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2. Molecular Kinetic Simulations of Transient and Steady Wave Propagation into a Planet’s Exosphere

Author

Lucia Tian, Robert E. Johnson, Orenthal J. Tucker, Adam K. Woodson, Hayley N. Williamson, and Shane R. Carberry Mogan

Subjects
molecular kinetics, atmospheric waves, planetary exospheres, Meteorology. Climatology, QC851-999
Abstract

The vertical propagation of wave energy into a planet’s exosphere, a process that affects atmospheric evolution, is calculated here using 1D molecular kinetic simulations. Effects sensitive to molecular interactions are examined by comparing simulation results to solutions of linear fluid models for steady wave activity using parameters associated with Mars’ upper atmosphere. In addition to correctly describing the wave behavior in the exobase region, these simulations directly yield nonlinear effects such as atmospheric heating. They also readily include the transient behavior due to the onset and decay of waves propagating into the rarefied region of a planet’s atmosphere. This is a first step in understanding the effects of variable wave activity in the region where the atmosphere evolves from collisional to collisionless.

Published
2023
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3. Callisto’s atmosphere: First evidence for H2, and the implications this has for Europa’s and Ganymede’s atmosphere

Author

Shane Carberry Mogan, Orenthal J. Tucker, Robert E. Johnson, Lorenz Roth, Juan Alday, Audrey Vorburger, Peter Wurz, Andre Galli, H. Todd Smith, Apurva V. Oza, Lucas Liuzzo, and Andrew R. Poppe

Abstract

We explore the parameter space for the contribution to Callisto's H corona observed by the Hubble Space Telescope from sublimated H2O and radiolytically produced H2 using the Direct Simulation Monte Carlo (DSMC) method. The spatial morphology of this corona produced via photo- and magnetospheric electron impact-induced dissociation is described by tracking the motion of and simulating collisions between the hot H atoms and thermal molecules including a near-surface O2 component. Our results presented indicate that sublimated H2O produced from the surface ice, whether assumed to be intimately mixed with or distinctly segregated from the dark non-ice or ice-poor regolith, cannot explain the observed structure of the H corona. On the other hand, a global H2 component can reproduce the observation, and is also capable of producing the enhanced electron densities observed at high altitudes by Galileo's plasma-wave instrument, providing the first evidence of H2 in Callisto's atmosphere. Finally, we discuss the implications of these results, in particular how they compare to Europa and Ganymede.

Published
2023

5. Mismatch repair operates at the replication fork in direct competition with mismatch extension by DNA polymerase δ

Author

Roland Klassen, Venkat Gangavarapu, Robert E. Johnson, Louise Prakash, and Satya Prakash

Subjects
Cell Biology, Molecular Biology, Biochemistry, Research Article
Abstract

DNA mismatch repair (MMR) in eukaryotes is believed to occur post-replicatively, wherein nicks or gaps in the nascent DNA strand are suggested to serve as strand discrimination signals. However, how such signals are generated in the nascent leading strand has remained unclear. Here we examine the alternative possibility that MMR occurs in conjunction with the replication fork. To this end, we utilize mutations in the PCNA interacting peptide (PIP) domain of the Pol3 or Pol32 subunit of DNA polymerase δ (Polδ) and show that these pip mutations suppress the greatly elevated mutagenesis in yeast strains harboring the pol3-01 mutation defective in Polδ proofreading activity. And strikingly, they suppress the synthetic lethality of pol3-01 pol2-4 double mutant strains, which arises from the vastly enhanced mutability due to defects in the proofreading functions of both Polδ and Polε. Our finding that suppression of elevated mutagenesis in pol3-01 by the Polδ pip mutations requires intact MMR supports the conclusion that MMR operates at the replication fork in direct competition with other mismatch removal processes and with extension of synthesis from the mispair by Polδ. Furthermore, the evidence that Polδ pip mutations eliminate almost all the mutability of pol2-4 msh2Δ or pol3-01 pol2-4 adds strong support for a major role of Polδ in replication of both the leading and lagging DNA strands.

