2024

Active processes on chromatin

Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression

In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that…

Cover of Computer Methods in Applied Mechanics and Engineering

A random field model for anisotropic strain energy functions and its application for uncertainty quantification in vascular mechanics

This paper deals with the construction of random field models for spatially-dependent anisotropic strain energy functions indexed by complex geometries. The approach relies on information theory and the principle of maximum entropy, which are invoked in order to construct the family of first-order marginal probability distributions in accordance with fundamental constraints such as polyconvexity, coerciveness…

Graphic showing weekday frequency of usage of smart devices.

Assessment of ownership of smart devices and the acceptability of digital health data sharing

Smart portable devices- smartphones and smartwatches- are rapidly being adopted by the general population, which has brought forward an opportunity to use the large volumes of physiological, behavioral, and activity data continuously being collected by these devices in naturalistic settings to perform research, monitor health, and track disease. While these data can serve to revolutionize…

Primitives of PTM-Mamba

PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks

Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to…

Cover of Computational Science journal

HarVI: Real-Time Intervention Planning for Coronary Artery Disease Using Machine Learning

Virtual planning tools that provide intuitive user interaction and immediate hemodynamic feedback are crucial for cardiologists to effectively treat coronary artery disease. Current FDA-approved tools for coronary intervention planning require days of preliminary processing and rely on conventional 2D displays for hemodynamic evaluation. Immersion offered by extended reality (XR) has been found to benefit intervention…

ROC curves comparing diagnostic performance with sensitivity metrics table.

Diagnostic Performance of Coronary Angiography Derived Computational Fractional Flow Reserve

Computational fluid dynamics can compute fractional flow reserve (FFR) accurately. However, existing models are limited by either the intravascular hemodynamic phenomarkers that can be captured or the fidelity of geometries that can be modeled. This study aimed to validate a new coronary angiography‐based FFR framework, FFRHARVEY, and examine intravascular hemodynamics to identify new biomarkers that…

Coronary angiogram showing vascular structure with marked regions.

Establishing the longitudinal hemodynamic mapping framework for wearable-driven coronary digital twins

Understanding the evolving nature of coronary hemodynamics is crucial for early disease detection and monitoring progression. We require digital twins that mimic a patient’s circulatory system by integrating continuous physiological data and computing hemodynamic patterns over months. Current models match clinical flow measurements but are limited to single heartbeats. To this end, we introduced the…

Overview of the communication tasks involved in distributed fluid-structure interaction computations.

Designing a GPU-Accelerated Communication Layer for Efficient Fluid-Structure Interaction Computations on Heterogeneous Systems

As biological research demands simulations with increasingly larger cell counts, optimizing these models for largescale deployment on heterogeneous supercomputing resources becomes crucial. This requires the redesign of fluid-structure interaction tasks written around distributed data structures built for CPU-based systems, where design flexibility and overall memory footprint are key considerations, to instead be performant on CPU-GPU…