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Xiaofeng Qian

Publications and source records attributed to Xiaofeng Qian.

8 recordsLinked to original sources

Critical line of an n-component cubic model.

We consider a special case of the -component cubic model on the square lattice, for which an expansion exists in Ising-type graphs. We construct a transfer matrix and perform a finite-size-scaling analysis to determine the critical points for several values of . Furthermore we determine several universal quantities, including three critical exponents. For , these results agree well with the theoretical predictions for the critical branch. This model is also a special case of the model of Domany and Riedel. It appears that the self-dual plane of the latter model contains the exactly known critical points of the and 2 cubic models. For this reason we have checked whether this is also the case for . However, this possibility is excluded by our numerical results.

Journal Article↗

Leucine motif-dependent tyrosine autophosphorylation of type III receptor tyrosine kinases.

Activation loop tyrosine autophosphorylation is an essential requirement for full kinase activation of receptor tyrosine kinases (RTKs). However, mechanisms involved are not fully understood. In general, kinase domains of RTKs are folded into two main lobes, NH2- and COOH-terminal lobes. The COOH-terminal lobe of vascular endothelial growth factor receptor-2 (VEGFR-2) is folded into seven alpha-helices (alphaD-alphaI). In the studies presented here we demonstrate that leucine residues of helix I (alphaI) regulate tyrosine autophosphorylation and phosphotransferase activity of VEGFR-2. The presence of leucines 1158, 1161, and 1162 are essential for tyrosine autophosphorylation and kinase activation of VEGFR-2 and are involved in helix-helix packing via hydrophobic interactions. The presence of leucine 1158 is critical for kinase activation of VEGFR-2 and appears to interact with alphaE, alphaF, alphaH, and beta7. The analogous residue, leucine 957 on platelet-derived growth factor receptor-beta and leucine 910 on colony stimulating factor-1R are also found to be critical for tyrosine autophosphorylation of these receptors. Leucines 1161 and 1162 are also involved in helix-helix packing but they play a less critical role in VEGFR-2 activation. Thus, we conclude that leucine motif-mediated helix-helix interactions are critical for kinase regulation of type III RTKs. This mechanism is likely to be shared with other kinases and might provide a basis for the design of a novel class of tyrosine kinase inhibitors.

Adenosine Triphosphate↗

Dilute Potts model in two dimensions.

We study the two-dimensional dilute q-state Potts model by means of transfer-matrix and Monte Carlo methods. Using the random-cluster representation, we include noninteger values of q. We locate phase transitions in the three-dimensional parameter space of q, the Potts coupling K>>0, and the chemical potential of the vacancies. The critical plane is found to contain a line of fixed points that divides into a critical branch and a tricritical one, just as predicted by the renormalization scenario formulated by Nienhuis et al for the dilute Potts model. The universal properties along the line of fixed points agree with the theoretical predictions. We also determine the density of the vacancies along these branches. For q=2-squareroot of 2 we obtain the phase diagram in a three-dimensional parameter space that also includes a coupling V> or = 0 between the vacancies. For q=2, the latter space contains the Blume-Capel model as a special case. We include a determination of the tricritical point of this model, as well as an analysis of percolation clusters constructed on tricritical Potts configurations for noninteger q. This percolation study is based on Monte Carlo algorithms that include local updates flipping between Potts sites and vacancies. The bond updates are performed locally for and by means of a cluster algorithm for q>1. The updates for q>1 use a number of operations per site independent of the system size.

Journal Article↗

Simulation algorithms for the random-cluster model.

We compare the performance of Monte Carlo algorithms for the simulation of the random-cluster representation of the q-state Potts model for continuous values of q. In particular we consider a local bond update method, a statistical reweighting method of percolation configurations, and a cluster algorithm, all of which generate Boltzmann statistics. The dynamic exponent z of the cluster algorithm appears to be quite small, and to assume the values of the Swendsen-Wang algorithm for q = 2 and 3. The cluster algorithm appears to be much more efficient than our versions of the other two methods for the simulation of the random-cluster model. The higher efficiency of the cluster method with respect to the local method is primarily due to the fact that the computer time usage of the local method increases more rapidly with system size; the difference between the dynamic exponents is less important.

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Triangular Ising model with nearest- and next-nearest-neighbor couplings in a field.

