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Integrated sequence and immunology filovirus database at Los Alamos

The Ebola outbreak of 2013–15 infected more than 28,000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. We report that as this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.

60 APPLIED LIFE SCIENCES↗

Fermion-bag inspired Hamiltonian lattice field theory for fermionic quantum criticality

Motivated by the fermion-bag approach, in this work we construct a new class of Hamiltonian lattice field theories that can help us to study fermionic quantum critical points, particularly those with four-fermion interactions. Although these theories are constructed in discrete time with a finite temporal lattice spacing ϵ, when ϵ → 0, conventional continuous-time Hamiltonian lattice field theories are recovered. The fermion-bag algorithms run relatively faster when ϵ = 1 as compared to ϵ → 0 but still allow us to compute universal quantities near the quantum critical point even at such a large value of ϵ. As an example of this new approach, here we study the $N_f$ = 1 Gross-Neveu chiral-Ising universality class in 2 + 1 dimensions by calculating the critical scaling of the staggered mass order parameter. We show that we are able to study lattice sizes up to 100 2 sites when ϵ = 1, while with comparable resources we can reach lattice sizes of only up to 64 2 when ϵ → 0. The critical exponents obtained in both these studies match within errors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

TH-E-17A-02: High-Pitch and Sparse-View Helical 4D CT Via Iterative Image Reconstruction Method Based On Tensor Framelet

Purpose: 4D CT is routinely performed during radiation therapy treatment planning of thoracic and abdominal cancers. Compared with the cine mode, the helical mode is advantageous in temporal resolution. However, a low pitch (∼0.1) for 4D CT imaging is often required instead of the standard pitch (∼1) for static imaging, since standard image reconstruction based on analytic method requires the low-pitch scanning in order to satisfy the data sufficient condition when reconstructing each temporal frame individually. In comparison, the flexible iterative method enables the reconstruction of all temporal frames simultaneously, so that the image similarity among frames can be utilized to possibly perform high-pitch and sparse-view helical 4D CT imaging. The purpose of this work is to investigate such an exciting possibility for faster imaging with lower dose. Methods: A key for highpitch and sparse-view helical 4D CT imaging is the simultaneous reconstruction of all temporal frames using the prior that temporal frames are continuous along the temporal direction. In this work, such a prior is regularized through the sparsity transform based on spatiotemporal tensor framelet (TF) as a multilevel and high-order extension of total variation transform. Moreover, GPU-based fast parallel computing of X-ray transform and its adjoint together with split Bregman method is utilized for solving the 4D image reconstruction problem efficiently and accurately. Results: The simulation studies based on 4D NCAT phantoms were performed with various pitches (i.e., 0.1, 0.2, 0.5, and 1) and sparse views (i.e., 400 views per rotation instead of standard >2000 views per rotation), using 3D iterative individual reconstruction method based on 3D TF and 4D iterative simultaneous reconstruction method based on 4D TF respectively. Conclusion: The proposed TF-based simultaneous 4D image reconstruction method enables high-pitch and sparse-view helical 4D CT with lower dose and faster speed.

60 APPLIED LIFE SCIENCES↗

CHiPBETA

High-accuracy water level data are needed to resolve the temporal and spatial hydraulic response to pumping in aquifers. However, the water-level data are typically affected by physical process unrelated to the aquifer pumping such as barometric pressure changes, tides, earthquakes, {\etc}. We have developed a computational framework to correct for barometric and Earth tide effects using linear regression deconvolution, as an initial guess for a nonlinear residual minimization to account for pumping effects. The pumping effects are predicted using the Theis equation with initialization by Jacob's method. After minimizing the residuals between the observed data and Theis predicted pumping effects, the algorithm estimates storativity and transmissivity of the aquifer. The algorithm also provides information about the measurement accuracy of the collected water-level data. The computational framework CHiPBETA is developed in Python and demonstrated to analyze synthetic and real data.

