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At least 91 records · Page 5Linked to original sources
PubMed1998

A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes.

For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps.

Biophysics↗
PubMed1990

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.

A protein is defined as an indexed string of elements at each level in the hierarchy of protein structure: sequence, secondary structure, super-secondary structure, etc. The elements, for example, residues or secondary structure segments such as helices or beta-strands, are associated with a series of properties and can be involved in a number of relationships with other elements. Element-by-element dissimilarity matrices are then computed and used in the alignment procedure based on the sequence alignment algorithm of Needleman & Wunsch, expanded by the simulated annealing technique to take into account relationships as well as properties. The utility of this method for exploring the variability of various aspects of protein structure and for comparing distantly related proteins is demonstrated by multiple alignment of serine proteinases, aspartic proteinase lobes and globins.

Amino Acid Sequence↗
PubMed2006

Dynamic programming of CD8+ T cell trafficking after live viral immunization.

After viral infection, activated T cells are present in multiple tissues regardless of the infection route. How these cells acquire pleiotropic homing ability is unclear. By using a cutaneous vaccinia virus infection model, we demonstrate that regulation of T cell trafficking is multiphasic. Upon completion of three cell divisions, CD8+ T cells upregulated specific skin-homing molecules within draining lymph nodes (LN). By 60 hr after infection, some activated T cells reached the infected tissue, while others entered distant antigen-free LN. These latter cells continued to divide and acquire additional tissue-homing molecules in this new setting, independent of antigen presentation. After viral clearance, the initial skin-homing imprint became the predominant homing phenotype on memory cells and provided superior protection against secondary cutaneous challenge. These observations demonstrate a mechanism by which T cells provide both immediate tissue-specific immune control at the pathogen entry site and a more flexible systemic protection against pathogen dissemination.

Animals↗
PubMed2006

Dynamic programming algorithms for comparing multineuronal spike trains via cost-based metrics and alignments.

Cost-based metrics formalize notions of distance, or dissimilarity, between two spike trains, and are applicable to single- and multineuronal responses. As such, these metrics have been used to characterize neural variability and neural coding. By examining the structure of an efficient algorithm [Aronov D, 2003. Fast algorithm for the metric-space analysis of simultaneous responses of multiple single neurons. J Neurosci Methods 124(2), 175-79] implementing a metric for multineuronal responses, we determine criteria for its generalization, and identify additional efficiencies that are applicable when related dissimilarity measures are computed in parallel. The generalized algorithm provides the means to test a wide range of coding hypotheses.

Action Potentials↗
PubMed2002

Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data.

Solutes analysed with LC-MS are characterised by their retention times and mass spectra, and quantified by the intensities measured. This highly selective information can be extracted by multiway modelling. However, for full use and interpretability it is necessary that the assumptions made for the model are valid. For PARAFAC modelling, the assumption is a trilinear data structure. With LC-MS, several factors, e.g. non-linear detector response and ionisation suppression may introduce deviations from trilinearity. The single largest problem, however, is the retention time shifts not related to the true sample variations. In this paper, a time warping algorithm for alignment of LC-MS data in the chromatographic direction has been examined. Several refinements have been implemented and the features are demonstrated for both simulated and real data. With moderate time shifts present in the data, pre-processing with this algorithm yields approximately trilinear data for which reasonable models can be made.

Chromatography, Liquid↗
PubMed2003

Dynamic programming of CD8+ T lymphocyte responses.

The initial encounter with an antigen-presenting cell (APC) is the primary force behind the expansion, differentiation and survival of naive T cells. Using an APC that permits temporal control of priming, we examined whether the duration of antigenic stimulation can influence the functional development of CD8+ cytotoxic T lymphocytes (CTLs) in vivo. Whereas CTLs given a 4-h stimulus underwent an abortive clonal expansion with transient surface CD25 expression, those given a 20-h stimulus sustained CD25 up-regulation, proliferated extensively, and efficiently mediated destruction of peripheral target tissues. Our results show that an instructional program preceding the first cell division integrates differences in signal strength into the decision to activate versus tolerize specific CTL clones.

Animals↗