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3,118 results on '"Parker, Stephen"'

1. Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits

Author

Brotman, Sarah M., El-Sayed Moustafa, Julia S., Guan, Li, Broadaway, K. Alaine, Wang, Dongmeng, Jackson, Anne U., Welch, Ryan, Currin, Kevin W., Tomlinson, Max, Vadlamudi, Swarooparani, Stringham, Heather M., Roberts, Amy L., Lakka, Timo A., Oravilahti, Anniina, Fernandes Silva, Lilian, Narisu, Narisu, Erdos, Michael R., Yan, Tingfen, Bonnycastle, Lori L., Raulerson, Chelsea K., Raza, Yasrab, Yan, Xinyu, Parker, Stephen C. J., Kuusisto, Johanna, Pajukanta, Päivi, Tuomilehto, Jaakko, Collins, Francis S., Boehnke, Michael, Love, Michael I., Koistinen, Heikki A., Laakso, Markku, Mohlke, Karen L., Small, Kerrin S., and Scott, Laura J.

Published
2025
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6. Grain boundary segregation and phase separation in ceria-zirconia from atomistic simulation

Author

Underwood, Tom L., Vigorito, Susanna, Molinari, Marco, Purton, John, Wilding, Nigel B., Irvine, John T. S., and Parker, Stephen C.

Subjects
Condensed Matter - Materials Science, Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Statistical Mechanics, Physics - Computational Physics
Abstract

Doping is the most common strategy employed in the development of new and improved materials. However, predicting the effects of doping on the atomic-scale structure of a material is often difficult or limited to high-end experimental techniques. Doping can induce phase separation in a material, undermining the material's stability. A further complication is that dopant atoms can segregate to interfaces in a material such as grain boundaries (GBs), with consequences for key macroscopic properties of the material such as its conductivity. Here, we describe a computational methodology based on semi-grand canonical Monte Carlo which can be used to probe these phenomena at the atomic scale for metal oxide solid solutions. The methodology can provide precise predictions of the thermodynamic conditions at which phase separation occurs. It can also provide the segregation patterns exhibited by GBs at given conditions. We apply the methodology to one of the most important catalytic materials, ceria-zirconia. Our calculations reveal an interesting richness in the GB segregation in this system. Most GBs we examined exhibited continuous increases in Zr segregation upon Zr doping, with a concomitant reduction in the formation enthalpies of the GBs. However, a few GBs exhibited no segregation at low temperatures. We also observed evidence of first-order complexion transitions in some GBs.

Published
2023

7. Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis

Author

Tenney, Alan P, Di Gioia, Silvio Alessandro, Webb, Bryn D, Chan, Wai-Man, de Boer, Elke, Garnai, Sarah J, Barry, Brenda J, Ray, Tammy, Kosicki, Michael, Robson, Caroline D, Zhang, Zhongyang, Collins, Thomas E, Gelber, Alon, Pratt, Brandon M, Fujiwara, Yuko, Varshney, Arushi, Lek, Monkol, Warburton, Peter E, Van Ryzin, Carol, Lehky, Tanya J, Zalewski, Christopher, King, Kelly A, Brewer, Carmen C, Thurm, Audrey, Snow, Joseph, Facio, Flavia M, Narisu, Narisu, Bonnycastle, Lori L, Swift, Amy, Chines, Peter S, Bell, Jessica L, Mohan, Suresh, Whitman, Mary C, Staffieri, Sandra E, Elder, James E, Demer, Joseph L, Torres, Alcy, Rachid, Elza, Al-Haddad, Christiane, Boustany, Rose-Mary, Mackey, David A, Brady, Angela F, Fenollar-Cortés, María, Fradin, Melanie, Kleefstra, Tjitske, Padberg, George W, Raskin, Salmo, Sato, Mario Teruo, Orkin, Stuart H, Parker, Stephen CJ, Hadlock, Tessa A, Vissers, Lisenka ELM, van Bokhoven, Hans, Jabs, Ethylin Wang, Collins, Francis S, Pennacchio, Len A, Manoli, Irini, and Engle, Elizabeth C

