Browsing Mathematical Modelling with Multidisciplinary Applications (M3A) by Title
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Coarsegraining RNA nanostructures for molecular dynamics simulations
(Physical Biology, 20101231)A series of coarsegrained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed ... 
Combining stochastic and deterministic approaches within high efficiency molecular simulations
(Central European Journal of Mathematics, 20131231)Generalized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). ... 
Comparative analysis of different methods of modeling the thermal effect of circulating blood flow during RF cardiac ablation
(IEEE Transactions on Biomedical Engineering, 20160101)Our aim was to compare the different methods of modeling the effect of circulating blood flow on the thermal lesion dimensions created by radio frequency (RF) cardiac ablation and on the maximum blood temperature. Computational ... 
Complex angular momentum theory of statetostate integral cross sections: Resonance effects in the $F + HD \to HF(v' = 3) + D$ reaction
(Physical Chemistry Chemical Physics, 20151231)Statetostate reactive integral cross sections (ICSs) are often affected by quantum mechanical resonances, especially near a reactive threshold. An ICS is usually obtained by summing partial waves at a given value of ... 
Complex systems in finance: Monte Carlo evaluation of first passage time density functions
(Procedia Computer Science, 20101231)Many examples of complex systems are provided by applications in finance and economics areas. Some of intrinsic features of such systems lie with the fact that their parts are interacting in a nontrivial dynamic manner ... 
Computational aspects of MonteCarlo simulations of the first passage time for multivariate transformed Brownian motions with jumps
(International Journal of Computational Methods, 20131231)Many problems in science, engineering, and finance require the information on the first passage time (FPT) of a stochastic process. Mathematically, such problems are often reduced to the evaluation of the probability density ... 
Computational Model for Prediction of the Occurrence of Steam Pops during Irrigated Radiofrequency Catheter Ablation
(Computing in Cardiology 43, 2016)Radiofrequency catheter ablation (RFCA) is a curative treatment for cardiac arrhythmias. Although globally a pretty safe procedure, it may present some risk. Steam pop is a serious complication that can occur during RFCA ... 
A computational model integrating brain electrophysiology and metabolism highlights the key role of extracellular potassium and oxygen
(Journal of Theoretical Biology, 20180226)The human brain is a small organ which uses a disproportional amount of the total metabolic energy pro duction in the body. While it is well understood that the most significant energy sink is the maintenance of the ... 
A computational model of openirrigated radiofrequency catheter ablation accounting for mechanical properties of the cardiac tissue
(2018)Radiofrequency catheter ablation (RFCA) is an effective treatment for cardiac arrhythmias. Although generally safe, it is not completely exempt from the risk of complications. The great flexibility of computational models ... 
Computational modeling of openirrigated electrodes for radiofrequency cardiac ablation including blood motionsaline flow interaction
(PLoS One, 2016)Radiofrequency catheter ablation (RFCA) is a routine treatment for cardiac arrhythmias. During RFCA, the electrodetissue interface temperature should be kept below 80°C to avoid thrombus formation. Openirrigated electrodes ... 
A computational multiscale model of cortical spreading depression propagation
(Computers and Mathematics with Applications, 20161219)Cortical Spreading Depression (CSD) is a disruption of the brain hemostasis that, originating in the visual cortex and traveling towards the frontal lobe, temporarily impairs the normal functioning of neurons. Although, ... 
Computational predictive modeling of integrated cerebral metabolism, electrophysiology and hemodynamics
(20190212)Understanding the energetic requirement of brain cells during resting state and during high neuronal activity is a very active research area where mathematical models have contributed significantly by providing a context ... 
Computer software for understanding resonances and resonancerelated phenomena in chemical reactions
(Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 20141231)In numerical modelling of chemical reactions one calculates the scattering matrix for the required values of energy and angular momentum. Having done so, one still faces the nontrivial task of extracting detailed information ... 
Computing the eigenvalues of realistic Daphnia models by pseudospectral methods
(SIAM Journal on Scientific Computing, 20151231)This work deals with physiologically structured populations of the Daphnia type. Their biological modeling poses several computational challenges. In such models, indeed, the evolution of a size structured consumer described ... 
A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630
(Metabolic Engineering, 201906)Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branchedchain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, ... 
ConductanceBased Refractory Density Approach for a Population of Bursting Neurons
(Bulletin of Mathematical Biology, 2019)The conductancebased refractory density (CBRD) approach is a parsimonious mathematicalcomputational framework for modeling interact ing populations of regular spiking neurons, which, however, has not been yet extended ... 
Constant pressure hybrid Monte Carlo simulations in GROMACS
(Journal of Molecular Modeling, 20141231)Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPTGSHMC, combines ... 
Corrections to finitesize scaling in the $\varphi^4$ model on square lattices
(International Journal of Modern Physics C, 20160101)Corrections to scaling in the twodimensional (2D) scalar (Formula presented.) model are studied based on nonperturbative analytical arguments and Monte Carlo (MC) simulation data for different lattice sizes L ((Formula ... 
Coupled magnetothermoelectromechanical effects and electronic properties of quantum dots
(Journal of Computational and Theoretical Nanoscience, 20131231)For the first time, we systemically analyze the influence of magnetothermoelectromechanical effects on the band structure calculations by using the fully coupled model. We focus on three different types of quantum dots ... 
Crystal growth as an excitable medium
(Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 20121231)Crystal growth has been widely studied for many years, and, since the pioneering work of Burton, Cabrera and Frank, spirals and target patterns on the crystal surface have been understood as forms of tangential crystal ...