Published
2023

6. Electron impact ionization in the icy Galilean satellites’ atmospheres

Author

Shane R. Carberry Mogan, Robert E. Johnson, Audrey Vorburger, and Lorenz Roth

Subjects
Earth and Planetary Astrophysics (astro-ph.EP), Physics - Space Physics, FOS: Physical sciences, Space Physics (physics.space-ph), Atomic and Molecular Physics, and Optics, Astrophysics - Earth and Planetary Astrophysics
Abstract

Electron impact ionization is critical in producing the ionospheres on many planetary bodies and, as discussed here, is critical for interpreting spacecraft and telescopic observations of the tenuous atmospheres of the icy Galilean satellites of Jupiter (Europa, Ganymede, and Callisto), which form an interesting planetary system. Fortunately, laboratory measurements, extrapolated by theoretical models, were developed and published over a number of years by K. Becker and colleagues (see Deutsch et al. 2009) to provide accurate electron impact ionization cross sections for atoms and molecules, which are crucial to correctly interpret these measurements. Because of their relevance for the Jovian icy satellites we provide useful fits to the complex, semi-empirical Deutsch-Mark formula for energy-dependent electron impact ionization cross-sections of gas-phase water products (i.e., H2O, H2, O2, H, O). These are then used with measurements of the thermal plasma in the Jovian magnetosphere to produce ionization rates for comparison with solar photo-ionization rates at the icy Galilean satellites.

Published
2023

7. Callisto's Atmosphere: First Evidence for H 2 and Constraints on H 2 O

Author

Shane R. Carberry Mogan, Orenthal J. Tucker, Robert E. Johnson, Lorenz Roth, Juan Alday, Audrey Vorburger, Peter Wurz, Andre Galli, H. Todd Smith, Benoit Marchand, and Apurva V. Oza

Subjects
Earth and Planetary Astrophysics (astro-ph.EP), Geophysics, Space and Planetary Science, Geochemistry and Petrology, 530 Physics, 520 Astronomy, Earth and Planetary Sciences (miscellaneous), FOS: Physical sciences, 620 Engineering, Astrophysics - Earth and Planetary Astrophysics
Abstract

We explore the parameter space for the contribution to Callisto's H corona observed by the Hubble Space Telescope (Roth et al. 2017a) from sublimated H2O and radiolytically produced H2 using the Direct Simulation Monte Carlo (DSMC) method. The spatial morphology of this corona produced via photo- and magnetospheric electron impact-induced dissociation is described by tracking the motion of and simulating collisions between the hot H atoms and thermal molecules including a near-surface O2 component. Our results indicate that sublimated H2O produced from the surface ice, whether assumed to be intimately mixed with or distinctly segregated from the dark non-ice or ice-poor regolith, cannot explain the observed structure of the H corona. On the other hand, a global H2 component can reproduced the observation, and is also capable of producing the enhanced electron densities observed at high altitudes by Galileo's plasma-wave instrument (Gurnett et al., 1997, 2000), providing the first evidence of H2 in Callisto's atmosphere. The range of H2 surface densities explored, under a variety of conditions, that are consistent with these observations is ~(0.4-1)x10^8 cm^-3. The simulated H2 escape rates and estimated lifetimes suggest that Callisto has a neutral H2 torus. We also place a rough upper limit on the peak H2O number density (

