Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Transport properties in a gated heterostructure with a trapezoidal AlxGa1-xAs barrier layer

By replacing the flat (Ga1-xAlx)As barrier layer with a trapezoidal AlxGa1-xAs barrier layer, a conventional heterostructure can be operated in enhancement mode. The sheet density of two-dimensional electron gas (2DEG) in the structure can be tuned linearly from N-2D = 0.3 x 10(11) cm(-2) to N-2D = 4.3 x 10(11) cm(-2) by changing the bias on the top gate. The present scheme for gated heterostructures is easy to fabricate and does not require the use of self-alignment photolithography or the deposition of insulating layers. In addition, this scheme facilitates the initial electrical contact to 2DEG. Although, the highest electron mobility obtained for the moment is limited by the background doping level of heterostructures, the mobility should be improved substantially in the future. (C) 2009 Elsevier B.V. All rights reserved.

Symmetry and optical transition rule for low-dimensional semiconductor system with spin-orbit interaction and magnetic field

Starting from effective mass Hamiltonian, we systematically investigate the symmetry of low-dimensional structures with spin-orbit interaction and transverse magnetic field. The position-dependent potentials are assumed to be space symmetric, which is ever-present in theory and experiment research. By group theory, we analyze degeneracy in different cases. Spin-orbit interaction makes the transition between Zeeman sub-levels possible, which is originally forbidden within dipole approximation. However, a transition rule given in this paper for the first time shows that the transition between some levels is forbidden for space symmetric potentials. (C) 2009 Elsevier Ltd. All rights reserved.

Single-mode condition for silicon rib waveguides with trapezoidal cross-section

Single-mode condition for silicon rib waveguides with trapezoidal cross-section was obtained using a numerical method based on imaginary-distance beam propagation method with non-uniform discretization. Both quasi-transverse-electric and quasi-transverse-magnetic modes were investigated. Simulated single-mode condition is given by a modified equation. Comparison with reported results shows that the Marcatili's method is in a better agreement with our results. (C) 2003 Elsevier B.V. All rights reserved.

Multimode interference 3-dB coupler in silicon-on-insulator based on silicon rib waveguides with trapezoidal cross section

A 3-dB multimode interference optical coupler based on rib waveguides with trapezoidal cross section was designed and fabricated on silicon-on-insulator wafer. Potassium hydroxide (KOH) anisotropic chemical etching of silicon was used to fabricate the waveguides to obtain smooth interface. A modified finite-difference beam propagation method was used to simulate the multimode rib waveguide with slope interfaces. The rms roughness of etching interface is as small as 1.49 nm. The propagation loss of the waveguide is 1.3 dB/cm at wavelength of 1.55 mum. The fabricated 3-dB coupler has a good uniformity of 0.2 dB.

LIPID MICRORESISTOR AS MIMICKING OLFACTORY SENSOR - THE RULE OF THE RESPONSE OF LIPIDS TO C-1-C-4 ALCOHOLS

Phosphatidylcholine (PC) and six other PC-similar lipids are coated on interdigital electrodes, IEs, as sensitive membranes. Eight alcohols (C-1-C-4) are tested in a flow system at room temperature. It is found that all responses are log(response)-log(concentration) linear relations. These results agree with Steven's law in psychophysics. Moreover, the thresholds of the sensors are coincident with human olfactory thresholds. The authors have analysed the data of the lipid hypothesis suggested by Kurihara et al. We have found that this hypothesis is also in agreement with Steven's law. Lipid microresistors are real mimicking olfactory sensors. A definition of an olfactory sensor is suggested.

