Browsing Modelling and Simulation in Life and Materials Sciences by Title
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Causality, 'superluminality', and reshaping in undersized waveguides
(20121231)We analyse the reshaping mechanism leading to apparently 'superluminal' advancement of a pulse traversing an undersized section of a waveguide. For frequencies below the first inelastic threshold (cut off one), there are ... 
Chemicalgarden formation, morphology, and composition. I. Effect of the nature of the cations
(20111231)We have grown chemical gardens in different sodium silicate solutions from several metalion saltscalcium chloride, manganese chloride, cobalt chloride, and nickel sulfatewith cations from period 4 of the periodic table. ... 
Chemicalgarden formation, morphology, and composition. II. Chemical gardens in microgravity
(20111231)We studied the growth of metalion silicate chemical gardens under Earth gravity (1 g) and microgravity (μg) conditions. Identical sets of reaction chambers from an automated system (the Silicate Garden Habitat or SGHab) ... 
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 ... 
Classification of resonance Regge trajectories and a modified Mulholland formula
(20111231)We employ a simple potential model to analyze the effects which a Regge trajectory, correlating with a bound or a metastable state at zero angular momentum, has on an integral cross section. A straightforward modification ... 
Coarsegraining RNA nanostructures for molecular dynamics simulations
(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 ... 
Combining stochastic and deterministic approaches within high efficiency molecular simulations
(20131231)Generalized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). ... 
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 ... 
Complex angular momentum theory of statetostate integral cross sections: Resonance effects in the $F + HD \to HF(v' = 3) + D$ reaction
(20151231)Statetostate reactive integral cross sections (ICSs) are often affected by quantum mechanical resonances, especially near a reactive threshold. An ICS is usually obtained by summing partial waves at a given value of ... 
Complex systems in finance: Monte Carlo evaluation of first passage time density functions
(20101231)Many examples of complex systems are provided by applications in finance and economics areas. Some of intrinsic features of such systems lie with the fact that their parts are interacting in a nontrivial dynamic manner ... 
Computational Analysis of Pulsed Radiofrequency Ablation in Treating Chronic Pain
(201906)In this paper, a parametric study has been conducted to evaluate the effects of frequency and duration of the short burst pulses during pulsed radiofrequency ablation (RFA) in treating chronic pain. Affecting the brain and ... 
Computational aspects of MonteCarlo simulations of the first passage time for multivariate transformed Brownian motions with jumps
(20131231)Many problems in science, engineering, and finance require the information on the first passage time (FPT) of a stochastic process. Mathematically, such problems are often reduced to the evaluation of the probability density ... 
Computer software for understanding resonances and resonancerelated phenomena in chemical reactions
(20141231)In numerical modelling of chemical reactions one calculates the scattering matrix for the required values of energy and angular momentum. Having done so, one still faces the nontrivial task of extracting detailed information ... 
Computing the eigenvalues of realistic Daphnia models by pseudospectral methods
(20151231)This work deals with physiologically structured populations of the Daphnia type. Their biological modeling poses several computational challenges. In such models, indeed, the evolution of a size structured consumer described ... 
A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630
(201906)Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branchedchain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, ... 
Constant pressure hybrid Monte Carlo simulations in GROMACS
(20141231)Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPTGSHMC, combines ... 
Corrections to finitesize scaling in the $\varphi^4$ model on square lattices
(20160101)Corrections to scaling in the twodimensional (2D) scalar (Formula presented.) model are studied based on nonperturbative analytical arguments and Monte Carlo (MC) simulation data for different lattice sizes L ((Formula ... 
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 ... 
Coupled magnetothermoelectromechanical effects and electronic properties of quantum dots
(20131231)For the first time, we systemically analyze the influence of magnetothermoelectromechanical effects on the band structure calculations by using the fully coupled model. We focus on three different types of quantum dots ... 
Coupled thermoelectromechanical models for thermal ablation of biological tissues and heat relaxation time effects
(2019)Thermal ablation is a widely applied electrosurgical process in medical treatment of soft biological tissues. Numerical modeling and simulations play an important role in prediction of temperature distribution and ...