The authors study the Ising model on the triangular lattice with nearest-neighbor couplings K(nn) , next-nearest-neighbor couplings K(nnn) >0 , and a magnetic field H . This work is done by means of finite-size scaling of numerical results of transfer matrix calculations, and Monte Carlo simulations. We determine the phase diagram and confirm the character of the critical manifolds. The emphasis of this work is on the antiferromagnetic case K(nn) <0 , but we also explore the ferromagnetic regime K(nn) >/=0 for H=0 . For K(nn) <0 and H=0 we locate a critical phase presumably covering the whole range -infinity< K(nn) <0 . For K(nn) <0 , H not equal 0 we locate a plane of phase transitions containing a line of tricritical three-state Potts transitions. In the limit H-->infinity this line leads to a tricritical model of hard hexagons with an attractive next-nearest-neighbor potential.

Journal Article↗

Critical frontier of the triangular Ising antiferromagnet in a field.

We study the critical line of the triangular Ising antiferromagnet in an external magnetic field by means of a finite-size analysis of results obtained by transfer-matrix and Monte Carlo techniques. We compare the shape of the critical line with predictions of two different theoretical scenarios. Both scenarios, while plausible, involve assumptions. The first scenario is based on the generalization of the model to a vertex model, and the assumption that the exact analytic form of the critical manifold of this vertex model is determined by the zeroes of an O(2) gauge-invariant polynomial in the vertex weights. However, it is not possible to fit the coefficients of such polynomials of orders up to 10, such as to reproduce the numerical data for the critical points. The second theoretical prediction is based on the assumption that a renormalization mapping exists of the Ising model on the Coulomb gas, and analysis of the resulting renormalization equations. It leads to a shape of the critical line that is inconsistent with the first prediction, but consistent with the numerical data.

Journal Article↗

A dual role for an aspartic acid in glycosylasparaginase autoproteolysis.

Glycosylasparaginase uses an autoproteolytic processing mechanism, through an N-O acyl shift, to generate a mature/active enzyme from a single-chain precursor. Structures of glycosylasparaginase precursors in complex with a glycine inhibitor have revealed the backbone in the immediate vicinity of the scissile peptide bond to be in a distorted trans conformation, which is believed to be the driving force for the N-O acyl shift to break the peptide bond. Here we report the effects of point mutation D151N. In addition to the loss of the base essential in autoproteolysis, this mutation also eradicates the backbone distortion near the scissile peptide bond. Binding of the glycine inhibitor to the autoproteolytic site of the D151N mutant does not restore the backbone distortion. Therefore, Asp151 plays a dual role, acting as the general base to activate the nucleophile and holding the distorted trans conformation that is critical for initiating an N-O acyl shift.

Aspartic Acid↗

Heat shock protein 90-independent activation of truncated hepadnavirus reverse transcriptase.

The reverse transcriptase (RT) encoded by hepadnaviruses (hepatitis B viruses) is a multifunctional protein critical for several aspects of viral assembly and replication. Reverse transcription is triggered by the specific interaction between the RT and an RNA signal located on the viral pregenomic RNA, termed epsilon, and is initiated through a novel protein priming mechanism whereby the RT itself serves as a protein primer and epsilon serves as the obligatory template. Using the RT from duck hepatitis B virus as a model, we previously demonstrated that RT-epsilon interaction and protein priming require the assistance of a host cell chaperone complex, heat shock protein 90 (Hsp90) and its co-chaperones, which associates with the RT and facilitates the folding of the RT into an active conformation. We now report that extensive truncation removing the entire C-terminal RNase H domain and part of the central RT domain could relieve this dependence on Hsp90 for RT folding such that the truncated RT variants could function in epsilon interaction and protein priming independently of Hsp90. The presence of certain nonionic or zwitterionic detergent was sufficient to establish and maintain the truncated RT proteins in an active, albeit labile, state. Furthermore, we were able to refold an RT truncation variant de novo after complete denaturation. In contrast, the full-length RT and also RT variants with less-extensive C-terminal truncations required Hsp90 for activation. Surprisingly, the presence of detergent plus some yet-to-be-identified cytoplasmic factor(s) led to a dramatic suppression of the RT activities. These results have important implications for RT folding and conformational maturation, Hsp90 chaperone function, and potential inhibition of RT functions by host cell factors.

Animals↗