daniel; van Eerde, André; Ökvist, Mats; Kienhöfer, Alexander; Kast, Peter; Hilvert, Donald; Krengel, Ute

2014-12-09

For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.

Isotopologue-selective excitation studied via optical-optical double resonance using the E3 Σ1+(63S1) ←A3Π0+(53P1) ←X1Σ0+(51S0) transitions in CdAr and CdKr van der Waals complexes

NASA Astrophysics Data System (ADS)

Urbańczyk, T.; Dudek, J.; Koperski, J.

2018-06-01

A method of experimental selection of molecular isotopologues using optical-optical double resonance (OODR) scheme and supersonic beam source of van der Waals (vdW) complexes is presented. Due to an appropriately large isotopic shift, the proper choice of a wavenumber of a sufficiently narrowband laser in the first transition of OODR scheme can lead to a selective isotopologue excitation to the intermediate state. Thanks to this approach, it is possible to select some of the isotopologues which subsequently give a contribution to laser induced fluorescence (LIF) signal originated from the final state of OODR. In this article, results of tests of the proposed method that employs the E3 Σ1+ ←A3Π0+ ←X1Σ0+ transitions in two vdW complexes, CdKr and CdAr, are presented and analysed.

Modeling the dynamic responses of riparian vegetation and salmon habitat in the Oregon Coast Range with state-and-transition models

Treesearch

Steven M. Wondzell; Agnieszka Przeszlowska; Dirk Pflugmacher; Miles A. Hemstrom; Peter A. Bisson

2012-01-01

Interactions between landuse and ecosystem change are complex, especially in riparian zones. To date, few models are available to project the influence of alternative landuse practices, natural disturbance and plant succession on the likely future conditions of riparian zones and aquatic habitats across large spatial extents. A state and transition approach was used to...

Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron†

PubMed Central

Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; St Maurice, Martin

2012-01-01

Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg2+-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we solved the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and cupferron, to 2.2-Å resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state/intermediate since its binding affinity to 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, cupferron, and the ground state analogue (S)-atrolacatate reveal that the para-carbon of the substrate phenyl ring moves by 0.8–1.2 Å between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to MR with bound (S)-atrolactate, the intermediate-Mg2+ distance shortens, suggesting a tighter complex with the catalytic Mg2+. In addition, Tyr 54 moves nearer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle. PMID:22264153

XANES, EXAFS and Kbeta spectroscopic studies of the oxygen-evolving complex in Photosystem II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robblee, John Henry

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S 3 → [S 4] → S 0 transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kβ X-ray emission spectroscopy (Kb XES) to this problem for the first time. The Kβ XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electronmore » paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S 2 → S 3 transition, in contrast to the S 0 → S 1 and S 1 → S 2 transitions, does not involve a Mn-centered oxidation. This is rationalized by manganese μ-oxo bridge radical formation during the S 2 → S 3 transition. Using extended X-ray absorption fine structure (EXAFS) spectroscopy, the local environment of the Mn atoms in the S 0 state has been structurally characterized. These results show that the Mn-Mn distance in one of the di-μ-oxo-bridged Mn-Mn moieties increases from 2.7 Å in the S 1} state to 2.85 Å in the S 0 state. Furthermore, evidence is presented that shows three di-μ-oxo binuclear Mn 2 clusters may be present in the OEC, which is contrary to the widely held theory that two such clusters are present in the OEC. The EPR properties of the S 0 state have been investigated and a characteristic ''multiline'' signal in the S 0 state has been discovered in the presence of methanol. This provides the first direct confirmation that the native S 0 state is paramagnetic. In addition, this signal was simulated using parameters derived from three possible oxidation states of Mn in the S 0 state. The dichroic nature of X-rays from synchrotron radiation and single-crystal Mn complexes have been exploited to selectively probe Mn-ligand bonds using XANES and EXAFS spectroscopy. The results from single-crystal Mn complexes show that dramatic dichroism exists in these complexes, and are suggestive of a promising future for single-crystal studies of PS II.« less

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

PubMed

Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

2010-06-03

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

PubMed Central

Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

2010-01-01

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590

Imaging ultrafast excited state pathways in transition metal complexes by X-ray transient absorption and scattering using X-ray free electron laser source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Lin X.; Shelby, Megan L.; Lestrange, Patrick J.

2016-01-01

This report will describe our recent studies of transition metal complex structural dynamics on the fs and ps time scales using an X-ray free electron laser source, Linac Coherent Light Source (LCLS). Ultrafast XANES spectra at the Ni K-edge of nickel(II) tetramesitylporphyrin (NiTMP) were successfully measured for optically excited state at a timescale from 100 fs to 50 ps, providing insight into its sub-ps electronic and structural relaxation processes. Importantly, a transient reduced state Ni(I) (π, 3dx2-y2) electronic state is captured through the interpretation of a short-lived excited state absorption on the low-energy shoulder of the edge, which is aidedmore » by the computation of X-ray transitions for postulated excited electronic states. The observed and computed inner shell to valence orbital transition energies demonstrate and quantify the influence of electronic configuration on specific metal orbital energies. A strong influence of the valence orbital occupation on the inner shell orbital energies indicates that one should not use the transition energy from 1s to other orbitals to draw conclusions about the d-orbital energies. For photocatalysis, a transient electronic configuration could influence d-orbital energies up to a few eV and any attempt to steer the reaction pathway should account for this to ensure that external energies can be used optimally in driving desirable processes. NiTMP structural evolution and the influence of the porphyrin macrocycle conformation on relaxation kinetics can be likewise inferred from this study.« less

Parents' perspectives on caring for children after solid organ transplant.

PubMed

Lerret, Stacee M; Johnson, Norah L; Haglund, Kristin A

2017-07-01

To explore parents' experiences of the transition from hospital to home and complex chronic illness management following their children's solid organ transplant (SOT). Qualitative component of a larger mixed methods longitudinal study. Parents of SOT recipients were interviewed three times following hospital discharge from five major pediatric transplant hospitals in the United States. Analysis of parent interviews (N = 48) resulted in three themes that characterized the phases of transition to home and complex chronic illness care. Three themes, corresponding to the three time periods of data collection, included "getting back to normal" at 3 weeks, "becoming routine" at 3 months, and "facing a future" at 6 months. Challenges families experienced over the course of their transition are also described. The transition from hospital to home and complex chronic condition care is challenging and changes over time. Nurses are called upon to prepare parents to become knowledgeable and confident to care for the child after hospital discharge. Nurses can best support families in transition after SOT by anticipating and understanding their dynamic challenging complex care needs. © 2017 Wiley Periodicals, Inc.

Generating probabilistic Boolean networks from a prescribed transition probability matrix.

PubMed

Ching, W-K; Chen, X; Tsing, N-K

2009-11-01

Probabilistic Boolean networks (PBNs) have received much attention in modeling genetic regulatory networks. A PBN can be regarded as a Markov chain process and is characterised by a transition probability matrix. In this study, the authors propose efficient algorithms for constructing a PBN when its transition probability matrix is given. The complexities of the algorithms are also analysed. This is an interesting inverse problem in network inference using steady-state data. The problem is important as most microarray data sets are assumed to be obtained from sampling the steady-state.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Rotational cross sections and rate coefficients of aluminium monoxide AlO(X2Σ+) induced by its collision with He(1 S) at low temperature

NASA Astrophysics Data System (ADS)

Tchakoua, Théophile; Nkot Nkot, Pierre René; Fifen, Jean Jules; Nsangou, Mama; Motapon, Ousmanou

2018-06-01

We present the first potential energy surface (PES) for the AlO(X2Σ+)-He(1 S) van der Waals complex. This PES has been calculated at the RCCSD(T) level of theory. The mixed Gaussian/Exponential Extrapolation Scheme of complete basis set [CBS(D,T,Q)] was employed. The PES was fitted using global analytical method. This fitted PES was used subsequently in the close-coupling approach for the computation of the state-to-state collisional excitation cross sections of the fine-structure levels of the AlO-He complex. Collision energies were taken up to 2500 cm-1 and they yield after thermal averaging, state-to-state rate coefficients up to 300 K. The propensity rules between the lowest fine-structure levels were studied. These rules show, on one hand, a strong propensity in favour of odd ΔN transitions, and on the other hand, that cross sections and collisional rate coefficients for Δj = ΔN transitions are larger than those for Δj ≠ ΔN transitions.

Time-resolved vibrational spectroscopy detects protein-based intermediates in the photosynthetic oxygen-evolving cycle.

PubMed

Barry, Bridgette A; Cooper, Ian B; De Riso, Antonio; Brewer, Scott H; Vu, Dung M; Dyer, R Brian

2006-05-09

Photosynthetic oxygen production by photosystem II (PSII) is responsible for the maintenance of aerobic life on earth. The production of oxygen occurs at the PSII oxygen-evolving complex (OEC), which contains a tetranuclear manganese (Mn) cluster. Photo-induced electron transfer events in the reaction center lead to the accumulation of oxidizing equivalents on the OEC. Four sequential photooxidation reactions are required for oxygen production. The oxidizing complex cycles among five oxidation states, called the S(n) states, where n refers to the number of oxidizing equivalents stored. Oxygen release occurs during the S(3)-to-S(0) transition from an unstable intermediate, known as the S(4) state. In this report, we present data providing evidence for the production of an intermediate during each S state transition. These protein-derived intermediates are produced on the microsecond to millisecond time scale and are detected by time-resolved vibrational spectroscopy on the microsecond time scale. Our results suggest that a protein-derived conformational change or proton transfer reaction precedes Mn redox reactions during the S(2)-to-S(3) and S(3)-to-S(0) transitions.

Direct measurement of the low temperature spin state transitions in La1-xSrxCoO3 (0.05 < x < 0.3)

NASA Astrophysics Data System (ADS)

Gulec, A.; Klie, R. F.

2014-12-01

Sr-doped LaCoO3 has a complex magnetic phase diagram, which is believed to be directly correlated to changes in the crystal structure and ordering of the Co3+ spin states. In this work, we study the low temperature Co3+-ion spin state transitions in Sr-doped LaCoO3 around the critical doping concentration where a metal to insulator transition has been observed using electron energy-loss spectroscopy of the O K-edge combined with the Co L-edge fine structure. We measure the local spin state of the Co3+-ions and we demonstrate that the Co3+ spin-state transition only occurs in La0.95Sr0.05CoO3 single-crystal materials in the temperature range accessible by LN2 in-situ cooling, while no structural symmetry change is observed. The presence of this low-temperature spin-state transition in La1-xSrxCoO3 (x < 0.17) has been proposed as the origin of the percolative magnetic ordering in doped LaCoO3.

Mechanochemical effect in the iron(III) spin crossover complex [Fe(3-MeO-salenEt2]PF6 as studied by heat capacity calorimetry.

PubMed

Sorai, Michio; Burriel, Ramón; Westrum, Edgar F; Hendrickson, David N

2008-04-10

Magnetic and thermal properties of the iron(III) spin crossover complex [Fe(3MeO-salenEt)(2)]PF(6) are very sensitive to mechanochemical perturbations. Heat capacities for unperturbed and differently perturbed samples were precisely determined by adiabatic calorimetry at temperatures in the 10-300 K range. The unperturbed compound shows a cooperative spin crossover transition at 162.31 K, presenting a hysteresis of 2.8 K. The anomalous enthalpy and entropy contents of the transition were evaluated to be Delta(trs)H = 5.94 kJ mol(-1) and Delta(trs)S = 36.7 J K(-1) mol(-1), respectively. By mechanochemical treatments, (1) the phase transition temperature was lowered by 1.14 K, (2) the enthalpy and entropy gains at the phase transition due to the spin crossover phenomenon were diminished to Delta(trs)H = 4.94 kJ mol(-1) and Delta(trs)S = 31.1 J K(-1) mol(-1), and (3) the lattice heat capacities were larger than those of the unperturbed sample over the whole temperature range. In spite of different mechanical perturbations (grinding with a mortar and pestle and grinding in a ball-mill), two sets of heat capacity measurements provided basically the same results. The mechanochemical perturbation exerts its effect more strongly on the low-spin state than on the high-spin state. It shows a substantial increase of the number of iron(III) ions in the high-spin state below the transition temperature. The heat capacities of the diamagnetic cobalt(III) analogue [Co(3MeO-salenEt)(2)]PF(6) also were measured. The lattice heat capacity of the iron compounds has been estimated from either the measurements on the cobalt complex using a corresponding states law or the effective frequency distribution method. These estimations have been used for the evaluation of the transition anomaly.

Probing the transition state for nucleic acid hybridization using phi-value analysis.

PubMed

Kim, Jandi; Shin, Jong-Shik

2010-04-27

Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

Quantitative Interpretation of Multifrequency Multimode EPR Spectra of Metal Containing Proteins, Enzymes, and Biomimetic Complexes.

PubMed

Petasis, Doros T; Hendrich, Michael P

2015-01-01

Electron paramagnetic resonance (EPR) spectroscopy has long been a primary method for characterization of paramagnetic centers in materials and biological complexes. Transition metals in biological complexes have valence d-orbitals that largely define the chemistry of the metal centers. EPR spectra are distinctive for metal type, oxidation state, protein environment, substrates, and inhibitors. The study of many metal centers in proteins, enzymes, and biomimetic complexes has led to the development of a systematic methodology for quantitative interpretation of EPR spectra from a wide array of metal containing complexes. The methodology is now contained in the computer program SpinCount. SpinCount allows simulation of EPR spectra from any sample containing multiple species composed of one or two metals in any spin state. The simulations are quantitative, thus allowing determination of all species concentrations in a sample directly from spectra. This chapter will focus on applications to transition metals in biological systems using EPR spectra from multiple microwave frequencies and modes. © 2015 Elsevier Inc. All rights reserved.

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

Luminescent low-valent rhenium complexes with 1,2-bis(dialkylphosphino)ethane ligands. synthesis and X-ray crystallographic, electrochemical, and spectroscopic characterization.

PubMed

Messersmith, Stephania J; Kirschbaum, Kristin; Kirchhoff, Jon R

2010-04-19

A series of low-valent rhenium phosphine complexes with the general formula [Re(dmpe)(3-x)(depe)(x)](2+/+) (x = 0-3), where dmpe is 1,2-bis(dimethylphosphino)ethane and depe is 1,2-bis(diethylphosphino)ethane, were synthesized and characterized. The reaction of [Re(benzil)(PPh(3))Cl(3)] with the appropriate phosphine yielded the homoleptic tris complexes [Re(dmpe)(3)](+) and [Re(depe)(3)](2+), while the mixed-ligand complexes [Re(dmpe)(2)(depe)](+) and [Re(dmpe)(depe)(2)](2+) were prepared from [Re(dmpe)(2)Cl(2)](+) and [Re(depe)(2)Cl(2)](+), respectively. The oxidation state of the final product strongly depends on the donating properties of the ligand. Each complex, however, exhibits a diffusion-controlled, reversible one-electron transfer between Re(I) and Re(II) with formal reduction potentials, E degrees ', ranging from -0.09 to -0.28 V versus a ferrocene external standard. Subsequent oxidation to Re(III) was found to be chemically irreversible. UV-vis and luminescence spectroelectrochemical techniques were used to study the spectral properties of the Re(I) and Re(II) forms. The Re(II) complexes are red in color and exhibit absorption features from 350 to 600 nm; the lowest-energy transition was assigned as a sigma(P) to dpi(Re) ligand-to-metal charge-transfer (LMCT) transition. Excitation into the lowest-energy absorption band revealed rare examples of luminescent (Phi approximately 0.07) LMCT excited states from d(5) transition-metal complexes in a room temperature solution. Structural characterization of salts of both oxidation states of [Re(dmpe)(2)(depe)](2+/+) was also performed.

Characterizing Transitions Between Decadal States of the Tropical Pacific using State Space Reconstruction

NASA Astrophysics Data System (ADS)

Ramesh, N.; Cane, M. A.

2017-12-01

The complex coupled ocean-atmosphere system of the Tropical Pacific generates variability on timescales from intraseasonal to multidecadal. Pacific Decadal Variability (PDV) is among the key drivers of global climate, with effects on hydroclimate on several continents, marine ecosystems, and the rate of global mean surface temperature rise under anthropogenic greenhouse gas forcing. Predicting phase shifts in the PDV would therefore be highly useful. However, the small number of PDV phase shifts that have occurred in the observational record pose a substantial challenge to developing an understanding of the mechanisms that underlie decadal variability. In this study, we use a 100,000-year unforced simulation from an intermediate-complexity model of the Tropical Pacific region that has been shown to produce PDV comparable to that in the real world. We apply the Simplex Projection method to the NINO3 index from this model to reconstruct a shadow manifold that preserves the topology of the true attractor of this system. We find that the high- and low-variance phases of PDV emerge as a pair of regimes in a 3-dimensional state space, and that the transitions between decadal states lie in a highly predictable region of the attractor. We then use a random forest algorithm to develop a physical interpretation of the processes associated with these highly-predictable transitions. We find that transitions to low-variance states are most likely to occur approximately 2.5 years after an El Nino event, and that ocean-atmosphere variables in the southeastern Tropical Pacific play a crucial role in driving these transitions.

Theoretical studies on the photophysical properties of luminescent pincer gold(iii) arylacetylide complexes: the role of π-conjugation at the C-deprotonated [C^N^C] ligand† †Electronic supplementary information (ESI) available: Experimental details of synthesis, characterization, and photophysical properties of complex 3-endo, additional computational details, and the Cartesian coordinates of the optimized structures. CCDC 1034529. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03697b

PubMed Central

Chan, Kaai Tung; Chang, Xiaoyong

2015-01-01

We have performed theoretical analyses of the photophysical properties of a series of cyclometalated gold(iii) arylacetylide complexes, [(C^N^C)AuIIIC 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CPh-4-OMe], with different extents of π-conjugation at the doubly C-deprotonated [C^N^C] ligand via replacement of one of the phenyl moieties in the non-conjugated CH^N^C ligand (1) by a naphthalenyl (2) or a fluorenyl moiety (3-exo and 3-endo; HCH^N^CH = 2,6-diphenylpyridine). Conforming to the conventional wisdom that extended π-conjugation imposes rigidity on the structure of the 3IL(ππ*(C^N^C)) excited state (IL = intraligand), the calculated Huang–Rhys factors for the 3IL → S0 transition follow the order: 1 > 2 > 3-exo ∼ 3-endo, which corroborates qualitatively the experimental non-radiative decay rate constants, knr: 1 ≫ 2 > 3-exo, but not 3-endo. Density Functional Theory (DFT) calculations revealed that there is an additional triplet excited state minimum of 3LLCT character (LLCT = ligand-to-ligand charge transfer; 3[π(C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CPh-4-OMe) → π*(C^N^C)]) for complexes 1 and 3-endo. This 3LLCT excited state, possessing a large out-of-plane torsional motion between the planes of the C^N^C and arylacetylide ligands, has a double minimum anharmonic potential energy surface along this torsional coordinate which leads to enhanced Franck–Condon overlap between the 3LLCT excited state and the ground state. Together with the larger spin–orbit coupling (SOC) and solvent reorganization energy for the 3LLCT → S0 transition compared with those for the 3IL → S0 transition, the calculated knr values for the 3LLCT → S0 transition are more than 690- and 1500-fold greater than the corresponding 3IL → S0 transition for complexes 1 and 3-endo respectively. Importantly, when this 3LLCT → S0 decay channel is taken into consideration, the non-radiative decay rate constant knr could be reproduced quantitatively and in the order of: 1 ≫ 3-endo, 2 > 3-exo. This challenges the common view that the facile non-radiative decay rate of transition metal complexes is due to the presence of a low-lying metal-centred 3dd or 3LMCT excited state (LMCT = ligand-to-metal charge transfer). By analysis of the relative order of MOs of the chromophoric [C^N^C] cyclometalated and arylacetylide ligands, one may discern why complexes 1 and 3-endo have a low-lying 3LLCT excited state while 3-exo does not. PMID:29403639

Folding thermodynamics of model four-strand antiparallel beta-sheet proteins.

PubMed Central

Jang, Hyunbum; Hall, Carol K; Zhou, Yaoqi

2002-01-01

The thermodynamic properties for three different types of off-lattice four-strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration R(g)(2), the root-mean-squared pair separation fluctuation Delta(B), the specific heat C(v), the internal energy of the system E, and the Lindemann disorder parameter Delta(L). Despite these models' simplicity, they exhibit a complex set of protein transitions, consistent with those observed in experimental studies on real proteins. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. The high temperature transitions, i.e., the collapse transition and the disordered-to-ordered globule transition, exist for all three beta-strand proteins, although the native-state geometry of the three model proteins is different. However the low temperature transitions, i.e., the folding transition and the liquid-to-solid transition, strongly depend on the native-state geometry of the model proteins and the size of the bias gap. PMID:11806908

Stability analysis for virus spreading in complex networks with quarantine and non-homogeneous transition rates

NASA Astrophysics Data System (ADS)

Alarcon-Ramos, L. A.; Schaum, A.; Rodríguez Lucatero, C.; Bernal Jaquez, R.

2014-03-01

Virus propagations in complex networks have been studied in the framework of discrete time Markov process dynamical systems. These studies have been carried out under the assumption of homogeneous transition rates, yielding conditions for virus extinction in terms of the transition probabilities and the largest eigenvalue of the connectivity matrix. Nevertheless the assumption of homogeneous rates is rather restrictive. In the present study we consider non-homogeneous transition rates, assigned according to a uniform distribution, with susceptible, infected and quarantine states, thus generalizing the previous studies. A remarkable result of this analysis is that the extinction depends on the weakest element in the network. Simulation results are presented for large free-scale networks, that corroborate our theoretical findings.

Efficient determination of the Markovian time-evolution towards a steady-state of a complex open quantum system

NASA Astrophysics Data System (ADS)

Jonsson, Thorsteinn H.; Manolescu, Andrei; Goan, Hsi-Sheng; Abdullah, Nzar Rauf; Sitek, Anna; Tang, Chi-Shung; Gudmundsson, Vidar

2017-11-01

Master equations are commonly used to describe time evolution of open systems. We introduce a general computationally efficient method for calculating a Markovian solution of the Nakajima-Zwanzig generalized master equation. We do so for a time-dependent transport of interacting electrons through a complex nano scale system in a photon cavity. The central system, described by 120 many-body states in a Fock space, is weakly coupled to the external leads. The efficiency of the approach allows us to place the bias window defined by the external leads high into the many-body spectrum of the cavity photon-dressed states of the central system revealing a cascade of intermediate transitions as the system relaxes to a steady state. The very diverse relaxation times present in the open system, reflecting radiative or non-radiative transitions, require information about the time evolution through many orders of magnitude. In our approach, the generalized master equation is mapped from a many-body Fock space of states to a Liouville space of transitions. We show that this results in a linear equation which is solved exactly through an eigenvalue analysis, which supplies information on the steady state and the time evolution of the system.

Stable singlet carbenes as mimics for transition metal centers

PubMed Central

Martin, David; Soleilhavoup, Michele

2011-01-01

This perspective summarizes recent results, which demonstrate that stable carbenes can activate small molecules (CO, H2, NH3 and P4) and stabilize highly reactive intermediates (main group elements in the zero oxidation state and paramagnetic species). These two tasks were previously exclusive for transition metal complexes. PMID:21743834

Photoregeneration of bovine rhodopsin from its signaling state.

PubMed

Arnis, S; Hofmann, K P

1995-07-25

In rhodopsin, 11-cis-retinal is bound by a protonated Schiff base and acts as a strong antagonist, which holds the receptor in its inactive ground state conformation. Light induces cis-/trans-retinal isomerization and a sequence of thermal transitions through intermediates. The active conformation that catalyzes GDP/GTP exchange in the G-protein (Gt) is generated from the metarhodopsin II intermediate (MII) and mediated by Schiff base proton translocation and proton uptake from the aqueous phase. In the stable nucleotide-free MII-Gt complex, any thermal transition of MII into other forms of rhodopsin is blocked. We have now studied how Gt affects flash-induced photochemical conversions of MII. Difference spectra from measured absorption changes show that MII photolyzes through two parallel pathways, with fast (1 ms) and slow (50 ms) kinetics (12 degrees C, pH 6). The slow pathway regenerates rhodopsin (9- or 11-cis) via Schiff base reprotonation and proton release. We infer a cis-isomerized early photoproduct (reverted meta, RM) preceding these thermal transitions. When MII is photolyzed in the MII-Gt complex, the slow absorption change is abolished, indicating that Gt blocks the completion of the regeneration process. This is due to the formation of a stable RM-Gt complex, as shown by successive photolysis of MII, RM, and ground state rhodopsin, and the application of GTP gamma S at different stages. The complex dissociates with GTP gamma S, and rhodopsin relaxes to the ground state. The results indicate that cis-retinal and Gt can bind to the receptor at the same time. We discuss the result that the protonations in the meta II state uncouple retinal geometry from Gt interaction.

Nudged-elastic band method with two climbing images: Finding transition states in complex energy landscapes

DOE PAGES

Zarkevich, Nikolai A.; Johnson, Duane D.

2015-01-09

The nudged-elastic band (NEB) method is modified with concomitant two climbing images (C2-NEB) to find a transition state (TS) in complex energy landscapes, such as those with a serpentine minimal energy path (MEP). If a single climbing image (C1-NEB) successfully finds the TS, then C2-NEB finds it too. Improved stability of C2-NEB makes it suitable for more complex cases, where C1-NEB misses the TS because the MEP and NEB directions near the saddle point are different. Generally, C2-NEB not only finds the TS, but guarantees, by construction, that the climbing images approach it from the opposite sides along the MEP.more » In addition, C2-NEB provides an accuracy estimate from the three images: the highest-energy one and its climbing neighbors. C2-NEB is suitable for fixed-cell NEB and the generalized solid-state NEB.« less

Assignment of Pre-edge Features in the Ru K-edge X-ray Absorption Spectra of Organometallic Ruthenium Complexes

PubMed Central

Getty, Kendra; Delgado-Jaime, Mario Ulises

2010-01-01

The nature of the lowest energy bound-state transition in the Ru K-edge X-ray Absorption Spectra for a series of Grubbs-type ruthenium complexes was investigated. The pre-edge feature was unambiguously assigned as resulting from formally electric dipole forbidden Ru 4d←1s transitions. The intensities of these transitions are extremely sensitive to the ligand environment and the symmetry of the metal centre. In centrosymmetric complexes the pre-edge is very weak since it is limited by the weak electric quadrupole intensity mechanism. By contrast, upon breaking centrosymmetry, Ru 5p-4d mixing allows for introduction of electric dipole allowed character resulting in a dramatic increase in the pre-edge intensity. The information content of this approach is explored as it relates to complexes of importance in olefin metathesis and its relevance as a tool for the study of reactive intermediates. PMID:20151030

Complex quantum network geometries: Evolution and phase transitions

NASA Astrophysics Data System (ADS)

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Complex quantum network geometries: Evolution and phase transitions.

PubMed

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Binding energies and spatial structures of small carrier complexes in monolayer transition-metal dichalcogenides via diffusion Monte Carlo

DOE PAGES

Mayers, Matthew Z.; Berkelbach, Timothy C.; Hybertsen, Mark S.; ...

2015-10-09

Ground-state diffusion Monte Carlo is used to investigate the binding energies and intercarrier radial probability distributions of excitons, trions, and biexcitons in a variety of two-dimensional transition-metal dichalcogenide materials. We compare these results to approximate variational calculations, as well as to analogous Monte Carlo calculations performed with simplified carrier interaction potentials. Our results highlight the successes and failures of approximate approaches as well as the physical features that determine the stability of small carrier complexes in monolayer transition-metal dichalcogenide materials. In conclusion, we discuss points of agreement and disagreement with recent experiments.

Square-antiprismatic eight-coordinate complexes of divalent first-row transition metal cations: a density functional theory exploration of the electronic-structural landscape.

PubMed

Conradie, Jeanet; Patra, Ashis K; Harrop, Todd C; Ghosh, Abhik

2015-02-16

Density functional theory (in the form of the PW91, BP86, OLYP, and B3LYP exchange-correlation functionals) has been used to map out the low-energy states of a series of eight-coordinate square-antiprismatic (D2d) first-row transition metal complexes, involving Mn(II), Fe(II), Co(II), Ni(II), and Cu(II), along with a pair of tetradentate N4 ligands. Of the five complexes, the Mn(II) and Fe(II) complexes have been synthesized and characterized structurally and spectroscopically, whereas the other three are as yet unknown. Each N4 ligand consists of a pair of terminal imidazole units linked by an o-phenylenediimine unit. The imidazole units are the strongest ligands in these complexes and dictate the spatial disposition of the metal three-dimensional orbitals. Thus, the dx(2)-y(2) orbital, whose lobes point directly at the coordinating imidazole nitrogens, has the highest orbital energy among the five d orbitals, whereas the dxy orbital has the lowest orbital energy. In general, the following orbital ordering (in order of increasing orbital energy) was found to be operative: dxy < dxz = dyz ≤ dz(2) < dx(2)-y(2). The square-antiprism geometry does not lead to large energy gaps between the d orbitals, which leads to an S = 2 ground state for the Fe(II) complex. Nevertheless, the dxy orbital has significantly lower energy relative to that of the dxz and dyz orbitals. Accordingly, the ground state of the Fe(II) complex corresponds unambiguously to a dxy(2)dxz(1)dyz(1)dz(2)(1)dx(2)-y(2)(1) electronic configuration. Unsurprisingly, the Mn(II) complex has an S = 5/2 ground state and no low-energy d-d excited states within 1.0 eV of the ground state. The Co(II) complex, on the other hand, has both a low-lying S = 1/2 state and multiple low-energy S = 3/2 states. Very long metal-nitrogen bonds are predicted for the Ni(II) and Cu(II) complexes; these bonds may be too fragile to survive in solution or in the solid state, and the complexes may therefore not be isolable. Overall, the different exchange-correlation functionals provided a qualitatively consistent and plausible picture of the low-energy d-d excited states of the complexes.

Dielectric Response at THz Frequencies of Mg Water Complexes Interacting with O3 Calculated by Density Functional Theory

DTIC Science & Technology

2012-10-24

of the atoms in a chemical system , at the maximal peak of the energy surface separating reactants from products . In the transition state every normal...Hada, M. Ehara, K. Toyota , R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda , O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E...calculations of ground state resonance structure associated with water complexes of Mg and the interaction of these complexes with Ozone using DFT. The

The solvation of the ground and transition states in the reaction of ortho-palladized acetanilide with styrene in organic solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakodynskaya, I.K.; Neverov, A.A; Ryabov, A.D.

1986-07-01

The rate of the reaction of di-mu-chlorobis(acetanilidato-2C, 0) dipalladium(II) with styrene leading to 2-acetaminostilbene was found in 11 organic solvents. In all media, the reaction has second-order kinetics. The free energy, enthalpy and entropy of activation were determined in each solvent. The data for the solubility of the starting Pd(II) complex were used to determine the free energy for the transfer of the ground state of this reaction from a standard solvent (heptane) to the other solvents. The analogous transfer functions were calculated for the transition state. The correlation of the transfer functions of the starting and transition states ofmore » this reaction with empirical solvent parameters was examined.« less

From metadynamics to dynamics.

PubMed

Tiwary, Pratyush; Parrinello, Michele

2013-12-06

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

From Metadynamics to Dynamics

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; Parrinello, Michele

2013-12-01

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

Distinct collective states due to trade-off between attractive and repulsive couplings

NASA Astrophysics Data System (ADS)

Sathiyadevi, K.; Chandrasekar, V. K.; Senthilkumar, D. V.; Lakshmanan, M.

2018-03-01

We investigate the effect of repulsive coupling together with an attractive coupling in a network of nonlocally coupled oscillators. To understand the complex interaction between these two couplings we introduce a control parameter in the repulsive coupling which plays a crucial role in inducing distinct complex collective patterns. In particular, we show the emergence of various cluster chimera death states through a dynamically distinct transition route, namely the oscillatory cluster state and coherent oscillation death state as a function of the repulsive coupling in the presence of the attractive coupling. In the oscillatory cluster state, the oscillators in the network are grouped into two distinct dynamical states of homogeneous and inhomogeneous oscillatory states. Further, the network of coupled oscillators follow the same transition route in the entire coupling range. Depending upon distinct coupling ranges, the system displays different number of clusters in the death state and oscillatory state. We also observe that the number of coherent domains in the oscillatory cluster state exponentially decreases with increase in coupling range and obeys a power-law decay. Additionally, we show analytical stability for observed solitary state, synchronized state, and incoherent oscillation death state.

Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120

PubMed Central

Korkut, Anil; Hendrickson, Wayne A.

2012-01-01

HIV envelope glycoproteins undergo large-scale conformational changes as they interact with cellular receptors to cause the fusion of viral and cellular membranes that permits viral entry to infect targeted cells. Conformational dynamics in HIV gp120 are also important in masking conserved receptor epitopes from being detected for effective neutralization by the human immune system. Crystal structures of HIV gp120 and its complexes with receptors and antibody fragments provide high-resolution pictures of selected conformational states accessible to gp120. Here we describe systematic computational analyses of HIV gp120 plasticity in such complexes with CD4 binding fragments, CD4 mimetic proteins, and various antibody fragments. We used three computational approaches: an isotropic elastic network analysis of conformational plasticity, a full atomic normal mode analysis, and simulation of conformational transitions with our coarse-grained virtual atom molecular mechanics (VAMM) potential function. We observe collective sub-domain motions about hinge points that coordinate those motions, correlated local fluctuations at the interfacial cavity formed when gp120 binds to CD4, and concerted changes in structural elements that form at the CD4 interface during large-scale conformational transitions to the CD4-bound state from the deformed states of gp120 in certain antibody complexes. PMID:23300605

The electronic and transport properties of monolayer transition metal dichalcogenides: a complex band structure analysis

NASA Astrophysics Data System (ADS)

Szczesniak, Dominik

Recently, monolayer transition metal dichalcogenides have attracted much attention due to their potential use in both nano- and opto-electronics. In such applications, the electronic and transport properties of group-VIB transition metal dichalcogenides (MX2 , where M=Mo, W; X=S, Se, Te) are particularly important. Herein, new insight into these properties is presented by studying the complex band structures (CBS's) of MX2 monolayers while accounting for spin-orbit coupling effects. By using the symmetry-based tight-binding model a nonlinear generalized eigenvalue problem for CBS's is obtained. An efficient method for solving such class of problems is presented and gives a complete set of physically relevant solutions. Next, these solutions are characterized and classified into propagating and evanescent states, where the latter states present not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gaps, which describe the tunneling currents in the MX2 materials. The importance of CBS's and tunneling currents is demonstrated by the analysis of the quantum transport across MX2 monolayers within phase field matching theory. Present work has been prepared within the Qatar Energy and Environment Research Institute (QEERI) grand challenge ATHLOC project (Project No. QEERI- GC-3008).

Theoretical study of the reactions of the hydroselenyl radical (HSe●) with the selenenic radical (HSeO●).

PubMed

Vega-Teijido, Mauricio Angel; Kieninger, Martina; Ventura, Oscar N

2017-12-05

The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe ● , RSe - , RSeO ● , and RSeO - , among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe ● ) and selenenic (HSeO ● ) radicals, in which the possible products, intermediates, and transition-state structures were investigated. Density functional theory (DFT) was applied at the B3LYP/6-311++G(3df,3pd) level and the Ahlrichs Coulomb fitting basis sets were employed with an effective core potential (ECP) for both Se atoms. The same procedure was used to calculate the electronic density. All calculations were also performed using the M06-2X functional, which describes weaker bonds better than B3LYP does. In the reaction of interest, the so-called CR complex (HSe····SeOH) is formed initially. After passing through the transition state TS1, cis-HSeSeOH is obtained as a product. If a low barrier is then overcome (passing through the transition state TS32), the trans-HSeSeOH species is obtained. The CR complex can also rearrange into the intermediate INT after overcoming the barrier presented by the transition state TS2. Additionally, the decomposition of INT to H 2 O and 1 Se 2 is possible through another transition state. This reaction is not included in this study. We also observed a second possible route for the conversion of INT to one of the HSeSeOH species; this route occurs through two pathways (with transition states TS31 and TS32). A comparison of some of the results with those obtained for sulfur analogs along the same pathways is also presented in this work. Graphical abstract Electronic envelopes for HSeO ● and HSe ● radicals.

Edge states at the interface of non-Hermitian systems

NASA Astrophysics Data System (ADS)

Yuce, C.

2018-04-01

Topological edge states appear at the interface of two topologically distinct Hermitian insulators. We study the extension of this idea to non-Hermitian systems. We consider P T -symmetric and topologically distinct non-Hermitian insulators with real spectra and study topological edge states at the interface of them. We show that P T symmetry is spontaneously broken at the interface during the topological phase transition. Therefore, topological edge states with complex energy eigenvalues appear at the interface. We apply our idea to a complex extension of the Su-Schrieffer-Heeger model.

Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states

PubMed Central

Jang, Sumin; Choubey, Sandeep; Furchtgott, Leon; Zou, Ling-Nan; Doyle, Adele; Menon, Vilas; Loew, Ethan B; Krostag, Anne-Rachel; Martinez, Refugio A; Madisen, Linda; Levi, Boaz P; Ramanathan, Sharad

2017-01-01

The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state. Using the inferred discrete cell states to build a probabilistic model for the underlying gene regulatory network, we further predict and experimentally verify that these states have unique response to perturbations, thus defining them functionally. Our study provides a framework to infer the dynamics of differentiation from single cell transcriptomics data and to build predictive models of the gene regulatory networks that drive the sequence of cell fate decisions during development. DOI: http://dx.doi.org/10.7554/eLife.20487.001 PMID:28296635

Investigations of the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies

NASA Astrophysics Data System (ADS)

Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

2017-03-01

The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species.

Coherent manipulation of mononuclear lanthanide-based single-molecule magnets

NASA Astrophysics Data System (ADS)

Datta, Saiti; Ghosh, Sanhita; Krzystek, Jurek; Hill, Stephen; Del Barco, Enrique; Cardona-Serra, Salvador; Coronado, Eugenio

2010-03-01

Using electron spin echo (ESE) spectroscopy, we report measurements of the longitudinal (T1) and transverse (T2) relaxation times of diluted single-crystals containing recently discovered mononuclear lanthanide-based single-molecule magnets (SMMs) encapsulated in polyoxometallate cages [AlDamen et al. J. Am. Chem. Soc. 130, 8874 -- 8875 (2008)]. This encapsulation offers the potential for preserving bulk SMM properties outside of a crystal, e.g. in molecular spintronic devices. The magnetic anisotropy in these complexes arises from the spin-orbit splitting of the ground state J multiplet of the lanthanide ion in the presence of a ligand field. At low frequencies only hyperfine-split transitions within the lowest ground state ±mJ doublet are observed. Spin relaxation times were measured for a holmium complex, and the results were compared for different hyperfine transitions and crystal dilutions. Clear Rabi oscillations were also observed, indicating that one can manipulate the spin coherently in these complexes.

A method of transition conflict resolving in hierarchical control

NASA Astrophysics Data System (ADS)

Łabiak, Grzegorz

2016-09-01

The paper concerns the problem of automatic solving of transition conflicts in hierarchical concurrent state machines (also known as UML state machine). Preparing by the designer a formal specification of a behaviour free from conflicts can be very complex. In this paper, it is proposed a method for solving conflicts through transition predicates modification. Partially specified predicates in the nondeterministic diagram are transformed into a symbolic Boolean space, whose points of the space code all possible valuations of transition predicates. Next, all valuations under partial specifications are logically multiplied by a function which represents all possible orthogonal predicate valuations. The result of this operation contains all possible collections of predicates, which under given partial specification make that the original diagram is conflict free and deterministic.

Variational Identification of Markovian Transition States

NASA Astrophysics Data System (ADS)

Martini, Linda; Kells, Adam; Covino, Roberto; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

2017-07-01

We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5 , and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

High-lying single-particle modes, chaos, correlational entropy, and doubling phase transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoyanov, Chavdar; Zelevinsky, Vladimir

Highly excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phononlike modes of the core. In the framework of the quasiparticle-phonon model, we consider the structure of resulting complex configurations, using the 1k{sub 17/2} orbital in {sup 209}Pb as an example. Although, on the level of one- and two-phonon admixtures, the fully chaotic Gaussian orthogonal ensemble regime is not reached, the eigenstates of the model carry a significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the systemmore » undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks. This phase transition is clearly detected by correlational entropy.« less

Sequencing chess

NASA Astrophysics Data System (ADS)

Atashpendar, Arshia; Schilling, Tanja; Voigtmann, Thomas

2016-10-01

We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important.

Characterization of Dynamical Phase Transitions in Quantum Jump Trajectories Beyond the Properties of the Stationary State

NASA Astrophysics Data System (ADS)

Lesanovsky, Igor; van Horssen, Merlijn; Guţă, Mădălin; Garrahan, Juan P.

2013-04-01

We describe how to characterize dynamical phase transitions in open quantum systems from a purely dynamical perspective, namely, through the statistical behavior of quantum jump trajectories. This approach goes beyond considering only properties of the steady state. While in small quantum systems dynamical transitions can only occur trivially at limiting values of the controlling parameters, in many-body systems they arise as collective phenomena and within this perspective they are reminiscent of thermodynamic phase transitions. We illustrate this in open models of increasing complexity: a three-level system, the micromaser, and a dissipative version of the quantum Ising model. In these examples dynamical transitions are accompanied by clear changes in static behavior. This is however not always the case, and, in general, dynamical phases need to be uncovered by observables which are strictly dynamical, e.g., dynamical counting fields. We demonstrate this via the example of a class of models of dissipative quantum glasses, whose dynamics can vary widely despite having identical (and trivial) stationary states.

Characterization of dynamical phase transitions in quantum jump trajectories beyond the properties of the stationary state.

PubMed

Lesanovsky, Igor; van Horssen, Merlijn; Guţă, Mădălin; Garrahan, Juan P

2013-04-12

We describe how to characterize dynamical phase transitions in open quantum systems from a purely dynamical perspective, namely, through the statistical behavior of quantum jump trajectories. This approach goes beyond considering only properties of the steady state. While in small quantum systems dynamical transitions can only occur trivially at limiting values of the controlling parameters, in many-body systems they arise as collective phenomena and within this perspective they are reminiscent of thermodynamic phase transitions. We illustrate this in open models of increasing complexity: a three-level system, the micromaser, and a dissipative version of the quantum Ising model. In these examples dynamical transitions are accompanied by clear changes in static behavior. This is however not always the case, and, in general, dynamical phases need to be uncovered by observables which are strictly dynamical, e.g., dynamical counting fields. We demonstrate this via the example of a class of models of dissipative quantum glasses, whose dynamics can vary widely despite having identical (and trivial) stationary states.

General magnetic transition dipole moments for electron paramagnetic resonance.

PubMed

Nehrkorn, Joscha; Schnegg, Alexander; Holldack, Karsten; Stoll, Stefan

2015-01-09

We present general expressions for the magnetic transition rates in electron paramagnetic resonance (EPR) experiments of anisotropic spin systems in the solid state. The expressions apply to general spin centers and arbitrary excitation geometry (Voigt, Faraday, and intermediate). They work for linear and circular polarized as well as unpolarized excitation, and for crystals and powders. The expressions are based on the concept of the (complex) magnetic transition dipole moment vector. Using the new theory, we determine the parities of ground and excited spin states of high-spin (S=5/2) Fe(III) in hemin from the polarization dependence of experimental EPR line intensities.

Transition from propagating localized states to spatiotemporal chaos in phase dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brand, H.R.; Deissler, R.J.; Brand, H.R.

1998-10-01

We study the nonlinear phase equation for propagating patterns. We investigate the transition from a propagating localized pattern to a space-filling spatiotemporally disordered pattern and discuss in detail to what extent there are propagating localized states that breathe in time periodically, quasiperiodically, and chaotically. Differences and similarities to the phenomena occurring for the quintic complex Ginzburg-Landau equation are elucidated. We also discuss for which experimentally accessible systems one could observe the phenomena described. {copyright} {ital 1998} {ital The American Physical Society}

Facilitating a Major Staffing Transition in a State Psychiatric Hospital With Changes to Nursing Orientation.

PubMed

Birnbaum, Shira; Sperber-Weiss, Doreen; Dimitrios, Timothy; Eckel, Donald; Monroy-Miller, Cherry; Monroe, Janet J; Friedman, Ross; Ologbosele, Mathias; Epo, Grace; Sharpe, Debra; Zarski, Yongsuk

A large state psychiatric hospital experienced a state-mandated Reduction in Force that resulted in the abrupt loss and rapid turnover of more than 40% of its nursing and paraprofessional staff. The change exemplified current national trends toward downsizing and facility closure. This article describes revisions to the nursing orientation program that supported cost containment and fidelity to mission and clinical practices during the transition. An existing nursing orientation program was reconfigured in alignment with principles of rational instructional design and a core-competencies model of curriculum development, evidence-based practices that provided tactical clarity and commonality of purpose during a complex and emotionally charged transition period. Program redesign enabled efficiencies that facilitated the transition, with no evidence of associated negative effects. The process described here offers an example for hospitals facing similar workforce reorganization in an era of public sector downsizing.

A specific transition state for S-peptide combining with folded S-protein and then refolding

PubMed Central

Goldberg, Jonathan M.; Baldwin, Robert L.

1999-01-01

We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the α-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the α-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of −0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state. PMID:10051587

Jet-Cooled Infrared Laser Spectroscopy in the Umbrella νb{2} Vibration Region of NH_3: Improving the Potential Energy Surface Model of the NH_3-Ar Van Der Waals Complex

NASA Astrophysics Data System (ADS)

Asselin, Pierre; Jabri, Atef; Potapov, Alexey; Loreau, Jérome; van der Avoird, Ad

2017-06-01

Taking advantage of our sensitive laser spectrometer coupled to a pulsed slit jet, we recorded near the νb{2} vibration a series of rovibrational transitions of the NH_3-Ar van der Waals (vdW) complex. These transitions involve in the ground vibrational state several internal rotor states corresponding to the ortho{NH_3} and para{NH_3} spin modifications of the complex. They are labeled by Σ_{a}(j,k), Σ_{s}(j,k), Π_{a}(j,k) and Π_{s}(j,k) where Σ(K=0) and Π(K=1) indicate the projection K of the total rotational angular momentum J on the vdW axis, the superscripts s and a designate a symmetric or antisymmetric NH_3 inversion wave function, and j, k quantum numbers indicate the correlation between the internal-rotor state of the complex and the j, k rotational state of the free NH_3 monomer. Five bands have been identified, only one of which was partly observed before. They include transitions starting from the Σ_{a}(j=0 or j=1) state without any internal angular momentum, consequently they can be assigned from the band contour of a linear-molecule-like K=0, ΔJ=1 transition. The energies and splittings of the rovibrational levels of the νb{2}=1←0 spectrum derived from the analysis of the Π_{s}, Σ_{s}(j=1)← Σ_{a}(j=0), k=0 bands and mostly of the Σ_{s}, Π_{s} and Σ_{a}(j=1)←Σ_{a}(j=1), k=1 bands bring relevant information about the νb{2} dependence of the NH_3-Ar interaction, the rovibrational dynamics of the NH_3-Ar complex and provide a sensitive test of a recently developed 4D potential energy surface that includes explicitly its dependence on the umbrella motion. P. Asselin, Y. Berger, T. R. Huet, R. Motiyenko, L. Margulès, R. J. Hendricks, M. R. Tarbutt, S. Tokunaga, B. Darquié, PCCP 19, 4576 (2017), G. T. Fraser, A.S. Pine and W. A. Kreiner, J. Chem. Phys. 94, 7061 (1991). J. Loreau, J. Liévin, Y. Scribano and A. van der Avoird, J. Chem. Phys. 141, 224303 (2014).

Scan Rate Dependent Spin Crossover Iron(II) Complex with Two Different Relaxations and Thermal Hysteresis fac-[Fe(II)(HL(n-Pr))3]Cl·PF6 (HL(n-Pr) = 2-Methylimidazol-4-yl-methylideneamino-n-propyl).

PubMed

Fujinami, Takeshi; Nishi, Koshiro; Hamada, Daisuke; Murakami, Keishiro; Matsumoto, Naohide; Iijima, Seiichiro; Kojima, Masaaki; Sunatsuki, Yukinari

2015-08-03

Solvent-free spin crossover Fe(II) complex fac-[Fe(II)(HL(n-Pr))3]Cl·PF6 was prepared, where HL(n-Pr) denotes 2-methylimidazol-4-yl-methylideneamino-n-propyl. The magnetic susceptibility measurements at scan rate of 0.5 K min(-1) showed two successive spin transition processes consisting of the first spin transition T1 centered at 122 K (T1↑ = 127.1 K, T1↓ = 115.8 K) and the second spin transition T2 centered at ca. 105 K (T2↑ = 115.8 K, T2↓ = 97.2 K). The magnetic susceptibility measurements at the scan rate of 2.0, 1.0, 0.5, 0.25, and 0.1 K min(-1) showed two scan speed dependent spin transitions, while the Mössbauer spectra detected only the first spin transition T1. The crystal structures were determined at 160, 143, 120, 110, 95 K in the cooling mode, and 110, 120, and 130 K in the warming mode so as to follow the spin transition process of high-spin HS → HS(T1) → HS(T2) → low-spin LS → LS(T2) → LS(T1) → HS. The crystal structures at all temperatures have a triclinic space group P1̅ with Z = 2. The complex-cation has an octahedral N6 coordination geometry with three bidentate ligands and assume a facial-isomer with Δ- and Λ-enantimorphs. Three imidazole groups of fac-[Fe(II)(HL(n-Pr))3](2+) are hydrogen-bonded to three Cl(-) ions. The 3:3 NH(imidazole)···Cl(-) hydrogen-bonds form a stepwise ladder assembly structure, which is maintained during the spin transition process. The spin transition process is related to the structural changes of the FeN6 coordination environment, the order-disorder of PF6(-) anion, and the conformation change of n-propyl groups. The Fe-N bond distance in the HS state is longer by 0.2 Å than that in the LS state. Disorder of PF6(-) anion is not observed in the LS state but in the HS state. The conformational changes of n-propyl groups are found in the spin transition processes except for HS → HS(T1) → HS(T2).

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution.

PubMed

Wernet, Ph; Kunnus, K; Josefsson, I; Rajkovic, I; Quevedo, W; Beye, M; Schreck, S; Grübel, S; Scholz, M; Nordlund, D; Zhang, W; Hartsock, R W; Schlotter, W F; Turner, J J; Kennedy, B; Hennies, F; de Groot, F M F; Gaffney, K J; Techert, S; Odelius, M; Föhlisch, A

2015-04-02

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16 - 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution

NASA Astrophysics Data System (ADS)

Wernet, Ph.; Kunnus, K.; Josefsson, I.; Rajkovic, I.; Quevedo, W.; Beye, M.; Schreck, S.; Grübel, S.; Scholz, M.; Nordlund, D.; Zhang, W.; Hartsock, R. W.; Schlotter, W. F.; Turner, J. J.; Kennedy, B.; Hennies, F.; de Groot, F. M. F.; Gaffney, K. J.; Techert, S.; Odelius, M.; Föhlisch, A.

2015-04-01

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16,17,18,19 and 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Luminescent molecular rods - transition-metal alkynyl complexes.

PubMed

Yam, Vivian Wing-Wah; Wong, Keith Man-Chung

2005-01-01

A number of transition-metal complexes have been reported to exhibit rich luminescence, usually originating from phosphorescence. Such luminescence properties of the triplet excited state with a large Stoke's shift, long lifetime, high luminescence quantum yield as well as lower excitation energy, are envisaged to serve as an ideal candidate in the area of potential applications for chemosensors, dye-sensitized solar cells, flat panel displays, optics, new materials and biological sciences. Organic alkynes (poly-ynes), with extended or conjugatedπ-systems and rigid structure with linear geometry, have become a significant research area due to their novel electronic and physical properties and their potential applications in nanotechnology. Owing to the presence of unsaturated sp-hybridized carbon atoms, the alkynyl unit can serve as a versatile building block in the construction of alkynyl transition-metal complexes, not only throughσ-bonding but also viaπ-bonding interactions. By incorporation of linear alkynyl groups into luminescent transition-metal complexes, the alkynyl moiety with goodσ-donor,π-donor andπ-acceptor abilities is envisaged to tune or perturb the emission behaviors, including emission energy (color), intensity and lifetime by its role as an auxiliary ligand as well as to govern the emission origin from its direct involvement. This review summarizes recent efforts on the synthesis of luminescent rod-like alkynyl complexes with different classes of transition metals and details the effects of the introduction of alkynyl groups on the luminescence properties of the complexes.

Bifurcation analysis and phase diagram of a spin-string model with buckled states.

PubMed

Ruiz-Garcia, M; Bonilla, L L; Prados, A

2017-12-01

We analyze a one-dimensional spin-string model, in which string oscillators are linearly coupled to their two nearest neighbors and to Ising spins representing internal degrees of freedom. String-spin coupling induces a long-range ferromagnetic interaction among spins that competes with a spin-spin antiferromagnetic coupling. As a consequence, the complex phase diagram of the system exhibits different flat rippled and buckled states, with first or second order transition lines between states. This complexity translates to the two-dimensional version of the model, whose numerical solution has been recently used to explain qualitatively the rippled to buckled transition observed in scanning tunneling microscopy experiments with suspended graphene sheets. Here we describe in detail the phase diagram of the simpler one-dimensional model and phase stability using bifurcation theory. This gives additional insight into the physical mechanisms underlying the different phases and the behavior observed in experiments.

Quantum vertex model for reversible classical computing.

PubMed

Chamon, C; Mucciolo, E R; Ruckenstein, A E; Yang, Z-C

2017-05-12

Mappings of classical computation onto statistical mechanics models have led to remarkable successes in addressing some complex computational problems. However, such mappings display thermodynamic phase transitions that may prevent reaching solution even for easy problems known to be solvable in polynomial time. Here we map universal reversible classical computations onto a planar vertex model that exhibits no bulk classical thermodynamic phase transition, independent of the computational circuit. Within our approach the solution of the computation is encoded in the ground state of the vertex model and its complexity is reflected in the dynamics of the relaxation of the system to its ground state. We use thermal annealing with and without 'learning' to explore typical computational problems. We also construct a mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating an approach to reversible classical computation based on state-of-the-art implementations of quantum annealing.

Quantum vertex model for reversible classical computing

NASA Astrophysics Data System (ADS)

Chamon, C.; Mucciolo, E. R.; Ruckenstein, A. E.; Yang, Z.-C.

2017-05-01

Mappings of classical computation onto statistical mechanics models have led to remarkable successes in addressing some complex computational problems. However, such mappings display thermodynamic phase transitions that may prevent reaching solution even for easy problems known to be solvable in polynomial time. Here we map universal reversible classical computations onto a planar vertex model that exhibits no bulk classical thermodynamic phase transition, independent of the computational circuit. Within our approach the solution of the computation is encoded in the ground state of the vertex model and its complexity is reflected in the dynamics of the relaxation of the system to its ground state. We use thermal annealing with and without `learning' to explore typical computational problems. We also construct a mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating an approach to reversible classical computation based on state-of-the-art implementations of quantum annealing.

Bifurcation analysis and phase diagram of a spin-string model with buckled states

NASA Astrophysics Data System (ADS)

Ruiz-Garcia, M.; Bonilla, L. L.; Prados, A.

2017-12-01

We analyze a one-dimensional spin-string model, in which string oscillators are linearly coupled to their two nearest neighbors and to Ising spins representing internal degrees of freedom. String-spin coupling induces a long-range ferromagnetic interaction among spins that competes with a spin-spin antiferromagnetic coupling. As a consequence, the complex phase diagram of the system exhibits different flat rippled and buckled states, with first or second order transition lines between states. This complexity translates to the two-dimensional version of the model, whose numerical solution has been recently used to explain qualitatively the rippled to buckled transition observed in scanning tunneling microscopy experiments with suspended graphene sheets. Here we describe in detail the phase diagram of the simpler one-dimensional model and phase stability using bifurcation theory. This gives additional insight into the physical mechanisms underlying the different phases and the behavior observed in experiments.

Democracy's Orphans: Rights, Responsibility, and the Role of the State in the Lives of Incarcerated Youth

ERIC Educational Resources Information Center

Gardner, Joby

2010-01-01

Transition to adulthood is increasingly complex, extended, and challenging. Working-class Brown and Black young men face very difficult transitions, as they are overrepresented in the justice system, poverty, foster care, special education, and among victims of violence. What effects do these developments have on young people's places in free…

Generalized concurrence in boson sampling.

PubMed

Chin, Seungbeom; Huh, Joonsuk

2018-04-17

A fundamental question in linear optical quantum computing is to understand the origin of the quantum supremacy in the physical system. It is found that the multimode linear optical transition amplitudes are calculated through the permanents of transition operator matrices, which is a hard problem for classical simulations (boson sampling problem). We can understand this problem by considering a quantum measure that directly determines the runtime for computing the transition amplitudes. In this paper, we suggest a quantum measure named "Fock state concurrence sum" C S , which is the summation over all the members of "the generalized Fock state concurrence" (a measure analogous to the generalized concurrences of entanglement and coherence). By introducing generalized algorithms for computing the transition amplitudes of the Fock state boson sampling with an arbitrary number of photons per mode, we show that the minimal classical runtime for all the known algorithms directly depends on C S . Therefore, we can state that the Fock state concurrence sum C S behaves as a collective measure that controls the computational complexity of Fock state BS. We expect that our observation on the role of the Fock state concurrence in the generalized algorithm for permanents would provide a unified viewpoint to interpret the quantum computing power of linear optics.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Devine, Jessalyn A.; Babin, Mark C.; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M.