Banner, Eric↗

Interactive Web Application for Traffic Simulation Data Management and Visualization

As traffic simulation software becomes more effective for realistically simulating and analyzing traffic dynamics and vehicle interactions on the mesoscopic and microscopic level, the management, dissemination, and collaborative visualization of traffic simulation results produced by individual transportation planners presents a significant challenge. Existing online content management systems have a very limited capability in allowing users to query specific traffic simulation scenarios and geospatially visualize simulation results through shareable and interactive web interfaces. This paper presents a web-based application for promoting the archiving, sharing, and visualization of large-scale traffic simulation outputs. The application is developed to enhance cyber-physical controls, communications, and public education for collaborative transportation planning. Unique features of the web application include: (a) allowing users to upload their new traffic simulation scenarios (parameters and outputs), as well as search existing scenarios using easily accessible interfaces; (b) optimizing simulation output files with heterogeneous data formats and projected coordinate systems for web-based storage and management using a scalable and searchable data/metadata standard; (c) standardizing user-uploaded simulation outputs using web interfaces and data processing libraries with parallel computing capacity; and (d) providing shareable web visual interfaces for visualizing the traffic flow and signal information stored in simulation outputs (e.g., regional traffic patterns and individual vehicle interactions) and visually comparing multiple simulation outputs both spatially and temporally. Furthermore, the paper presents the conceptual design and implementation of this application, and demonstrates the application’s performance for sharing, comparing, and visualizing simulation outputs from VISSIM and SUMO, two commonly used traffic simulation software programs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Advanced Atmospheric Ensemble Modeling Techniques

Ensemble modeling (EM), the creation of multiple atmospheric simulations for a given time period, has become an essential tool for characterizing uncertainties in model predictions. We explore two novel ensemble modeling techniques: (1) perturbation of model parameters (Adaptive Programming, AP), and (2) data assimilation (Ensemble Kalman Filter, EnKF). The current research is an extension to work from last year and examines transport on a small spatial scale (<100 km) in complex terrain, for more rigorous testing of the ensemble technique. Two different release cases were studied, a coastal release (SF6) and an inland release (Freon) which consisted of two release times. Observations of tracer concentration and meteorology are used to judge the ensemble results. In addition, adaptive grid techniques have been developed to reduce required computing resources for transport calculations. Using a 20- member ensemble, the standard approach generated downwind transport that was quantitatively good for both releases; however, the EnKF method produced additional improvement for the coastal release where the spatial and temporal differences due to interior valley heating lead to the inland movement of the plume. The AP technique showed improvements for both release cases, with more improvement shown in the inland release. This research demonstrated that transport accuracy can be improved when models are adapted to a particular location/time or when important local data is assimilated into the simulation and enhances SRNL’s capability in atmospheric transport modeling in support of its current customer base and local site missions, as well as our ability to attract new customers within the intelligence community.

54 ENVIRONMENTAL SCIENCES↗

Short term collaborations of the NEAMS Center of Excellence: third wave

A primary goal of the Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program is to develop the next generation of simulations tools to support the design and deployment of commercial nuclear power. The mission of the NEAMS Center of Excellence for Thermal-fluids Applications in Nuclear Energy is to advance this goal by providing leadership, best practices, research, and support and training for computational thermal-fluids applications in nuclear energy. This is accomplished by leveraging expertise in the NEAMS tools to solve challenging problems in fluid flow and heat transfer. The NEAMS tools provide simulation capabilities covering a range of temporal and spatial scales and the Center connects stakeholders in industry with the expertise to use these tools to their fullest. This addresses a pressing need, facilitating advanced reactor development and commercialization.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Volumetric Rendering on Wavelet-Based Adaptive Grid

