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Article
Open AccessIntrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes
K-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution. We want to reveal the evolution rules of genome sequences by studying the k-mer spectra of genome...
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Article
Quantum conformational transition in biological macromolecule
Recently we proposed a quantum theory on the conformational change of biomolecule, deduced several equations on protein folding rate from the first principles and discussed the experimental tests of the theory...
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Article
Open AccessStatistical analyses of protein folding rates from the view of quantum transition
Understanding protein folding rate is the primary key to unlock the fundamental physics underlying protein structure and its folding mechanism. Especially, the temperature dependence of the folding rate remain...
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Article
Quantum theory on protein folding
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobi...
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Article
Prediction of Protein Secondary Structure Using Feature Selection and Analysis Approach
The prediction of the secondary structure of a protein from its amino acid sequence is an important step towards the prediction of its three-dimensional structure. However, the accuracy of ab initio secondary ...
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Article
Open AccessProtein photo-folding and quantum folding theory
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from quantum folding theory by use of a field-theoretical method. Al...
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Article
Open AccessThe dynamical contact order: Protein folding rate parameters based on quantum conformational transitions
Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain. According to the quantum theory of conformational dynamics, we propose the dynamical contact order (DCO) d...
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Article
Use of tetrapeptide signals for protein secondary-structure prediction
This paper develops a novel sequence-based method, tetra-peptide-based increment of diversity with quadratic discriminant analysis (TPIDQD for short), for protein secondary-structure prediction. The proposed T...
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Messenger RNA Information: Its Implication in Protein Structure Determination and Others
Three problems on mRNA information in protein-coding regions are discussed: first, how the mRNA sequence information (tRNA gene copy number) is related to protein secondary structure; second, how the mRNA stru...
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Article
Open AccessPhysicochemical attack against solid tumors based on the reversal of direction of entropy flow: an attempt to introduce thermodynamics in anticancer therapy
There are many differences between healthy tissue and growing tumor tissue, including metabolic, structural and thermodynamic differences. Both structural and thermodynamic differences can be used to follow th...
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Article
Open AccessUltrasound absorption and entropy production in biological tissue: a novel approach to anticancer therapy
The entropy production of tumorous cells is higher than that of normal cells, and entropy flow is therefore directed from tumorous toward healthy cells. This results in information concerning the cancer propag...
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Article
Prediction for Target Sites of Small Interfering RNA Duplexes in SARS Coronavirus
RNA interference is used for SARS-related pharmaceutical research and development. Following bioinformatic method twenty seven 21~25 base-long sequence segments in SARS-CoV genome are predicted as the optimal ...
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Article
Short segmental duplication: parsimony in growth of microbial genomes
We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long (2 to 10-mers) in microbial complete genomes with corresponding distributions obtained from random sequences and...
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Article
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 ofmutational deterioration. The global mutational deterioration(GMD) function is defined th...
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Article
Fuzzy classification of nucleotide sequences and bacterial evolution
A new method for reconstructing evolutionary relationship among bacteria by use of rRNA sequence data is proposed. The method is based on the concept of fuzzy classification of probabilitiesp(i), p(i/j) andp(i/j*...
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Article
The statistical correlation of nucleotides in protein-coding DNA sequences
The statistical correlation of nucleotides in a DNA sequence is described by a set of redundanciesD 1,D 2,D 3,... By calculation of {D n} of 2341 co...
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Article
A statistical theory of amino acid mutation
Assuming that the observed mutation frequency of an amino acid depends on two factors. The first is mutation coefficient which describes the rate of the nucleotide substitution stochastically and the second is...
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Article
The phenomenology ofSU 2,L ×SU 2,R ×U 1,L+R gauge theory
By use of experimental data on high-energy weak interactions the masses of new gauge bosons are determined in a self-consistent way. The decay width and branching ratio of gauge bosons are calculated.