Golden-rule treatment on the ClO/ClO+ electron-transfer system

The structures, properties and electron transfer reactivity of the ClO/ClO+ coupling system are studied in this paper at ab initio (HF and MP2) levels and the density functional theory (DFT: B3LYP, B3P86, B3PW91) levels employing 6311 + G(3df) basis set and on the basis of the golden-rule of the time-dependent perturbation theory. Investigations indicate that the results got from the B3LYP method employing 6-311 + G(3df) basis set is in excellent agreement with the experiment. The activation energies, the stabilization energies and the electronic coupling matrix elements have also been calculated by using the B3LYP/6-311 + G(3df) method, and then the electron transfer rates are determined at this level. The electronic coupling matrix element of EC.6 is very small, only 0.03 kcal/mol, while that of EC.7 is the biggest, being 12.41 kcal/mol, the corresponding electron transfer rate is also the fastest among these seven encounter complexes. The averaged electron transfer rate is about 1.672 X 10(11) M-1 s(-1). It is indicated that the structures optimized by B3LYP method are more reliable than the results got from the other four methods. It also testified that the electronic coupling matrix element is the vital factor that significantly affects the electron transfer rate. (C) 2003 Elsevier B.V. All rights reserved.

Theoretical study on the ClO/ClO- system electron-transfer reactivity by the golden-rule

The structures, properties and electron transfer reactivity of the ClO/ClO- coupling system are studied in this paper at ab initio (UHF and UMP2) levels and the Density Functional Theory (DFT: UB3LYP, UB3P86, UB3PW91) levels employing 6311 + G(3df) basis set and on the basis of the Golden-rule of the time-dependent perturbation theory. Investigations indicate that the results obtained using the UB3LYP method employing 6-311 + G(3df) basis set is in excellent agreement with the experiment. For this coupling system, six stable coupling modes have been found which correspond to six different encounter complexes and denote six different electron transfer mechanism: four O-O directly linked structures (one collinear: D-h, one anti-parallel: C-s, two twist: C-2) and two Cl-O linked structures (cis- and anti- C-s structures). The activation energies, the stabilization energies and the electronic coupling matrix elements have also been calculated for the electron transfer reactions via these six different mechanism at the UB3LYP/6-311 + G(3df) level, and then the electron transfer rates are determined at the same level. The most favorable coupling mode to the electron transfer is the anti-parallel mechanism. The averaged electron transfer rate is about 5.58 X 10(11) M-1 s(-1). It is also implied that the B3LYP method can give more reasonable results for the electron transfer reactivity of this system. (C) 2003 Elsevier B.V. All rights reserved.

Theoretical estimation of thermodynamic properties of the system PS/PPO on the basis of modified combining rule of Sanchez-Lacombe lattice fluid model

The three scaling parameters described in Sanchez-Lacombe lattice fluid theory (SLLFT), T*, P* and rho* of pure polystyrene (PS), pure poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) and their mixtures are obtained by fitting corresponding experimental pressure volume-temperature data with equation-of-state of SLLFT. A modified combining rule in SLLFT used to match the volume per mer, v* of the PS/PPO mixtures was advanced and the enthalpy of mixing and Flory-Huggins (FH) interaction parameter were calculated using the new rule. It is found that the difference between the new rule and the old one presented by Sanchez and Lacombe is quite small in the calculation of the enthalpy of mixing and FH interaction parameter and the effect of volume-combining rule on the calculation of thermodynamic properties is much smaller than that of energy-combining rule. But the relative value of interaction parameter changes much due to the new volume-based combining rule. This effect can affect the position of phase diagram very much, which is reported elsewhere [Macromolecules 34 (2001) 6291]

A rule to design high spin molecules with hetero-spin centers

The series of biradicals with m-phenylene coupling unit and hetero-spin centers were calculated compared with those possessing home-spin centers using AM1-CI method. A simple rule was proposed to design high spin molecules with ferromagnetic coupling unit and hetero-spin centers. Two neutral (or charged) hetero-spin centers resulted in high spin ground state, one neutral and another charged hetero-spin centers correspond to low spin ground state. The latter was ascribed to the huge splitting of two partially occupied molecular orbitals.

Fully developed laminar flow and heat transfer in smooth trapezoidal microchannel

Numerical analysis of fully developed laminar slip flow and heat transfer in trapezoidal micro-channels has been studied with uniform wall heat flux boundary conditions. Through coordinate transformation, the governing equations are transformed from physical plane to computational domain, and the resulting equations are solved by a finite-difference scheme. The influences of velocity slip and temperature jump on friction coefficient and Nusselt number are investigated in detail. The calculation also shows that the aspect ratio and base angle have significant effect on flow and heat transfer in trapezoidal micro-channel. (c) 2005 Elsevier Ltd. All rights reserved.