Numerical modeling of physical phenomena frequently involves processes across a wide range of spatial and temporal scales. In the last two decades, the advancements in wavelet-based numerical methodologies to solve partial differential equations, combined with the unique properties of wavelet analysis to resolve localized structures of the solution on dynamically adaptive computational meshes, make it feasible to perform large-scale numerical simulations of a variety of physical systems on a dynamically adaptive computational mesh that changes both in space and time. Volumetric visualization of the solution is an essential part of scientific computing, yet the existing volumetric visualization techniques do not take full advantage of multi-resolution wavelet analysis and are not fully tailored for visualization of a compressed solution on the wavelet-based adaptive computational mesh. Our objective is to explore the alternatives for the visualization of time-dependent data on space-time varying adaptive mesh using volume rendering while capitalizing on the available sparse data representation. Two alternative formulations are explored. The first one is based on volumetric ray casting of multi-scale datasets in wavelet space. Rather than working with the wavelets at the finest possible resolution, a partial inverse wavelet transform is performed as a preprocessing step to obtain scaling functions on a uniform grid at a user-prescribed resolution. As a result, a solution in physical space is represented by a superposition of scaling functions on a coarse regular grid and wavelets on an adaptive mesh. An efficient and accurate ray casting algorithm is based just on these coarse scaling functions. Additional details are added during the ray tracing by taking an appropriate number of wavelets into account based on support overlap with the interpolation point, wavelet coefficient magnitude, and other characteristics, such as opacity accumulation (front to back ordering) and deviation from frontal viewing direction. The second approach is based on complementing of wavelet-based adaptive mesh to the traditional Adaptive Mesh Refinement (AMR) mesh. Both algorithms are illustrated and compared to the existing volume visualization software for Rayleigh-Benard thermal convection and electron density data sets in terms of rendering time and visual quality for different data compression of both wavelet-based and AMR adaptive meshes.

Vezolainen, Alexei V.↗

Petascale Application of a Coupled CPU-GPU Algorithm for Simulation and Analysis of Multiphase Flow Solutions in Porous Medium Systems, In: 2014 IEEE 28th International Parallel and Distributed Processing Symposium

Large-scale simulation can provide a wide range of information needed to develop and validate theoretical models for multiphase flow in porous medium systems. In this paper, we consider a coupled solution in which a multiphase flow simulator is coupled to an analysis approach used to extract the interfacial geometries as the flow evolves. This has been implemented using MPI to target heterogeneous nodes equipped with GPUs. The GPUs evolve the multiphase flow solution using the lattice Boltzmann method while the CPUs compute up scaled measures of the morphology and topology of the phase distributions and their rate of evolution. Our approach is demonstrated to scale to 4,096 GPUs and 65,536 CPU cores to achieve a maximum performance of 244,754 million-lattice-node updates per second (MLUPS) in double precision execution on Titan. In turn, this approach increases the size of systems that can be considered by an order of magnitude compared with previous work and enables detailed in situ tracking of averaged flow quantities at temporal resolutions that were previously impossible. Furthermore, it virtually eliminates the need for post-processing and intensive I/O and mitigates the potential loss of data associated with node failures.

Computer Science↗

Multigrid Reduction in Time for Nonlinear Parabolic Problems: A Case Study

The need for parallelism in the time dimension is being driven by changes in computer architectures, where performance increases are now provided through greater concurrency, not faster clock speeds. This creates a bottleneck for sequential time marching schemes because they lack parallelism in the time dimension. Multigrid reduction in time (MGRIT) is an iterative procedure that allows for temporal parallelism by utilizing multigrid reduction techniques and a multilevel hierarchy of coarse time grids. MGRIT has been shown to be effective for linear problems, with speedups of up to 50 times. The goal of this work is the efficient solution of nonlinear problems with MGRIT, where efficiency is defined as achieving similar performance when compared to an equivalent linear problem. The benchmark nonlinear problem is the p-Laplacian, where p=4 corresponds to a well-known nonlinear diffusion equation and p=2 corresponds to the standard linear diffusion operator, our benchmark linear problem. The key difficulty encountered is that the nonlinear time-step solver becomes progressively more expensive on coarser time levels as the time-step size increases. To overcome such difficulties, multigrid research has historically targeted an accumulated body of experience regarding how to choose an appropriate solver for a specific problem type. To that end, this paper develops a library of MGRIT optimizations and modifications, most important an alternate initial guess for the nonlinear time-step solver and delayed spatial coarsening, that will allow many nonlinear parabolic problems to be solved with parallel scaling behavior comparable to the corresponding linear problem.

