Topologically invariant reaction coordinates for simulating multistate chemical reactions.

Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

Accurate screened exchange band structures for the transition metal monoxides MnO, FeO, CoO and NiO.

We report calculations of the band structures and density of states of the four transition metal monoxides MnO, FeO, CoO and NiO using the hybrid density functional sX-LDA ('screened exchange local density approximation'). Late transition metal oxides are prototypical examples of strongly correlated materials, which pose challenges for electronic structure methods. We compare our results with available experimental data and show that our calculations generally yield accurate predictions for the fundamental band gaps and valence bands, in favourable agreement with previously reported theoretical studies. For MnO, the band gaps are still underestimated, suggesting additional many-body effects that are not captured by our screened hybrid functional approach.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Carbon source/sink function of a subtropical, eutrophic lake determined from an overall mass balance and a gas exchange and carbon burial balance

Although studies on carbon burial in lake sediments have shown that lakes are disproportionately important carbon sinks, many studies on gaseous carbon exchange across the water-air interface have demonstrated that lakes are supersaturated with CO2 and CH4 causing a net release of CO2 and CH4 to the atmosphere. In order to more accurately estimate the net carbon source/sink function of lake ecosystems, a more comprehensive carbon budget is needed, especially for gaseous carbon exchange across the water-air interface. Using two methods, overall mass balance and gas exchange and carbon burial balance, we assessed the carbon source/sink function of Lake Donghu, a subtropical, eutrophic take, from April 2003 to March 2004. With the overall mass balance calculations, total carbon input was 14 905 t, total carbon output was 4950 1, and net carbon budget was +9955 t, suggesting that Lake Donghu was a great carbon sink. For the gas exchange and carbon burial balance, gaseous carbon (CO2 and CH4) emission across the water-air interface totaled 752 t while carbon burial in the lake sediment was 9477 t. The ratio of carbon emission into the atmosphere to carbon burial into the sediment was only 0.08. This low ratio indicates that Lake Donghu is a great carbon sink. Results showed good agreement between the two methods with both showing Lake Donghu to be a great carbon sink. This results from the high primary production of Lake Donghu, substantive allochthonous carbon inputs and intensive anthropogenic activity. Gaseous carbon emission accounted for about 15% of the total carbon output, indicating that the total output would be underestimated without including gaseous carbon exchange. (C) 2007 Elsevier Ltd. All rights reserved.

Hydrodynamics in an expanded bed of large size ion-exchange resin, and natural product adsorption

Successful applications of expanded bed adsorption (EBA) technology have been widely reported in the literature for protein purification. Little has been reported on the recovery of natural products and active components of Chinese herbal preparations using EBA technology. In this study, the hydrodynamic behavior in an expanded bed of cation resin, 001 x 7 Styrene-DVB, was investigated. Ephedrine hydrochloride (EH) was used as a model natural product to test the dynamic binding capacity (DBC) in the expanded bed. EBA of EH directly from a feedstock containing powdered herbs has also been investigated. These particles are different from commercially available expanded bed adsorbents by virtue of their large size (20S to 1030 gm). When the adsorbent bed is expanded to approximately 1.3 to 1.5 times its settled bed height, the axial liquid-phase dispersion coefficient was found to be of the order 10(-5) m(2) s(-1), which falls into the range 1.0 x 10(-6) to 1.0 X 10(-5) m(2) s(-1) observed previously in protein purification. Because of the favorable column efficiency (low axial dispersion coefficient), the recovery yield and purification factor values of EH directly from a feedstock reached 86.5% and 18, respectively. The results suggest that EBA technology holds promise for the recovery of natural products and active components of Chinese herbal preparations.

Analysis of steric mass-action model for protein adsorption equilibrium onto porous anion-exchange adsorbent

The ion-exchange equilibrium of bovine serum albumin (BSA) to an anion exchanger, DEAE Spherodex M, has been studied by batch adsorption experiments at pH values ranging from 5.26 to 7.6 and ionic strengths from 10 to 117.1 mmol/l. Using the unadjustable adsorption equilibrium parameters obtained from batch experiments, the applicability of the steric mass-action (SMA) model was analyzed for describing protein ion-exchange equilibrium in different buffer systems. The parametric sensitivity analysis was performed by perturbing each of the model parameters, while holding the rest constant. The simulation results showed that, at high salt concentrations or low pHs close to the isoelectric point of the protein, the precision of the model prediction decreased. Parametric sensitivity analysis showed that the characteristic charge and protein steric factor had the largest effects on ion-exchange equilibrium, while the effect of equilibrium constant was about 70%-95% smaller than those of characteristic charge and steric factor under all conditions investigated. The SMA model with the relationship between the adjusted characteristic charge and the salt concentration can well predict the protein adsorption isotherms in a wide pH range from 5.84 to 7.6. It is considered that the SMA model could be further improved by taking into account the effect of salt concentration on the intermolecular interactions of proteins. (c) 2006 Elsevier Ltd. All rights reserved.

