Bae-Yeun Ha, University of Waterloo

Research

biomolecular crowding computer simulations confined polymers inclusions in a polymer brush interactions of lipid membranes with amphiphilic peptides membrane biophysics polymer physics approach to chromosome organization

Latest papers

Computational study of bacterial chromosome organization by H-NS-mediated cross-linking and molecular crowding.
The Journal of chemical physics · 2026 · senior author
Variations of the Depletion Zones around Inclusions Explain the Complexity of Brush-Induced Depletion Interactions.
Journal of chemical theory and computation · 2025
Compaction and clustering of a heterogeneous polymer by biomolecular crowding.
The Journal of chemical physics · 2024 · senior author

All 28 publications

Latest funding

Physical and computational modeling of biomolecular crowding, confinement, organization, and interactions
NSERC · 2022 · Principal investigator
$72,000
Building physical models for biomolecular organization and interactions
NSERC · 2016 · Principal investigator
$162,000
Biomolecular electrostatics, confinement, and dynamics
NSERC · 2011 · Principal investigator
$110,000

All 5 grants and awards

28 publications.

01

Computational study of bacterial chromosome organization by H-NS-mediated cross-linking and molecular crowding.

Jung Y, Sadeghi A, Ha BY

The Journal of chemical physics2026Senior author

DOI: 10.1063/5.0325597 PMID: 42117660

02

Variations of the Depletion Zones around Inclusions Explain the Complexity of Brush-Induced Depletion Interactions.

Yong D, Yu JW, Ha BY, Hyeon C

Journal of chemical theory and computation2025

DOI: 10.1021/acs.jctc.5c00334 PMID: 40471983

03

Compaction and clustering of a heterogeneous polymer by biomolecular crowding.

Sadeghi A, Hyeon C, Jung Y, Ha BY

The Journal of chemical physics2024Senior author

DOI: 10.1063/5.0226892 PMID: 39530373

04

Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS.

Jung Y, Sadeghi A, Ha BY

Scientific reports2024Senior author

DOI: 10.1038/s41598-023-50355-2 PMID: 38167921

05

Modeling selectivity of antimicrobial peptides: how it depends on the presence of host cells and cell density.

Lee S, Schefter BR, Taheri-Araghi S, Ha BY

RSC advances2023Senior author

DOI: 10.1039/d3ra06030f PMID: 38020026

06

Interplay between nematic and cholesteric interactions in self-consistent field theory.

Spencer RKW, Ha BY, Saeidi N

Physical review. E2022

DOI: 10.1103/physreve.105.054501 PMID: 35706232

07

Self-consistent field theory of chiral nematic worm-like chains.

Spencer RKW, Ha BY, Saeidi N

The Journal of chemical physics2022

DOI: 10.1063/5.0078937 PMID: 35317576

08

Modeling the Protective Role of Bacterial Lipopolysaccharides against Membrane-Rupturing Peptides.

Nourbakhsh S, Yu L, Ha BY

The journal of physical chemistry. B2021Senior author

DOI: 10.1021/acs.jpcb.1c02330 PMID: 34319722

09

Collapse transition of a heterogeneous polymer in a crowded medium.

Jung Y, Ha BY

The Journal of chemical physics2021Senior author

DOI: 10.1063/5.0056446 PMID: 34364346

10

Characteristic time for the end monomers of a spherically confined polymer to find a nano-pore.

Hoseinpoor SM, Nikoofard N, Ha BY

The Journal of chemical physics2021Senior author

DOI: 10.1063/5.0040551 PMID: 33752364

Physical and computational modeling of biomolecular crowding, confinement, organization, and interactions

Principal investigatorNSERC2022Discovery Grants Program - Individual

Principal investigators: Ha, Bae-Yeun

Keywords: biomolecular crowding; confined polymers; polymer physics approach to chromosome organization; computer simulations; membrane biophysics; interactions of lipid membranes with amphiphilic peptides; inclusions in a polymer brush

$72,000

Building physical models for biomolecular organization and interactions

Principal investigatorNSERC2016Discovery Grants Program - Individual

Principal investigators: Ha, Bae-Yeun

$162,000

Biomolecular electrostatics, confinement, and dynamics

Principal investigatorNSERC2011Discovery Grants Program - Individual

Principal investigators: Ha, BaeYeun

$110,000

Theoretical studies in charged biomolecules

Principal investigatorNSERC2006Discovery Grants Program - Individual

Principal investigators: Ha, BaeYeun

$157,000

Ligand binding and stability of bilayer membranes

Principal investigatorNSERC2002Discovery Grants Program - Individual

Principal investigators: Ha, BaeYeun

$92,000

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

Frequent collaborators

Mohammad Kohandel

Applied Mathematics

1 shared papers, latest 2006

Write to this professor

A short, specific email works best. This draft uses one of their recent papers; replace the parts in brackets with your own details before sending.

Applying for

Paper to mentionMention their NSERC grant from 2022

Subject: Prospective PhD student: biomolecular crowding Dear Professor Ha, My name is [your name], and I am a [your current degree or role] at [your institution]. I am applying for a PhD position starting in [term and year]. I read your paper "Computational study of bacterial chromosome organization by H-NS-mediated cross-linking and molecular crowding." (2026), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] I also saw your NSERC-funded project "Physical and computational modeling of biomolecular crowding, confinement, organization, and interactions" (2022), and I would be glad to contribute to work in that direction. Are you accepting new PhD students for [term and year]? I have attached my CV and transcripts, and I would be glad to talk at a time that suits you. Thank you for your time. Kind regards, [your name]