Modelling and Simulation in Life and Materials Sciences
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Wigner's friends, tunnelling times and Feynman's "only mystery of quantum mechanics"
(20220113)Recent developments in elementary quantum mechanics have seen a number of extraordinary claims regarding quantum behaviour, and even questioning internal consistency of the theory. These are, we argue, different disguises ... 
The topology of higherorder complexes associated with brain hubs in human connectomes
(20201201)Higherorder connectivity in complex systems described by simplexes of different orders provides a geometry for simplexbased dynamical variables and interactions. Simplicial complexes that constitute a functional geometry ... 
Tunnelling times, Larmor clock, and the elephant in the room
(20210511)A controversy surrounding the “tunnelling time problem” stems from the seeming inability of quantum mechanics to provide, in the usual way, a definition of the duration a particle is supposed to spend in a given region of ... 
Multiscale Modelling and Simulation of Advanced Battery Materials
(2021)Development of efficient strategies for the rational design of materials involved in the production and storage of renewable energy is essential for accelerating the transition to a lowcarbon economy. To contribute to ... 
Unveiling Interfacial LiIon Dynamics in Li7La3Zr2O12/PEO(LiTFSI) Composite PolymerCeramic Solid Electrolytes for AllSolidState Lithium Batteries
(20210623)Unlocking the full potential of solidstate electrolytes (SSEs) is key to enabling safer and moreenergy dense technologies than today’s Liion batteries. In particular, composite materials comprising a conductive, flexible ... 
A Tool for Custom Construction of QMC and RQMC Point Sets
(2021)We present LatNet Builder, a software tool to find good parameters for lattice rules, polynomial lattice rules, and digital nets in base 2, for quasiMonte Carlo (QMC) and randomized quasiMonte Carlo (RQMC) sampling over ... 
Density Estimation by Monte Carlo and QuasiMonte Carlo
(2021)Estimating the density of a continuous random variable $X$ has been studied extensively in statistics, in the setting where $n$ independent observations of $X$ are given a priori and one wishes to estimate the density from ... 
Monte Carlo and QuasiMonte Carlo Density Estimation via Conditioning
(2021)Estimating the unknown density from which a given independent sample originates is more difficult than estimating the mean, in the sense that for the best popular nonparametric density estimators, the mean integrated ... 
Variance Reduction with ArrayRQMC for TauLeaping Simulation of Stochastic Biological and Chemical Reaction Networks
(2021)We explore the use of ArrayRQMC, a randomized quasiMonte Carlo method designed for the simulation of Markov chains, to reduce the variance when simulating stochastic biological or chemical reaction networks with ... 
Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models
(2019)In combination with advanced mechanistic modeling and the generation of highquality multidimensional data sets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show ... 
Chemoinformaticguided engineering of polyketide synthases
(2019)Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A central challenge in PKS design is replacing a partially reductive module with a ... 
ART: A machine learning Automated Recommendation Tool for synthetic biology
(2019)Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable ... 
Modeling latent infection transmissions through biosocial stochastic dynamics
(202008)The events of the recent SARSCoV2 epidemics have shown the importance of social factors, especially given the large number of asymptomatic cases that effectively spread the virus, which can cause a medical emergency to ... 
Coupled Electromechanical Behavior of Microtubules
(2019)n this contribution, the coupled electromechanical behavior of the microtubules has been systematically investigated utilizing a continuumbased finite element framework. A threedimensional computational model of a mi ... 
Thermal ablation of biological tissues in disease treatment: A review of computational models and future directions
(202003)Percutaneous thermal ablation has proved to be an effective modality for treating both benign and malignant tumors in various tissues. Among these modalities, radiofrequency ablation (RFA) is the most promising and widely ... 
Atomistic to continuum model for studying mechanical properties of RNA nanotubes
(202006)With rapid advancements in the emerging field of RNA nanotechnology, its current and potential applications, new important problems arise in our quest to better understand properties of RNA nanocomplexes. In this paper, ... 
Common principles and best practices for engineering microbiomes
(2019)Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue hat structuring research ... 
Kinetic Parameter Estimation from Spectroscopic Data for a MultiStage SolidLiquid Pharmaceutical Process
(20200807)Laboratory and process measurements from spectroscopic instruments are ubiquitous in pharma processes, and directly using the data can pose a number of challenges for kinetic model building. Moreover, scaling up from ... 
Optimization of an Externally Mixed Biogas Plant Using a Robust CFD Method
(202004)Biogas plants have to be continuously or periodically mixed to ensure the homogenization of fermenting and fresh substrate. Externally installed mixers provide easier access than submerged mixers but concerns of ... 
Valleydependent Lorentz force and AharonovBohm phase in strained graphene pn junction
(2019)Veselago lens focusing in graphene pn junction is promising for realizations of new generation electron optics devices. However, the effect of the straininduced AharonovBohm interference in a pn junction has not been ...