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Comparative study of forward and backward test-kinetic simulation approaches

Gabriel Voitcu, Marius Echim, Richard Marchand
2012 Computer Physics Communications  
In this paper we perform a comparative study of the forward and backward Liouville mapping applied to the modeling of ring-shaped and non-gyrotropic velocity distribution functions of particles injected  ...  The test-kinetic method is used to compute the velocity distribution function in various areas of a proton cloud moving in the vicinity of a region with a sharp transition of the magnetic field and a non-uniform  ...  Conclusions In this paper we performed a comparative study of the forward and backward Liouville approaches corresponding to the test-kinetic simulation method that integrates numerically test-particle  ... 
doi:10.1016/j.cpc.2012.07.005 fatcat:xeerqyoryrdylpw7mzsh2fa3sy

Interpretation of binding kinetics in fluorescence recovery after photobleaching experiments using a novel stochastic simulation strategy

Dimitris Glotsos, Spiros Kostopoulos, Kostas Ninos, Dionisis Cavouras
2009 Molecular Simulation  
In this study, a new approach for the interpretation of FRAP curves is presented based on the stochastic simulation of binding kinetics.  ...  Predictions of recovery times of FRAP curves and sum of residuals revealed a good agreement.  ...  We would like to thank the Institute of Genomics and Bioinformatics of Graz University of Technology for its contribution in the preliminary steps of this work.  ... 
doi:10.1080/08927020903015353 fatcat:qscye4tkivda3g4do6kcq7som4

Testing for microscopic reversibility in the gating of maxi K+ channels using two-dimensional dwell-time distributions

L. Song, K.L. Magleby
1994 Biophysical Journal  
If microscopic reversibility is obeyed, then the number of forward and backward transitions per unit time for each individual reaction step will, on average, be identical and, consequently, the gating  ...  No significant differences were observed between the forward and backward analysis of the two-dimensional dwell-time distributions, suggesting time reversibility.  ...  Owen McManus for providing some of the data that were analyzed for this study, and Dr. W. Ferguson for carrying out some of the preliminary analysis. This work was supported in part by grants to K.  ... 
doi:10.1016/s0006-3495(94)80458-8 pmid:7919030 pmcid:PMC1225338 fatcat:aolta2xsmfdcfnmipa5sjn3pdq

Reexamining the origin of the directionality of myosin V

Raphael Alhadeff, Arieh Warshel
2017 Proceedings of the National Academy of Sciences of the United States of America  
We show that the energy of the power stroke and the barriers involved in it are of minor consequence to the selectivity of forward over backward steps and instead suggest that the selective release of  ...  With the help of Langevin Dynamics (LD) simulations, Monte Carlo (MC) simulations, and a technique we term SLiK (Segmental LD integrated Kinetics), we solve the kinetic equation and reach the conclusion  ...  Author contributions: R.A. and A.W. designed research; R.A. performed research; R.A. and A.W. analyzed data; and R.A. and A.W. wrote the paper.  ... 
doi:10.1073/pnas.1711214114 pmid:28894003 pmcid:PMC5625930 fatcat:gxgydw7x3baehdhps42czmxjpu

Lattice-Boltzmann Simulation of Lipase Separation via Bioaffinity Chromatography: Imposing Dirichlet or Danckwerts Inlet Condition

José A. Rabi, Eliana S. Kamimura
2016 Procedia Engineering  
One may instead impose Danckwerts condition and the goal of this work was to compare breakthrough curves simulated via LBM under each condition above.  ...  Numerical breakthrough curves were compared with experimental data and the expected "S" shape was reproduced in LBM simulations.  ...  9) where k = 1 and k = 2 refer to forward and backward streaming directions, respectively.  ... 
doi:10.1016/j.proeng.2016.08.362 fatcat:ga7e4rgrabhe7arohii6optica

Evaporation sampled by stationary molecular dynamics simulation

Matthias Heinen, Jadran Vrabec
2019 Journal of Chemical Physics  
Relatively large systems are simulated, allowing for a detailed study of velocity distribution functions.  ...  Particles constituting the vapor reservoir, forward flux j + , and backward flux j − are colored green, red, and blue, respectively.  ...  ACKNOWLEDGMENTS This work contributes to the Collaborative Research Center SFB-TRR 75 of Deutsche Forschungsgemeinschaft (DFG) and was funded under Grant No. VR 6/9-2.  ... 
doi:10.1063/1.5111759 fatcat:ey6bkitxljc45bmkmnbknimxo4

Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

Michael M. H. Graf, Manuela Maurer, Chris Oostenbrink
2016 Journal of Computational Chemistry  
Previous free-energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and  ...  backward thermodynamic integration processes (i.e., hysteresis).  ...  With a total simulation time of only 10 ns, the OSP approach is most efficient in terms of calculation time compared to all other tested methods.  ... 
doi:10.1002/jcc.24488 pmid:27634475 pmcid:PMC5082540 fatcat:ce2lb6upnfcerp6b7kbgelmsea

Ion Dynamics in the Meso-scale 3-D Kelvin–Helmholtz Instability: Perspectives From Test Particle Simulations

Xuanye Ma, Peter Delamere, Katariina Nykyri, Brandon Burkholder, Stefan Eriksson, Yu-Lun Liou
2021 Frontiers in Astronomy and Space Sciences  
This study applies different test particle approaches and cross validates the different results against one another to investigate the behavior of different ion species (i.e., H+ and O+), which include  ...  Test particle simulation provides such a bridge to connect the MHD scale to the kinetic scale.  ...  This is essentially a cross-scale problem, requiring hybrid or even PIC simulation. The results from the forward tracing and the backward tracing methods are quantitatively comparable.  ... 
doi:10.3389/fspas.2021.758442 fatcat:42zpl3ii2vhnreh7ocbeidpieq