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH3OH → HF + CH3O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH3OHF- anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy.

PubMed

Weichman, Marissa L; DeVine, Jessalyn A; Babin, Mark C; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH 3 OH → HF + CH 3 O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH 3 OHF - anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.

PubMed

Xu, Shenyuan; Long, Brian N; Boris, Gabriel H; Chen, Anqi; Ni, Shuisong; Kennedy, Michael A

2017-12-01

K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras-GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shenyuan; Long, Brian N.; Boris, Gabriel H.

K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras–GTP complex, the switch I region undergoes amore » significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.« less

Statistical mechanics of complex economies

NASA Astrophysics Data System (ADS)

Bardoscia, Marco; Livan, Giacomo; Marsili, Matteo

2017-04-01

In the pursuit of ever increasing efficiency and growth, our economies have evolved to remarkable degrees of complexity, with nested production processes feeding each other in order to create products of greater sophistication from less sophisticated ones, down to raw materials. The engine of such an expansion have been competitive markets that, according to general equilibrium theory (GET), achieve efficient allocations under specific conditions. We study large random economies within the GET framework, as templates of complex economies, and we find that a non-trivial phase transition occurs: the economy freezes in a state where all production processes collapse when either the number of primary goods or the number of available technologies fall below a critical threshold. As in other examples of phase transitions in large random systems, this is an unintended consequence of the growth in complexity. Our findings suggest that the Industrial Revolution can be regarded as a sharp transition between different phases, but also imply that well developed economies can collapse if too many intermediate goods are introduced.

Optical population of iodine molecule ion-pair states via MI2 vdW complexes, M = I2, Xe, of valence states correlating with the third, I(2 P 1/2) + I(2 P 1/2), dissociation limit

NASA Astrophysics Data System (ADS)

Lukashov, S. S.; Poretsky, S. A.; Pravilov, A. M.; Khadikova, E. I.; Shevchenko, E. V.

2010-10-01

The first results of measurements and analysis of excitation spectra of the λlum = 3250 Å luminescence corresponding to I2( D0{/u +} → X0{/g +}) transition as well as luminescence at λlum = 3400 Å, where I2( D'2 g → A'2 u and/or β1 g → A1 u ) transitions occur, observed after three-step, λ1 + λ f + λ1, λ1 = 5321-5508.2 Å, λ f = 10644.0 Å, laser excitation of pure iodine vapour and I2 + Xe mixtures at room temperature via MI2 vdW complexes, M = I2, Xe, of the I2(0{/g +}, 1 u ( bb)) valence states correlating with the third, I(2 P 1/2) + I(2 P 1/2) (I2( bb)), dissociation limit are presented. Luminescence spectra in the λlum = 2200-3500 Å spectral range are also analyzed. Strong luminescence from the I2(D) and, probably, I2(D' and β) states is observed. We discuss three alternative mechanisms of optical population of the IP state. In our opinion, the mechanism including the MI2 complexes is the most probable.

Functional Analyses of the Plant Photosystem I–Light-Harvesting Complex II Supercomplex Reveal That Light-Harvesting Complex II Loosely Bound to Photosystem II Is a Very Efficient Antenna for Photosystem I in State II[W

PubMed Central

Galka, Pierre; Santabarbara, Stefano; Khuong, Thi Thu Huong; Degand, Hervé; Morsomme, Pierre; Jennings, Robert C.; Boekema, Egbert J.; Caffarri, Stefano

2012-01-01

State transitions are an important photosynthetic short-term response that allows energy distribution balancing between photosystems I (PSI) and II (PSII). In plants when PSII is preferentially excited compared with PSI (State II), part of the major light-harvesting complex LHCII migrates to PSI to form a PSI-LHCII supercomplex. So far, little is known about this complex, mainly due to purification problems. Here, a stable PSI-LHCII supercomplex is purified from Arabidopsis thaliana and maize (Zea mays) plants. It is demonstrated that LHCIIs loosely bound to PSII in State I are the trimers mainly involved in state transitions and become strongly bound to PSI in State II. Specific Lhcb1-3 isoforms are differently represented in the mobile LHCII compared with S and M trimers. Fluorescence analyses indicate that excitation energy migration from mobile LHCII to PSI is rapid and efficient, and the quantum yield of photochemical conversion of PSI-LHCII is substantially unaffected with respect to PSI, despite a sizable increase of the antenna size. An updated PSI-LHCII structural model suggests that the low-energy chlorophylls 611 and 612 in LHCII interact with the chlorophyll 11145 at the interface of PSI. In contrast with the common opinion, we suggest that the mobile pool of LHCII may be considered an intimate part of the PSI antenna system that is displaced to PSII in State I. PMID:22822202

Adaptive particle filter for robust visual tracking

NASA Astrophysics Data System (ADS)

Dai, Jianghua; Yu, Shengsheng; Sun, Weiping; Chen, Xiaoping; Xiang, Jinhai

2009-10-01

Object tracking plays a key role in the field of computer vision. Particle filter has been widely used for visual tracking under nonlinear and/or non-Gaussian circumstances. In particle filter, the state transition model for predicting the next location of tracked object assumes the object motion is invariable, which cannot well approximate the varying dynamics of the motion changes. In addition, the state estimate calculated by the mean of all the weighted particles is coarse or inaccurate due to various noise disturbances. Both these two factors may degrade tracking performance greatly. In this work, an adaptive particle filter (APF) with a velocity-updating based transition model (VTM) and an adaptive state estimate approach (ASEA) is proposed to improve object tracking. In APF, the motion velocity embedded into the state transition model is updated continuously by a recursive equation, and the state estimate is obtained adaptively according to the state posterior distribution. The experiment results show that the APF can increase the tracking accuracy and efficiency in complex environments.

Plants Actively Avoid State Transitions upon Changes in Light Intensity: Role of Light-Harvesting Complex II Protein Dephosphorylation in High Light1[OPEN

PubMed Central

Suorsa, Marjaana; Rantala, Marjaana; Aro, Eva-Mari

2015-01-01

Photosystem II (PSII) core and light-harvesting complex II (LHCII) proteins in plant chloroplasts undergo reversible phosphorylation upon changes in light intensity (being under control of redox-regulated STN7 and STN8 kinases and TAP38/PPH1 and PSII core phosphatases). Shift of plants from growth light to high light results in an increase of PSII core phosphorylation, whereas LHCII phosphorylation concomitantly decreases. Exactly the opposite takes place when plants are shifted to lower light intensity. Despite distinct changes occurring in thylakoid protein phosphorylation upon light intensity changes, the excitation balance between PSII and photosystem I remains unchanged. This differs drastically from the canonical-state transition model induced by artificial states 1 and 2 lights that concomitantly either dephosphorylate or phosphorylate, respectively, both the PSII core and LHCII phosphoproteins. Analysis of the kinase and phosphatase mutants revealed that TAP38/PPH1 phosphatase is crucial in preventing state transition upon increase in light intensity. Indeed, tap38/pph1 mutant revealed strong concomitant phosphorylation of both the PSII core and LHCII proteins upon transfer to high light, thus resembling the wild type under state 2 light. Coordinated function of thylakoid protein kinases and phosphatases is shown to secure balanced excitation energy for both photosystems by preventing state transitions upon changes in light intensity. Moreover, PROTON GRADIENT REGULATION5 (PGR5) is required for proper regulation of thylakoid protein kinases and phosphatases, and the pgr5 mutant mimics phenotypes of tap38/pph1. This shows that there is a close cooperation between the redox- and proton gradient-dependent regulatory mechanisms for proper function of the photosynthetic machinery. PMID:25902812

Impact of zeolite-Y framework on the geometry and reactivity of Ru (III) benzimidazole complexes - A DFT study

NASA Astrophysics Data System (ADS)

Selvaraj, Tamilmani; Rajalingam, Renganathan; Balasubramanian, Viswanathan

2018-03-01

A detailed comparative Density Functional Theory (DFT) study is made to understand the structural changes of the guest complex due to steric and electronic interactions with the host framework. In this study, Ru(III) benzimidazole and 2- ethyl Ru(III) benzimidazole complexes encapsulated in a supercage of zeolite Y. The zeolitic framework integrity is not disturbed by the intrusion of the large guest complex. A blue shift in the d-d transition observed in the UV-Visible spectroscopic studies of the zeolite encapsulated complexes and they shows a higher catalytic efficiency. Encapsulation of zeolite matrix makes the metal center more viable to nucleophilic attack and favors the phenol oxidation reaction. Based on the theoretical calculations, transition states and structures of reaction intermediates involved in the catalytic cycles are derived.

Investigations of the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies.

PubMed

Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

2017-03-05

The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species. Copyright © 2016 Elsevier B.V. All rights reserved.

Catastrophic Shifts in Semiarid Vegetation-Soil Systems May Unfold Rapidly or Slowly.

PubMed

Karssenberg, Derek; Bierkens, Marc F P; Rietkerk, Max

2017-12-01

Under gradual change of a driver, complex systems may switch between contrasting stable states. For many ecosystems it is unknown how rapidly such a critical transition unfolds. Here we explore the rate of change during the degradation of a semiarid ecosystem with a model coupling the vegetation and geomorphological system. Two stable states-vegetated and bare-are identified, and it is shown that the change between these states is a critical transition. Surprisingly, the critical transition between the vegetated and bare state can unfold either rapidly over a few years or gradually over decennia up to millennia, depending on parameter values. An important condition for the phenomenon is the linkage between slow and fast ecosystems components. Our results show that, next to climate change and disturbance rates, the geological and geomorphological setting of a semiarid ecosystem is crucial in predicting its fate.

Phosphoryl transfer reaction snapshots in crystals: Insights into the mechanism of protein kinase a catalytic subunit

DOE PAGES

Das, Amit; Gerlits, Oksana O.; Heller, William T.; ...

2015-06-19

To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal structures of the Michaelis complex mimics of the PKA catalytic subunit (PKAc) were obtained with either peptide inhibitors or ATP analogs. Here we utilized Ca 2+ ions and sulfur in place of the nucleophilic oxygen in a 20-residue pseudo-substrate peptide (CP20) and ATP to produce a close mimic of the Michaelis complex. In the ternary reactant complex,more » the thiol group of Cys-21 of the peptide is facing Asp-166 and the sulfur atom is positioned for an in-line phosphoryl transfer. Replacement of Ca 2+ cations with Mg 2+ ions resulted in a complex with trapped products of ATP hydrolysis: phosphate ion and ADP. As a result, the present structural results in combination with the previously reported structures of the transition state mimic and phosphorylated product complexes complete the snapshots of the phosphoryl transfer reaction by PKAc, providing us with the most thorough picture of the catalytic mechanism to date.« less

Near-infrared-emitting heteroleptic cationic iridium complexes derived from 2,3-diphenylbenzo[g]quinoxaline as in vitro theranostic photodynamic therapy agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Li; Yin, Huimin; Cui, Peng

Five heteroleptic cationic iridium complexes with a π-expansive cyclometalating 2,3-diphenylbenzo[g] quinoxaline (dpbq) ligand (C^N ligand) and different diimine ligands (N^N ligands) (i.e. 2,2’-bipyridine (bpy, 1), phenanthroline (phen, 2), 2-(2-pyridinyl)quinoline (pqu, 3), 2,2’-bisquinoline (bqu, 4), and 2-(quinolin-2-yl)quinoxaline (quqo, 5)) were synthesized and characterized. The lowest-energy singlet electronic transitions (S1 states) were mainly dpbq ligand-centred 1ILCT (intraligand charge transfer)/1MLCT (metal to ligand charge transfer) transitions mixed with some 1π,π* transitions for complexes 1–4 with increased contributions from 1LLCT (ligand to ligand charge transfer) in 3 and 4. For complex 5, the S1 state was switched to the 1LLCT/1MLCT transitions. All five complexesmore » displayed weak near-infrared (NIR) phosphorescence, with maximal emission output spanning 700–1400 nm and quantum yields being on the order of 10-3. The triplet state absorptions of 1–4 all resembled that of the [Ir(dpbq)2Cl]2 dimer with lifetimes of ca. 400 ns, while the TA spectrum of 5 possessed the characteristics of both the quqo ligand and the [Ir(dpbq)2Cl]2 dimer with a bi-exponential decay of ca. 5 μs and 400 ns. While the photophysics of these complexes differ slightly, their theranostic photodynamic therapy (PDT) effects varied drastically. All of the complexes were biologically active toward melanoma cells. Complexes 2 and 3 were the most cytotoxic, with 230–340 nM activity and selectivity factors for melanoma cells over normal skin fibroblasts of 34 to 40 fold. Complexes 2, 3, and 5 became very potent cytotoxins with light activation, with EC50 values as low as 12–18 nM. This potent nanomolar light-triggered activity combined with a lower dark toxicity resulted in 5 having a phototherapeutic index (PI) margin of almost 275. The bpy coligand led to the least amount of dark toxicity of 1, while phen and pqu produced cytotoxic but selective complexes 2 and 3. The quqo coligand produced the most potent complex 5 for in vitro PDT, both in terms of photocytotoxicity and PI. All Ir(III) complexes exhibited very bright NIR phosphorescence in melanoma cells. The wide range of cytotoxicity and photocytotoxicity effects within a relatively small class of complexes highlights the importance of the identity of the coligand in the biological activity of the π-expansive biscyclometalated Ir(III) complexes, and their bright NIR emission in live cells demonstrates their potential as theranostic PDT agents.« less

Dissipation processes in the insulating skyrmion compound Cu2OSeO3

NASA Astrophysics Data System (ADS)

Levatić, I.; Šurija, V.; Berger, H.; Živković, I.

2014-12-01

We present a detailed study of the phase diagram surrounding the skyrmion lattice (SkL) phase of Cu2OSe2O3 using high-precision magnetic ac susceptibility measurements. An extensive investigation of transition dynamics around the SkL phase using the imaginary component of the susceptibility revealed that at the conical-to-SkL transition a broad dissipation region exists with a complex frequency dependence. The analysis of the observed behavior within the SkL phase indicates a distribution of relaxation times intrinsically related to SkL. At the SkL-to-paramagnet transition a narrow first-order peak is found that exhibits a strong frequency and magnetic field dependence. Surprisingly, very similar dependence has been discovered for the first-order transition below the SkL phase, i.e., where the system enters the helical and conical state(s), indicating similar processes across the order-disorder transition.

Preparation of the polyelectrolyte complex hydrogel of biopolymers via a semi-dissolution acidification sol-gel transition method and its application in solid-state supercapacitors

NASA Astrophysics Data System (ADS)

Zhao, Jian; Chen, Yu; Yao, Ying; Tong, Zong-Rui; Li, Pu-Wang; Yang, Zi-Ming; Jin, Shao-Hua

2018-02-01

Hydrogels have drawn many attentions as the solid-state electrolytes in flexible solid-state supercapacitors (SCs) recently. Among them, the polyelectrolyte complex hydrogel (PECH) electrolytes of natural polymers are more competitive because of their environmentally friendly property and low cost. However, while mixing two biopolymer solutions with opposite charges, the strong electrostatic interactions between the cationic and anionic biopolymers may result in precipitates instead of hydrogels. Here we report a novel method, semi-dissolution acidification sol-gel transition (SD-A-SGT), for the preparation of the PECH of chitosan (CTS) and sodium alginate (SA), with the controllable sol-gel transition and uniform composition and successfully apply it as the hydrogel electrolyte of solid-state supercapacitors (SCs). The CTS-SA PECH exhibits an extremely high ionic conductivity of 0.051 S·cm-1 and reasonable mechanical properties with a tensile strength of 0.29 MPa and elongation at break of 109.5%. The solid-state SC fabricated with the CTS-SA PECH and conventional polyaniline (PANI) nanowire electrodes provided a high specific capacitance of 234.6 F·g-1 at 5 mV·s-1 and exhibited excellent cycling stability with 95.3% capacitance retention after 1000 cycles. Our work may pave a novel avenue to the preparation of biodegradable PECHs of full natural polymers, and promote the development of environmentally friendly electronic devices.

Cell responses to single pheromone molecules may reflect the activation kinetics of olfactory receptor molecules.

PubMed

Minor, A V; Kaissling, K-E

2003-03-01

Olfactory receptor cells of the silkmoth Bombyx mori respond to single pheromone molecules with "elementary" electrical events that appear as discrete "bumps" a few milliseconds in duration, or bursts of bumps. As revealed by simulation, one bump may result from a series of random openings of one or several ion channels, producing an average inward membrane current of 1.5 pA. The distributions of durations of bumps and of gaps between bumps in a burst can be fitted by single exponentials with time constants of 10.2 ms and 40.5 ms, respectively. The distribution of burst durations is a sum of two exponentials; the number of bumps per burst obeyed a geometric distribution (mean 3.2 bumps per burst). Accordingly the elementary events could reflect transitions among three states of the pheromone receptor molecule: the vacant receptor (state 1), the pheromone-receptor complex (state 2), and the activated complex (state 3). The calculated rate constants of the transitions between states are k(21)=7.7 s(-1), k(23)=16.8 s(-1), and k(32)=98 s(-1).

Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

PubMed

Nose, Holliness; Chen, Yu; Rodgers, M T

2013-05-23

The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana.

PubMed

Silva, Anderson Tadeu; Ligterink, Wilco; Hilhorst, Henk W M

2017-11-01

Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.

Theoretical treatment of the processes involving the dipole transitions to the lowest exciton states in hexagonal semiconductors

NASA Astrophysics Data System (ADS)

Semenova, L. E.

2018-04-01

The treatment of the two-photon transitions to the An=1 exciton level and the resonant Raman scattering of light by LO-phonons is given for the hexagonal semiconductors A2B6, taking into account the influence of the complex top valence band and anisotropy of the exciton effective mass.

Taking Systems Medicine to Heart.

PubMed

Trachana, Kalliopi; Bargaje, Rhishikesh; Glusman, Gustavo; Price, Nathan D; Huang, Sui; Hood, Leroy E

2018-04-27

Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine. © 2018 American Heart Association, Inc.

Evolution of complexity in the volvocine algae: transitions in individuality through Darwin's eye.

PubMed

Herron, Matthew D; Michod, Richard E

2008-02-01

The transition from unicellular to differentiated multicellular organisms constitutes an increase in the level complexity, because previously existing individuals are combined to form a new, higher-level individual. The volvocine algae represent a unique opportunity to study this transition because they diverged relatively recently from unicellular relatives and because extant species display a range of intermediate grades between unicellular and multicellular, with functional specialization of cells. Following the approach Darwin used to understand "organs of extreme perfection" such as the vertebrate eye, this jump in complexity can be reduced to a series of small steps that cumulatively describe a gradual transition between the two levels. We use phylogenetic reconstructions of ancestral character states to trace the evolution of steps involved in this transition in volvocine algae. The history of these characters includes several well-supported instances of multiple origins and reversals. The inferred changes can be understood as components of cooperation-conflict-conflict mediation cycles as predicted by multilevel selection theory. One such cycle may have taken place early in volvocine evolution, leading to the highly integrated colonies seen in extant volvocine algae. A second cycle, in which the defection of somatic cells must be prevented, may still be in progress.

Hidden Markov models reveal complexity in the diving behaviour of short-finned pilot whales

PubMed Central

Quick, Nicola J.; Isojunno, Saana; Sadykova, Dina; Bowers, Matthew; Nowacek, Douglas P.; Read, Andrew J.

2017-01-01

Diving behaviour of short-finned pilot whales is often described by two states; deep foraging and shallow, non-foraging dives. However, this simple classification system ignores much of the variation that occurs during subsurface periods. We used multi-state hidden Markov models (HMM) to characterize states of diving behaviour and the transitions between states in short-finned pilot whales. We used three parameters (number of buzzes, maximum dive depth and duration) measured in 259 dives by digital acoustic recording tags (DTAGs) deployed on 20 individual whales off Cape Hatteras, North Carolina, USA. The HMM identified a four-state model as the best descriptor of diving behaviour. The state-dependent distributions for the diving parameters showed variation between states, indicative of different diving behaviours. Transition probabilities were considerably higher for state persistence than state switching, indicating that dive types occurred in bouts. Our results indicate that subsurface behaviour in short-finned pilot whales is more complex than a simple dichotomy of deep and shallow diving states, and labelling all subsurface behaviour as deep dives or shallow dives discounts a significant amount of important variation. We discuss potential drivers of these patterns, including variation in foraging success, prey availability and selection, bathymetry, physiological constraints and socially mediated behaviour. PMID:28361954

Steady state and time resolved optical characterization studies of Zn 2SnO 4 nanowires for solar cell applications

DOE PAGES

Yakami, Baichhabi R.; Poudyal, Uma; Nandyala, Shashank R.; ...

2016-10-25

Nanowires are a promising option for sensitized solar cells, sensors, and display technology. Most of the work thus far has focused on binary oxides for these nanowires, but ternary oxides have advantages in additional control of optical and electronic properties. Here, we report on the diffuse reflectance, Low Temperature and Room Temperature Photoluminescence (PL), PL excitation spectrum, and Time Resolved PL (TRPL) of Zinc Tin Oxide (ZTO) nanowires grown by Chemical Vapor Deposition. The PL from the ZTO nanowires does not exhibit any band gap or near gap emission, and the diffuse reflectance measurement confirms that these ZTO nanowires havemore » a direct forbidden transition. The broad PL spectrum reveals two Gaussian peaks centered at 1.86 eV (red) and 2.81 eV (blue), representing two distinct defect states or complexes. The PL spectra were further studied by the Time Resolved Emission Spectrum and intensity dependent PL and TRPL. The time resolved measurements show complex non-exponential decays at all wavelengths, indicative of defect to defect transitions, and the red emissive states decay much slower than the blue emissive states. The effects of annealing in air and vacuum are studied to investigate the origin of the defect states in the nanowires, showing that the blue states are related to oxygen vacancies. We propose an energy band model for the nanowires containing defect states within the band gap and the associated transitions between these states that are consistent with our measurements.« less

Steady state and time resolved optical characterization studies of Zn 2SnO 4 nanowires for solar cell applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yakami, Baichhabi R.; Poudyal, Uma; Nandyala, Shashank R.

Nanowires are a promising option for sensitized solar cells, sensors, and display technology. Most of the work thus far has focused on binary oxides for these nanowires, but ternary oxides have advantages in additional control of optical and electronic properties. Here, we report on the diffuse reflectance, Low Temperature and Room Temperature Photoluminescence (PL), PL excitation spectrum, and Time Resolved PL (TRPL) of Zinc Tin Oxide (ZTO) nanowires grown by Chemical Vapor Deposition. The PL from the ZTO nanowires does not exhibit any band gap or near gap emission, and the diffuse reflectance measurement confirms that these ZTO nanowires havemore » a direct forbidden transition. The broad PL spectrum reveals two Gaussian peaks centered at 1.86 eV (red) and 2.81 eV (blue), representing two distinct defect states or complexes. The PL spectra were further studied by the Time Resolved Emission Spectrum and intensity dependent PL and TRPL. The time resolved measurements show complex non-exponential decays at all wavelengths, indicative of defect to defect transitions, and the red emissive states decay much slower than the blue emissive states. The effects of annealing in air and vacuum are studied to investigate the origin of the defect states in the nanowires, showing that the blue states are related to oxygen vacancies. We propose an energy band model for the nanowires containing defect states within the band gap and the associated transitions between these states that are consistent with our measurements.« less

Norharmane rhenium(I) polypyridyl complexes: synthesis, structural and spectroscopic characterization.

PubMed

Maisuls, Iván; Wolcan, Ezequiel; Piro, Oscar E; Etcheverría, Gustavo A; Petroselli, Gabriela; Erra-Ballsels, Rosa; Cabrerizo, Franco M; Ruiz, Gustavo T

2015-10-21

Two novel Re(i) complexes with the general formula fac-[Re(CO)3(L)(nHo)]CF3SO3, where L = 2,2'-bipyridine (bpy) or 1,10 phenanthroline (phen) and nHo (9H-pyrido[3,4-b]indole; norharmane) have been synthesized. The Re(i)-nHo complexes were characterized by structural X-ray diffraction, (1)H and (13)C NMR, UV-vis absorption and FT-IR spectroscopy, and by a combination of two mass spectrometry techniques, namely ESI-MS and UV-MALDI-MS. All characterizations showed that nHo is coordinated to the metal atom by the pyridine nitrogen of the molecule. X-ray structural analysis revealed that the crystal lattices for both complexes are further stabilized by a strong >N-HO bond between the pyrrole NH group of the pyridoindole ligand and one oxygen atom of the trifluoromethanesulfonate counter-ion. Ground state geometry optimization by DFT calculations showed that in fluid solution the nHo ligand may rotate freely. The nature of the electronic transitions of Re(CO)3(bpy)(nHo)(+) were established by TD-DFT calculations. The set of the most important electronic transitions present in this complex are comprised of π→π* electronic transitions centered on bpy and nHo moieties, LLCTnHo→COs, MLLCTRe(CO)3→bpy and LLCTnHo→bpy transitions. Additionally, TD-DFT calculations predict the existence of another two intense MLLCTRe(CO)3→nHo electronic transitions. Calculated UV-vis absorption spectra are in good agreement with the corresponding experimental data for the bpy-containing complex.

Grip on health: A complex systems approach to transform health care.

PubMed

van Wietmarschen, Herman A; Wortelboer, Heleen M; van der Greef, Jan

2018-02-01

This article addresses the urgent need for a transition in health care to deal with the increasing prevalence of chronic diseases and associated rapid rise of health care costs. Chronic diseases evolve and are predominantly related to lifestyle and environment. A shift is needed from a reductionist repair mode of thinking, toward a more integrated biopsychosocial way of thinking about health. The aim of this article is to discuss the opportunities that complexity science offer for transforming health care toward optimal treatment and prevention of chronic lifestyle diseases. Health and health care is discussed from a complexity science perspective. The benefits of concepts developed in the field of complexity science for stimulating transitions in health care are explored. Complexity science supports the elucidation of the essence of health processes. It provides a unique perspective on health with a focus on the relationships within networks of dynamically interacting factors and the emergence of health out of the organization of those relationships. Novel types of complexity science-based intervention strategies are being developed. The first application in practice is the integrated obesity treatment program currently piloted in the Netherlands, focusing on health awareness and healing relationships. Complexity science offers various theories and methods to capture the path toward unhealthy and healthy states, facilitating the development of a dynamic integrated biopsychosocial perspective on health. This perspective offers unique insights into health processes for patients and citizens. In addition, dynamic models driven by personal data provide simulations of health processes and the ability to detect transitions between health states. Such models are essential for aligning and reconnecting the many institutions and disciplines involved in the health care sector and evolve toward an integrated health care ecosystem. © 2016 John Wiley & Sons, Ltd.

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

NASA Astrophysics Data System (ADS)

Lichtenberg, Dennis L.

During this period some important breakthroughs were accomplished in understanding the relationships between molecular ionization energies and bond energies in transition metal complexes, in understanding the electronic factors of carbon-hydrogen bond activation by transition metals, in characterizing small molecule bonding interactions with transition metals, and in investigating intermolecular interactions in thin films of transition metal complexes. The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies was developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. The relationship was used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. The ionization energies were also used to correlate the rates of carbonyl substitution reactions of (eta(sup 5)-C5H4X)Rh(CO)2 complexes, and to reveal the factors that control the stability of the transition state. The investigations of the fundamental interactions of C-H sigma and sigma* orbitals metals were continued with study of eta(sup 3)-1-methylallyl metal complexes. Direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal was obtained. The ability to observe the electronic effects of intermolecular interactions by comparing the ionizations of metal complexes in the gas phase with the ionizations of thin solid organometallic films prepared in ultra-high vacuum was established. Most significantly, the scanning tunneling microscope imaging of these thin films was accomplished.

Theoretical studies for excited-state tautomerization in the 7-azaindole-(CH3OH)n (n = 1 and 2) complexes in the gas phase.

PubMed

Fang, Hua; Kim, Yongho

2011-12-01

The excited-state tautomerization of 7-azaindole (7AI) complexes bonded with either one or two methanol molecule(s) was studied by systematic quantum mechanical calculations in the gas phases. Electronic structures and energies for the reactant, transition state (TS), and product were computed at the complete active space self-consistent field (CASSCF) levels with the second-order multireference perturbation theory (MRPT2) to consider the dynamic electron correlation. The time-dependent density functional theory (TDDFT) was also used for comparison. The excited-state double proton transfer (ESDPT) in 7AI-CH(3)OH occurs in a concerted but asynchronous mechanism. Similarly, such paths are also found in the two transition states during the excited-state triple proton transfer (ESTPT) of the 7AI-(CH(3)OH)(2) complex. In the first TS, the pyrrole ring proton first migrated to methanol, while in the second the methanol proton moved first to the pyridine ring. The CASSCF level with the MRPT2 correction showed that the former path was much preferable to the latter, and the ESDPT is much slower than the ESTPT. Additionally, the vibrational-mode enhanced tautomerization in the 7AI-(CH(3)OH)(2) complex was also studied. We found that the excitation of the low-frequency mode shortens the reaction path to increase the tautomerization rate. Overall, most TDDFT methods used in this study predicted different TS structures and barriers from the CASSCF methods with MRPT2 corrections. © 2011 American Chemical Society

Trinuclear ruthenium dioxolene complexes based on the bridging ligand hexahydroxytriphenylene: electrochemistry, spectroscopy, and near-infrared electrochromic behaviour associated with a reversible seven-membered redox chain.

PubMed

Grange, Christopher S; Meijer, Anthony J H M; Ward, Michael D

2010-01-07

The trinuclear complexes [{(R2bipy)2Ru}3(mu3-HHTP)](PF6)3 [1(PF6)3, R = H; 2(PF6)3, R = 4-tBu] contain three {Ru(R2bipy)2}2+ fragments connected to the triangular tris-chelating ligand hexahydroxytriphenylene (H6HHTP). This bridging ligand contains three dioxolene-type binding sites, each of which can reversibly convert between dianionic catecholate (cat), monoanionic semiquinone (sq) or neutral quinone (q) redox states. The bridging ligand as a whole can therefore exist in seven different redox states from fully reduced [cat,cat,cat]6- through to fully oxidised, neutral [q,q,q]. Cyclic voltammetry of 1(PF6)3 in MeCN reveals six redox processes of which the three at more positive potentials (the sq/q couples) are reversible but the three at more negative potentials (the sq/cat couples) are irreversible with distorted wave shapes due to the insolubility of the reduced forms of the complex. In contrast, the more soluble complex 2(PF6)3 displays six reversible one-electron redox processes making all components of a seven-membered redox chain accessible. UV/Vis/NIR spectro-electrochemical studies reveal rich spectroscopic behaviour, with--in particular--very intense transitions in the near-IR region in many of the oxidation states associated with Ru(II)-->(dioxolene) MLCT and bridging ligand centred pi-pi* transitions. TDDFT calculations were used to analyse the electronic spectra in all seven oxidation states; the calculated spectra generally show very good agreement with experiment, which has allowed a fairly complete assignment of the low-energy transitions. The strong electrochromism of the complexes in the near-IR region has formed the basis of an optical window in which a thin film of 1(PF6)3 or 2(PF6)3 on a conductive glass surface can be reversibly and rapidly switched between redox states that alternate between strongly absorbing or near-transparent at 1100 nm, with--for 2(PF6)3--the switching being stable and reversible in water over thousands of cycles.

State transitions and feedback mechanisms control hydrology in the constructed catchment ´Chicken Creeḱ

NASA Astrophysics Data System (ADS)

Schaaf, Wolfgang; Gerwin, Werner; Hinz, Christoph; Zaplata, Markus

2016-04-01

Landscapes and ecosystems are complex systems with many feedback mechanisms acting between the various abiotic and biotic components. The knowledge about these interacting processes is mainly derived from mature ecosystems. The initial development of ecosystem complexity may involve state transitions following catastrophic shifts, disturbances or transgression of thresholds. The Chicken Creek catchment was constructed in 2005 in the mining area of Lusatia/Germany to study processes and feedback mechanisms during ecosystem evolution. The hillslope-shaped 6 ha site has defined boundary conditions and well-documented inner structures. The dominating substrate above the underlying clay layer is Pleistocene sandy material representing mainly the lower C horizon of the former landscape. Since 2005, the unrestricted, unmanaged development of the catchment was intensively monitored. During the ten years since then, we observed characteristic state transitions in catchment functioning driven by feedbacks between original substrate properties, surface structures, soil development and vegetation succession. Whereas surface runoff induced by surface crusting and infiltration dominated catchment hydrology in the first years, the impact of vegetation on hydrological pathways and groundwater levels became more and more evident during the last years. Discharge from the catchment changed from episodic events driven by precipitation and surface runoff to groundwater driven. This general picture is overlain by spatial patterns and single episodic events of external drivers. The scientific value of the Chicken Creek site with known boundary conditions and structure information could help in disentangling general feedback mechanisms between hydrologic, pedogenic, biological and geomorphological processes as well as a in gaining a more integrative view of succession and its drivers during the transition from initial, less complex systems to more mature ecosystems. Long-term time series of data are a key for a better understanding of these processes and the effects on ecosystem resilience and self-organization.

A theory for bioinorganic chemical reactivity of oxometal complexes and analogous oxidants: the exchange and orbital-selection rules.

PubMed

Usharani, Dandamudi; Janardanan, Deepa; Li, Chunsen; Shaik, Sason

2013-02-19

Over the past decades metalloenzymes and their synthetic models have emerged as an area of increasing research interest. The metalloenzymes and their synthetic models oxidize organic molecules using oxometal complexes (OMCs), especially oxoiron(IV)-based ones. Theoretical studies have helped researchers to characterize the active species and to resolve mechanistic issues. This activity has generated massive amounts of data on the relationship between the reactivity of OMCs and the transition metal's identity, oxidation state, ligand sphere, and spin state. Theoretical studies have also produced information on transition state (TS) structures, reaction intermediates, barriers, and rate-equilibrium relationships. For example, the experimental-theoretical interplay has revealed that nonheme enzymes carry out H-abstraction from strong C-H bonds using high-spin (S = 2) oxoiron(IV) species with four unpaired electrons on the iron center. However, other reagents with higher spin states and more unpaired electrons on the metal are not as reactive. Still other reagents carry out these transformations using lower spin states with fewer unpaired electrons on the metal. The TS structures for these reactions exhibit structural selectivity depending on the reactive spin states. The barriers and thermodynamic driving forces of the reactions also depend on the spin state. H-Abstraction is preferred over the thermodynamically more favorable concerted insertion into C-H bonds. Currently, there is no unified theoretical framework that explains the totality of these fascinating trends. This Account aims to unify this rich chemistry and understand the role of unpaired electrons on chemical reactivity. We show that during an oxidative step the d-orbital block of the transition metal is enriched by one electron through proton-coupled electron transfer (PCET). That single electron elicits variable exchange interactions on the metal, which in turn depend critically on the number of unpaired electrons on the metal center. Thus, we introduce the exchange-enhanced reactivity (EER) principle, which predicts the preferred spin state during oxidation reactions, the dependence of the barrier on the number of unpaired electrons in the TS, and the dependence of the deformation energy of the reactants on the spin state. We complement EER with orbital-selection rules, which predict the structure of the preferred TS and provide a handy theory of bioinorganic oxidative reactions. These rules show how EER provides a Hund's Rule for chemical reactivity: EER controls the reactivity landscape for a great variety of transition-metal complexes and substrates. Among many reactivity patterns explained, EER rationalizes the abundance of high-spin oxoiron(IV) complexes in enzymes that carry out bond activation of the strongest bonds. The concepts used in this Account might also be applicable in other areas such as in f-block chemistry and excited-state reactivity of 4d and 5d OMCs.

Synthesis, characterization, and photophysical properties of a thiophene-functionalized bis(pyrazolyl) pyridine (BPP) tricarbonyl rhenium(I) complex.

PubMed

Lytwak, Lauren A; Stanley, Julie M; Mejía, Michelle L; Holliday, Bradley J

2010-09-07

A bromo tricarbonyl rhenium(I) complex with a thiophene-functionalized bis(pyrazolyl) pyridine ligand (L), ReBr(L)(CO)(3) (1), has been synthesized and characterized by variable temperature and COSY 2-D (1)H NMR spectroscopy, single-crystal X-ray diffraction, and photophysical methods. Complex 1 is highly luminescent in both solution and solid-state, consistent with phosphorescence from an emissive (3)MLCT excited state with an additional contribution from a LC (3)(pi-->pi*) transition. The single-crystal X-ray diffraction structure of the title ligand is also reported.

Gas-phase kinetics study of reaction of OH radical with CH3NHNH2 by second-order multireference perturbation theory.

PubMed

Sun, Hongyan; Zhang, Peng; Law, Chung K

2012-05-31

The gas-phase kinetics of H-abstraction reactions of monomethylhydrazine (MMH) by OH radical was investigated by second-order multireference perturbation theory and two-transition-state kinetic model. It was found that the abstractions of the central and terminal amine H atoms by the OH radical proceed through the formation of two hydrogen bonded preactivated complexes with energies of 6.16 and 5.90 kcal mol(-1) lower than that of the reactants, whereas the abstraction of methyl H atom is direct. Due to the multireference characters of the transition states, the geometries and ro-vibrational frequencies of the reactant, transition states, reactant complexes, and product complexes were optimized by the multireference CASPT2/aug-cc-pVTZ method, and the energies of the stationary points of the potential energy surface were refined at the QCISD(T)/CBS level via extrapolation of the QCISD(T)/cc-pVTZ and QCISD(T)/cc-pVQZ energies. It was found that the abstraction reactions of the central and two terminal amine H atoms of MMH have the submerged energy barriers with energies of 2.95, 2.12, and 1.24 kcal mol(-1) lower than that that of the reactants respectively, and the abstraction of methyl H atom has a real energy barrier of 3.09 kcal mol(-1). Furthermore, four MMH radical-H(2)O complexes were found to connect with product channels and the corresponding transition states. Consequently, the rate coefficients of MMH + OH for the H-abstraction of the amine H atoms were determined on the basis of a two-transition-state model, with the total energy E and angular momentum J conserved between the two transition-state regions. In units of cm(3) molecule(-1) s(-1), the rate coefficient was found to be k(1) = 3.37 × 10(-16)T(1.295) exp(1126.17/T) for the abstraction of the central amine H to form the CH(3)N(•)NH(2) radical, k(2) = 2.34 × 10(-17)T(1.907) exp(1052.26/T) for the abstraction of the terminal amine H to form the trans-CH(3)NHN(•)H radical, k(3) = 7.41 × 10(-20)T(2.428) exp(1343.20/T) for the abstraction of the terminal amine H to form the cis-CH(3)NHN(•)H radical, and k(4) = 9.13 × 10(-21)T(2.964) exp(-114.09/T) for the abstraction of the methyl H atom to form the C(•)H(2)NHNH(2) radical, respectively. Assuming that the rate coefficients are additive, the total rate coefficient of these theoretical predictions quantitatively agrees with the measured rate constant at temperatures of 200-650 K, with no adjustable parameters.

Structural, electronic, and optical properties of representative Cu-flavonoid complexes.

PubMed

Lekka, Ch E; Ren, Jun; Meng, Sheng; Kaxiras, Efthimios

2009-05-07

We present density functional theory (DFT) results on the structural, electronic, and optical properties of Cu-flavonoid complexes for molar ratios 1:1, 1:2, and 1:3. We find that the preferred chelating site is close to the 4-oxo group and in particular the 3-4 site followed by the 3'-4' dihydroxy group in ring B. For the Cu-quercetin complexes, the large bathochromic shift of the first absorbance band upon complexation, which is in good agreement with experimental UV-vis spectra, results from the reduction of the electronic energy gap. The HOMO states for these complexes are characterized by pi-bonding between the Cu d orbitals and the C, O p orbitals except for the case of 1:1 complex (spin minority), which corresponds to sigma-type bonds. The LUMO states are attributed to the contribution of Cu p(z) orbitals. Consequently, the main features of the first optical absorption maxima are essentially due to pi --> pi transitions, while the 1:1 complex exhibits also sigma --> pi transitions. Our optical absorption calculations based on time-dependent DFT demonstrate that the 1:1 complex is responsible for the spectroscopic features at pH 5.5, whereas the 1:2 complex is mainly the one responsible for the characteristic spectra at pH 7.4. These theoretical predictions explain in detail the behavior of the optical absorption for the Cu-flavonoid complexes observed in experiments and are thus useful in elucidating the complexation mechanism and antioxidant activity of flavonoids.

Numerical simulation of a device with two spin crossover complexes: application for temperature and pressure sensors

NASA Astrophysics Data System (ADS)

Linares, Jorge; Eddine Allal, Salah; Dahoo, Pierre Richard; Garcia, Yann

2017-12-01

The spin-crossover (SCO) phenomenon is related to the ability of a transition metal to change its spin state vs. a given perturbation. For an iron(II) SCO complexes the reversible changes involve the diamagnetic low-spin (S = 0) and the paramagnetic high-spin (HS S = 2) states [1,2,3]. In this contribution we simulate the HS Fraction (nHS) for different set values of temperature and pressure for a device using two SCO complexes with weak elastic interactions. We improve the calculation given by Linares et al. [4], taking also into account different volume (VHS, VLS) changes of the SCO. We perform all the calculation in the frame work of an Ising-like model solved in the mean-field approximation. The two SCO show in the case of “weak elastic interactions”, gradual spin transitions such that both temperature and pressure values can be obtained from the optical observation in the light of calculations discussed in this article.

Synthesis and characterization of heterometallic uranyl pyridinedicarboxylate compounds

NASA Astrophysics Data System (ADS)

Jayasinghe, Ashini S.; Payne, Maurice K.; Forbes, Tori Z.

2017-10-01

The incorporation of transition metals into hybrid uranyl materials can result in more diverse structural topologies and variations in physical and chemical properties. To explore the impact of transition metals on the uranyl cation, five uranium containing bimetallic chain compounds, [(UO2)M(PDC)2(H2O)4]·4(H2O) (PDC = 2,6 pyridinedicarboxylate; M = Ni2+, Co2+, Fe2+, Zn2+, and Cu2+) were synthesized by evaporation of aqueous solutions at room temperature. The uranyl cation is complex by two PDC ligands and the transition metal cations bond to the complex to form a one-dimensional chain topology. The presence of the transition metal leads to the presence of a stronger uranyl oxo bonds as shown by the single-crystal X-ray diffraction data and the Raman spectra. Solid state diffuse reflectance UV/Visible spectra confirmed the presence of the transition metals in the structure by the broad bands that appeared at relevant wavelengths.

Role of Plastid Protein Phosphatase TAP38 in LHCII Dephosphorylation and Thylakoid Electron Flow

PubMed Central

Pribil, Mathias; Pesaresi, Paolo; Hertle, Alexander; Barbato, Roberto; Leister, Dario

2010-01-01

Short-term changes in illumination elicit alterations in thylakoid protein phosphorylation and reorganization of the photosynthetic machinery. Phosphorylation of LHCII, the light-harvesting complex of photosystem II, facilitates its relocation to photosystem I and permits excitation energy redistribution between the photosystems (state transitions). The protein kinase STN7 is required for LHCII phosphorylation and state transitions in the flowering plant Arabidopsis thaliana. LHCII phosphorylation is reversible, but extensive efforts to identify the protein phosphatase(s) that dephosphorylate LHCII have been unsuccessful. Here, we show that the thylakoid-associated phosphatase TAP38 is required for LHCII dephosphorylation and for the transition from state 2 to state 1 in A. thaliana. In tap38 mutants, thylakoid electron flow is enhanced, resulting in more rapid growth under constant low-light regimes. TAP38 gene overexpression markedly decreases LHCII phosphorylation and inhibits state 1→2 transition, thus mimicking the stn7 phenotype. Furthermore, the recombinant TAP38 protein is able, in an in vitro assay, to directly dephosphorylate LHCII. The dependence of LHCII dephosphorylation upon TAP38 dosage, together with the in vitro TAP38-mediated dephosphorylation of LHCII, suggests that TAP38 directly acts on LHCII. Although reversible phosphorylation of LHCII and state transitions are crucial for plant fitness under natural light conditions, LHCII hyperphosphorylation associated with an arrest of photosynthesis in state 2 due to inactivation of TAP38 improves photosynthetic performance and plant growth under state 2-favoring light conditions. PMID:20126264

Financial Symmetry and Moods in the Market

PubMed Central

Savona, Roberto; Soumare, Maxence; Andersen, Jørgen Vitting

2015-01-01

This paper studies how certain speculative transitions in financial markets can be ascribed to a symmetry break that happens in the collective decision making. Investors are assumed to be bounded rational, using a limited set of information including past price history and expectation on future dividends. Investment strategies are dynamically changed based on realized returns within a game theoretical scheme with Nash equilibria. In such a setting, markets behave as complex systems whose payoff reflect an intrinsic financial symmetry that guarantees equilibrium in price dynamics (fundamentalist state) until the symmetry is broken leading to bubble or anti-bubble scenarios (speculative state). We model such two-phase transition in a micro-to-macro scheme through a Ginzburg-Landau-based power expansion leading to a market temperature parameter which modulates the state transitions in the market. Via simulations we prove that transitions in the market price dynamics can be phenomenologically explained by the number of traders, the number of strategies and amount of information used by agents, all included in our market temperature parameter. PMID:25856392

Financial symmetry and moods in the market.

PubMed

Savona, Roberto; Soumare, Maxence; Andersen, Jørgen Vitting

2015-01-01

This paper studies how certain speculative transitions in financial markets can be ascribed to a symmetry break that happens in the collective decision making. Investors are assumed to be bounded rational, using a limited set of information including past price history and expectation on future dividends. Investment strategies are dynamically changed based on realized returns within a game theoretical scheme with Nash equilibria. In such a setting, markets behave as complex systems whose payoff reflect an intrinsic financial symmetry that guarantees equilibrium in price dynamics (fundamentalist state) until the symmetry is broken leading to bubble or anti-bubble scenarios (speculative state). We model such two-phase transition in a micro-to-macro scheme through a Ginzburg-Landau-based power expansion leading to a market temperature parameter which modulates the state transitions in the market. Via simulations we prove that transitions in the market price dynamics can be phenomenologically explained by the number of traders, the number of strategies and amount of information used by agents, all included in our market temperature parameter.

Classical Spin Nematic Transition in LiGa0.95In0.05Cr4O8

NASA Astrophysics Data System (ADS)

Wawrzyńczak, R.; Tanaka, Y.; Yoshida, M.; Okamoto, Y.; Manuel, P.; Casati, N.; Hiroi, Z.; Takigawa, M.; Nilsen, G. J.

2017-08-01

We present the results of a combined 7Li -NMR and diffraction study on LiGa0.95In0.05Cr4O8, a member of the LiGa1 -xInxCr4O8 "breathing" pyrochlore family. Via specific heat and NMR measurements, we find that the complex sequence of first-order transitions observed for LiGaCr4O8 is replaced by a single second-order transition at Tf=11 K . Neutron and x-ray diffraction rule out both structural symmetry lowering and magnetic long-range order as the origin of this transition. Instead, reverse Monte Carlo fitting of the magnetic diffuse scattering indicates that the low-temperature phase may be described as a collinear spin nematic state, characterized by a quadrupolar order parameter. This state also shows signs of short-range order between collinear spin arrangements on tetrahedra, revealed by mapping the reverse Monte Carlo spin configurations onto a three-state color model.

Platinum CCC-NHC benzimidazolyl pincer complexes: synthesis, characterization, photostability, and theoretical investigation of a blue-green emitter.

PubMed

Huckaba, Aron J; Cao, Bei; Hollis, T Keith; Valle, Henry U; Kelly, John T; Hammer, Nathan I; Oliver, Allen G; Webster, Charles Edwin

2013-06-28

The recently reported metallation/transmetallation route for the synthesis of CCC-bis(NHC) pincer ligand architectures was extended to 1,3-bis(3'-(trimethylsilylmethyl)-benzimidizol-1'-yl)benzene. The precursor was metallated with Zr(NMe2)4 and transmetallated to Pt using [Pt(COD)Cl2]. This Pt complex was found to resist photobleaching under UV irradiation in ambient conditions. Density functional theory (DFT) computations were used to generate the emission spectrum of the complex and reveal that this spectrum is the result of a transition from the triplet excited state (T1) to the ground state (S0). The Pt complex's molecular structure was determined by X-ray crystallography. The UV-vis absorption and emission spectra in solution and the solid-state emission spectra are reported. The solid-state photostability data and the radiative lifetime is also reported.

Re-evaluating the Cu K pre-edge XAS transition in complexes with covalent metal–ligand interactions† †Electronic supplementary information (ESI) available: Experimental methods; UV-vis absorption spectrum and crystallographic data for 3; fits to Cu K pre-edge XANES spectra; details of DFT, CASSCF, and MR-DDCI3 computational experiments; optimized atomic coordinates for all complexes. CCDC 1031118 and 1031119. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03294b Click here for additional data file. Click here for additional data file.

PubMed Central

Williams, Kamille D.; Dai, Xuliang; Sproules, Stephen; DeBeer, Serena

2015-01-01

Three [Me2NN]Cu(η2-L2) complexes (Me2NN = HC[C(Me)NAr]2; L2 = PhNO (2), (3), PhCH 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CH2 (4); Ar = 2,6-Me2-C6H3; ArF = 3,5-(CF3)2-C6H3) have been studied by Cu K-edge X-ray absorption spectroscopy, as well as single- and multi-reference computational methods (DFT, TD-DFT, CASSCF, MRCI, and OVB). The study was extended to a range of both known and theoretical compounds bearing 2p-element donors as a means of deriving a consistent view of how the pre-edge transition energy responds in systems with significant ground state covalency. The ground state electronic structures of many of the compounds under investigation were found to be strongly influenced by correlation effects, resulting in ground state descriptions with majority contributions from a configuration comprised of a Cu(ii) metal center anti-ferromagentically coupled to radical anion O2, PhNO, and ligands. In contrast, the styrene complex 4, which displays a Cu K pre-edge transition despite its formal d10 electron configuration, exhibits what can best be described as a Cu(i):(styrene)0 ground state with strong π-backbonding. The Cu K pre-edge features for these complexes increase in energy from 1 to 4, a trend that was tracked to the percent Cu(ii)-character in the ground state. The unexpected shift to higher pre-edge transition energies with decreasing charge on copper (Q Cu) contributed to an assignment of the pre-edge features for these species as arising from metal-to-ligand charge transfer instead of the traditional Cu1s → Cu3d designation. PMID:29308158

Exploration of metastability and hidden phases in correlated electron crystals visualized by femtosecond optical doping and electron crystallography

PubMed Central

Han, Tzong-Ru T.; Zhou, Faran; Malliakas, Christos D.; Duxbury, Phillip M.; Mahanti, Subhendra D.; Kanatzidis, Mercouri G.; Ruan, Chong-Yu

2015-01-01

Characterizing and understanding the emergence of multiple macroscopically ordered electronic phases through subtle tuning of temperature, pressure, and chemical doping has been a long-standing central issue for complex materials research. We report the first comprehensive studies of optical doping–induced emergence of stable phases and metastable hidden phases visualized in situ by femtosecond electron crystallography. The electronic phase transitions are triggered by femtosecond infrared pulses, and a temperature–optical density phase diagram is constructed and substantiated with the dynamics of metastable states, highlighting the cooperation and competition through which the macroscopic quantum orders emerge. These results elucidate key pathways of femtosecond electronic switching phenomena and provide an important new avenue to comprehensively investigate optical doping–induced transition states and phase diagrams of complex materials with wide-ranging applications. PMID:26601190

There Is More to Mind Reading than Having Theory of Mind Concepts: New Directions in Theory of Mind Research

ERIC Educational Resources Information Center

Samson, Dana; Apperly, Ian A.

2010-01-01

For more than 30 years, researchers have focused on the important transition that children undergo between the ages of 3 and 5, when they start to solve mind-reading problems that require reasoning about complex mental states, such as beliefs. The main question for debate has been whether, during that transition, children acquire new concepts…

Identifying early-warning signals of critical transitions with strong noise by dynamical network markers

PubMed Central

Liu, Rui; Chen, Pei; Aihara, Kazuyuki; Chen, Luonan

2015-01-01

Identifying early-warning signals of a critical transition for a complex system is difficult, especially when the target system is constantly perturbed by big noise, which makes the traditional methods fail due to the strong fluctuations of the observed data. In this work, we show that the critical transition is not traditional state-transition but probability distribution-transition when the noise is not sufficiently small, which, however, is a ubiquitous case in real systems. We present a model-free computational method to detect the warning signals before such transitions. The key idea behind is a strategy: “making big noise smaller” by a distribution-embedding scheme, which transforms the data from the observed state-variables with big noise to their distribution-variables with small noise, and thus makes the traditional criteria effective because of the significantly reduced fluctuations. Specifically, increasing the dimension of the observed data by moment expansion that changes the system from state-dynamics to probability distribution-dynamics, we derive new data in a higher-dimensional space but with much smaller noise. Then, we develop a criterion based on the dynamical network marker (DNM) to signal the impending critical transition using the transformed higher-dimensional data. We also demonstrate the effectiveness of our method in biological, ecological and financial systems. PMID:26647650

Specificity in transition state binding: the Pauling model revisited.

PubMed

Amyes, Tina L; Richard, John P

2013-03-26

Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared with that of the free enzyme. Evidence is presented that supports a model in which the binding energy of the phosphite dianion piece, or the phosphodianion group of the whole substrate, is utilized to drive an enzyme conformational change from an inactive open form E(O) to an active closed form E(C), by closure of a phosphodianion gripper loop. Members of the enolase and haloalkanoic acid dehalogenase superfamilies use variable capping domains to interact with nonreacting portions of the substrate and sequester the substrate from interaction with bulk solvent. Interactions of this capping domain with the phenyl group of mandelate have been shown to activate mandelate racemase for catalysis of deprotonation of α-carbonyl carbon. We propose that an important function of these capping domains is to utilize the binding interactions with nonreacting portions of the substrate to activate the enzyme for catalysis.

Specificity in Transition State Binding: The Pauling Model Revisited

PubMed Central

Amyes, Tina L.; Richard, John P.

2013-01-01

Linus Pauling proposed that the large rate accelerations for enzymes are due to the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogs of the transition states for enzymatic reactions often act as tight-binding binding inhibitors provided early support for this simple and elegant proposal. We review experimental results which support the proposal that Pauling’s model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of CoA are responsible for a rate increase of 3 × 1012-fold, which is close to the estimated total 5 × 1013-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide a ca. 12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5′-monophosphate decarboxylase and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6 – 8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared with the free enzyme. Evidence is presented that supports a model in which the binding energy of the phosphite dianion piece, or the phosphodianion group of the whole substrate, is utilized to drive an enzyme conformational change from an inactive open form EO to an active closed form EC, by closure of a phosphodianion gripper loop. Members of the enolase and haloalkanoic acid dehalogenase superfamilies use variable capping domains to interact with nonreacting portions of the substrate and sequester the substrate from interaction with bulk solvent. Interactions of this capping domain with the phenyl group of mandelate have been shown to activate mandelate racemase for catalysis of deprotonation of α-carbonyl carbon. We propose that an important function of these capping domains is to utilize the binding interactions with nonreacting portions of the substrate to activate the enzyme for catalysis. PMID:23327224

Signatures for a nuclear quantum phase transition from E 0 and E 2 observables in Gd isotopes

NASA Astrophysics Data System (ADS)

Wiederhold, J.; Kern, R.; Lizarazo, C.; Pietralla, N.; Werner, V.; Jolos, R. V.; Bucurescu, D.; Florea, N.; Ghita, D.; Glodariu, T.; Lica, R.; Marginean, N.; Marginean, R.; Mihai, C.; Mihai, R.; Mitu, I. O.; Negret, A.; Nita, C.; Olacel, A.; Pascu, S.; Stroe, L.; Toma, S.; Turturica, A.

2018-05-01

Nuclei are complex quantum objects due to complex nucleon-nucleon interactions. They can undergo rather rapid changes in structure as a function of nucleon number. A well known region of such a shape transition is the rare-earth region around N = 90, where accessible nuclei range from spherical nuclei at the closed neutron shell at N = 82 to deformed nuclei. For a better understanding of this phenomenon, it is of interest to study empirical signatures like the E2 transition strength B(E2;{2}1+\\to {0}1+) or the E0 excitation strength {ρ }2(E0;{0}1+\\to {0}2+). The nuclide 152Gd with 88 neutrons is located close to the quantum phase transition at N = 90. The lifetime τ ({0}2+) of 152Gd has been measured using fast electronic scintillation timing (FEST) with an array of HPGe- and LaBr3- detectors. Excited states of 152Gd were populated via an (α,n)-reaction on a gold-backed 149Sm target. The measured lifetime of τ ({0}2+)=96(6)\\text{ps} corresponds to a reduced transition strength of B(E2;{0}2+\\to {2}1+)=111(7) W.u. and an E0 transition strength of ρ 2(E0) = 39(3) · 10‑3 to the ground state. This result provides experimental support for the validity of a correlation between E0 and E2 strengths that is a novel indicator for a quantum phase transition. This work was published as J. Wiederhold et al., Phys. Rev. C 94, 044302 (2016).

