Studies performed at single-cell resolution have demonstrated the physiological significance of cell-to-cell variability. Various types of mathematical models and systems analyses of biological networks have further been used to gain a better understanding of the sources and regulatory mechanisms of such variability. In this work, we present a novel sensitivity analysis method, called molecular density function perturbation (MDFP), for the dynamical analysis of cellular heterogeneity. The proposed analysis is based on introducing perturbations to the density or distribution function of the cellular state variables at specific time points, and quantifying how such perturbations affect the state distribution at later time points. We applied the MDFP analysis to a model of a signal transduction pathway involving TRAIL (tumor necrosis factor-related apoptosis-inducing ligand)-induced apoptosis in HeLa cells. The MDFP analysis shows that caspase-8 activation regulates the timing of the swit... [more]

The error-in-variables-model (EVM) is the most statistically correct non-linear parameter estimation technique for reactivity ratio estimation. However, many polymer researchers are unaware of the advantages of EVM and therefore still choose to use rather erroneous or approximate methods. The procedure is straightforward but it is often avoided because it is seen as mathematically and computationally intensive. Therefore, the goal of this work is to make EVM more accessible to all researchers through a series of focused case studies. All analyses employ a MATLAB-based computational package for copolymerization reactivity ratio estimation. The basis of the package is previous work in our group over many years. This version is an improvement, as it ensures wider compatibility and enhanced flexibility with respect to copolymerization parameter estimation scenarios that can be considered.

Crystallization behavior of hexadecane (C16H34), octadecane (C18H38), eicosane (C20H42), and docosane (C22H46) dispersions of similar mean droplet diameter (x50.2 ≈ 15 µm) was investigated in quiescent systems and compared to crystallization under mechanical stress. In quiescent systems, the required supercooling decreased with increasing chain length of the alkanes to initiate crystallization. Crystallization of alkane dispersions under mechanical stress resulted in similar onset crystallization supercooling, as during quiescent crystallization. Increase of mechanical stress did not affect the onset crystallization supercooling within alkane dispersions.

Lignocellulose is an abundant and renewable resource that holds great promise for sustainable bioprocessing. However, unpretreated lignocellulose is recalcitrant to direct utilization by most microbes. Current methods to overcome this barrier include expensive pretreatment steps to liberate cellulose and hemicellulose from lignin. Anaerobic gut fungi possess complex cellulolytic machinery specifically evolved to decompose crude lignocellulose, but they are not yet genetically tractable and have not been employed in industrial bioprocesses. Here, we aim to exploit the biomass-degrading abilities of anaerobic fungi by pairing them with another organism that can convert the fermentable sugars generated from hydrolysis into bioproducts. By combining experiments measuring the amount of excess fermentable sugars released by the fungal enzymes acting on crude lignocellulose, and a novel dynamic flux balance analysis algorithm, we screened potential consortia partners by qualitative suitabilit... [more]

Dinoflagellates are the large group of marine phytoplankton with primary studies interest regarding their symbiosis with coral reef and the abilities to form harmful algae blooms (HABs). Toxin produced by dinoflagellates during events of HABs cause severe negative impact both in the economy and health sector. However, attempts to understand the dinoflagellates genomic features are hindered by their complex genome organization. Transcriptomics have been employed to understand dinoflagellates genome structure, profile genes and gene expression. RNA-seq is one of the latest methods for transcriptomics study. This method is capable of profiling the dinoflagellates transcriptomes and has several advantages, including highly sensitive, cost effective and deeper sequence coverage. Thus, in this review paper, the current workflow of dinoflagellates RNA-seq starts with the extraction of high quality RNA and is followed by cDNA sequencing using the next-generation sequencing platform, dinoflagel... [more]

This experimental and theoretical study deals with the thermal spontaneous polymerization of n-butyl acrylate (n-BA). The polymerization was carried out in solution (n-heptane as the solvent) at 200 and 220 °C without adding any conventional initiators. It was studied with the five different n-BA/n-heptane volume ratios: 50/50, 70/30, 80/20, 90/10, and 100/0. Extensive experimental data presented here show significant monomer conversion at all temperatures and concentrations confirming the occurrence of the thermal self-initiation of the monomer. The order, frequency factor, and activation energy of the thermal self-initiation reaction of n-BA were estimated from n-BA conversion, using a macroscopic mechanistic model. The estimated reaction order agrees well with the order obtained via our quantum chemical calculations. Furthermore, the frequency factor and activation energy estimates agree well with the corresponding values that we already reported for bulk polymerization of n-BA.