Published
2022

9. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Author

Mohammad Raza, Alison E. Mather, Gilberto Betancor, Ian Merrick, Ben Taylor, Mathew A. Beale, Helen Ward, Samir Dervisevic, Michelle Cronin, Aaron R. Jeffries, Louise Smith, Steven Rudder, Mara K. N. Lawniczak, Sascha Ott, Ashok Dadrah, Luke Bedford, Gabrielle Vernet, Erik M. Volz, Rahul Batra, Johnny Debebe, Caoimhe McKerr, Samantha McGuigan, Oliver Megram, Katie Jones, Mailis Maes, Rebecca Dewar, Emma Swindells, Robert E. Johnson, Myra Hosmillo, Wen C Yew, Vineet Patel, Scott Aj Thurston, Matthew Bashton, Luke B Snell, Lynn Monaghan, David Buck, Gregory R Young, Garren Scott, Louis du Plessis, Sara Kumziene-Summerhayes, David M. Aanensen, Carl Jones, Nadine Holmes, Bernardo Gutierrez, Elizabeth Wastenge, Stavroula F Louka, Dennis Wang, Richard I. Gregory, M. Estée Török, Alistair C. Darby, Ulf Schaefer, Marc Niebel, David Robertson, E. Thomson, Carol Churcher, Patrick C McClure, Scott Elliott, Sarah Jeremiah, Katerina Galai, Matthew W. Loose, Megan Mayhew, Adhyana I K Mahanama, Angeliki Karamani, Naomi R Park, David J. Williams, Lance Turtle, Lucy R. Frost, Alicia Thornton, Jennifier Liddle, M Morgan, Tim Wyatt, Paul W Bird, Chloe Bishop, Esther Robinson, Alasdair MacLean, Inigo Martincorena, Bridget A. Knight, Emma Meader, Thomas R. Connor, Hermione J. Webster, Peter Muir, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Hannah E Bridgewater, David Simpson, Radoslaw Poplawski, Angus I. Best, David Baker, Laura Letchford, Cassie Breen, Yann Bourgeois, Matthew Gemmell, Nikki Smith, Alison Holmes, Iliana Georgana, Christophe Fraser, Natasha Jesudason, Johnathan M Evans, Rachael Stanley, Lesley-Anne Williams, Jessica Lynch, Hannah Lowe, Eleri Wilson-Davies, Paul A. Baker, Alex Makunin, James Bonfield, Helen Adams, Christopher Fearn, Peter J. Diggle, Harry D Wilson, Carmen F. Manso, Nichola Duckworth, D Haw, Anna L. Casey, Audrey Farbos, Sam Haldenby, Vicki Chalker, Roberto Amato, Elen De Lacy, Ben Farr, Eric Witele, Buddhini Samaraweera, G MacIntyre-Cockett, Husam Osman, Jane Greenaway, Justin O'Grady, Sally Forrest, Andrew Nelson, Monika Pusok, A Lloyd, Edward Barton, James W. Harrison, Sophie Palmer, Amanda Symmonds, James Shepherd, Nazreen F. Hadjirin, Stephen L. Michell, Mohammed O Hassan-Ibrahim, Fiona Ashcroft, Daniel Mair, Richard H. Myers, Dianne Irish-Tavares, Hannah C. Howson-Wells, Jacqui Prieto, Christine Sambles, Andrew Hesketh, Alp Aydin, Sónia Gonçalves, Tabitha Mahungu, Tanzina Haque, Nicholas Ellaby, Karen Oliver, Hannah Paul, Joanne Watts, Claire McMurray, Lisa J Levett, Darren Smith, Simon Cottrell, Joanna Warwick-Dugdale, Pinglawathee Madona, Matthew J. Dorman, Lizzie Meadows, Ali R Awan, Leanne M Kermack, Jennifer Hart, Angie Lackenby, Carol Scott, Michael Spencer Chapman, Lucille Rainbow, Kyriaki Nomikou, Julianne R Brown, Juan Ledesma, Adam P Westhorpe, Giri Shankar, Karlie Fallon, Tim J Sloan, Joanne Watkins, Robert Impey, Sue Edwards, Rebecca C H Brown, Robin J Moll, Karla Spellman, Laura Gifford, Jamie Young, Adrienn Angyal, Graham Phillip Taylor, Robin Manley, Gavin Dabrera, Michelle Wantoch, Rachel Williams, David Heyburn, Mirko Menegazzo, Derrick W. Crook, Gaia Nebbia, Rachel Nelson, Elaine