Methods and systems of four-valued genomic sequencing and macromolecular analysis

1. A machine implemented method of executing four-valued logic in a semantic network for genome sequencing and analysis, the method comprising:

defining a logic system having a NOT logical connective denoted as “ ,” an AND logical connective denoted as “ ,” and an OR logical connective denoted as “ ,” wherein false values are represented with an “F” symbol, true values are represented by a “T” symbol, undefined values are represented by a “U” symbol, and defined values are represented by a “D” symbol, such that for a property P false values are in a set { P}, true values are in a set {P}, undefined values are in a set{ }, defined values are in a set {P, P},

wherein said logic system is proven complete and w-consistent by a set of statements comprising:

F is T, T is F, U is D, D is U;

F F is F, F T is F, F U is F, F D is F;

T F is F, T T is T, T U is U, T D is D;

U F is F, U T is U, U U is U, U D is F;

D F is F, D T is D, D U is F, D D is D;

F F is F, F T is T, F U is U, F D is D;

T F is T, T T is T, T U is T, T D is T;

U F is U, U T is T, U U is U, U D is T; and

D F is D, D T is T, D U is T, D D is D;

generating a semantic network representing digitally stored information, said semantic network comprising a plurality of object nodes representing inputted genetic sequences and a plurality of relationships between said plurality of object nodes, by:

providing a first vector and a second vector in digital memory for each of said plurality of object nodes, each of said first vector and said second vector being a dynamically allocated array having a plurality of index positions each with a size of one bit;

linearly encoding semantic information for an object node by storing two bits that together encode a false value, true value, undefined value, or defined value, a first bit of said two bits being stored at an index position within the first vector associated with the object node, and a second bit of said two bits being stored at the same index position within the second vector associated with the object node;

linearly encoding syntactic information associated with said plurality of relationships in said digital memory; and

testing conditionals or quantifying variables in said semantic network during successive recursive steps in a predicate calculus using said logic system, the false values, true values, undefined values, and defined values in the semantic information associated with said plurality of object nodes, and the syntactic information associated with said plurality of relationships,

wherein linear encoding of semantic information and said syntactic information optimizes short term memory, maximizes long term storage, and optimizes communication and memory between different knowledge sources or processes.

2. The method of claim 1 , further comprising applying phrase structure rewrite rule on said plurality of object nodes in said semantic network.

3. The method of claim 2 , further comprising implementing a top/down, bottom/up parser configured of a plurality of syntactic parses of a grammar.

4. The method of claim 3 , wherein said top/down, bottom/up parsers is coupled with a system clock, a runtime stack and heap, a processor, machine readable instructions contained on non-transitory media, a database of rewrite rules, a database storing said semantic network, and a database storing said syntactic information and said semantic information.

5. The method of claim 4 , wherein said plurality of syntactic parses of a grammar provides syntactic pattern matching abilities when modeling pattern matching for DNA sequences.

6. The method of claim 5 , further comprising dynamic modeling of DNA in Monte Carlo simulations, for the use of whole genomic sequences.

7. The method of claim 5 , wherein said processor is a specialized processor.

8. A machine implemented method of executing four-valued logic in a semantic network for macromolecular analysis, the method comprising:

defining a logic system having a NOT logical connective denoted as “ ,” an AND logical connective denoted as “ ,” and an OR logical connective denoted as “ ,” wherein false values are represented with an “F” symbol, true values are represented by a “T” symbol, undefined values are represented by a “U” symbol, and defined values are represented by a “D” symbol, such that for a property P false values are in a set { P}, true values are in a set {P}, undefined values are in a set{ }, defined values are in a set {P, P},

wherein said logic system is proven complete and w-consistent by a set of statements comprising:

F is T, T is F, U is D, D is U;

F F is F, F T is F, F U is F, F D is F;

T F is F, T T is T, T U is U, T D is D;

U F is F, U T is U, U U is U, U D is F;

D F is F, D T is D, D U is F, D D is D;

F F is F, F T is T, F U is U, F D is D;

T F is T, T T is T, T U is T, T D is T;

