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Sensitivity of the inverse wave crest problem

Pearu Peterson, E van Groesen
2001 Wave motion  
In a previous paper [1] the inverse problem for wave crests was introduced and a solution strategy for two-wave interactions was given. Here these solutions are actually constructed, in particular for the cases with small interaction angle, moderate phase shifts, and/or symmetric interactions. Two detailed examples are presented and analyzed. The sensitivity of the method is investigated, and conclusions about the practical applicability are given.
doi:10.1016/s0165-2125(01)00076-2 fatcat:s3n3zic2x5hjzovpa4dnuuefbe

Symbolic flux analysis for genome-scale metabolic networks

David W Schryer, Marko Vendelin, Pearu Peterson
2011 BMC Systems Biology  
With the advent of genomic technology, the size of metabolic networks that are subject to analysis is growing. A common task when analyzing metabolic networks is to find all possible steady state regimes. There are several technical issues that have to be addressed when analyzing large metabolic networks including accumulation of numerical errors and presentation of the solution to the researcher. One way to resolve those technical issues is to analyze the network using symbolic methods. The
more » ... of this paper is to develop a routine that symbolically finds the steady state solutions of large metabolic networks. Results: A symbolic Gauss-Jordan elimination routine was developed for analyzing large metabolic networks. This routine was tested by finding the steady state solutions for a number of curated stoichiometric matrices with the largest having about 4000 reactions. The routine was able to find the solution with a computational time similar to the time used by a numerical singular value decomposition routine. As an advantage of symbolic solution, a set of independent fluxes can be suggested by the researcher leading to the formation of a desired flux basis describing the steady state solution of the network. These independent fluxes can be constrained using experimental data. We demonstrate the application of constraints by calculating a flux distribution for the central metabolic and amino acid biosynthesis pathways of yeast. Conclusions: We were able to find symbolic solutions for the steady state flux distribution of large metabolic networks. The ability to choose a flux basis was found to be useful in the constraint process and provides a strong argument for using symbolic Gauss-Jordan elimination in place of singular value decomposition.
doi:10.1186/1752-0509-5-81 pmid:21605414 pmcid:PMC3130677 fatcat:7q56irzu5vefbe4wzuwateez5e

Cross-Bridge Group Ensembles Describing Cooperativity in Thermodynamically Consistent Way

Mari Kalda, Pearu Peterson, Marko Vendelin
2016 Biophysical Journal  
The aim of this work is to incorporate cooperativity into Huxley-type cross-bridge model in thermodynamically consistent way. While the Huxley-type models assume that cross-bridges act independently from each other, we take into account that each cross-bridge is influenced by its neighbors and cooperativity is induced by tropomyosin movement. For that, we introduce ensembles of cross-bridge groups connected by elastic tropomyosin. By taking into account that the mechanical displacement of
more » ... yosin induces free energy change of the cross-bridge group ensemble, we develop the formalism for thermodynamically consistent description of the cooperativity in muscle contraction. An example model was composed to test the approach. The model parameters were found by optimization from the linear relation between oxygen consumption and stress-strain area as well as experimentally measured stress dynamics of rat trabecula. We have found a good agreement between the optimized model solution and experimental data. Simulations also showed that it is possible to study cooperativity with the approach developed in this work.
doi:10.1016/j.bpj.2015.11.2481 fatcat:yfxk2omzwnc4jplgmprsv3ao2y

Mapping Diffusion Coefficients of Fluorescent Dyes in Cardiomyocytes

Ardo Illaste, Martin Laasmaa, Pearu Peterson, Rikke Birkedal, Marko Vendelin
2011 Biophysical Journal  
Peterson, Rikke Birkedal, Marko Vendelin.  ...  RBT]) and ISS (Champaign, IL) for the use of the Alba confocal FLIM. 2546-Pos 2547-Pos Board B533 Mapping Diffusion Coefficients of Fluorescent Dyes in Cardiomyocytes Ardo Illaste, Martin Laasmaa, Pearu  ... 
doi:10.1016/j.bpj.2010.12.2759 fatcat:c74hwhxndjcbpmfrumbhn657we

