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Pathology foundation models (PFMs) have demonstrated strong representational capabilities through self-supervised pre-training on large-scale, unannotated histopathology image datasets. However, their diverse yet opaque pretraining…
Background: Quantitative susceptibility mapping (QSM) of the brain is an advanced MRI technique for assessing tissue characteristics based on magnetic susceptibility, which varies with the composition of the tissue, such as iron, calcium,…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Optically addressable spins are a promising platform for quantum information science due to their combination of a long-lived qubit with a spin-optical interface for external qubit control and read out. The ability to chemically synthesize…
In this work, we present a computational formulation based on continuum mechanics to study the interaction of fluid membranes embedded with semiflexible filaments. This is motivated by systems in membrane biology, such as cytoskeletal…
Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the energy landscape of natural proteins. Finding low-energy…
With the advent of exascale computing, effective load balancing in massively parallel software applications is critically important for leveraging the full potential of high performance computing systems. Load balancing is the distribution…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Computing the electronic structure of molecules with high precision is a central challenge in the field of quantum chemistry. Despite the enormous success of approximate methods, tackling this problem exactly with conventional computers is…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time intervals up to tens of $\mu$s, while many key events occur…
AlphaFold has achieved groundbreaking advancements in protein structure prediction, exerting profound influence across biology, medicine, and drug discovery. However, its reliance on multiple sequence alignment (MSA) is inherently…
We introduce and explore an approach for constructing force fields for small molecules, which combines intuitive low body order empirical force field terms with the concepts of data driven statistical fits of recent machine learned…
The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we…
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena from how cells send and receive…
The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Surface parameterization plays an essential role in numerous computer graphics and geometry processing applications. Traditional parameterization approaches are designed for high-quality meshes laboriously created by specialized 3D…