U F is U, U T is T, U U is U, U D is T; and

D F is D, D T is T, D U is T, D D is D;

generating a semantic network representing digitally stored information, said semantic network comprising a plurality of object nodes representing macro molecular mechanics and a plurality of relationships between said plurality of object nodes, by:

providing a first vector and a second vector in digital memory for each of said plurality of object nodes, each of said first vector and said second vector being a dynamically allocated array having a plurality of index positions each with a size of one bit;

linearly encoding semantic information for an object node by storing two bits that together encode a false value, true value, undefined value, or defined value, a first bit of said two bits being stored at an index position within the first vector associated with the object node, and a second bit of said two bits being stored at the same index position within the second vector associated with the object node;

linearly encoding syntactic information associated with said plurality of relationships in said digital memory; and

testing conditionals or quantifying variables in said semantic network during successive recursive steps in a predicate calculus using said logic system, the false values, true values, undefined values, and defined values in the semantic information associated with said plurality of object nodes, and the syntactic information associated with said plurality of relationships,

wherein linear encoding of said semantic information and said syntactic information optimizes short term memory, maximizes long term storage, and optimizes communication and memory between different knowledge sources or processes, and;

wherein defined values and undefined values represent different genetic types and molecular structures in said semantic network.

9. A system for the hybrid modeling of genetic sequences and macromolecular structures for chemical discoveries in key lock systems and induced fit systems, the system comprising:

a computing device comprising a central processing unit, a runtime stack and heap, a top down / bottom up parser, and a system clock;

a logic system defined in memory of said computing device, said logic system having a NOT logical connective denoted as “ ,” an AND logical connective denoted as “ ,” and an OR logical connective denoted as “ ,” wherein false values are represented with an “F” symbol, true values are represented by a “T” symbol, undefined values are represented by a “U” symbol, and defined values are represented by a “D” symbol, such that for a property P false values are in a set { P}, true values are in a set {P}, undefined values are in a set { }, and defined values are in a set {P, P},

wherein said logic system is proven complete and w-consistent by a set of statements comprising:

F is T, T is F, U is D, D is U;

F F is F, F T is F, F U is F, F D is F;

T F is F, T T is T, T U is U, T D is D;

U F is F, U T is U, U U is U, U D is F;

D F is F, D T is D, D U is F, D D is D;

F F is F, F T is T, F U is U, F D is D;

T F is T, T T is T, T U is T, T D is T;

U F is U, U T is T, U U is U, U D is T;

D F is D, D T is T, D U is T, D D is D; and

a non-transitory computer readable medium storing machine readable instructions for causing said computing device to perform the steps of:

generating a semantic network representing digitally stored information, said semantic network comprising a plurality of object nodes representing genetic sequences and macromolecular structures and a plurality of relationships between said plurality of object nodes, by:

providing a first vector and a second vector in digital memory for each of said plurality of object nodes, each of said first vector and said second vector being a dynamically allocated array having a plurality of index positions each with a size of one bit;

linearly encoding semantic information for an object node by storing two bits that together encode a false value, true value, undefined value, or defined value, a first bit of said two bits being stored at an index position within the first vector associated with the object node, and a second bit of said two bits being stored at the same index position within the second vector associated with the object node;

linearly encoding syntactic information associated with said plurality of relationships in said digital memory; and

testing of conditionals or quantifying variables in said semantic network during successive recursive steps in a predicate calculus using said logic system, the false values, true values, undefined values, and defined values in the semantic information associated with said plurality of object nodes, and the syntactic information associated with said plurality of relationships,

wherein linear encoding of said semantic information and said syntactic information optimizes short term memory, maximizes long term storage, and optimizes communication and memory between different knowledge databases.

10. The system of claim 9 , said machine readable instructions further comprising applying a phrase structure rewrite rule on said plurality of object nodes in said semantic network for testing and passing of the rewrite rule, a word size of the system imposing a chunking factor in a testing of conditionals in theoretic time O(C).

11. The system of claim 9 , wherein said first vector and said second vector for each of said plurality of object nodes is stored in a database of vectors, said plurality of object nodes and said plurality of relationships is stored in a semantic network database, a plurality of grammar phrase structure implementations is stored in a grammar database, and logical connectives of said logic system are stored in a logical connectives database.

12. The system of claim 9 , wherein said top/down, bottom/up parser is configured to perform a plurality of syntactic parses of a grammar to efficiently model the growth of a statistical summation in a search space.

13. The system of claim 9 , wherein said machine readable instructions further comprise instructions for dynamic macromolecular modeling of DNA in Monte Carlo simulations using physical properties of the DNA.