Using experimental data obtained from in vitro bioaugmentation studies of a sand filter community of 13 bacterial species, we develop an individual-based model representing the in silico counterpart of this synthetic microbial community. We assess the inter-species interactions, first by identifying strain identity effects in the data then by synthesizing these effects into a competition structure for our model. Pairwise competition outcomes are determined based on interaction effects in terms of functionality. We also consider non-deterministic competition, where winning probabilities are assigned based on the relative intrinsic competitiveness of each strain. Our model is able to reproduce the key qualitative dynamics observed in in vitro experiments with similar synthetic sand filter communities. Simulation outcomes can be explained based on the underlying competition structures and the resulting spatial dynamics. Our results highlight the importance of community diversity and in pa... [more]

The problem of scheduling multiproduct and multipurpose batch processes has been studied for more than 30 years using math programming and heuristics. In most formulations, the manufacturing recipes are represented by simplified models using state task network (STN) or resource task network (RTN), transfers of materials are assumed to be instantaneous, constraints due to shared utilities are often ignored, and scheduling horizons are kept small due to the limits on the problem size that can be handled by the solvers. These limitations often result in schedules that are not actionable. A simulation model, on the other hand, can represent a manufacturing recipe to the smallest level of detail. In addition, a simulator can provide a variety of built-in capabilities that model the assignment decisions, coordination logic and plant operation rules. The simulation based schedules are more realistic, verifiable, easy to adapt for changing plant conditions and can be generated in a short perio... [more]

In this study, the solvent based extraction of artemisinin from Artemisia annua L. using acetone in percolation mode is compared to the method of pressurized hot water extraction. Both techniques are simulated by a physico-chemical process model. The model as well as the model parameter determination, including the thermal degradation of artemisinin are shown and discussed. For the conventional extraction, a solvent screening is performed considering various organic solvents. A temperature screening is presented for the systematic design of the pressurized hot water extraction. The best temperature with regards to thermal decomposition and high productivity was found to be 80 °C. Both, conventional percolation and Pressurized Hot Water Extraction (PHWE) are suitable for the extraction of artemisinin. The extraction curves show a high conformity with the simulation results.

Dynamic optimization offers a great potential for maximizing performance of continuous processes from startup to shutdown by obtaining optimal trajectories for the control variables. However, numerical procedures for dynamic optimization can become prohibitively costly upon a sufficiently fine discretization of control trajectories, especially for large-scale dynamic process models. On the other hand, a coarse discretization of control trajectories is often incapable of representing the optimal solution, thereby leading to reduced performance. In this paper, a new control discretization approach for dynamic optimization of continuous processes is proposed. It builds upon turnpike theory in optimal control and exploits the solution structure for constructing the optimal trajectories and adaptively deciding the locations of the control discretization points. As a result, the proposed approach can potentially yield the same, or even improved, optimal solution with a coarser discretization... [more]

A novel formulation for combined scheduling and control of multi-product, continuous chemical processes is introduced in which nonlinear model predictive control (NMPC) and noncyclic continuous-time scheduling are efficiently combined. A decomposition into nonlinear programming (NLP) dynamic optimization problems and mixed-integer linear programming (MILP) problems, without iterative alternation, allows for computationally light solution. An iterative method is introduced to determine the number of production slots for a noncyclic schedule during a prediction horizon. A filter method is introduced to reduce the number of MILP problems required. The formulation’s closed-loop performance with both process disturbances and updated market conditions is demonstrated through multiple scenarios on a benchmark continuously stirred tank reactor (CSTR) application with fluctuations in market demand and price for multiple products. Economic performance surpasses cyclic scheduling in all scenarios... [more]

Performance of integrated production scheduling and advanced process control with disturbances is summarized and reviewed with four progressive stages of scheduling and control integration and responsiveness to disturbances: open-loop segregated scheduling and control, closed-loop segregated scheduling and control, open-loop scheduling with consideration of process dynamics, and closed-loop integrated scheduling and control responsive to process disturbances and market fluctuations. Progressive economic benefit from dynamic rescheduling and integrating scheduling and control is shown on a continuously stirred tank reactor (CSTR) benchmark application in closed-loop simulations over 24 h. A fixed horizon integrated scheduling and control formulation for multi-product, continuous chemical processes is utilized, in which nonlinear model predictive control (NMPC) and continuous-time scheduling are combined.

Dry reforming is a very interesting process for synthesis gas generation from CH 4 and CO 2 but suffers from low hydrogen yields due to the reverse water⁻gas shift reaction (WGS). For this reason, membranes are often used for hydrogen separation, which in turn leads to coke formation at the process temperatures suitable for the membranes. To avoid these problems, this work shows the possibility of using nickel self-supported membranes for hydrogen separation at a temperature of 800 ∘ C. The higher temperature effectively suppresses coke formation. The paper features the analysis of the dry reforming reaction in a nickel membrane reactor without additional catalyst. The measurement campaign targeted coke formation and conversion of the methane feedstock. The nickel approximately 50% without hydrogen separation. The hydrogen removal led to an increase in methane conversion to 60⁻90%.

