Bubble nucleation and cooperativity in DNA melting

Physical Review Letters

Volumn 94, Issue 3, 2005, Pages

  Ares, S ^a,b   Voulgarakis, N K ^c   Rasmussen, K O ^a   Bishop, A R ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSIDAD CARLOS III DE MADRID   (Spain)

^c UNIVERSITY OF CRETE   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE-THYMINE (AT); GUANINE-CYTOSINE (GC); PEYRARD-BISHOP-DAUXOIS MODEL; THERMAL BUBBLES; TWO-STATE TRANSITIONS;

DNA; DNA SEQUENCES; LIGHT ABSORPTION; MATHEMATICAL MODELS; MELTING; MONTE CARLO METHODS; NUCLEATION; POTENTIAL ENERGY; THERMODYNAMICS; ULTRAVIOLET RADIATION;

BUBBLES (IN FLUIDS);

DNA;

CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFORMATION; DNA DENATURATION; EVALUATION STUDY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHASE TRANSITION; STRUCTURE ACTIVITY RELATION; TRANSITION TEMPERATURE;

BASE SEQUENCE; COMPUTER SIMULATION; DNA; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; PHASE TRANSITION; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSITION TEMPERATURE;

EID: 18144371205     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.94.035504     Document Type: Article

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22. We have used periodic boundary conditions for the bubble-in-the-middle sequences and open boundary conditions for the bubble-at-the-end sequences. While it may appear most reasonable to apply open boundary conditions, in both cases, we consistently find that such boundary conditions lead to a much too large propensity for openings at the ends of the DNA molecule. This represents a clear problem of the model that we are working towards improving.