Publications - Computational Aerobiology Lab

2026

#22

Condensate-Like Dynamics in Respiratory Aerosols Shape the Behavior of an Airborne Virus

Wauer, NA†; Calvó-Tusell, C†; Dommer, AC; Casalino, L; Kearns, FL; Caparotta, M; Rosenfeld, MA; Morris, CK; Amaro, RE.*

Under Review (2026)

Under Review

#21

Enzymes at the Ocean-Atmosphere Boundary: Lipase Modulation of Lipid Packing and Water Loss in Sea Spray Aerosols

Rubio, PB†; Davasam, A†; Wauer, NA†; Dommer, AC.; Man, L; Grassian, V; Amaro, RE.*

ACS Earth Space Chem. (2026)

DOI: 10.1021/acsearthspacechem.6c00108

#20

Compartment-Guided Assembly of Large-Scale Molecular Models with Bentopy

Westendorp, MSS†; Stevens, JA†; Brown, CM; Dommer, AC; Wassenaar, TA; Bruininks, BMH; Marrink, SJ.*

Protein Science (2026)

DOI: 10.1002/pro.70480

2025

#19

Understanding Aerosol-Mediated Disease Transmission

Dommer, AC; Amaro, RE;* Prather, KA.*

ACS Cent. Sci. 2025, 11, 12, 2319-2328

DOI: 10.1021/acscentsci.5c00364

#18

All-Atom Virus Simulations to Tackle Airborne Disease

Dommer, AC; Wauer, NA; Marrink, SJ;* Amaro, RE.*

Curr. Opin. Struct. Biol. 2025, 92, 103048

DOI: 10.1016/j.sbi.2025.103048

2024

#17

Interfacial Enrichment of Lauric Acid Assisted by Long Chain Fatty Acids, Acidity, and Salinity at Sea Spray Aerosol Surfaces

Dommer, AC† and Rogers, M;† Carter-Fenk, KA; Wauer, NA; Davasam, A; Rubio, PB; Allen, HC;* Amaro, RE.*

J. Phys. Chem. A. 2024, 128, 34, 7195-7207

DOI: 10.1021/acs.jpca.4c03335

2023

#16

Revealing the Impacts of Chemical Complexity on Submicron Sea Spray Aerosol Morphology

Dommer, AC; Wauer, NA; Angle, KJ; Davasam, A; Rubio, PB; Luo, M; Morris, CK; Prather, KA; Grassian, VH;* Amaro, RE.*

ACS Cent. Sci. 2023, 9, 6, 1088-1103

DOI: 10.1021/acscentsci.3c00184

#15

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

Dommer, AC†, Casalino, L,† and Kearns, FL†; Rosenfeld, MA; Wauer, NA; Ahn, S-H; Russo, J; Oliveira, S; Morris, C; Bogetti, A; Trifan, A; Brace, A; Sztain, T; Clyde, A; Ma, H; Chennubhotla, C; Lee, H; Turilli, M; Khalid, S; Tamayo-Mendoza, T; Welborn, M; Christensen, A; Smith, D; Qiao, Z; Sirumalla, S; O’Connor, M; Manby, F; Anandkumar, A; Hardy, D; Phillips, J; Stern, A; Romero, J; Clark, D; Dorrell, M; Maiden, T; Huang, L; McCalpin, J; Woods, C; Williams, M; Barker, B; Rajapaksha, H; Pitts, R; Gibbs, T; Stone, J; Zuckerman, D; Mulholland, A; Miller, T; Jha, S; Ramanathan, A;* Chong, L;* Amaro, R.*

Int. J. High Perform. Comput. Appl. 2023, 37, 1, 28-44

DOI: 10.1177/10943420221128233

2022

#14

Amino Acids are Driven to the Interface by Salts and Acidic Environments

Angle, KA; Nowak, CM; Davasam, A; Dommer, AC; Wauer, NA; Amaro, RE;* Grassian, VH.*

J. Phys. Chem. Lett. 2022, 13, 12, 2824-2829

DOI: 10.1021/acs.jpclett.2c00321

2021

#13

Calcium bridging drives polysaccharide co-adsorption to a proxy sea surface microlayer

Carter-Fenk, KA; Dommer, AC; Fiamingo, ME; Kim, JJ; Amaro, RE;* Allen, HC.*

Phys. Chem. Chem. Phys. 2021, 23, 16401-16416

DOI: 10.1039/D1CP01407B

#12

Cation-driven lipopolysaccharide morphological changes impact nitric acid heterogeneous reactivity in sea spray aerosols