The Antiparallel Dimerization of Myosin X Imparts Bundle Selectivity for Processive Motility

Matthew A. Caporizzo, Claire E. Fishman, Osamu Sato, Ryan M. Jamiolkowski, Mitsuo Ikebe, Yale E. Goldman
2018 Biophysical Journal  
and mechanical kinetics of the dimer.  ...  This study aims to determine if antiparallel dimerization of myosin X imparts selectivity toward actin bundles by comparing the motility of parallel and antiparallel dimers of myosin X on single and fascin-bundled  ...  The work was supported by National Institutes of Health grants R01-GM086352 and R35-GM118139 to Y.E.G. and T32-HL007954 to M.A.C., University of Texas STARS PLUS award to M.I., and National Science Foundation  ... 
doi:10.1016/j.bpj.2018.01.038 pmid:29590597 pmcid:PMC5883617 fatcat:57cgt27w2rgsfeqi3i4dutrape

Simulation of heat transfer to separation Air flow in a concentric pipe

C.S. Oon, A. Al-Shamma'a, S.N. Kazi, B.T. Chew, A. Badarudin, E. Sadeghinezhad
2014 International Communications in Heat and Mass Transfer  
The experimental data shows slightly lower distribution of surface temperature compared to simulation data.  ...  Computational simulation by using standard k-ε turbulence model was performed to investigate numerically the characteristic of backward-facing step flow in a concentric configuration.  ...  Besides the experimental and theoretical approaches, numerical simulation has established itself as the most practical and viable alternative to study and to understand different engineering problems.  ... 
doi:10.1016/j.icheatmasstransfer.2014.07.008 fatcat:ifs2vtcejbeabn56fcqzejzv5i

Statistical Error for Cosmic Rays Modulation Evaluated by SDE Backward in Time Method for 1D Model

Viacheslav Mykhailenko, Pavol Bobik
2022 Fluids  
The error dependence on simulation statistics and energy is presented for different combinations of input parameters.  ...  This work presents the estimation of statistical error of solution of Fokker–Planck equation by the 1D backward in time stochastic differential equations method.  ...  Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/fluids7020046 fatcat:7aalkkutdjhj7cks5ujb4sl5xq

Dynamic Modeling of Reversible Methanolysis ofJatropha curcasOil to Biodiesel

Azhari M. Syam, Hamidah A. Hamid, Robiah Yunus, Umer Rashid
2013 The Scientific World Journal  
The kinetics study revealed that the reverse reactions were significantly slower than forward reactions. The activation energies ranged from 6.5 to 44.4 KJ mol−1.  ...  Many kinetics studies on methanolysis assumed the reactions to be irreversible.  ...  Acknowledgment The authors acknowledge the Higher Education Ministry of Malaysia for the financial support through the FRGS Scheme (via vot. 5523422).  ... 
doi:10.1155/2013/268385 pmid:24363616 pmcid:PMC3865725 fatcat:7cp7jyvecbdufbp2tyombubtka

Evaluation of Lagrangian footprint model using data from wind tunnel convective boundary layer

N. Kljun, P. Kastner-Klein, E. Fedorovich, M.W. Rotach
2004 Agricultural and Forest Meteorology  
Furthermore, a comparison of two footprint model approaches ('forwardin-time' and 'backward-in-time' trajectories) was carried out using the same core model.  ...  It was found that the dispersion patterns and the concentration footprints compared well with the wind-tunnel data.  ...  TRAPOS, and by the Swiss Commission for Technology and Innovation (KTI) in the framework of EUROTRAC II (grants 3532.1 and 4092.1).  ... 
doi:10.1016/j.agrformet.2004.07.013 fatcat:dgbscvibkzb45p7twek6iwwwvq

Toward Modeling Context-Specific EMT Regulatory Networks Using Temporal Single Cell RNA-Seq Data

Daniel Ramirez, Vivek Kohar, Mingyang Lu
2020 Frontiers in Molecular Biosciences  
In particular, we observe distinct paths during the forward and backward transitions, as is evident from the dynamics of major regulators such as NF-KB (e.g., NFKB2 and RELB) and AP-1 (e.g., FOSL1 and  ...  We expect the integration of top-down bioinformatics and bottom-up systems biology modeling to be a powerful and generally applicable approach to elucidate gene regulatory mechanisms of cellular state  ...  We evaluated the quality of gene networks by comparing the simulated and experimental gene expression data (see section "Materials and Methods").  ... 
doi:10.3389/fmolb.2020.00054 pmid:32391378 pmcid:PMC7190801 fatcat:kp5rvvmqvbbkzapbhf2ksm6bna

Development of a Backward–Forward Stochastic Particle Tracking Model for Identification of Probable Sedimentation Sources in Open Channel Flow

Chelsie Chia-Hsin Liu, Christina W. Tsai, Yu-Ying Huang
2021 Mathematics  
According to the results of the case study of source identification, the regions with higher sediment concentrations computed by only backward simulations do not necessarily imply a higher likelihood of  ...  One can then verify if a specific area might be a probable source by cross-checking the values of influence functions calculated backward and forward, respectively.  ...  Hung and Wen-Jia Liu from National Taiwan University for their kind assistance with this manuscript. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/math9111263 fatcat:ujkmvolucbhbtgbthimwvoujvm
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