Mitochondrial Proteins and Molecular Interaction with Cardiolipin at Atomistic Level

Jaanus Karo, Marko Vendelin, Pearu Peterson
2013 Biophysical Journal  
Journal of Molecular Biology 234(3): 779-815 3417-Pos Board B572 Mitochondrial Proteins and Molecular Interaction with Cardiolipin at Atomistic Level Jaanus Karo, Marko Vendelin, Pearu Peterson.  ... 
doi:10.1016/j.bpj.2012.11.3673 fatcat:3dlplwnxo5g37gkhwp4ye7lz4m

Real-Time Determination of Sarcomere Length of a Single Cardiomyocyte during Contraction

Mari Kalda, Marko Vendelin, Pearu Peterson
2013 Biophysical Journal  
Peterson.  ...  We also discuss our package for LAMMPS. 2608-Pos Board B627 Real-Time Determination of Sarcomere Length of a Single Cardiomyocyte during Contraction Mari Kalda, Marko Vendelin, Pearu Peterson.  ... 
doi:10.1016/j.bpj.2012.11.2812 fatcat:mrqti33umjdznis3pmj3vp3fiq

Cross-Bridge Group Ensembles Describing Cooperativity in Thermodynamically Consistent Way

Mari Kalda, Pearu Peterson, Marko Vendelin, L. Michel Espinoza-Fonseca
2015 PLoS ONE  
The aim of this work is to incorporate cooperativity into Huxley-type cross-bridge model in thermodynamically consistent way. While the Huxley-type models assume that cross-bridges act independently from each other, we take into account that each cross-bridge is influenced by its neighbors and cooperativity is induced by tropomyosin movement. For that, we introduce ensembles of cross-bridge groups connected by elastic tropomyosin. By taking into account that the mechanical displacement of
more » ... yosin induces free energy change of the cross-bridge group ensemble, we develop the formalism for thermodynamically consistent description of the cooperativity in muscle contraction. An example model was composed to test the approach. The model parameters were found by optimization from the linear relation between oxygen consumption and stress-strain area as well as experimentally measured stress dynamics of rat trabecula. We have found a good agreement between the optimized model solution and experimental data. Simulations also showed that it is possible to study cooperativity with the approach developed in this work.
doi:10.1371/journal.pone.0137438 pmid:26361396 pmcid:PMC4567334 fatcat:3jssdqv6gff25b6qmbn3d5lyga

Application of Regularized Richardson-Lucy Algorithm for Deconvolution of Confocal Microscopy Images

Martin Laasmaa, Marko Vendelin, Pearu Peterson
2011 Biophysical Journal  
Peterson.  ...  represented in a basis where they are sparse. 751-Pos Board B551 Application of Regularized Richardson-Lucy Algorithm for Deconvolution of Confocal Microscopy Images Martin Laasmaa, Marko Vendelin, Pearu  ... 
doi:10.1016/j.bpj.2010.12.963 fatcat:24f6y2bbqzdphonajuv7d2gaby

Mathematical Model of Oxygen Labeling to Study Heart Energy Transfer

David W. Schryer, Pearu Peterson, Ardo Illaste, Marko Vendelin
2012 Biophysical Journal  
Schryer, Pearu Peterson, Ardo Illaste, Marko Vendelin. Laboratory of Systems Biology, Tallinn, Estonia.  ... 
doi:10.1016/j.bpj.2011.11.777 fatcat:gotgly7c5vgtfkwgi4js2lrkk4

Incorporating Cooperativity into Huxley-Type Cross-Bridge Models in Thermodynamically Consistent Way

Mari Kalda, Pearu Peterson, Marko Vendelin
2012 Biophysical Journal  
Peterson, Marko Vendelin.  ...  affinity-states with higher Ca 2þ -affinity as activation progresses. 1809-Pos Board B579 Incorporating Cooperativity into Huxley-Type Cross-Bridge Models in Thermodynamically Consistent Way Mari Kalda, Pearu  ... 
doi:10.1016/j.bpj.2011.11.1950 fatcat:bmeszowfhbeijecbswjlkpw5h4

