Modelling and Simulation in Life and Materials Sciences
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No Time at the End of the Tunnel
(Communications Physics – Nature, 20180821)Modern attosecond experiments seek to provide an insight into a long standing question: “how much time does a tunnelling particle spend in the barrier?” Traditionally, quantum theory relates this duration to the delay ... 
Multistage splitting integrators for sampling with modified Hamiltonian Monte Carlo methods
(Journal of Computational Physics, 20180717)Modified Hamiltonian Monte Carlo (MHMC) methods combine the ideas behind two popular sampling approaches: Hamiltonian Monte Carlo (HMC) and importance sampling. As in the HMC case, the bulk of the computational cost of ... 
Synthesis of Monodisperse Spherical Nanocrystals
(20160129)Nanoparticles, small units of matter with dimensions in the range 1100 nm, exhibit many advantageous sizedependent magnetic, electrical, chemical and optical prop erties, which are not observed at the microscale or ... 
On the Analysis of TrajectoryBased Search Algorithms: When is it Beneficial to Reject Improvements?
(Algorithmica, 2018)We investigate popular trajectorybased algorithms inspired by biology and physics to answer a question of general significance: when is it beneficial to reject improvements? A distinguishing factor of SSWM (Strong Selection ... 
Probabilistic Modelling of Classical and Quantum Systems
(20180614)While probabilistic modelling has been widely used in the last decades, the quantitative prediction in stochastic modelling of real physical problems remains a great challenge and requires sophisticated mathematical models ... 
Adapting Hybrid Monte Carlo methods for solving complex problems in life and materials sciences
(20180511)Efficient sampling is the key to success of molecular simulation of complex physical systems. Still, a unique recipe for achieving this goal is unavailable. Hybrid Monte Carlo (HMC) is a promising sampling tool offering a ... 
A Machine Learning Approach to Predict Metabolic Pathway Dynamics from Time Series Multiomics Data
(npj Systems Biology and Applications, 201805)New synthetic biology capabilities hold the promise of dramatically improving our ability to engineer biological systems. However, a fundamental hurdle in realizing this potential is our inability to accurately predict ... 
Revealing the Mechanism of Sodium Diffusion in NaxFePO4 Using an Improved Force Field
(Journal of Physical Chemistry C, 20180402)Olivine NaFePO4 is a promising cathode material for Naion batteries. Intermediate phases such as Na0.66FePO4 govern phase stability during intercalationdeintercalation processes, yet little is known about Na+ diffusion ... 
Modelling of Thermal Sterilization of highmoisture snack foods: feasibility analysis and optimization
(Food and Bioprocess Technology, 201801)Highmoisture snacks, such as steamed buns and rice cakes, are traditional and popular in Asian countries. However, their shelf life is short, primarily due to microbial spoilage. Current manufacturing methods address this ... 
An even simpler understanding of quantum weak values
(Annals of Physics, 201801)We explain the properties and clarify the meaning of quantum weak values using only the basic notions of elementary quantum mechanics. 
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 ... 
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 ...