Mathematical Modelling with Multidisciplinary Applications (M3A)
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A spacefractional Monodomain model for cardiac electrophysiology combining anisotropy and heterogeneity on realistic geometries
(20171004)Classical models of electrophysiology do not typically account for the effects of high structural heterogeneity in the spatiotemporal description of excitation waves propagation. We consider a modification of the Monodomain ... 
The Experiment Data Depot: A WebBased Software Tool for Biological Experimental Data Storage, Sharing, and Visualization
(ACS Synthetic Biology, 20170930)Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large ... 
Discretizations of the spectral fractional Laplacian on general domains with Dirichlet, Neumann, and Robin boundary conditions
(20170428)In this work, we propose novel discretisations of the spectral fractional Laplacian on bounded domains based on the integral formulation of the operator via the heatsemigroup formalism. Specifically, we combine suitable ... 
Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation
(Langmuir, 20171024)The modified Hamiltonian Monte Carlo (MHMC) methods, i.e., importance sampling methods that use modified Hamiltonians within a Hybrid Monte Carlo (HMC) framework, often outperform in sampling efficiency standard techniques ... 
Maximal regularity in $l_p$ spaces for discrete time fractional shifted equations
(Journal of Differential Equations, 20170501)In this paper, we are presenting a new method based on operatorvalued Fourier multipliers to \ characterize the existence and uniqueness of $\ell_p$solutions for discrete time fractional models in the form $$ ... 
FluxEnabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism
(Frontiers in Bioengineering and Biotechnology, 20170531)13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference ... 
Lowtraffic limit and firstpassage times for a simple model of the continuous double auction
(Physica A: Statistical Mechanics and its Applications, 201705)We consider a simplified model of the continuous double auction where prices are integers varying from 1 to $N$ with limit orders and market orders, but quantity per order limited to a single share. For this model, the ... 
Reexamination of continuous fuzzy measurement on twolevel systems
(PHYSICAL REVIEW A, 20170410)Imposing restrictions on the Feynman paths of the monitored system has in the past been proposed as a universal modelfree approach to continuous quantum measurements. Here we revisit this proposition and demonstrate that ... 
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
(BMC Bioinformatics, 20170101)Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ... 
Assessment of van der Waals inclusive density functional theory methods for layered electroactive materials
(Physical Chemistry Chemical Physics, 20170101)Computationaldriven materials discovery requires efficient and accurate methods. Density functional theory (DFT) meets these two requirements for many classes of materials. However, DFTbased methods have limitations. One ... 
Enhancing sampling in atomistic simulations of solid state materials for batteries: a focus on olivine NaFePO$_4$
(Theoretical Chemistry Accounts, 20170307)The study of ion transport in electrochemically active materials for energy storage systems requires simulations on quantum, atomistic and mesoscales. The methods accessing these scales not only have to be effective but ... 
'Superluminal paradox' in wave packet propagation and its quantum mechanical resolution
(Annals of Physics, 20131231)We analyse in detail the reshaping mechanism leading to apparently 'superluminal' advancement of a wave packet traversing a classically forbidden region. In the coordinate representation, a barrier is shown to act as an ... 
Runaway electrification of friable selfreplicating granular matter
(Langmuir, 20131231)We establish that the nonlinear dynamics of collisions between particles favors the charging of an insulating, friable, selfreplicating granular material that undergoes nucleation, growth, and fission processes; we ... 
Numerical equilibrium analysis for structured consumer resource models
(Bulletin of Mathematical Biology, 20101231)In this paper, we present methods for a numerical equilibrium and stability analysis for models of a size structured population competing for an unstructured resource. We concentrate on cases where two model parameters are ... 
Influence of electromechanical effects and wetting layers on band structures of AlN/GaN quantum dots and spin control
(Journal of Applied Physics, 20101231)In a series of recent papers we demonstrated that coupled electromechanical effects can lead to pronounced contributions in band structure calculations of low dimensional semiconductor nanostructures (LDSNs) such as quantum ... 
Band structures of laterally coupled quantum dots, accounting for electromechanical effects
(Journal of Physics: Conference Series, 20101231)In a series of recent papers we demonstrated that coupled electromechanical effects can lead to pronounced contributions in band structure calculations of low dimensional semiconductor nanostructures (LDSNs) such as quantum ... 
Manipulation of single electron spin in a GaAs quantum dot through the application of geometric phases: The Feynman disentangling technique
(Physical Review B  Condensed Matter and Materials Physics, 20101231)The spin of a single electron in an electrically defined quantum dot in a twodimensional electron gas can be manipulated by moving the quantum dot adiabatically in a closed loop in the twodimensional plane under the ... 
Higherorder nonlinear electromechanical effects in wurtzite GaN/AlN quantum dots
(Journal of Physics Condensed Matter, 20101231)As we demonstrated earlier, conventional mathematical models based on linear approximations may be inadequate in the analysis of properties of lowdimensional nanostructures and band structure calculations. In this work, ... 
Geometry and temperature dependent thermal conductivity of diamond nanowires: A nonequilibrium molecular dynamics study
(Physica E: LowDimensional Systems and Nanostructures, 20101231)Using nonequilibrium molecular dynamics methods, the analysis of geometry and temperature dependent thermal conductivities of diamond nanowires is carried out. It is found that at the same temperature conditions, thermal ... 
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 ...