Practicum Abstracts

Numerical Analysis and Acceleration of Particle-Particle Particle-Mesh Method using Cabana

Solving long horizon optimal control with distributed optimization and randomized numerical linear algebra.

The Strength and Impacts of Atmospheric Rivers in the ERA5 & HENS using TempestExtremes

Bayesian Variable Selection on Quantum Computers

Physics-informed diagnostics: improving PINN performance with information-based model selection

Flow Matching for Probabalistic Forecasting of Time Series

Developing and evaluating deep learning segmentation models in the biological and medical domain.

Application of Topological Data Analysis to Amorphous Materials

Randomized preconditioning based on approximate range deflation

Distributed Subgraph GNN Training with Local Graph Clustering

Watermarking scientific data

Multiphase Modeling of Cohesive Particle-Laden Flows

Mitigating Memorization In Language Models

Patterns of generalization in pretrained neural data models.

Inverse Design of Upconverting Nanoparticles via Deep Learning on Physics-Infused Heterogeneous Graphs

Butterfly factorization from matrix-vector products

Probabilistic Noise Conversion for Simulating Open Quantum Systems

Surface snow properties at the SAIL site

Reinforcement Learning for De Novo Molecule Design in Photovoltaic Cell Applications

Evaluating Methods of Calculating Connectivity from Functional MRI

Load Balancing Nyx Cosmological Code

Does In-Context Operator Learning Generalize to Domain-Shifted Settings?

Learning Polarizable Force Field Parameters for Ionic Liquids using Graph-Neural Networks

Iterative Phasing with Noise Projection for Fluctuation X-Ray Scattering

Disentangling order-4 tensors using Riemannian optimization

Development and Implementation of Optimized PEXSI Algorithms for Twisted Bilayer Graphene Systems

Relativistic Fluid Modeling for Wake-Field Acceleration Plasmas in WarpX

Extreme Events in a Data-Driven Deep Learning Weather Model: Fuzzy Verification and FourCastNet

Adaptive Remapping for PIC Methods

Fluctuating Hydrodynamics and the Rayleigh-Plateau Instability

TBD: Exploration into Quantum Speech Processing using Quantum Pixel Representations and Compression for Keyword Recognition

Method development for high-throughput polarization calculations

Advancing Free-Form Deformation for Aerodynamic Design

Revisiting approaches for binning and taxonomic annotation of the coccolithophore Emiliania huxleyi in environmental samples

Proposal for near-term quantum simulation of strongly-correlated molecules with Rydberg Atom Arrays

Estimating MAG Quality

Kernel View of Quantum Machine Learning on Array Data

Evolutionary Analysis of Prophage Genomes

BarrierNet: Adapting Message Passing Neural Networks to Refine the Search for optimal reaction networks in Lithium Ion Battery Solid Electrolyte Interfaces

Simulating Supermassive Black Holes in Nyx

Quantum Subspace Diagonalization

Modeling Superluminous Type 1a Supernovae

Randomized Sampling for Training Hypergraph Neural Networks

Simulating U(1) gauge theories using quantum computers

Uncovering eukaryotes from a 20-year metagenomic time series from Lake Mendota

Multimodal analysis of plant root composition as a function of drought

6D Bricks: Extending the Bricks Data Layout for Near-Roofline Performance in High-Dimensional Application Code

Molecular Dataset Summarization

Disentangling the Relative Impacts of Temperature and VPD on Tropical Forest GPP

Using Reference Map Technique in AMReX to model microswimmers

Learning Quantum Error Models

SNIFS Software and Pipeline Upgrades

Preconditioning Techniques for the Marginalized Graph Kernel

An acceleration framework for parameter estimation using implicit sampling and adaptive

Ultrafast Electron Detector Enabled by High Performance Computing

Direct evaluation of dynamical large-deviation rate functions using a variational ansatz

Application of AMReX to an Eulerian method to simulate fluid-structure interactions

Genome Constellation

Climate Science, Deep Learning, and Pattern Discovery: The Madden-Julian Oscillation as a Test Case

Computational discovery of novel two-dimensional CO2 reduction photocatalysts

Charged Pion Scattering with Massive QED

Dynamical Models of Biological Subtraction in Genetic Circuits

Exploring methods to compress deep neural networks using union of intersections

Exploration of the Electronic Landscape

Dynamic Load Balancing for Storm Surge Applications

Spark Based Metagenome Assembler

Computational Optimization of Biosynthetic Gene Clusters

Numerical Methods for the Drag-Coupled Particles in Viscous Flow

Network design for quantifying urban CO2 emissions: Assessing tradeoffs between precision and network density

Analysis of high throughput screens using CRISPRi and adapting CRISPRi for probing phage infections

High-dimensional variable selection and shrinkage in pseudolikelihood estimators of the inverse covariance matrix

"Automating Image Processing for Planet and TNO Searches in PTF" (unofficial)

A Hartree-Fock Application using UPC++ and the New DArray Library

Robust Estimation of Auditory Cortex Tuning and Connectivity

Parallel algorithms for maximum-cardinality high-weight graph matching

Reactive force field modelling of silicate sorption on the hematite r-plane

FASTERp: A Feature Array Search Tool for Estimating Resemblance of protein sequences

Bidi: scalable bit-distance calculations using MPI + OpenCL

A convolutional free-space propagator for Maxwell's equations in free-space with application to PIC methods