Ultrafast relaxation dynamics of amine-substituted bipyridyl ruthenium(II) complexes

NASA Astrophysics Data System (ADS)

Song, Hongwei; Wang, Xian; Yang, WenWen; He, Guiying; Kuang, Zhuoran; Li, Yang; Xia, Andong; Zhong, Yu-Wu; Kong, Fan'ao

2017-09-01

The excited state properties of a series of ruthenium(II) amine-substituted bipyridyl complexes, [Ru(bpy)n(NNbpy)3-n]2+, were investigated by steady-state and transient absorption spectroscopy, as well as quantum chemical calculations. The steady-state absorption spectra of these complexes in CH3CN show a distinct red-shift of the 1MLCT absorption with increasing numbers of amine substituent, whereas the emission spectra indicate an energy gap order of [Ru(bpy)3]2+ > [Ru(bpy)2(NNbpy)]2+ > [Ru(NNbpy)3]2+ > [Ru(bpy)(NNbpy)2]2+. Nanosecond, femtosecond transient absorption and electrochemical measurements suggest that NNbpy ligand has a strong influence on the electronic and emission properties of these complexes, due to electron-rich amine substituent. We illustrate how the numbers of amine substituent modulate the spectroscopic properties of transition metal complexes, which is related to the design of new electro-active systems with novel photoelectrochemical properties.

Phase Transitions of an Epidemic Spreading Model in Small-World Networks

NASA Astrophysics Data System (ADS)

Hua, Da-Yin; Gao, Ke

2011-06-01

We propose a modified susceptible-infected-refractory-susceptible (SIRS) model to investigate the global oscillations of the epidemic spreading in Watts—Strogatz (WS) small-world networks. It is found that when an individual immunity does not change or decays slowly in an immune period, the system can exhibit complex transition from an infecting stationary state to a large amplitude sustained oscillation or an absorbing state with no infection. When the immunity decays rapidly in the immune period, the transition to the global oscillation disappears and there is no oscillation. Furthermore, based on the spatio-temporal evolution patterns and the phase diagram, it is disclosed that a long immunity period takes an important role in the emergence of the global oscillation in small-world networks.

State-of-the-art thermochemical and kinetic computations for astrochemical complex organic molecules: formamide formation in cold interstellar clouds as a case study

PubMed Central

Vazart, Fanny; Calderini, Danilo; Puzzarini, Cristina; Skouteris, Dimitrios

2017-01-01

We propose an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model. Formamide has been selected as a case study in view of its interest as a precursor in the abiotic amino acid synthesis. After validation of the level of theory chosen for describing the potential energy surface, we have investigated several pathways of the OH+CH2NH and NH2+HCHO reaction channels. Our results indicate that both reaction channels are essentially barrier-less (in the sense that all relevant transition states lie below or only marginally above the reactants) and can, therefore, occur under the low temperature conditions of interstellar objects provided that tunneling is taken into the proper account. PMID:27689448

Spectra, energy levels, and energy transition of lanthanide complexes with cinnamic acid and its derivatives

NASA Astrophysics Data System (ADS)

Zhou, Kaining; Feng, Zhongshan; Shen, Jun; Wu, Bing; Luo, Xiaobing; Jiang, Sha; Li, Li; Zhou, Xianju

2016-04-01

High resolution spectra and luminescent lifetimes of 6 europium(III)-cinnamic acid complex {[Eu2L6(DMF)(H2O)]·nDMF·H2O}m (L = cinnamic acid I, 4-methyl-cinnamic acid II, 4-chloro-cinnamic acid III, 4-methoxy-cinnamic acid IV, 4-hydroxy-cinnamic acid V, 4-nitro-cinnamic acid VI; DMF = N, N-dimethylformamide, C3H7NO) were recorded from 8 K to room temperature. The energy levels of Eu3 + in these 6 complexes are obtained from the spectra analysis. It is found that the energy levels of the central Eu3 + ions are influenced by the nephelauxetic effect, while the triplet state of ligand is lowered by the p-π conjugation effect of the para-substituted functional groups. The best energy matching between the ligand triplet state and the central ion excited state is found in complex I. While the other complexes show poorer matching because the gap of 5D0 and triplet state contracts.

Statistical Analysis of the First Passage Path Ensemble of Jump Processes

NASA Astrophysics Data System (ADS)

von Kleist, Max; Schütte, Christof; Zhang, Wei

2018-02-01

The transition mechanism of jump processes between two different subsets in state space reveals important dynamical information of the processes and therefore has attracted considerable attention in the past years. In this paper, we study the first passage path ensemble of both discrete-time and continuous-time jump processes on a finite state space. The main approach is to divide each first passage path into nonreactive and reactive segments and to study them separately. The analysis can be applied to jump processes which are non-ergodic, as well as continuous-time jump processes where the waiting time distributions are non-exponential. In the particular case that the jump processes are both Markovian and ergodic, our analysis elucidates the relations between the study of the first passage paths and the study of the transition paths in transition path theory. We provide algorithms to numerically compute statistics of the first passage path ensemble. The computational complexity of these algorithms scales with the complexity of solving a linear system, for which efficient methods are available. Several examples demonstrate the wide applicability of the derived results across research areas.

Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM

PubMed Central

Boyd, Andrew D; ‘John’ Li, Jianrong; Kenost, Colleen; Joese, Binoy; Min Yang, Young; Kalagidis, Olympia A; Zenku, Ilir; Saner, Donald; Bahroos, Neil; Lussier, Yves A

2015-01-01

In the United States, International Classification of Disease Clinical Modification (ICD-9-CM, the ninth revision) diagnosis codes are commonly used to identify patient cohorts and to conduct financial analyses related to disease. In October 2015, the healthcare system of the United States will transition to ICD-10-CM (the tenth revision) diagnosis codes. One challenge posed to clinical researchers and other analysts is conducting diagnosis-related queries across datasets containing both coding schemes. Further, healthcare administrators will manage growth, trends, and strategic planning with these dually-coded datasets. The majority of the ICD-9-CM to ICD-10-CM translations are complex and nonreciprocal, creating convoluted representations and meanings. Similarly, mapping back from ICD-10-CM to ICD-9-CM is equally complex, yet different from mapping forward, as relationships are likewise nonreciprocal. Indeed, 10 of the 21 top clinical categories are complex as 78% of their diagnosis codes are labeled as “convoluted” by our analyses. Analysis and research related to external causes of morbidity, injury, and poisoning will face the greatest challenges due to 41 745 (90%) convolutions and a decrease in the number of codes. We created a web portal tool and translation tables to list all ICD-9-CM diagnosis codes related to the specific input of ICD-10-CM diagnosis codes and their level of complexity: “identity” (reciprocal), “class-to-subclass,” “subclass-to-class,” “convoluted,” or “no mapping.” These tools provide guidance on ambiguous and complex translations to reveal where reports or analyses may be challenging to impossible. Web portal: http://www.lussierlab.org/transition-to-ICD9CM/ Tables annotated with levels of translation complexity: http://www.lussierlab.org/publications/ICD10to9 PMID:25681260

Magnesium, zinc, aluminium and gallium hydride complexes of the transition metals.

PubMed

Butler, Michael J; Crimmin, Mark R

2017-01-24

The preparation and applications of heterobimetallic complexes continue to occupy researchers in the fields of organometallic, main group, and coordination chemistry. This interest stems from the promise these complexes hold as precursors to materials, reagents in synthesis and as new catalysis. Here we survey and organise the state-of-the-art understanding of the TM-H-M linkage (M = Mg, Zn, Al, Ga). We discuss the structure and bonding in these complexes, their known reactivity, and their largely unrealised potential in catalysis.

Design and construction of a double inversion recombination switch for heritable sequential genetic memory.

PubMed

Ham, Timothy S; Lee, Sung K; Keasling, Jay D; Arkin, Adam P

2008-07-30

Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and "remembers" its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable.

Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

PubMed Central

Ham, Timothy S.; Lee, Sung K.; Keasling, Jay D.; Arkin, Adam P.

2008-01-01

Background Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. Methodology/Principal Findings In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and “remembers” its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. Conclusions/Significance We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable. PMID:18665232

Photoinduced energy transfer in transition metal complex oligomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-04-01

The work we have done over the past three years has been directed toward the preparation, characterization and photophysical examination of mono- and bimetallic diimine complexes. The work is part of a broader project directed toward the development of stable, efficient, light harvesting arrays of transition metal complex chromophores. One focus has been the synthesis of rigid bis-bidentate and bis-tridentate bridging ligands. We have managed to make the ligand bphb in multigram quantities from inexpensive starting materials. The synthetic approach used has allowed us prepare a variety of other ligands which may have unique applications (vide infra). We have prepared,more » characterized and examined the photophysical behavior of Ru(II) and Re(I) complexes of the ligands. Energy donor/acceptor complexes of bphb have been prepared which exhibit nearly activationless energy transfer. Complexes of Ru(II) and Re(I) have also been prepared with other polyunsaturated ligands in which two different long lived ( > 50 ns) excited states exist; results of luminescence and transient absorbance measurements suggest the two states are metal-to-ligand charge transfer and ligand localized {pi}{r_arrow}{pi}* triplets. Finally, we have developed methods to prepare polymetallic complexes which are covalently bound to various surfaces. The long term objective of this work is to make light harvesting arrays for the sensitization of large band gap semiconductors. Details of this work are provided in the body of the report.« less

DEPRESSIVE SYMPTOMS AND FUNCTIONAL TRANSITIONS OVER TIME IN OLDER PERSONS

PubMed Central

Barry, Lisa C.; Murphy, Terrence E.; Gill, Thomas M.

2010-01-01

Objective We determined the association between clinically significant depressive symptoms, often referred to as depression, and subsequent transitions between no disability, mild disability, severe disability, and death. Design Prospective cohort study. Setting General community in greater New Haven, Connecticut, from March 23, 1998, to December 31, 2008. Participants Seven-hundred fifty four persons, aged 70 years or older. Measurements Monthly assessments of disability in essential activities of daily living and assessments of depressive symptoms every 18 months using a short-form of the Center for Epidemiologic Studies of Depression Scale for up to 129 months. Results Depressed participants were more likely than those who were non-depressed to transition from a state of no disability to mild (HR= 1.52; 95% CI 1.25, 1.85) and severe disability (HR=1.57; 95% CI 1.22, 2.01), and from a state of mild disability to severe disability (HR=1.33; 95% CI 1.06, 1.65); and were less likely to transition from a state of mild disability to no disability (HR=0.69; 95% CI 0.57, 0.85) and from a state of severe disability to no disability (HR=0.50; 95% CI 0.31, 0.79). Conclusions Depressive symptoms are associated with transitions into and out of disabled states, and with increased likelihood of transitioning from mild to severe disability. More broadly, our findings underscore the complexity of the relationship between depressive symptoms and disability. Future work is needed to evaluate the likely reciprocal relationship between depression and functional transitions in older persons. PMID:21873834

Excited state dynamics of the astaxanthin radical cation

NASA Astrophysics Data System (ADS)

Amarie, Sergiu; Förster, Ute; Gildenhoff, Nina; Dreuw, Andreas; Wachtveitl, Josef

2010-07-01

Femtosecond transient absorption spectroscopy in the visible and NIR and ultrafast fluorescence spectroscopy were used to examine the excited state dynamics of astaxanthin and its radical cation. For neutral astaxanthin, two kinetic components corresponding to time constants of 130 fs (decay of the S 2 excited state) and 5.2 ps (nonradiative decay of the S 1 excited state) were sufficient to describe the data. The dynamics of the radical cation proved to be more complex. The main absorption band was shifted to 880 nm (D 0 → D 3 transition), showing a weak additional band at 1320 nm (D 0 → D 1 transition). We found, that D 3 decays to the lower-lying D 2 within 100 fs, followed by a decay to D 1 with a time constant of 0.9 ps. The D 1 state itself exhibited a dual behavior, the majority of the population is transferred to the ground state in 4.9 ps, while a small population decays on a longer timescale of 40 ps. Both transitions from D 1 were found to be fluorescent.

High-Resolution Study of the Perturbation in the CO Triplet Band

NASA Astrophysics Data System (ADS)

Momona, M.; Kanamori, H.; Sakurai, K.

1993-05-01

Seven hundred absorption lines have been observed in the discharge plasma of He and CO in the 12600-12 800 cm-1 region with Doppler-limited resolution by a near-infrared diode laser spectrometer. Out of complex spectral patterns, more than 400 lines were assigned to the CO triplet band, d3Δ(v‧ = 2) - a3Π (v″ = 1). The upper state of this transition is known to be severely perturbed. The measurement of all the spin subbands of the 3Δ - 3Π transition allowed us to reanalyze the perturbation of the d3Δ (v = 2) state with the highly vibrationally excited state, v = 9, in the a3Π state. Diode laser spectroscopy with high sensitivity and Doppler-limited resolution revealed the overtone band transition from v = 1 to v = 9 within the a3Π state and the Λ-type doubling in the d3Δ state. Those interesting phenomena can be understood as a result of the perturbation and were successfully reproduced by the eigenvectors determined in this analysis.

Highly excited symmetry-breaking infrared and THz transitions in methanol-D 1

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Indranath

2004-06-01

In this paper, symmetry-breaking transitions have been identified in the Fourier transform infrared (FTIR) and Terra Hertz (THz) fast scan spectra of asymmetrically deuterated methanol CH 2DOH involving three quanta of the lowest lying vibrational state ( ν1). These transitions have an upper state belonging to highly excited torsional state with the torsional quantum number v=11 (e 5) (with the axial component of total rotational angular momentum K=5 and 6) in the Internal Axis Method (IAM) formalism developed by Quade and his co-workers [J. Mol. Spectrosc. 146 (1991) 238; J. Mol. Spectrosc. 146 (1991) 252], which was later extended by Mukhopadhyay [Spectrochim. Acta A 53 (1997) 2457; Spectrochim. Acta A 53 (1997) 1947] to include highly excited torsional-rotational states. The originating lower states belong to the o 1 ( v=3) with K=4 and 5. In analogy with pure methanol these transitions terminate to the third excited torsional state, which has very small torsional matrix elements to be observable in normal FTIR spectra. The location of the e 5 states suggests that the calculated energy levels using the parameters of Liu and Quade [J. Mol. Spectrosc. 146 (1991) 252] are reasonable and very helpful to assign such highly excited transitions, considering that their studies include low angular momentum states. In addition the very existence of these transitions proves that the matrix elements calculated by Mukhopadhyay [Spectrochim. Acta A 53 (1997) 1947] are very useful and dependable. Thus they represent a valuable tool for entangling the complex spectrum of this asymmetrically deuterated methanol. In order to provide confirmatory evidence the THz spectra obtained using the Fast Scanning Submillimeter Spectroscopy Technique (FASSST) at the Ohio State University [Rev. Instr. 68 (1997) 1675; Anal. Chem. 70 (1998) 719A] were searched for the ground state transitions that can be calculated precisely from IR combination relations. All the transitions that can be predicted with K=4 and 5 in the o 1 states are indeed identified in the FASSST spectrum. To our knowledge this is the first reported work involving direct transitions to such highly excited torsional state of CH 2DOH. This work will enable the determination of higher order barrier terms and provide enough understanding of the energy levels for the identification of many unidentified transitions. To our knowledge, this is the first time such high frequency symmetry-breaking transitions have been observed in asymmetrically deuterated methanol.

Structure of the Deactive State of Mammalian Respiratory Complex I.

PubMed

Blaza, James N; Vinothkumar, Kutti R; Hirst, Judy

2018-02-06

Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Rotational and angular distributions of NO products from NO-Rg(Rg = He, Ne, Ar) complex photodissociation

DOE PAGES

Heather L. Holmes-Ross; Hall, Gregory E.; Valenti, Rebecca J.; ...

2016-01-29

In this study, we present the results of an investigation into the rotational and angular distributions of the NO A ~ state fragment following photodissociation of the NO-He, NO-Ne and NO-Ar van der Waals complexed excited via the A ~ ← X ~ transition. For each complex the dissociation is probed for several values of E a, the available energy above the dissociation threshold.

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.

PubMed

Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

2016-01-01

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions.

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

PubMed Central

Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

2016-01-01

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions. PMID:27243223

Thermal stability of bubble domains in ferromagnetic discs

NASA Astrophysics Data System (ADS)

Hrkac, G.; Bance, S.; Goncharov, A.; Schrefl, T.; Suess, D.

2007-05-01

The transition and thermal stability of disc-shaped ferromagnetic particles at the temperature of T = 300 K with a uniaxial anisotropy along the symmetry axis from a bi-domain to a single domain state has been studied. The nudge elastic band method was used to map the energy landscape and to calculate the energy barrier between the transition states. For single FePt disc-shaped particles with perpendicular anisotropy three transition configurations have been found: single domain, stripe- and stable bubble domains at zero applied field. The single domain configuration along the positive anisotropy axis is reached by an annihilation process of the domain wall and the all-down state by a complex domain expansion process. Magnetization configurations in two interacting discs show an increase in thermal stability compared with single disc systems, which is attributed to the interacting magnetostatic energy between the two particles.

Insights into the nature of DNA binding of AbrB-like transcription factors

PubMed Central

Sullivan, Daniel M.; Bobay, Benjamin G.; Kojetin, Douglas J.; Thompson, Richele J.; Rance, Mark; Strauch, Mark A.; Cavanagh, John

2008-01-01

Summary Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these ‘transition-state regulator’ proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel shift assays, mutagenic and NMR studies to generate a structural model of the complex between AbrBN55 and its cognate promoter, abrB8. These investigations have enabled us to generate the first model for the specific nature of the transition-state regulator-DNA interaction. PMID:19000822

Taking Ockham's razor to enzyme dynamics and catalysis.

PubMed

Glowacki, David R; Harvey, Jeremy N; Mulholland, Adrian J

2012-01-29

The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

Kinetic, Spectroscopic, and Theoretical Assessment of Associative and Dissociative Methanol Dehydration Routes in Zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Andrew J.; Iglesia, Enrique

Mechanistic interpretations of rates and in situ IR spectra combined with density functionals that account for van der Waals interactions of intermediates and transition states within confining voids show that associative routes mediate the formation of dimethyl ether from methanol on zeolitic acids at the temperatures and pressures of practical dehydration catalysis. Methoxy-mediated dissociative routes become prevalent at higher temperatures and lower pressures, because they involve smaller transition states with higher enthalpy, but also higher entropy, than those in associative routes. These enthalpy–entropy trade-offs merely reflect the intervening role of temperature in activation free energies and the prevalence of moremore » complex transition states at low temperatures and high pressures. This work provides a foundation for further inquiry into the contributions of H-bonded methanol and methoxy species in homologation and hydrocarbon synthesis reactions from methanol.« less

Synthesis and Properties of Ortho-Nitro-Fe Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, A.; Mishra, Niyati; Sharma, R.

2011-07-15

Ortho-Nitro-Fe complex (Transition metal complex) has synthesized by chemical route method and properties of made complex has characterized by X-Ray diffraction (XRD), Moessbauer spectroscopy, Fourier transformation infra-red spectroscopy (FTIR) and X-Ray photoelectron spectroscopy (XPS). XRD analysis shows that sample is crystalline in nature and having particle size in the range of few nano meters. Moessbauer spectroscopy at room temperature shows the oxidation state of Iron (central metal ion) after complaxasion. FTIR spectra of the complex confirms the coordination of metal ion with ligand.

Influence of molecular designs on polaronic and vibrational transitions in a conjugated push-pull copolymer

NASA Astrophysics Data System (ADS)

Cobet, Christoph; Gasiorowski, Jacek; Menon, Reghu; Hingerl, Kurt; Schlager, Stefanie; White, Matthew S.; Neugebauer, Helmut; Sariciftci, N. Serdar; Stadler, Philipp

2016-10-01

Electron-phonon interactions of free charge-carriers in doped pi-conjugated polymers are conceptually described by 1-dimensional (1D) delocalization. Thereby, polaronic transitions fit the 1D-Froehlich model in quasi-confined chains. However, recent developments in conjugated polymers have diversified the backbones to become elaborate heterocylcic macromolecules. Their complexity makes it difficult to investigate the electron-phonon coupling. In this work we resolve the electron-phonon interactions in the ground and doped state in a complex push-pull polymer. We focus on the polaronic transitions using in-situ spectroscopy to work out the differences between single-unit and push-pull systems to obtain the desired structural- electronic correlations in the doped state. We apply the classic 1D-Froehlich model to generate optical model fits. Interestingly, we find the 1D-approach in push-pull polarons in agreement to the model, pointing at the strong 1D-character and plain electronic structure of the push-pull structure. In contrast, polarons in the single-unit polymer emerge to a multi- dimensional problem difficult to resolve due to their anisotropy. Thus, we report an enhancement of the 1D-character by the push-pull concept in the doped state - an important view in light of the main purpose of push-pull polymers for photovoltaic devices.

Radiative, nonradiative, and mixed-decay transitions of rare-earth ions in dielectric media

NASA Astrophysics Data System (ADS)

Burshtein, Zeev

2010-09-01

We present and discuss in a comprehensive, deductive, and simplified manner, issues of nonradiative transitions involvement in fluorescence of ions embedded in dielectric solid matrices. The semiclassical approach is favored over a full quantum description, and empiric quantities are introduced from the start. One issue is nonradiative single-phonon transitions when the energy gap between the adjacent electronic ion states is smaller than the cutoff matrix phonon energy. Another issue is transitions in a complex energy scheme, where some visible and near-visible transitions are radiative and others are nonradiative. A refined Füchtbauer-Ladenburg recipe for calculation of the stimulated emission spectrum on the basis of measurable absorption and fluorescence emission spectra is worked out. The last issue is multiphonon nonradiative transitions occurring when the energy gap between adjacent electronic ion states is larger than the cutoff matrix phonon energy. Transition probabilities were calculated on the basis of anharmonicity of the effective potential supporting the internal atomic basis vibrations. An expression in a closed form is obtained, similar to the empiric ``energy gap'' law, however, with parameters related to specific host material properties and the actual transition in the ion. Comparison to existing experimental evidence is presented and discussed in detail.

Rationalizing the role of structural motif and underlying electronic structure in the finite temperature behavior of atomic clusters

NASA Astrophysics Data System (ADS)

Susan, Anju; Joshi, Kavita

2014-04-01

Melting in finite size systems is an interesting but complex phenomenon. Many factors affect melting and owing to their interdependencies it is a challenging task to rationalize their roles in the phase transition. In this work, we demonstrate how structural motif of the ground state influences melting transition in small clusters. Here, we report a case with clusters of aluminum and gallium having same number of atoms, valence electrons, and similar structural motif of the ground state but drastically different melting temperatures. We have employed Born-Oppenheimer molecular dynamics to simulate the solid-like to liquid-like transition in these clusters. Our simulations have reproduced the experimental trends fairly well. Further, the detailed analysis of isomers has brought out the role of the ground state structure and underlying electronic structure in the finite temperature behavior of these clusters. For both clusters, isomers accessible before cluster melts have striking similarities and does have strong influence of the structural motif of the ground state. Further, the shape of the heat capacity curve is similar in both the cases but the transition is more spread over for Al36 which is consistent with the observed isomerization pattern. Our simulations also suggest a way to characterize transition region on the basis of accessibility of the ground state at a specific temperature.

Development of Instrumentation for Boundary Layer Transition Detection

DTIC Science & Technology

1991-01-01

assistance of Maj. Aaron Byerley were largely responsible for my decision to stay on. 4t Contents Abstract Acknowledgements Nomenclature Chapter 1...The use of shr sensitive liquid crystals in aerodynamic measurements has been a mor wPu imovation. Two different prcesses can be employed to...transition location. The steady-state heat transfer technique is unsuited for use on complex geometries, may be time consuming , and has an element of

Two-photon direct frequency comb spectroscopy of alkali atoms

NASA Astrophysics Data System (ADS)

Palm, Christopher; Pradhananga, Trinity; Nguyen, Khoa; Montcrieffe, Caitlin; Kimball, Derek

2012-11-01

We have studied transition frequencies and excited state hyperfine structure in rubidium using 2-photon transitions excited directly with the frequency-doubled output of a erbium fiber optical frequency comb. The frequency comb output is directed in two counterpropagating directions through a vapor cell containing the rubidium vapor. A pair of optical filters is used to select teeth of the comb in order to identify the transition wavelengths. A photomultiplier tube (PMT) measures fluorescence from a decay channel wavelength selected with another optical filter. Using different combinations of filters enables a wide range of transitions to be investigated. By scanning the repetition rate, a Doppler-free spectrum can be obtained enabling kHz-resolution spectral measurements. An interesting dependence of the 2-photon spectrum on the energy of the intermediate state of the 2-photon transition is discussed. Our investigations are laying the groundwork for a long-term research program to use direct frequency comb spectroscopy to understand the complex spectra of rare-earth atoms.

Vibrational energy flow controls internal conversion in a transition metal complex.

PubMed

Hedley, Gordon J; Ruseckas, Arvydas; Samuel, Ifor D W

2010-09-02

Internal conversion (IC) between excited electronic states is a fundamental photophysical process that is important for understanding protection from UV radiation, energy transfer pathways and electron injection in artificial photosynthetic systems and organic solar cells. We have studied IC between three singlet MLCT states in an iridium complex using femtosecond fluorescence spectroscopy. Very fast IC with a time constant of <20 fs is observed from the highest state and a much slower relaxation to the lowest energy singlet state on a 70 fs time scale. The abrupt slowdown of the relaxation rate occurs when there is >0.6 eV of vibrational energy stored in the complex that has to be dissipated by intramolecular vibrational redistribution before further IC to the lower energy states can occur. These results show that the ability to dissipate vibrational energy can control the relaxation process in this class of materials.

Near-saturated red emitters: four-coordinate copper(i) halide complexes containing 8-(diphenylphosphino)quinoline and 1-(diphenylphosphino)naphthalene ligands.

PubMed

Liu, Li-Ping; Li, Qian; Xiang, Song-Po; Liu, Li; Zhong, Xin-Xin; Liang, Chen; Li, Guang Hua; Hayat, Tasawar; Alharbi, Njud S; Li, Fa-Bao; Zhu, Nian-Yong; Wong, Wai-Yeung; Qin, Hai-Mei; Wang, Lei

2018-06-07

Recently, highly emissive neutral copper halide complexes have received much attention. Here, a series of four-coordinate mononuclear Cu(i) halide complexes, [CuX(dpqu)(dpna)] (dpqu = 8-(diphenylphosphino)quinoline, dpna = 1-(diphenylphosphino)naphthalene, X = I (1), Br (2) and Cl (3)), were synthesized, and their molecular structures and photophysical properties were investigated. These complexes exhibit near-saturated red emission in the solid state at room temperature and have peak emission wavelengths at 669-691 nm with microsecond lifetimes (τ = 0.46-1.80 μs). Small S1-T1 energy gaps in the solid state indicate that the emission occurs from a thermally activated excited singlet state at ambient temperature. The emission of the complexes 1-3 mainly originates from MLCT transition. The solution-processed devices of complex 1 exhibit stable red emission with a CIE(x, y) of (0.62, 0.38) for a doped device and (0.63, 0.37) for a non-doped device.

a Theoretical Search for AN Electronic Spectrum of the He-BeO Complex

NASA Astrophysics Data System (ADS)

Gardner, Adrian; Heaven, Michael

2014-06-01

The surprisingly high dissociation energy of the He-Be bond in the He-BeO complex was first reported 25 years ago. Following which, a number of theoretical studies have investigated similar closed shell helium containing complexes. However, despite these investigations, a complex containing a strong He-X bond has thus far eluded experimental detection. In this work, potential energy surfaces of electronically excited states of the He-BeO complex have been calculated employing high level CASSCF+MRCI+Q methodologies and utilizing extended basis sets. Several excited states show strong interactions between helium and BeO lying in Franck-Condon accessible windows of electronic transitions arising from the vibrationless electronic ground state. It is hoped that the conclusions of this study will result in the observation an electronic spectrum of this long hypothesized strongly bound complex in the near future. W. Koch, J. R. Collins and G. Frenking, Chem. Phys. Lett. 1986, 132 330-333.

Generic approach to access barriers in dehydrogenation reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

Generic approach to access barriers in dehydrogenation reactions

DOE PAGES

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

2018-03-08

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Critical Slowing Down Governs the Transition to Neuron Spiking

PubMed Central

Meisel, Christian; Klaus, Andreas; Kuehn, Christian; Plenz, Dietmar

2015-01-01

Many complex systems have been found to exhibit critical transitions, or so-called tipping points, which are sudden changes to a qualitatively different system state. These changes can profoundly impact the functioning of a system ranging from controlled state switching to a catastrophic break-down; signals that predict critical transitions are therefore highly desirable. To this end, research efforts have focused on utilizing qualitative changes in markers related to a system’s tendency to recover more slowly from a perturbation the closer it gets to the transition—a phenomenon called critical slowing down. The recently studied scaling of critical slowing down offers a refined path to understand critical transitions: to identify the transition mechanism and improve transition prediction using scaling laws. Here, we outline and apply this strategy for the first time in a real-world system by studying the transition to spiking in neurons of the mammalian cortex. The dynamical system approach has identified two robust mechanisms for the transition from subthreshold activity to spiking, saddle-node and Hopf bifurcation. Although theory provides precise predictions on signatures of critical slowing down near the bifurcation to spiking, quantitative experimental evidence has been lacking. Using whole-cell patch-clamp recordings from pyramidal neurons and fast-spiking interneurons, we show that 1) the transition to spiking dynamically corresponds to a critical transition exhibiting slowing down, 2) the scaling laws suggest a saddle-node bifurcation governing slowing down, and 3) these precise scaling laws can be used to predict the bifurcation point from a limited window of observation. To our knowledge this is the first report of scaling laws of critical slowing down in an experiment. They present a missing link for a broad class of neuroscience modeling and suggest improved estimation of tipping points by incorporating scaling laws of critical slowing down as a strategy applicable to other complex systems. PMID:25706912

Oscillating potential well in the complex plane and the adiabatic theorem

NASA Astrophysics Data System (ADS)

Longhi, Stefano

2017-10-01

A quantum particle in a slowly changing potential well V (x ,t ) =V ( x -x0(ɛ t ) ) , periodically shaken in time at a slow frequency ɛ , provides an important quantum mechanical system where the adiabatic theorem fails to predict the asymptotic dynamics over time scales longer than ˜1 /ɛ . Specifically, we consider a double-well potential V (x ) sustaining two bound states spaced in frequency by ω0 and periodically shaken in a complex plane. Two different spatial displacements x0(t ) are assumed: the real spatial displacement x0(ɛ t ) =A sin(ɛ t ) , corresponding to ordinary Hermitian shaking, and the complex one x0(ɛ t ) =A -A exp(-i ɛ t ) , corresponding to non-Hermitian shaking. When the particle is initially prepared in the ground state of the potential well, breakdown of adiabatic evolution is found for both Hermitian and non-Hermitian shaking whenever the oscillation frequency ɛ is close to an odd resonance of ω0. However, a different physical mechanism underlying nonadiabatic transitions is found in the two cases. For the Hermitian shaking, an avoided crossing of quasienergies is observed at odd resonances and nonadiabatic transitions between the two bound states, resulting in Rabi flopping, can be explained as a multiphoton resonance process. For the complex oscillating potential well, breakdown of adiabaticity arises from the appearance of Floquet exceptional points at exact quasienergy crossing.

State-selective optimization of local excited electronic states in extended systems

NASA Astrophysics Data System (ADS)

Kovyrshin, Arseny; Neugebauer, Johannes

2010-11-01

Standard implementations of time-dependent density-functional theory (TDDFT) for the calculation of excitation energies give access to a number of the lowest-lying electronic excitations of a molecule under study. For extended systems, this can become cumbersome if a particular excited state is sought-after because many electronic transitions may be present. This often means that even for systems of moderate size, a multitude of excited states needs to be calculated to cover a certain energy range. Here, we present an algorithm for the selective determination of predefined excited electronic states in an extended system. A guess transition density in terms of orbital transitions has to be provided for the excitation that shall be optimized. The approach employs root-homing techniques together with iterative subspace diagonalization methods to optimize the electronic transition. We illustrate the advantages of this method for solvated molecules, core-excitations of metal complexes, and adsorbates at cluster surfaces. In particular, we study the local π →π∗ excitation of a pyridine molecule adsorbed at a silver cluster. It is shown that the method works very efficiently even for high-lying excited states. We demonstrate that the assumption of a single, well-defined local excitation is, in general, not justified for extended systems, which can lead to root-switching during optimization. In those cases, the method can give important information about the spectral distribution of the orbital transition employed as a guess.

Wetting transitions on patterned surfaces with diffuse interaction potentials embedded in a Young-Laplace formulation

NASA Astrophysics Data System (ADS)

Pashos, G.; Kokkoris, G.; Papathanasiou, A. G.; Boudouvis, A. G.

2016-01-01

The Minimum Energy Paths (MEPs) of wetting transitions on pillared surfaces are computed with the Young-Laplace equation, augmented with a pressure term that accounts for liquid-solid interactions. The interactions are smoothed over a short range from the solid phase, therefore facilitating the numerical solution of problems concerning wetting on complex surface patterns. The patterns may include abrupt geometric features, e.g., arrays of rectangular pillars, where the application of the unmodified Young-Laplace is not practical. The MEPs are obtained by coupling the augmented Young-Laplace with the modified string method from which the energy barriers of wetting transitions are eventually extracted. We demonstrate the method on a wetting transition that is associated with the breakdown of superhydrophobic behavior, i.e., the transition from the Cassie-Baxter state to the Wenzel state, taking place on a superhydrophobic pillared surface. The computed energy barriers quantify the resistance of the system to these transitions and therefore, they can be used to evaluate superhydrophobic performance or provide guidelines for optimal pattern design.

Rates of transition between amyloid and neurodegeneration biomarker states and to dementia among non-demented individuals: a population-based cohort study

PubMed Central

Jack, Clifford R.; Therneau, Terry M.; Wiste, Heather J.; Weigand, Stephen D.; Knopman, David S.; Lowe, Val J.; Mielke, Michelle M.; Vemuri, Prashanthi; Roberts, Rosebud O.; Machulda, Mary M.; Senjem, Matthew L.; Gunter, Jeffrey L.; Rocca, Walter A.; Petersen, Ronald C.

2016-01-01

Summary Background We previously observed in a cross-sectional analysis that frequencies of amyloid and neurodegeneration biomarker states varied greatly by age among cognitively non-impaired participants, suggesting dynamic within-person processes. Our objective in this longitudinal study was to estimate rates of transitioning from a less- to a more-abnormal biomarker state by age among non-demented individuals, as well as rates of transitioning to dementia by biomarker state. Methods All participants (n=4049) were non-demented at baseline. A subset of 1541 underwent multi-modality imaging. Amyloid PET was used to classify individuals as amyloid positive (A+) or negative (A−). FDG PET and MRI were used to classify individuals as neurodegeneration positive (N+) or negative (N−). All observations from the 4049 individuals were used in a multi-state model to estimate four different age-specific biomarker state transition rates among non-demented individuals: A−N− to A+N−; A−N− to A−N+ (suspected non-Alzheimer pathology, SNAP); A+N− to A+N+; A−N+ (SNAP) to A+N+. We also estimated two age-specific rates to dementia: A+N+ to dementia; and A−N+ (SNAP) to dementia. Using these state-to-state transition rates, we estimated biomarker state frequencies by age. Findings All transition rates were low at age 50 and (with one exception) were well-characterized by an exponential increase with age. The rates per 100-person years at ages 65 versus 85 were 1.6 versus 17.2 for A−N− to A−N+, 6.1 versus 20.8 for A+N− to A+N+, 2.6 versus 13.2 for A−N+ to A+N+, 0.8 versus 7.0 for A+N+ to dementia, and 0.6 versus 1.7 for A−N+ to dementia. The one exception to an exponential increase with age was the transition rate from A−N− to A+N− which increased from 4.0 transitions per 100 person-years at age 65 to approximately 7 transitions per 100 person-years in the 70s and then plateaued beyond that age. Estimated biomarker frequencies by age from the multistate model were similar to cross-sectional biomarker frequencies. Interpretation Dynamic state-to-state transition rates illustrate important measurable aspects of the changing biology underlying brain aging. The biomarker states we describe relate to both AD and non-AD processes. Our transition rates suggest that brain aging can be conceptualized as a nearly inevitable acceleration toward worse biomarker and clinical states. The one exception was that transition to amyloidosis without neurodegeneration was most dynamic from age 60 to 70 and then plateaued beyond that age. We found that simple transition rates can explain complex, highly interdependent biomarker state frequencies in our sample. PMID:26597325

Two-State Reactivity in Low-Valent Iron-Mediated C-H Activation and the Implications for Other First-Row Transition Metals.

PubMed

Sun, Yihua; Tang, Hao; Chen, Kejuan; Hu, Lianrui; Yao, Jiannian; Shaik, Sason; Chen, Hui

2016-03-23

C-H bond activation/functionalization promoted by low-valent iron complexes has recently emerged as a promising approach for the utilization of earth-abundant first-row transition metals to carry out this difficult transformation. Herein we use extensive density functional theory and high-level ab initio coupled cluster calculations to shed light on the mechanism of these intriguing reactions. Our key mechanistic discovery for C-H arylation reactions reveals a two-state reactivity (TSR) scenario in which the low-spin Fe(II) singlet state, which is initially an excited state, crosses over the high-spin ground state and promotes C-H bond cleavage. Subsequently, aryl transmetalation occurs, followed by oxidation of Fe(II) to Fe(III) in a single-electron transfer (SET) step in which dichloroalkane serves as an oxidant, thus promoting the final C-C coupling and finalizing the C-H functionalization. Regeneration of the Fe(II) catalyst for the next round of C-H activation involves SET oxidation of the Fe(I) species generated after the C-C bond coupling. The ligand sphere of iron is found to play a crucial role in the TSR mechanism by stabilization of the reactive low-spin state that mediates the C-H activation. This is the first time that the successful TSR concept conceived for high-valent iron chemistry is shown to successfully rationalize the reactivity for a reaction promoted by low-valent iron complexes. A comparative study involving other divalent middle and late first-row transition metals implicates iron as the optimum metal in this TSR mechanism for C-H activation. It is predicted that stabilization of low-spin Mn(II) using an appropriate ligand sphere should produce another promising candidate for efficient C-H bond activation. This new TSR scenario therefore emerges as a new strategy for using low-valent first-row transition metals for C-H activation reactions.

A computational study of the CO dissociation in cyclopentadienyl ruthenium complexes relevant to the racemization of alcohols.

PubMed

Stewart, Beverly; Nyhlen, Jonas; Martín-Matute, Belén; Bäckvall, Jan-E; Privalov, Timofei

2013-01-28

The formation of an active 16-electron ruthenium sec-alkoxide complex via loss of the CO ligand is an important step in the mechanism of the racemization of sec-alcohols by (η(5)-Ph(5)C(5))Ru(CO)(2)X ruthenium complexes with X = Cl and O(t)Bu. Here we show with accurate DFT calculations the potential energy profile of the CO dissociation pathway for a series of relevant (η(5)-Ph(5)C(5))Ru(CO)(2)X complexes, where X = Cl, O(t)Bu, H and COO(t)Bu. We have found that the CO dissociation energy increases in the following order: O(t)Bu (lowest), Cl, COO(t)Bu and H (highest). Using the distance between ruthenium and C(CO), r = Ru-C(CO), as a constraint, and by optimizing all other degrees of freedom for a range of Ru-CO distances, we obtained relative energies, ΔE(r) and geometries of a sufficient number of transient structures with the elongated Ru-CO bond up to r = 3.4 Å. Our calculations provide a quantitative understanding of the CO ligand dissociation in (η(5)-Ph(5)C(5))Ru(CO)(2)Cl and (η(5)-Ph(5)C(5))Ru(CO)(2)(O(t)Bu) complexes, which is relevant to the mechanism of their catalytic activity in the racemization of alcohols. We recently reported that exchange of the CO ligand by isotopically labeled (13)CO in the Ru-O(t)Bu complex occurs twenty times faster than that in the Ru-Cl complex. This corresponds to a difference of 1.8 kcal mol(-1) in the CO dissociation energy (at room temperature). This is in very good agreement with the calculated difference between the two potential energy curves for Ru-O(t)Bu and Ru-Cl complexes, which is about 1.8-2 kcal mol(-1) around the corresponding transition states of the CO dissociation. The calculated difference in the total energy for CO dissociation in (η(5)-Ph(5)C(5))Ru(CO)(2)X complexes is related to the stabilization provided by the X group in the final 16-electron complexes, which are formed via product-like transition states. In addition to the calculated transition states of CO dissociation in Ru-O(t)Bu and Ru-Cl complexes, the calculated transient structures with the elongated Ru-CO bond provide insight into how the geometry of the ruthenium complex with a potent heteroatom donor group (X) gradually changes when one of the COs is dissociating.

Electronic structural changes of Mn in the oxygen-evolving complex of photosystem II during the catalytic cycle.

PubMed

Glatzel, Pieter; Schroeder, Henning; Pushkar, Yulia; Boron, Thaddeus; Mukherjee, Shreya; Christou, George; Pecoraro, Vincent L; Messinger, Johannes; Yachandra, Vittal K; Bergmann, Uwe; Yano, Junko

2013-05-20

The oxygen-evolving complex (OEC) in photosystem II (PS II) was studied in the S0 through S3 states using 1s2p resonant inelastic X-ray scattering spectroscopy. The spectral changes of the OEC during the S-state transitions are subtle, indicating that the electrons are strongly delocalized throughout the cluster. The result suggests that, in addition to the Mn ions, ligands are also playing an important role in the redox reactions. A series of Mn(IV) coordination complexes were compared, particularly with the PS II S3 state spectrum to understand its oxidation state. We find strong variations of the electronic structure within the series of Mn(IV) model systems. The spectrum of the S3 state best resembles those of the Mn(IV) complexes Mn3(IV)Ca2 and saplnMn2(IV)(OH)2. The current result emphasizes that the assignment of formal oxidation states alone is not sufficient for understanding the detailed electronic structural changes that govern the catalytic reaction in the OEC.

Excited State Energetics and Dynamics of Large Molecules, Complexes and Clusters

DTIC Science & Technology

1988-07-01

tetracene. Ar (n=l-5) complexes, providing central information on microscopic solvent shifts. These studies were extended to M-metal atom com - plexes...corresponding to the bare molecule. At higher 2. Experimental stagnation pressures of Ar (p = 80-150 Toff) the contributions of van der Waals DPB. Ar, com - Our...gas aromatic-molecule complexes were docu- So - S1 transition of the trans-stilbene (TS)-Ar com - mented experimentally to lie in the rango - 30- plex

Abstraction kinetics of H-atom by OH radical from pinonaldehyde (C10H16O2): ab initio and transition-state theory calculations.

PubMed

Dash, Manas Ranjan; Rajakumar, B

2012-06-21

The kinetics and abstraction rate coefficients of hydroxyl radical (OH) reaction with pinonaldehyde were computed using G3(MP2) theory and transition-state theory (TST) between 200 and 400 K. Structures of the reactants, reaction complexes (RCs), product complexes (PCs), transition states (TSs), and products were optimized at the MP2(FULL)/6-31G* level of theory. Fifteen transition states were identified for the title reaction and confirmed by intrinsic reaction coordinate (IRC) calculations. The contributions of all the individual hydrogens in the substrate molecule to the total reaction are computed. The quantum mechanical tunneling effect was computed using Wigner's and Eckart's methods (both symmetrical and unsymmetrical methods). The reaction exhibits a negative temperature dependent rate coefficient, k(T) = (1.97 ± 0.34) × 10(-13) exp[(1587 ± 48)/T] cm(3) molecule(-1) s(-1), k(T) = (3.02 ± 0.56) × 10(-13) exp[(1534 ± 52/T] cm(3) molecule(-1) s(-1), and k(T) = (4.71 ± 1.85) × 10(-14) exp[(2042 ± 110)/T] cm(3) molecule(-1) s(-1) with Wigner's, Eckart's symmetrical, and Eckart's unsymmetrical tunneling corrections, respectively. Theoretically calculated rate coefficients are found to be in good agreement with the experimentally measured ones and other theoretical results. It is shown that hydrogen abstraction from -CHO position is the major channel, whereas H-abstraction from -COCH(3) is negligible. The atmospheric lifetime of pinonaldehyde is computed to be few hours and found to be in excellent agreement with the experimentally estimated ones.

Ultraviolet laser spectroscopy of jet-cooled CaNC and SrNC free radicals: Observation of bent excited electronic states

NASA Astrophysics Data System (ADS)

Greetham, Gregory M.; Ellis, Andrew M.

2000-11-01

New electronic transitions of the CaNC and SrNC free radicals have been identified in the near ultraviolet. For CaNC one new system, labeled the D˜-X˜ transition, was observed in the 31 500-33 400 cm-1 region. Two new transitions were found for SrNC, the D˜-X˜ and Ẽ-X˜ systems spanning 29 100-31 000 and 32 750-34 000 cm-1, respectively. Jet-cooled laser excitation spectra yield complex vibrational structure, much of which is attributed to excitation of the bending vibration. This has been used to infer that the molecule adopts a nonlinear equilibrium geometry in the upper electronic state in all three band systems, in contrast to the linear ground electronic state. This structural change is accounted for by the increased diffuseness of the unpaired electron in the excited states, which favors deviation from linearity. All three new excited states are assigned 2A' symmetry and correlate with 2Σ+ states in the linear molecule limit. Tentative estimates for the barriers to linearity in the D˜ 2A' states of CaNC and SrNC have been determined as ˜700 and ˜1050 cm-1, respectively.

Timescales of Coherent Dynamics in the Light Harvesting Complex 2 (LH2) of Rhodobacter sphaeroides.

PubMed

Fidler, Andrew F; Singh, Ved P; Long, Phillip D; Dahlberg, Peter D; Engel, Gregory S

2013-05-02

The initial dynamics of energy transfer in the light harvesting complex 2 from Rhodobacter sphaeroides were investigated with polarization controlled two-dimensional spectroscopy. This method allows only the coherent electronic motions to be observed revealing the timescale of dephasing among the excited states. We observe persistent coherence among all states and assign ensemble dephasing rates for the various coherences. A simple model is utilized to connect the spectroscopic transitions to the molecular structure, allowing us to distinguish coherences between the two rings of chromophores and coherences within the rings. We also compare dephasing rates between excited states to dephasing rates between the ground and excited states, revealing that the coherences between excited states dephase on a slower timescale than coherences between the ground and excited states.

A novel high light-inducible carotenoid-binding protein complex in the thylakoid membranes of Synechocystis PCC 6803

PubMed Central

Daddy, Soumana; Zhan, Jiao; Jantaro, Saowarath; He, Chenliu; He, Qingfang; Wang, Qiang

2015-01-01

Synechocystis sp. PCC 6803 is a model cyanobacterium extensively used to study photosynthesis. Here we reveal a novel high light-inducible carotenoid-binding protein complex (HLCC) in the thylakoid membranes of Synechocystis PCC 6803 cells exposed to high intensity light. Zeaxanthin and myxoxanthophyll accounted for 29.8% and 54.8%, respectively, of the carotenoids bound to the complex. Using Blue-Native PAGE followed by 2D SDS-PAGE and mass spectrometry, we showed that the HLCC consisted of Slr1128, IsiA, PsaD, and HliA/B. We confirmed these findings by SEAD fluorescence cross-linking and anti-PsaD immuno-coprecipitation analyses. The expression of genes encoding the protein components of the HLCC was enhanced by high light illumination and artificial oxidative stress. Deletion of these proteins resulted in impaired state transition and increased sensitivity to oxidative and/or high light stress, as indicated by increased membrane peroxidation. Therefore, the HLCC protects thylakoid membranes from extensive photooxidative damage, likely via a mechanism involving state transition. PMID:25820628

Novel thermoelectric properties of complex transition-metal oxides.

PubMed

Terasaki, Ichiro; Iwakawa, Manabu; Nakano, Tomohito; Tsukuda, Akira; Kobayashi, Wataru

2010-01-28

We report how the thermopower of complex transition-metal oxides is susceptible to small changes in material parameters. In the A-site ordered perovskite oxide R(2/3)Cu(3)Ti(3.6)Ru(0.4)O(12), the thermopower changes from 15 to -100 microV K(-1) at 300 K in going from R = La to Er. We associate this with the hybridization between Cu 3d and Ru 4d electrons, which depends on R. For stronger hybridization, the Cu 3d electrons become more itinerant leading to positive thermopower. In the A-site ordered perovskite cobalt oxide Sr(3)YCo(4)O(10.5), the spin state of the Co(3+) ions determines the magnitude of the thermopower, where partial isovalent substitution (Ca for Sr and Rh for Co) enhances the thermopower whilst keeping the resistivity intact. These substitutions stabilize the low spin state of the Co(3+) ions, which affects the thermopower through the entropy of the background for the carriers. We propose that the control of the magnetism plays a pivotal role in determining the thermopower in a certain class of complex oxides.

A novel high light-inducible carotenoid-binding protein complex in the thylakoid membranes of Synechocystis PCC 6803.

PubMed

Daddy, Soumana; Zhan, Jiao; Jantaro, Saowarath; He, Chenliu; He, Qingfang; Wang, Qiang

2015-03-30

Synechocystis sp. PCC 6803 is a model cyanobacterium extensively used to study photosynthesis. Here we reveal a novel high light-inducible carotenoid-binding protein complex (HLCC) in the thylakoid membranes of Synechocystis PCC 6803 cells exposed to high intensity light. Zeaxanthin and myxoxanthophyll accounted for 29.8% and 54.8%, respectively, of the carotenoids bound to the complex. Using Blue-Native PAGE followed by 2D SDS-PAGE and mass spectrometry, we showed that the HLCC consisted of Slr1128, IsiA, PsaD, and HliA/B. We confirmed these findings by SEAD fluorescence cross-linking and anti-PsaD immuno-coprecipitation analyses. The expression of genes encoding the protein components of the HLCC was enhanced by high light illumination and artificial oxidative stress. Deletion of these proteins resulted in impaired state transition and increased sensitivity to oxidative and/or high light stress, as indicated by increased membrane peroxidation. Therefore, the HLCC protects thylakoid membranes from extensive photooxidative damage, likely via a mechanism involving state transition.

Revisiting the polytopal rearrangements in penta-coordinate d7-metallocomplexes: modified Berry pseudorotation, octahedral switch, and butterfly isomerization.

PubMed

Asatryan, Rubik; Ruckenstein, Eli; Hachmann, Johannes

2017-08-01

This paper provides a first-principles theoretical investigation of the polytopal rearrangements and fluxional behavior of five-coordinate d 7 -transition metal complexes. Our work is primarily based on a potential energy surface analysis of the iron tetracarbonyl hydride radical HFe˙(CO) 4 . We demonstrate the existence of distorted coordination geometries in this prototypical system and, for the first time, introduce three general rearrangement mechanisms, which account for the non-ideal coordination. The first of these mechanisms constitutes a modified version of the Berry pseudorotation via a square-based pyramidal C 4v transition state that connects two chemically identical edge-bridged tetrahedral stereoisomers of C 2v symmetry. It differs from the classical Berry mechanism, which involves two regular D 3h equilibrium structures and a C 4v transition state. The second mechanism is related to the famous "tetrahedral jump" hypothesis, postulated by Muetterties for a number of d 6 HML 4 and H 2 ML 4 complexes. Here, our study suggests two fluxional rearrangement pathways via distinct types of C 2v transition states. Both pathways of this mechanism can be described as a single-ligand migration to a vacant position of an "octahedron", thus interchanging (switching) the apical and basal ligands of the initial quasi-square pyramidal isomer, which is considered as an idealized octahedron with a vacancy. Accordingly, we call this mechanism "octahedral switch". The third mechanism follows a butterfly-type isomerization featuring a key-angle deformation, and we thus call it "butterfly isomerization". It connects the quasi-square pyramidal and edge-bridged tetrahedral isomers of HFe˙(CO) 4 through a distorted edge-bridged tetrahedral transition state of C s symmetry. Our paper discusses the overall features of the isomers and rearrangement mechanisms as well as their implications. We rationalize the existence of each stationary point through an electronic structure analysis and argue their relevance for isolobal analogues of HFe˙(CO) 4 .

Deuterium kinetic isotope effects on the dissociation of a protein-fatty acid complex in the gas phase.

PubMed

Liu, Lan; Michelsen, Klaus; Kitova, Elena N; Schnier, Paul D; Brown, Alex; Klassen, John S

2012-04-04

Deuterium kinetic isotope effects (KIEs) are reported for the first time for the dissociation of a protein-ligand complex in the gas phase. Temperature-dependent rate constants were measured for the loss of neutral ligand from the deprotonated ions of the 1:1 complex of bovine β-lactoglobulin (Lg) and palmitic acid (PA), (Lg + PA)(n-) → Lg(n-) + PA, at the 6- and 7- charge states. At 25 °C, partial or complete deuteration of the acyl chain of PA results in a measurable inverse KIE for both charge states. The magnitude of the KIEs is temperature dependent, and Arrhenius analysis of the rate constants reveals that deuteration of PA results in a decrease in activation energy. In contrast, there is no measurable deuterium KIE for the dissociation of the (Lg + PA) complex in aqueous solution at pH 8. Deuterium KIEs were calculated using conventional transition-state theory with an assumption of a late dissociative transition state (TS), in which the ligand is free of the binding pocket. The vibrational frequencies of deuterated and non-deuterated PA in the gas phase and in various solvents (n-hexane, 1-chlorohexane, acetone, and water) were established computationally. The KIEs calculated from the corresponding differences in zero-point energies account qualitatively for the observation of an inverse KIE but do not account for the magnitude of the KIEs nor their temperature dependence. It is proposed that the dissociation of the (Lg + PA) complex in aqueous solution also proceeds through a late TS in which the acyl chain is extensively hydrated such that there is no significant differential change in the vibrational frequencies along the reaction coordinate and, consequently, no significant KIE.

Direct coupled-channels deperturbation analysis of the A{sup 1}Σ{sup +} ∼ b{sup 3}Π complex in LiCs with experimental accuracy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalczyk, P., E-mail: Pawel.Kowalczyk@fuw.edu.pl; Jastrzebski, W.; Szczepkowski, J.

2015-06-21

We have carried out the direct deperturbation analysis of about 780 rovibronic term values of the strongly spin-orbit (SO) coupled A{sup 1}Σ{sup +} and b{sup 3}Π states of the {sup 7}Li{sup 133}Cs molecule recorded by polarization labelling spectroscopy technique. The explicit A{sup 1}Σ{sup +} ∼ b{sup 3}Π{sub Ω=0,1,2} coupled-channels treatment allowed us to reproduce 95% experimental term values with a standard deviation of 0.05 cm{sup −1} which is close to the accuracy of the present experiment. The initial potential energy curves (PECs) of the mutually perturbed states and SO matrix elements were ab initio evaluated in the basis of themore » spin-averaged wave functions. The empirically refined PECs and SO functions, along with the theoretical transition dipole moments, were used to predict energy and radiative properties of the A ∼ b complex for low J levels of both {sup 7}Li{sup 133}Cs and {sup 6}Li{sup 133}Cs isotopologues. The reasonable candidates for the stimulated Raman transitions between initial Feshbach resonance states, the mixed levels of the A ∼ b complex, and absolute ground X{sup 1}Σ{sup +} (v = 0 and J = 0) state were identified.« less

Synthesis of a metal oxide with a room-temperature photoreversible phase transition.

PubMed

Ohkoshi, Shin-Ichi; Tsunobuchi, Yoshihide; Matsuda, Tomoyuki; Hashimoto, Kazuhito; Namai, Asuka; Hakoe, Fumiyoshi; Tokoro, Hiroko

2010-07-01

Photoinduced phase-transition materials, such as chalcogenides, spin-crossover complexes, photochromic organic compounds and charge-transfer materials, are of interest because of their application to optical data storage. Here we report a photoreversible metal-semiconductor phase transition at room temperature with a unique phase of Ti(3)O(5), lambda-Ti(3)O(5). lambda-Ti(3)O(5) nanocrystals are made by the combination of reverse-micelle and sol-gel techniques. Thermodynamic analysis suggests that the photoinduced phase transition originates from a particular state of lambda-Ti(3)O(5) trapped at a thermodynamic local energy minimum. Light irradiation causes reversible switching between this trapped state (lambda-Ti(3)O(5)) and the other energy-minimum state (beta-Ti(3)O(5)), both of which are persistent phases. This is the first demonstration of a photorewritable phenomenon at room temperature in a metal oxide. lambda-Ti(3)O(5) satisfies the operation conditions required for a practical optical storage system (operational temperature, writing data by short wavelength light and the appropriate threshold laser power).

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

PubMed Central

Koorehdavoudi, Hana; Bogdan, Paul

2016-01-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity. PMID:27297496

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

NASA Astrophysics Data System (ADS)

Koorehdavoudi, Hana; Bogdan, Paul

2016-06-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity.

Polynomial law for controlling the generation of n-scroll chaotic attractors in an optoelectronic delayed oscillator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Márquez, Bicky A., E-mail: bmarquez@ivic.gob.ve; Suárez-Vargas, José J., E-mail: jjsuarez@ivic.gob.ve; Ramírez, Javier A.

2014-09-01

Controlled transitions between a hierarchy of n-scroll attractors are investigated in a nonlinear optoelectronic oscillator. Using the system's feedback strength as a control parameter, it is shown experimentally the transition from Van der Pol-like attractors to 6-scroll, but in general, this scheme can produce an arbitrary number of scrolls. The complexity of every state is characterized by Lyapunov exponents and autocorrelation coefficients.

Oxygen atom transfer reactions of iridium and osmium complexes: theoretical study of characteristic features and significantly large differences between these two complexes.

