chemical master eqn, aij*h = prob of i->j transition in time h (Markov model)
Name chem_master1
Group Watson
Matrix ID 1854
Num Rows 40,401
Num Cols 40,401
Nonzeros 201,201
Pattern Entries 201,201
Kind 2D/3D Problem
Symmetric No
Date 2007
Author L. Watson and J. Zhang
Editor T. Davis
Structural Rank 40,401
Structural Rank Full true
Num Dmperm Blocks 1
Strongly Connect Components 1
Num Explicit Zeros 0
Pattern Symmetry 100%
Numeric Symmetry 0%
Cholesky Candidate no
Positive Definite no
Type real
Download MATLAB Rutherford Boeing Matrix Market
The ODE system \frac{dp}{dt}=Qp is what we call a chemical master equation (a 
Kolmogorov's backward/forward equation). Q is a sparse asymmetric matrix,     
whose off-diagonal entries are non-negative and row sum to zero. On each row, 
q_{ij}h gives the probability the system makes a transition from current state
i to some other state j, in small time interval h. By "state", we mean a      
possible combination of number of molecules in each chemical species. Now, h  
is small enough so that only one reaction happens.  In this way q_{ij} is     
nonzero only if there exists a chemical reaction that connects state i and j, 
i.e. j=i+s_k, s_k's are constant state vectors that correspond to every       
reaction.  Say we have M reactions, then there are at most M+1 nonzero        
entries on each row of Q.  On the other hand, the number of possible          
combination of molecules is huge, which means the dimension of Q is huge.     
The linear system we want to solve is (I - Q/lambda)x=b, and we have          
to solve it several times. (Here lambda is a constant).  Problem.A is the Q   
matrix.  This is a small test problem; the largest has dimension 10^8.        
It has the nonzero pattern of a 201-by-201 mesh, minus 300 entries on the     
+1 and -1 diagonal.