parareal↗

Learning stochastic dynamics with statistics-informed neural network

We introduce a machine-learning framework named statistics-informed neural network (SINN) for learning stochastic dynamics from data. This new architecture was theoretically inspired by a universal approximation theorem for stochastic systems, which we introduce in this paper, and the projection-operator formalism for stochastic modeling. Here, we devise mechanisms for training the neural network model to reproduce the correct statistical behavior of a target stochastic process. Numerical simulation results demonstrate that a well-trained SINN can reliably approximate both Markovian and non-Markovian stochastic dynamics. We demonstrate the applicability of SINN to coarse-graining problems and the modeling of transition dynamics. Furthermore, we show that the obtained reduced-order model can be trained on temporally coarse-grained data and hence is well suited for rare-event simulations.

97 MATHEMATICS AND COMPUTING↗

Melt pool temperature measurement and monitoring during laser powder bed fusion based additive manufacturing via single-camera two-wavelength imaging pyrometry (STWIP)

Melt pool (MP) temperature is one of the determining factors and a key signature for evaluating the properties of printed components in metal additive manufacturing (AM). The state-of-the-art measurement systems are hindered, primarily by the large-scale data acquisition and processing demands. In this work, we introduce a novel coaxial, high-speed, single-camera two-wavelength imaging pyrometer (STWIP) system as opposed to the typical utilization of multiple cameras for measuring MP temperature profiles in laser powder bed fusion (LPBF) processes. Developed on a commercial LPBF machine (EOS M290), the STWIP system demonstrated its ability to quantitatively monitor the MP temperature and its variation for 50 layers at high framerates (>30,000 fps) for a real-world application (standard fatigue specimens) print. High performance computing is employed to analyze the acquired big data (MP images), for determining each MP's average temperature and 2D temperature profile. The MP temperature evolution in the gage section of a fatigue specimen is also examined at a temporal resolution of 1 ms, by evaluating the MP temperatures in the samples' first, middle, and last layers. This report is the first of its kind on monitoring MP temperature distribution and evolution at such a large, detailed scale for longer durations in practical applications.

42 ENGINEERING↗

Impact of Distinct Origin Locations on the Life Cycles of Landfalling Atmospheric Rivers Over the U.S. West Coast

An atmospheric river (AR) event represents strong poleward moisture transport and is defined as a series of spatiotemporally connected instantaneous AR objects. Utilizing an AR tracking algorithm with a depth-first search (a widely used algorithm in computer science), we examine the life cycle characteristics of AR events that make landfall over the U.S. West Coast by their distinct origin locations. We report landfalling AR events from the Northwest Pacific (120°E–170°W, WLAR events) temporally last longer (5.3 versus 3.6 days on average) and have stronger intensity of integrated vapor transport (508 versus 388 kg m -1 s -1 on average) than those originating from the Northeast Pacific (125°W–170°W, ELAR events). A persistent tripole geopotential height anomaly pattern over the North Pacific modulates the origin locations and propagation of landfalling AR events. WLAR events are associated with anomalous highs over northeastern Asia and the Northeast Pacific and an anomalous low over the central North Pacific. This pattern provides favorable conditions for WLAR events to start, propagate northeastward, and make landfall in the northwestern West Coast. WLAR events contribute approximately 25% of the total winter precipitation over Washington and British Columbia. ELAR events are associated with a similar tripole pattern to the WLAR events with an eastward shift. The anomalous low over the Northeast Pacific helps ELAR events to start, propagate northeastward, and make landfall in the southwestern West Coast. Precipitation induced by ELAR events contributes up to 30% of total winter precipitation over California.