PubMed

Ishikawa, Atsushi; Nakao, Yoshihide; Sato, Hirofumi; Sakaki, Shigeyoshi

2009-09-07

Oxygen atom transfer reaction between ML(3)=O and ML(3) (L = 2,4,6-trimethylphenyl (Mes) for M = Ir and L = 2,6-diisopropylphenylimide (NAr) for M = Os) was theoretically investigated by DFT method. The optimized geometry of (Mes)(3)Ir-O-Ir(Mes)(3) agrees well with the experimental one, although those of (CH(3))(3)Ir-O-Ir(CH(3))(3) and Ph(3)Ir-O-IrPh(3) are much different from the experimental one of the Mes complex. These results indicate that the bulky ligand plays important roles to determine geometry of the mu-oxo dinuclear Ir complex. Theoretical study of the real systems presents clear pictures of these oxygen atom transfer reactions, as follows: In the Ir reaction system, (i) the mu-oxo bridged dinuclear complex is more stable than the infinite separation system in potential energy surface, indicating this is incomplete oxygen atom transfer reaction which does not occur at very low temperature, (ii) unsymmetrical transition state is newly found, in which one Ir-O distance is longer than the other one, (iii) unsymmetrical local minimum is also newly found between the transition state and the infinite separation system, and (iv) activation barrier (E(a)) is very small. In the Os reaction system, (v) the transition state is symmetrical, while no intermediate is observed unlike the Ir reaction system, and (vi) E(a) is very large. These results are consistent with the experimental results that the reaction rapidly occurs in the Ir system but very slowly in the Os system, and that the mu-oxo bridged dinuclear intermediate is detected in the Ir system but not in the Os system. To elucidate the reasons of these differences between Ir and Os systems, the E(a) value is decomposed into the nuclear and electronic factors. The former is the energy necessary to distort ML(3) and ML(3)=O moieties from their equilibrium geometries to those in the transition state. The latter depends on donor-acceptor interaction between ML(3)=O and ML(3). The nuclear factor is much larger in the Os system than in the Ir system and it contributes to about 70% of the difference in E(a). The energy gap between the donor orbital of ML(3) and the acceptor orbital of ML(3)=O is much larger in the Os system than in the Ir system, which also contributes to the lower E(a) value of the Ir system than that of the Os system.

High-Permeability Magnetic Polymer Additives for Lightweight Electromagnetic Shielding

DTIC Science & Technology

2015-08-01

organometallic complexes containing Fe2+ cations. [Cp] = cyclopentadiene; [Py] = pyrrole ; [Imid] = imidazole. ΔEmag values calculated with DFT using the...27 Table A-6 Energy difference between high- and low-spin magnetic states in transition metal ion- pyrrole (Py) complexes...2-],52 pyrrole (C4NH5),53 and other heterocyclic ligands.36,54 The cyclopentadienyl ligand, in particular, is ubiquitous in organometallic chemistry

Exploring a strongly non-Markovian behavior

NASA Astrophysics Data System (ADS)

Alba, Vasyl; Berman, Gordon; Bialek, William; Shaevitz, Joshua

Is there some simplicity or universality underlying the complexities of natural animal behavior? Using the walking fruit fly as a model system, we have shown that unconstrained behaviors can be categorized into roughly one hundred discrete states, which all individuals from a single species visit repeatedly. In each state, the fly executes stereotyped movements, and the transitions between states are organized hierarchically. The sequences of states, however, are strongly non-Markovian: correlations persist for orders of magnitude longer than expected from the state-to-state transition probabilities, and there are hints of power law decay. But with 100 states, further analysis is difficult. Here we develop a generalization of the information bottleneck method to compress these states into a more compact description that preserves as much of the temporal correlations as possible. We find that, even on compressing down to just two states, this coarse grained description of behavior captures the long ranged correlations. Power law decays are clearer in this reduced representation, which opens the way for more quantitative analysis.

Infrared spectra and tunneling dynamics of the N2-D2O and OC-D2O complexes in the v2 bend region of D2O.

PubMed

Zhu, Yu; Zheng, Rui; Li, Song; Yang, Yu; Duan, Chuanxi

2013-12-07

The rovibrational spectra of the N2-D2O and OC-D2O complexes in the v2 bend region of D2O have been measured in a supersonic slit jet expansion using a rapid-scan tunable diode laser spectrometer. Both a-type and b-type transitions were observed for these two complexes. All transitions are doubled, due to the heavy water tunneling within the complexes. Assuming the tunneling splittings are the same in K(a) = 0 and K(a) = 1, the band origins, all three rotational and several distortion constants of each tunneling state were determined for N2-D2O in the ground and excited vibrational states, and for OC-D2O in the excited vibrational state, respectively. The averaged band origin of OC-D2O is blueshifted by 2.241 cm(-1) from that of the v2 band of the D2O monomer, compared with 1.247 cm(-1) for N2-D2O. The tunneling splitting of N2-D2O in the ground state is 0.16359(28) cm(-1), which is about five times that of OC-D2O. The tunneling splittings decrease by about 26% for N2-D2O and 23% for OC-D2O, respectively, upon excitation of the D2O bending vibration, indicating an increase of the tunneling barrier in the excited vibrational state. The tunneling splittings are found to have a strong dependence on intramolecular vibrational excitation as well as a weak dependence on quantum number K(a).

Edge states in the climate system: exploring global instabilities and critical transitions

NASA Astrophysics Data System (ADS)

Lucarini, Valerio; Bódai, Tamás

2017-07-01

Multistability is a ubiquitous feature in systems of geophysical relevance and provides key challenges for our ability to predict a system’s response to perturbations. Near critical transitions small causes can lead to large effects and—for all practical purposes—irreversible changes in the properties of the system. As is well known, the Earth climate is multistable: present astronomical and astrophysical conditions support two stable regimes, the warm climate we live in, and a snowball climate characterized by global glaciation. We first provide an overview of methods and ideas relevant for studying the climate response to forcings and focus on the properties of critical transitions in the context of both stochastic and deterministic dynamics, and assess strengths and weaknesses of simplified approaches to the problem. Following an idea developed by Eckhardt and collaborators for the investigation of multistable turbulent fluid dynamical systems, we study the global instability giving rise to the snowball/warm multistability in the climate system by identifying the climatic edge state, a saddle embedded in the boundary between the two basins of attraction of the stable climates. The edge state attracts initial conditions belonging to such a boundary and, while being defined by the deterministic dynamics, is the gate facilitating noise-induced transitions between competing attractors. We use a simplified yet Earth-like intermediate complexity climate model constructed by coupling a primitive equations model of the atmosphere with a simple diffusive ocean. We refer to the climatic edge states as Melancholia states and provide an extensive analysis of their features. We study their dynamics, their symmetry properties, and we follow a complex set of bifurcations. We find situations where the Melancholia state has chaotic dynamics. In these cases, we have that the basin boundary between the two basins of attraction is a strange geometric set with a nearly zero codimension, and relate this feature to the time scale separation between instabilities occurring on weather and climatic time scales. We also discover a new stable climatic state that is similar to a Melancholia state and is characterized by non-trivial symmetry properties.

Role of glutamate-104 in generating a transition state analogue inhibitor at the active site of cytidine deaminase.

PubMed

Carlow, D C; Short, S A; Wolfenden, R

1996-01-23

The 19F-NMR resonance of 5-[19F]fluoropyrimidin-2-one ribonucleoside moves upfield when it is bound by wild-type cytidine deaminase from Escherichia coli, in agreement with UV and X-ray spectroscopic indications that this inhibitor is bound as the rate 3,4-hydrated species 5-fluoro-3,4-dihydrouridine, a transition state analogue inhibitor resembling an intermediate in direct water attack on 5-fluorocytidine. Comparison of pKa values of model compounds indicates that the equilibrium constant for 3,4-hydration of this inhibitor in free solution is 3.5 x 10(-4) M, so that the corrected dissociation constant of 5-fluoro-3,4-dihydrouridine from the wild-type enzyme is 3.9 x 10(-11) M. Very different behavior is observed for a mutant enzyme in which alanine replaces Glu-104 at the active site, and kcat has been reduced by a factor of 10(8). 5-[19F]Fluoropyrimidin-2-one ribonucleoside is strongly fluorescent, making it possible to observe that the mutant enzyme binds this inhibitor even more tightly (Kd = 4.4 x 10(-8) M) than does the native enzyme (Kd = 1.1 x 10(-7) M). 19F-NMR indicates, however, that the E104A mutant enzyme binds the inhibitor without modification, in a form that resembles the substrate in the ground state. These results are consistent with a major role for Glu-104, not only in stabilizing the ES++ complex in the transition state, but also in destabilizing the ES complex in the ground state.

Photoinduced energy transfer in transition metal complex oligomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-06-01

The work done over the past three years has been directed toward the preparation, characterization and photophysical examination of mono- and bimetallic diimine complexes. The work is part of a broader project directed toward the development of stable, efficient, light harvesting arrays of transition metal complex chromophores. One focus has been the synthesis of rigid bis-bidentate and bis-tridentate bridging ligands. The authors have managed to make the ligand bphb in multigram quantities from inexpensive starting materials. The synthetic approach used has allowed them to prepare a variety of other ligands which may have unique applications (vide infra). They have prepared,more » characterized and examined the photophysical behavior of Ru(II) and Re(I) complexes of the ligands. Energy donor/acceptor complexes of bphb have been prepared which exhibit nearly activationless energy transfer. Complexes of Ru(II) and Re(I) have also been prepared with other polyunsaturated ligands in which two different long lived (> 50 ns) excited states exist; results of luminescence and transient absorbance measurements suggest the two states are metal-to-ligand charge transfer and ligand localized {pi}{r_arrow}{pi}* triplets. Finally, the authors have developed methods to prepare polymetallic complexes which are covalently bound to various surfaces. The long term objective of this work is to make light harvesting arrays for the sensitization of large band gap semiconductors. Details of this work are provided in the body of the report.« less

DFT Study of Optical Properties of Pt-based Complexes

NASA Astrophysics Data System (ADS)

Oprea, Corneliu I.; Dumbravǎ, Anca; Moscalu, Florin; Nicolaides, Atnanassios; Gîrţu, Mihai A.

2010-01-01

We report Density Functional Theory (DFT) calculations providing the geometrical and electronic structures, as well as the vibrational and optical properties of the homologous series of Pt-pyramidalized olefin complexes (CH2)n-(C8H10)Pt(PH3)2, where n = 0, 1, and 2, in their neutral and oxidized states. All complexes were geometry optimized for the singlet ground state in vacuum using DFT methods with B3LYP exchange-correlation functional and the Effective Core Potential LANL2DZ basis set, within the frame of Gaussian03 quantum chemistry package. We find the coordination geometry of Pt to be distorted square planar, with dihedral angles ranging from 0°, for n = 0 and 1, which have C2V symmetry to 3.4°, for n = 2 with C2 symmetry. The Mulliken charge analysis allows a discussion of the oxidation state of the Pt ion. Electronic transitions were calculated at the same level of theory by means of Time Dependant-DFT. For n = 2 the electronic absorption bands are located in the UV region of the spectrum, the transitions being assigned to metal to ligand charge transfers. The relevance of these Pt-based compounds as possible pigments for dye-sensitized solar cells is discussed.

Insights into the crystal-packing effects on the spin crossover of [Fe(II)(1-bpp)](2+)-based materials.

PubMed

Vela, Sergi; Novoa, Juan J; Ribas-Arino, Jordi

2014-12-28

Iron(II) complexes of the [Fe(II)(1-bpp2)](2+) type (1-bpp = 2,6-di(pyrazol-1-yl)pyridine) have been intensively investigated in the context of crystal engineering of switchable materials because their spin-crossover (SCO) properties dramatically depend on the counterions. Here, by means of DFT + U calculations at the molecular and solid state levels we provide a rationale for the different SCO behaviour of the BF4(-) and ClO4(-) salts of the parent complex; the former features Fe(II) complexes with a regular coordination geometry and undergoes a spin transition, whereas the Fe(II) complexes of the latter adopt a distorted structure and remain in the high-spin state at all temperatures. The different SCO behaviour of both salts can be explained on the basis of a combination of thermodynamic and kinetic effects. The shape of the SCO units at high temperature is thermodynamically controlled by the intermolecular interactions between the SCO units and counterions within the crystal. The spin trapping at low temperatures in the ClO4(-) salt, in turn, is traced back to a kinetic effect because our calculations have revealed the existence of a more stable polymorph having SCO units in their low-spin state that feature a regular structure. From the computational point of view, it is the first time that the U parameter is fine-tuned on the basis of CASPT2 calculations, thereby enabling an accurate description of the energetics of the spin transition at both molecular and solid-state levels.

Development of luminescent sensors based on transition metal complexes for the detection of nitroexplosives.

PubMed

Sathish, Veerasamy; Ramdass, Arumugam; Velayudham, Murugesan; Lu, Kuang-Lieh; Thanasekaran, Pounraj; Rajagopal, Seenivasan

2017-12-12

The detection of chemical explosives is a major area of research interest and is essential for the military as well as homeland security to counter the catastrophic effects of global terrorism. In recent years, tremendous effort has been devoted to the development of luminescent materials for the detection of explosives in the vapor, solution, and solid states with a high degree of selectivity and sensitivity and a rapid response time. Apart from the wide range of organic fluorescent chemosensors, transition metal complexes play a prominent role in the sensing of nitroaromatic explosives owing to their rich photophysical characteristics. This review briefly summarizes the salient features of the design and preparation of transition metal (Zn(ii), Ir(iii), Pd(ii), Pt(ii), Re(i) and Ru(ii)) complexes/metallacycles/metallosupramolecules with emphasis on their photophysical properties, sensing behavior, mechanism of action, and the driving forces for detecting explosives and future prospects and challenges. Most of the probes that have been reported to date act as "turn-off" luminescent sensors because their emission (intensity, lifetime, and quantum yield) is eventually quenched upon sensing with nitroaromatic compounds (NACs) through photo-induced electron or energy transfer. These unique properties of transition metal complexes in response to explosives open up new vistas for the development of real world applications such as on-site detection, in-field security, forensic research, etc.

Ultrafast time-resolved carotenoid to-bacteriochlorophyll energy transfer in LH2 complexes from photosynthetic bacteria.

PubMed

Cong, Hong; Niedzwiedzki, Dariusz M; Gibson, George N; LaFountain, Amy M; Kelsh, Rhiannon M; Gardiner, Alastair T; Cogdell, Richard J; Frank, Harry A

2008-08-28

Steady-state and ultrafast time-resolved optical spectroscopic investigations have been carried out at 293 and 10 K on LH2 pigment-protein complexes isolated from three different strains of photosynthetic bacteria: Rhodobacter (Rb.) sphaeroides G1C, Rb. sphaeroides 2.4.1 (anaerobically and aerobically grown), and Rps. acidophila 10050. The LH2 complexes obtained from these strains contain the carotenoids, neurosporene, spheroidene, spheroidenone, and rhodopin glucoside, respectively. These molecules have a systematically increasing number of pi-electron conjugated carbon-carbon double bonds. Steady-state absorption and fluorescence excitation experiments have revealed that the total efficiency of energy transfer from the carotenoids to bacteriochlorophyll is independent of temperature and nearly constant at approximately 90% for the LH2 complexes containing neurosporene, spheroidene, spheroidenone, but drops to approximately 53% for the complex containing rhodopin glucoside. Ultrafast transient absorption spectra in the near-infrared (NIR) region of the purified carotenoids in solution have revealed the energies of the S1 (2(1)Ag-)-->S2 (1(1)Bu+) excited-state transitions which, when subtracted from the energies of the S0 (1(1)Ag-)-->S2 (1(1)Bu+) transitions determined by steady-state absorption measurements, give precise values for the positions of the S1 (2(1)Ag-) states of the carotenoids. Global fitting of the ultrafast spectral and temporal data sets have revealed the dynamics of the pathways of de-excitation of the carotenoid excited states. The pathways include energy transfer to bacteriochlorophyll, population of the so-called S* state of the carotenoids, and formation of carotenoid radical cations (Car*+). The investigation has found that excitation energy transfer to bacteriochlorophyll is partitioned through the S1 (1(1)Ag-), S2 (1(1)Bu+), and S* states of the different carotenoids to varying degrees. This is understood through a consideration of the energies of the states and the spectral profiles of the molecules. A significant finding is that, due to the low S1 (2(1)Ag-) energy of rhodopin glucoside, energy transfer from this state to the bacteriochlorophylls is significantly less probable compared to the other complexes. This work resolves a long-standing question regarding the cause of the precipitous drop in energy transfer efficiency when the extent of pi-electron conjugation of the carotenoid is extended from ten to eleven conjugated carbon-carbon double bonds in LH2 complexes from purple photosynthetic bacteria.

Decrease in Hysteresis of Planetary Climate for Planets with Long Solar Days

NASA Astrophysics Data System (ADS)

Abbot, Dorian S.; Bloch-Johnson, Jonah; Checlair, Jade; Farahat, Navah X.; Graham, R. J.; Plotkin, David; Popovic, Predrag; Spaulding-Astudillo, Francisco

2018-02-01

The ice-albedo feedback on rapidly rotating terrestrial planets in the habitable zone can lead to abrupt transitions (bifurcations) between a warm and a snowball (ice-covered) state, bistability between these states, and hysteresis in planetary climate. This is important for planetary habitability because snowball events may trigger rises in the complexity of life, but could also endanger complex life that already exists. Recent work has shown that planets tidally locked in synchronous rotation states will transition smoothly into the snowball state rather than experiencing bifurcations. Here we investigate the structure of snowball bifurcations on planets that are tidally influenced, but not synchronously rotating, so that they experience long solar days. We use PlaSIM, an intermediate-complexity global climate model, with a thermodynamic mixed layer ocean and the Sun’s spectrum. We find that the amount of hysteresis (the range in stellar flux for which there is bistability in climate) is significantly reduced for solar days with lengths of tens of Earth days, and disappears for solar days of hundreds of Earth days. These results suggest that tidally influenced planets orbiting M and K stars that are not synchronously rotating could have much less hysteresis associated with the snowball bifurcations than they would if they were rapidly rotating. This implies that the amount of time it takes them to escape a snowball state via CO2 outgassing would be greatly reduced, as would the period of cycling between the warm and snowball state if they have low CO2 outgassing rates.

Spectra, energy levels, and energy transition of lanthanide complexes with cinnamic acid and its derivatives.

PubMed

Zhou, Kaining; Feng, Zhongshan; Shen, Jun; Wu, Bing; Luo, Xiaobing; Jiang, Sha; Li, Li; Zhou, Xianju

2016-04-05

High resolution spectra and luminescent lifetimes of 6 europium(III)-cinnamic acid complex {[Eu2L6(DMF)(H2O)]·nDMF·H2O}m (L=cinnamic acid I, 4-methyl-cinnamic acid II, 4-chloro-cinnamic acid III, 4-methoxy-cinnamic acid IV, 4-hydroxy-cinnamic acid V, 4-nitro-cinnamic acid VI; DMF=N, N-dimethylformamide, C3H7NO) were recorded from 8 K to room temperature. The energy levels of Eu(3+) in these 6 complexes are obtained from the spectra analysis. It is found that the energy levels of the central Eu(3+) ions are influenced by the nephelauxetic effect, while the triplet state of ligand is lowered by the p-π conjugation effect of the para-substituted functional groups. The best energy matching between the ligand triplet state and the central ion excited state is found in complex I. While the other complexes show poorer matching because the gap of (5)D0 and triplet state contracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Perspective. Extremely fine tuning of doping enabled by combinatorial molecular-beam epitaxy

DOE PAGES

Wu, J.; Bozovic, I.

2015-04-06

Chemical doping provides an effective method to control the electric properties of complex oxides. However, the state-of-art accuracy in controlling doping is limited to about 1%. This hampers elucidation of the precise doping dependences of physical properties and phenomena of interest, such as quantum phase transitions. Using the combinatorial molecular beam epitaxy, we improve the accuracy in tuning the doping level by two orders of magnitude. We illustrate this novel method by two examples: a systematic investigation of the doping dependence of interface superconductivity, and a study of the competing ground states in the vicinity of the insulator-to-superconductor transition.

A Numerical Scheme for Ordinary Differential Equations Having Time Varying and Nonlinear Coefficients Based on the State Transition Matrix

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2002-01-01

A variable order method of integrating initial value ordinary differential equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. While it is more complex than most other methods, it produces exact solutions at arbitrary time step size when the time variation of the system can be modeled exactly by a polynomial. Solutions to several nonlinear problems exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with an exact solution and with solutions obtained by established methods.

Heavy atom labeled nucleotides for measurement of kinetic isotope effects.

PubMed

Weissman, Benjamin P; Li, Nan-Sheng; York, Darrin; Harris, Michael; Piccirilli, Joseph A

2015-11-01

Experimental analysis of kinetic isotope effects represents an extremely powerful approach for gaining information about the transition state structure of complex reactions not available through other methodologies. The implementation of this approach to the study of nucleic acid chemistry requires the synthesis of nucleobases and nucleotides enriched for heavy isotopes at specific positions. In this review, we highlight current approaches to the synthesis of nucleic acids enriched site specifically for heavy oxygen and nitrogen and their application in heavy atom isotope effect studies. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

Communication: Evaluating non-empirical double hybrid functionals for spin-state energetics in transition-metal complexes

NASA Astrophysics Data System (ADS)

Wilbraham, Liam; Adamo, Carlo; Ciofini, Ilaria

2018-01-01

The computationally assisted, accelerated design of inorganic functional materials often relies on the ability of a given electronic structure method to return the correct electronic ground state of the material in question. Outlining difficulties with current density functionals and wave function-based approaches, we highlight why double hybrid density functionals represent promising candidates for this purpose. In turn, we show that PBE0-DH (and PBE-QIDH) offers a significant improvement over its hybrid parent functional PBE0 [as well as B3LYP* and coupled cluster singles and doubles with perturbative triples (CCSD(T))] when computing spin-state splitting energies, using high-level diffusion Monte Carlo calculations as a reference. We refer to the opposing influence of Hartree-Fock (HF) exchange and MP2, which permits higher levels of HF exchange and a concomitant reduction in electronic density error, as the reason for the improved performance of double-hybrid functionals relative to hybrid functionals. Additionally, using 16 transition metal (Fe and Co) complexes, we show that low-spin states are stabilised by increasing contributions from MP2 within the double hybrid formulation. Furthermore, this stabilisation effect is more prominent for high field strength ligands than low field strength ligands.

Optical population of gerade and ungerade iodine ion-pair states via MI2 vdW complexes of valence states correlating with the third dissociation limit, M = I2, Xe

NASA Astrophysics Data System (ADS)

Lukashov, S. S.; Poretsky, S. A.; Pravilov, A. M.

2012-05-01

The results of measurements and analysis of excitation spectra of the λlum = 2350 Ǻ luminescence corresponding to I2(D0+u → X0+g) transition as well as luminescence at λlum = 3400 Ǻ, where I2(D'2g → A'2u and/or β1g → A1u) transitions occur, observed after three-step, λ1 + λf + λ1, λ1 = 5321-5508.2 Ǻ, λf = 10644.0 Ǻ, laser excitation of pure iodine vapour and I2 + Xe mixtures at room temperature are presented. Luminescence spectra in the λlum = 2200-3500 Ǻ spectral range are also analyzed. We discuss three alternative mechanisms of optical population of the IP states. In our opinion, the mechanism including the MI2, M = I2, Xe, complexes is the most probable at least in the λ1 ≈ 5321-5480 Ǻ, λ1 ≈ 5508 Ǻ spectral ranges and for population of the states which luminescence occur at λlum ≈ 3400 Ǻ.

Cytochrome b 6 f function and localization, phosphorylation state of thylakoid membrane proteins and consequences on cyclic electron flow.

PubMed

Dumas, Louis; Chazaux, Marie; Peltier, Gilles; Johnson, Xenie; Alric, Jean

2016-09-01

Both the structure and the protein composition of thylakoid membranes have an impact on light harvesting and electron transfer in the photosynthetic chain. Thylakoid membranes form stacks and lamellae where photosystem II and photosystem I localize, respectively. Light-harvesting complexes II can be associated to either PSII or PSI depending on the redox state of the plastoquinone pool, and their distribution is governed by state transitions. Upon state transitions, the thylakoid ultrastructure and lateral distribution of proteins along the membrane are subject to significant rearrangements. In addition, quinone diffusion is limited to membrane microdomains and the cytochrome b 6 f complex localizes either to PSII-containing grana stacks or PSI-containing stroma lamellae. Here, we discuss possible similarities or differences between green algae and C3 plants on the functional consequences of such heterogeneities in the photosynthetic electron transport chain and propose a model in which quinones, accepting electrons either from PSII (linear flow) or NDH/PGR pathways (cyclic flow), represent a crucial control point. Our aim is to give an integrated description of these processes and discuss their potential roles in the balance between linear and cyclic electron flows.

Time-dependent density functional theory study of the luminescence properties of gold phosphine thiolate complexes.

PubMed

Guidez, Emilie B; Aikens, Christine M

2015-04-09

The origin of the emission of the gold phosphine thiolate complex (TPA)AuSCH(CH3)2 (TPA = 1,3,5-triaza-7-phosphaadamantanetriylphosphine) is investigated using time-dependent density functional theory (TDDFT). This system absorbs light at 3.6 eV, which corresponds mostly to a ligand-to-metal transition with some interligand character. The P-Au-S angle decreases upon relaxation in the S1 and T1 states. Our calculations show that these two states are strongly spin-orbit coupled at the ground state geometry. Ligand effects on the optical properties of this complex are also discussed by looking at the simple AuP(CH3)3SCH3 complex. The excitation energies differ by several tenths of an electronvolt. Excited state optimizations show that the excited singlet and triplet of the (TPA)AuSCH(CH3)2 complex are bent. On the other hand, the Au-S bond breaks in the excited state for the simple complex, and TDDFT is no longer an adequate method. The excited state energy landscape of gold phosphine thiolate systems is very complex, with several state crossings. This study also shows that the formation of the [(TPA)AuSCH(CH3)2]2 dimer is favorable in the ground state. The inclusion of dispersion interactions in the calculations affects the optimized geometries of both ground and excited states. Upon excitation, the formation of a Au-Au bond occurs, which results in an increase in energy of the low energy excited states in comparison to the monomer. The experimentally observed emission of the (TPA)AuSCH(CH3)2 complex at 1.86 eV cannot be unambiguously assigned and may originate from several excited states.

Transition state-finding strategies for use with the growing string method.

PubMed

Goodrow, Anthony; Bell, Alexis T; Head-Gordon, Martin

2009-06-28

Efficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of the transition state structure in order to converge, particularly for complex reaction systems. The growing string method (GSM) [B. Peters et al., J. Chem. Phys. 120, 7877 (2004)] does not require an initial guess of the transition state; however, the calculation is still computationally intensive due to repeated calls to the quantum mechanics code. Recent modifications to the GSM [A. Goodrow et al., J. Chem. Phys. 129, 174109 (2008)] have reduced the total computational time for converging to a transition state by a factor of 2 to 3. In this work, three transition state-finding strategies have been developed to complement the speedup of the modified-GSM: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy. The hybrid strategy initiates the string calculation at a low level of theory (HF/STO-3G), which is then refined at a higher level of theory (B3LYP/6-31G(*)). The energy-weighted strategy spaces points along the reaction pathway based on the energy at those points, leading to a higher density of points where the energy is highest and finer resolution of the transition state. The substring strategy is similar to the hybrid strategy, but only a portion of the low-level string is refined using a higher level of theory. These three strategies have been used with the modified-GSM and are compared in three reactions: alanine dipeptide isomerization, H-abstraction in methanol oxidation on VO(x)/SiO(2) catalysts, and C-H bond activation in the oxidative carbonylation of toluene to p-toluic acid on Rh(CO)(2)(TFA)(3) catalysts. In each of these examples, the substring strategy was proved most effective by obtaining a better estimate of the transition state structure and reducing the total computational time by a factor of 2 to 3 compared to the modified-GSM. The applicability of the substring strategy has been extended to three additional examples: cyclopropane rearrangement to propylene, isomerization of methylcyclopropane to four different stereoisomers, and the bimolecular Diels-Alder condensation of 1,3-butadiene and ethylene to cyclohexene. Thus, the substring strategy used in combination with the modified-GSM has been demonstrated to be an efficient transition state-finding strategy for a wide range of types of reactions.

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nithianantham, Stanley; Shilton, Brian H

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nithianantham, Stanley; Shilton, Brian H

2011-09-28

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Vibronic Boson Sampling: Generalized Gaussian Boson Sampling for Molecular Vibronic Spectra at Finite Temperature.

PubMed

Huh, Joonsuk; Yung, Man-Hong

2017-08-07

Molecular vibroic spectroscopy, where the transitions involve non-trivial Bosonic correlation due to the Duschinsky Rotation, is strongly believed to be in a similar complexity class as Boson Sampling. At finite temperature, the problem is represented as a Boson Sampling experiment with correlated Gaussian input states. This molecular problem with temperature effect is intimately related to the various versions of Boson Sampling sharing the similar computational complexity. Here we provide a full description to this relation in the context of Gaussian Boson Sampling. We find a hierarchical structure, which illustrates the relationship among various Boson Sampling schemes. Specifically, we show that every instance of Gaussian Boson Sampling with an initial correlation can be simulated by an instance of Gaussian Boson Sampling without initial correlation, with only a polynomial overhead. Since every Gaussian state is associated with a thermal state, our result implies that every sampling problem in molecular vibronic transitions, at any temperature, can be simulated by Gaussian Boson Sampling associated with a product of vacuum modes. We refer such a generalized Gaussian Boson Sampling motivated by the molecular sampling problem as Vibronic Boson Sampling.

Model-Checking with Edge-Valued Decision Diagrams

NASA Technical Reports Server (NTRS)

Roux, Pierre; Siminiceanu, Radu I.

2010-01-01

We describe an algebra of Edge-Valued Decision Diagrams (EVMDDs) to encode arithmetic functions and its implementation in a model checking library along with state-of-the-art algorithms for building the transition relation and the state space of discrete state systems. We provide efficient algorithms for manipulating EVMDDs and give upper bounds of the theoretical time complexity of these algorithms for all basic arithmetic and relational operators. We also demonstrate that the time complexity of the generic recursive algorithm for applying a binary operator on EVMDDs is no worse than that of Multi-Terminal Decision Diagrams. We have implemented a new symbolic model checker with the intention to represent in one formalism the best techniques available at the moment across a spectrum of existing tools: EVMDDs for encoding arithmetic expressions, identity-reduced MDDs for representing the transition relation, and the saturation algorithm for reachability analysis. We compare our new symbolic model checking EVMDD library with the widely used CUDD package and show that, in many cases, our tool is several orders of magnitude faster than CUDD.

Syntheses, crystal and band structures, and optical properties of a selenidoantimonate and an iron polyselenide

NASA Astrophysics Data System (ADS)

Liu, Guang-Ning; Zhu, Wen-Juan; Zhang, Ming-Jian; Xu, Bo; Liu, Qi-Sheng; Zhang, Zhen-Wei; Li, Cuncheng

2014-10-01

A new selenidoantimonate (CH3NH4)[Mn(phen)2](SbSe4)·phen (1, phen=1,10-phenanthroline) and an iron polyselenide [Fe(phen)2](Se4) (2) were obtained under hydro(solvo)thermal conditions. Compound 1 represents the first example of a selenidoantimonate anion as a ligand to a transition-metal π-conjugated ligand complex cation. Compound 2 containing a κ2Se1,Se4 chelating tetraselenide ligand, represents the only example of a tetraselenide ligand to a Fe complex cation. Compounds 1 and 2 exhibit optical gaps of 1.71 and 1.20 eV, respectively and their thermal stabilities have been investigated by thermogravimetric analyses. The electronic band structure along with the density of states calculated by the DFT method indicate that the optical absorptions mainly originate from the charge transitions from the Se 4p and Mn 3d states to the phen p-π* orbital for 1 and the Se 4p and Fe 3d states to the phen p-π* orbital for 2.

Relaxor-ferroelectric crossover in (B i1 /2K1 /2)Ti O3 : Origin of the spontaneous phase transition and the effect of an applied external field

NASA Astrophysics Data System (ADS)

Hagiwara, Manabu; Ehara, Yoshitaka; Novak, Nikola; Khansur, Neamul H.; Ayrikyan, Azatuhi; Webber, Kyle G.; Fujihara, Shinobu

2017-07-01

The temperature evolution of polar order in an A -site complex perovskite (B i1 /2K1 /2)Ti O3 (BKT) has been investigated by measurements of dielectric permittivity, depolarization current, and stress-stain curves at elevated temperatures. Upon cooling from high temperatures, BKT first enters a relaxor state and then spontaneously transforms into a ferroelectric state. The analyses of temperature and frequency dependence of permittivity have revealed that polar nanoregions of the relaxor phase appear at temperatures higher than 560°C, and also that their freezing at 296°C triggers the spontaneous relaxor-ferroelectric transition. We discuss the key factors determining the development of long-range polar order in A -site complex perovskites through a comparison with the relaxor (B i1 /2N a1 /2)Ti O3 . We also show that application of biasing electric fields and compressive stresses to BKT favors its ferroelectric phase, resulting in a significant shift of the relaxor-ferroelectric transition temperature towards higher temperatures. Based on the obtained results, electric field-temperature and stress-temperature phase diagrams are firstly determined for BKT.

Polarization-induced interference within electromagnetically induced transparency for atoms of double-V linkage

NASA Astrophysics Data System (ADS)

Sun, Yuan; Liu, Chang; Chen, Ping-Xing; Liu, Liang

2018-02-01

People have been paying attention to the role of atoms' complex internal level structures in the research of electromagnetically induced transparency (EIT) for a long time, where the various degenerate Zeeman levels usually generate complex linkage patterns for the atomic transitions. It turns out, with special choices of the atomic states and the atomic transitions' linkage structure, clear signatures of quantum interference induced by the probe and coupling light's polarizations can emerge from a typical EIT phenomena. We propose to study a four-state system with double-V linkage pattern for the transitions and analyze the polarization-induced interference under the EIT condition. We show that such interference arises naturally under mild conditions on the optical field and atom manipulation techniques. Moreover, we construct a variation form of double-M linkage pattern where the polarization-induced interference enables polarization-dependent cross modulation between incident weak lights that can be effective even at the few-photon level. The theme is to gain more insight into the essential question: how can we build a nontrivial optical medium where incident lights experience polarization-dependent nonlinear optical interactions, valid for a wide range of incidence intensities down to the few-photon level?

Analysis of Complexity Evolution Management and Human Performance Issues in Commercial Aircraft Automation Systems

NASA Technical Reports Server (NTRS)

Vakil, Sanjay S.; Hansman, R. John

2000-01-01

Autoflight systems in the current generation of aircraft have been implicated in several recent incidents and accidents. A contributory aspect to these incidents may be the manner in which aircraft transition between differing behaviours or 'modes.' The current state of aircraft automation was investigated and the incremental development of the autoflight system was tracked through a set of aircraft to gain insight into how these systems developed. This process appears to have resulted in a system without a consistent global representation. In order to evaluate and examine autoflight systems, a 'Hybrid Automation Representation' (HAR) was developed. This representation was used to examine several specific problems known to exist in aircraft systems. Cyclomatic complexity is an analysis tool from computer science which counts the number of linearly independent paths through a program graph. This approach was extended to examine autoflight mode transitions modelled with the HAR. A survey was conducted of pilots to identify those autoflight mode transitions which airline pilots find difficult. The transitions identified in this survey were analyzed using cyclomatic complexity to gain insight into the apparent complexity of the autoflight system from the perspective of the pilot. Mode transitions which had been identified as complex by pilots were found to have a high cyclomatic complexity. Further examination was made into a set of specific problems identified in aircraft: the lack of a consistent representation of automation, concern regarding appropriate feedback from the automation, and the implications of physical limitations on the autoflight systems. Mode transitions involved in changing to and leveling at a new altitude were identified across multiple aircraft by numerous pilots. Where possible, evaluation and verification of the behaviour of these autoflight mode transitions was investigated via aircraft-specific high fidelity simulators. Three solution approaches to concerns regarding autoflight systems, and mode transitions in particular, are presented in this thesis. The first is to use training to modify pilot behaviours, or procedures to work around known problems. The second approach is to mitigate problems by enhancing feedback. The third approach is to modify the process by which automation is designed. The Operator Directed Process forces the consideration and creation of an automation model early in the design process for use as the basis of the software specification and training.

η6-Cycloparaphenylene transition metal complexes: synthesis, structure, photophysical properties, and application to the selective monofunctionalization of cycloparaphenylenes.

PubMed

Kubota, Natsumi; Segawa, Yasutomo; Itami, Kenichiro

2015-01-28

The synthesis, structure, photophysical properties, and reactivity of cycloparaphenylenes (CPPs) coordinated to group 6 transition metal fragments are described. The η(6)-coordination of [9]CPP or [12]CPP with M(CO)6 (M = Cr, Mo, W) afforded the corresponding [n]CPP-M(CO)3 complexes (n = 9, 12; M = Cr, Mo, W). In the (1)H NMR spectra of these complexes, characteristic upfield-shifted singlet signals corresponding to the four hydrogen atoms attached to the coordinated C6H4 ring of the CPPs were observed at 5.4-5.9 ppm. The complex [9]CPP-Cr(CO)3 could be successfully isolated in spite of its instability. X-ray crystallographic analysis and computational studies of [9]CPP-Cr(CO)3 revealed that chromium-CPP coordination occurs at the convex surface of [9]CPP both in the solid state and in solution. TD-DFT calculations suggested that the emerging high-wavenumber absorption peak upon coordination of [9]CPP to Cr(CO)3 should be assigned to a weak HOMO-LUMO transition. Moreover, by using the complex [9]CPP-Cr(CO)3, a rapid and highly monoselective CPP functionalization has been achieved. The established one-pot method, consisting of complexation, deprotonation, nucleophilic substitution, and decomplexation steps, yielded silyl-, boryl-, and methoxycarbonyl-substituted CPPs in up to 93% yield relative to reacted starting material.

Long-lived room temperature deep-red/near-IR emissive intraligand triplet excited state (3IL) of naphthalimide in cyclometalated platinum(II) complexes and its application in upconversion.

PubMed

Wu, Wenting; Guo, Huimin; Wu, Wanhua; Ji, Shaomin; Zhao, Jianzhang

2011-11-21

[C(^)NPt(acac)] (C(^)N = cyclometalating ligand; acac = acetylacetonato) complexes in which the naphthalimide (NI) moiety is directly cyclometalated (NI as the C donor of the C-Pt bond) were synthesized. With 4-pyrazolylnaphthalimide, isomers with five-membered (Pt-2) and six-membered (Pt-3) chelate rings were obtained. With 4-pyridinylnaphthalimide, only the complex with a five-membered chelate ring (Pt-4) was isolated. A model complex with 1-phenylpyrazole as the C(^)N ligand was prepared (Pt-1). Strong absorption of visible light (ε = 21,900 M(-1) cm(-1) at 443 nm for Pt-3) and room temperature (RT) phosphorescence at 630 nm (Pt-2 and Pt-3) or 674 nm (Pt-4) were observed. Long-lived phosphorescences were observed for Pt-2 (τ(P) = 12.8 μs) and Pt-3 (τ(P) = 61.9 μs). Pt-1 is nonphosphorescent at RT in solution because of the acac-localized T(1) excited state [based on density functional theory (DFT) calculations and spin density analysis], but a structured emission band centered at 415 nm was observed at 77 K. Time-resolved transient absorption spectra and spin density analysis indicated a NI-localized intraligand triplet excited state ((3)IL) for complexes Pt-2, Pt-3, and Pt-4. DFT calculations on the transient absorption spectra (T(1) → T(n) transitions, n > 1) also support the (3)IL assignment of the T(1) excited states of Pt-2, Pt-3, and Pt-4. The complexes were used as triplet sensitizers for triplet-triplet-annihilation (TTA) based upconversion, and the results show that Pt-3 is an efficient sensitizer with an upconversion quantum yield of up to 14.1%, despite its low phosphorescence quantum yield of 5.2%. Thus, we propose that the sensitizer molecules at the triplet excited state that are otherwise nonphosphorescent were involved in the TTA upconversion process, indicating that weakly phosphorescent or nonphosphorescent transition-metal complexes can be used as triplet sensitizers for TTA upconversion.

Electronic Structure of Transition Metal Clusters, Actinide Complexes and Their Reactivities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan Balasubramanian

2009-07-18

This is a continuing DOE-BES funded project on transition metal and actinide containing species, aimed at the electronic structure and spectroscopy of transition metal and actinide containing species. While a long term connection of these species is to catalysis and environmental management of high-level nuclear wastes, the immediate relevance is directly to other DOE-BES funded experimental projects at DOE-National labs and universities. There are a number of ongoing gas-phase spectroscopic studies of these species at various places, and our computational work has been inspired by these experimental studies and we have also inspired other experimental and theoretical studies. Thus ourmore » studies have varied from spectroscopy of diatomic transition metal carbides to large complexes containing transition metals, and actinide complexes that are critical to the environment. In addition, we are continuing to make code enhancements and modernization of ALCHEMY II set of codes and its interface with relativistic configuration interaction (RCI). At present these codes can carry out multi-reference computations that included up to 60 million configurations and multiple states from each such CI expansion. ALCHEMY II codes have been modernized and converted to a variety of platforms such as Windows XP, and Linux. We have revamped the symbolic CI code to automate the MRSDCI technique so that the references are automatically chosen with a given cutoff from the CASSCF and thus we are doing accurate MRSDCI computations with 10,000 or larger reference space of configurations. The RCI code can also handle a large number of reference configurations, which include up to 10,000 reference configurations. Another major progress is in routinely including larger basis sets up to 5g functions in thee computations. Of course higher angular momenta functions can also be handled using Gaussian and other codes with other methods such as DFT, MP2, CCSD(T), etc. We have also calibrated our RECP methods with all-electron Douglas-Kroll relativistic methods. We have the capabilities for computing full CI extrapolations including spin-orbit effects and several one-electron properties and electron density maps including spin-orbit effects. We are continuously collaborating with several experimental groups around the country and at National Labs to carry out computational studies on the DOE-BES funded projects. The past work in the last 3 years was primarily motivated and driven by the concurrent or recent experimental studies on these systems. We were thus significantly benefited by coordinating our computational efforts with experimental studies. The interaction between theory and experiment has resulted in some unique and exciting opportunities. For example, for the very first time ever, the upper spin-orbit component of a heavy trimer such as Au{sub 3} was experimentally observed as a result of our accurate computational study on the upper electronic states of gold trimer. Likewise for the first time AuH{sub 2} could be observed and interpreted clearly due to our computed potential energy surfaces that revealed the existence of a large barrier to convert the isolated AuH{sub 2} back to Au and H{sub 2}. We have also worked on yet to be observed systems and have made predictions for future experiments. We have computed the spectroscopic and thermodynamic properties of transition metal carbides transition metal clusters and compared our electronic states to the anion photodetachment spectra of Lai Sheng Wang. Prof Mike Morse and coworkers(funded also by DOE-BES) and Prof Stimle and coworkers(also funded by DOE-BES) are working on the spectroscopic properties of transition metal carbides and nitrides. Our predictions on the excited states of transition metal clusters such as Hf{sub 3}, Nb{sub 2}{sup +} etc., have been confirmed experimentally by Prof. Lombardi and coworkers using resonance Raman spectroscopy. We have also been studying larger complexes critical to the environmental management of high-level nuclear wastes. In collaboration with experimental colleague Prof Hieno Nitsche (Berkeley) and Dr. Pat Allen (Livermore, EXAFS) we have studied the uranyl complexes with silicates and carbonates. It should be stressed that although our computed ionization potential of uranium oxide was in conflict with the existing experimental data at the time, a subsequent gas-phase experimental work by Prof Mike Haven and coworkers published as communication in JACS confirmed our computed result to within 0.1 eV. This provides considerable confidence that the computed results in large basis sets with highly-correlated wave functions have excellent accuracies and they have the capabilities to predict the excited states also with great accuracy. Computations of actinide complexes (Uranyl and plutonyl complexes) are critical to management of high-level nuclear wastes.« less

Multiple tipping points and optimal repairing in interacting networks

PubMed Central

Majdandzic, Antonio; Braunstein, Lidia A.; Curme, Chester; Vodenska, Irena; Levy-Carciente, Sary; Eugene Stanley, H.; Havlin, Shlomo

2016-01-01

Systems composed of many interacting dynamical networks—such as the human body with its biological networks or the global economic network consisting of regional clusters—often exhibit complicated collective dynamics. Three fundamental processes that are typically present are failure, damage spread and recovery. Here we develop a model for such systems and find a very rich phase diagram that becomes increasingly more complex as the number of interacting networks increases. In the simplest example of two interacting networks we find two critical points, four triple points, ten allowed transitions and two ‘forbidden' transitions, as well as complex hysteresis loops. Remarkably, we find that triple points play the dominant role in constructing the optimal repairing strategy in damaged interacting systems. To test our model, we analyse an example of real interacting financial networks and find evidence of rapid dynamical transitions between well-defined states, in agreement with the predictions of our model. PMID:26926803

Detecting phase boundaries of quantum spin-1/2 XXZ ladder via bipartite and multipartite entanglement transitions

NASA Astrophysics Data System (ADS)

Singha Roy, Sudipto; Dhar, Himadri Shekhar; Rakshit, Debraj; Sen(De), Aditi; Sen, Ujjwal

2017-12-01

Phase transition in quantum many-body systems inevitably causes changes in certain physical properties which then serve as potential indicators of critical phenomena. Besides the traditional order parameters, characterization of quantum entanglement has proven to be a computationally efficient and successful method for detection of phase boundaries, especially in one-dimensional models. Here we determine the rich phase diagram of the ground states of a quantum spin-1/2 XXZ ladder by analyzing the variation of bipartite and multipartite entanglements. Our study characterizes the different ground state phases and notes the correspondence with known results, while highlighting the finer details that emerge from the behavior of ground state entanglement. Analysis of entanglement in the ground state provides a clearer picture of the complex ground state phase diagram of the system using only a moderate-size model.

Improvement of driving safety in road traffic system

NASA Astrophysics Data System (ADS)

Li, Ke-Ping; Gao, Zi-You

2005-05-01

A road traffic system is a complex system in which humans participate directly. In this system, human factors play a very important role. In this paper, a kind of control signal is designated at a given site (i.e., signal point) of the road. Under the effect of the control signal, the drivers will decrease their velocities when their vehicles pass the signal point. Our aim is to transit the traffic flow states from disorder to order and then improve the traffic safety. We have tested this technique for the two-lane traffic model that is based on the deterministic Nagel-Schreckenberg (NaSch) traffic model. The simulation results indicate that the traffic flow states can be transited from disorder to order. Different order states can be observed in the system and these states are safer.

Rotational study of the NH{sub 3}–CO complex: Millimeter-wave measurements and ab initio calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Surin, L. A., E-mail: surin@ph1.uni-koeln.de; Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya Str. 5, 142190 Troitsk, Moscow; Potapov, A.

2015-03-21

The rotational spectrum of the van der Waals complex NH{sub 3}–CO has been measured with the intracavity OROTRON jet spectrometer in the frequency range of 112–139 GHz. Newly observed and assigned transitions belong to the K = 0–0, K = 1–1, K = 1–0, and K = 2–1 subbands correlating with the rotationless (j{sub k}){sub NH3} = 0{sub 0} ground state of free ortho-NH{sub 3} and the K = 0–1 and K = 2–1 subbands correlating with the (j{sub k}){sub NH3} = 1{sub 1} ground state of free para-NH{sub 3}. The (approximate) quantum number K is the projection of themore » total angular momentum J on the intermolecular axis. Some of these transitions are continuations to higher J values of transition series observed previously [C. Xia et al., Mol. Phys. 99, 643 (2001)], the other transitions constitute newly detected subbands. The new data were analyzed together with the known millimeter-wave and microwave transitions in order to determine the molecular parameters of the ortho-NH{sub 3}–CO and para-NH{sub 3}–CO complexes. Accompanying ab initio calculations of the intermolecular potential energy surface (PES) of NH{sub 3}–CO has been carried out at the explicitly correlated coupled cluster level of theory with single, double, and perturbative triple excitations and an augmented correlation-consistent triple zeta basis set. The global minimum of the five-dimensional PES corresponds to an approximately T-shaped structure with the N atom closest to the CO subunit and binding energy D{sub e} = 359.21 cm{sup −1}. The bound rovibrational levels of the NH{sub 3}–CO complex were calculated for total angular momentum J = 0–6 on this intermolecular potential surface and compared with the experimental results. The calculated dissociation energies D{sub 0} are 210.43 and 218.66 cm{sup −1} for ortho-NH{sub 3}–CO and para-NH{sub 3}–CO, respectively.« less

Chimera at the phase-flip transition of an ensemble of identical nonlinear oscillators

NASA Astrophysics Data System (ADS)

Gopal, R.; Chandrasekar, V. K.; Senthilkumar, D. V.; Venkatesan, A.; Lakshmanan, M.

2018-06-01

A complex collective emerging behavior characterized by coexisting coherent and incoherent domains is termed as a chimera state. We bring out the existence of a new type of chimera in a nonlocally coupled ensemble of identical oscillators driven by a common dynamic environment. The latter facilitates the onset of phase-flip bifurcation/transitions among the coupled oscillators of the ensemble, while the nonlocal coupling induces a partial asynchronization among the out-of-phase synchronized oscillators at this onset. This leads to the manifestation of coexisting out-of-phase synchronized coherent domains interspersed by asynchronous incoherent domains elucidating the existence of a different type of chimera state. In addition to this, a rich variety of other collective behaviors such as clusters with phase-flip transition, conventional chimera, solitary state and complete synchronized state which have been reported using different coupling architectures are found to be induced by the employed couplings for appropriate coupling strengths. The robustness of the resulting dynamics is demonstrated in ensembles of two paradigmatic models, namely Rössler oscillators and Stuart-Landau oscillators.

Ultrafast photo-induced hidden phases in strained manganite thin films

NASA Astrophysics Data System (ADS)

Zhang, Jingdi; McLeod, A. S.; Zhang, Gu-Feng; Stoica, Vladimir; Jin, Feng; Gu, Mingqiang; Gopalan, Venkatraman; Freeland, John W.; Wu, Wenbin; Rondinelli, James; Wen, Haidan; Basov, D. N.; Averitt, R. D.

Correlated transition metal oxides (TMOs) are particularly sensitive to external control because of energy degeneracy in a complex energy landscape that promote a plethora of metastable states. However, it remains a grand challenge to actively control and fully explore the rich landscape of TMOs. Dynamic control with pulsed photons can overcome energetic barriers, enabling access to transient or metastable states that are not thermally accessible. In the past, we have demonstrated that mode-selective single-laser-pulse excitation of a strained manganite thin film La2/3Ca1/3MnO3 initiates a persistent phase transition from an emergent antiferromagnetic insulating ground state to a ferromagnetic metallic metastable state. Beyond the photo-induced insulator to metal transition, we recently discovered a new peculiar photo-induced hidden phase, identified by an experimental approach that combines ultrafast pump-probe spectroscopy, THz spectroscopy, X-ray diffraction, cryogenic near-field spectroscopy and SHG probe. This work is funded by the DOE, Office of Science, Office of Basic Energy Science under Award Numbers DE-SC0012375 and DE-SC0012592.

Quantification of brain macrostates using dynamical nonstationarity of physiological time series.

PubMed

Latchoumane, Charles-Francois Vincent; Jeong, Jaeseung

2011-04-01

The brain shows complex, nonstationarity temporal dynamics, with abrupt micro- and macrostate transitions during its information processing. Detecting and characterizing these transitions in dynamical states of the brain is a critical issue in the field of neuroscience and psychiatry. In the current study, a novel method is proposed to quantify brain macrostates (e.g., sleep stages or cognitive states) from shifts of dynamical microstates or dynamical nonstationarity. A ``dynamical microstate'' is a temporal unit of the information processing in the brain with fixed dynamical parameters and specific spatial distribution. In this proposed approach, a phase-space-based dynamical dissimilarity map (DDM) is used to detect transitions between dynamically stationary microstates in the time series, and Tsallis time-dependent entropy is applied to quantify dynamical patterns of transitions in the DDM. We demonstrate that the DDM successfully detects transitions between microstates of different temporal dynamics in the simulated physiological time series against high levels of noise. Based on the assumption of nonlinear, deterministic brain dynamics, we also demonstrate that dynamical nonstationarity analysis is useful to quantify brain macrostates (sleep stages I, II, III, IV, and rapid eye movement (REM) sleep) from sleep EEGs with an overall accuracy of 77%. We suggest that dynamical nonstationarity is a useful tool to quantify macroscopic mental states (statistical integration) of the brain using dynamical transitions at the microscopic scale in physiological data.

Machine learning phases of matter

NASA Astrophysics Data System (ADS)

Carrasquilla, Juan; Melko, Roger G.

2017-02-01

Condensed-matter physics is the study of the collective behaviour of infinitely complex assemblies of electrons, nuclei, magnetic moments, atoms or qubits. This complexity is reflected in the size of the state space, which grows exponentially with the number of particles, reminiscent of the `curse of dimensionality' commonly encountered in machine learning. Despite this curse, the machine learning community has developed techniques with remarkable abilities to recognize, classify, and characterize complex sets of data. Here, we show that modern machine learning architectures, such as fully connected and convolutional neural networks, can identify phases and phase transitions in a variety of condensed-matter Hamiltonians. Readily programmable through modern software libraries, neural networks can be trained to detect multiple types of order parameter, as well as highly non-trivial states with no conventional order, directly from raw state configurations sampled with Monte Carlo.

Landscapes with megabasins: Polyamorphism in liquids and biopolymers and the role of nucleation in folding and folding diseases

NASA Astrophysics Data System (ADS)

Angell, C. A.

1997-02-01

We show how energy landscape concepts can rationalize the observations on glassforming liquids over the whole range of behavior, strong to fragile. In particular, we show how the existence of landscapes with both strong and fragile megabasins can provide a basis for understanding the nature of quasi-first-order transitions between amorphous states such as those observed to occur in the glassy states of “strong” glassformers. We show how this propensity originates in the liquid state and then emphasize the analogy provided, at the mesoscopic level, by the folding transition in proteins. Recognition that the folding transition is an equilibrium first-order transition between polyamorphic forms of a complex system implies recognition of the need for a nucleation step in the process. When nucleated phase transitions are kinetically retarded, their probability can be influenced by time-temperature history and by the presence of nucleating agents. Nucleation events are statistically rare in mesoscopic systems, hence the ability to fold rapidly should require special features in the folding molecular structure or the presence of nucleating agents. We propose that the unwanted folding events leading to pathogenic forms of certain proteins (prions) can be stimulated by nucleating agents, which thus may be the unidentified infectious agents in “mad cow” disease and related maladies.

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mori, Toshifumi, E-mail: mori@ims.ac.jp; Saito, Shinji, E-mail: shinji@ims.ac.jp

Molecular dynamics simulations have become an important tool in studying protein dynamics over the last few decades. Atomistic simulations on the order of micro- to milliseconds are becoming feasible and are used to study the state-of-the-art experiments in atomistic detail. Yet, analyzing the high-dimensional-long-temporal trajectory data is still a challenging task and sometimes leads to contradictory results depending on the analyses. To reveal the dynamic aspect of the trajectory, here we propose a simple approach which uses a time correlation function matrix and apply to the folding/unfolding trajectory of FiP35 WW domain [Shaw et al., Science 330, 341 (2010)]. Themore » approach successfully characterizes the slowest mode corresponding to the folding/unfolding transitions and determines the free energy barrier indicating that FiP35 is not an incipient downhill folder. The transition dynamics analysis further reveals that the folding/unfolding transition is highly heterogeneous, e.g., the transition path time varies by ∼100 fold. We identify two misfolded states and show that the dynamic heterogeneity in the folding/unfolding transitions originates from the trajectory being trapped in the misfolded and half-folded intermediate states rather than the diffusion driven by a thermal noise. The current results help reconcile the conflicting interpretations of the folding mechanism and highlight the complexity in the folding dynamics. This further motivates the need to understand the transition dynamics beyond a simple free energy picture using simulations and single-molecule experiments.« less

Correlation of Solid State and Solution Coordination Numbers with Infrared Spectroscopy in Five-, Six-, and Eight-Coordinate Transition Metal Complexes of DOTAM.

PubMed

Nagata, Maika K C T; Brauchle, Paul S; Wang, Sen; Briggs, Sarah K; Hong, Young Soo; Laorenza, Daniel W; Lee, Andrea G; Westmoreland, T David

2016-08-16

Three new DOTAM (1,4,7,10-tetrakis(acetamido)-1,4,7,10-tetraazacyclododecane) complexes have been synthesized and characterized by X-ray crystallography: [Co(DOTAM)]Cl 2 •3H 2 O, [Ni(DOTAM)]Cl 2 •4H 2 O, and [Cu(DOTAM)](ClO 4 ) 2 •H 2 O. Solid state and solution IR spectroscopic features for a series of [M(DOTAM)] 2+ complexes (M=Mn, Co, Cu, Ni, Ca, Zn) correlate with solid state and solution coordination numbers. [Co(DOTAM)] 2+ , [Ni(DOTAM)] 2+ , and [Zn(DOTAM)] 2+ are demonstrated to be six-coordinate in both the solid state and in solution, while [Mn(DOTAM)] 2+ and [Ca(DOTAM)] 2+ are eight-coordinate in the solid state and remain so in solution. [Cu(DOTAM)] 2+ , which is five-coordinate by X-ray crystallography, is shown to increase its coordination number in solution to six-coordinate.

Ab initio calculations of the effects of H+ and NH4+ on the initial decomposition of HMX.

