Biomedical subjects

Xiaofeng Qian

Publications and source records attributed to Xiaofeng Qian.

5 recordsLinked to original sources

PubMed2005

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.

Journal Article↗

PubMed2004

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↗

PubMed2004

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↗

PubMed2003

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↗

PubMed2003

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↗