54 ENVIRONMENTAL SCIENCES↗

elm-diagnostics

elm-diagnostics is a Python package for computing diagnostic analyses and visualizations for the E3SM Land Model (ELM) component and is meant to support new feature development in ELM. The tool reads model history files and performs quantitative analyses including budget-closure checking, variable transformations, temporal aggregations, and statistical summaries to support model evaluation, validation, and scientific interpretation. The framework is designed for extensibility, with modular architecture enabling straightforward addition of new diagnostic methods, derived variables, analysis types, visualization approaches, and model-specific adaptations

Hoffman, Matt [Los Alamos National Laboratory]↗

Development of a Novel Electrical Characterization Technique for Measuring Hidden Joint Contacts in Weapons Cavities (LDRD Final Report 218470)

This report summarizes research performed in the context of a REHEDS LDRD project that explores methods for measuring electrical properties of vessel joints. These properties, which include contact points and associated contact resistance, are “hidden” in the sense that they are not apparent from a computer-assisted design (CAD) description or visual inspection. As is demonstrated herein, the impact of this project is the development of electromagnetic near-field scanning capabilities that allow weapon cavity joints to be characterized with high spatial and/or temporal resolution. Such scans provide insight on the hidden electrical properties of the joint, allowing more detailed and accurate models of joints to be developed, and ultimately providing higher fidelity shielding effectiveness (SE) predictions. The capability to perform high-resolution temporal scanning of joints under vibration is also explored, using a multitone probing concept, allowing time-varying properties of joints to be characterized and the associated modulation to SE to be quantified.

42 ENGINEERING↗

CRCNS US-France Research Proposal: Collaborative Research: Encoding reward expectation in Drosophilia

The fruit fly Drosophila melanogaster has been a valuable model for investigating the genetic and neural bases that underlie learning and memory. Early and most current studies use basic behavior conditioning protocols to study learning in controlled laboratory settings. More recently, the ability to transgenically manipulate many of the brain neurons in the fruit fly with exquisite specificity, and the recent knowledge of the synaptic ‘connectome’ of the fruit fly brain, makes these animals almost unique as a comprehensive model for studies of learning, memory and motivated behavior. In fact, the connectome has revealed many types of new connections that had until now been overlooked. Within this context, the thesis of this proposal is that studies of learning and memory will be greatly enhanced by using more sophisticated means for evaluating memory representations, such as have been developed in vertebrates, and combining those studies with information from the connectome guided by computational modelling. We propose to push beyond the boundaries of existing conditioning protocols for fruit flies to investigate more complex memory representations. In particular, we will investigate the function of reinforcement pathways in relation to the absence of expected reinforcement. More specifically, we propose a series of experiments designed to investigate the memory representations in fruit flies when an expected consequence of a Conditioned Stimulus (CS) fails to occur. Although studies have evaluated how this failure can establish extinction memory for the CS, our studies will go beyond studying extinction. Specifically, we predict that in Drosophila when a CS is associated with a failed expectation of an appetitive food reinforcement it will acquire aversive value, and vice versa for a failed expectation of an aversive reinforcer. We combine these studies with manipulations of reinforcement pathways in the CNS inspired from the connectome, iteratively knitted in with established computational models. Intellectual Merit: The concept of reinforcement expectation and incentive contrast have been influential in the development of studies of associative learning in mammals. These questions are particularly challenging to answer in vertebrates because they require exquisite cellular, temporal, and genetic specificity of experimental manipulations. The recent development of work with identified neurons and their connectomes makes the larval and adult fly brains ripe as models for pushing our understanding of neural bases for these higher- order conditioning phenomena. Broader Impacts: Public health: These analyses and the conceptual framework of prediction error processing underlying them have a profound impact on our understanding of reinforcement-related behavior in humans, including monetary rewards and the mnemonic consequences of traumatic experiences, and for pathologies of the dopamine reinforcement system. Educational: This project will provide interdisciplinary training for postdoctoral researchers, Ph.D. and undergraduate students. The PIs will act as co-supervisors or mentors of students working in the different labs via face-to-face and internet-based technologies. We will also work with ASU’s award-winning Ask- A-Biologist program. This is an online science program designed to enrich the learning experiences of students of all ages and to provide classroom material for use by K-12 teachers. We will develop an extension of a game developed under a prior NSF award, and the new game will include modules to teach K-12 students about how insects learn. We will also integrate into the AAB site a program developed by a collaborator (B Gerber) at the Leibniz Institut für Neurobiologie, Magdeburg, and now in use in schools in Germany, to teach K-12 students how to train animals using the fruit fly larval learning paradigm. Underrepresented groups: All PIs will work with their university offices of Academic Diversity and Equal Opportunity for reaching underrepresented students.