F2PY: a tool for connecting Fortran and Python programs

Pearu Peterson
2009 International Journal of Computational Science and Engineering (IJCSE)  
F2PY (a Fortran to PYthon interface generator) was specifically designed to create Python wrappers to large Fortran libraries (Peterson et al., 2001) , and has already gained substantial popularity: currently  ... 
doi:10.1504/ijcse.2009.029165 fatcat:id3s7lx3yvesrpf27f75itjlne

Isotopomeric 13C Labeling of Amino Acids Reveal Compartmentation in Saccharomyces uvarum

David W. Schryer, Pearu Peterson, Toomas Paalme, Marko Vendelin
2009 Biophysical Journal  
Schryer 1 , Pearu Peterson 1 , Toomas Paalme 2 , Marko Vendelin 1 . 1 Laboratory of Systems Biology, Institute of Cybernetics at Tallinn University of Technology, Tallinn, Estonia, 2 Department of Food  ... 
doi:10.1016/j.bpj.2008.12.1537 fatcat:evlpjtd2arcuzgi4t5izp4irru

Determination of Regional Diffusion Coefficients of Fluorescent ATP in Rat Cardiomyocytes

Ardo Illaste, Martin Laasmaa, David Schryer, Rikke Birkedal, Pearu Peterson, Marko Vendelin
2010 Biophysical Journal  
Peterson, Marko Vendelin.  ...  by NIH-P41 P41-RRO3155 and P50-GM076516 3896-Pos Determination of Regional Diffusion Coefficients of Fluorescent ATP in Rat Cardiomyocytes Ardo Illaste, Martin Laasmaa, David Schryer, Rikke Birkedal, Pearu  ... 
doi:10.1016/j.bpj.2009.12.4107 fatcat:b4mvofgzcfburlfvtyk6epimcq

Using Raster Image Correlation Spectroscopy for the Detection of ADP/ATP Diffusion Restrictions in Rat Cardiomyocytes

Päivo Simson, Marko Vendelin, Pearu Peterson
2013 Biophysical Journal  
Peterson.  ...  We also discuss our package for LAMMPS. 2608-Pos Board B627 Real-Time Determination of Sarcomere Length of a Single Cardiomyocyte during Contraction Mari Kalda, Marko Vendelin, Pearu Peterson.  ... 
doi:10.1016/j.bpj.2012.11.2813 fatcat:qtrj6melx5fmrniwtc7d23hjte

Analysis of Molecular Movement Reveals Latticelike Obstructions to Diffusion in Heart Muscle Cells

Ardo Illaste, Martin Laasmaa, Pearu Peterson, Marko Vendelin
2012 Biophysical Journal  
Intracellular diffusion in muscle cells is known to be restricted. Although characteristics and localization of these restrictions is yet to be elucidated, it has been established that ischemia-reperfusion injury reduces the overall diffusion restriction. Here we apply an extended version of raster image correlation spectroscopy to determine directional anisotropy and coefficients of diffusion in rat cardiomyocytes. Our experimental results indicate that diffusion of a smaller molecule (1127 MW
more » ... fluorescently labeled ATTO633-ATP) is restricted more than that of a larger one (10,000 MW Alexa647-dextran), when comparing diffusion in cardiomyocytes to that in solution. We attempt to provide a resolution to this counterintuitive result by applying a quantitative stochastic model of diffusion. Modeling results suggest the presence of periodic intracellular barriers situated ∼1 μm apart having very low permeabilities and a small effect of molecular crowding in volumes between the barriers. Such intracellular structuring could restrict diffusion of molecules of energy metabolism, reactive oxygen species, and apoptotic signals, enacting a significant role in normally functioning cardiomyocytes as well as in pathological conditions of the heart.
doi:10.1016/j.bpj.2012.01.012 pmid:22385844 pmcid:PMC3283817 fatcat:nutw4eypjnhb7derdsg4y2ytom
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