### Recent Submissions

• #### Synthesis of Monodisperse Spherical Nanocrystals ﻿

(2016-01-29)
Nanoparticles, small units of matter with dimensions in the range 1-100 nm, exhibit many advantageous size-dependent magnetic, electrical, chemical and optical prop- erties, which are not observed at the microscale or ...
• #### On the Analysis of Trajectory-Based Search Algorithms: When is it Beneficial to Reject Improvements? ﻿

(Algorithmica, 2018)
We investigate popular trajectory-based 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 ﻿

(2018-06-14)
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 ...
• #### An RBF-FD closest point method for solving PDEs on surfaces ﻿

(Journal of Computational Physics, 2018)
Partial differential equations (PDEs) on surfaces appear in many applications throughout the natural and applied sciences. The classical closest point method (Ruuth and Merriman, J. Comput. Phys. 227(3):1943-1961, ...
• #### Adapting Hybrid Monte Carlo methods for solving complex problems in life and materials sciences ﻿

(2018-05-11)
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, 2018-05)
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, 2018-04-02)
Olivine NaFePO4 is a promising cathode material for Na-ion batteries. Intermediate phases such as Na0.66FePO4 govern phase stability during intercalation-deintercalation processes, yet little is known about Na+ diffusion ...
• #### Modelling of Thermal Sterilization of high-moisture snack foods: feasibility analysis and optimization ﻿

(Food and Bioprocess Technology, 2018-01)
High-moisture 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 ...
• #### Unlocking datasets by calibrating populations of models to data density: a study in atrial electrophysiology ﻿

The understanding of complex physical or biological systems nearly always requires a characterization of the variability that underpins these processes. In addition, the data used to calibrate these models may also often ...
• #### An even simpler understanding of quantum weak values ﻿

(Annals of Physics, 2018-01)
We explain the properties and clarify the meaning of quantum weak values using only the basic notions of elementary quantum mechanics.
• #### A space-fractional Monodomain model for cardiac electrophysiology combining anisotropy and heterogeneity on realistic geometries ﻿

(2017-10-04)
Classical models of electrophysiology do not typically account for the effects of high structural heterogeneity in the spatio-temporal description of excitation waves propagation. We consider a modification of the Monodomain ...
• #### The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization ﻿

(ACS Synthetic Biology, 2017-09-30)
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 ﻿

(2017-04-28)
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 heat-semigroup formalism. Specifically, we combine suitable ...
• #### Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation ﻿

(Langmuir, 2017-10-24)
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, 2017-05-01)
In this paper, we are presenting a new method based on operator-valued Fourier multipliers to \- characterize the existence and uniqueness of $\ell_p$-solutions for discrete time fractional models in the form  ...
• #### Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism ﻿

(Frontiers in Bioengineering and Biotechnology, 2017-05-31)
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 ...
• #### Low-traffic limit and first-passage times for a simple model of the continuous double auction ﻿

(Physica A: Statistical Mechanics and its Applications, 2017-05)
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 two-level systems ﻿

(PHYSICAL REVIEW A, 2017-04-10)
Imposing restrictions on the Feynman paths of the monitored system has in the past been proposed as a universal model-free 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, 2017-01-01)
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, 2017-01-01)
Computational-driven materials discovery requires efficient and accurate methods. Density functional theory (DFT) meets these two requirements for many classes of materials. However, DFT-based methods have limitations. One ...