Electrical control of dynamic spin splitting induced by exchange interaction as revealed by time-resolved Kerr rotation in a degenerate spin-polarized electron gas

Manipulation of the spin degree of freedom has been demonstrated in a spin-polarized electron plasma in a heterostructure by using exchange-interaction-induced dynamic spin splitting rather than the Rashba and Dresselhaus types, as revealed by time-resolved Kerr rotation. The measured spin splitting increases from 0.256 meV to 0.559 meV as the bias varies from -0.3 V to -0.6 V. Both the sign switch of the Kerr signal and the phase reversal of Larmor precessions have been observed with biases, which all fit into the framework of exchange-interaction-induced spin splitting. The electrical control of it may provide a new effective scheme for manipulating spin-selected transport in spin FET-like devices. Copyright (C) EPLA, 2008.

Anisotropic exchange splitting of excitons in (001)GaAs/Al0.3Ga0.7As superlattice studied by reflectance difference spectroscopy

Anisotropic exchange splitting (AES) is induced by the joint effects of the electron-hole exchange interaction and the symmetry reduction in quantum wells and quantum dots. A model has been developed to quantitatively obtain the electron-hole exchange energy and the hole-mixing energy of quantum wells and superlattices. In this model, the AES and the degree of polarization can both be obtained from the reflectance difference spectroscopy. Thus the electron-hole exchange energy and the hole-mixing energy can be completely separated and quantitatively deduced. By using this model, a (001)5 nm GaAs/7 nm Al0.3Ga0.7As superlattice sample subjected to [110] uniaxial strains has been investigated in detail. The n=1 heavy-hole (1H1E) exciton can be analyzed by this model. We find that the AES of quantum wells can be linearly tuned by the [110] uniaxial strains. The small uniaxial strains can only influence the hole-mixing interaction of quantum wells, but have almost no contribution to the electron-hole exchange interaction. (c) 2008 American Institute of Physics.

Electric-field tuning s-d exchange interaction in quantum dots

We investigate theoretically the electron-hole pair states in CdTe quantum dot (QD) containing a single Mn2+ ion by the magneto-optical spectrum tuned by the electric field. It is shown that the electric field does not only tune the spin splitting via the sp-d exchange interaction but also affect significantly the anticrossing behavior in the photoluminescence spectrum. This anticrossing is caused by the s-d exchange interaction and/or the hole mixing effect, which depends sensitively on the shape of the QD. (C) 2008 American Institute of Physics.

Properties of exchange interaction in Yb3Fe5O12 under extreme conditions

In Yb3Fe5O12, the exchange effective field can be expressed as H-eff = -lambda center dot center dot center dot M-Fe = -lambda chi(eff)center dot center dot center dot H-e = -gamma center dot center dot center dot H-e where gamma is named as the exchange field parameter and H-e is the external magnetic field. Then, in this paper, by the discussions on the characteristics of the exchange field parameter gamma, the properties of exchange interaction in ytterbium iron garnet (Yb3Fe5O12) are analyzed under extreme conditions (high magnetic fields and low temperatures). Our theory suggests that the exchange field parameter gamma is the function of the temperatures under different external magnetic fields, and gamma = a+b center dot center dot center dot T+c center dot center dot center dot T-2, where the coefficients a, b, c are associated with the external magnetic fields and the magnetized directions. Thus, the temperature-dependence, field-dependence and anisotropic characteristics of the exchange interaction in Yb3Fe5O12 are revealed. Also, excellent fits to the available experiments are obtained. (C) 2009 Elsevier B.V. All rights reserved.

Evidence of ultrafast energy exchange-induced soft'mode of phonons and lattice instability: a nanotime effect

With a series of supportive experimental phenomena as induced by ion beam bombardment, energetic beaminduced athermal activation process in Si is demonstrated. This is correlated with phenomena induced by ultrafast energy exchange in condensed matter in general. A critical modelling is presented on the above process and a universal concept: the ultrafast energy exchange-induced soft mode of phonons and the lattice instability in condensed matter are proposed.

Interplay between s-d exchange interaction and Rashba effect: Spin-polarized transport

The authors investigate the spin-polarized transport properties of a two-dimensional electron gas in a n-type diluted magnetic narrow gap semiconductor quantum well subjected to perpendicular magnetic and electric fields. Interesting beating patterns in the magnetoresistance are found which can be tuned significantly by varying the electric field. A resonant enhancement of spin-polarized current is found which is induced by the competition between the s-d exchange interaction and the Rashba effect [Y. A. Bychkov and E. I. Rashba, J. Phys. C 17, 6039 (1984)]. (c) 2006 American Institute of Physics.

Interlayer segregation in magnetic multilayers and its influence on exchange coupling

Experimental results show that the exchange coupling field (H-ex) of NiFe/FeMn for Ta/NiFe/FeMn/Ta multilayers is higher than that for spin-valve multilayers Ta/NiFe/Cu/NiFe/FeMn/Ta. X-ray photoelectron spectroscopy shows that Cu atoms segregate to the NiFe/FeMn interface for Ta/NiFe/Cu/NiFe/FeMn/Ta multilayers. While studying Ta/X(X=Bi,Pb,Ag,In)/NiFe/FeMn multilayers, we also find that X atoms segregate to the NiFe/FeMn interface, which results in a decrease of the H-ex. However, a small amount of Bi, Pb, etc. deposited between Cu and pinned NiFe layer for Ta/NiFe/Cu/NiFe/FeMn/Ta multilayers can increase H-ex. (C) 2003 American Institute of Physics.