• A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism 

  Roell, G.W.; Schenk, C.; Anthony, W.E.; Carr, R.R.; Ponukumati, A.; Kim, J.; Akhmatskaya, E.; Foston, M.; Dantas, G.; Moon, T.S.; Tang, Y.J.; Garcia Martin, H. (2023)

  Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 ...

• Impact of Glucose on the Nanostructure and Mechanical Properties of Calcium-Alginate Hydrogels 

  Lopez-Sanchez, P.; Assifaoui, A.; Cousin, F.; Moser, J.; Bonilla, M.R.; Ström, A. (2022-02-01)

  Alginate is a polysaccharide obtained from brown seaweed that is widely used in food, pharmaceutical, and biotechnological applications due to its versatility as a viscosifier and gelling agent. Here, we investigated the ...

• Coupled stochastic systems of Skorokhod type: well-posedness of a mathematical model and its applications 

  Thieu, T.K.T; Muntean, A.; Melnik, R. (2022)

  Population dynamics with complex biological interactions, accounting for uncertainty quantification, is critical for many application areas. However, due to the complexity of biological systems, the mathematical formulation ...

• Effects of noise on leaky integrate-and-fire neuron models for neuromorphic computing applications 

  Thieu, T.K.T; Melnik, R. (2022)

  Artificial neural networks (ANNs) have been extensively used for the description of problems arising from biological systems and for constructing neuromorphic computing models. The third generation of ANNs, namely, ...

• Effects of random inputs and short-term synaptic plasticity in a LIF conductance model for working memory applications 

  Thieu, TKT.; Melnik, R. (2022)

  Working memory (WM) has been intensively used to enable the temporary storing of information for processing purposes, playing an important role in the execution of various cognitive tasks. Recent studies have shown that ...

• Nonlocal Models in the Analysis of Brain Neurodegenerative Protein Dynamics with Application to Alzheimer's Disease 

  Pal, S.; Melnik, R. (2021)

  It is well known that today nearly one in six of the world’s population has to deal with neurodegenerative disorders. While a number of medical devices have been developed for the detection, prevention, and treatments of ...

• Partition Constant of Binary Mixtures for the Equilibrium between a Bulk and a Confined Phase 

  Cortés, H.E.; Scherlis, D. A.; Factorovich, M. H. (2022-09-15)

  It is well-known that the thermodynamic, kinetic and structural properties of fluids, and in particular of water and its solutions, can be drastically affected in nanospaces. A possible consequence of nanoscale confinement ...

• Existence, Uniqueness, and Numerical Modeling of Wine Fermentation Based on Integro-Differential Equations 

  Schenk, C.; Schulz, V. (2022)

  Predictive modeling is key for saving time and resources in manufacturing processes such as fermentation arising in food and chemical manufacturing. To make reliable predictions, realistic models representing the most ...

• Numerical Regge pole analysis of resonance structures in state-to-state reactive differential cross sections 

  Akhmatskaya, E.; Sokolovski, D. (2022-04-19)

  This is the third (and the last) code in a collection of three programs [Sokolovski et al. (2011), Akhmatskaya et al. (2014)] dedicated to the analysis of numerical data, obtained in an accurate simulation of an atom-diatom ...

• On the interfacial lithium dynamics in Li7La3Zr2O12:poly(ethylene oxide) (LiTFSI) composite polymer-ceramic solid electrolytes under strong polymer phase confinement 

  Rincón, M.; Cortés, H.E.; Carrasco, J.; Akhmatskaya, E.; Garcia, F. (2022-05-27)

  A better molecular-level understanding of Li+ diffusion through ceramic/polymer interfaces is key to designing high-performance composite solid-state electrolytes for all-solid-state batteries. By considering as a case ...

• Wigner's friends, tunnelling times and Feynman's "only mystery of quantum mechanics" 

  Sokolovsksi, D.; Akhmatskaya, E. (2022-01-13)

  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 higher-order complexes associated with brain hubs in human connectomes 

  Andjelkovic, M.; Bosiljka, T.; Melnik, R. (2020-12-01)

  Higher-order connectivity in complex systems described by simplexes of different orders provides a geometry for simplex-based dynamical variables and interactions. Simplicial complexes that constitute a functional geometry ...

• Tunnelling times, Larmor clock, and the elephant in the room 

  Sokolovski, D.; Akhmatskaya, E. (2021-05-11)

  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 

  Rincón, M.; García-Daza, F.; Fernández-Pendás, M.; Carrasco, J.; Akhmatskaya, E. (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 low-carbon economy. To contribute to ...

• Unveiling Interfacial Li-Ion Dynamics in Li7La3Zr2O12/PEO(LiTFSI) Composite Polymer-Ceramic Solid Electrolytes for All-Solid-State Lithium Batteries 

  Rincón, M.; García Daza, F.A.; Ranque, P.; Aguesse, F.; Carrasco, J.; Akhmatskaya, E. (2021-06-23)

  Unlocking the full potential of solid-state electrolytes (SSEs) is key to enabling safer and more-energy dense technologies than today’s Li-ion batteries. In particular, composite materials comprising a conductive, flexible ...

• A Tool for Custom Construction of QMC and RQMC Point Sets 

  Godin, M.; Marion, P.; L'Ecuyer, P.; Puchhammer, F. (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 quasi-Monte Carlo (QMC) and randomized quasi-Monte Carlo (RQMC) sampling over ...

• Density Estimation by Monte Carlo and Quasi-Monte Carlo 

  L'Ecuyer, P.; Puchhammer, F. (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 Quasi-Monte Carlo Density Estimation via Conditioning 

  L'Ecuyer, P.; Puchhammer, F.; Ben Abdellah, A. (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 non-parametric density estimators, the mean integrated ...

• Variance Reduction with Array-RQMC for Tau-Leaping Simulation of Stochastic Biological and Chemical Reaction Networks 

  Puchhammer, F.; Ben Abdellah, A.; L'Ecuyer, P. (2021)

  We explore the use of Array-RQMC, a randomized quasi-Monte 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 

  Zhang, J.; Petersen, S.; Radivojevic, T.; Ramirez, A.; Pérez, A.; Abeliuk, E.; Sánchez, B.; Costello, Z.; Chen, Y.; Fero, M.; Garcia Martin, H.; Nielsen, J.; Keasling, J.; Jensen, M. (2019)

  In combination with advanced mechanistic modeling and the generation of high-quality multi-dimensional data sets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show ...

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