Metagenomic Assembly by K-mer Histogram Peelback

Estimating urban carbon dioxide fluxes at high resolution from in situ observations

Hydrodynamic Simulations of high multiplicity proton proton collisions at a center of mass energy of 13 TeV

Adaptive mesh refinement (AMR) and embedded boundaries (EB) in Chombo

High-speed visualization of/interaction with ALS data for previewing algorithm parameter tweaks

Monte Carlo Radiation Transport in Compact Binary Merger Disks

Inferring the ecological niches of thousands of microbial species using synthetic ecosystems

The Shape of Climate: Topological Data Analysis on Climate Data

Solving 1,000 Puzzles with 8 Billion Small Pieces: Assembling Draft Genomes from the Cow Rumen Metagenome

Accuracy checks of Chombo's mapped multiblock framework

Parallelizing three-dimensional viscoelastic models

Shirley Compact Basis

High resolution global constraints on atmospheric carbon dioxide with a novel statistical framework

Time Integration and Nonlinear Solvers for the Speedup of the Discontinuous Galerkin Finite Element Method

Model-based detection of interactions from time-series data

Simulation of Porous Media Flow in a Nuclear Waste Repository

Fluctuating Hydrodynamics

Low Mach Number Fluctuating Hydrodynamics

Grouping molecules of similar orientation in single-molecule diffraction experiments

Developing a Fast Algorithm for Classifying Unknown Proteins

Global constraints on atmospheric CO2 concentrations and CO2 sources

Detecting genomic-level regulatory strategies in Shewanella MR-1

Modeling stratified tidal flow with adaptive mesh refinement

Stochastic Population Dynamics in Structured Populations

Exploration of Novel Parallel Algorithms for Short Read Assembly

Driving biofuel production with a synthetic oscillator

Electronic structure calculations to screen solar PV materials

A Comparison of Helicos and Illumina RNA-sequencing platforms

Engineering gold nanostructures for surface-enhanced Raman spectroscopy

Overall group: Chombo my work: Artificial Viscosity for 4th order accurate Finite Volume Schemes

DeepSky

Atmospheric Modeling using Chombo

Calculation of Side Chain Conformational Entropy and the Discrimination of Native Protein Structures from Decoy Sets

Can yields of a biofuel candidate Isopentenol be increased using oscillatory promoters?

Computational Analysis of CRISPR Mechanism, Function, and Evolution

The Design of Orthogonal Components for a Transcription Attenuation System

High Performance 3-D Image Reconstruction for Molecular Structure Determination

Application of adaptive mesh refinement to particle-in-cell methods

Extremum-Preserving Limiters for the Piecewise Linear Method and Piecewise Parabolic Method

Automated Sorting of Large All Versus All BLAST Datasets

Modeling Ideal MHD collimation from differential rotation using an upwinding scheme with adaptive mesh refinement

Quaternary structure and stability of glycine mutated Amyloid Beta fibrils

Stochastic modeling of HIV Tat-transactivation

Algorithm Refinement for the Stochastic Burgers' Equation

A Numerical Study of the Kelvin-Helmholtz Instability on Large Amplitude Internal Waves

Towards a Mechanistic Model of Agonist-Induced Calcium Signaling in Macrophage Cells

Tomography of molecular machines central to mechanotransduction in hair cells

Transfer-matrix approach to phonon defect scattering in three-dimensional carbon structures with thermoelectric applications

"Prediction of Regulatory Motifs Controlling the Expression and Processing of MicroRNA Genes in Drosophila" "Prediction of Regulatory Motifs Controlling the Expression and Processing of MicroRNA Ge

Improving the Performance of the Scaled Matrix/Vector Multiplication with Vector Addition in Tau3P, an Electromagnetic Solver.

A Fourth Order Accurate Adaptive Mesh Refinement Method for Poisson's Equation

Characterization of a Pulse-Generating Gene Circuit Using Quantitative Real-Time PCR

Automatic segmentation and labeling of images of different cell types

Learning RNA Secondary Structure using Marginalized Kernels on Graphs

Inference of Protein-DNA Binding Specificity From Structure

Numerical Simulations of the Lyman Alpha Forest

Polymorphisms in Ciona intestinalis

Investigation of quantum well states in Copper-Cobalt thin films.

Implementing an embedded boundary algorithm for gas dymamics in EBChombo.

Parallelization of the Ewald Summation Method in Molecular Dynamics

Modeling Multiphase Fluid Flow with Level Set Methods

RNA Gene Finding In Eukaryote

Project 1 (A) "Archiving the 1999 AMANDA Data Set" Project 2 (B) "Enlarging the Gamma-Ray Burst Sample for AMANDA"

Computational Neuroscience of C. Elegans and Mammalian Retinal Ganglion Cells During Development

Measuring the Extensional Elasticity of the Red Blood Cell Using Micropipette Aspiration

Implementation Issues in Haptic Visualization

Numerical Experiments with Optimal Predictions Method

Image Recovery Using Multiple Holograms

Using the Space Transformations to solve the Three Dimensional Flow Equation

Integration of physical and genetic genome maps

Slug Tests Under Saturated/Unsaturated Flow: A Richard's Equation Perspective

Parallel Computation using OVERFLOW: Overlapping Grid Navier-Stokes Flow Solver

Examination of Image Reconstruction from Transmission Data