O'Toole, Luke Foulser, Katherine L Harper, Fatima Downing, Hassan Hartman, Nathan Moore, Gemma L. Kay, Matthew Wyles, Thanh Le-Viet, Edith Vamos, John Sillitoe, Lesley Shirley, Nicholas J. Loman, Iona Willingham, Elihu Aranday-Cortes, Ian B Vipond, Jeremy Mirza, Alberto C Cerda, Michelle L Michelsen, Steven Riley, Alison Cox, Igor Siveroni, Nadua Bayzid, Shavanthi Rajatileka, Giselda Bucca, Benjamin J Cogger, Tim Boswell, Matthew J. Bull, Stephen Carmichael, Lisa Berry, Frances Bolt, Kylie E. C. Ainslie, Martyn Guest, Sarojini Pandey, Katherine L. Bellis, Shane A. McCarthy, Christopher Ruis, Fei Sang, David Bonsall, Danni Weldon, Alex Alderton, Lee Graham, Amy Trebes, Sally Corden, Adrian W Signell, Tanya Golubchik, Huw Gulliver, Rocio Martinez Nunez, Dinesh Aggarwal, Tanya Curran, Jonathan K. Ball, Sharif Shaaban, Paul Randell, Jillian Durham, Alec Birchley, Matilde Mori, Joana Dias, Katherine A Twohig, Grant Hall, Antony D Hale, Alan McNally, Jonathan D. Edgeworth, Safiah Afifi, Andrew Rambaut, Katherine Smollett, David N. Lee, Tamyo Mbisa, Shahjahan Miah, Steven Rushton, Grace Taylor-Joyce, Hannah M Pymont, Chloe L Fisher, Cordelia Langford, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Kathleen A. Williamson, Anna Price, Holli Carden, Khalil Abudahab, Joanne D. Stockton, Meera Unnikrishnan, Jennifer Collins, Emma Moles-Garcia, Michaela John, Christine Kitchen, Tranprit Saluja, Ian Harrison, Lily Tong, Thomas G. Thompson, Thomas Helmer, Amita Patel, Siona Silveira, Deborah Ashby, Claire M Bewshea, Anita Justice, Brendan A I Payne, Alexander J. Trotter, Nikos Manesis, Katie F. Loveson, Cristina V. Ariani, Wendy Chatterton, Robert J. Munn, Julian A. Hiscox, Robert Beer, Judith Breuer, Caroline E. Walters, Liam Crawford, Ara Darzi, Will P. M. Rowe, Cariad Evans, Matthew Parker, Tammy V Merrill, Louise Aigrain, Joshua Quick, Leigh M Jackson, Samuel M. Nicholls, Jonathan W. Moore, John A Hartley, Graham P. Taylor, Cherian Koshy, Shirelle Burton-Fanning, Sheila Waugh, Catherine Moore, Danielle C. Groves, Peijun Zhang, Sahar Eldirdiri, Derek Fairley, Tim E. A. Peto, Jack Cd Lee, Sharon Glaysher, Liam Prestwood, Hannah Dent, Anita Kenyon, Stephen P. Kidd, Nick Levene, Igor Starinskij, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Laia Fina, Angela Marchbank, Daniel Bradshaw, Marina Escalera Zamudio, Scott Goodwin, Andrew D Beggs, Seema Nickbakhsh, Trevor Robinson, Christina Atchison, David K. Jackson, Kathy Li, Rory Gunson, Sunando Roy, Graham S Cooke, Steven Liggett, Yasmin Chaudhry, Anoop Chauhan, Ben Temperton, Mariateresa de Cesare, Paul E Brown, Li Xu-McCrae, Martin P McHugh, Catherine Ludden, Wendy Smith, Danielle Leek, Divya K. Shah, Judith Heaney, Dominic P. Kwiatkowski, Kate M. Johnson, Robin Howe, Malorie Perry, Tetyana I. Vasylyeva, David F. Bibby, Haowei Wang, Steve Palmer, Nicholas W Machin, Charlotte A Williams, Bree Gatica-Wilcox, Angie Green, John A. Todd, Paul Elliott, Noel Craine, Jeffrey K. J. Cheng, Kate Templeton, Jonathan Hubb, Joshua Maksimovic, Christl A. Donnelly, Monique Andersson, Christopher Holmes, Dimitris Grammatopoulos, Christopher B. Williams, David G Partridge, Aminu S Jahun, Alexander Adams, Marius Cotic, Sarah Essex, Christopher J. Moore, Trudy Workman, Nicola