Differential activation of neuronal populations can improve the efficacy of clinical devices such as sensory or cortical prostheses. Improving stimulus specificity will facilitate targeted neuronal activation to convey biologically realistic percepts. In order to deliver more complex stimuli to a neuronal population, stimulus optimization techniques must be developed that will enable a single electrode to activate subpopulations of neurons. However, determining the stimulus needed to evoke targeted neuronal activity is challenging. To find the most selective waveform for a particular population, we apply an optimization-based search routine, Powell’s conjugate direction method, to systematically search the stimulus waveform space. This routine utilizes a 1-D sigmoid activation model and a 2-D strength⁻duration curve to measure neuronal activation throughout the stimulus waveform space. We implement our search routine in both an experimental study and a simulation study to characterize... [more]

Tuberculosis (TB) is one of the most common infectious diseases worldwide. It is estimated that one-third of the world’s population is infected with TB. Most have the latent stage of the disease that can later transition to active TB disease. TB is spread by aerosol droplets containing Mycobacterium tuberculosis (Mtb). Mtb bacteria enter through the respiratory system and are attacked by the immune system in the lungs. The bacteria are clustered and contained by macrophages into cellular aggregates called granulomas. These granulomas can hold the bacteria dormant for long periods of time in latent TB. The bacteria can be perturbed from latency to active TB disease in a process called granuloma activation when the granulomas are compromised by other immune response events in a host, such as HIV, cancer, or aging. Dysregulation of matrix metalloproteinase 1 (MMP-1) has been recently implicated in granuloma activation through experimental studies, but the mechanism is not well understood.... [more]

Calculation of evaporation requires accurate thermophysical properties of the liquid. Such data are well-known for conventional fossil fuels. In contrast, e.g., thermal conductivity or dynamic viscosity of the fuel vapor are rarely available for modern liquid fuels. To overcome this problem, molecular models can be used. Currently, the measurement-based properties of n-heptane and diesel oil are compared with estimated values, using the state-of-the-art molecular models to derive the temperature-dependent material properties. Then their effect on droplet evaporation was evaluated. The critical parameters were liquid density, latent heat of vaporization, boiling temperature, and vapor thermal conductivity where the estimation affected the evaporation time notably. Besides a general sensitivity analysis, evaporation modeling in a practical burner ended up with similar results. By calculating droplet motion, the evaporation number, the evaporation-to-residence time ratio can be derived. A... [more]

The pennate diatom Phaeodactylum tricornutum is a model organism able to synthesize industrially-relevant molecules. Commercial-scale cultivation currently requires large monocultures, prone to bio-contamination. However, little is known about the identity of the invading organisms. To reduce the complexity of natural systems, we systematically investigated the microbiome of non-axenic P. tricornutum cultures from a culture collection in reproducible experiments. The results revealed a dynamic bacterial community that developed differently in “complete” and “minimal” media conditions. In complete media, we observed an accelerated “culture crash”, indicating a more stable culture in minimal media. The identification of only four bacterial families as major players within the microbiome suggests specific roles depending on environmental conditions. From our results we propose a network of putative interactions between P. tricornutum and these main bacterial factions. We demonstrate that,... [more]

The moisture content of biomass affects its processing for applications such as electricity or steam. In this study, the effects of variation in moisture content of banagrass and energycane was evaluated using techno-economic analysis and life-cycle assessments. A 25% loss of moisture was assumed as a variation that was achieved by field drying the biomass. Techno-economic analysis revealed that high moisture in the biomass was not economically feasible. Comparing banagrass with energycane, the latter was more economically feasible; thanks to the low moisture and ash content in energycane. About 32 GWh/year of electricity was produced by field drying 60,000 dry MT/year energycane. The investment for different scenarios ranged between $17 million and $22 million. Field-dried energycane was the only economically viable option that recovered the investment after 11 years of operation. This scenario was also more environmentally friendly, releasing 16-gCO₂ equivalent/MJ of electricity prod... [more]

The systematic design of an advanced and efficient control strategy for controlling critical quality attributes of the tablet compaction operation is necessary to increase the robustness of a continuous pharmaceutical manufacturing process and for real time release. A process model plays a very important role to design, evaluate and tune the control system. However, much less attention has been made to develop a validated control relevant model for tablet compaction process that can be systematically applied for design, evaluation, tuning and thereby implementation of the control system. In this work, a dynamic tablet compaction model capable of predicting linear and nonlinear process responses has been successfully developed and validated. The nonlinear model is based on a series of transfer functions and static polynomial models. The model has been applied for control system design, tuning and evaluation and thereby facilitate the control system implementation into the pilot-plant wi... [more]

