Browsing Modelling and Simulation in Life and Materials Sciences by Title
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A differential equation with statedependent delay from cell population biology
(Journal of Differential Equations, 20151231)We analyze a differential equation, describing the maturation of a stem cell population, with a statedependent delay, which is implicitly defined via the solution of an ODE. We elaborate smoothness conditions for the model ... 
A model for stem cell population dynamics with regulated maturation delay
(Discrete and Continuous Dynamical Systems Series A, 20111231)We develop a structured population model for the maturation process of stem cells in the form of a statedependent delay differential equation. Moreover, results on existence, uniqueness and positivity of solutions as well ... 
A stylized model for the continuous double auction
(Lecture Notes in Economics and Mathematical Systems, 20121231)A stylized phenomenological model for the continuous double auction is introduced. This model is equivalent to two uncoupled M/M/1 queues. The conditions for statistical equilibrium (ergodicity) are derived. The results ... 
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 ... 
Adaptive multistage integrators for optimal energy conservation in molecular simulations
(Journal of Computational Physics, 20161001)We introduce a new Adaptive Integration Approach (AIA) to be used in a wide range of molecular simulations. Given a simulation problem and a step size, the method automatically chooses the optimal scheme out of an available ... 
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 ... 
Analytical evaluation of the performance of contactBased messaging applications
(Computer Networks, 20160301)Communications in mobile opportunistic networks, instead of using the Internet infrastructure, take place upon the establishment of ephemeral contacts among mobile nodes using direct communication. In this paper, we ... 
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 ... 
Atomistic Insight into Ion Transport and Conductivity in Ga/AlSubstituted Li$_7$La$_3$Zr$_2$O$_{12}$ Solid Electrolytes
(ACS Applied Materials & Interfaces, 20181212)Garnetstructured Li$_{7}$La$_{3}$Zr$_{2}$O$_{12}$ is a promising solid electrolyte for nextgeneration solidstate Li batteries. However, sufficiently fast Liion mobility required for battery applications only emerges ... 
Band structures of cylindrical AlN/GaN quantum dots with fully coupled piezoelectric models
(Proceedings of SPIE  The International Society for Optical Engineering, 20101231)We study the coupled electromechanical effects in the band structure calculations of low dimensional semiconductor nanostructures (LDSNs) such as AlN/GaN quantum dots. Some effects in these systems are essentially nonlinear. ... 
Band structures of laterally coupled quantum dots, accounting for electromechanical effects
(Journal of Physics: Conference Series, 20101231)In a series of recent papers we demonstrated that coupled electromechanical effects can lead to pronounced contributions in band structure calculations of low dimensional semiconductor nanostructures (LDSNs) such as quantum ... 
Breast cancer dormancy can be maintained by small numbers of micrometastases
(Cancer Research, 20101231)Late relapse of breast cancer can occur more than 25 years after primary diagnosis. During the intervening years between initial treatment and relapse, occult cancers are maintained in an apparent state of dormancy that ... 
Brinicles as a case of inverse chemical gardens
(Langmuir, 20131231)Brinicles are hollow tubes of ice from centimeters to meters in length that form under floating sea ice in the polar oceans when dense, cold brine drains downward from sea ice to seawater close to its freezing point. When ... 
Causality, 'superluminality', and reshaping in undersized waveguides
(ECCOMAS 2012  European Congress on Computational Methods in Applied Sciences and Engineering, eBook Full Papers, 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
(Langmuir, 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
(Langmuir, 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) ... 
Classification of resonance Regge trajectories and a modified Mulholland formula
(Physics Letters, Section A: General, Atomic and Solid State Physics, 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
(Physical Biology, 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
(Central European Journal of Mathematics, 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). ... 
Complex angular momentum theory of statetostate integral cross sections: Resonance effects in the $F + HD \to HF(v' = 3) + D$ reaction
(Physical Chemistry Chemical Physics, 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 ...