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, Animals, Mice, Facial Paralysis, GATA2 Transcription Factor, Motor Neurons, Neurogenesis, Neurons, Efferent, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Hereditary congenital facial paresis type 1 (HCFP1) is an autosomal dominant disorder of absent or limited facial movement that maps to chromosome 3q21-q22 and is hypothesized to result from facial branchial motor neuron (FBMN) maldevelopment. In the present study, we report that HCFP1 results from heterozygous duplications within a neuron-specific GATA2 regulatory region that includes two enhancers and one silencer, and from noncoding single-nucleotide variants (SNVs) within the silencer. Some SNVs impair binding of NR2F1 to the silencer in vitro and in vivo and attenuate in vivo enhancer reporter expression in FBMNs. Gata2 and its effector Gata3 are essential for inner-ear efferent neuron (IEE) but not FBMN development. A humanized HCFP1 mouse model extends Gata2 expression, favors the formation of IEEs over FBMNs and is rescued by conditional loss of Gata3. These findings highlight the importance of temporal gene regulation in development and of noncoding variation in rare mendelian disease.

Published
2023

9. Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood

Author

Jakubek, Yasminka A., Ma, Xiaolong, Stilp, Adrienne M., Yu, Fulong, Bacon, Jason, Wong, Justin W., Aguet, Francois, Ardlie, Kristin, Arnett, Donna K., Barnes, Kathleen, Bis, Joshua C., Blackwell, Tom, Becker, Lewis C., Boerwinkle, Eric, Bowler, Russell P., Budoff, Matthew J., Carson, April P., Chen, Jiawen, Cho, Michael H., Coresh, Josef, Cox, Nancy J., de Vries, Paul S., DeMeo, Dawn L., Fardo, David W., Fornage, Myriam, Guo, Xiuqing, Hall, Michael E., Heard-Costa, Nancy, Hidalgo, Bertha, Irvin, Marguerite Ryan, Johnson, Andrew D., Jorgenson, Eric, Kenny, Eimear E., Kessler, Michael D., Levy, Daniel, Li, Yun, Lima, Joao A.C., Liu, Yongmei, Locke, Adam E., Loos, Ruth J.F., Machiela, Mitchell J., Mathias, Rasika A., Mitchell, Braxton D., Murabito, Joanne M., Mychaleckyj, Josyf C., North, Kari E., Orchard, Peter, Parker, Stephen C.J., Pershad, Yash, Peyser, Patricia A., Pratte, Katherine A., Psaty, Bruce M., Raffield, Laura M., Redline, Susan, Rich, Stephen S., Rotter, Jerome I., Shah, Sanjiv J., Smith, Jennifer A., Smith, Aaron P., Smith, Albert, Taub, Margaret A., Tiwari, Hemant K., Tracy, Russell, Tuftin, Bjoernar, Bick, Alexander G., Sankaran, Vijay G., Reiner, Alexander P., Scheet, Paul, and Auer, Paul L.

Published
2025
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10. FixItFelix: improving genomic analysis by fixing reference errors

Author

Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F, Farek, Jesse, Soto, Daniela C, Parker, Stephen CJ, Smith, Albert V, Dennis, Megan Y, Zook, Justin M, and Sedlazeck, Fritz J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Mental health, Humans, Genomics, Genome, Human, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Reference, GRCh38, T2T-CHM13, Variant, SNV, INDEL, Medically relevant genes, Remapping, GIAB, eQTL, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies.

Published
2023

13. Genetic risk converges on regulatory networks mediating early type 2 diabetes

Author

Walker, John T., Saunders, Diane C., Rai, Vivek, Chen, Hung-Hsin, Orchard, Peter, Dai, Chunhua, Pettway, Yasminye D., Hopkirk, Alexander L., Reihsmann, Conrad V., Tao, Yicheng, Fan, Simin, Shrestha, Shristi, Varshney, Arushi, Petty, Lauren E., Wright, Jordan J., Ventresca, Christa, Agarwala, Samir, Aramandla, Radhika, Poffenberger, Greg, Jenkins, Regina, Mei, Shaojun, Hart, Nathaniel J., Phillips, Sharon, Kang, Hakmook, Greiner, Dale L., Shultz, Leonard D., Bottino, Rita, Liu, Jie, Below, Jennifer E., Parker, Stephen C. J., Powers, Alvin C., and Brissova, Marcela