PubMed

Wang, Luoxin; Tuo, Xinlin; Yi, Changhai; Wang, Xiaogong

2008-10-01

In this work, the effects of H(+) and NH(4)(+) on the initial decomposition of HMX were investigated on the basis of the B3P86/6-31G** and B3LYP/6-31G* calculations. Three initial decomposition pathways including the N-NO(2) bond fission, HONO elimination and C-N bond dissociation were considered for the complexes formed by HMX with H(+) (PHMX1 and PHMX2) or with NH(4)(+) (AHMX). We found that H(+) and NH(4)(+) did not evidently induce the HMX to trigger the N-NO(2) heterolysis because the energy barrier of N-NO(2) heterolysis was found to be higher than the bond dissociation energy of N-NO(2) homolytic cleavage. Meanwhile, the transition state barriers of the HONO elimination from the complexes were found to be similar to that from the isolated HMX, which means that the HONO elimination reaction of HMX was not affected by the H(+) and NH(4)(+). As for the ring-opening reaction of HMX due to the C-N bond dissociation, the calculated potential energy profile showed that the energy of the complex (AHMX) went uphill along the C-N bond length and no transition state existed on the curve. However, the transition state energy barriers of C-N bond dissociation were calculated to be only 5.0 kcal/mol and 5.5 kcal/mol for the PHMX1 and PHMX2 complexes, respectively, which were much lower than the C-N bond dissociation energy of isolated HMX. Moreover, among the three initial decomposition reactions, the C-N bond dissociation was also the most energetically favorable pathway for the PHMX1 and PHMX2. Our calculation results showed that the H(+) can significantly promote the initial thermal decomposition of C-N bond of HMX, which, however, is influenced by NH(4)(+) slightly.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

PubMed Central

Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

Chimera states and the interplay between initial conditions and non-local coupling

NASA Astrophysics Data System (ADS)

Kalle, Peter; Sawicki, Jakub; Zakharova, Anna; Schöll, Eckehard

2017-03-01

Chimera states are complex spatio-temporal patterns that consist of coexisting domains of coherent and incoherent dynamics. We study chimera states in a network of non-locally coupled Stuart-Landau oscillators. We investigate the impact of initial conditions in combination with non-local coupling. Based on an analytical argument, we show how the coupling phase and the coupling strength are linked to the occurrence of chimera states, flipped profiles of the mean phase velocity, and the transition from a phase- to an amplitude-mediated chimera state.

Chimera states and the interplay between initial conditions and non-local coupling.

PubMed

Kalle, Peter; Sawicki, Jakub; Zakharova, Anna; Schöll, Eckehard

2017-03-01

Chimera states are complex spatio-temporal patterns that consist of coexisting domains of coherent and incoherent dynamics. We study chimera states in a network of non-locally coupled Stuart-Landau oscillators. We investigate the impact of initial conditions in combination with non-local coupling. Based on an analytical argument, we show how the coupling phase and the coupling strength are linked to the occurrence of chimera states, flipped profiles of the mean phase velocity, and the transition from a phase- to an amplitude-mediated chimera state.

Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM.

PubMed

Boyd, Andrew D; Li, Jianrong John; Kenost, Colleen; Joese, Binoy; Yang, Young Min; Kalagidis, Olympia A; Zenku, Ilir; Saner, Donald; Bahroos, Neil; Lussier, Yves A

2015-05-01

In the United States, International Classification of Disease Clinical Modification (ICD-9-CM, the ninth revision) diagnosis codes are commonly used to identify patient cohorts and to conduct financial analyses related to disease. In October 2015, the healthcare system of the United States will transition to ICD-10-CM (the tenth revision) diagnosis codes. One challenge posed to clinical researchers and other analysts is conducting diagnosis-related queries across datasets containing both coding schemes. Further, healthcare administrators will manage growth, trends, and strategic planning with these dually-coded datasets. The majority of the ICD-9-CM to ICD-10-CM translations are complex and nonreciprocal, creating convoluted representations and meanings. Similarly, mapping back from ICD-10-CM to ICD-9-CM is equally complex, yet different from mapping forward, as relationships are likewise nonreciprocal. Indeed, 10 of the 21 top clinical categories are complex as 78% of their diagnosis codes are labeled as "convoluted" by our analyses. Analysis and research related to external causes of morbidity, injury, and poisoning will face the greatest challenges due to 41 745 (90%) convolutions and a decrease in the number of codes. We created a web portal tool and translation tables to list all ICD-9-CM diagnosis codes related to the specific input of ICD-10-CM diagnosis codes and their level of complexity: "identity" (reciprocal), "class-to-subclass," "subclass-to-class," "convoluted," or "no mapping." These tools provide guidance on ambiguous and complex translations to reveal where reports or analyses may be challenging to impossible.Web portal: http://www.lussierlab.org/transition-to-ICD9CM/Tables annotated with levels of translation complexity: http://www.lussierlab.org/publications/ICD10to9. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: A review

DOE PAGES

Reichhardt, Charles; Olson Reichhardt, Cynthia Jane

2016-12-20

Here, we review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic andmore » plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.« less

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: a review

NASA Astrophysics Data System (ADS)

Reichhardt, C.; Olson Reichhardt, C. J.

2017-02-01

We review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic and plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.

Theoretical Investigation of the Electronic Structure of Fe(II) Complexes at Spin-State Transitions

PubMed Central

2013-01-01

The electronic structure relevant to low spin (LS)↔high spin (HS) transitions in Fe(II) coordination compounds with a FeN6 core are studied. The selected [Fe(tz)6]2+ (1) (tz = 1H-tetrazole), [Fe(bipy)3]2+ (2) (bipy = 2,2′-bipyridine), and [Fe(terpy)2]2+ (3) (terpy = 2,2′:6′,2″-terpyridine) complexes have been actively studied experimentally, and with their respective mono-, bi-, and tridentate ligands, they constitute a comprehensive set for theoretical case studies. The methods in this work include density functional theory (DFT), time-dependent DFT (TD-DFT), and multiconfigurational second order perturbation theory (CASPT2). We determine the structural parameters as well as the energy splitting of the LS–HS states (ΔEHL) applying the above methods and comparing their performance. We also determine the potential energy curves representing the ground and low-energy excited singlet, triplet, and quintet d6 states along the mode(s) that connect the LS and HS states. The results indicate that while DFT is well suited for the prediction of structural parameters, an accurate multiconfigurational approach is essential for the quantitative determination of ΔEHL. In addition, a good qualitative agreement is found between the TD-DFT and CASPT2 potential energy curves. Although the TD-DFT results might differ in some respect (in our case, we found a discrepancy at the triplet states), our results suggest that this approach, with due care, is very promising as an alternative for the very expensive CASPT2 method. Finally, the two-dimensional (2D) potential energy surfaces above the plane spanned by the two relevant configuration coordinates in [Fe(terpy)2]2+ were computed at both the DFT and CASPT2 levels. These 2D surfaces indicate that the singlet–triplet and triplet–quintet states are separated along different coordinates, i.e., different vibration modes. Our results confirm that in contrast to the case of complexes with mono- and bidentate ligands, the singlet–quintet transitions in [Fe(terpy)2]2+ cannot be described using a single configuration coordinate. PMID:25821416

Identification of the protein folding transition state from molecular dynamics trajectories

NASA Astrophysics Data System (ADS)

Muff, S.; Caflisch, A.

2009-03-01

The rate of protein folding is governed by the transition state so that a detailed characterization of its structure is essential for understanding the folding process. In vitro experiments have provided a coarse-grained description of the folding transition state ensemble (TSE) of small proteins. Atomistic details could be obtained by molecular dynamics (MD) simulations but it is not straightforward to extract the TSE directly from the MD trajectories, even for small peptides. Here, the structures in the TSE are isolated by the cut-based free-energy profile (cFEP) using the network whose nodes and links are configurations sampled by MD and direct transitions among them, respectively. The cFEP is a barrier-preserving projection that does not require arbitrarily chosen progress variables. First, a simple two-dimensional free-energy surface is used to illustrate the successful determination of the TSE by the cFEP approach and to explain the difficulty in defining boundary conditions of the Markov state model for an entropically stabilized free-energy minimum. The cFEP is then used to extract the TSE of a β-sheet peptide with a complex free-energy surface containing multiple basins and an entropic region. In contrast, Markov state models with boundary conditions defined by projected variables and conventional histogram-based free-energy profiles are not able to identify the TSE of the β-sheet peptide.

Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics.

PubMed

Darkhovskii, M B; Pletnev, I V; Tchougréeff, A L

2003-11-15

A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie-Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d-shell. The quantum mechanical EHCF part is limited to the metal ion d-shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. Copyright 2003 Wiley Periodicals, Inc.

Highly versatile heteroditopic ligand scaffolds for accommodating group 8, 9 & 11 heterobimetallic complexes.

PubMed

Gatus, Mark R D; Bhadbhade, Mohan; Messerle, Barbara A

2017-10-24

Two highly versatile xanthene scaffolds containing pairs of heteroditopic ligands were found to be capable of accommodating a range of transition metal ions, including Au(i), Ir(i), Ir(iii), Rh(i), and Ru(ii) to generate an array of heterobimetallic complexes. The metal complexes were fully characterised and proved to be stable in the solid and solution state, with no observed metal-metal scrambling. Heterobimetallic complexes containing the Rh(i)/Ir(i) combinations were tested as catalysts for the two-step dihydroalkoxylation reaction of alkynediols and sequential hydroamination/hydrosilylation reaction of alkynamines.

Magnesium, zinc, aluminium and gallium hydride complexes of the transition metals† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6cc05702k

PubMed Central

Butler, Michael J.

2017-01-01

The preparation and applications of heterobimetallic complexes continue to occupy researchers in the fields of organometallic, main group, and coordination chemistry. This interest stems from the promise these complexes hold as precursors to materials, reagents in synthesis and as new catalysis. Here we survey and organise the state-of-the-art understanding of the TM–H–M linkage (M = Mg, Zn, Al, Ga). We discuss the structure and bonding in these complexes, their known reactivity, and their largely unrealised potential in catalysis. PMID:28070586

Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

PubMed Central

Linscott, Joshua A.; Kapilashrami, Kanishk; Wang, Zhen; Senevirathne, Chamara; Bothwell, Ian R.; Blum, Gil; Luo, Minkui

2016-01-01

Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)–PKMT–substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MS-based method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-l-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13C KIE of 1.04, an inverse intrinsic α-secondary CD3 KIE of 0.90, and a small but statistically significant inverse CD3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35–2.40 Å and 2.00–2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steady-state kinetics with the SAM analog Se-adenosyl-l-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors. PMID:27940912

Pressure Dependence of Gas-Phase Reaction Rates

ERIC Educational Resources Information Center

De Persis, Stephanie; Dollet, Alain; Teyssandier, Francis

2004-01-01

It is presented that only simple concepts, mainly taken from activated-complex or transition-state theory, are required to explain and analytically describe the influence of pressure on gas-phase reaction kinetics. The simplest kind of elementary gas-phase reaction is a unimolecular decomposition reaction.

Structural and topological phase transitions on the German Stock Exchange

NASA Astrophysics Data System (ADS)

Wiliński, M.; Sienkiewicz, A.; Gubiec, T.; Kutner, R.; Struzik, Z. R.

2013-12-01

We find numerical and empirical evidence for dynamical, structural and topological phase transitions on the (German) Frankfurt Stock Exchange (FSE) in the temporal vicinity of the worldwide financial crash. Using the Minimal Spanning Tree (MST) technique, a particularly useful canonical tool of the graph theory, two transitions of the topology of a complex network representing the FSE were found. The first transition is from a hierarchical scale-free MST representing the stock market before the recent worldwide financial crash, to a superstar-like MST decorated by a scale-free hierarchy of trees representing the market’s state for the period containing the crash. Subsequently, a transition is observed from this transient, (meta)stable state of the crash to a hierarchical scale-free MST decorated by several star-like trees after the worldwide financial crash. The phase transitions observed are analogous to the ones we obtained earlier for the Warsaw Stock Exchange and more pronounced than those found by Onnela-Chakraborti-Kaski-Kertész for the S&P 500 index in the vicinity of Black Monday (October 19, 1987) and also in the vicinity of January 1, 1998. Our results provide an empirical foundation for the future theory of dynamical, structural and topological phase transitions on financial markets.

Strain-Engineered Oxygen Vacancies in CaMnO3 Thin Films.

PubMed

Chandrasena, Ravini U; Yang, Weibing; Lei, Qingyu; Delgado-Jaime, Mario U; Wijesekara, Kanishka D; Golalikhani, Maryam; Davidson, Bruce A; Arenholz, Elke; Kobayashi, Keisuke; Kobata, Masaaki; de Groot, Frank M F; Aschauer, Ulrich; Spaldin, Nicola A; Xi, Xiaoxing; Gray, Alexander X

2017-02-08

We demonstrate a novel pathway to control and stabilize oxygen vacancies in complex transition-metal oxide thin films. Using atomic layer-by-layer pulsed laser deposition (PLD) from two separate targets, we synthesize high-quality single-crystalline CaMnO 3 films with systematically varying oxygen vacancy defect formation energies as controlled by coherent tensile strain. The systematic increase of the oxygen vacancy content in CaMnO 3 as a function of applied in-plane strain is observed and confirmed experimentally using high-resolution soft X-ray absorption spectroscopy (XAS) in conjunction with bulk-sensitive hard X-ray photoemission spectroscopy (HAXPES). The relevant defect states in the densities of states are identified and the vacancy content in the films quantified using the combination of first-principles theory and core-hole multiplet calculations with holistic fitting. Our findings open up a promising avenue for designing and controlling new ionically active properties and functionalities of complex transition-metal oxides via strain-induced oxygen-vacancy formation and ordering.

Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butkus, Vytautas; Gelzinis, Andrius; Valkunas, Leonas

2015-06-07

Energy transfer processes and coherent phenomena in the fucoxanthin–chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Q{sub y} transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Q{submore » y} transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.« less

Transition metal ferrocenyl dithiocarbamates functionalized dye-sensitized solar cells with hydroxy as an anchoring group

NASA Astrophysics Data System (ADS)

Yadav, Reena; Waghadkar, Yogesh; Kociok-Köhn, Gabriele; Kumar, Abhinav; Rane, Sunit B.; Chauhan, Ratna

2016-12-01

Three new transition-metal dithiocarbamates involving ferrocene (Fc), namely [Co(FcCH2EtOHdtc)3] (Co), [M(FcCH2EtOHdtc)2] M = Ni (Ni), Cu (Cu) (EtOHdtc = N-ethanol dithiocarbamate), have been synthesized and characterized by microanalyses, FTIR, 1H and 13C NMR spectroscopies and single crystal X-ray diffraction technique. The peak broadening in the 1H spectrum of the copper complex indicates the paramagnetic behavior of this compound. The observed single quasi-reversible cyclic voltammograms for the complexes indicate the stabilization of a metal center (except copper) other than Fe in their characteristic oxidation state. These complexes have been used as photo-sensitizer in dye-sensitized solar cells which indicates that Co displays the best photosensitization property with an overall conversion efficiency of 3.25 ± 0.04%. The low cell efficiency of Ni and Cu complexes may be due to slow regeneration of the dye by iodine/iodide redox couple followed by charge injection into TiO2.

Photodissociation spectroscopy and ab initio calculations for the Sr +-N 2 complex

NASA Astrophysics Data System (ADS)

Massaouti, Maria; Fanourgakis, George S.; Velegrakis, Michalis

2010-04-01

Electronic vibrationally resolved spectra of the Sr +-N 2 complex have been recorded in two energy regions 20 284-22 988 cm -1 and 15 576-16 380 cm -1. In the high energy region, two progressions are present and they are attributed to the (2) 2Π 3/2,1/2 ← X2Σ+ transitions assuming a linear molecule. This linear configuration is supported from the observed spin-orbit splitting of these excited states as well as from electronic structure calculations. The lower energy spectrum shows a structure, which ends up to a continuum. Considering the complex as an anharmonic oscillator, the spectroscopic constants and the dissociation energies of the corresponding states are determined.

Molecular basis of the fructose-2,6-bisphosphatase reaction of PFKFB3: Transition state and the C-terminal function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cavalier, Michael C.; Kim, Song-Gun; Neau, David

2012-03-22

The molecular basis of fructose-2,6-bisphosphatase (F-2,6-P{sub 2}ase) of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB) was investigated using the crystal structures of the human inducible form (PFKFB3) in a phospho-enzyme intermediate state (PFKFB3-P {center_dot} F-6-P), in a transition state-analogous complex (PFKFB3 {center_dot} AlF{sub 4}), and in a complex with pyrophosphate (PFKFB3 {center_dot} PP{sub i}) at resolutions of 2.45, 2.2, and 2.3 {angstrom}, respectively. Trapping the PFKFB3-P {center_dot} F-6-P intermediate was achieved by flash cooling the crystal during the reaction, and the PFKFB3 {center_dot} AlF{sub 4} and PFKFB3 {center_dot} PP{sub i} complexes were obtained by soaking. The PFKFB3 {center_dot} AlF{sub 4} and PFKFB3 {center_dot} PP{sub i}more » complexes resulted in removing F-6-P from the catalytic pocket. With these structures, the structures of the Michaelis complex and the transition state were extrapolated. For both the PFKFB3-P formation and break down, the phosphoryl donor and the acceptor are located within {approx}5.1 {angstrom}, and the pivotal point 2-P is on the same line, suggesting an 'in-line' transfer with a direct inversion of phosphate configuration. The geometry suggests that NE2 of His253 undergoes a nucleophilic attack to form a covalent N-P bond, breaking the 2O-P bond in the substrate. The resulting high reactivity of the leaving group, 2O of F-6-P, is neutralized by a proton donated by Glu322. Negative charges on the equatorial oxygen of the transient bipyramidal phosphorane formed during the transfer are stabilized by Arg252, His387, and Asn259. The C-terminal domain (residues 440-446) was rearranged in PFKFB3 {center_dot} PP{sub i}, implying that this domain plays a critical role in binding of substrate to and release of product from the F-2,6-P{sub 2}ase catalytic pocket. These findings provide a new insight into the understanding of the phosphoryl transfer reaction.« less

Chapter 8: Selective Stoichiometric and Catalytic Reactivity in the Confines of a Chiral Supramolecular Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

University of California, Berkeley; Lawrence Berkeley National Laboratory; Raymond, Kenneth

2007-09-27

Nature uses enzymes to activate otherwise unreactive compounds in remarkable ways. For example, DNases are capable of hydrolyzing phosphate diester bonds in DNA within seconds,[1-3]--a reaction with an estimated half-life of 200 million years without an enzyme.[4] The fundamental features of enzyme catalysis have been much discussed over the last sixty years in an effort to explain the dramatic rate increases and high selectivities of enzymes. As early as 1946, Linus Pauling suggested that enzymes must preferentially recognize and stabilize the transition state over the ground state of a substrate.[5] Despite the intense study of enzymatic selectivity and ability tomore » catalyze chemical reactions, the entire nature of enzyme-based catalysis is still poorly understood. For example, Houk and co-workers recently reported a survey of binding affinities in a wide variety of enzyme-ligand, enzyme-transition-state, and synthetic host-guest complexes and found that the average binding affinities were insufficient to generate many of the rate accelerations observed in biological systems.[6] Therefore, transition-state stabilization cannot be the sole contributor to the high reactivity and selectivity of enzymes, but rather, other forces must contribute to the activation of substrate molecules. Inspired by the efficiency and selectivity of Nature, synthetic chemists have admired the ability of enzymes to activate otherwise unreactive molecules in the confines of an active site. Although much less complex than the evolved active sites of enzymes, synthetic host molecules have been developed that can carry out complex reactions with their cavities. While progress has been made toward highly efficient and selective reactivity inside of synthetic hosts, the lofty goal of duplicating enzymes specificity remains.[7-9] Pioneered by Lehn, Cram, Pedersen, and Breslow, supramolecular chemistry has evolved well beyond the crown ethers and cryptands originally studied.[10-12] Despite the increased complexity of synthetic host molecules, most assembly conditions utilize self-assembly to form complex highly-symmetric structures from relatively simple subunits. For supramolecular assemblies able to encapsulate guest molecules, the chemical environment in each assembly--defined by the size, shape, charge, and functional group availability--greatly influences the guest-binding characteristics.[6, 13-17]« less

Monitoring the kinetics of the pH driven transition of the anthrax toxin prepore to the pore by biolayer interferometry and surface plasmon resonance

PubMed Central

Naik, Subhashchandra; Brock, Susan; Akkaladevi, Narahari; Tally, Jon; Mcginn-Straub, Wesley; Zhang, Na; Gao, Phillip; Gogol, E. P.; Pentelute, B. L.; Collier, R. John; Fisher, Mark T.

2013-01-01

Domain 2 of the anthrax protective antigen (PA) prepore heptamer unfolds and refolds during endosome acidification to generate an extended 100 Å beta barrel pore that inserts into the endosomal membrane. The PA pore facilitates the pH dependent unfolding and translocation of bound toxin enzymic components, lethal factor (LF) and/or edema factor (EF), from the endosome into the cytoplasm. We constructed immobilized complexes of the prepore with the PA-binding domain of LF (LFN) to monitor the real-time prepore to pore kinetic transition using surface plasmon resonance (SPR) and bio-layer interferometry (BLI). The kinetics of this transition increased as the solution pH was decreased from pH 7.5 to pH 5.0, mirroring acidification of the endosome. Once transitioned, the LFN-PA pore complex was removed from the BLI biosensor tip and deposited onto EM grids, where the PA pore formation was confirmed by negative stain electron microscopy. When the soluble receptor domain (ANTRX2/CMG2) binds the immobilized PA prepore, the transition to the pore state was observed only after the pH was lowered to early or late endosomal pH conditions (5.5 to 5.0 respectively). Once the pore formed, the soluble receptor readily dissociated from the PA pore. Separate binding experiments with immobilized PA pores and soluble receptor indicate that the receptor has a weakened propensity to bind to the transitioned pore. This immobilized anthrax toxin platform can be used to identify or validate potential antimicrobial lead compounds capable of regulating and/or inhibiting anthrax toxin complex formation or pore transitions. PMID:23964683

Monitoring the kinetics of the pH-driven transition of the anthrax toxin prepore to the pore by biolayer interferometry and surface plasmon resonance.

PubMed

Naik, Subhashchandra; Brock, Susan; Akkaladevi, Narahari; Tally, Jon; McGinn-Straub, Wesley; Zhang, Na; Gao, Phillip; Gogol, E P; Pentelute, B L; Collier, R John; Fisher, Mark T

2013-09-17

Domain 2 of the anthrax protective antigen (PA) prepore heptamer unfolds and refolds during endosome acidification to generate an extended 100 Å β barrel pore that inserts into the endosomal membrane. The PA pore facilitates the pH-dependent unfolding and translocation of bound toxin enzymic components, lethal factor (LF) and/or edema factor, from the endosome to the cytoplasm. We constructed immobilized complexes of the prepore with the PA-binding domain of LF (LFN) to monitor the real-time prepore to pore kinetic transition using surface plasmon resonance and biolayer interferometry (BLI). The kinetics of this transition increased as the solution pH was decreased from 7.5 to 5.0, mirroring acidification of the endosome. Once it had undergone the transition, the LFN-PA pore complex was removed from the BLI biosensor tip and deposited onto electron microscopy grids, where PA pore formation was confirmed by negative stain electron microscopy. When the soluble receptor domain (ANTRX2/CMG2) binds the immobilized PA prepore, the transition to the pore state was observed only after the pH was lowered to early (pH 5.5) or late (pH 5.0) endosomal pH conditions. Once the pore formed, the soluble receptor readily dissociated from the PA pore. Separate binding experiments with immobilized PA pores and the soluble receptor indicate that the receptor has a weakened propensity to bind to the transitioned pore. This immobilized anthrax toxin platform can be used to identify or validate potential antimicrobial lead compounds capable of regulating and/or inhibiting anthrax toxin complex formation or pore transitions.

Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.

PubMed

Jung, Young-Sang; Cai, Mengli; Clore, G Marius

2010-02-05

The solution structure of the IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state and the active site Cys-10 of IIB(Chb) was substituted by serine to prevent intermolecular disulfide bond formation. Binding is weak with a K(D) of approximately 1.3 mm. The two complementary interaction surfaces are largely hydrophobic, with the protruding active site loop (residues 9-16) of IIB(Chb) buried deep within the active site cleft formed at the interface of two adjacent subunits of the IIA(Chb) trimer. The central hydrophobic portion of the interface is surrounded by a ring of polar and charged residues that provide a relatively small number of electrostatic intermolecular interactions that serve to correctly align the two proteins. The conformation of the active site loop in unphosphorylated IIB(Chb) is inconsistent with the formation of a phosphoryl transition state intermediate because of steric hindrance, especially from the methyl group of Ala-12 of IIB(Chb). Phosphorylation of IIB(Chb) is accompanied by a conformational change within the active site loop such that its path from residues 11-13 follows a mirror-like image relative to that in the unphosphorylated state. This involves a transition of the phi/psi angles of Gly-13 from the right to left alpha-helical region, as well as smaller changes in the backbone torsion angles of Ala-12 and Met-14. The resulting active site conformation is fully compatible with the formation of the His-89-P-Cys-10 phosphoryl transition state without necessitating any change in relative translation or orientation of the two proteins within the complex.

Bound-bound transitions in the emission spectra of Ba+-He excimer

NASA Astrophysics Data System (ADS)

Moroshkin, P.; Kono, K.

2016-05-01

We present an experimental and theoretical study of the emission and absorption spectra of the Ba+ ions and Ba+*He excimer quasimolecules in the cryogenic Ba-He plasma. We observe several spectral features in the emission spectrum, which we assign to the electronic transitions between bound states of the excimer correlating to the 6 2P3 /2 and 5 2D3 /2 ,5 /2 states of Ba+. The resulting Ba+(5 2DJ) He is a metastable electronically excited complex with orbital angular momentum L =2 , thus expanding the family of known metal-helium quasimolecules. It might be suitable for high-resolution spectroscopic studies and for the search for new polyatomic exciplex structures.

Identification of Second Shell Coordination in Transition Metal Species Using Theoretical XANES: Example of Ti–O–(C, Si, Ge) Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spanjers, Charles S.; Guillo, Pascal; Tilley, T. Don

X-ray absorption near-edge structure (XANES) is a common technique for elucidating oxidation state and first shell coordination geometry in transition metal complexes, among many other materials. However, the structural information obtained from XANES is often limited to the first coordination sphere. In this study, we show how XANES can be used to differentiate between C, Si, and Ge in the second coordination shell of Ti–O–(C, Si, Ge) molecular complexes based on differences in their Ti K-edge XANES spectra. Experimental spectra were compared with theoretical spectra calculated using density functional theory structural optimization and ab initio XANES calculations. The unique featuresmore » for second shell C, Si, and Ge present in the Ti K pre-edge XANES are attributed to the interaction between the Ti center and the O–X (X = C, Si, or Ge) antibonding orbitals.« less

Mitochondrial network complexity emerges from fission/fusion dynamics.

PubMed

Zamponi, Nahuel; Zamponi, Emiliano; Cannas, Sergio A; Billoni, Orlando V; Helguera, Pablo R; Chialvo, Dante R

2018-01-10

Mitochondrial networks exhibit a variety of complex behaviors, including coordinated cell-wide oscillations of energy states as well as a phase transition (depolarization) in response to oxidative stress. Since functional and structural properties are often interwinded, here we characterized the structure of mitochondrial networks in mouse embryonic fibroblasts using network tools and percolation theory. Subsequently we perturbed the system either by promoting the fusion of mitochondrial segments or by inducing mitochondrial fission. Quantitative analysis of mitochondrial clusters revealed that structural parameters of healthy mitochondria laid in between the extremes of highly fragmented and completely fusioned networks. We confirmed our results by contrasting our empirical findings with the predictions of a recently described computational model of mitochondrial network emergence based on fission-fusion kinetics. Altogether these results offer not only an objective methodology to parametrize the complexity of this organelle but also support the idea that mitochondrial networks behave as critical systems and undergo structural phase transitions.

Electric-Field Control of Oxygen Vacancies and Magnetic Phase Transition in a Cobaltite/Manganite Bilayer

NASA Astrophysics Data System (ADS)

Cui, B.; Song, C.; Li, F.; Zhong, X. Y.; Wang, Z. C.; Werner, P.; Gu, Y. D.; Wu, H. Q.; Saleem, M. S.; Parkin, S. S. P.; Pan, F.

2017-10-01

Manipulation of oxygen vacancies (VO ) in single oxide layers by varying the electric field can result in significant modulation of the ground state. However, in many oxide multilayers with strong application potentials, e.g., ferroelectric tunnel junctions and solid-oxide fuel cells, understanding VO behavior in various layers under an applied electric field remains a challenge, owing to complex VO transport between different layers. By sweeping the external voltage, a reversible manipulation of VO and a corresponding fixed magnetic phase transition sequence in cobaltite/manganite (SrCoO3 -x/La0.45Sr0.55MnO3 -y ) heterostructures are reported. The magnetic phase transition sequence confirms that the priority of electric-field-induced VO formation or annihilation in the complex bilayer system is mainly determined by the VO formation energies and Gibbs free-energy differences, which is supported by theoretical analysis. We not only realize a reversible manipulation of the magnetic phase transition in an oxide bilayer but also provide insight into the electric-field control of VO engineering in heterostructures.

A chemometric method to identify enzymatic reactions leading to the transition from glycolytic oscillations to waves

NASA Astrophysics Data System (ADS)

Zimányi, László; Khoroshyy, Petro; Mair, Thomas

2010-06-01

In the present work we demonstrate that FTIR-spectroscopy is a powerful tool for the time resolved and noninvasive measurement of multi-substrate/product interactions in complex metabolic networks as exemplified by the oscillating glycolysis in a yeast extract. Based on a spectral library constructed from the pure glycolytic intermediates, chemometric analysis of the complex spectra allowed us the identification of many of these intermediates. Singular value decomposition and multiple level wavelet decomposition were used to separate drifting substances from oscillating ones. This enabled us to identify slow and fast variables of glycolytic oscillations. Most importantly, we can attribute a qualitative change in the positive feedback regulation of the autocatalytic reaction to the transition from homogeneous oscillations to travelling waves. During the oscillatory phase the enzyme phosphofructokinase is mainly activated by its own product ADP, whereas the transition to waves is accompanied with a shift of the positive feedback from ADP to AMP. This indicates that the overall energetic state of the yeast extract determines the transition between spatially homogeneous oscillations and travelling waves.

A Forty Year Odyssey in Metallo-Organic Chemistry.

PubMed

Nicholas, Kenneth M

2015-07-17

In this invited Perspective, I provide a personal account highlighting several of my group's research contributions in metallo-organic chemistry over the past 40 years. Our early work focused primarily in stoichiometric structure/reactivity of transition metal-organic compounds and their use in organic synthesis. More recent efforts have centered on the discovery and development of new metal-catalyzed organic reactions via reactive metal-organic intermediates. The major research findings that are described here include (1) propargyl-cobalt complexes as electrophilic agents for C-C and C-Nu coupling; (2) the activation of carbon dioxide by metal complexes; (3) metal-promoted C-H nitrogenation reactions; (4) oxo-metal catalyzed deoxygenation reactions; and (5) catalyst discovery via dynamic templating with substrate- and transition-state analogues.

Phase Transition in a Healthy Human Heart Rate

NASA Astrophysics Data System (ADS)

Kiyono, Ken; Struzik, Zbigniew R.; Aoyagi, Naoko; Togo, Fumiharu; Yamamoto, Yoshiharu

2005-07-01

A healthy human heart rate displays complex fluctuations which share characteristics of physical systems in a critical state. We demonstrate that the human heart rate in healthy individuals undergoes a dramatic breakdown of criticality characteristics, reminiscent of continuous second order phase transitions. By studying the germane determinants, we show that the hallmark of criticality—highly correlated fluctuations—is observed only during usual daily activity, and a breakdown of these characteristics occurs in prolonged, strenuous exercise and sleep. This finding is the first reported discovery of the dynamical phase transition phenomenon in a biological control system and will be a key to understanding the heart rate control system in health and disease.

Origin of Stereodivergence in Cooperative Asymmetric Catalysis with Simultaneous Involvement of Two Chiral Catalysts.

PubMed

Bhaskararao, Bangaru; Sunoj, Raghavan B

2015-12-23

Accomplishing high diastereo- and enantioselectivities simultaneously is a persistent challenge in asymmetric catalysis. The use of two chiral catalysts in one-pot conditions might offer new avenues to this end. Chirality transfer from a catalyst to product gets increasingly complex due to potential chiral match-mismatch issues. The origin of high enantio- and diastereoselectivities in the reaction between a racemic aldehyde and an allyl alcohol, catalyzed by using axially chiral iridium phosphoramidites PR/S-Ir and cinchona amine is established through transition-state modeling. The multipoint contact analysis of the stereocontrolling transition state revealed how the stereodivergence could be achieved by inverting the configuration of the chiral catalysts that are involved in the activation of the reacting partners. While the enantiocontrol is identified as being decided in the generation of PR/S-Ir-π-allyl intermediate from the allyl alcohol, the diastereocontrol arises due to the differential stabilizations in the C-C bond formation transition states. The analysis of the weak interactions in the transition states responsible for chiral induction revealed that the geometric disposition of the quinoline ring at the C8 chiral carbon of cinchona-enamine plays an anchoring role. The quinolone ring is noted as participating in a π-stacking interaction with the phenyl ring of the Ir-π-allyl moiety in the case of PR with the (8R,9R)-cinchona catalyst combination, whereas a series of C-H···π interactions is identified as vital to the relative stabilization of the stereocontrolling transition states when PR is used with (8S,9S)-cinchona.

Density function theoretical study on the complex involved in Th atom-activated C-C bond in C2H6

NASA Astrophysics Data System (ADS)

Qing-Qing, Wang; Peng, Li; Tao, Gao; Hong-Yan, Wang; Bing-Yun, Ao

2016-06-01

Density functional theory (DFT) calculations are performed to investigate the reactivity of Th atom toward ethane C-C bond activation. A comprehensive description of the reaction mechanisms leading to two different reaction products is presented. We report a complete exploration of the potential energy surfaces by taking into consideration different spin states. In addition, the intermediate and transition states along the reaction paths are characterized. Total, partial, and overlap population density of state diagrams and analyses are also presented. Furthermore, the natures of the chemical bonding of intermediate and transition states are studied by using topological method combined with electron localization function (ELF) and Mayer bond order. Infrared spectrum (IR) is obtained and further discussed based on the optimized geometries. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160, 21401173, and 11364023).

Establishing Dual Electrogenerated Chemiluminescence and Multi-Color Electrochromism in Functional Ionic Transition Metal Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puodziukynaite, Egle; Oberst, Justin L.; Dyer, Aubrey L.

A combination of electrochromism and electroluminescence in functional materials could lead to single-layer dual electrochromic/electroluminescent (EC/EL) display devices, capable of simultaneous operation in emissive and reflective modes. Whereas such next generation displays could provide optimal visibility in any ambient lighting situation, materials available that exhibit such characteristics in the active layer are limited due to the required intrinsic multifunctionality (i.e., redox activity, electroluminescence, electrochromism, and ion conductivity) and to date can only be achieved via the rational design of ionic transition-metal complexes. Reported herein is the synthesis and characterization of a new family of acrylate-containing ruthenium (tris)bipyridine-based coordination complexes withmore » multifunctional characteristics. Potential use of the presented compounds in EC/EL devices is established, as they are applied as cross-linked electrochromic films and electrochemiluminescent layers in light-emitting electrochemical cell devices. Electrochromic switching of the polymeric networks between yellow, orange, green, brown and transmissive states is demonstrated, and electrochemiluminescent devices based on the complexes synthesized show red-orange to deep red emission with λ{sub max} ranging from 680 to 722 nm and luminance up to 135 cd/m{sup 2}. Additionally, a dual EC/EL device prototype is presented where light emission and multicolor electrochromism occur from the same pixel comprised of a single active layer, demonstrating a true combination of these properties in ionic transition-metal complexes.« less

Establishing Dual Electrogenerated Chemiluminescence and Multicolor Electrochromism in Functional Ionic Transition-Metal Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puodziukynaite, Egle; Oberst, Justin L.; Dyer, Aubrey L.

A combination of electrochromism and electroluminescence in functional materials could lead to single-layer dual electrochromic/electroluminescent (EC/EL) display devices, capable of simultaneous operation in emissive and reflective modes. Whereas such next generation displays could provide optimal visibility in any ambient lighting situation, materials available that exhibit such characteristics in the active layer are limited due to the required intrinsic multifunctionality (i.e., redox activity, electroluminescence, electrochromism, and ion conductivity) and to date can only be achieved via the rational design of ionic transition-metal complexes. Reported herein is the synthesis and characterization of a new family of acrylate-containing ruthenium (tris)bipyridine-based coordination complexes withmore » multifunctional characteristics. Potential use of the presented compounds in EC/EL devices is established, as they are applied as cross-linked electrochromic films and electrochemiluminescent layers in light-emitting electrochemical cell devices. Electrochromic switching of the polymeric networks between yellow, orange, green, brown and transmissive states is demonstrated, and electrochemiluminescent devices based on the complexes synthesized show red-orange to deep red emission with λmax ranging from 680 to 722 nm and luminance up to 135 cd/m². Additionally, a dual EC/EL device prototype is presented where light emission and multicolor electrochromism occur from the same pixel comprised of a single active layer, demonstrating a true combination of these properties in ionic transition-metal complexes.« less

Identifying quantum phase transitions with adversarial neural networks

NASA Astrophysics Data System (ADS)

Huembeli, Patrick; Dauphin, Alexandre; Wittek, Peter

2018-04-01

The identification of phases of matter is a challenging task, especially in quantum mechanics, where the complexity of the ground state appears to grow exponentially with the size of the system. Traditionally, physicists have to identify the relevant order parameters for the classification of the different phases. We here follow a radically different approach: we address this problem with a state-of-the-art deep learning technique, adversarial domain adaptation. We derive the phase diagram of the whole parameter space starting from a fixed and known subspace using unsupervised learning. This method has the advantage that the input of the algorithm can be directly the ground state without any ad hoc feature engineering. Furthermore, the dimension of the parameter space is unrestricted. More specifically, the input data set contains both labeled and unlabeled data instances. The first kind is a system that admits an accurate analytical or numerical solution, and one can recover its phase diagram. The second type is the physical system with an unknown phase diagram. Adversarial domain adaptation uses both types of data to create invariant feature extracting layers in a deep learning architecture. Once these layers are trained, we can attach an unsupervised learner to the network to find phase transitions. We show the success of this technique by applying it on several paradigmatic models: the Ising model with different temperatures, the Bose-Hubbard model, and the Su-Schrieffer-Heeger model with disorder. The method finds unknown transitions successfully and predicts transition points in close agreement with standard methods. This study opens the door to the classification of physical systems where the phase boundaries are complex such as the many-body localization problem or the Bose glass phase.

Strain-induced topological transition in SrRu 2O 6 and CaOs 2O 6

DOE PAGES

Ochi, Masayuki; Arita, Ryotaro; Trivedi, Nandini; ...

2016-05-24

The topological property of SrRumore » $$_2$$O$$_6$$ and isostructural CaOs$$_2$$O$$_6$$ under various strain conditions is investigated using density functional theory. Based on an analysis of parity eigenvalues, we anticipate that a three-dimensional strong topological insulating state should be realized when band inversion is induced at the A point in the hexagonal Brillouin zone. For SrRu$$_2$$O$$_6$$, such a transition requires rather unrealistic tuning, where only the $c$ axis is reduced while other structural parameters are unchanged. However, given the larger spin-orbit coupling and smaller lattice constants in CaOs$$_2$$O$$_6$$, the desired topological transition does occur under uniform compressive strain. Our study paves a way to realize a topological insulating state in a complex oxide, which has not been experimentally demonstrated so far.« less

Three-state Potts model on non-local directed small-world lattices

NASA Astrophysics Data System (ADS)

Ferraz, Carlos Handrey Araujo; Lima, José Luiz Sousa

2017-10-01

In this paper, we study the non-local directed Small-World (NLDSW) disorder effects in the three-state Potts model as a form to capture the essential features shared by real complex systems where non-locality effects play a important role in the behavior of these systems. Using Monte Carlo techniques and finite-size scaling analysis, we estimate the infinite lattice critical temperatures and the leading critical exponents in this model. In particular, we investigate the first- to second-order phase transition crossover when NLDSW links are inserted. A cluster-flip algorithm was used to reduce the critical slowing down effect in our simulations. We find that for a NLDSW disorder densities p

Transition Characteristic Analysis of Traffic Evolution Process for Urban Traffic Network

PubMed Central

Chen, Hong; Li, Yang

2014-01-01

The characterization of the dynamics of traffic states remains fundamental to seeking for the solutions of diverse traffic problems. To gain more insights into traffic dynamics in the temporal domain, this paper explored temporal characteristics and distinct regularity in the traffic evolution process of urban traffic network. We defined traffic state pattern through clustering multidimensional traffic time series using self-organizing maps and construct a pattern transition network model that is appropriate for representing and analyzing the evolution progress. The methodology is illustrated by an application to data flow rate of multiple road sections from Network of Shenzhen's Nanshan District, China. Analysis and numerical results demonstrated that the methodology permits extracting many useful traffic transition characteristics including stability, preference, activity, and attractiveness. In addition, more information about the relationships between these characteristics was extracted, which should be helpful in understanding the complex behavior of the temporal evolution features of traffic patterns. PMID:24982969

Phase transitions in nanocomposites of hydrogen-bonded dimeric liquid crystals with mesogenic and non-mesogenic components

NASA Astrophysics Data System (ADS)

Katranchev, Boyko; Petrov, Minko

2016-02-01

Microtextural polarization, phase transitions, and electro-optical effects are studied in a series of nanocomposites, grown by mixing alkyloxybenzoic acids (nOBAs), displaying hydrogen-bonded dimeric liquid crystal (LC) state, with non-mesogens (single-walled carbon nanotubes (SWCNTs), perfluorooctanoic acid) or mesogens (bent-core LC compound D14F3). Each of the studied nanocomposites, in which the nOBA serves as a matrix, forms complexes with bent-shaped dimeric, caused by the interaction between the dopant structural units and the dimer rings. This feature, coordinated with the surface anchoring, bulk and electrical effects, leads to drastic reduction of the LC system symmetry. As a result, transitions from achiral (characteristic for the pristine nOBA) to chiral states (including ferroelectric smectic C with C2 symmetry and ferroelectric smectic CG with the lowest C1 triclinic one) take place. The functionalization of the SWCNTs causes drastic increase of the ferroelectricity.

Efficient Deterministic Finite Automata Minimization Based on Backward Depth Information.

PubMed

Liu, Desheng; Huang, Zhiping; Zhang, Yimeng; Guo, Xiaojun; Su, Shaojing

2016-01-01

Obtaining a minimal automaton is a fundamental issue in the theory and practical implementation of deterministic finite automatons (DFAs). A minimization algorithm is presented in this paper that consists of two main phases. In the first phase, the backward depth information is built, and the state set of the DFA is partitioned into many blocks. In the second phase, the state set is refined using a hash table. The minimization algorithm has a lower time complexity O(n) than a naive comparison of transitions O(n2). Few states need to be refined by the hash table, because most states have been partitioned by the backward depth information in the coarse partition. This method achieves greater generality than previous methods because building the backward depth information is independent of the topological complexity of the DFA. The proposed algorithm can be applied not only to the minimization of acyclic automata or simple cyclic automata, but also to automata with high topological complexity. Overall, the proposal has three advantages: lower time complexity, greater generality, and scalability. A comparison to Hopcroft's algorithm demonstrates experimentally that the algorithm runs faster than traditional algorithms.

The value of information for woodland management: Updating a state–transition model

USGS Publications Warehouse

Morris, William K.; Runge, Michael C.; Vesk, Peter A.

2017-01-01

Value of information (VOI) analyses reveal the expected benefit of reducing uncertainty to a decision maker. Most ecological VOI analyses have focused on population models rarely addressing more complex community models. We performed a VOI analysis for a complex state–transition model of Box-Ironbark Forest and Woodland management. With three management alternatives (limited harvest/firewood removal (HF), ecological thinning (ET), and no management), managing the system optimally (for 150 yr) with the original information would, on average, increase the amount of forest in a desirable state from 19% to 35% (a 16-percentage point increase). Resolving all uncertainty would, on average, increase the final percentage to 42% (a 19-percentage point increase). However, only resolving the uncertainty for a single parameter was worth almost two-thirds the value of resolving all uncertainty. We found the VOI to depend on the number of management options, increasing as the management flexibility increased. Our analyses show it is more cost-effective to monitor low-density regrowth forest than other states and more cost-effective to experiment with the no-management alternative than the other management alternatives. Importantly, the most cost-effective strategies did not include either the most desired forest states or the least understood management strategy, ET. This implies that managers cannot just rely on intuition to tell them where the most VOI will lie, as critical uncertainties in a complex system are sometimes cryptic.

Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation

PubMed Central

Ramrath, David J. F.; Lancaster, Laura; Sprink, Thiemo; Mielke, Thorsten; Loerke, Justus; Noller, Harry F.; Spahn, Christian M. T.

2013-01-01

During protein synthesis, coupled translocation of messenger RNAs (mRNA) and transfer RNAs (tRNA) through the ribosome takes place following formation of each peptide bond. The reaction is facilitated by large-scale conformational changes within the ribosomal complex and catalyzed by elongtion factor G (EF-G). Previous structural analysis of the interaction of EF-G with the ribosome used either model complexes containing no tRNA or only a single tRNA, or complexes where EF-G was directly bound to ribosomes in the posttranslocational state. Here, we present a multiparticle cryo-EM reconstruction of a translocation intermediate containing two tRNAs trapped in transit, bound in chimeric intrasubunit ap/P and pe/E hybrid states. The downstream ap/P-tRNA is contacted by domain IV of EF-G and P-site elements within the 30S subunit body, whereas the upstream pe/E-tRNA maintains tight interactions with P-site elements of the swiveled 30S head. Remarkably, a tight compaction of the tRNA pair can be seen in this state. The translocational intermediate presented here represents a previously missing link in understanding the mechanism of translocation, revealing that the ribosome uses two distinct molecular ratchets, involving both intra- and intersubunit rotational movements, to drive the synchronous movement of tRNAs and mRNA. PMID:24324168

trans-Methylpyridine cyclen versus cross-bridged trans-methylpyridine cyclen. Synthesis, acid-base and metal complexation studies (metal = Co2+, Cu2+, and Zn2+).

PubMed

Bernier, Nicolas; Costa, Judite; Delgado, Rita; Félix, Vítor; Royal, Guy; Tripier, Raphaël

2011-05-07

The synthesis of the cross-bridged cyclen CRpy(2) {4,10-bis((pyridin-2-yl)methyl)-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane}, a constrained analogue of the previously described trans-methylpyridine cyclen Cpy(2) is reported. The additional ethylene bridge confers to CRpy(2) proton-sponge type behaviour which was explored by NMR and potentiometric studies. Transition metal complexes have been synthesized (by complexation of both ligands with Co(2+), Cu(2+) and Zn(2+)) and characterized in solution and in the solid state. The single crystal X-ray structures of [CoCpy(2)](2+), [CuCpy(2)](2+) and [ZnCpy(2)](2+) complexes were determined. Stability constants of the complexes, including those of the cross-bridged derivative, were determined using potentiometric titration data and the kinetic inertness of the [CuCRpy(2)](2+) complex in an acidic medium (half-life values) was evaluated by spectrophotometry. The pre-organized structure of the cross-bridged ligand imposes an additional strain for the complexation leading to complexes with smaller thermodynamic stability in comparison with the related non-bridged ligand. The electrochemical study involving cyclic voltammetry underlines the importance of the ethylene cross-bridge on the redox properties of the transition metal complexes.

Resilience and tipping points of an exploited fish population over six decades.

PubMed

Vasilakopoulos, Paraskevas; Marshall, C Tara

2015-05-01

Complex natural systems with eroded resilience, such as populations, ecosystems and socio-ecological systems, respond to small perturbations with abrupt, discontinuous state shifts, or critical transitions. Theory of critical transitions suggests that such systems exhibit fold bifurcations featuring folded response curves, tipping points and alternate attractors. However, there is little empirical evidence of fold bifurcations occurring in actual complex natural systems impacted by multiple stressors. Moreover, resilience of complex systems to change currently lacks clear operational measures with generic application. Here, we provide empirical evidence for the occurrence of a fold bifurcation in an exploited fish population and introduce a generic measure of ecological resilience based on the observed fold bifurcation attributes. We analyse the multivariate development of Barents Sea cod (Gadus morhua), which is currently the world's largest cod stock, over six decades (1949-2009), and identify a population state shift in 1981. By plotting a multivariate population index against a multivariate stressor index, the shift mechanism was revealed suggesting that the observed population shift was a nonlinear response to the combined effects of overfishing and climate change. Annual resilience values were estimated based on the position of each year in relation to the fitted attractors and assumed tipping points of the fold bifurcation. By interpolating the annual resilience values, a folded stability landscape was fit, which was shaped as predicted by theory. The resilience assessment suggested that the population may be close to another tipping point. This study illustrates how a multivariate analysis, supported by theory of critical transitions and accompanied by a quantitative resilience assessment, can clarify shift mechanisms in data-rich complex natural systems. © 2014 John Wiley & Sons Ltd.

Electronic Excited States of Tungsten(0) Arylisocyanides.

PubMed

Kvapilová, Hana; Sattler, Wesley; Sattler, Aaron; Sazanovich, Igor V; Clark, Ian P; Towrie, Michael; Gray, Harry B; Záliš, Stanislav; Vlček, Antonín

2015-09-08

W(CNAryl)6 complexes containing 2,6-diisopropylphenyl isocyanide (CNdipp) are powerful photoreductants with strongly emissive long-lived excited states. These properties are enhanced upon appending another aryl ring, e.g., W(CNdippPh(OMe2))6; CNdippPh(OMe2) = 4-(3,5-dimethoxyphenyl)-2,6-diisopropylphenylisocyanide (Sattler et al. J. Am. Chem. Soc. 2015, 137, 1198-1205). Electronic transitions and low-lying excited states of these complexes were investigated by time-dependent density functional theory (TDDFT); the lowest triplet state was characterized by time-resolved infrared spectroscopy (TRIR) supported by density functional theory (DFT). The intense absorption band of W(CNdipp)6 at 460 nm and that of W(CNdippPh(OMe2))6 at 500 nm originate from transitions of mixed ππ*(C≡N-C)/MLCT(W → Aryl) character, whereby W is depopulated by ca. 0.4 e(-) and the electron-density changes are predominantly localized along two equatorial molecular axes. The red shift and intensity rise on going from W(CNdipp)6 to W(CNdippPh(OMe2))6 are attributable to more extensive delocalization of the MLCT component. The complexes also exhibit absorptions in the 300-320 nm region, owing to W → C≡N MLCT transitions. Electronic absorptions in the spectrum of W(CNXy)6 (Xy = 2,6-dimethylphenyl), a complex with orthogonal aryl orientation, have similar characteristics, although shifted to higher energies. The relaxed lowest W(CNAryl)6 triplet state combines ππ* excitation of a trans pair of C≡N-C moieties with MLCT (0.21 e(-)) and ligand-to-ligand charge transfer (LLCT, 0.24-0.27 e(-)) from the other four CNAryl ligands to the axial aryl and, less, to C≡N groups; the spin density is localized along a single Aryl-N≡C-W-C≡N-Aryl axis. Delocalization of excited electron density on outer aryl rings in W(CNdippPh(OMe2))6 likely promotes photoinduced electron-transfer reactions to acceptor molecules. TRIR spectra show an intense broad bleach due to ν(C≡N), a prominent transient upshifted by 60-65 cm(-1), and a weak down-shifted feature due to antisymmetric C≡N stretch along the axis of high spin density. The TRIR spectral pattern remains unchanged on the femtosecond-nanosecond time scale, indicating that intersystem crossing and electron-density localization are ultrafast (<100 fs).

Infrared and Microwave Spectra of Ne-WATER Complex

NASA Astrophysics Data System (ADS)

Liu, Xunchen; Thomas, Javix; Xu, Yunjie; Hou, Dan; Li, Hui

2016-06-01

The binary complex of rare gas atom and water is an ideal model to study the anisotropic potential energy surface of van der Waals interaction and the large amplitude motion. Although Xe-H_2O, Kr-H_2O, Ar-H_2O, Ar-D_2O and even Ne-D_2O complexes were studied by microwave or high resolution infrared spectroscopy, the lighter Ne-H_2O complex has remained unidentified. In this talk, we will present the theoretical and experimental investigation of the Ne-H_2O complex. A four-dimension PES for H_2O-Ne which only depended on the intramolecular (Q2) normal-mode coordinate of H2O monomer was calculated in this work to determine the rovibrational energy levels and mid-infrared transitions. Aided with the calculated transitions, we were able to assigned the high resolution mid-infrared spectra of both 20Ne-H_2O and 22Ne-H_2O complexes that are generated with a pulsed supersonic molecular beam in a multipass direct absorption spectrometer equiped with an external cavity quantum cascade laser at 6 μm. Several bands of both para and ortho Ne-H2O were assigned and fitted using the Hamiltonian with strong Coriolis and angular-radical coupling terms. The predicted groud state energy levels are then confirmed by the J=1-0 and J=2-1 transitions measurement using a cavity based Fourier transform microwave spectrometer.

First-principles characterization of native-defect-related optical transitions in ZnO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyons, J. L.; Varley, J. B.; Steiauf, D.

We investigate the electrical and optical properties of oxygen vacancies (VO), zinc vacancies (V Zn), hydrogenated V Zn, and isolated dangling bonds in ZnO using hybrid functional calculations. While the formation energy of V O is high in n-type ZnO, indicating that this center is unlikely to form, our results for optical absorption signals associated with V O are consistent with those observed in irradiated samples, and give rise to emission with a peak at less than 1 eV. Under realistic growth conditions, we find that VZn is the lowest-energy native defect in n-type ZnO, acting as an acceptor thatmore » is likely to compensate donor doping. Turning to optical transitions, we first examine N O as a case study, since N-related transitions have been identified in experiments on ZnO. Here, we also examine how hydrogen, often unintentionally present in ZnO, forms stable complexes with V Zn and modifies its optical properties. Compared with isolated V Zn, V Zn-H complexes have charge-state transition levels lower in the band gap as well as have lower formation energies. These complexes also lead to characteristic vibrational frequencies which compare favorably with experiment. Oxygen dangling bonds show behavior mostly consistent with V Zn, while zinc dangling bonds give rise to transition levels near the ZnO conduction-band minimum and emission peaking near 2.4 eV. Lastly, we discuss our results in view of the available experimental literature.« less

First-principles characterization of native-defect-related optical transitions in ZnO

DOE PAGES

Lyons, J. L.; Varley, J. B.; Steiauf, D.; ...

2017-07-21

We investigate the electrical and optical properties of oxygen vacancies (VO), zinc vacancies (V Zn), hydrogenated V Zn, and isolated dangling bonds in ZnO using hybrid functional calculations. While the formation energy of V O is high in n-type ZnO, indicating that this center is unlikely to form, our results for optical absorption signals associated with V O are consistent with those observed in irradiated samples, and give rise to emission with a peak at less than 1 eV. Under realistic growth conditions, we find that VZn is the lowest-energy native defect in n-type ZnO, acting as an acceptor thatmore » is likely to compensate donor doping. Turning to optical transitions, we first examine N O as a case study, since N-related transitions have been identified in experiments on ZnO. Here, we also examine how hydrogen, often unintentionally present in ZnO, forms stable complexes with V Zn and modifies its optical properties. Compared with isolated V Zn, V Zn-H complexes have charge-state transition levels lower in the band gap as well as have lower formation energies. These complexes also lead to characteristic vibrational frequencies which compare favorably with experiment. Oxygen dangling bonds show behavior mostly consistent with V Zn, while zinc dangling bonds give rise to transition levels near the ZnO conduction-band minimum and emission peaking near 2.4 eV. Lastly, we discuss our results in view of the available experimental literature.« less

Convergence of Transition Probability Matrix in CLVMarkov Models

NASA Astrophysics Data System (ADS)

Permana, D.; Pasaribu, U. S.; Indratno, S. W.; Suprayogi, S.

2018-04-01

A transition probability matrix is an arrangement of transition probability from one states to another in a Markov chain model (MCM). One of interesting study on the MCM is its behavior for a long time in the future. The behavior is derived from one property of transition probabilty matrix for n steps. This term is called the convergence of the n-step transition matrix for n move to infinity. Mathematically, the convergence of the transition probability matrix is finding the limit of the transition matrix which is powered by n where n moves to infinity. The convergence form of the transition probability matrix is very interesting as it will bring the matrix to its stationary form. This form is useful for predicting the probability of transitions between states in the future. The method usually used to find the convergence of transition probability matrix is through the process of limiting the distribution. In this paper, the convergence of the transition probability matrix is searched using a simple concept of linear algebra that is by diagonalizing the matrix.This method has a higher level of complexity because it has to perform the process of diagonalization in its matrix. But this way has the advantage of obtaining a common form of power n of the transition probability matrix. This form is useful to see transition matrix before stationary. For example cases are taken from CLV model using MCM called Model of CLV-Markov. There are several models taken by its transition probability matrix to find its convergence form. The result is that the convergence of the matrix of transition probability through diagonalization has similarity with convergence with commonly used distribution of probability limiting method.