59 BASIC BIOLOGICAL SCIENCES↗

Projecting Antarctica's contribution to future sea level rise from basal ice shelf melt using linear response functions of 16 ice sheet models (LARMIP-2)

Abstract. The sea level contribution of the Antarctic ice sheet constitutes a large uncertainty in future sea level projections. Here we apply a linear response theory approach to 16 state-of-the-art ice sheet models to estimate the Antarctic ice sheet contribution from basal ice shelf melting within the 21st century. The purpose of this computation is to estimate the uncertainty of Antarctica's future contribution to global sea level rise that arises from large uncertainty in the oceanic forcing and the associated ice shelf melting. Ice shelf melting is considered to be a major if not the largest perturbation of the ice sheet's flow into the ocean. However, by computing only the sea level contribution in response to ice shelf melting, our study is neglecting a number of processes such as surface-mass-balance-related contributions. In assuming linear response theory, we are able to capture complex temporal responses of the ice sheets, but we neglect any self-dampening or self-amplifying processes. This is particularly relevant in situations in which an instability is dominating the ice loss. The results obtained here are thus relevant, in particular wherever the ice loss is dominated by the forcing as opposed to an internal instability, for example in strong ocean warming scenarios. In order to allow for comparison the methodology was chosen to be exactly the same as in an earlier study (Levermann et al., 2014) but with 16 instead of 5 ice sheet models. We include uncertainty in the atmospheric warming response to carbon emissions (full range of CMIP5 climate model sensitivities), uncertainty in the oceanic transport to the Southern Ocean (obtained from the time-delayed and scaled oceanic subsurface warming in CMIP5 models in relation to the global mean surface warming), and the observed range of responses of basal ice shelf melting to oceanic warming outside the ice shelf cavity. This uncertainty in basal ice shelf melting is then convoluted with the linear response functions of each of the 16 ice sheet models to obtain the ice flow response to the individual global warming path. The model median for the observational period from 1992 to 2017 of the ice loss due to basal ice shelf melting is 10.2 mm, with a likely range between 5.2 and 21.3 mm. For the same period the Antarctic ice sheet lost mass equivalent to 7.4 mm of global sea level rise, with a standard deviation of 3.7 mm (Shepherd et al., 2018) including all processes, especially surface-mass-balance changes. For the unabated warming path, Representative Concentration Pathway 8.5 (RCP8.5), we obtain a median contribution of the Antarctic ice sheet to global mean sea level rise from basal ice shelf melting within the 21st century of 17 cm, with a likely range (66th percentile around the mean) between 9 and 36 cm and a very likely range (90th percentile around the mean) between 6 and 58 cm. For the RCP2.6 warming path, which will keep the global mean temperature below 2 ∘C of global warming and is thus consistent with the Paris Climate Agreement, the procedure yields a median of 13 cm of global mean sea level contribution. The likely range for the RCP2.6 scenario is between 7 and 24 cm, and the very likely range is between 4 and 37 cm. The structural uncertainties in the method do not allow for an interpretation of any higher uncertainty percentiles. We provide projections for the five Antarctic regions and for each model and each scenario separately. The rate of sea level contribution is highest under the RCP8.5 scenario. The maximum within the 21st century of the median value is 4 cm per decade, with a likely range between 2 and 9 cm per decade and a very likely range between 1 and 14 cm per decade.

54 ENVIRONMENTAL SCIENCES↗

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

59 BASIC BIOLOGICAL SCIENCES↗