Locally Balanced Constraints

Three new constraints are introduced in this paper. These constraints are characterized by limitations on the Hamming weight of every subword of some fixed even length ℓ. In the (ℓ, δ)-locally-balanced constraint, the Hamming weight of every length-ℓ subword is bounded between ℓ/2 — δ and ℓ/2 + δ. The strong-(ℓ,δ)-locally-balanced constraint imposes the locally- balanced constraint for any subword whose length is at least ℓ. Lastly, the Hamming weight of every length-ℓ subword which satisfies the (ℓ, δ)-locally-bounded constraint is at most ℓ/2 — δ. It is shown that the capacity of the strong-(ℓ, δ)-locally-balanced constraint does not depend on the value of ℓ and is identical to the capacity of the (2δ + 1)-RDS constraint. The latter constraint limits the difference between the number of zeros and ones in every prefix of the word to be at most 2δ + 1. This value is also a lower bound on the capacity of the (ℓ, δ)-locally-balanced constraint, while a corresponding upper bound is given as well. Lastly, it is shown that if δ is not large enough, namely for $\delta < \sqrt \ell /2$, then the capacity of the (ℓ, δ)-locally-bounded constraint approaches 1 as ℓ increases.

[1]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1974, Nature.

[2]  Jehoshua Bruck,et al.  Attaining the 2nd Chargaff Rule by Tandem Duplications , 2018, 2018 IEEE International Symposium on Information Theory (ISIT).

[3]  Mehul Motani,et al.  On code design for simultaneous energy and information transfer , 2014, 2014 Information Theory and Applications Workshop (ITA).

[4]  David Mitchell,et al.  A test of Chargaff's second rule. , 2006, Biochemical and biophysical research communications.

[5]  Elza Erkip,et al.  Constrained Codes for Joint Energy and Information Transfer , 2014, IEEE Transactions on Communications.

[6]  Olgica Milenkovic,et al.  Portable and Error-Free DNA-Based Data Storage , 2016, Scientific Reports.

[7]  Mehul Motani,et al.  Subblock-Constrained Codes for Real-Time Simultaneous Energy and Information Transfer , 2015, IEEE Transactions on Information Theory.

[8]  Jian Ma,et al.  DNA-Based Storage: Trends and Methods , 2015, IEEE Transactions on Molecular, Biological and Multi-Scale Communications.

[9]  Donald E. Knuth,et al.  Efficient balanced codes , 1986, IEEE Trans. Inf. Theory.

[10]  C. H,et al.  Handbook of enumerative combinatorics , 2022 .

[11]  E. Chargaff Structure and function of nucleic acids as cell constituents. , 1951, Federation proceedings.

[12]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[13]  Robert N Grass,et al.  Robust chemical preservation of digital information on DNA in silica with error-correcting codes. , 2015, Angewandte Chemie.

[14]  Yaniv Erlich,et al.  DNA Fountain enables a robust and efficient storage architecture , 2016, Science.

[15]  E. Chargaff,et al.  Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. , 1968, Proceedings of the National Academy of Sciences of the United States of America.

[16]  E. Chargaff Chemical specificity of nucleic acids and mechanism of their enzymatic degradation , 1950, Experientia.