Early warning signals for critical transitions in a thermoacoustic system

PubMed Central

Gopalakrishnan, E. A.; Sharma, Yogita; John, Tony; Dutta, Partha Sharathi; Sujith, R. I.

2016-01-01

Dynamical systems can undergo critical transitions where the system suddenly shifts from one stable state to another at a critical threshold called the tipping point. The decrease in recovery rate to equilibrium (critical slowing down) as the system approaches the tipping point can be used to identify the proximity to a critical transition. Several measures have been adopted to provide early indications of critical transitions that happen in a variety of complex systems. In this study, we use early warning indicators to predict subcritical Hopf bifurcation occurring in a thermoacoustic system by analyzing the observables from experiments and from a theoretical model. We find that the early warning measures perform as robust indicators in the presence and absence of external noise. Thus, we illustrate the applicability of these indicators in an engineering system depicting critical transitions. PMID:27767065

Critical Behaviors in Contagion Dynamics.

PubMed

Böttcher, L; Nagler, J; Herrmann, H J

2017-02-24

We study the critical behavior of a general contagion model where nodes are either active (e.g., with opinion A, or functioning) or inactive (e.g., with opinion B, or damaged). The transitions between these two states are determined by (i) spontaneous transitions independent of the neighborhood, (ii) transitions induced by neighboring nodes, and (iii) spontaneous reverse transitions. The resulting dynamics is extremely rich including limit cycles and random phase switching. We derive a unifying mean-field theory. Specifically, we analytically show that the critical behavior of systems whose dynamics is governed by processes (i)-(iii) can only exhibit three distinct regimes: (a) uncorrelated spontaneous transition dynamics, (b) contact process dynamics, and (c) cusp catastrophes. This ends a long-standing debate on the universality classes of complex contagion dynamics in mean field and substantially deepens its mathematical understanding.

Evidence for changes in the nucleotide conformation in the active site of H(+)-ATPase as determined by pulsed EPR spectroscopy.

PubMed

Schneider, B; Sigalat, C; Amano, T; Zimmermann, J L

2000-12-19

The conformation of di- and triphosphate nucleosides in the active site of ATPsynthase (H(+)-ATPase) from thermophilic Bacillus PS3 (TF1) and their interaction with Mg(2+)/Mn(2+) cations have been investigated using EPR, ESEEM, and HYSCORE spectroscopies. For a ternary complex formed by a stoichiometric mixture of TF1, Mn(2+), and ADP, the ESEEM and HYSCORE data reveal a (31)P hyperfine interaction with Mn(2+) (|A((31)P)| approximately 5.20 MHz), significantly larger than that measured for the complex formed by Mn(2+) and ADP in solution (|A((31)P)| approximately 4.50 MHz). The Q-band EPR spectrum of the Mn.TF1.ADP complex indicates that the Mn(2+) binds in a slightly distorted environment with |D| approximately 180 x 10(-4) cm(-1) and |E| approximately 50 x 10(-4) cm(-1). The increased hyperfine coupling with (31)P in the presence of TF1 reflects the specific interaction between the central Mn(2+) and the ADP beta-phosphate, illustrating the role of the enzyme active site in positioning the phosphate chain of the substrate for efficient catalysis. Results with the ternary Mn.TF1.ATP and Mn.TF1.AMP-PNP complexes are interpreted in a similar way with two hyperfine couplings being resolved for each complex (|A((31)P(beta))| approximately 4.60 MHz and |A((31)P(gamma))| approximately 5.90 MHz with ATP, and |A((31)P(beta))| approximately 4.20 MHz and |A((31)P(gamma))| approximately 5.40 MHz with AMP-PNP). In these complexes, the increased hyperfine coupling with (31)P(gamma) compared with (31)P(beta) reflects the smaller Mn.P distance with the gamma-phosphate compared with the beta-phosphate as found in the crystal structure of the analogous enzyme from mitochondria [3.53 vs 3.70 A (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628)] and the different binding modes of the two phosphate groups. The ESEEM and HYSCORE data of a complex formed with Mn(2+), ATP, and the isolated beta subunit show that the (31)P hyperfine coupling is close to that measured in the absence of the protein, indicating a poorly structured nucleotide site in the isolated beta subunit in the presence of ATP. The inhibition data obtained for TF1 incubated in the presence of Mg(2+), ADP, Al(NO(3))(3), and NaF indicate the formation of the inhibited complex with the transition state analogue namely Mg.TF1.ADP.AlF(x) with the equilibrium dissociation constant K(D) = 350 microM and rate constant k = 0.02 min(-1). The ESEEM and HYSCORE data obtained for an inhibited TF1 sample, Mn.TF1.ADP.AlF(x), confirm the formation of the transition state analogue with distinct spectroscopic footprints that can be assigned to Mn.(19)F and Mn.(27)Al hyperfine interactions. The (31)P(beta) hyperfine coupling that is measured in the inhibited complex with the transition state analogue (|A((31)P(beta))| approximately 5.10 MHz) is intermediate between those measured in the presence of ADP and ATP and suggests an increase in the bond between Mn and the P(beta) from ADP upon formation of the transition state.

Bifurcation Phenomena of Opinion Dynamics in Complex Networks

NASA Astrophysics Data System (ADS)

Guo, Long; Cai, Xu

In this paper, we study the opinion dynamics of Improved Deffuant model (IDM), where the convergence parameter μ is a function of the opposite’s degree K according to the celebrity effect, in small-world network (SWN) and scale-free network (SFN). Generically, the system undergoes a phase transition from the plurality state to the polarization state and to the consensus state as the confidence parameter ɛ increasing. Furthermore, the evolution of the steady opinion s * as a function of ɛ, and the relation between the minority steady opinion s_{*}^{min} and the individual connectivity k also have been analyzed. Our present work shows the crucial role of the confidence parameter and the complex system topology in the opinion dynamics of IDM.

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding

PubMed Central

Tischer, Alexander; Auton, Matthew

2013-01-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497

Structural evaluation of crystalline ternary γ-cyclodextrin complex.

PubMed

Higashi, Kenjirou; Ideura, Saori; Waraya, Haruka; Moribe, Kunikazu; Yamamoto, Keiji

2011-01-01

The structure of a crystalline γ-cyclodextrin (γ-CD) ternary complex containing salicylic acid (SA) and flurbiprofen (FBP) prepared by sealed heating was investigated. FBP/γ-CD inclusion complex was prepared by coprecipitation; its molar ratio was determined as 1/1. Powder X-ray diffraction measurements showed that the molecular packing of γ-CD changed from hexagonal to monoclinic columnar form by sealed heating of SA with dried FBP/γ-CD inclusion complex, indicating ternary complex formation. The stoichiometry of SA/FBP/γ-CD was estimated as 2/1/1. Solid-state transformation of γ-CD molecular packing upon water vapor adsorption and desorption was irreversible for this ternary complex, in contrast to the reversible transition for the FBP/γ-CD inclusion complex. The ternary complex contained one FBP molecule in the cavity of γ-CD and two SA molecules in the intermolecular space between neighboring γ-CD column stacks. Infrared and (13) C solid-state NMR spectroscopies revealed that the molecular states of SA and FBP changed upon ternary complex formation. In the complex, dimer FBP molecules were sandwiched between two γ-CD molecules whereas each monomer SA molecule was present in the intermolecular space of γ-CD. Ternary complex formation was also observed for other drug-guest systems using naproxen and ketoprofen. Thus, the complex can be used to formulate variety of drugs. Copyright © 2010 Wiley-Liss, Inc. and the American Pharmacists Association

A theoretical study of the dynamic behavior of alkane hydroxylation by a compound I model of cytochrome P450.

PubMed

Yoshizawa, K; Kamachi, T; Shiota, Y

2001-10-10

Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory. The nuclei of the reacting system are propagated from a transition state to a reactant or product direction according to classical dynamics on a Born-Oppenheimer potential energy surface. Geometric and energetic changes in both low-spin doublet and high-spin quartet states are followed along the ethane to ethanol reaction pathway, which is partitioned into two chemical steps: the first is the H-atom abstraction from ethane by the iron-oxo species of Compound I and the second is the rebound step in which the resultant iron-hydroxo complex and the ethyl radical intermediate react to form the ethanol complex. Molecular vibrations of the C-H bond being dissociated and the O-H bond being formed are significantly activated before and after the transition state, respectively, in the H-atom abstraction. The principal reaction coordinate that can represent the first chemical step is the C-H distance or the O-H distance while other geometric parameters remain almost unchanged. The rebound process begins with the iron-hydroxo complex and the ethyl radical intermediate and ends with the formation of the ethanol complex, the essential process in this reaction being the formation of the C-O bond. The H-O-Fe-C dihedral angle corresponds to the principal reaction coordinate for the rebound step. When sufficient kinetic energy is supplied to this rotational mode, the rebound process should efficiently take place. Trajectory calculations suggest that about 200 fs is required for the rebound process under specific initial conditions, in which a small amount of kinetic energy (0.1 kcal/mol) is supplied to the transition state exactly along the reaction coordinate. An important issue about which normal mode of vibration is activated during the hydroxylation reaction is investigated in detail from trajectory calculations. A large part of the kinetic energy is distributed to the C-H and O-H stretching modes before and after the transition state for the H-atom abstraction, respectively, and a small part of the kinetic energy is distributed to the Fe-O and Fe-S stretching modes and some characteristic modes of the porphyrin ring. The porphyrin marker modes of nu(3) and nu(4) that explicitly involve Fe-N stretching motion are effectively enhanced in the hydroxylation reaction. These vibrational modes of the porphyrin ring can play an important role in the energy transfer during the enzymatic process.

Effective on-site Coulomb interaction and electron configurations in transition-metal complexes from constraint density functional theory

NASA Astrophysics Data System (ADS)

Nawa, Kenji; Nakamura, Kohji; Akiyama, Toru; Ito, Tomonori; Weinert, Michael

Effective on-site Coulomb interactions (Ueff) and electron configurations in the localized d and f orbitals of metal complexes in transition-metal oxides and organometallic molecules, play a key role in the first-principles search for the true ground-state. However, wide ranges of values in the Ueff parameter of a material, even in the same ionic state, are often reported. Here, we revisit this issue from constraint density functional theory (DFT) by using the full-potential linearized augmented plane wave method. The Ueff parameters for prototypical transition-metal oxides, TMO (TM =Mn, Fe, Co, Ni), were calculated by the second derivative of the total energy functional with respect to the d occupation numbers inside the muffin-tin (MT) spheres as a function of the sphere radius. We find that the calculated Ueff values depend significantly on the MT radius, with a variation of more than 3 eV when the MT radius changes from 2.0 to 2.7 a.u., but importantly an identical valence band structure can be produced in all the cases, with an approximate scaling of Ueff. This indicates that a simple transferability of the Ueff value among different calculation methods is not allowed. We further extend the constraint DFT to treat various electron configurations of the localized d-orbitals in organometallic molecules, TMCp2 (TM =Cr, Mn, Fe, Co, Ni), and find that the calculated Ueff values can reproduce the experimentally determined ground-state electron configurations.

Synthesis, Structure, and Conformational Dynamics of Rhodium and Iridium Complexes of Dimethylbis(2-pyridyl)borate.

PubMed

Pennington-Boggio, Megan K; Conley, Brian L; Richmond, Michael G; Williams, Travis J

2014-12-14

Rhodium(I) and Iridium(I) borate complexes of the structure [Me 2 B(2-py) 2 ]ML 2 (L 2 = (tBuNC) 2 , (CO) 2 , (C 2 H 4 ) 2 , cod, dppe) were prepared and structurally characterized (cod = 1,5-cyclooctadiene; dppe = 1,2-diphenylphosphinoethane). Each contains a boat-configured chelate ring that participates in a boat-to-boat ring flip. Computational evidence shows that the ring flip proceeds through a transition state that is near planarity about the chelate ring. We observe an empirical, quantitative correlation between the barrier of this ring flip and the π acceptor ability of the ancillary ligand groups on the metal. The ring flip barrier correlates weakly to the Tolman and Lever ligand parameterization schemes, apparently because these combine both σ and π effects while we propose that the ring flip barrier is dominated by π bonding. This observation is consistent with metal-ligand π interactions becoming temporarily available only in the near-planar transition state of the chelate ring flip and not the boat-configured ground state. Thus, this is a first-of-class observation of metal-ligand π bonding governing conformational dynamics.

Synthesis, Structure, and Conformational Dynamics of Rhodium and Iridium Complexes of Dimethylbis(2-pyridyl)borate†

PubMed Central

Pennington-Boggio, Megan K.; Conley, Brian L.; Richmond, Michael G.; Williams, Travis J.

2014-01-01

Rhodium(I) and Iridium(I) borate complexes of the structure [Me2B(2-py)2]ML2 (L2 = (tBuNC)2, (CO)2, (C2H4)2, cod, dppe) were prepared and structurally characterized (cod = 1,5-cyclooctadiene; dppe = 1,2-diphenylphosphinoethane). Each contains a boat-configured chelate ring that participates in a boat-to-boat ring flip. Computational evidence shows that the ring flip proceeds through a transition state that is near planarity about the chelate ring. We observe an empirical, quantitative correlation between the barrier of this ring flip and the π acceptor ability of the ancillary ligand groups on the metal. The ring flip barrier correlates weakly to the Tolman and Lever ligand parameterization schemes, apparently because these combine both σ and π effects while we propose that the ring flip barrier is dominated by π bonding. This observation is consistent with metal-ligand π interactions becoming temporarily available only in the near-planar transition state of the chelate ring flip and not the boat-configured ground state. Thus, this is a first-of-class observation of metal-ligand π bonding governing conformational dynamics. PMID:25435645

Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation.

PubMed

Jamshidi, Shirin; Jalili, Seifollah; Rafii-Tabar, Hashem

2015-01-01

Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.

Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline.

PubMed

Jarzembska, Katarzyna N; Kamiński, Radosław; Durka, Krzysztof; Woźniak, Krzysztof

2018-05-10

This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å -1 ) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.

Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.

PubMed

Karain, Wael I

2017-11-28

Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis. We start from the assumption that a protein has a "baseline" recurrence structure over a given period of time. Any statistically significant deviation from this recurrence structure, as inferred from complexity measures provided by recurrence quantification analysis, is considered a transition in the dynamics of the protein. We apply this technique to a 132 ns long molecular dynamics simulation of the β-Lactamase Inhibitory Protein BLIP. We are able to detect conformational transitions in the nanosecond range in the recurrence dynamics of the BLIP protein during the simulation. The results compare favorably to those extracted using the principal component analysis technique. The recurrence quantification analysis based bootstrap technique is able to detect transitions between different dynamics states for a protein over different time scales. It is not limited to linear dynamics regimes, and can be generalized to any time scale. It also has the potential to be used to cluster frames in molecular dynamics trajectories according to the nature of their recurrence dynamics. One shortcoming for this method is the need to have large enough time windows to insure good statistical quality for the recurrence complexity measures needed to detect the transitions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stein, R.L.

A procedure for the analysis of observed isotope effects on rates of complex reactions is outlined which can be applied to kinetic isotope effect data for any reaction having a virtual transition state whose structure can be varied by adjusting a reaction parameter. This procedure is applied to the basic hydrolysis of p-nitroacetanilide. 3 tables. (DLC)

The behavior of exciplex decay processes and interplay of radiationless transition and preliminary reorganization mechanisms of electron transfer in loose and tight pairs of reactants.

PubMed

Kuzmin, Michael G; Soboleva, Irina V; Dolotova, Elena V

2007-01-18

Exciplex emission spectra and rate constants of their decay via internal conversion and intersystem crossing are studied and discussed in terms of conventional radiationless transition approach. Exciplexes of 9-cyanophenanthrene with 1,2,3-trimethoxybenzene and 1,3,5-trimethoxybenzene were studied in heptane, toluene, butyl acetate, dichloromethane, butyronitrile, and acetonitrile. A better description of spectra and rate constants is obtained using 0-0 transition energy and Gauss broadening of vibrational bands rather than the free energy of electron transfer and reorganization energy. The coincidence of parameters describing exciplex emission spectra and dependence of exciplex decay rate constants on energy gap gives the evidence of radiationless quantum transition mechanism rather than thermally activated medium reorganization mechanism of charge recombination in exciplexes and excited charge transfer complexes (contact radical ion pairs) as well as in solvent separated radical ion pairs. Radiationless quantum transition mechanism is shown to provide an appropriate description also for the main features of exergonic excited-state charge separation reactions if fast mutual transformations of loose and tight pairs of reactants are considered. In particular, very fast electron transfer (ET) in tight pairs of reactants with strong electronic coupling of locally excited and charge transfer states can prevent the observation of an inverted region in bimolecular excited-state charge separation even for highly exergonic reactions.

Microwave Spectrum and Structure of the Methane-Propane Complex

NASA Astrophysics Data System (ADS)

Peterson, Karen I.; Lin, Wei; Arsenault, Eric A.; Choi, Yoon Jeong; Novick, Stewart E.

2017-06-01

Methane is exceptional in its solid-phase orientational disorder that persists down to 24 K. Only below that temperature does the structure become partially ordered, and full crystallinity requires even lower temperatures and high pressures. Not surprisingly, methane appears to freely rotate in most van der Waals complexes, although two notable exceptions are CH_4-HF and CH_4-C_5H_5N. Of interest to us is how alkane interactions affect the methane rotation. Except for CH_4-CH_4, rotationally-resolved spectra of alkane-alkane complexes have not been studied. To fill this void, we present the microwave spectrum of CH_4-C_3H_8 which is the smallest alkane complex with a practical dipole moment. The microwave spectrum of CH_4-C_3H_8 was measured using the Fourier Transform microwave spectrometer at Wesleyan University. In the region between 7100 and 25300 MHz, we observed approximately 70 transitions that could plausibly be attributed to the CH_4-C_3H_8 complex (requiring high power and the proper mixture of gases). Of these, 16 were assigned to the A-state (lowest internal rotor state of methane) and four to the F-state. The A-state transitions were fitted with a Watson Hamiltonian using nine spectroscopic constants of which A = 7553.8144(97) MHz, B = 2483.9183(35) MHz, and C = 2041.8630(21) MHz. The A rotational constant is only 1.5 MHz higher than that of Ar-C_3H_8 and, since the a-axis of the complex passes approximately through the centers of mass of the subunits, this indicates a similar relative orientation. Thus, we find that the CH_4 is located above the plane of the propane. The center-of-mass separation of the subunits in CH_4-C_3H_8 is calculated to be 3.993 Å, 0.16 Å longer than the Ar-C_3H_8 distance of 3.825 Å, a reasonable difference considering the larger van der Waals radius of CH_4. The four F-state lines, which were about twice as strong as the A-state lines, could be fitted to A, B, and C rotational constants, and further analysis is in progress.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gendron, Frederic; Fleischauer, Valerie R.; Duignan, Thomas J.

Here, we present a combined ab initio theoretical and experimental study of the magnetic circular dichroism (MCD) spectrum of the octahedral UCl 6- complex ion in the UV-Vis spectral region. The ground state is an orbitally non-degenerate doublet E 5/2u and the MCD is a $C$-term spectrum caused by spin–orbit coupling. Calculations of the electronic spectrum at various levels of theory indicate that differential dynamic electron correlation has a strong influence on the energies of the dipole-allowed transitions and the envelope of the MCD spectrum. The experimentally observed bands are assigned to dipole-allowed ligand-to-metal charge transfer into the 5f shell,more » and 5f to 6d transitions. Charge transfer excitations into the U 6d shell appear at much higher energies. The MCD-allowed transitions can be assigned via their signs of the $C$-terms: Under O h double group symmetry, E 5/2u → E 5/2g transitions have negative $C$-terms whereas E 5/2u → F 3/2g transitions have positive $C$-terms if the ground state g-factor is negative, as it is the case for UCl 6-.« less

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

PubMed Central

Kurkcuoglu, Zeynep; Doruker, Pemra

2016-01-01

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

How Accurate Are Transition States from Simulations of Enzymatic Reactions?

PubMed Central

2015-01-01

The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics. PMID:24860275

Order parameter aided efficient phase space exploration under extreme conditions

NASA Astrophysics Data System (ADS)

Samanta, Amit

Physical processes in nature exhibit disparate time-scales, for example time scales associated with processes like phase transitions, various manifestations of creep, sintering of particles etc. are often much higher than time the system spends in the metastable states. The transition times associated with such events are also orders of magnitude higher than time-scales associated with vibration of atoms. Thus, an atomistic simulation of such transition events is a challenging task. Consequently, efficient exploration of configuration space and identification of metastable structures in condensed phase systems is challenging. In this talk I will illustrate how we can define a set of coarse-grained variables or order parameters and use these to systematically and efficiently steer a system containing thousands or millions of atoms over different parts of the configuration. This order parameter aided sampling can be used to identify metastable states, transition pathways and understand the mechanistic details of complex transition processes. I will illustrate how this sampling scheme can be used to study phase transition pathways and phase boundaries in prototypical materials, like SiO2 and Cu under high-pressure conditions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Identifying States of a Financial Market

NASA Astrophysics Data System (ADS)

Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

2012-09-01

The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical ``market states''. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

Identifying states of a financial market.

PubMed

Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

2012-01-01

The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

Ab initio calculations of supramolecular complexes of fullerene C60 with CdTe and CdS

NASA Astrophysics Data System (ADS)

Kvyatkovskii, O. E.; Zakharova, I. B.; Ziminov, V. M.

2014-06-01

This paper presents the results of ab initio quantum-chemical calculations of supramolecular complexes C60CdHal, [C60]4CdHal, and [C60]6CdHal (Hal = S, Te), which simulate the defects forming in fullerite during the absorption or adsorption of cadmium telluride (sulfide). Calculations of the electronic structure of complexes with inclusion of their relaxation to the equilibrium state have been performed in terms of the density functional theory with the B3LYP hybrid functional. The obtained enthalpies of formation of complexes show that their formation leads to the energy gain of the order of 0.5-1.5 eV depending on the complex type. It has been shown that the formation of tetrahedral complexes [C60]4CdTe with the intercalated CdTe molecule is possible only with a considerable distortion of the tetrahedral void. The energy spectrum of low-lying excited electron states for the linear and octahedral complexes has been calculated. It has been found that a decrease in symmetry with the formation of complexes leads to the appearance of excited states of allowed singlet transitions in the electron spectrum, which are forbidden in optical spectra of initial components.

Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches

NASA Astrophysics Data System (ADS)

Ramírez-Solís, A.; Poteau, R.; Vela, A.; Daudey, J. P.

2005-04-01

The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Instability and Death of Spiral Wave in a Two-Dimensional Array of Hindmarsh-Rose Neurons

NASA Astrophysics Data System (ADS)

Wang, Chun-Ni; Ma, Jun; Tang, Jun; Li, Yan-Long

2010-02-01

Spiral wave could be observed in the excitable media, the neurons are often excitable within appropriate parameters. The appearance and formation of spiral wave in the cardiac tissue is linked to monomorphic ventricular tachycardia that can denervate into polymorphic tachycardia and ventricular fibrillation. The neuronal system often consists of a large number of neurons with complex connections. In this paper, we theoretically study the transition from spiral wave to spiral turbulence and homogeneous state (death of spiral wave) in two-dimensional array of the Hindmarsh-Rose neuron with completely nearest-neighbor connections. In our numerical studies, a stable rotating spiral wave is developed and selected as the initial state, then the bifurcation parameters are changed to different values to observe the transition from spiral wave to homogeneous state, breakup of spiral wave and weak change of spiral wave, respectively. A statistical factor of synchronization is defined with the mean field theory to analyze the transition from spiral wave to other spatial states, and the snapshots of the membrane potentials of all neurons and time series of mean membrane potentials of all neurons are also plotted to discuss the change of spiral wave. It is found that the sharp changing points in the curve for factor of synchronization vs. bifurcation parameter indicate sudden transition from spiral wave to other states. And the results are independent of the number of neurons we used.

Aging, memory, and nonhierarchical energy landscape of spin jam

NASA Astrophysics Data System (ADS)

Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

2016-10-01

The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes.

Synthesis and CV Studies of Dithiol-terminated Metal Terpyridine Complexes

NASA Technical Reports Server (NTRS)

Asano, Sylvia; Fan, Wendy; Ng, Hou-Tee; Han, Jie; Meyyappan, M.

2003-01-01

Transition metal coordination complexes possess unique electronic structures that should be a good model for studying electronic transport behavior at a molecular level. The discrete, multiple redox states, low redox potential and the superb ability to establish contact with other molecular and electronic components by coordination chemistry have made this a subject of investigation for their possible application as active electronic components in molecular devices. We present the synthesis and electrochemical characterization of 4'-thioacetylphenyl-2'2:6',2"-terpyridine iron(II) complex and compare it with a model bis-terpyridine iron(II) complex by cyclic voltammetry. With the use of different working electrodes, the behavior of these complexes show different electron transfer rates.

The Correlation Entropy as a Measure of the Complexity of High-Lying Single-Particle Modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoyanov, Chavdar; Zelevinsky, Vladimir; Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824-1321

Highly-excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phonon-like modes of the core. In the framework of the quasiparticle-phonon model we consider the structure of resulting complex configurations using the 1k17/2 orbital in 209Pb as an example. The eigenstates of the model carry significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the system undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks.

Luminescence of the (O2(a(1)Δ(g)))2 collisional complex in the temperature range of 90-315 K: Experiment and theory.

PubMed

Zagidullin, M V; Pershin, A A; Azyazov, V N; Mebel, A M

2015-12-28

Experimental and theoretical studies of collision induced emission of singlet oxygen molecules O2(a(1)Δg) in the visible range have been performed. The rate constants, half-widths, and position of peaks for the emission bands of the (O2(a(1)Δg))2 collisional complex centered around 634 nm (2) and 703 nm (3) have been measured in the temperature range of 90-315 K using a flow-tube apparatus that utilized a gas-liquid chemical singlet oxygen generator. The absolute values of the spontaneous emission rate constants k2 and k3 are found to be similar, with the k3/k2 ratio monotonically decreasing from 1.1 at 300 K to 0.96 at 90 K. k2 slowly decreases with decreasing temperature but a sharp increase in its values is measured below 100 K. The experimental results were rationalized in terms of ab initio calculations of the ground and excited potential energy and transition dipole moment surfaces of singlet electronic states of the (O2)2 dimole, which were utilized to compute rate constants k2 and k3 within a statistical model. The best theoretical results reproduced experimental rate constants with the accuracy of under 40% and correctly described the observed temperature dependence. The main contribution to emission process (2), which does not involve vibrational excitation of O2 molecules at the ground electronic level, comes from the spin- and symmetry-allowed 1(1)Ag←(1)B3u transition in the rectangular H configuration of the dimole. Alternatively, emission process (3), in which one of the monomers becomes vibrationally excited in the ground electronic state, is found to be predominantly due to the vibronically allowed 1(1)Ag←2(1)Ag transition induced by the asymmetric O-O stretch vibration in the collisional complex. The strong vibronic coupling between nearly degenerate excited singlet states of the dimole makes the intensities of vibronically and symmetry-allowed transitions comparable and hence the rate constants k2 and k3 close to one another.

Rate of recovery from perturbations as a means to forecast future stability of living systems.

PubMed

Ghadami, Amin; Gourgou, Eleni; Epureanu, Bogdan I

2018-06-18

Anticipating critical transitions in complex ecological and living systems is an important need because it is often difficult to restore a system to its pre-transition state once the transition occurs. Recent studies demonstrate that several indicators based on changes in ecological time series can indicate that the system is approaching an impending transition. An exciting question is, however, whether we can predict more characteristics of the future system stability using measurements taken away from the transition. We address this question by introducing a model-less forecasting method to forecast catastrophic transition of an experimental ecological system. The experiment is based on the dynamics of a yeast population, which is known to exhibit a catastrophic transition as the environment deteriorates. By measuring the system's response to perturbations prior to transition, we forecast the distance to the upcoming transition, the type of the transition (i.e., catastrophic/non-catastrophic) and the future equilibrium points within a range near the transition. Experimental results suggest a strong potential for practical applicability of this approach for ecological systems which are at risk of catastrophic transitions, where there is a pressing need for information about upcoming thresholds.

Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states

PubMed Central

Schlau-Cohen, Gabriela S.; Wang, Quan; Southall, June; Cogdell, Richard J.; Moerner, W. E.

2013-01-01

Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities. PMID:23776245

Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states.

PubMed

Schlau-Cohen, Gabriela S; Wang, Quan; Southall, June; Cogdell, Richard J; Moerner, W E

2013-07-02

Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities.

Factors associated with successful transition among children with disabilities in eight European countries

PubMed Central

2017-01-01

Introduction This research paper aims to assess factors reported by parents associated with the successful transition of children with complex additional support requirements that have undergone a transition between school environments from 8 European Union member states. Methods Quantitative data were collected from 306 parents within education systems from 8 EU member states (Bulgaria, Cyprus, Greece, Ireland, the Netherlands, Romania, Spain and the UK). The data were derived from an online questionnaire and consisted of 41 questions. Information was collected on: parental involvement in their child’s transition, child involvement in transition, child autonomy, school ethos, professionals’ involvement in transition and integrated working, such as, joint assessment, cooperation and coordination between agencies. Survey questions that were designed on a Likert-scale were included in the Principal Components Analysis (PCA), additional survey questions, along with the results from the PCA, were used to build a logistic regression model. Results Four principal components were identified accounting for 48.86% of the variability in the data. Principal component 1 (PC1), ‘child inclusive ethos,’ contains 16.17% of the variation. Principal component 2 (PC2), which represents child autonomy and involvement, is responsible for 8.52% of the total variation. Principal component 3 (PC3) contains questions relating to parental involvement and contributed to 12.26% of the overall variation. Principal component 4 (PC4), which involves transition planning and coordination, contributed to 11.91% of the overall variation. Finally, the principal components were included in a logistic regression to evaluate the relationship between inclusion and a successful transition, as well as whether other factors that may have influenced transition. All four principal components were significantly associated with a successful transition, with PC1 being having the most effect (OR: 4.04, CI: 2.43–7.18, p<0.0001). Discussion To support a child with complex additional support requirements through transition from special school to mainstream, governments and professionals need to ensure children with additional support requirements and their parents are at the centre of all decisions that affect them. It is important that professionals recognise the educational, psychological, social and cultural contexts of a child with additional support requirements and their families which will provide a holistic approach and remove barriers for learning. PMID:28636649

Factors associated with successful transition among children with disabilities in eight European countries.

PubMed

Ravenscroft, John; Wazny, Kerri; Davis, John M

2017-01-01

This research paper aims to assess factors reported by parents associated with the successful transition of children with complex additional support requirements that have undergone a transition between school environments from 8 European Union member states. Quantitative data were collected from 306 parents within education systems from 8 EU member states (Bulgaria, Cyprus, Greece, Ireland, the Netherlands, Romania, Spain and the UK). The data were derived from an online questionnaire and consisted of 41 questions. Information was collected on: parental involvement in their child's transition, child involvement in transition, child autonomy, school ethos, professionals' involvement in transition and integrated working, such as, joint assessment, cooperation and coordination between agencies. Survey questions that were designed on a Likert-scale were included in the Principal Components Analysis (PCA), additional survey questions, along with the results from the PCA, were used to build a logistic regression model. Four principal components were identified accounting for 48.86% of the variability in the data. Principal component 1 (PC1), 'child inclusive ethos,' contains 16.17% of the variation. Principal component 2 (PC2), which represents child autonomy and involvement, is responsible for 8.52% of the total variation. Principal component 3 (PC3) contains questions relating to parental involvement and contributed to 12.26% of the overall variation. Principal component 4 (PC4), which involves transition planning and coordination, contributed to 11.91% of the overall variation. Finally, the principal components were included in a logistic regression to evaluate the relationship between inclusion and a successful transition, as well as whether other factors that may have influenced transition. All four principal components were significantly associated with a successful transition, with PC1 being having the most effect (OR: 4.04, CI: 2.43-7.18, p<0.0001). To support a child with complex additional support requirements through transition from special school to mainstream, governments and professionals need to ensure children with additional support requirements and their parents are at the centre of all decisions that affect them. It is important that professionals recognise the educational, psychological, social and cultural contexts of a child with additional support requirements and their families which will provide a holistic approach and remove barriers for learning.

The Low Molecular Weight Protein PsaI Stabilizes the Light-Harvesting Complex II Docking Site of Photosystem I.

PubMed

Plöchinger, Magdalena; Torabi, Salar; Rantala, Marjaana; Tikkanen, Mikko; Suorsa, Marjaana; Jensen, Poul-Erik; Aro, Eva Mari; Meurer, Jörg

2016-09-01

PsaI represents one of three low molecular weight peptides of PSI. Targeted inactivation of the plastid PsaI gene in Nicotiana tabacum has no measurable effect on photosynthetic electron transport around PSI or on accumulation of proteins involved in photosynthesis. Instead, the lack of PsaI destabilizes the association of PsaL and PsaH to PSI, both forming the light-harvesting complex (LHC)II docking site of PSI. These alterations at the LHCII binding site surprisingly did not prevent state transition but led to an increased incidence of PSI-LHCII complexes, coinciding with an elevated phosphorylation level of the LHCII under normal growth light conditions. Remarkably, LHCII was rapidly phosphorylated in ΔpsaI in darkness even after illumination with far-red light. We found that this dark phosphorylation also occurs in previously described mutants impaired in PSI function or state transition. A prompt shift of the plastoquinone (PQ) pool into a more reduced redox state in the dark caused an enhanced LHCII phosphorylation in ΔpsaI Since the redox status of the PQ pool is functionally connected to a series of physiological, biochemical, and gene expression reactions, we propose that the shift of mutant plants into state 2 in darkness represents a compensatory and/or protective metabolic mechanism. This involves an increased reduction and/or reduced oxidation of the PQ pool, presumably to sustain a balanced excitation of both photosystems upon the onset of light. © 2016 American Society of Plant Biologists. All rights reserved.

Model Checking - My 27-Year Quest to Overcome the State Explosion Problem

NASA Technical Reports Server (NTRS)

Clarke, Ed

2009-01-01

Model Checking is an automatic verification technique for state-transition systems that are finite=state or that have finite-state abstractions. In the early 1980 s in a series of joint papers with my graduate students E.A. Emerson and A.P. Sistla, we proposed that Model Checking could be used for verifying concurrent systems and gave algorithms for this purpose. At roughly the same time, Joseph Sifakis and his student J.P. Queille at the University of Grenoble independently developed a similar technique. Model Checking has been used successfully to reason about computer hardware and communication protocols and is beginning to be used for verifying computer software. Specifications are written in temporal logic, which is particularly valuable for expressing concurrency properties. An intelligent, exhaustive search is used to determine if the specification is true or not. If the specification is not true, the Model Checker will produce a counterexample execution trace that shows why the specification does not hold. This feature is extremely useful for finding obscure errors in complex systems. The main disadvantage of Model Checking is the state-explosion problem, which can occur if the system under verification has many processes or complex data structures. Although the state-explosion problem is inevitable in worst case, over the past 27 years considerable progress has been made on the problem for certain classes of state-transition systems that occur often in practice. In this talk, I will describe what Model Checking is, how it works, and the main techniques that have been developed for combating the state explosion problem.

Dark States in the Light-Harvesting complex 2 Revealed by Two-dimensional Electronic Spectroscopy

PubMed Central

Ferretti, Marco; Hendrikx, Ruud; Romero, Elisabet; Southall, June; Cogdell, Richard J.; Novoderezhkin, Vladimir I.; Scholes, Gregory D.; van Grondelle, Rienk

2016-01-01

Energy transfer and trapping in the light harvesting antennae of purple photosynthetic bacteria is an ultrafast process, which occurs with a quantum efficiency close to unity. However the mechanisms behind this process have not yet been fully understood. Recently it was proposed that low-lying energy dark states, such as charge transfer states and polaron pairs, play an important role in the dynamics and directionality of energy transfer. However, it is difficult to directly detect those states because of their small transition dipole moment and overlap with the B850/B870 exciton bands. Here we present a new experimental approach, which combines the selectivity of two-dimensional electronic spectroscopy with the availability of genetically modified light harvesting complexes, to reveal the presence of those dark states in both the genetically modified and the wild-type light harvesting 2 complexes of Rhodopseudomonas palustris. We suggest that Nature has used the unavoidable charge transfer processes that occur when LH pigments are concentrated to enhance and direct the flow of energy. PMID:26857477

Dark States in the Light-Harvesting complex 2 Revealed by Two-dimensional Electronic Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferretti, Marco; Hendrikx, Ruud; Romero, Elisabet

Energy transfer and trapping in the light harvesting antennae of purple photosynthetic bacteria is an ultrafast process, which occurs with a quantum efficiency close to unity. However the mechanisms behind this process have not yet been fully understood. Recently it was proposed that low-lying energy dark states, such as charge transfer states and polaron pairs, play an important role in the dynamics and directionality of energy transfer. However, it is difficult to directly detect those states because of their small transition dipole moment and overlap with the B850/B870 exciton bands. Here we present a new experimental approach, which combines themore » selectivity of two-dimensional electronic spectroscopy with the availability of genetically modified light harvesting complexes, to reveal the presence of those dark states in both the genetically modified and the wild-type light harvesting 2 complexes of Rhodopseudomonas palustris. In conclusion, we suggest that Nature has used the unavoidable charge transfer processes that occur when LH pigments are concentrated to enhance and direct the flow of energy.« less

Dark States in the Light-Harvesting complex 2 Revealed by Two-dimensional Electronic Spectroscopy

DOE PAGES

Ferretti, Marco; Hendrikx, Ruud; Romero, Elisabet; ...

2016-02-09

Energy transfer and trapping in the light harvesting antennae of purple photosynthetic bacteria is an ultrafast process, which occurs with a quantum efficiency close to unity. However the mechanisms behind this process have not yet been fully understood. Recently it was proposed that low-lying energy dark states, such as charge transfer states and polaron pairs, play an important role in the dynamics and directionality of energy transfer. However, it is difficult to directly detect those states because of their small transition dipole moment and overlap with the B850/B870 exciton bands. Here we present a new experimental approach, which combines themore » selectivity of two-dimensional electronic spectroscopy with the availability of genetically modified light harvesting complexes, to reveal the presence of those dark states in both the genetically modified and the wild-type light harvesting 2 complexes of Rhodopseudomonas palustris. In conclusion, we suggest that Nature has used the unavoidable charge transfer processes that occur when LH pigments are concentrated to enhance and direct the flow of energy.« less

Engineering the oxygen coordination in digital superlattices

NASA Astrophysics Data System (ADS)

Cook, Seyoung; Andersen, Tassie K.; Hong, Hawoong; Rosenberg, Richard A.; Marks, Laurence D.; Fong, Dillon D.

2017-12-01

The oxygen sublattice in complex oxides is typically composed of corner-shared polyhedra, with transition metals at their centers. The electronic and chemical properties of the oxide depend on the type and geometric arrangement of these polyhedra, which can be controlled through epitaxial synthesis. Here, we use oxide molecular beam epitaxy to create SrCoOx:SrTiO3 superlattices with tunable oxygen coordination environments and sublattice geometries. Using synchrotron X-ray scattering in combination with soft X-ray spectroscopy, we find that the chemical state of Co can be varied with the polyhedral arrangement, with higher Co oxidation states increasing the valence band maximum. This work demonstrates a new strategy for engineering unique electronic structures in the transition metal oxides using short-period superlattices.

NSR&D FY15 Final Report. Modeling Mechanical, Thermal, and Chemical Effects of Impact

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Christopher Curtis; Ma, Xia; Zhang, Duan Zhong

2015-11-02

The main goal of this project is to develop a computer model that explains and predicts coupled mechanical, thermal and chemical responses of HE under impact and friction insults. The modeling effort is based on the LANL-developed CartaBlanca code, which is implemented with the dual domain material point (DDMP) method to calculate complex and coupled thermal, chemical and mechanical effects among fluids, solids and the transitions between the states. In FY 15, we have implemented the TEPLA material model for metal and performed preliminary can penetration simulation and begun to link with experiment. Currently, we are working on implementing amore » shock to detonation transition (SDT) model (SURF) and JWL equation of state.« less

Density functional theory study on Herzberg-Teller contribution in Raman scattering from 4-aminothiophenol-metal complex and metal-4-aminothiophenol-metal junction

NASA Astrophysics Data System (ADS)

Liu, Shasha; Zhao, Xiuming; Li, Yuanzuo; Zhao, Xiaohong; Chen, Maodu

2009-06-01

Density functional theory (DFT) and time-dependent DFT calculations have been performed to investigate the Raman scattering spectra of metal-molecule complex and metal-molecule-metal junction architectures interconnected with 4-aminothiophenol (PATP) molecule. The simulated profiles of normal Raman scattering (NRS) spectra for the two complexes (Ag2-PATP and PATP-Au2) and the two junctions (Ag2-PATP-Au2 and Au2-PATP-Ag2) are similar to each other, but exhibit obviously different Raman intensities. Due to the lager static polarizabilities of the two junctions, which directly influence the ground state chemical enhancement in NRS spectra, the calculated normal Raman intensities of them are stronger than those of two complexes by the factor of 102. We calculate preresonance Raman scattering (RRS) spectra with incident light at 1064 nm, which is much lower than the S1 electronic transition energy of complexes and junctions. Ag2-PATP-Au2 and Au2-PATP-Ag2 junctions yield higher Raman intensities than those of Ag2-PATP and PATP-Au2 complexes, especially for b2 modes. This effect is mainly attributed to charge transfer (CT) between the metal gap and the PAPT molecule which results in the occurrence of CT resonance enhancement. The calculated pre-RRS spectra strongly depend on the electronic transition state produced by new structures. With excitation at 514.5 nm, the calculated pre-RRS spectra of two complexes and two junctions are stronger than those of with excitation at 1064 nm. A charge difference densities methodology has been used to visually describe chemical enhancement mechanism of RRS spectrum. This methodology aims at visualizing intermolecular CT which provides direct evidence of the Herzberg-Teller mechanism.

Anaerobiosis Induced State Transition: A Non Photochemical Reduction of PQ Pool Mediated by NDH in Arabidopsis thaliana

PubMed Central

Tirupathi, Malavath; Subramanyam, Rajagopal

2012-01-01

Background Non photochemical reduction of PQ pool and mobilization of LHCII between PSII and PSI are found to be linked under abiotic stress conditions. The interaction of non photochemical reduction of PQ pool and state transitions associated physiological changes are critically important under anaerobic condition in higher plants. Methodology/Findings The present study focused on the effect of anaerobiosis on non-photochemical reduction of PQ pool which trigger state II transition in Arabidopsis thaliana. Upon exposure to dark-anaerobic condition the shape of the OJIP transient rise is completely altered where as in aerobic treated leaves the rise is unaltered. Rise in F o and F J was due to the loss of oxidized PQ pool as the PQ pool becomes more reduced. The increase in Fo′ was due to the non photochemical reduction of PQ pool which activated STN7 kinase and induced LHCII phosphorylation under anaerobic condition. Further, it was observed that the phosphorylated LHCII is migrated and associated with PSI supercomplex increasing its absorption cross-section. Furthermore, evidences from crr2-2 (NDH mutant) and pgr5 mutants (deficient in non NDH pathway of cyclic electron transport) have indicated that NDH is responsible for non photochemical reduction of the PQ pool. We propose that dark anaerobic condition accelerates production of reducing equivalents (such as NADPH by various metabolic pathways) which reduce PQ pool and is mediated by NDH leading to state II transition. Conclusions/Significance Anaerobic condition triggers non photochemical reduction of PQ pool mediated by NDH complex. The reduced PQ pool activates STN7 kinase leading to state II transition in A. thaliana. PMID:23185453

Dynamics of Sleep Stage Transitions in Health and Disease

NASA Astrophysics Data System (ADS)

Kishi, Akifumi; Struzik, Zbigniew R.; Natelson, Benjamin H.; Togo, Fumiharu; Yamamoto, Yoshiharu

2007-07-01

Sleep dynamics emerges from complex interactions between neuronal populations in many brain regions. Annotated sleep stages from electroencephalography (EEG) recordings could potentially provide a non-invasive way to obtain valuable insights into the mechanisms of these interactions, and ultimately into the very nature of sleep regulation. However, to date, sleep stage analysis has been restricted, only very recently expanding the scope of the traditional descriptive statistics to more dynamical concepts of the duration of and transitions between vigilance states and temporal evaluation of transition probabilities among different stages. Physiological and/or pathological implications of the dynamics of sleep stage transitions have, to date, not been investigated. Here, we study detailed duration and transition statistics among sleep stages in healthy humans and patients with chronic fatigue syndrome, known to be associated with disturbed sleep. We find that the durations of waking and non-REM sleep, in particular deep sleep (Stages III and IV), during the nighttime, follow a power-law probability distribution function, while REM sleep durations follow an exponential function, suggestive of complex underlying mechanisms governing the onset of light sleep. We also find a substantial number of REM to non-REM transitions in humans, while this transition is reported to be virtually non-existent in rats. Interestingly, the probability of this REM to non-REM transition is significantly lower in the patients than in controls, resulting in a significantly greater REM to awake, together with Stage I to awake, transition probability. This might potentially account for the reported poor sleep quality in the patients because the normal continuation of sleep after either the lightest or REM sleep is disrupted. We conclude that the dynamical transition analysis of sleep stages is useful for elucidating yet-to-be-determined human sleep regulation mechanisms with a pathophysiological implication.

Modulation of the brain's functional network architecture in the transition from wake to sleep

PubMed Central

Larson-Prior, Linda J.; Power, Jonathan D.; Vincent, Justin L.; Nolan, Tracy S.; Coalson, Rebecca S.; Zempel, John; Snyder, Abraham Z.; Schlaggar, Bradley L.; Raichle, Marcus E.; Petersen, Steven E.

2013-01-01

The transition from quiet wakeful rest to sleep represents a period over which attention to the external environment fades. Neuroimaging methodologies have provided much information on the shift in neural activity patterns in sleep, but the dynamic restructuring of human brain networks in the transitional period from wake to sleep remains poorly understood. Analysis of electrophysiological measures and functional network connectivity of these early transitional states shows subtle shifts in network architecture that are consistent with reduced external attentiveness and increased internal and self-referential processing. Further, descent to sleep is accompanied by the loss of connectivity in anterior and posterior portions of the default-mode network and more locally organized global network architecture. These data clarify the complex and dynamic nature of the transitional period between wake and sleep and suggest the need for more studies investigating the dynamics of these processes. PMID:21854969

Frustration across the periodic table: heterolytic cleavage of dihydrogen by metal complexes.

PubMed

Bullock, R Morris; Chambers, Geoffrey M

2017-08-28

This perspective examines frustrated Lewis pairs (FLPs) in the context of heterolytic cleavage of H 2 by transition metal complexes, with an emphasis on molecular complexes bearing an intramolecular Lewis base. FLPs have traditionally been associated with main group compounds, yet many reactions of transition metal complexes support a broader classification of FLPs that includes certain types of transition metal complexes with reactivity resembling main group-based FLPs. This article surveys transition metal complexes that heterolytically cleave H 2 , which vary in the degree that the Lewis pairs within these systems interact. Many of the examples include complexes bearing a pendant amine functioning as the base with the metal functioning as the hydride acceptor. Consideration of transition metal compounds in the context of FLPs can inspire new innovations and improvements in transition metal catalysis.This article is part of the themed issue 'Frustrated Lewis pair chemistry'. © 2017 The Author(s).

Multiple dimensions of transitions in complex socio-ecological systems - A case from China

NASA Astrophysics Data System (ADS)

Liu, Wei; Yang, Wu; Vina, Andres; Schröter, Dagmar; Liu, Jianguo

2013-04-01

Transitions in complex socio-ecological systems are intermediate phases between two successive and more stable periods or states and involve various societal, ecological, and biophysical changes that are often non-linear and inter-related. Understanding transitions is challenging but important for managing socio-ecological systems for achieving environmental sustainability and improving human well-being. Long-term and intensive research is warranted to disclose common patterns and mechanisms of socio-ecological transitions and to develop ideas and methods for studying and planning sustainable transitions. Based on a long-term research on human-nature relationships in Wolong Nature Reserve in China, we studied multiple concurrent social, economic, and ecological transitions during the last 15 years. As a UNESCO biosphere reserve, Wolong lies within a global biodiversity hotspot and a World Heritage site. It contains the largest populations of the world-famous endangered giant pandas and several thousand other animal and plant species. Like most nature reserves in China and many other developing countries, Wolong is also home to many local residents who undertake a variety of activities that involve interaction with ecosystem. For the majority of the 20th century, local people in Wolong lived under poverty line in a closed subsistence-based agricultural economy. Their demands on for wood (as fuel and raw materials) from the natural forests were high and resulted in severe deforestation, habitat degradation, and landslides. Since late 1990s, a series of major economic (e.g., tourism development) and environmental (e.g., payment for ecosystem services programs) policies have been implemented in the reserve as adaptive strategies to cope with poverty and ecological degradation. Within a decade, we have observed major transitions in land use (i.e., from extractive use to non-consumptive use), economic structure (i.e., from a subsistence-based agricultural economy to an open economy relying on tourism and cash crop), and energy consumption (i.e., decline in biomass fuel by three quarters and tripling in electricity use). We further analyzed their impacts on local people's well-being and discuss the possible explanatory framework for the observed socio-ecological transition as a whole. This study not only has direct implications for sustainability transition in developing countries but also increases our understanding of the complexity of human-nature interactions and their effects on the resilience of complex socio-ecological systems.

Spectroscopy of selected metal-containing diatomic molecules

NASA Astrophysics Data System (ADS)

Gordon, Iouli E.

Fourier transform infrared emission spectra of MnH and MnD were observed in the ground X7Sigma+ electronic state. The vibration-rotation bands from v = 1 → 0 to v = 3 → 2 for MnH, and from v = 1 → 0 to v = 4 → 3 for MnD were recorded at an instrumental resolution of 0.0085 cm-1. Spectroscopic constants were determined for each vibrational level and equilibrium constants were found from a Dunham-type fit. The equilibrium vibrational constant oe for MnH was found to be 1546.84518(65) cm-1, the equilibrium rotational constant Be was found to be 5.6856789(103) cm-1 and the equilibrium bond distance re was determined to be 1.7308601(47) A. New high resolution emission spectra of CoH and CoD molecules have been recorded in the 640 nm to 3.5 mum region using a Fourier transform spectrometer. Many bands were observed for the A'3phi- X3phi electronic transition of CoH and CoD. In addition, a new [13.3]4 electronic state was found by observing the [13.3]4-X3phi3 and [13.3]4- X3phi4 transitions in the spectrum of CoD. Analysis of the transitions with DeltaO = 0, +/-1 provided more accurate values of spin-orbit splittings between O = 4 and O = 3 components. The ground state for both molecules was fitted both to band and Dunham-type constants. The estimated band constants of the perturbed upper states were also obtained. The emission spectrum of gas-phase YbO has been investigated using a Fourier transform spectrometer. A total of 8 red-degraded bands in the range 9 800--11 300 cm-1 were recorded at a resolution of 0.04 cm-1. Because of the multiple isotopomers present in the spectra, only 3 bands were rotationally analyzed. Perturbations were identified in two of these bands and all 3 transitions were found to terminate at the X1Sigma+ ground electronic state. The electronic configurations that give rise to the observed states are discussed and molecular parameters for all of the analyzed bands are reported. Electronic spectra of the previously unobserved EuH and EuD molecules were studied by means of Fourier transform spectroscopy and laser-induced fluorescence. The extreme complexity of these transitions made rotational assignments of EuH bands impossible. However, the spin-spin interaction constant, lambda, and Fermi contact parameter, bF, in the ground X9Sigma- electronic state were estimated for the 151EuH and 153EuH isotopologues. Electronic spectra of SmH, SmCl, TmH and ErF molecules were recorded for the first time using Fourier transform spectrometer. The poor signal to noise ratio of the observed bands coupled with their complexity prevented a rotational analysis. The electronic states that may be involved in the observed transitions are discussed.

Spectroscopy of selected metal-containing diatomic molecules

NASA Astrophysics Data System (ADS)

Gordon, Iouli

Fourier transform infrared emission spectra of MnH and MnD were observed in the ground X7[sigma]+ electronic state. The vibration-rotation bands from v = 1 to 0 to v = 3 to 2 for MnH, and from v = 1 to 0 to v = 4 to 3 for MnD were recorded at an instrumental resolution of 0. 0085 cm-1. Spectroscopic constants were determined for each vibrational level and equilibrium constants were found from a Dunham-type fit. The equilibrium vibrational constant [omega]e for MnH was found to be 1546. 84518(65) cm-1, the equilibrium rotational constant Be was found to be 5. 6856789(103) cm-1 and the equilibrium bond distance re was determined to be 1. 7308601(47) ?. New high resolution emission spectra of CoH and CoD molecules have been recorded in the 640 nm to 3. 5 _m region using a Fourier transform spectrometer. Many bands were observed for the A'3?-X3? electronic transition of CoH and CoD. In addition, a new [13. 3]4 electronic state was found by observing the [13. 3]4- X3?3 and [13. 3]4-X3?4 transitions in the spectrum of CoD. Analysis of the transitions with [delta][omega] = 0, ?1 provided more accurate values of spin-orbit splittings between [omega] = 4 and [omega] = 3 components. The ground state for both molecules was fitted both to band and Dunham-type constants. The estimated band constants of the perturbed upper states were also obtained. The emission spectrum of gas-phase YbO has been investigated using a Fourier transform spectrometer. A total of 8 red-degraded bands in the range 9 800 ? 11 300 cm-1 were recorded at a resolution of 0. 04 cm-1. Because of the multiple isotopomers present in the spectra, only 3 bands were rotationally analyzed. Perturbations were identified in two of these bands and all 3 transitions were found to terminate at the X1[sigma]+ ground electronic state. The electronic configurations that give rise to the observed states are discussed and molecular parameters for all of the analyzed bands are reported. Electronic spectra of the previously unobserved EuH and EuD molecules were studied by means of Fourier transform spectroscopy and laser-induced fluorescence. The extreme complexity of these transitions made rotational assignments of EuH bands impossible. However, the spin-spin interaction constant, [lambda], and Fermi contact parameter, bF, in the ground X9[sigma]- electronic state were estimated for the 151EuH and 153EuH isotopologues. Electronic spectra of SmH, SmCl, TmH and ErF molecules were recorded for the first time using Fourier transform spectrometer. The poor signal to noise ratio of the observed bands coupled with their complexity prevented a rotational analysis. The electronic states that may be involved in the observed transitions are discussed.

Stationary properties of maximum-entropy random walks.

PubMed

Dixit, Purushottam D

2015-10-01

Maximum-entropy (ME) inference of state probabilities using state-dependent constraints is popular in the study of complex systems. In stochastic systems, how state space topology and path-dependent constraints affect ME-inferred state probabilities remains unknown. To that end, we derive the transition probabilities and the stationary distribution of a maximum path entropy Markov process subject to state- and path-dependent constraints. A main finding is that the stationary distribution over states differs significantly from the Boltzmann distribution and reflects a competition between path multiplicity and imposed constraints. We illustrate our results with particle diffusion on a two-dimensional landscape. Connections with the path integral approach to diffusion are discussed.

Catastrophic shifts in vegetation-soil systems may unfold rapidly or slowly independent of the rate of change in the system driver

NASA Astrophysics Data System (ADS)

Karssenberg, Derek; Bierkens, Marc

2014-05-01

Complex systems may switch between contrasting stable states under gradual change of a driver. Such critical transitions often result in considerable long-term damage because strong hysteresis impedes reversion, and the transition becomes catastrophic. Critical transitions largely reduce our capability of forecasting future system states because it is hard to predict the timing of their occurrence [2]. Moreover, for many systems it is unknown how rapidly the critical transition unfolds when the tipping point has been reached. The rate of change during collapse, however, is important information because it determines the time available to take action to reverse a shift [1]. In this study we explore the rate of change during the degradation of a vegetation-soil system on a hillslope from a state with considerable vegetation cover and large soil depths, to a state with sparse vegetation and a bare rock or negligible soil depths. Using a distributed, stochastic model coupling hydrology, vegetation, weathering and water erosion, we derive two differential equations describing the vegetation and the soil system, and their interaction. Two stable states - vegetated and bare - are identified by means of analytical investigation, and it is shown that the change between these two states is a critical transition as indicated by hysteresis. Surprisingly, when the tipping point is reached under a very slow increase of grazing pressure, the transition between the vegetated and the bare state can either unfold rapidly, over a few years, or gradually, occurring over decennia up to millennia. These differences in the rate of change during the transient state are explained by differences in bedrock weathering rates. This finding emphasizes the considerable uncertainty associated with forecasting catastrophic shifts in ecosystems, which is due to both difficulties in forecasting the timing of the tipping point and the rate of change when the transition unfolds. References [1] Hughes, T. P., Linares, C., Dakos, V., van de Leemput, I. a, & van Nes, E. H. (2013). Living dangerously on borrowed time during slow, unrecognized regime shifts. Trends in ecology & evolution, 28(3), 149-55. [2] Karssenberg, D., & Bierkens, M. F. P. (2012). Early-warning signals (potentially) reduce uncertainty in forecasted timing of critical shifts. Ecosphere, 3(2).

Dynamical modeling and analysis of large cellular regulatory networks

NASA Astrophysics Data System (ADS)

Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.