Dommer, AC† and Lee, C†; Schiffer, JM; Amaro, RE;* Grassian, VH;* Prather, KA.*

J. Phys. Chem. Lett. 2021, 12, 20, 5023-5029

DOI: 10.1021/acs.jpclett.1c00810

#11

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

Dommer, AC†, Casalino, L†, and Gaieb, Z†; Barros, EP; Sztain, T; Ahn, S; Trifan, A; Brace, A; Ma, H; Lee, H; Bogetti, A; Khalid, S; Chong, L; Simmerling, C; Hardy, DJ; Maia, JD; Phillips, JC; Kurth, T; Stern, A; Huang, L; McCalpin, J; Tatineni, M; Gibbs, T; Stone, JE; Jha, S; Ramanathan, A;* Amaro, RE.*

Int. J. High Perform. Comput. Appl. 2021, 35 (5)

DOI: 10.1177/10943420211006452

2020

#10

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

Yu, A; Pak, AJ; He, P; Monje-Galvan, V; Casalino, L; Gaieb, Z; Dommer, AC; Amaro, RE; Voth, GA.*

Biophys. J. 2020, 120, 6, 1097-1104

DOI: 10.1016/j.bpj.2020.10.048

#9

The flexibility of ACE2 in the context of SARS-CoV-2 Infection

Barros, EP; Casalino, L; Gaieb, Z; Dommer, AC; Wang, Y; Fallon, L; Raguette, L; Belfon, K; Simmerling, C; Amaro, RE.*

Biophys. J. 2020, 120, 6, 1072-1084

DOI: 10.1016/j.bpj.2020.10.036

#8

Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein

Casalino, L† and Gaieb, Z†; Goldsmith, JA; Hjorth, C; Dommer, AC; Harbison, AM; Fogarty, CA; Barros, EP; Taylor, BC; McLellan, JS; Fadda, E; Amaro, RE.*

ACS Cent. Sci. 2020, 6, 10, 1722-1734

DOI: 10.1021/acscentsci.0c01056

#7

Insights into the Behavior of Nonanoic Acid and Its Conjugate Base at the Air/Water Interface Through a Combined Experimental and Theoretical Approach

Luo, M; Wauer, NA; Angle, KJ; Dommer, AC; Song, M; Novak, CM; Amaro, RE; Grassian, VH.*

Chem. Sci. 2020, 11, 10647-10656

DOI: 10.1039/D0SC02354J

#6

Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism

Durrant, J† and Kochanek, S†; Casalino, L; Ieong, P; Dommer, AC; Amaro, RE.*

ACS Cent. Sci. 2020, 6, 2, 189-196

DOI: 10.1021/acscentsci.9b01071

2019

#5

Surfactant Charge Modulates Lipase-Embedded Monolayer Stability at Marine-Relevant Aerosol Surfaces

Dommer, AC† and Luo, M†; Schiffer, JM; Rez, DJ; Mitchell, AR; Amaro, RE;* Grassian, VH.*

Langmuir 2019, 35 (27), 9050-9060

DOI: 10.1021/acs.langmuir.9b00689

2018

#4

Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target

Amaro, RE; Ieong, P; Huber, G; Dommer, AC; Alasdair, S; Bush, R; Durrant, J; Votapka, LA.*

ACS Cent. Sci. 2018, 4 (11), 1570-1577

DOI: 10.1021/acscentsci.8b00666

#3

Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols

Schiffer, JM; Luo, M; Dommer, A. C; Thoron, G; Pendergraft, M; Santander, MV; Lucero, D; De Barros, EP; Prather, KA; Grassian, VH; Amaro, RE.*

J. Phys. Chem. Lett. 2018, 9, 14, 3839-3849

DOI: 10.1021/acs.jpclett.8b01363

2016

#2

A Miniature Marine Aerosol Reference Tank (MiniMART) as a Compact Breaking Wave Analogue

Stokes, MD; Deane, G; Collins, DB; Cappa, C; Bertram, T; Dommer, AC; Schill, S; Forestieri, S; Survilo, M.*

Atmos. Meas. Tech. 2016, 9 (9), 4257-4267

DOI: 10.5194/amt-9-4257-2016

#1

Sea Spray Aerosol Structure and Composition Using Cryogenic Transmission Electron Microscopy

Patterson, JP; Collins, DB; Michaud, JM; Axson, JL; Sultana, CM; Moser, T; Dommer, AC; Conner, J; Grassian, VH; Stokes, MD; Deane, GB; Evans, JE; Burkart, MD; Prather, KA; Gianneschi, NC.*

ACS Cent. Sci. 2016, 2 (1), 40-47

DOI: 10.1021/acscentsci.5b0034