Sheriff, Helen L Lowe, Ewan M. Harrison, Dorota Jamrozy, Rachel Jones, Ellen Higginson, Erwan Acheson, Christopher R. Jones, Oliver G. Pybus, Francesc Coll, Sian Morgan, Paul J. Parsons, Patawee Asamaphan, Veena Raviprakash, Andrew R. Bassett, Declan Bradley, Laura Atkinson, Anthony Underwood, Graciela Sluga, Sally Kay, Ellena Brooks, Oliver Eales, Andrew Whitwham, Surendra Parmar, Angela Cowell, Nicole Pacchiarini, Theocharis Tsoleridis, Jason Coombes, Robert Davies, Flavia Flaviani, Benita Percival, Jenna Nichols, Natasha M. Johnson, Salman Goudarzi, Hibo Asad, Amanda Bradley, Hannah Jones, Chrystala Constantinidou, Georgina M McManus, Minal Patel, Steven Leonard, Rebecca Williams Bmbs, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Amy Ash, John Danesh, Corin Yeats, Claudia Wierzbicki, Kordo Saeed, John Boyes, Michael A. Quail, Sharon J. Peacock, Nabil-Fareed Alikhan, Jon-Paul Keatley, Claudio Fronterre, Garry Scarlett, James McKenna, Thushan I de Silva, Malte L Pinckert, Kate B. Cook, Amy Gaskin, Rajiv Shah, Matthew T. G. Holden, Sophie J Prosolek, Nathaniel Storey, Ryan P George, Lindsay Coupland, Jenifer Mason, Matthew Carlile, Thomas D Stanton, Guy Mollett, Siddharth Mookerjee, Mary Ramsay, Steven Platt, Stephen W Attwood, Susanne Stonehouse, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Mark Whitehead, Catherine Bresner, Stefanie V Lensing, Louissa R Macfarlane-Smith, Colin P. Smith, Wendy Hogsden, Charlotte Nelson, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Samuel Robson, Zoltán Molnár, Emma L. Wise, Sian Ellard, Kim S Smith, Alice Broos, Manjinder Khakh, Kathryn A Jackson, Claire Cormie, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Meera Chand, Debra Padgett, Cassandra S Malone, James V. Price, Themoula Charalampous, Ronan A Lyons, Natalie Groves, Stefan Rooke, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Michelle Lister, Carlos Balcazar, Ana da Silva Filipe, Ben Warne, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Rose K Davidson, Angela Helen Beckett, Ember Hilvers, Kathryn McCluggage, Eileen Gallagher, Charlotte Beaver, Nick Cortes, Alisha Davies, Yusri Taha, Leah Ensell, Emanuela Pelosi, Elias Allara, Cressida Auckland, Eleanor Drury, Richard Eccles, Adela Alcolea-Medina, William L Hamilton, Rich Livett, Rachel Blacow, Margaret Hughes, Sarah François, Melisa Louise Fenton, Liz Ratcliffe, Verity Hill, Stephanie Hutchings, Kathryn Ann Harris, Emma Betteridge, William D. Fuller, Sophia T Girgis, Louise Berry, Gemma Clark, Nicholas M Redshaw, Richard Hopes, Leonardo de Oliveira Martins, Alexander J Keeley, Beth Blane, Wendy S. Barclay, Victoria Wright, Anita Lucaci, Luke R. Green, Fenella D. Halstead, Sarah Wyllie, Iraad F. Bronner, Áine O'Toole, Ravi Gupta, Leanne Kane, Clare M. McCann, Michael R Chapman, David W Eyre, Kelly Bicknell, Aileen G. Rowan, Sara Rey, Shazaad Ahmad, Diana Rajan, S Taylor, Sarah J. O'Brien, Alessandro M Carabelli, Amelia Joseph, Max Whiteley, Riaz Jannoo, Victoria Blakey, Martin D. Curran, David J. Studholme, Harmeet K Gill, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Julian Tang, Clare Pearson, Mark Kristiansen, Miren Iturriza-Gomara, National Institute for Health Research, and UK Research and Innovation