2013-06-01

The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

Liquid-gas phase transitions and C K symmetry in quantum field theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishimura, Hiromichi; Ogilvie, Michael C.; Pangeni, Kamal

A general field-theoretic framework for the treatment of liquid-gas phase transitions is developed. Starting from a fundamental four-dimensional field theory at nonzero temperature and density, an effective three-dimensional field theory is derived. The effective field theory has a sign problem at finite density. Although finite density explicitly breaks charge conjugation C , there remains a symmetry under C K , where K is complex conjugation. Here, we consider four models: relativistic fermions, nonrelativistic fermions, static fermions and classical particles. The interactions are via an attractive potential due to scalar field exchange and a repulsive potential due to massive vector exchange.more » The field-theoretic representation of the partition function is closely related to the equivalence of the sine-Gordon field theory with a classical gas. The thermodynamic behavior is extracted from C K -symmetric complex saddle points of the effective field theory at tree level. In the cases of nonrelativistic fermions and classical particles, we find complex saddle point solutions but no first-order transitions, and neither model has a ground state at tree level. The relativistic and static fermions show a liquid-gas transition at tree level in the effective field theory. The liquid-gas transition, when it occurs, manifests as a first-order line at low temperature and high density, terminated by a critical end point. The mass matrix controlling the behavior of correlation functions is obtained from fluctuations around the saddle points. Due to the C K symmetry of the models, the eigenvalues of the mass matrix are not always real but can be complex. This then leads to the existence of disorder lines, which mark the boundaries where the eigenvalues go from purely real to complex. The regions where the mass matrix eigenvalues are complex are associated with the critical line. In the case of static fermions, a powerful duality between particles and holes allows for the analytic determination of both the critical line and the disorder lines. Depending on the values of the parameters, either zero, one, or two disorder lines are found. Our numerical results for relativistic fermions give a very similar picture.« less

Liquid-gas phase transitions and C K symmetry in quantum field theories

DOE PAGES

Nishimura, Hiromichi; Ogilvie, Michael C.; Pangeni, Kamal

2017-04-04

A general field-theoretic framework for the treatment of liquid-gas phase transitions is developed. Starting from a fundamental four-dimensional field theory at nonzero temperature and density, an effective three-dimensional field theory is derived. The effective field theory has a sign problem at finite density. Although finite density explicitly breaks charge conjugation C , there remains a symmetry under C K , where K is complex conjugation. Here, we consider four models: relativistic fermions, nonrelativistic fermions, static fermions and classical particles. The interactions are via an attractive potential due to scalar field exchange and a repulsive potential due to massive vector exchange.more » The field-theoretic representation of the partition function is closely related to the equivalence of the sine-Gordon field theory with a classical gas. The thermodynamic behavior is extracted from C K -symmetric complex saddle points of the effective field theory at tree level. In the cases of nonrelativistic fermions and classical particles, we find complex saddle point solutions but no first-order transitions, and neither model has a ground state at tree level. The relativistic and static fermions show a liquid-gas transition at tree level in the effective field theory. The liquid-gas transition, when it occurs, manifests as a first-order line at low temperature and high density, terminated by a critical end point. The mass matrix controlling the behavior of correlation functions is obtained from fluctuations around the saddle points. Due to the C K symmetry of the models, the eigenvalues of the mass matrix are not always real but can be complex. This then leads to the existence of disorder lines, which mark the boundaries where the eigenvalues go from purely real to complex. The regions where the mass matrix eigenvalues are complex are associated with the critical line. In the case of static fermions, a powerful duality between particles and holes allows for the analytic determination of both the critical line and the disorder lines. Depending on the values of the parameters, either zero, one, or two disorder lines are found. Our numerical results for relativistic fermions give a very similar picture.« less

Microwave measurements of proton tunneling and structural parameters for the propiolic acid-formic acid dimer.

PubMed

Daly, Adam M; Douglass, Kevin O; Sarkozy, Laszlo C; Neill, Justin L; Muckle, Matt T; Zaleski, Daniel P; Pate, Brooks H; Kukolich, Stephen G

2011-10-21

Microwave spectra of the propiolic acid-formic acid doubly hydrogen bonded complex were measured in the 1 GHz to 21 GHz range using four different Fourier transform spectrometers. Rotational spectra for seven isotopologues were obtained. For the parent isotopologue, a total of 138 a-dipole transitions and 28 b-dipole transitions were measured for which the a-dipole transitions exhibited splittings of a few MHz into pairs of lines and the b-type dipole transitions were split by ~580 MHz. The transitions assigned to this complex were fit to obtain rotational and distortion constants for both tunneling levels: A(0+) = 6005.289(8), B(0+) = 930.553(8), C(0+) = 803.9948(6) MHz, Δ(0+)(J) = 0.075(1), Δ(0+)(JK) = 0.71(1), and δ(0+)(j) = -0.010(1) kHz and A(0-) = 6005.275(8), B(0-) = 930.546(8), C(0-) = 803.9907(5) MHz, Δ(0-)(J) = 0.076(1), Δ(0-)(JK) = 0.70(2), and δ(0-)(j) = -0.008(1) kHz. Double resonance experiments were used on some transitions to verify assignments and to obtain splittings for cases when the b-dipole transitions were difficult to measure. The experimental difference in energy between the two tunneling states is 291.428(5) MHz for proton-proton exchange and 3.35(2) MHz for the deuterium-deuterium exchange. The vibration-rotation coupling constant between the two levels, F(ab), is 120.7(2) MHz for the proton-proton exchange. With one deuterium atom substituted in either of the hydrogen-bonding protons, the tunneling splittings were not observed for a-dipole transitions, supporting the assignment of the splitting to the concerted proton tunneling motion. The spectra were obtained using three Flygare-Balle type spectrometers and one chirped-pulse machine at the University of Virginia. Rotational constants and centrifugal distortion constants were obtained for HCOOH···HOOCCCH, H(13)COOH···HOOCCCH, HCOOD···HOOCCCH, HCOOH···DOOCCCH, HCOOD···DOOCCCH, DCOOH···HOOCCCH, and DCOOD···HOOCCCH. High-level ab initio calculations provided initial rotational constants for the complex, structural parameters, and some details of the proton tunneling potential energy surface. A least squares fit to the isotopic data reveals a planar structure that is slightly asymmetric in the OH distances. The formic OH···O propiolic hydrogen bond length is 1.8 Å and the propiolic OH···O formic hydrogen bond length is 1.6 Å, for the equilibrium configuration. The magnitude of the dipole moment was experimentally determined to be 1.95(3) × 10(-30) C m (0.584(8) D) for the 0(+) states and 1.92(5) × 10(-30) C m (0.576(14) D) for the 0(-) states. © 2011 American Institute of Physics

Electrically active induced energy levels and metastability of B and N vacancy-complexes in 4H–SiC

NASA Astrophysics Data System (ADS)

Igumbor, E.; Olaniyan, O.; Mapasha, R. E.; Danga, H. T.; Omotoso, E.; Meyer, W. E.

2018-05-01

Electrically active induced energy levels in semiconductor devices could be beneficial to the discovery of an enhanced p or n-type semiconductor. Nitrogen (N) implanted into 4H–SiC is a high energy process that produced high defect concentrations which could be removed during dopant activation annealing. On the other hand, boron (B) substituted for silicon in SiC causes a reduction in the number of defects. This scenario leads to a decrease in the dielectric properties and induced deep donor and shallow acceptor levels. Complexes formed by the N, such as the nitrogen-vacancy centre, have been reported to play a significant role in the application of quantum bits. In this paper, results of charge states thermodynamic transition level of the N and B vacancy-complexes in 4H–SiC are presented. We explore complexes where substitutional N/N or B/B sits near a Si (V) or C (V) vacancy to form vacancy-complexes (NV, NV, NV, NV, BV, BV, BV and BV). The energies of formation of the N related vacancy-complexes showed the NV to be energetically stable close to the valence band maximum in its double positive charge state. The NV is more energetically stable in the double negative charge state close to the conduction band minimum. The NV on the other hand, induced double donor level and the NV induced a double acceptor level. For B related complexes, the BV and BV were energetically stable in their single positive charge state close to the valence band maximum. As the Fermi energy is varied across the band gap, the neutral and single negative charge states of the BV become more stable at different energy levels. B and N related complexes exhibited charge state controlled metastability behaviour.

Multi-state succession in wetlands: a novel use of state and transition models

USGS Publications Warehouse

Zweig, Christa L.; Kitchens, Wiley M.

2009-01-01

The complexity of ecosystems and mechanisms of succession are often simplified by linear and mathematical models used to understand and predict system behavior. Such models often do not incorporate multivariate, nonlinear feedbacks in pattern and process that include multiple scales of organization inherent within real-world systems. Wetlands are ecosystems with unique, nonlinear patterns of succession due to the regular, but often inconstant, presence of water on the landscape. We develop a general, nonspatial state and transition (S and T) succession conceptual model for wetlands and apply the general framework by creating annotated succession/management models and hypotheses for use in impact analysis on a portion of an imperiled wetland. The S and T models for our study area, Water Conservation Area 3A South (WCA3), Florida, USA, included hydrologic and peat depth values from multivariate analyses and classification and regression trees. We used the freeware Vegetation Dynamics Development Tool as an exploratory application to evaluate our S and T models with different management actions (equal chance [a control condition], deeper conditions, dry conditions, and increased hydrologic range) for three communities: slough, sawgrass (Cladium jamaicense), and wet prairie. Deeper conditions and increased hydrologic range behaved similarly, with the transition of community states to deeper states, particularly for sawgrass and slough. Hydrology is the primary mechanism for multi-state transitions within our study period, and we show both an immediate and lagged effect on vegetation, depending on community state. We consider these S and T succession models as a fraction of the framework for the Everglades. They are hypotheses for use in adaptive management, represent the community response to hydrology, and illustrate which aspects of hydrologic variability are important to community structure. We intend for these models to act as a foundation for further restoration management and experimentation which will refine transition and threshold concepts. 

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

PubMed

Sagarik, Kritsana; Phonyiem, Mayuree; Lao-ngam, Charoensak; Chaiwongwattana, Sermsiri

2008-04-21

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

Resilience | Science Inventory | US EPA

EPA Pesticide Factsheets

Resilience is an important framework for understanding and managing complex systems of people and nature that are subject to abrupt and nonlinear change. The idea of ecological resilience was slow to gain acceptance in the scientific community, taking thirty years to become widely accepted (Gunderson 2000, cited under Original Definition). Currently, the concept is commonplace in academics, management, and policy. Although the idea has quantitative roots in the ecological sciences and was proposed as a measurable quality of ecosystems, the broad use of resilience led to an expansion of definitions and applications. Holling’s original definition, presented in 1973 (Holling 1973, cited under Original Definition), was simply the amount of disturbance that a system can withstand before it shifts into an alternative stability domain. Ecological resilience, therefore, emphasizes that the dynamics of complex systems are nonlinear, meaning that these systems can transition, often abruptly, between dynamic states with substantially different structures, functions, and processes. The transition of ecological systems from one state to another frequently has important repercussions for humans. Recent definitions are more normative and qualitative, especially in the social sciences, and a competing definition, that of engineering resilience, is still often used. Resilience is an emergent phenomenon of complex systems, which means it cannot be deduced from the behavior of t

Photochemistry of Metal-Metal Bonded Transition Element Complexes

DTIC Science & Technology

1980-12-12

longest-lived metal - metal bonded complex in 298 K fluid solution is of tl.e order of _10-6 a in lifetime (7). Thus, excited state reactions of any kind must...may be greater since cage escape of Re(CO)5 radicals may be less thin unity. There is a solvent viscosity effect on the disappearance quantum yield of...M2 (CO) 1 0 in the presence of 12,consistent with a solvent cage effect (11). In polar solvents (pyridine, THF, alcohols, etc.) the photochemistry of

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding.

PubMed

Tischer, Alexander; Auton, Matthew

2013-09-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. © 2013 The Protein Society.

Computation of rare transitions in the barotropic quasi-geostrophic equations

NASA Astrophysics Data System (ADS)

Laurie, Jason; Bouchet, Freddy

2015-01-01

We investigate the theoretical and numerical computation of rare transitions in simple geophysical turbulent models. We consider the barotropic quasi-geostrophic and two-dimensional Navier-Stokes equations in regimes where bistability between two coexisting large-scale attractors exist. By means of large deviations and instanton theory with the use of an Onsager-Machlup path integral formalism for the transition probability, we show how one can directly compute the most probable transition path between two coexisting attractors analytically in an equilibrium (Langevin) framework and numerically otherwise. We adapt a class of numerical optimization algorithms known as minimum action methods to simple geophysical turbulent models. We show that by numerically minimizing an appropriate action functional in a large deviation limit, one can predict the most likely transition path for a rare transition between two states. By considering examples where theoretical predictions can be made, we show that the minimum action method successfully predicts the most likely transition path. Finally, we discuss the application and extension of such numerical optimization schemes to the computation of rare transitions observed in direct numerical simulations and experiments and to other, more complex, turbulent systems.

Focused Research Group in Correlated Electron and Complex Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ziqiang

While the remarkable physical properties of correlated and complex electronic materials hold great promise for technological applications, one of the key values of the research in this field is its profound impact on fundamental physics. The transition metal oxides, pnictides, and chalcogenides play a key role and occupy an especially important place in this field. The basic reason is that the outer shell of transition metals contains the atomic d-orbitals that have small spatial extent, but not too small to behave as localized orbtials. These d-electrons therefore have a small wave function overlap in a solid, e.g. in an octahedralmore » environment, and form energy bands that are relatively narrow and on the scale of the short-range intra-atomic Coulomb repulsion (Hubbard U). In this intermediate correlation regime lies the challenge of the many-body physics responsible for new and unconventional physical properties. The study of correlated electron and complex materials represents both the challenge and the vitality of condensed matter and materials physics and often demands close collaborations among theoretical and experimental groups with complementary techniques. Our team has a track record and a long-term research goal of studying the unusual complexities and emergent behaviors in the charge, spin, and orbital sectors of the transition metal compounds in order to gain basic knowledge of the quantum electronic states of matter. During the funding period of this grant, the team continued their close collaborations between theory, angle-resolved photoemission spectroscopy, and scanning tunneling microscopy and made significant progress and contributions to the field of iron-based superconductors, copper-oxide high-temperature superconductors, triangular lattice transition metal oxide cobaltates, strontium ruthenates, spin orbital coupled iridates, as well as topological insulators and other topological quantum states of matter. These results include both new discoveries and the resolution to outstanding and unresolved issues. It should be emphasized that the DOE funding provided the crucial support for the close and meaningful collaborations of the focused research group that go far beyond simply putting the research papers from each group together. Indeed, the majority of the publications involved multiple PIs and collaborations between theory and experiments.« less

Tunicamycins: translocase-I inhibitors that target bacterial cell wall and mammalian N-glycoproteins. The potential for selective inhibitors

USDA-ARS?s Scientific Manuscript database

Tunicamycins are a heterologous family of nucleoside antibiotics that target the biosynthesis of bacterial peptidoglycan and eukaryotic N-glycoproteins. The mechanism of action is known, with the tunicamycin-Mg2+ complex established as a transition state analog for hexosamine-1-phosphate: prenol pho...

Oak woodland vegetation dynamics: a state and transition approach

Treesearch

Melvin R. George; Maximo F. Alonso

2008-01-01

California’s oak-woodlands are a complex, often multi-layered mosaic of grassland, shrubland, and woodland patches. While soil type and depth, topography, aspect, and geological substrate influence the distribution of these patches, disturbance and biological interactions are also important determinants of the patchy distribution of these plant communities. Fire...

First-Principles Studies of the Excited States and Optical Properties of Xanthene Derivative Chromophores

NASA Astrophysics Data System (ADS)

Hamed, Samia; Sharifzadeh, Sahar; Neaton, Jeffrey

2014-03-01

Elucidation of the energy transfer mechanism in natural photosynthetic systems remains an exciting challenge. In particular, biomimetic protein-pigment complexes provide a unique study space in which individual parameters are adjusted and the impact of those changes captured. Here, we compute the excited state properties of a group of xanthene-derivative chromophores to be employed in the construction of new biomimetic light harvesting frameworks. Excitation energies, transition dipoles, and natural transition orbitals for the low-lying singlet and triplet states of these experimentally-relevant chromophores are obtained from first-principles density functional theory. The performance of several exchange-correlation functionals, including an optimally-tuned range-separated hybrid, are evaluated and compared with many body perturbation theory and experiment. Finally, we will discuss the implication of our results for the bottom-up design of new chromophores. This work is supported by the DOE and computational resources are provided by NERSC.

Slow Photoelectron Velocity-Map Imaging of Cryogenically Cooled Anions

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Neumark, Daniel M.

2018-04-01

Slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled anions (cryo-SEVI) is a powerful technique for elucidating the vibrational and electronic structure of neutral radicals, clusters, and reaction transition states. SEVI is a high-resolution variant of anion photoelectron spectroscopy based on photoelectron imaging that yields spectra with energy resolution as high as 1-2 cm‑1. The preparation of cryogenically cold anions largely eliminates hot bands and dramatically narrows the rotational envelopes of spectral features, enabling the acquisition of well-resolved photoelectron spectra for complex and spectroscopically challenging species. We review the basis and history of the SEVI method, including recent experimental developments that have improved its resolution and versatility. We then survey recent SEVI studies to demonstrate the utility of this technique in the spectroscopy of aromatic radicals, metal and metal oxide clusters, nonadiabatic interactions between excited states of small molecules, and transition states of benchmark bimolecular reactions.

Tunable Electron-Electron Interactions in LaAlO 3 / SrTiO 3 Nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Guanglei; Tomczyk, Michelle; Tacla, Alexandre B.

The interface between the two complex oxides LaAlO 3 and SrTiO 3 has remarkable properties that can be locally reconfigured between conducting and insulating states using a conductive atomic force microscope. Prior investigations of “sketched” quantum dot devices revealed a phase in which electrons form pairs, implying a strongly attractive electron-electron interaction. Here, we show that these devices with strong electron-electron interactions can exhibit a gate-tunable transition from a pair-tunneling regime to a single-electron (Andreev bound state) tunneling regime where the interactions become repulsive. The electron-electron interaction sign change is associated with a Lifshitz transition where the d xz andmore » d yz bands start to become occupied. This electronically tunable electron-electron interaction, combined with the nanoscale reconfigurability of this system, provides an interesting starting point towards solid-state quantum simulation.« less

Tunable Electron-Electron Interactions in LaAlO 3 / SrTiO 3 Nanostructures

DOE PAGES

Cheng, Guanglei; Tomczyk, Michelle; Tacla, Alexandre B.; ...

2016-12-01

The interface between the two complex oxides LaAlO 3 and SrTiO 3 has remarkable properties that can be locally reconfigured between conducting and insulating states using a conductive atomic force microscope. Prior investigations of “sketched” quantum dot devices revealed a phase in which electrons form pairs, implying a strongly attractive electron-electron interaction. Here, we show that these devices with strong electron-electron interactions can exhibit a gate-tunable transition from a pair-tunneling regime to a single-electron (Andreev bound state) tunneling regime where the interactions become repulsive. The electron-electron interaction sign change is associated with a Lifshitz transition where the d xz andmore » d yz bands start to become occupied. This electronically tunable electron-electron interaction, combined with the nanoscale reconfigurability of this system, provides an interesting starting point towards solid-state quantum simulation.« less

Single-molecule chemo-mechanical unfolding reveals multiple transition state barriers in a small single-domain protein

NASA Astrophysics Data System (ADS)

Guinn, Emily J.; Jagannathan, Bharat; Marqusee, Susan

2015-04-01

A fundamental question in protein folding is whether proteins fold through one or multiple trajectories. While most experiments indicate a single pathway, simulations suggest proteins can fold through many parallel pathways. Here, we use a combination of chemical denaturant, mechanical force and site-directed mutations to demonstrate the presence of multiple unfolding pathways in a simple, two-state folding protein. We show that these multiple pathways have structurally different transition states, and that seemingly small changes in protein sequence and environment can strongly modulate the flux between the pathways. These results suggest that in vivo, the crowded cellular environment could strongly influence the mechanisms of protein folding and unfolding. Our study resolves the apparent dichotomy between experimental and theoretical studies, and highlights the advantage of using a multipronged approach to reveal the complexities of a protein's free-energy landscape.

Structure of the carboxypeptidase B complex with N-sulfamoyl-L-phenylalanine - a transition state analog of non-specific substrate.

PubMed

Akparov, Valery; Timofeev, Vladimir; Khaliullin, Ilyas; Švedas, Vytas; Kuranova, Inna

2018-03-01

Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However, its ability to discriminate substrates with hydrophobic, hydrophilic, and charged side chains is not well understood. We report structure of CPB complex with a transition state analog N-sulfamoyl-L-phenylalanine solved at 1.74Å. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center. Side chain of the non-specific substrate analog SPhe in comparison with that of specific substrate analog SArg (reported earlier) not only loses favorable electrostatic interactions and two hydrogen bonds with Asp255 and three fixed water molecules, but is forced to be in the unfavorable hydrophilic environment. Thus, Ser207, Gly253, Tyr248, and Asp255 residues play major role in the substrate recognition by S1'-subsite.

Efficient Deterministic Finite Automata Minimization Based on Backward Depth Information

PubMed Central

Liu, Desheng; Huang, Zhiping; Zhang, Yimeng; Guo, Xiaojun; Su, Shaojing

2016-01-01

Obtaining a minimal automaton is a fundamental issue in the theory and practical implementation of deterministic finite automatons (DFAs). A minimization algorithm is presented in this paper that consists of two main phases. In the first phase, the backward depth information is built, and the state set of the DFA is partitioned into many blocks. In the second phase, the state set is refined using a hash table. The minimization algorithm has a lower time complexity O(n) than a naive comparison of transitions O(n2). Few states need to be refined by the hash table, because most states have been partitioned by the backward depth information in the coarse partition. This method achieves greater generality than previous methods because building the backward depth information is independent of the topological complexity of the DFA. The proposed algorithm can be applied not only to the minimization of acyclic automata or simple cyclic automata, but also to automata with high topological complexity. Overall, the proposal has three advantages: lower time complexity, greater generality, and scalability. A comparison to Hopcroft’s algorithm demonstrates experimentally that the algorithm runs faster than traditional algorithms. PMID:27806102

Platinum(II) diimine complexes with catecholate ligands bearing imide electron-acceptor groups: synthesis, crystal structures, (spectro)electrochemical and EPR studies, and electronic structure.

PubMed

Shavaleev, Nail M; Davies, E Stephen; Adams, Harry; Best, Jonathan; Weinstein, Julia A

2008-03-03

A series of catechols with attached imide functionality (imide = phthalimide PHT, 1,8-naphthalimide NAP, 1,4,5,8-naphthalenediimide NDI, and NAP-NDI) has been synthesized and coordinated to the Pt (II)(bpy*) moiety, yielding Pt(bpy*)(cat-imide) complexes (bpy* = 4,4'-di- tert-butyl-2,2'-bipyridine). X-ray crystal structures of PHT and NAP complexes show a distorted square-planar arrangement of ligands around the Pt center. Both complexes form "head-to-tail" dimers in the solid state through remarkably short unsupported Pt...Pt contacts of 3.208 (PHT) and 3.378 A (NAP). The Pt(bpy*)(cat-imide) complexes are shown to combine optical (absorption) and electrochemical properties of the catecholate (electron-donor) and imide (electron-acceptor) groups. The complexes show a series of reversible reduction processes in the range from -0.5 to -1.9 V vs Fc (+)/Fc, which are centered on either bpy* or imide groups, and a reversible oxidation process at +0.07 to +0.14 V, which is centered on the catecholate moiety. A combination of UV-vis absorption spectroscopy, cyclic voltammetry, UV-vis spectroelectrochemistry, and EPR spectroscopy has allowed assignment of the nature of frontier orbitals in Pt(bpy*)(cat-imide) complexes. The HOMO in Pt(bpy*)(cat-imide) is centered on the catechol ligand, while the LUMO is localized either on bpy* or on the imide group, depending on the nature of the imide group involved. Despite the variations in the nature of the LUMO, the lowest-detectable electronic transition in all Pt(bpy*)(cat-imide) complexes has predominantly ligand-to-ligand (catechol-to-diimine) charge-transfer nature (LLCT) and involves a bpy*-based unoccupied molecular orbital in all cases. The LLCT transition in all Pt(bpy*)(cat-imide) complexes appears at 530 nm in CH2Cl2 and is strongly negatively solvatochromic. The energy of this transition is remarkably insensitive to the imide group present, indicating lack of electronic communication between the imide and the catechol moieties within the cat-imide ligand. The high extinction coefficient, approximately 6 x 10(3) L mol(-1) cm(-1) of this predominantly LLCT transition is the result of the Pt orbital contribution, as revealed by EPR spectroscopy of the complexes in various redox states. The CV profile of the oxidation process of Pt(bpy*)(cat-imide) in CH2Cl2 and DMF is concentration dependent, as was shown for NDI and PHT complexes as typical examples. Oxidation appears as a simple diffusion-limited process at low concentrations, with an increasing anodic-to-cathodic peak separation eventually resolving as two independent consecutive waves as the concentration of the complex increases. It is suggested that aggregation of the complexes in the diffusion layer in the course of oxidation is responsible for the observed concentration dependence. Overall, the Pt(bpy*)(cat-imide) complexes are electrochromic compounds in which a series of stepwise reversible redox processes in the potential range from 0.2 to -2 V (vs Fc (+)/Fc) leads to tuneable absorbencies between 300 and 850 nm.

Shape Transitional Nuclei: What can we learn from the Yrare States? or Hello the Double Vacuum; Goodbye β-vibrations!

NASA Astrophysics Data System (ADS)

Sharpey-Schafer, J. F.; Mullins, S. M.; Bark, R. A.; Gueorguieva, E.; Kau, J.; Komati, F.; Lawrie, J. J.; Maine, P.; Minkova, A.; Murray, S. H. T.; Ncapayi, N. J.; Vymers, P.

2008-05-01

The results of our measurements on the yrare states up to spin 20ℏ in 152,154,155Gd, using (α,xn) reactions and the AFRODITE γ-ray spectrometer, are presented. We find that in 155Gd the decay scheme is divided into levels feeding the [505]11/2- band, that is extruded by the prolate deformation from the h11/2 orbital, and levels feeding the i13/2[651]3/2+ intruder orbital and the h9/2[521]3/2- orbital. The decay scheme of 154Gd is very complex. We find no evidence for the existence of β-vibrational levels below 1.5 MeV. We discover that the level scheme can be best understood as a set of collective states built on the ground state configuration |01+> plus a ``congruent'' set of collective states based on the |02+> state at 681 keV. The data suggest that this second vacuum has reduced pairing. Our data do not support IBA and phonon interpretations of these transitional nuclei.

Simple Deterministically Constructed Recurrent Neural Networks

NASA Astrophysics Data System (ADS)

Rodan, Ali; Tiňo, Peter

A large number of models for time series processing, forecasting or modeling follows a state-space formulation. Models in the specific class of state-space approaches, referred to as Reservoir Computing, fix their state-transition function. The state space with the associated state transition structure forms a reservoir, which is supposed to be sufficiently complex so as to capture a large number of features of the input stream that can be potentially exploited by the reservoir-to-output readout mapping. The largely "black box" character of reservoirs prevents us from performing a deeper theoretical investigation of the dynamical properties of successful reservoirs. Reservoir construction is largely driven by a series of (more-or-less) ad-hoc randomized model building stages, with both the researchers and practitioners having to rely on a series of trials and errors. We show that a very simple deterministically constructed reservoir with simple cycle topology gives performances comparable to those of the Echo State Network (ESN) on a number of time series benchmarks. Moreover, we argue that the memory capacity of such a model can be made arbitrarily close to the proved theoretical limit.

Observation of a Rare Earth Ion–Extractant Complex Arrested at the Oil–Water Interface During Solvent Extraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bu, Wei; Yu, Hao; Luo, Guangming

2014-09-11

Selective extraction of metal ions from a complex aqueous mixture into an organic phase is used to separate toxic or radioactive metals from polluted environments and nuclear waste, as well as to produce industrially relevant metals, such as rare earth ions. Selectivity arises from the choice of an extractant amphiphile, dissolved in the organic phase, which interacts preferentially with the target metal ion. The extractant-mediated process of ion transport from an aqueous to an organic phase takes place at the aqueous–organic interface; nevertheless, little is known about the molecular mechanism of this process despite its importance. Although state-of-the-art X-ray scatteringmore » is uniquely capable of probing molecular ordering at a liquid–liquid interface with subnanometer spatial resolution, utilizing this capability to investigate interfacial dynamical processes of short temporal duration remains a challenge. We show that a temperature-driven adsorption transition can be used to turn the extraction on and off by controlling adsorption and desorption of extractants at the oil–water interface. Lowering the temperature through this transition immobilizes a supramolecular ion–extractant complex at the interface during the extraction of rare earth erbium ions. Under the conditions of these experiments, the ion–extractant complexes condense into a two-dimensional inverted bilayer, which is characterized on the molecular scale with synchrotron X-ray reflectivity and fluorescence measurements. Raising the temperature above the transition leads to Er ion extraction as a result of desorption of ion–extractant complexes from the interface into the bulk organic phase. XAFS measurements of the ion–extractant complexes in the bulk organic phase demonstrate that they are similar to the interfacial complexes.« less

Dynamics of electronic transitions and reemission spectra of attosecond electromagnetic pulses

NASA Astrophysics Data System (ADS)

Matveev, V. I.; Makarov, D. N.

2014-05-01

The processes of reemission of attosecond electromagnetic pulses by systems in nonstationary states have been considered. The probabilities of the reemission of attosecond electromagnetic pulses at the resonance charge exchange of a proton on a hydrogen atom and at the decay of a quasistationary state, as well as the probabilities of the reemission of attosecond pulses by a system in a resonance external field, have been calculated as examples. The developed method can be applied to more complex targets, including targets in the collision state, and to various chemical reactions.

Johari-Goldstein Relaxation Far Below Tg: Experimental Evidence for the Gardner Transition in Structural Glasses?

NASA Astrophysics Data System (ADS)

Geirhos, K.; Lunkenheimer, P.; Loidl, A.

2018-02-01

Experimental evidence for the Gardner transition, theoretically predicted to arise deep in the glassy state of matter, is scarce. At this transition, the energy landscape sensed by the particles forming the glass is expected to become more complex. In the present Letter, we report the dielectric response of two typical glass formers with well-pronounced Johari-Goldstein β relaxation, following this response down to unprecedented low temperatures, far below the glass transition. As the Johari-Goldstein process is believed to arise from the local structure of the energy landscape, its investigation seems an ideal tool to seek evidence for the Gardner transition. Indeed, we find an unusual broadening of the β relaxation below about 110 K for sorbitol and 100 K for xylitol, in excess of the expected broadening arising from a distribution of energy barriers. These results are well consistent with the presence of the Gardner transition in canonical structural glass formers.

Thermodynamic, crystallographic, and dielectric study of the nature of glass transitions in cyclo-octanol

NASA Astrophysics Data System (ADS)

Puertas, Ricardo; Rute, Maria A.; Salud, Josep; López, David O.; Diez, Sergio; van Miltenburg, J. Kees; Pardo, Luis C.; Tamarit, Josep Ll.; Barrio, Maria; Pérez-Jubindo, Miguel A.; de La Fuente, Maria R.

2004-06-01

The stable solid polymorphism of cyclooctanol (C8H16O, for short C8 OH) is revealed to be a complex problem and only two stable solid phases, denoted on cooling from the liquid as phases I and II, are found using static (thermodynamic and x-ray diffraction) as well as dynamic (dielectric spectroscopy) experimental techniques. Both solid phases are known to exhibit glass transitions if they are cooled down fast enough to prevent transition to ordered crystalline states. Although glass transitions corresponding to both phases had been well documented by means of specific heat measurements, x-ray measurements constitute, as far as we know, the first evidence from the structural point of view. In addition, a great amount of dielectric works devoted to phase I and its glass transition, were published in the past but next to nothing relating to the dielectric properties of phase II and its glass transition. The nature of the disorder of phase II will be discussed.

Formation of novel transition metal hydride complexes with ninefold hydrogen coordination

PubMed Central

Takagi, Shigeyuki; Iijima, Yuki; Sato, Toyoto; Saitoh, Hiroyuki; Ikeda, Kazutaka; Otomo, Toshiya; Miwa, Kazutoshi; Ikeshoji, Tamio; Orimo, Shin-ichi

2017-01-01

Ninefold coordination of hydrogen is very rare, and has been observed in two different hydride complexes comprising rhenium and technetium. Herein, based on a theoretical/experimental approach, we present evidence for the formation of ninefold H- coordination hydride complexes of molybdenum ([MoH9]3−), tungsten ([WH9]3−), niobium ([NbH9]4−) and tantalum ([TaH9]4−) in novel complex transition-metal hydrides, Li5MoH11, Li5WH11, Li6NbH11 and Li6TaH11, respectively. All of the synthesized materials are insulated with band gaps of approximately 4 eV, but contain a sufficient amount of hydrogen to cause the H 1s-derived states to reach the Fermi level. Such hydrogen-rich materials might be of interest for high-critical-temperature superconductivity if the gaps close under compression. Furthermore, the hydride complexes exhibit significant rotational motions associated with anharmonic librations at room temperature, which are often discussed in relation to the translational diffusion of cations in alkali-metal dodecahydro-closo-dodecaborates and strongly point to the emergence of a fast lithium conduction even at room temperature. PMID:28287143

Entropy, complexity, and Markov diagrams for random walk cancer models.

PubMed

Newton, Paul K; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

2014-12-19

The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.

Entropy, complexity, and Markov diagrams for random walk cancer models

NASA Astrophysics Data System (ADS)

Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

2014-12-01

The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.

Insight into the structure of photosynthetic LH2 aggregate from spectroscopy simulations.

PubMed

Rancova, Olga; Sulskus, Juozas; Abramavicius, Darius

2012-07-12

Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.

Free-energy landscape of ion-channel voltage-sensor–domain activation

PubMed Central

Delemotte, Lucie; Kasimova, Marina A.; Klein, Michael L.; Tarek, Mounir; Carnevale, Vincenzo

2015-01-01

Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations. PMID:25535341

Free-energy landscape of ion-channel voltage-sensor-domain activation.

PubMed

Delemotte, Lucie; Kasimova, Marina A; Klein, Michael L; Tarek, Mounir; Carnevale, Vincenzo

2015-01-06

Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations.

Status in calculating electronic excited states in transition metal oxides from first principles.

PubMed

Bendavid, Leah Isseroff; Carter, Emily Ann

2014-01-01

Characterization of excitations in transition metal oxides is a crucial step in the development of these materials for photonic and optoelectronic applications. However, many transition metal oxides are considered to be strongly correlated materials, and their complex electronic structure is challenging to model with many established quantum mechanical techniques. We review state-of-the-art first-principles methods to calculate charged and neutral excited states in extended materials, and discuss their application to transition metal oxides. We briefly discuss developments in density functional theory (DFT) to calculate fundamental band gaps, and introduce time-dependent DFT, which can model neutral excitations. Charged excitations can be described within the framework of many-body perturbation theory based on Green's functions techniques, which predominantly employs the GW approximation to the self-energy to facilitate a feasible solution to the quasiparticle equations. We review the various implementations of the GW approximation and evaluate each approach in its calculation of fundamental band gaps of many transition metal oxides. We also briefly review the related Bethe-Salpeter equation (BSE), which introduces an electron-hole interaction between GW-derived quasiparticles to describe accurately neutral excitations. Embedded correlated wavefunction theory is another framework used to model localized neutral or charged excitations in extended materials. Here, the electronic structure of a small cluster is modeled within correlated wavefunction theory, while its coupling to its environment is represented by an embedding potential. We review a number of techniques to represent this background potential, including electrostatic representations and electron density-based methods, and evaluate their application to transition metal oxides.

Trans influence on the rate of reductive elimination. Reductive elimination of amines from isomeric arylpalladium amides with unsymmetrical coordination spheres.

PubMed

Yamashita, Makoto; Cuevas Vicario, Jose V; Hartwig, John F

2003-12-31

To determine the trans effect on the rates of reductive eliminations from arylpalladium(II) amido complexes, the reactions of arylpalladium amido complexes bearing symmetrical and unsymmetrical DPPF (DPPF = bis(diphenylphosphino)ferrocene) derivatives were studied. THF solutions of LPd(Ar)(NMeAr') (L = DPPF, DPPF-OMe, DPPF-CF3, DPPF-OMe,Ph, DPPF-Ph,CF3, and DPPF-OMe,CF3; Ar = C6H4-4-CF3; Ar' = C6H4-4-CH3, Ph, and C6H4-4-OMe) underwent C-N bond forming reductive elimination at -15 C to form the corresponding N-methyldiarylamine in high yield. Complexes ligated by symmetrical DPPF derivatives with electron-withdrawing substituents on the DPPF aryl groups underwent reductive elimination faster than complexes ligated by symmetrical DPPF derivatives with electron-donating substituents on the ligand aryl groups. Studies of arylpalladium amido complexes containing unsymmetrical DPPF ligands revealed several trends. First, the complex with the weaker donor trans to nitrogen and the stronger donor trans to the palladium-bound aryl group underwent reductive elimination faster than the regioisomeric complex with the stronger donor trans to nitrogen and the weaker donor trans to the palladium-bound aryl group. Second, the effect of varying the substituents on the phosphorus donor trans to the nitrogen was larger than the effect of varying the substituents on the phosphorus donor trans to the palladium-bound aryl group. Third, the difference in rate between the isomeric arylpalladium amido complexes was similar in magnitude to the differences in rates resulting from conventional variation of substituents on the symmetric phosphine ligands. This result suggests that the geometry of the complex is equal in importance to the donating ability of the dative ligands. The ratio of the differences in rates of reaction of the isomeric complexes was similar to the relative populations of the two geometric isomers. This result and consideration of transition state geometries suggest that the reaction rates are controlled more by substituent effects on ground state stability than on transition state energies. In addition, variation of the aryl group at the amido nitrogen showed systematically that complexes with more electron-donating groups at nitrogen undergo faster reductive elimination than those with less electron-donating groups at nitrogen.

First Principles Based Simulation of Reaction-Induced Phase Transition in Hydrogen Storage and Other Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ge, Qingfeng

2014-08-31

This major part of this proposal is simulating hydrogen interactions in the complex metal hydrides. Over the period of DOE BES support, key achievements include (i) Predicted TiAl 3Hx as a precursor state for forming TiAl 3 through analyzing the Ti-doped NaAlH 4 and demonstrated its catalytic role for hydrogen release; (ii) Explored the possibility of forming similar complex structures with other 3d transition metals in NaAlH 4 as well as the impact of such complex structures on hydrogen release/uptake; (iii) Demonstrated the role of TiAl 3 in hydriding process; (iv) Predicted a new phase of NaAlH 4 that linksmore » to Na3AlH6 using first-principles metadynamics; (v) Examined support effect on hydrogen release from supported/encapsulated NaAlH 4; and (vi) Expanded research scope beyond hydrogen storage. The success of our research is documented by the peer-reviewed publications.« less

The perspectives of femtosecond imaging and spectroscopy of complex materials using electrons

NASA Astrophysics Data System (ADS)

Ruan, Chong-Yu; Duxbury, Phiilp M.; Berz, Martin

2014-09-01

The coexistence of various electronic and structural phases that are close in free-energy is a hallmark in strongly correlated electron systems with emergent properties, such as metal-insulator transition, colossal magnetoresistance, and high-temperature superconductivity. The cooperative phase transitions from one functional state to another can involve entanglements between the electronically and structurally ordered states, hence deciphering the fundamental mechanisms is generally difficult and remains very active in condensed matter physics and functional materials research. We outline the recent ultrafast characterizations of 2D charge-density wave materials, including the nonequilibrium electron dynamics unveiled by ultrafast optical spectroscopy-based techniques sensitive to the electronic order parameter. We also describe the most recent findings from ultrafast electron crystallography, which provide structural aspects to correlate lattice dynamics with electronic evolutions to address the two sides of a coin in the ultrafast switching of a cooperative state. Combining these results brings forth new perspectives and a fuller picture in understanding lightmatter interactions and various switching mechanisms in cooperative systems with many potential applications. We also discuss the prospects of implementing new ultrafast electron imaging as a local probe incorporated with femtosecond select-area diffraction, imaging and spectroscopy to provide a full scope of resolution to tackle the more challenging complex phase transitions on the femtosecond-nanometer scale all at once based on a recent understanding of the spacespace- charge-driven emittance limitation on the ultimate performance of these devices. The projection shows promising parameter space for conducting ultrafast electron micordiffraction at close to single-shot level, which is supported by the latest experimental characterization of such a system.

Three Conformational Snapshots of the Hepatitis Virus NS3 Helicase Reveal a Ratchet Translocation Mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gu, M.; Rice, C

2010-01-01

A virally encoded superfamily-2 (SF2) helicase (NS3h) is essential for the replication of hepatitis C virus, a leading cause of liver disease worldwide. Efforts to elucidate the function of NS3h and to develop inhibitors against it, however, have been hampered by limited understanding of its molecular mechanism. Here we show x-ray crystal structures for a set of NS3h complexes, including ground-state and transition-state ternary complexes captured with ATP mimics (ADP {center_dot} BeF{sub 3} and ADP {center_dot} AlF{sub 4}{sup -}). These structures provide, for the first time, three conformational snapshots demonstrating the molecular basis of action for a SF2 helicase. Uponmore » nucleotide binding, overall domain rotation along with structural transitions in motif V and the bound DNA leads to the release of one base from the substrate base-stacking row and the loss of several interactions between NS3h and the 3{prime} DNA segment. As nucleotide hydrolysis proceeds into the transition state, stretching of a 'spring' helix and another overall conformational change couples rearrangement of the (d)NTPase active site to additional hydrogen-bonding between NS3h and DNA. Together with biochemistry, these results demonstrate a 'ratchet' mechanism involved in the unidirectional translocation and define the step size of NS3h as one base per nucleotide hydrolysis cycle. These findings suggest feasible strategies for developing specific inhibitors to block the action of this attractive, yet largely unexplored drug target.« less

Resonance-enhanced two-photon ionization spectroscopy and theoretical calculations of 3,5-difluoroanisole and its Ar-containing complex.

PubMed

Zhang, Lijuan; Dong, Changwu; Cheng, Min; Hu, Lili; Du, Yikui; Zhu, Qihe; Zhang, Cunhao

2012-10-01

The structure and vibrations of 3,5-difluoroanisole (3,5-DFA) in the first electronically excited (S(1)) state were studied by mass-analyzed resonant two-photon ionization (R2PI) technique as well as the quantum chemical calculations. The ab initio and density functional theory (DFT) calculations reveal that only one structure is stable for each of the S(0), S(1), and D(0) states. In the one color R2PI spectrum, the band origin of the S(1)←S(0) electronic transition (0(0) band) of 3,5-DFA is found to be 37,595±3 cm(-1). In the S(1) state, most of the bands observed are related to the in-plane ring deformation and out-of-plane bending vibrations. The adiabatic ionization energy (IE) of 3,5-DFA is determined to be 70,096±15 cm(-1) by the two color R2PI technique, in agreement with the values predicted by the DFT approaches. The dihalogen-substitution effects on the molecular structure, vibrational frequencies, and electronic transition and ionization energies were discussed in detail. The van der Waals complex of 3,5-DFA with argon (3,5-DFA···Ar) was also observed and studied. The 0(0) band of 3,5-DFA···Ar complex is red-shifted by about 9 cm(-1) with respect to that of 3,5-DFA. Both the experimental data and the calculated results indicate that the formation of 3,5-DFA···Ar complex gives only a weak influence on the properties of 3,5-DFA moiety. Copyright © 2012 Elsevier B.V. All rights reserved.

Grover's unstructured search by using a transverse field

NASA Astrophysics Data System (ADS)

Jiang, Zhang; Rieffel, Eleanor; Wang, Zhihui

2017-04-01

We design a circuit-based quantum algorithm to search for a needle in a haystack, giving the same quadratic speedup achieved by Grover's original algorithm. In our circuit-based algorithm, the problem Hamiltonian (oracle) and a transverse field (instead of Grover's diffusion operator) are applied to the system alternatively. We construct a periodic time sequence such that the resultant unitary drives a closed transition between two states, which have high degrees of overlap with the initial state (even superposition of all states) and the target state, respectively. Let N =2n be the size of the search space. The transition rate in our algorithm is of order Θ(1 /√{ N}) , and the overlaps are of order Θ(1) , yielding a nearly optimal query complexity of T =√{ N}(π / 2√{ 2}) . Our algorithm is inspired by a class of algorithms proposed by Farhi et al., namely the Quantum Approximate Optimization Algorithm (QAOA); our method offers a route to optimizing the parameters in QAOA by restricting them to be periodic in time.

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging.

PubMed

Held, Michael; Schmitz, Michael H A; Fischer, Bernd; Walter, Thomas; Neumann, Beate; Olma, Michael H; Peter, Matthias; Ellenberg, Jan; Gerlich, Daniel W

2010-09-01

Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. Incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions and confusion between different functional states with similar morphology. We demonstrate generic applicability in different assays and perturbation conditions, including a candidate-based RNA interference screen for regulators of mitotic exit in human cells. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.

Ultrafast Spin Crossover in [FeII (bpy)3 ]2+ : Revealing Two Competing Mechanisms by Extreme Ultraviolet Photoemission Spectroscopy.

PubMed

Moguilevski, Alexandre; Wilke, Martin; Grell, Gilbert; Bokarev, Sergey I; Aziz, Saadullah G; Engel, Nicholas; Raheem, Azhr A; Kühn, Oliver; Kiyan, Igor Yu; Aziz, Emad F

2017-03-03

Photoinduced spin-flip in Fe II complexes is an ultrafast phenomenon that has the potential to become an alternative to conventional processing and magnetic storage of information. Following the initial excitation by visible light into the singlet metal-to-ligand charge-transfer state, the electronic transition to the high-spin quintet state may undergo different pathways. Here we apply ultrafast XUV (extreme ultraviolet) photoemission spectroscopy to track the low-to-high spin dynamics in the aqueous iron tris-bipyridine complex, [Fe(bpy) 3 ] 2+ , by monitoring the transient electron density distribution among excited states with femtosecond time resolution. Aided by first-principles calculations, this approach enables us to reveal unambiguously both the sequential and direct de-excitation pathways from singlet to quintet state, with a branching ratio of 4.5:1. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the formation of molecules and solid-state compounds from the AGB to the PN phases

NASA Astrophysics Data System (ADS)

García-Hernández, D. A.; Manchado, A.

2016-07-01

During the asymptoyic giant branch (AGB) phase, different elements are dredge- up to the stellar surface depending on progenitor mass and metallicity. When the mass loss increases at the end of the AGB, a circumstellar dust shell is formed, where different (C-rich or O-rich) molecules and solid-state compounds are formed. These are further processed in the transition phase between AGB stars and planetary nebulae (PNe) to create more complex organic molecules and inorganic solid-state compounds (e.g., polycyclic aromatic hydrocarbons, fullerenes, and graphene precursors in C-rich environments and oxides and crystalline silicates in O-rich ones). We present an observational review of the different molecules and solid-state materials that are formed from the AGB to the PN phases. We focus on the formation routes of complex fullerene (and fullerene-based) molecules as well as on the level of dust processing depending on metallicity.

Aging, memory, and nonhierarchical energy landscape of spin jam

PubMed Central

Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

2016-01-01

The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes. PMID:27698141

Frustration across the periodic table: heterolytic cleavage of dihydrogen by metal complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bullock, R. Morris; Chambers, Geoffrey M.

2017-07-24

This Perspective examines the field of Frustrated Lewis Pairs (FLPs) in the context of transition metal mediated heterolytic cleavage of H2, with a particular emphasis on molecular complexes bearing an intramolecular Lewis base. FLPs have traditionally been associated with group compounds, yet many transition metal reactions support a broader classification of FLPs to include certain types of transition metal complexes with reactivity resembling main group based FLPs. This article surveys transition metal complexes that heterolytically cleave H2, which vary in the degree that the Lewis pairs within these systems interact. Particular attention is focused on complexes bearing a pendant aminemore » function as the base. Consideration of transition metal compounds in the context of FLPs can inspire new innovations and improvements in transition metal catalysis.« less

Long-term population, productivity, and energy use trends in the sequence of leading capitalist nations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

LePoire, D. J.

2010-10-01

There are many theories on why sustainable science, technology, and commerce emerged first in Western Europe rather than elsewhere. A general theory is that the geography of Europe facilitated the development of diverse and independent states and resultant competition among them. Over the past 500 years, the sequence of leading states began with Portugal and the Netherlands on the edge of continental Western Europe, then moved to the British Isles, and finally moved across the Atlantic Ocean to the United States. The transitions of leadership from one state to another occurred about every 100 years. This sequence suggests that leadershipmore » moves from smaller states to larger states (although not to the largest existing state at the time), perhaps because larger states have the flexibility to develop more complex organizational processes and adapt new technology. To explore this theory further, this paper analyzes state population data at the beginning and end of each leadership period. The data reveal an accelerating initial population sequence. Further understanding is gained from comparing the populations of the preceding and succeeding states at the time of each transition: the succeeding state's population is usually about two times larger than that of the preceding state. It is also seen that over time, the new organizational processes and technologies developed by the leading state are diffused and adapted by other states. Evidence of the effects of this diffusion should be seen in the dynamics of relative productivity and energy use (since the relative advantage of new ideas and technology can be maintained for a short period of about 100 years). This paper investigates these trends in population, trade, and resources to provide insight on possible future transitions.« less

Seismology of adolescent neutron stars: Accounting for thermal effects and crust elasticity

NASA Astrophysics Data System (ADS)

Krüger, C. J.; Ho, W. C. G.; Andersson, N.

2015-09-01

We study the oscillations of relativistic stars, incorporating key physics associated with internal composition, thermal gradients and crust elasticity. Our aim is to develop a formalism which is able to account for the state-of-the-art understanding of the complex physics associated with these systems. As a first step, we build models using a modern equation of state including composition gradients and density discontinuities associated with internal phase transitions (like the crust-core transition and the point where muons first appear in the core). In order to understand the nature of the oscillation spectrum, we carry out cooling simulations to provide realistic snapshots of the temperature distribution in the interior as the star evolves through adolescence. The associated thermal pressure is incorporated in the perturbation analysis, and we discuss the presence of g -modes arising as a result of thermal effects. We also consider interface modes due to phase-transitions and the gradual formation of the star's crust and the emergence of a set of shear modes.

Ground-state oxygen holes and the metal–insulator transition in the negative charge-transfer rare-earth nickelates

PubMed Central

Bisogni, Valentina; Catalano, Sara; Green, Robert J.; Gibert, Marta; Scherwitzl, Raoul; Huang, Yaobo; Strocov, Vladimir N.; Zubko, Pavlo; Balandeh, Shadi; Triscone, Jean-Marc; Sawatzky, George; Schmitt, Thorsten

2016-01-01

The metal–insulator transition and the intriguing physical properties of rare-earth perovskite nickelates have attracted considerable attention in recent years. Nonetheless, a complete understanding of these materials remains elusive. Here we combine X-ray absorption and resonant inelastic X-ray scattering (RIXS) spectroscopies to resolve important aspects of the complex electronic structure of rare-earth nickelates, taking NdNiO3 thin film as representative example. The unusual coexistence of bound and continuum excitations observed in the RIXS spectra provides strong evidence for abundant oxygen holes in the ground state of these materials. Using cluster calculations and Anderson impurity model interpretation, we show that distinct spectral signatures arise from a Ni 3d8 configuration along with holes in the oxygen 2p valence band, confirming suggestions that these materials do not obey a conventional positive charge-transfer picture, but instead exhibit a negative charge-transfer energy in line with recent models interpreting the metal–insulator transition in terms of bond disproportionation. PMID:27725665

A set of new transition metal-based coordination complexes dependent upon Hpztza ligand (Hpztza=2-(5-(pyrazin-2-yl)-2H-tetrazol-2-yl) acetic acid)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang Jie; Shen Lei; Yang Gaowen, E-mail: ygwsx@126.com

2012-02-15

Reaction of MCl{sub 2}{center_dot}4H{sub 2}O (M=Zn, Cd, Mn, Co, Ni) with 2-(5-(pyrazin-2-yl)-2H-tetrazol-2-yl) acetic acid (Hpztza) yielded a set of new M(II)/pztza complexes, [Cd(pztza){sub 2}(H{sub 2}O){sub 6}]{center_dot}3H{sub 2}O{center_dot}(Hpztza) (1), [M(pztza){sub 2}(H{sub 2}O){sub 2}; M=Cd(2), Zn(7), Mn(9)], [Cd(pztza){sub 2}]{center_dot}2(CH{sub 3}OH) (3), [Co(pztza){sub 2}(H{sub 2}O){sub 2}]{center_dot}6H{sub 2}O (4), [Co(pztza)(H{sub 2}O)Cl] (6) and [M(pztza){sub 2}(H{sub 2}O){sub 2}]{center_dot}2H{sub 2}O [M=Co(5), Zn(8), Ni(10)]. These compounds were structurally characterized by elemental analysis, IR spectroscopy and X-ray single-crystal diffraction. Complex 1 featured a mononuclear structure, complexes 4, 5, 7, 8, 10 showed 1D chains and complexes 2, 3, 6, 9 displayed 2D layer structures. Furthermore, the luminescence propertiesmore » of 1-10 were investigated at room temperature in the solid state. - Graphical abstract: Ten new coordination polymers with 2-(5-(pyrazin-2-yl)-2H-tetrazol-2-yl) acetic acid (Hpztza) ligand have been synthesized and their structures have been characterized. All of the complexes show photoluminescence at room temperature. Highlights: Black-Right-Pointing-Pointer Ten novel transition metal-based coordination complexes with 2-(5-(pyrazin-2-yl)-2H-tetrazol-2-yl) acetic acid (Hpztza) are reported. Black-Right-Pointing-Pointer Complexes 1-10 are described as mononuclear structure, 1D and 2D frameworks with diverse architecture. Black-Right-Pointing-Pointer Six coordination complexes show emission at room temperature in the solid state.« less

Nonlinear absorption dynamics using field-induced surface hopping: zinc porphyrin in water.

PubMed

Röhr, Merle I S; Petersen, Jens; Wohlgemuth, Matthias; Bonačić-Koutecký, Vlasta; Mitrić, Roland

2013-05-10

We wish to present the application of our field-induced surface-hopping (FISH) method to simulate nonlinear absorption dynamics induced by strong nonresonant laser fields. We provide a systematic comparison of the FISH approach with exact quantum dynamics simulations on a multistate model system and demonstrate that FISH allows for accurate simulations of nonlinear excitation processes including multiphoton electronic transitions. In particular, two different approaches for simulating two-photon transitions are compared. The first approach is essentially exact and involves the solution of the time-dependent Schrödinger equation in an extended manifold of excited states, while in the second one only transiently populated nonessential states are replaced by an effective quadratic coupling term, and dynamics is performed in a considerably smaller manifold of states. We illustrate the applicability of our method to complex molecular systems by simulating the linear and nonlinear laser-driven dynamics in zinc (Zn) porphyrin in the gas phase and in water. For this purpose, the FISH approach is connected with the quantum mechanical-molecular mechanical approach (QM/MM) which is generally applicable to large classes of complex systems. Our findings that multiphoton absorption and dynamics increase the population of higher excited states of Zn porphyrin in the nonlinear regime, in particular in solution, provides a means for manipulating excited-state properties, such as transient absorption dynamics and electronic relaxation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles analysis of X-ray magnetic circular dichroism for transition metal complex oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ikeno, Hidekazu, E-mail: h-ikeno@21c.osakafu-u.ac.jp

2016-10-14

X-ray magnetic circular dichroism (XMCD) is widely used for the characterization of magnetism of materials. However, information from XMCD related to the atomic, electronic, and magnetic structures is not fully utilized due to the lack of reliable theoretical tools for spectral analysis. In this work, the first-principles configuration interaction (CI) calculations for X-ray absorption spectra developed by the author were extended for the calculation of XMCD, where the Zeeman energy was taken into the Hamiltonian of the CI to mimic magnetic polarization in the solid state. This technique was applied to interpret the L{sub 2,3} XMCD from 3d transition metalmore » complex oxides, such as NiFe{sub 2}O{sub 4} and FeTiO{sub 3}. The experimental XMCD spectra were quantitatively reproduced using this method. The oxidation states as well as the magnetic ordering between transition metal ions on crystallographically different sites in NiFe{sub 2}O{sub 4} can be unambiguously determined. A first-principles analysis of XMCD in FeTiO{sub 3} revealed the presence of Fe{sup 3+} and Ti{sup 3+} ions, which indicates that the charge transfer from Fe to Ti ions occurs. The origin of magnetic polarization of Ti ions in FeTiO{sub 3} was also discussed.« less

The effect of basis set and exchange-correlation functional on time-dependent density functional theory calculations within the Tamm-Dancoff approximation of the x-ray emission spectroscopy of transition metal complexes.

PubMed

Roper, Ian P E; Besley, Nicholas A

2016-03-21

The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals.

