FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2040743399> ?p ?o ?g. }

• W2040743399 endingPage "174" @default.
• W2040743399 startingPage "166" @default.
• W2040743399 abstract "Conventional normal-mode analysis of molecular vibrations requires computation and storage of the Hessian matrix. For a typical biological system such storage can reach several gigabytes posing difficulties for straightforward implementation. In this work we discuss an iterative block method to carry out full diagonalization of the Hessian while only storing a few vectors in memory. The iterative approach is based on the conjugate gradient formulation of the Davidson algorithm for simultaneous optimization of L roots, where in our case 10 < L < 300. The procedure is modified further by automatically adding a new vector into the search space for each locked (converged) root and keeping the new vector orthogonal to the eigenvectors previously determined. The higher excited states are then converged with the orthonormality constraint to the locked roots by applying a projector which is carried out using a read-rewind step done once per iteration. This allows for convergence of as many roots as desired without increasing the computer memory. The required Hessian-vector products are calculated on the fly as follows, Kp = dgp/dt, where K is the mass weighted Hessian, and gp is the gradient along p. The method has been implemented into the TINKER suite of molecular design codes. Preliminary results are presented for the normal modes of bacteriorhodopsin (bR) up to 300 cm-1 and for the high frequency range between 2840 and 3680 cm-1. There is evidence of a highly localized, noncollective mode at ∼1.4 cm-1, caused by long-range interactions acting between the cytoplasmic and extracellular domains of bR." @default.
• W2040743399 created "2016-06-24" @default.
• W2040743399 creator A5001114553 @default.
• W2040743399 creator A5042193191 @default.
• W2040743399 creator A5064654490 @default.
• W2040743399 date "2005-11-24" @default.
• W2040743399 modified "2023-09-27" @default.
• W2040743399 title "All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method" @default.
• W2040743399 cites W108302527 @default.
• W2040743399 cites W1506690472 @default.
• W2040743399 cites W1967737979 @default.
• W2040743399 cites W1971610885 @default.
• W2040743399 cites W1972244704 @default.
• W2040743399 cites W1972469106 @default.
• W2040743399 cites W1973049888 @default.
• W2040743399 cites W1973914966 @default.
• W2040743399 cites W1974211053 @default.
• W2040743399 cites W1975945758 @default.
• W2040743399 cites W1976607746 @default.
• W2040743399 cites W1988583358 @default.
• W2040743399 cites W2009596258 @default.
• W2040743399 cites W2012111359 @default.
• W2040743399 cites W2016763547 @default.
• W2040743399 cites W2027408247 @default.
• W2040743399 cites W2031249581 @default.
• W2040743399 cites W2033052540 @default.
• W2040743399 cites W203338483 @default.
• W2040743399 cites W2035262611 @default.
• W2040743399 cites W2039414855 @default.
• W2040743399 cites W2045607459 @default.
• W2040743399 cites W2045826869 @default.
• W2040743399 cites W2051142108 @default.
• W2040743399 cites W2052495184 @default.
• W2040743399 cites W2060248899 @default.
• W2040743399 cites W2061461605 @default.
• W2040743399 cites W2063962473 @default.
• W2040743399 cites W2066702764 @default.
• W2040743399 cites W2070719372 @default.
• W2040743399 cites W2077203661 @default.
• W2040743399 cites W2086257387 @default.
• W2040743399 cites W2091765441 @default.
• W2040743399 cites W2092675267 @default.
• W2040743399 cites W2093151204 @default.
• W2040743399 cites W2098077341 @default.
• W2040743399 cites W2103502821 @default.
• W2040743399 cites W2108946966 @default.
• W2040743399 cites W2114760564 @default.
• W2040743399 cites W2115357061 @default.
• W2040743399 cites W2117686912 @default.
• W2040743399 cites W2118191240 @default.
• W2040743399 cites W2122199548 @default.
• W2040743399 cites W2139487784 @default.
• W2040743399 cites W2140889378 @default.
• W2040743399 cites W2142578757 @default.
• W2040743399 cites W2155027540 @default.
• W2040743399 doi "https://doi.org/10.1021/ct050161z" @default.
• W2040743399 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26626391" @default.
• W2040743399 hasPublicationYear "2005" @default.
• W2040743399 type Work @default.
• W2040743399 sameAs 2040743399 @default.
• W2040743399 citedByCount "18" @default.
• W2040743399 countsByYear W20407433992012 @default.
• W2040743399 countsByYear W20407433992017 @default.
• W2040743399 countsByYear W20407433992018 @default.
• W2040743399 countsByYear W20407433992020 @default.
• W2040743399 countsByYear W20407433992021 @default.
• W2040743399 crossrefType "journal-article" @default.
• W2040743399 hasAuthorship W2040743399A5001114553 @default.
• W2040743399 hasAuthorship W2040743399A5042193191 @default.
• W2040743399 hasAuthorship W2040743399A5064654490 @default.
• W2040743399 hasConcept C11413529 @default.
• W2040743399 hasConcept C114614502 @default.
• W2040743399 hasConcept C121332964 @default.
• W2040743399 hasConcept C158693339 @default.
• W2040743399 hasConcept C159694833 @default.
• W2040743399 hasConcept C203616005 @default.
• W2040743399 hasConcept C2777210771 @default.
• W2040743399 hasConcept C28826006 @default.
• W2040743399 hasConcept C33923547 @default.
• W2040743399 hasConcept C41008148 @default.
• W2040743399 hasConcept C5806529 @default.
• W2040743399 hasConcept C62520636 @default.
• W2040743399 hasConcept C92951342 @default.
• W2040743399 hasConceptScore W2040743399C11413529 @default.
• W2040743399 hasConceptScore W2040743399C114614502 @default.
• W2040743399 hasConceptScore W2040743399C121332964 @default.
• W2040743399 hasConceptScore W2040743399C158693339 @default.
• W2040743399 hasConceptScore W2040743399C159694833 @default.
• W2040743399 hasConceptScore W2040743399C203616005 @default.
• W2040743399 hasConceptScore W2040743399C2777210771 @default.
• W2040743399 hasConceptScore W2040743399C28826006 @default.
• W2040743399 hasConceptScore W2040743399C33923547 @default.
• W2040743399 hasConceptScore W2040743399C41008148 @default.
• W2040743399 hasConceptScore W2040743399C5806529 @default.
• W2040743399 hasConceptScore W2040743399C62520636 @default.
• W2040743399 hasConceptScore W2040743399C92951342 @default.
• W2040743399 hasIssue "1" @default.
• W2040743399 hasLocation W20407433991 @default.

• next