Subjects
Delta, Adult, Male, 2019-20 coronavirus outbreak, COVID-19 Vaccines, Vaccination Coverage, Coronavirus disease 2019 (COVID-19), Adolescent, General Science & Technology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Vaccine Efficacy, Biology, Young Adult, Exponential growth, Ethnicity, Prevalence, Humans, Child, Aged, Family Characteristics, Multidisciplinary, High prevalence, COVID-19 Genomics UK (COG-UK) Consortium11‡, SARS-CoV-2, Age Factors, COVID-19, Middle Aged, Virology, Hospitalization, England, Socioeconomic Factors, COVID-19 Nucleic Acid Testing, Child, Preschool, Female, Self Report
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

Published
2021

10. The influence of upper boundary conditions on molecular kinetic atmospheric escape simulations

Author

Robert E. Johnson, Orenthal J. Tucker, and Shane R. Carberry Mogan

Subjects
Earth and Planetary Astrophysics (astro-ph.EP), Physics, Atmospheric escape, FOS: Physical sciences, Astronomy and Astrophysics, Mechanics, Kinetic energy, Space Physics (physics.space-ph), Atmosphere, Physics - Atmospheric and Oceanic Physics, Physics - Space Physics, Space and Planetary Science, Dynamical time scale, Atmospheric and Oceanic Physics (physics.ao-ph), Hill sphere, Astrophysics::Earth and Planetary Astrophysics, Specular reflection, Boundary value problem, Astrophysics - Earth and Planetary Astrophysics, Exosphere
Abstract

Molecular kinetic simulations are typically used to accurately describe the tenuous regions of the upper atmospheres on planetary bodies. These simulations track the motion of particles representing real atmospheric atoms and/or molecules subject to collisions, the object's gravity, and external influences. Because particles can end up in very large ballistic orbits, upper boundary conditions (UBC) are typically used to limit the domain size thereby reducing the time for the atmosphere to reach steady-state. In the absence of a clear altitude at which all molecules are removed, such as a Hill sphere, an often used condition is to choose an altitude at which collisions become infrequent so that particles on escape trajectories are removed. The remainder are then either specularly reflected back into the simulation domain or their ballistic trajectories are calculated analytically or explicitly tracked so they eventually re-enter the domain. Here we examine the effect of the choice of the UBC on the escape rate and the structure of the atmosphere near the nominal exobase in the convenient and frequently used 1D spherically symmetric approximation. Using Callisto as the example body, we show that the commonly used specular reflection UBC can lead to significant uncertainties when simulating a species with a lifetime comparable to or longer than a dynamical time scale, such as an overestimation of escape rates and an inflated exosphere. Therefore, although specular reflection is convenient, the molecular lifetimes and body's dynamical time scales need to be considered even when implementing the convenient 1D spherically symmetric simulations in order to accurately estimate the escape rate and the density and temperature structure in the transition regime.

Published
2021

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