Gas Phase Conformations and Methyl Internal Rotation for 2-PHENYLETHYL Methyl Ether and its Argon Van Der Waals Complex from Fourier Transform Microwave Spectroscopy

NASA Astrophysics Data System (ADS)

Gurusinghe, Ranil M.; Tubergen, Michael

2015-06-01

A mini-cavity microwave spectrometer was used to record the rotational spectra arising from 2-phenylethyl methyl ether and its weakly bonded argon complex in the frequency range of 10.5 - 22 GHz. Rotational spectra were found for two stable conformations of the monomer: anti-anti and gauche-anti, which are 1.4 kJ mol-1 apart in energy at wB97XD/6-311++G(d,p) level. Doubled rotational transitions, arising from internal motion of the methyl group, were observed for both conformers. The program XIAM was used to fit the rotational constants, centrifugal distortion constants, and barrier to internal rotation to the measured transition frequencies of the A and E internal rotation states. The best global fit values of the rotational constants for the anti-anti conformer are A= 3799.066(3) MHz, B= 577.95180(17) MHz, C= 544.7325(3) MHz and the A state rotational constants of the gauche-anti conformer are A= 2676.1202(7) MHz, B= 760.77250(2) MHz, C= 684.78901(2) MHz. The rotational spectrum of 2-phenylethyl methyl ether - argon complex is consistent with the geometry where argon atom lies above the plane of the benzene moiety of gauche-anti conformer. Tunneling splittings were too small to resolve within experimental accuracy, likely due to an increase in three fold potential barrier when the argon complex is formed. Fitted rotational constants are A= 1061.23373(16) MHz, B= 699.81754(7) MHz, C= 518.33553(7) MHz. The lowest energy solvated ether - water complex with strong intermolecular hydrogen bonding has been identified theoretically. Progress on the assignment of the water complex will also be presented.

Steady-state and time-resolved studies on the photophysical properties of fullerene-pyropheophorbide a complexes in polar and nonpolar solvents

NASA Astrophysics Data System (ADS)

Ermilov, E. A.; Al-Omari, S.; Helmreich, M.; Jux, N.; Hirsch, A.; Röder, B.

2004-04-01

A novel monofullerene-bis(pyropheophorbide a) dyad has been photophysically characterized by steady-state as well as time-resolved techniques. It was revealed that in this complex strong and fast quenching of the first excited singlet state of the pyropheophorbide a (pyroPheo) molecule occurs by efficient photoinduced electron transfer to the fullerene moiety in both polar (DMF) and nonpolar (toluene) solvents. In DMF the energy of the charge-separated state is 0.94 eV and it undergoes directly transition to the ground state resulting in a very low value of photosensitized singlet oxygen generation. In contrast to the situation in a polar solvent, in toluene the charge-separated state lies above the exited triplet state of pyroPheo as well as that of C 60. It has been shown that in a nonpolar solvent a sufficient amount of singlet oxygen was generated by energy transfer from the excited triplet state of pyroPheo which has been populated via relaxation of the charge-separated state.

Chromium complexes for luminescence, solar cells, photoredox catalysis, upconversion, and phototriggered NO release

PubMed Central

Büldt, Laura A.

2017-01-01

Some complexes of Cr(iii) and Cr(0) have long been known to exhibit interesting photophysical and photochemical properties, but in the past few years important conceptual progress was made. This Perspective focuses on the recent developments of Cr(iii) complexes as luminophores and dyes for solar cells, their application in photoredox catalysis, their use as sensitizers in upconversion processes, and their performance as photochemical nitric oxide sources. The example of a luminescent Cr(0) isocyanide complex illustrates the possibility of obtaining photoactive analogues of d6 metal complexes that are commonly made from precious metals such as Ru(ii) or Ir(iii). The studies highlighted herein illustrate the favorable excited-state properties of robust first-row transition metal complexes with broad application potential. PMID:29163886

Chromium complexes for luminescence, solar cells, photoredox catalysis, upconversion, and phototriggered NO release.

PubMed

Büldt, Laura A; Wenger, Oliver S

2017-11-01

Some complexes of Cr(iii) and Cr(0) have long been known to exhibit interesting photophysical and photochemical properties, but in the past few years important conceptual progress was made. This Perspective focuses on the recent developments of Cr(iii) complexes as luminophores and dyes for solar cells, their application in photoredox catalysis, their use as sensitizers in upconversion processes, and their performance as photochemical nitric oxide sources. The example of a luminescent Cr(0) isocyanide complex illustrates the possibility of obtaining photoactive analogues of d 6 metal complexes that are commonly made from precious metals such as Ru(ii) or Ir(iii). The studies highlighted herein illustrate the favorable excited-state properties of robust first-row transition metal complexes with broad application potential.

Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

NASA Astrophysics Data System (ADS)

Swinburne, Thomas D.; Perez, Danny

2018-05-01

A massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

Ionic Salt Effect on the Phase Transition of PS-b-P2VP Copolymers

NASA Astrophysics Data System (ADS)

Kim, Bokyung; An, Hyungju; Ryu, Du Yeol; Kim, Jehan

2009-03-01

Solid-state electrolytes have long been considered as suitable candidates owing to the simple and easy processes for rechargeable battery manufactures, compared to conventional liquid electrolyte counterparts. Especially, polymer/salt systems involving PMMA and PVP complex forms have been studied since they provide stable electrochemical characteristics as well as mechanical properties. We studied the phase behavior of PS-b-P2VP upon the salt addition by small angle x-ray scattering (SAXS) and depolarized light scattering. Transition temperatures of block copolymer were significantly influenced by the salt addition in addition to the changes of d-spacings, which is caused by the effective coordinative interaction between P2VP block and salt. This study suggests a simple approach to solid-state block copolymer electrolytes.

Method of Continuous Variations: Applications of Job Plots to the Study of Molecular Associations in Organometallic Chemistry[**

PubMed Central

Renny, Joseph S.; Tomasevich, Laura L.; Tallmadge, Evan H.; Collum, David B.

2014-01-01

Applications of the method of continuous variations—MCV or the Method of Job—to problems of interest to organometallic chemists are described. MCV provides qualitative and quantitative insights into the stoichiometries underlying association of m molecules of A and n molecules of B to form AmBn. Applications to complex ensembles probe associations that form metal clusters and aggregates. Job plots in which reaction rates are monitored provide relative stoichiometries in rate-limiting transition structures. In a specialized variant, ligand- or solvent-dependent reaction rates are dissected into contributions in both the ground states and transition states, which affords insights into the full reaction coordinate from a single Job plot. Gaps in the literature are identified and critiqued. PMID:24166797

Heterogeneous to homogeneous melting transition visualized with ultrafast electron diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

The ultrafast laser excitation of matters leads to non-equilibrium states with complex solid-liquid phase transition dynamics. We used electron diffraction at mega-electronvolt energies to visualize the ultrafast melting of gold on the atomic scale length. For energy densities approaching the irreversible melting regime, we first observed heterogeneous melting on time scales of 100 ps to 1000 ps, transitioning to homogeneous melting that occurs catastrophically within 10-20 ps at higher energy densities. We showed evidence for the heterogeneous coexistence of solid and liquid. We determined the ion and electron temperature evolution and found superheated conditions. Our results constrain the electron-ion couplingmore » rate, determine the Debye temperature and reveal the melting sensitivity to nucleation seeds.« less

Magnetic circular dichroism of UCl 6– in the ligand-to-metal charge-transfer spectral region

DOE PAGES

Gendron, Frederic; Fleischauer, Valerie R.; Duignan, Thomas J.; ...

2017-06-23

Here, we present a combined ab initio theoretical and experimental study of the magnetic circular dichroism (MCD) spectrum of the octahedral UCl 6- complex ion in the UV-Vis spectral region. The ground state is an orbitally non-degenerate doublet E 5/2u and the MCD is a $C$-term spectrum caused by spin–orbit coupling. Calculations of the electronic spectrum at various levels of theory indicate that differential dynamic electron correlation has a strong influence on the energies of the dipole-allowed transitions and the envelope of the MCD spectrum. The experimentally observed bands are assigned to dipole-allowed ligand-to-metal charge transfer into the 5f shell,more » and 5f to 6d transitions. Charge transfer excitations into the U 6d shell appear at much higher energies. The MCD-allowed transitions can be assigned via their signs of the $C$-terms: Under O h double group symmetry, E 5/2u → E 5/2g transitions have negative $C$-terms whereas E 5/2u → F 3/2g transitions have positive $C$-terms if the ground state g-factor is negative, as it is the case for UCl 6-.« less

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.

Transition metal-chelating surfactant micelle templates for facile synthesis of mesoporous silica nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Hye Sun; Department of Materials Science and Engineering, Yonsei University, Seoul 120-749; Kim, Won Hee

2012-01-15

Highly ordered mesoporous silica nanoparticles with tunable morphology and pore-size are prepared by the use of a transition metal-chelating surfactant micelle complex using Co{sup 2+}, Ni{sup 2+}, Cu{sup 2+}, and Zn{sup 2+} ions. These metal ions formed a metal-P123 micelle complex in an aqueous solution, while the metal ions are chelated to the hydrophilic domain such as the poly(ethylene oxide) group of a P123 surfactant. The different complexation abilities of the utilized transition metal ions play an important role in determining the formation of nano-sized ordered MSNs due to the different stabilization constant of the metal-P123 complex. Consequently, from amore » particle length of 1700 nm in the original mesoporous silica materials, the particle length of ordered MSNs through the metal-chelating P123 micelle templates can be reduced to a range of 180-800 nm. Furthermore, the variation of pore size shows a slight change from 8.8 to 6.6 nm. In particular, the Cu{sup 2+}-chelated MSNs show only decreased particle size to 180 nm. The stability constants for the metal-P123 complex are calculated on the basis of molar conductance measurements in order to elucidate the formation mechanism of MSNs by the metal-chelating P123 complex templates. In addition, solid-state {sup 29}Si, {sup 13}C-NMR and ICP-OES measurements are used for quantitative characterization reveal that the utilized metal ions affect only the formation of a metal-P123 complex in a micelle as a template. - Graphical abstract: Metal-chelating surfactant micelle templates support a simple and facile preparations of size-tunable ordered MSNs. Black-Small-Square Highlights: Black-Right-Pointing-Pointer Facile preparation of mesoporous silica nanoparticles (MSNs) was achieved by metal-chelating surfactant micelle complex using Co{sup 2+}, Ni{sup 2+}, Cu{sup 2+}, and Zn{sup 2+} ions. Black-Right-Pointing-Pointer Different complexation of metal ions plays an important role in determining the formation of nano-sized ordered MSNs. Black-Right-Pointing-Pointer Systematic characterization of the synthesized materials was achieved by solid-state {sup 29}Si and {sup 13}C-NMR techniques, BET, FT-IR, and XPS. Black-Right-Pointing-Pointer Stability constants for the metal-P123 complex are calculated on the basis of molar conductance measurements in order to elucidate the formation mechanism.« less

Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.

PubMed

Lai, Cheng-Tsung; Li, Huei-Jiun; Yu, Weixuan; Shah, Sonam; Bommineni, Gopal R; Perrone, Victoria; Garcia-Diaz, Miguel; Tonge, Peter J; Simmerling, Carlos

2015-08-04

Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.

Fourier-transform spectroscopy and deperturbation analysis of the spin-orbit coupled A{sup 1}Σ{sup +} and b{sup 3}Π states of KRb

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alps, K.; Kruzins, A.; Tamanis, M.

Fourier-transform A{sup 1}Σ{sup +} − b{sup 3}Π → X{sup 1}Σ{sup +} laser-induced fluorescence spectra were recorded for the natural mixture of {sup 39,41}K{sup 85,87}Rb isotopologues produced in a heatpipe oven. Overall 4200 rovibronic term values of the spin-orbit coupled A{sup 1}Σ{sup +} and b{sup 3}Π states were determined with an uncertainty of about 0.01 cm{sup −1} in the energy range [10 850, 14 200] cm{sup −1} covering rotational quantum numbers J′ ∈ [3, 280]. Direct deperturbation analysis of the A ∼ b complex performed within the framework of the A{sup 1}Σ{sup +} ∼ b{sup 3}Π{sub Ω=0,1,2} coupled-channel approach reproduced experimental data withmore » a standard deviation of 0.004 cm{sup −1}. Initial parameters of the internuclear potentials and spin-orbit coupling functions along with the relevant transition dipole moments were obtained by performing the quasi-relativistic electronic structure calculations. The mass-invariant molecular parameters obtained from the fit were used to predict energy and radiative properties of the A ∼ b complex for low J levels of {sup 39}K{sup 85}Rb as well as for {sup 41}K{sup 87}Rb isotopologues, allowing us to identify the most reasonable candidates for the stimulated Raman transitions between the initial uppermost vibrational levels of the a{sup 3}Σ{sup +} and X{sup 1}Σ{sup +} states, the intermediate levels of the A ∼ b complex, and the lowest absolute ground X{sup 1}Σ{sup +}(v = 0, J = 0) state.« less

Small Modifications to Network Topology Can Induce Stochastic Bistable Spiking Dynamics in a Balanced Cortical Model

PubMed Central

McDonnell, Mark D.; Ward, Lawrence M.

2014-01-01

Abstract Directed random graph models frequently are used successfully in modeling the population dynamics of networks of cortical neurons connected by chemical synapses. Experimental results consistently reveal that neuronal network topology is complex, however, in the sense that it differs statistically from a random network, and differs for classes of neurons that are physiologically different. This suggests that complex network models whose subnetworks have distinct topological structure may be a useful, and more biologically realistic, alternative to random networks. Here we demonstrate that the balanced excitation and inhibition frequently observed in small cortical regions can transiently disappear in otherwise standard neuronal-scale models of fluctuation-driven dynamics, solely because the random network topology was replaced by a complex clustered one, whilst not changing the in-degree of any neurons. In this network, a small subset of cells whose inhibition comes only from outside their local cluster are the cause of bistable population dynamics, where different clusters of these cells irregularly switch back and forth from a sparsely firing state to a highly active state. Transitions to the highly active state occur when a cluster of these cells spikes sufficiently often to cause strong unbalanced positive feedback to each other. Transitions back to the sparsely firing state rely on occasional large fluctuations in the amount of non-local inhibition received. Neurons in the model are homogeneous in their intrinsic dynamics and in-degrees, but differ in the abundance of various directed feedback motifs in which they participate. Our findings suggest that (i) models and simulations should take into account complex structure that varies for neuron and synapse classes; (ii) differences in the dynamics of neurons with similar intrinsic properties may be caused by their membership in distinctive local networks; (iii) it is important to identify neurons that share physiological properties and location, but differ in their connectivity. PMID:24743633

A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

PubMed

Xu, Guoyan G; Zhang, Yan; Mercedes-Camacho, Ana Y; Etzkorn, Felicia A

2011-11-08

The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.

Structure, bonding, and catalytic activity of monodisperse, transition-metal-substituted CeO2 nanoparticles.

PubMed

Elias, Joseph S; Risch, Marcel; Giordano, Livia; Mansour, Azzam N; Shao-Horn, Yang

2014-12-10

We present a simple and generalizable synthetic route toward phase-pure, monodisperse transition-metal-substituted ceria nanoparticles (M0.1Ce0.9O2-x, M = Mn, Fe, Co, Ni, Cu). The solution-based pyrolysis of a series of heterobimetallic Schiff base complexes ensures a rigorous control of the size, morphology and composition of 3 nm M0.1Ce0.9O2-x crystallites for CO oxidation catalysis and other applications. X-ray absorption spectroscopy confirms the dispersion of aliovalent (M(3+) and M(2+)) transition metal ions into the ceria matrix without the formation of any bulk transition metal oxide phases, while steady-state CO oxidation catalysis reveals an order of magnitude increase in catalytic activity with copper substitution. Density functional calculations of model slabs of these compounds confirm the stabilization of M(3+) and M(2+) in the lattice of CeO2. These results highlight the role of the host CeO2 lattice in stabilizing high oxidation states of aliovalent transition metal dopants that ordinarily would be intractable, such as Cu(3+), as well as demonstrating a rational approach to catalyst design. The current work demonstrates, for the first time, a generalizable approach for the preparation of transition-metal-substituted CeO2 for a broad range of transition metals with unparalleled synthetic control and illustrates that Cu(3+) is implicated in the mechanism for CO oxidation on CuO-CeO2 catalysts.

Mechanosensitive channels in bacteria as membrane tension reporters

NASA Technical Reports Server (NTRS)

Sukharev, S.

1999-01-01

The purpose of this short review is to discuss recent data on the molecular structure and mechanism of gating of MscL, a mechanosensitive channel of large conductance from Escherichia coli. MscL is the first isolated molecule shown to convert mechanical stress of the membrane into a simple response, the opening of a large aqueous pore. The functional complex appears to be a stable homo-pentamer of 15-kDa subunits, the gating transitions in which are driven by stretch forces conveyed through the lipid bilayer. We have measured the open probability of MscL and the kinetics of transitions as a function of membrane tension. The parameters extracted from the single-channel current recordings and dose-response curves such as the energy difference between the closed, open, and intermediate conducting states, and the transition-related changes in protein dimensions suggest a large conformational rearrangement of the channel complex. The estimations show that in native conditions MscL openings could be driven primarily by forces of osmotic nature. The thermodynamic and spatial parameters reasonably correlate with the available data on the structure of a single MscL subunit and multimeric organization of the complex. Combined with the functional analysis of mutations, these data give grounds to hypotheses on the nature of the channel mechanosensitivity.

Superconductor-insulator transition on annealed complex networks.

PubMed

Bianconi, Ginestra

2012-06-01

Cuprates show multiphase and multiscale complexity that has hindered physicists search for the mechanism of high T{c} for many years. Recently the interest has been addressed to a possible optimum inhomogeneity of dopants, defects, and interstitials, and the structural scale invariance of dopants detected by scanning micro-x-ray diffraction has been reported to promote the critical temperature. In order to shed light on critical phenomena on granular materials, here we propose a stylized model capturing the essential characteristics of the superconducting-insulator transition of a highly dynamical, heterogeneous granular material: the random transverse Ising model (RTIM) on annealed complex network. We show that when the networks encode for high heterogeneity of the expected degrees described by a power-law distribution, the critical temperature for the onset of the superconducting phase diverges to infinity as the power-law exponent γ of the expected degree distribution is less than 3, i.e., γ<3. Moreover we investigate the case in which the critical state of the electronic background is triggered by an external parameter g that determines an exponential cutoff in the power-law expected degree distribution characterized by an exponent γ. We find that for g=g{c} the critical temperature for the superconducting-insulator transition has a maximum if γ>3 and diverges if γ<3.

Stationary and oscillatory bound states of dissipative solitons created by third-order dispersion

NASA Astrophysics Data System (ADS)

Sakaguchi, Hidetsugu; Skryabin, Dmitry V.; Malomed, Boris A.

2018-06-01

We consider the model of fiber-laser cavities near the zero-dispersion point, based on the complex Ginzburg-Landau equation with the cubic-quintic nonlinearity, including the third-order dispersion (TOD) term. It is well known that this model supports stable dissipative solitons. We demonstrate that the same model gives rise to several families of robust bound states of the solitons, which exists only in the presence of the TOD. There are both stationary and dynamical bound states, with oscillating separation between the bound solitons. Stationary states are multistable, corresponding to different values of the separation. With the increase of the TOD coefficient, the bound state with the smallest separation gives rise the oscillatory state through the Hopf bifurcation. Further growth of TOD leads to a bifurcation transforming the oscillatory limit cycle into a strange attractor, which represents a chaotically oscillating dynamical bound state. Families of multistable three- and four-soliton complexes are found too, the ones with the smallest separation between the solitons again ending by a transition to oscillatory states through the Hopf bifurcation.

Engineering the oxygen coordination in digital superlattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, Seyoung; Andersen, Tassie K.; Hong, Hawoong

The oxygen sublattice in the complex oxides is typically composed of corner-shared polyhedra, with transition metals at their centers. The electronic and chemical properties of the oxide depend on the type and geometric arrangement of these polyhedra, which can be controlled through epitaxial synthesis. Here, we use oxide molecular beam epitaxy to create SrCoOx:SrTiO3 superlattices with tunable oxygen coordination environments and sublattice geometries. Using soft X-ray spectroscopy, we find that the chemical state of Co can be varied with the polyhedral arrangement, demonstrating a new strategy for achieving unique electronic properties in the transition metal oxides.

Ultra high resolution molecular beam cars spectroscopy with application to planetary atmospheric molecules

NASA Technical Reports Server (NTRS)

Byer, R. L.

1982-01-01

The measurement of high resolution pulsed and continuous wave (CW) coherent anti-Stokes Raman spectroscopy (CARS) measurements in pulsed and steady state supersonic expansions were demonstrated. Pulsed molecular beam sources were characterized, and saturation of a Raman transition and, for the first time, the Raman spectrum of a complex molecular cluster were observed. The observation of CW CARS spectra in a molecular expansion and the effects of transit time broadening is described. Supersonic expansion is established as a viable technique for high resolution Raman spectroscopy of cold molecules with resolutions of 100 MH2.

Emirati Women's Higher Educational Leadership Formation under Globalisation: Culture, Religion, Politics, and the Dialectics of Modernisation

ERIC Educational Resources Information Center

Samier, Eugenie

2015-01-01

The United Arab Emirates (UAE) is a small state transitioning from traditional communities into a modern society. This is a complex process: it involves instilling a national identity over tribal structures; modernising and technologising while retaining Islam; ensuring a high level of security while allowing for a liberal and relatively free…

Structural Studies on Intact Clostridium botulinum Neurotoxins Complexed with Inhibitors Leading to Drug Design

DTIC Science & Technology

2009-02-01

compounds via virtual screening. These compounds include small molecules – transition state analogues and benzimidazoles . Since there is a commonality in...Crystal structure of BoNT/E has been determined helping us to understand the faster action of BoNT/E compared to BoNT/A. • A subset of benzimidazole

Care Management's Challenges and Opportunities to Reduce the Rapid Rehospitalization of Frail Community-Dwelling Older Adults

ERIC Educational Resources Information Center

Golden, Adam G.; Tewary, Sweta; Dang, Stuti; Roos, Bernard A.

2010-01-01

Community-based frail older adults, burdened with complex medical and social needs, are at great risk for preventable rapid rehospitalizations. Although federal and state regulations are in place to address the care transitions between the hospital and nursing home, no such guidelines exist for the much larger population of community-dwelling…

Field-induced magnetic phase transitions and metastable states in Tb3Ni

NASA Astrophysics Data System (ADS)

Gubkin, A. F.; Wu, L. S.; Nikitin, S. E.; Suslov, A. V.; Podlesnyak, A.; Prokhnenko, O.; Prokeš, K.; Yokaichiya, F.; Keller, L.; Baranov, N. V.

2018-04-01

In this paper we report the detailed study of magnetic phase diagrams, low-temperature magnetic structures, and the magnetic field effect on the electrical resistivity of the binary intermetallic compound Tb3Ni . The incommensurate magnetic structure of the spin-density-wave type described with magnetic superspace group P 1121/a 1'(a b 0 ) 0 s s and propagation vector kIC=[" close="]1/2 ,1/2 ,0 ]">0.506 ,0.299 ,0 was found to emerge just below Néel temperature TN=61 K. Further cooling below 58 K results in the appearance of multicomponent magnetic states: (i) a combination of k1=[1/2 ,0 ,0 ] below 48 K. An external magnetic field suppresses the complex low-temperature antiferromagnetic states and induces metamagnetic transitions towards a forced ferromagnetic state that are accompanied by a substantial magnetoresistance effect due to the magnetic superzone effect. The forced ferromagnetic state induced after application of an external magnetic field along the b and c crystallographic axes was found to be irreversible below 3 and 8 K, respectively.

Partial information, market efficiency, and anomalous continuous phase transition

NASA Astrophysics Data System (ADS)

Yang, Guang; Zheng, Wenzhi; Huang, Jiping

2014-04-01

It is a common belief in economics and social science that if there is more information available for agents to gather in a human system, the system can become more efficient. The belief can be easily understood according to the well-known efficient market hypothesis. In this work, we attempt to challenge this belief by investigating a complex adaptive system, which is modeled by a market-directed resource-allocation game with a directed random network. We conduct a series of controlled human experiments in the laboratory to show the reliability of the model design. As a result, we find that even under a small information concentration, the system can still almost reach the optimal (balanced) state. Furthermore, the ensemble average of the system’s fluctuation level goes through a continuous phase transition. This behavior means that in the second phase if too much information is shared among agents, the system’s stability will be harmed instead, which differs from the belief mentioned above. Also, at the transition point, the ensemble fluctuations of the fluctuation level remain at a low value. This phenomenon is in contrast to the textbook knowledge about continuous phase transitions in traditional physical systems, namely, fluctuations will rise abnormally around a transition point since the correlation length becomes infinite. Thus, this work is of potential value to a variety of fields, such as physics, economics, complexity science, and artificial intelligence.

A craniometric perspective on the transition to agriculture in Europe.

PubMed

Pinhasi, Ron; von Cramon-Taubadel, Noreen

2012-02-01

Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.

Potential energy and dipole moment surfaces of the triplet states of the O2(X3Σg-) - O2(X3Σg-,a1Δg,b1Σg+) complex

NASA Astrophysics Data System (ADS)

Karman, Tijs; van der Avoird, Ad; Groenenboom, Gerrit C.

2017-08-01

We compute four-dimensional diabatic potential energy surfaces and transition dipole moment surfaces of O2-O2, relevant for the theoretical description of collision-induced absorption in the forbidden X3Σg- → a1Δg and X3Σg- → b1Σg+ bands at 7883 cm-1 and 13 122 cm-1, respectively. We compute potentials at the multi-reference configuration interaction (MRCI) level and dipole surfaces at the MRCI and complete active space self-consistent field (CASSCF) levels of theory. Potentials and dipole surfaces are transformed to a diabatic basis using a recent multiple-property-based diabatization algorithm. We discuss the angular expansion of these surfaces, derive the symmetry constraints on the expansion coefficients, and present working equations for determining the expansion coefficients by numerical integration over the angles. We also present an interpolation scheme with exponential extrapolation to both short and large separations, which is used for representing the O2-O2 distance dependence of the angular expansion coefficients. For the triplet ground state of the complex, the potential energy surface is in reasonable agreement with previous calculations, whereas global excited state potentials are reported here for the first time. The transition dipole moment surfaces are strongly dependent on the level of theory at which they are calculated, as is also shown here by benchmark calculations at high symmetry geometries. Therefore, ab initio calculations of the collision-induced absorption spectra cannot become quantitatively predictive unless more accurate transition dipole surfaces can be computed. This is left as an open question for method development in electronic structure theory. The calculated potential energy and transition dipole moment surfaces are employed in quantum dynamical calculations of collision-induced absorption spectra reported in Paper II [T. Karman et al., J. Chem. Phys. 147, 084307 (2017)].

Potential energy and dipole moment surfaces of the triplet states of the O2(X3Σg-) - O2(X3Σg-,a1Δg,b1Σg+) complex.

PubMed

Karman, Tijs; van der Avoird, Ad; Groenenboom, Gerrit C

2017-08-28

We compute four-dimensional diabatic potential energy surfaces and transition dipole moment surfaces of O 2 -O 2 , relevant for the theoretical description of collision-induced absorption in the forbidden X 3 Σ g -  → a 1 Δ g and X 3 Σ g -  → b 1 Σ g + bands at 7883 cm -1 and 13 122 cm -1 , respectively. We compute potentials at the multi-reference configuration interaction (MRCI) level and dipole surfaces at the MRCI and complete active space self-consistent field (CASSCF) levels of theory. Potentials and dipole surfaces are transformed to a diabatic basis using a recent multiple-property-based diabatization algorithm. We discuss the angular expansion of these surfaces, derive the symmetry constraints on the expansion coefficients, and present working equations for determining the expansion coefficients by numerical integration over the angles. We also present an interpolation scheme with exponential extrapolation to both short and large separations, which is used for representing the O 2 -O 2 distance dependence of the angular expansion coefficients. For the triplet ground state of the complex, the potential energy surface is in reasonable agreement with previous calculations, whereas global excited state potentials are reported here for the first time. The transition dipole moment surfaces are strongly dependent on the level of theory at which they are calculated, as is also shown here by benchmark calculations at high symmetry geometries. Therefore, ab initio calculations of the collision-induced absorption spectra cannot become quantitatively predictive unless more accurate transition dipole surfaces can be computed. This is left as an open question for method development in electronic structure theory. The calculated potential energy and transition dipole moment surfaces are employed in quantum dynamical calculations of collision-induced absorption spectra reported in Paper II [T. Karman et al., J. Chem. Phys. 147, 084307 (2017)].

Regulation of photochemical energy transfer accompanied by structural changes in thylakoid membranes of heat-stressed wheat.

PubMed

Marutani, Yoko; Yamauchi, Yasuo; Miyoshi, Akihito; Inoue, Kanako; Ikeda, Ken-ichi; Mizutani, Masaharu; Sugimoto, Yukihiro

2014-12-11

Photosystems of higher plants alleviate heat-induced damage in the presence of light under moderate stressed conditions; however, in the absence of light (i.e., in the dark), the same plants are damaged more easily. (Yamauchi and Kimura, 2011) We demonstrate that regulating photochemical energy transfer in heat-treated wheat at 40 °C with light contributed to heat tolerance of the photosystem. Chlorophyll fluorescence analysis using heat-stressed wheat seedlings in light showed increased non-photochemical quenching (NPQ) of chlorophyll fluorescence, which was due to thermal dissipation that was increased by state 1 to state 2 transition. Transmission electron microscopy revealed structural changes in thylakoid membranes, including unstacking of grana regions under heat stress in light. It was accompanied by the phosphorylation of thylakoid proteins such as D1 and D2 proteins and the light harvesting complex II proteins Lhcb1 and Lhcb2. These results suggest that heat stress at 40 °C in light induces state 1 to state 2 transition for the preferential excitation of photosystem I (PSI) by phosphorylating thylakoid proteins more strongly. Structural changes of thylakoid membrane also assist the remodeling of photosystems and regulation of energy distribution by transition toward state 2 probably contributes to plastoquione oxidation; thus, light-driven electrons flowing through PSI play a protective role against PSII damage under heat stress.

Separation of traveling and standing waves in a finite dispersive string with partial or continuous viscoelastic foundation

NASA Astrophysics Data System (ADS)

Cheng, Xiangle; Blanchard, Antoine; Tan, Chin An; Lu, Huancai; Bergman, Lawrence A.; McFarland, D. Michael; Vakakis, Alexander F.

2017-12-01

The free and forced vibrations of a linear string with a local spring-damper on a partial elastic foundation, as well as a linear string on a viscoelastic foundation conceptualized as a continuous distribution of springs and dampers, are studied in this paper. Exact, analytical results are obtained for the free and forced response to a harmonic excitation applied at one end of the string. Relations between mode complexity and energy confinement with the dispersion in the string system are examined for the steady-state forced vibration, and numerical methods are applied to simulate the transient evolution of energy propagation. Eigenvalue loci veering and normal mode localization are observed for weakly coupled subsystems, when the foundation stiffness is sufficiently large, for both the spatially symmetric and asymmetric systems. The forced vibration results show that nonproportional damping-induced mode complexity, for which there are co-existing regions of purely traveling waves and standing waves, is attainable for the dispersive string system. However, this wave transition phenomenon depends strongly on the location of the attached discrete spring-damper relative to the foundation and whether the excitation frequency Ω is above or below the cutoff frequency ωc. When Ω<ωc, the wave transition cannot be attained for a string on an elastic foundation, but is possible if the string is on a viscoelastic foundation. Although this study is primarily formulated for a harmonic boundary excitation at one end of the string, generalization of the mode complexity can be deduced for the steady-state forced response of the string-foundation system to synchronous end excitations and is confirmed numerically. This work represents a novel study to understand the wave transitions in a dispersive structural system and lays the groundwork for potentially effective passive vibration control strategies.

Integrating transition theory and bioecological theory: a theoretical perspective for nurses supporting the transition to adulthood for young people with medical complexity.

PubMed

Joly, Elizabeth

2016-06-01

To present a discussion of a theoretical perspective developed through integrating Meleis' Transition Theory and Bronfenbrenner's Bioecological Theory of Human Development to inform nursing and advanced nursing practice supporting the transition to adulthood for young people with medical complexity. Theoretical perspectives to inform nursing practice in supporting successful transition are limited, yet nurses frequently encounter young people with medical complexity during the transition to adulthood. Discussion paper. A literature search of CINAHL and Medline was conducted in 2014 and included articles from 2003-2014; informal discussions with families; the author's experiences in a transition program. The integrated theoretical perspective described in this paper can inform nurses and advanced practice nurses on contextual influences, program and intervention development across spheres of influence and outcomes for the transition to adulthood for young people with medical complexity. Young people and their families require effective reciprocal interactions with individuals and services across sectors to successfully transition to adulthood and become situated in the adult world. Intervention must also extend beyond the young person to include providers, services and health and social policy. Nurses can take a leadership role in supporting the transition to adulthood for young people with medical complexity through direct care, case management, education and research. It is integral that nurses holistically consider developmental processes, complexity and contextual conditions that promote positive outcomes during and beyond the transition to adulthood. © 2016 John Wiley & Sons Ltd.

β-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations . Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

NASA Astrophysics Data System (ADS)

Kupka, Teobald

1997-12-01

IR studies were preformed to determine possible transition metal ion binding sites of penicillin. the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M-L complexes with engagement of -COO - and/or -CONH- functional groups. The small shift of νCO towards higher frequencies rules out direct M-L interaction via β-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic β-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and CO stretching frequencies were discussed to determine the β-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.

Multifractality and Network Analysis of Phase Transition

PubMed Central

Li, Wei; Yang, Chunbin; Han, Jihui; Su, Zhu; Zou, Yijiang

2017-01-01

Many models and real complex systems possess critical thresholds at which the systems shift dramatically from one sate to another. The discovery of early-warnings in the vicinity of critical points are of great importance to estimate how far the systems are away from the critical states. Multifractal Detrended Fluctuation analysis (MF-DFA) and visibility graph method have been employed to investigate the multifractal and geometrical properties of the magnetization time series of the two-dimensional Ising model. Multifractality of the time series near the critical point has been uncovered from the generalized Hurst exponents and singularity spectrum. Both long-term correlation and broad probability density function are identified to be the sources of multifractality. Heterogeneous nature of the networks constructed from magnetization time series have validated the fractal properties. Evolution of the topological quantities of the visibility graph, along with the variation of multifractality, serve as new early-warnings of phase transition. Those methods and results may provide new insights about the analysis of phase transition problems and can be used as early-warnings for a variety of complex systems. PMID:28107414

Manipulating charge transfer excited state relaxation and spin crossover in iron coordination complexes with ligand substitution

DOE PAGES

Zhang, Wenkai; Kjaer, Kasper S.; Alonso-Mori, Roberto; ...

2016-08-25

Developing light-harvesting and photocatalytic molecules made with iron could provide a cost effective, scalable, and environmentally benign path for solar energy conversion. To date these developments have been limited by the sub-picosecond metal-to-ligand charge transfer (MLCT) electronic excited state lifetime of iron based complexes due to spin crossover – the extremely fast intersystem crossing and internal conversion to high spin metal-centered excited states. We revitalize a 30 year old synthetic strategy for extending the MLCT excited state lifetimes of iron complexes by making mixed ligand iron complexes with four cyanide (CN –) ligands and one 2,2'-bipyridine (bpy) ligand. This enablesmore » MLCT excited state and metal-centered excited state energies to be manipulated with partial independence and provides a path to suppressing spin crossover. We have combined X-ray Free-Electron Laser (XFEL) Kβ hard X-ray fluorescence spectroscopy with femtosecond time-resolved UV-visible absorption spectroscopy to characterize the electronic excited state dynamics initiated by MLCT excitation of [Fe(CN) 4(bpy)] 2–. The two experimental techniques are highly complementary; the time-resolved UV-visible measurement probes allowed electronic transitions between valence states making it sensitive to ligand-centered electronic states such as MLCT states, whereas the Kβ fluorescence spectroscopy provides a sensitive measure of changes in the Fe spin state characteristic of metal-centered excited states. Here, we conclude that the MLCT excited state of [Fe(CN) 4(bpy)] 2– decays with roughly a 20 ps lifetime without undergoing spin crossover, exceeding the MLCT excited state lifetime of [Fe(2,2'-bipyridine) 3] 2+ by more than two orders of magnitude.« less

A New Approach to Monte Carlo Simulations in Statistical Physics

NASA Astrophysics Data System (ADS)

Landau, David P.

2002-08-01

Monte Carlo simulations [1] have become a powerful tool for the study of diverse problems in statistical/condensed matter physics. Standard methods sample the probability distribution for the states of the system, most often in the canonical ensemble, and over the past several decades enormous improvements have been made in performance. Nonetheless, difficulties arise near phase transitions-due to critical slowing down near 2nd order transitions and to metastability near 1st order transitions, and these complications limit the applicability of the method. We shall describe a new Monte Carlo approach [2] that uses a random walk in energy space to determine the density of states directly. Once the density of states is known, all thermodynamic properties can be calculated. This approach can be extended to multi-dimensional parameter spaces and should be effective for systems with complex energy landscapes, e.g., spin glasses, protein folding models, etc. Generalizations should produce a broadly applicable optimization tool. 1. A Guide to Monte Carlo Simulations in Statistical Physics, D. P. Landau and K. Binder (Cambridge U. Press, Cambridge, 2000). 2. Fugao Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001); Phys. Rev. E64, 056101-1 (2001).

Magnetic circular dichroism and computational study of mononuclear and dinuclear iron(iv) complexes† †Electronic supplementary information (ESI) available: VT MCD spectra, VT and VTVH MCD intensity analysis of complex 1, energies, S x, S z values and Boltzmann populations of S = 1 magnetic sublevels as a function of the applied magnetic field, derivation of the excited states arising from the 1b2 → 2b1 transition, determination of the C-term sign of band 1 and the E(2e → 2a1) transitions for complex 1, VTVH MCD spectra, VTVH simulations and the computed MCD spectrum of complex 2. See DOI: 10.1039/c4sc03268c Click here for additional data file.

PubMed Central

Xue, Genqiang; Krivokapic, Itana; Petrenko, Taras

2015-01-01

High-valent iron(iv)-oxo species are key intermediates in the catalytic cycles of a range of O2-activating iron enzymes. This work presents a detailed study of the electronic structures of mononuclear ([FeIV(O)(L)(NCMe)]2+, 1, L = tris(3,5-dimethyl-4-methoxylpyridyl-2-methyl)amine) and dinuclear ([(L)FeIV(O)(μ-O)FeIV(OH)(L)]3+, 2) iron(iv) complexes using absorption (ABS), magnetic circular dichroism (MCD) spectroscopy and wave-function-based quantum chemical calculations. For complex 1, the experimental MCD spectra at 2–10 K are dominated by a broad positive band between 12 000 and 18 000 cm–1. As the temperature increases up to ∼20 K, this feature is gradually replaced by a derivative-shaped signal. The computed MCD spectra are in excellent agreement with experiment, which reproduce not only the excitation energies and the MCD signs of key transitions but also their temperature-dependent intensity variations. To further corroborate the assignments suggested by the calculations, the individual MCD sign for each transition is independently determined from the corresponding electron donating and accepting orbitals. Thus, unambiguous assignments can be made for the observed transitions in 1. The ABS/MCD data of complex 2 exhibit ten features that are assigned as ligand-field transitions or oxo- or hydroxo-to-metal charge transfer bands, based on MCD/ABS intensity ratios, calculated excitation energies, polarizations, and MCD signs. In comparison with complex 1, the electronic structure of the FeIV 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 O site is not significantly perturbed by the binding to another iron(iv) center. This may explain the experimental finding that complexes 1 and 2 have similar reactivities toward C–H bond activation and O-atom transfer. PMID:26417426

Theoretical study of inverted sandwich type complexes of 4d transition metal elements: interesting similarities to and differences from 3d transition metal complexes.

PubMed

Kurokawa, Yusaku I; Nakao, Yoshihide; Sakaki, Shigeyoshi

2012-03-08

Inverted sandwich type complexes (ISTCs) of 4d metals, (μ-η(6):η(6)-C(6)H(6))[M(DDP)](2) (DDPH = 2-{(2,6-diisopropylphenyl)amino}-4-{(2,6-diisopropylphenyl)imino}pent-2-ene; M = Y, Zr, Nb, Mo, and Tc), were investigated with density functional theory (DFT) and MRMP2 methods, where a model ligand AIP (AIPH = (Z)-1-amino-3-imino-prop-1-ene) was mainly employed. When going to Nb (group V) from Y (group III) in the periodic table, the spin multiplicity of the ground state increases in the order singlet, triplet, and quintet for M = Y, Zr, and Nb, respectively, like 3d ISTCs reported recently. This is interpreted with orbital diagram and number of d electrons. However, the spin multiplicity decreases to either singlet or triplet in ISTC of Mo (group VI) and to triplet in ISTC of Tc (group VII), where MRMP2 method is employed because the DFT method is not useful here. These spin multiplicities are much lower than the septet of ISTC of Cr and the nonet of that of Mn. When going from 3d to 4d, the position providing the maximum spin multiplicity shifts to group V from group VII. These differences arise from the size of the 4d orbital. Because of the larger size of the 4d orbital, the energy splitting between two d(δ) orbitals of M(AIP) and that between the d(δ) and d(π) orbitals are larger in the 4d complex than in the 3d complex. Thus, when occupation on the d(δ) orbital starts, the low spin state becomes ground state, which occurs at group VI. Hence, the ISTC of Nb (group V) exhibits the maximum spin multiplicity.

Transition to international classification of disease version 10, clinical modification: the impact on internal medicine and internal medicine subspecialties.

PubMed

Caskey, Rachel N; Abutahoun, Angelos; Polick, Anne; Barnes, Michelle; Srivastava, Pavan; Boyd, Andrew D

2018-05-04

The US health care system uses diagnostic codes for billing and reimbursement as well as quality assessment and measuring clinical outcomes. The US transitioned to the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) on October, 2015. Little is known about the impact of ICD-10-CM on internal medicine and medicine subspecialists. We used a state-wide data set from Illinois Medicaid specified for Internal Medicine providers and subspecialists. A total of 3191 ICD-9-CM codes were used for 51,078 patient encounters, for a total cost of US $26,022,022 for all internal medicine. We categorized all of the ICD-9-CM codes based on the complexity of mapping to ICD-10-CM as codes with complex mapping could result in billing or administrative errors during the transition. Codes found to have complex mapping and frequently used codes (n = 295) were analyzed for clinical accuracy of mapping to ICD-10-CM. Each subspecialty was analyzed for complexity of codes used and proportion of reimbursement associated with complex codes. Twenty-five percent of internal medicine codes have convoluted mapping to ICD-10-CM, which represent 22% of Illinois Medicaid patients, and 30% of reimbursements. Rheumatology and Endocrinology had the greatest proportion of visits and reimbursement associated with complex codes. We found 14.5% of ICD-9-CM codes used by internists, when mapped to ICD-10-CM, resulted in potential clinical inaccuracies. We identified that 43% of diagnostic codes evaluated and used by internists and that account for 14% of internal medicine reimbursements are associated with codes which could result in administrative errors.

Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

NASA Astrophysics Data System (ADS)

Shukla, P. K.; Mishra, P. C.; Suhai, S.

Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the other strongly carcinogenic methylating agents.

Quinonoid metal complexes: toward molecular switches.

PubMed

Dei, Andrea; Gatteschi, Dante; Sangregorio, Claudio; Sorace, Lorenzo

2004-11-01

The peculiar redox-active character of quinonoid metal complexes makes them extremely appealing to design materials of potential technological interest. We show here how the tuning of the properties of these systems can be pursued by using appropriate molecular synthetic techniques. In particular, we focus our attention on metal polyoxolene complexes exhibiting intramolecular electron transfer processes involving either the ligand and the metal ion or the two dioxolene moieties of a properly designed ligand thus inducing electronic bistability. The transition between the two metastable electronic states can be induced by different external stimuli such as temperature, pressure, light, or pH suggesting the use of these systems for molecular switches.

Applications of NIR spectroscopy to monitoring and analyzing the solid state during industrial crystallization processes.

PubMed

Févotte, G; Calas, J; Puel, F; Hoff, C

2004-04-01

Fiber-optic near infrared (NIR) spectroscopy was used to investigate several key features of the polymorphic transitions observed during the crystallization and the filtration of SaC, an Active Pharmaceutical Ingredient (API) produced by Sanofi-Synthelabo. Using few samples, the spectroscopic data were calibrated to provide measurements of the polymorphic composition of the solid product which is likely to appear in two crystalline forms or in the amorphous state. Both qualitative and quantitative methods were successfully evaluated to characterize the API. The NIR spectroscopy measurement was then applied to investigate the kinetic behavior of the phase transition phenomena against various operating conditions. From the viewpoint of industrial process development several applications are presented. The effects of temperature and seed crystal habits on the rate of transition of filtration cakes are briefly investigated; and a study of the effect of residual water in the solvent on the transition occurring during filtration is more deeply analyzed. The experimental results demonstrate that highly valuable information can be provided by the NIR spectroscopy measurements, when one aims at understanding more deeply and optimizing the consequences of various and complex phenomena involved during the solid processing chain.

First principles study of structural, electronic and optical properties of polymorphic forms of Rb 2Te

NASA Astrophysics Data System (ADS)

Alay-e-Abbas, S. M.; Shaukat, A.

2011-05-01

First-principles density functional theory calculations have been performed for structural, electronic and optical properties of three polymorphic forms of rubidium telluride. Our calculations show that the sequence of pressure induced phase transitions for Rb 2Te is Fm3¯m → Pnma → P6 3/mmc which is governed by the coordination numbers of the anions. From our calculated low transition pressure value for the Fm3¯m phase to the Pnma phase transition of Rb 2Te, the experimentally observed meta-stability of Fm3¯m phase at ambient conditions seems reasonable. The electronic band structure has been calculated for all the three phases and the change in the energy band gap is discussed for the transitioning phases. The energy band gaps obtained for the three phases of Rb 2Te decrease on going from the meta-stable phase to the high-pressure phases. Total and partial density of states for the polymorphs of Rb 2Te has been computed to elucidate the contribution of various atomic states on the electronic band structure. Furthermore, optical properties for all the polymorphic forms have been presented in form of the complex dielectric function.

Photoinduced Charge Shifts and Electron Transfer in Viologen-Tetraphenylborate Complexes: Push-Pull Character of the Exciplex.

PubMed

Santos, Willy G; Budkina, Darya S; Deflon, Victor M; Tarnovsky, Alexander N; Cardoso, Daniel R; Forbes, Malcolm D E

2017-06-14

Viologen-tetraarylborate ion-pair complexes were prepared and investigated by steady-state and time-resolved spectroscopic techniques such as fluorescence and femtosecond transient absorption. The results highlight a charge transfer transition that leads to changes in the viologen structure in the excited singlet state. Femtosecond transient absorption reveals the formation of excited-state absorption and stimulated emission bands assigned to the planar (k obs < 10 12 s -1 ) and twisted (k obs ∼ 10 10 s -1 ) structures between two pyridinium groups in the viologen ion. An efficient photoinduced electron transfer from the tetraphenylborate anionic moiety to the viologen dication was observed less than 1 μs after excitation. This is a consequence of the push-pull character of the electron donor twisted viologen structure, which helps formation of the borate triplet state. The borate triplet state is deactivated further via a second electron transfer process, generating viologen cation radical (V •+ ).

Pattern Driven Stress Localization

NASA Astrophysics Data System (ADS)

Croll, Andrew; Crosby, Alfred

2010-03-01

The self-assembly of patterns from isotropic initial states is a major driver of modern soft-matter research. This avenue of study is directed by the desire to understand the complex physics of the varied structures found in Nature, and by technological interest in functional materials that may be derived through biomimicry. In this work we show how a simple striped phase can respond with significant complexity to an appropriately chosen perturbation. In particular, we show how a buckled elastic plate transitions into a state of stress localization using a simple, self-assembled variation in surface topography. The collection of topographic boundaries act in concert to change the state from isotropic sinusoidal wrinkles, to sharp folds or creases separated by relatively flat regions. By varying the size of the imposed topographic pattern or the wavelength of the wrinkles, we construct a state diagram of the system. The localized state has implications for both biological systems, and for the control of non-linear pattern formation.

Temperature-dependent vibrational spectroscopy to study order-disorder transitions in charge transfer complexes

NASA Astrophysics Data System (ADS)

Isaac, Rohan; Goetz, Katelyn P.; Roberts, Drew; Jurchescu, Oana D.; McNeil, L. E.

2018-02-01

Charge-transfer (CT) complexes are a promising class of materials for the semiconductor industry because of their versatile properties. This class of compounds shows a variety of phase transitions, which are of interest because of their potential impact on the electronic characteristics. Here temperature-dependent vibrational spectroscopy is used to study structural phase transitions in a set of organic CT complexes. Splitting and broadening of infrared-active phonons in the complex formed between pyrene and pyromellitic dianhydride (PMDA) confirm the structural transition is of the order-disorder type and complement previous x-ray diffraction (XRD) results. We show that this technique is a powerful tool to characterize transitions, and apply it to a range of binary CT complexes composed of polyaromatic hyrdocarbons (anthracene, perylene, phenanthrene, pyrene, and stilbene) and PMDA. We extend the understanding of transitions in perylene-PMDA and pyrene-PMDA, and show that there are no order-disorder transitions present in anthracene-PMDA, stilbene-PMDA and phenanthrene-PMDA in the temperature range investigated here.

Single-Molecule Spectroscopy Unmasks the Lowest Exciton State of the B850 Assembly in LH2 from Rps. acidophila

PubMed Central

Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J.; Freiberg, Arvi; Köhler, Jürgen

2014-01-01

We have recorded fluorescence-excitation and emission spectra from single LH2 complexes from Rhodopseudomonas (Rps.) acidophila. Both types of spectra show strong temporal spectral fluctuations that can be visualized as spectral diffusion plots. Comparison of the excitation and emission spectra reveals that for most of the complexes the lowest exciton transition is not observable in the excitation spectra due to the cutoff of the detection filter characteristics. However, from the spectral diffusion plots we have the full spectral and temporal information at hand and can select those complexes for which the excitation spectra are complete. Correlating the red most spectral feature of the excitation spectrum with the blue most spectral feature of the emission spectrum allows an unambiguous assignment of the lowest exciton state. Hence, application of fluorescence-excitation and emission spectroscopy on the same individual LH2 complex allows us to decipher spectral subtleties that are usually hidden in traditional ensemble spectroscopy. PMID:24806933

Statistical moments of quantum-walk dynamics reveal topological quantum transitions.

PubMed

Cardano, Filippo; Maffei, Maria; Massa, Francesco; Piccirillo, Bruno; de Lisio, Corrado; De Filippis, Giulio; Cataudella, Vittorio; Santamato, Enrico; Marrucci, Lorenzo

2016-04-22

Many phenomena in solid-state physics can be understood in terms of their topological properties. Recently, controlled protocols of quantum walk (QW) are proving to be effective simulators of such phenomena. Here we report the realization of a photonic QW showing both the trivial and the non-trivial topologies associated with chiral symmetry in one-dimensional (1D) periodic systems. We find that the probability distribution moments of the walker position after many steps can be used as direct indicators of the topological quantum transition: while varying a control parameter that defines the system phase, these moments exhibit a slope discontinuity at the transition point. Numerical simulations strongly support the conjecture that these features are general of 1D topological systems. Extending this approach to higher dimensions, different topological classes, and other typologies of quantum phases may offer general instruments for investigating and experimentally detecting quantum transitions in such complex systems.

Statistical moments of quantum-walk dynamics reveal topological quantum transitions

PubMed Central

Cardano, Filippo; Maffei, Maria; Massa, Francesco; Piccirillo, Bruno; de Lisio, Corrado; De Filippis, Giulio; Cataudella, Vittorio; Santamato, Enrico; Marrucci, Lorenzo

2016-01-01

Many phenomena in solid-state physics can be understood in terms of their topological properties. Recently, controlled protocols of quantum walk (QW) are proving to be effective simulators of such phenomena. Here we report the realization of a photonic QW showing both the trivial and the non-trivial topologies associated with chiral symmetry in one-dimensional (1D) periodic systems. We find that the probability distribution moments of the walker position after many steps can be used as direct indicators of the topological quantum transition: while varying a control parameter that defines the system phase, these moments exhibit a slope discontinuity at the transition point. Numerical simulations strongly support the conjecture that these features are general of 1D topological systems. Extending this approach to higher dimensions, different topological classes, and other typologies of quantum phases may offer general instruments for investigating and experimentally detecting quantum transitions in such complex systems. PMID:27102945

Cumulative Exposure to Neighborhood Context: Consequences for Health Transitions over the Adult Life Course

PubMed Central

Clarke, Philippa; Morenoff, Jeffrey; Debbink, Michelle; Golberstein, Ezra; Elliott, Michael R.; Lantz, Paula M.

2012-01-01

Over the last two decades, research has assessed the relationship between neighborhood socioeconomic factors and individual health. However, existing research is based almost exclusively on cross-sectional data, ignoring the complexity in health transitions that may be shaped by long term residential exposures. We address these limitations by specifying distinct health transitions over multiple waves of a 15 year study of American adults. We focus on transitions between a hierarchy of health states, (free from health problems, onset of health problems, and death), not just gradients in a single health indicator over time, and use a cumulative measure of exposure to neighborhoods over adulthood. We find that cumulative exposure to neighborhood disadvantage has significant effects on functional decline and mortality. Research ignoring a persons’ history of exposure to residential contexts over the life course runs the risk of underestimating the role of neighborhood disadvantage on health. PMID:24465068

Inhibition of the hammerhead ribozyme by neomycin.

PubMed Central

Stage, T K; Hertel, K J; Uhlenbeck, O C

1995-01-01

A series of antibiotics was tested for stimulation or inhibition of the hammerhead ribozyme cleavage reaction. Neomycin was found to be a potent inhibitor of the reaction with a Kl of 13.5 microM. Two hammerheads with well-characterized kinetics were used to determine which steps in the reaction mechanism were inhibited by neomycin. The data suggest that neomycin interacts preferentially with the enzyme-substrate complex and that this interaction leads to a reduction in the cleavage rate by stabilizing the ground state of the complex and destabilizing the transition state of the cleavage step. A comparison of neomycin with other aminoglycosides and inhibitors of hammerhead cleavage implies that the ammonium ions of neomycin are important for the antibiotic-hammerhead interaction. PMID:7489494

Reprogramming of Escherichia coli K-12 Metabolism during the Initial Phase of Transition from an Anaerobic to a Micro-Aerobic Environment

PubMed Central

Trotter, Eleanor W.; Rolfe, Matthew D.; Hounslow, Andrea M.; Craven, C. Jeremy; Williamson, Michael P.; Sanguinetti, Guido; Poole, Robert K.; Green, Jeffrey

2011-01-01

Background Many bacteria undergo transitions between environments with differing O2 availabilities as part of their natural lifestyles and during biotechnological processes. However, the dynamics of adaptation when bacteria experience changes in O2 availability are understudied. The model bacterium and facultative anaerobe Escherichia coli K-12 provides an ideal system for exploring this process. Methods and Findings Time-resolved transcript profiles of E. coli K-12 during the initial phase of transition from anaerobic to micro-aerobic conditions revealed a reprogramming of gene expression consistent with a switch from fermentative to respiratory metabolism. The changes in transcript abundance were matched by changes in the abundances of selected central metabolic proteins. A probabilistic state space model was used to infer the activities of two key regulators, FNR (O2 sensing) and PdhR (pyruvate sensing). The model implied that both regulators were rapidly inactivated during the transition from an anaerobic to a micro-aerobic environment. Analysis of the external metabolome and protein levels suggested that the cultures transit through different physiological states during the process of adaptation, characterized by the rapid inactivation of pyruvate formate-lyase (PFL), a slower induction of pyruvate dehydrogenase complex (PDHC) activity and transient excretion of pyruvate, consistent with the predicted inactivation of PdhR and FNR. Conclusion Perturbation of anaerobic steady-state cultures by introduction of a limited supply of O2 combined with time-resolved transcript, protein and metabolite profiling, and probabilistic modeling has revealed that pyruvate (sensed by PdhR) is a key metabolic signal in coordinating the reprogramming of E. coli K-12 gene expression by working alongside the O2 sensor FNR during transition from anaerobic to micro-aerobic conditions. PMID:21980479

Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment.

PubMed

Trotter, Eleanor W; Rolfe, Matthew D; Hounslow, Andrea M; Craven, C Jeremy; Williamson, Michael P; Sanguinetti, Guido; Poole, Robert K; Green, Jeffrey

2011-01-01

Many bacteria undergo transitions between environments with differing O₂ availabilities as part of their natural lifestyles and during biotechnological processes. However, the dynamics of adaptation when bacteria experience changes in O₂ availability are understudied. The model bacterium and facultative anaerobe Escherichia coli K-12 provides an ideal system for exploring this process. Time-resolved transcript profiles of E. coli K-12 during the initial phase of transition from anaerobic to micro-aerobic conditions revealed a reprogramming of gene expression consistent with a switch from fermentative to respiratory metabolism. The changes in transcript abundance were matched by changes in the abundances of selected central metabolic proteins. A probabilistic state space model was used to infer the activities of two key regulators, FNR (O₂ sensing) and PdhR (pyruvate sensing). The model implied that both regulators were rapidly inactivated during the transition from an anaerobic to a micro-aerobic environment. Analysis of the external metabolome and protein levels suggested that the cultures transit through different physiological states during the process of adaptation, characterized by the rapid inactivation of pyruvate formate-lyase (PFL), a slower induction of pyruvate dehydrogenase complex (PDHC) activity and transient excretion of pyruvate, consistent with the predicted inactivation of PdhR and FNR. Perturbation of anaerobic steady-state cultures by introduction of a limited supply of O₂ combined with time-resolved transcript, protein and metabolite profiling, and probabilistic modeling has revealed that pyruvate (sensed by PdhR) is a key metabolic signal in coordinating the reprogramming of E. coli K-12 gene expression by working alongside the O₂ sensor FNR during transition from anaerobic to micro-aerobic conditions.