### Recent Submissions

• #### 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 ...
• #### 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 ...
• #### Enhancing sampling in atomistic simulations of solid state materials for batteries: a focus on olivine NaFePO$_4$ ﻿

(Theoretical Chemistry Accounts, 2017-03-07)
The study of ion transport in electrochemically active materials for energy storage systems requires simulations on quantum-, atomistic- and meso-scales. 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, 2013-12-31)
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 ...
• #### Runaway electrification of friable self-replicating granular matter ﻿

(Langmuir, 2013-12-31)
We establish that the nonlinear dynamics of collisions between particles favors the charging of an insulating, friable, self-replicating granular material that undergoes nucleation, growth, and fission processes; we ...
• #### Numerical equilibrium analysis for structured consumer resource models ﻿

(Bulletin of Mathematical Biology, 2010-12-31)
In this paper, we present methods for a numerical equilibrium and stability analysis for models of a size structured population competing for an unstructured resource. We concentrate on cases where two model parameters are ...
• #### Influence of electromechanical effects and wetting layers on band structures of AlN/GaN quantum dots and spin control ﻿

(Journal of Applied Physics, 2010-12-31)
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 ...
• #### Band structures of laterally coupled quantum dots, accounting for electromechanical effects ﻿

(Journal of Physics: Conference Series, 2010-12-31)
In a series of recent papers we demonstrated that coupled electro-mechanical effects can lead to pronounced contributions in band structure calculations of low dimensional semiconductor nanostructures (LDSNs) such as quantum ...
• #### Manipulation of single electron spin in a GaAs quantum dot through the application of geometric phases: The Feynman disentangling technique ﻿

(Physical Review B - Condensed Matter and Materials Physics, 2010-12-31)
The spin of a single electron in an electrically defined quantum dot in a two-dimensional electron gas can be manipulated by moving the quantum dot adiabatically in a closed loop in the two-dimensional plane under the ...
• #### Higher-order nonlinear electromechanical effects in wurtzite GaN/AlN quantum dots ﻿

(Journal of Physics Condensed Matter, 2010-12-31)
As we demonstrated earlier, conventional mathematical models based on linear approximations may be inadequate in the analysis of properties of low-dimensional nanostructures and band structure calculations. In this work, ...
• #### Geometry and temperature dependent thermal conductivity of diamond nanowires: A non-equilibrium molecular dynamics study ﻿

(Physica E: Low-Dimensional Systems and Nanostructures, 2010-12-31)
Using non-equilibrium molecular dynamics methods, the analysis of geometry and temperature dependent thermal conductivities of diamond nanowires is carried out. It is found that at the same temperature conditions, thermal ...
• #### Coarse-graining RNA nanostructures for molecular dynamics simulations ﻿

(Physical Biology, 2010-12-31)
A series of coarse-grained 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 ...
• #### Computational aspects of Monte-Carlo simulations of the first passage time for multivariate transformed Brownian motions with jumps ﻿

(International Journal of Computational Methods, 2013-12-31)
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 ...
• #### Global stability of a delayed SIRS epidemic model with a non-monotonic incidence rate ﻿

(Journal of Mathematical Analysis and Applications, 2011-12-31)
In this paper, we investigate a disease transmission model of SIRS type with latent period τ≥0 and the specific nonmonotone incidence rate, namely, For the basic reproduction number R0&gt;1, applying monotone iterative ...