Biomedical subjects

Xiaoqin Li

Publications and source records attributed to Xiaoqin Li.

5 recordsLinked to original sources

PubMed2004

Protein structure preference, tRNA copy number, and mRNA stem/loop content.

From statistical analyses of protein sequences for humans and Escherichia coli we found that the messenger RNA segment of m-codons (for m=2 to 6) with average high tRNA copy number (TCN) (larger than approximately 10.5 for humans or approximately 1.95 for E. coli) preferably code for the alpha helix and that with low TCN (smaller than approximately 7.5 for humans or approximately 1.7 for E. coli) preferably code for coil. Between them there is an intermediate region without correlation to structure preference. For the beta strand the preference/ avoidance tendency is not obvious. All strong preference-modes of TCN for protein secondary structures have been deduced. The mutual interaction between two factors--protein secondary structural type and codon TCN--is tested by F distribution. A phenomenological model on the relation between structure preference and translational efficiency or accuracy is proposed. It is pointed out that the structure preference of codons is related to the distribution of mRNA stem/loop content in three TCN regions.

Bacterial Proteins↗

PubMed2003

An all-optical quantum gate in a semiconductor quantum dot.

We report coherent optical control of a biexciton (two electron-hole pairs), confined in a single quantum dot, that shows coherent oscillations similar to the excited-state Rabi flopping in an isolated atom. The pulse control of the biexciton dynamics, combined with previously demonstrated control of the single-exciton Rabi rotation, serves as the physical basis for a two-bit conditional quantum logic gate. The truth table of the gate shows the features of an all-optical quantum gate with interacting yet distinguishable excitons as qubits. Evaluation of the fidelity yields a value of 0.7 for the gate operation. Such experimental capability is essential to a scheme for scalable quantum computation by means of the optical control of spin qubits in dots.

Journal Article↗

PubMed2002

Biexciton quantum coherence in a single quantum dot.

Nondegenerate (two-wavelength) two-photon absorption using coherent optical fields is used to show that there are two different quantum mechanical pathways leading to formation of the biexciton in a single quantum dot. Of specific importance to quantum information applications is the resulting coherent dynamics between the ground state and the biexciton from the pathway involving only optically induced exciton/biexciton quantum coherence. The data provide a direct measure of the biexciton decoherence rate which is equivalent to the decoherence of the Bell state in this system, as well as other critical optical parameters.

Journal Article↗

PubMed2002

Coding rules for amino acids in the genetic code: the genetic code is a minimal code of mutational deterioration.

Coding rules for amino acids in the genetic code are discussed from the point that the genetic code is a minimal code of mutational deterioration. The global mutational deterioration (GMD) function is defined through several parameters describing single base mutations and amino acid distances. The problem of searching for the global minimum of the GMD function is discussed in some detail. From GMD minimization under initial constraints we have succeeded in deducing the standard genetic code.

Amino Acids↗

PubMedDate not supplied

Construction of genetic code from evolutionary stability.

The construction of the genetic code is investigated based on a stability principle. The concept and formulation of mutational deterioration (MD) of the genetic code is proposed. It is proved that the degeneracies of codon multiplets obey the rule to best resist MD. The MD for each ideal multiplet of codons is expressed by four parameters and it takes on a minimum value for real distributions of codons in the multiplet. Then the global mutational deterioration (GMD) of code table is calculated and the minimal code is deduced. The domain-like distribution of hydrophobic and hydrophilic amino acids on the genetic code is explained from the minimization of GMD. It is demonstrated that the standard code is approximately GMD-minimal. By introducing some constraints that are related to the initial condition of the system, we have deduced the standard genetic code from the minimization of GMD. The minimization shows the general trend of evolutionary process to some stable state while the constraints reflect a 'frozen accident.' Many deviant codon assignments are also explained through MD minimization assuming the changeable degrees of degeneracies for some multiplets. So, a possible answer to the question of "Why are synonymous codons and amino acids distributed in the code table just as they are?" is given.

Biological Evolution↗