Modern data, such as occurring in chemical engineering, typically entail large collections of samples with numerous dimensional components (or attributes). Visualizing the samples in relation of these components can bring valuable insight. For example, one may be able to see how a certain chemical property is expressed in the samples taken. This could reveal if there are clusters and outliers that have specific distinguishing properties. Current multivariate visualization methods lack the ability to reveal these types of information at a sufficient degree of fidelity since they are not optimized to simultaneously present the relations of the samples as well as the relations of the samples to their attributes. We propose a display that is designed to reveal these multiple relations. Our scheme is based on the concept of RadViz, but enhances the layout with three stages of iterative refinement. These refinements reduce the layout error in terms of three essential relationships—sample to... [more]

Microbial Fuel Cells (MFCs) represent a still relatively new technology for liquid organic waste treatment and simultaneous recovery of energy and resources. Although the technology is quite appealing due its potential benefits, its practical application is still hampered by several drawbacks, such as systems instability (especially when attempting to scale-up reactors from laboratory prototypes), internally competing microbial reactions, and limited power generation. This paper is an attempt to address some of the issues related to MFC application in wastewater treatment with a simulation model. Reactor configuration, operational schemes, electrochemical and microbiological characterization, optimization methods and modelling strategies were reviewed and have been included in a mathematical simulation model written with a multidisciplinary, multi-perspective approach, considering the possibility of feeding real substrates to an MFC system while dealing with a complex microbiological p... [more]

Various distance metrics and their induced norms are employed in the quantitative modeling of evolutionary dynamics. Minimization of these distance metrics, when applied to evolutionary optimization, are hypothesized to result in different outcomes. Here, we apply the different distance metrics to the evolutionary trait dynamics brought about by the interaction between two competing species infected by parasites (exploiters). We present deterministic cases showing the distinctive selection outcomes under the Manhattan, Euclidean, and Chebyshev norms. Specifically, we show how they differ in the time of convergence to the desired optima (e.g., no disease), and in the egalitarian sharing of carrying capacity between the competing species. However, when randomness is introduced to the population dynamics of parasites and to the trait dynamics of the competing species, the distinctive characteristics of the outcomes under the three norms become indistinguishable. Our results provide theore... [more]

The development of molecularly imprinted polymers (MIPs) to target polyphenols present in vegetable extracts was here addressed. Polydatin was selected as a template polyphenol due to its relatively high size and amphiphilic character. Different MIPs were synthesized to explore preferential interactions between the functional monomers and the template molecule. The effect of solvent polarity on the molecular imprinting efficiency, namely owing to hydrophobic interactions, was also assessed. Precipitation and suspension polymerization were examined as a possible way to change MIPs morphology and performance. Solid phase extraction and batch/continuous sorption processes were used to evaluate the polyphenols uptake/release in individual/competitive assays. Among the prepared MIPs, a suspension polymerization synthesized material, with 4-vinylpyridine as the functional monomer and water/methanol as solvent, showed a superior performance. The underlying cause of such a significant outcome... [more]

Clinical trial planning of candidate drugs is an important task for pharmaceutical companies. In this paper, we propose two new multistage stochastic programming formulations (CM1 and CM2) to determine the optimal clinical trial plan under uncertainty. Decisions of a clinical trial plan include which clinical trials to start and their start times. Its objective is to maximize expected net present value of the entire clinical trial plan. Outcome of a clinical trial is uncertain, i.e., whether a potential drug successfully completes a clinical trial is not known until the clinical trial is completed. This uncertainty is modeled using an endogenous uncertain parameter in CM1 and CM2. The main difference between CM1 and CM2 is an additional binary variable, which tracks both start and end time points of clinical trials in CM2. We compare the sizes and solution times of CM1 and CM2 with each other and with a previously developed formulation (CM3) using different instances of clinical trial... [more]

We present a generalized state-space model formulation particularly motivated by an online scheduling perspective, which allows modeling (1) task-delays and unit breakdowns; (2) fractional delays and unit downtimes, when using discrete-time grid; (3) variable batch-sizes; (4) robust scheduling through the use of conservative yield estimates and processing times; (5) feedback on task-yield estimates before the task finishes; (6) task termination during its execution; (7) post-production storage of material in unit; and (8) unit capacity degradation and maintenance. Through these proposed generalizations, we enable a natural way to handle routinely encountered disturbances and a rich set of corresponding counter-decisions. Thereby, greatly simplifying and extending the possible application of mathematical programming based online scheduling solutions to diverse application settings. Finally, we demonstrate the effectiveness of this model on a case study from the field of bio-manufacturin... [more]