Published
2023
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16. Human vascularized macrophage-islet organoids to model immune-mediated pancreatic β cell pyroptosis upon viral infection

Author

Yang, Liuliu, Han, Yuling, Zhang, Tuo, Dong, Xue, Ge, Jian, Roy, Aadita, Zhu, Jiajun, Lu, Tiankun, Jeya Vandana, J., de Silva, Neranjan, Robertson, Catherine C., Xiang, Jenny Z., Pan, Chendong, Sun, Yanjie, Que, Jianwen, Evans, Todd, Liu, Chengyang, Wang, Wei, Naji, Ali, Parker, Stephen C.J., Schwartz, Robert E., and Chen, Shuibing

Published
2024
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20. Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program

Author

DiCorpo, Daniel, Gaynor, Sheila M, Russell, Emily M, Westerman, Kenneth E, Raffield, Laura M, Majarian, Timothy D, Wu, Peitao, Sarnowski, Chloé, Highland, Heather M, Jackson, Anne, Hasbani, Natalie R, de Vries, Paul S, Brody, Jennifer A, Hidalgo, Bertha, Guo, Xiuqing, Perry, James A, O’Connell, Jeffrey R, Lent, Samantha, Montasser, May E, Cade, Brian E, Jain, Deepti, Wang, Heming, D’Oliveira Albanus, Ricardo, Varshney, Arushi, Yanek, Lisa R, Lange, Leslie, Palmer, Nicholette D, Almeida, Marcio, Peralta, Juan M, Aslibekyan, Stella, Baldridge, Abigail S, Bertoni, Alain G, Bielak, Lawrence F, Chen, Chung-Shiuan, Chen, Yii-Der Ida, Choi, Won Jung, Goodarzi, Mark O, Floyd, James S, Irvin, Marguerite R, Kalyani, Rita R, Kelly, Tanika N, Lee, Seonwook, Liu, Ching-Ti, Loesch, Douglas, Manson, JoAnn E, Minster, Ryan L, Naseri, Take, Pankow, James S, Rasmussen-Torvik, Laura J, Reiner, Alexander P, Reupena, Muagututi’a Sefuiva, Selvin, Elizabeth, Smith, Jennifer A, Weeks, Daniel E, Xu, Huichun, Yao, Jie, Zhao, Wei, Parker, Stephen, Alonso, Alvaro, Arnett, Donna K, Blangero, John, Boerwinkle, Eric, Correa, Adolfo, Cupples, L Adrienne, Curran, Joanne E, Duggirala, Ravindranath, He, Jiang, Heckbert, Susan R, Kardia, Sharon LR, Kim, Ryan W, Kooperberg, Charles, Liu, Simin, Mathias, Rasika A, McGarvey, Stephen T, Mitchell, Braxton D, Morrison, Alanna C, Peyser, Patricia A, Psaty, Bruce M, Redline, Susan, Shuldiner, Alan R, Taylor, Kent D, Vasan, Ramachandran S, Viaud-Martinez, Karine A, Florez, Jose C, Wilson, James G, Sladek, Robert, Rich, Stephen S, Rotter, Jerome I, Lin, Xihong, Dupuis, Josée, Meigs, James B, Wessel, Jennifer, and Manning, Alisa K

Subjects
Biological Sciences, Genetics, Nutrition, Clinical Research, Human Genome, Precision Medicine, Biotechnology, Diabetes, Minority Health, 2.1 Biological and endogenous factors, Metabolic and endocrine, Good Health and Well Being, Diabetes Mellitus, Type 2, Fasting, Glucose, Humans, Insulin, National Heart, Lung, and Blood Institute (U.S.), Nerve Tissue Proteins, Polymorphism, Single Nucleotide, Receptors, Immunologic, United States, Biological sciences, Biomedical and clinical sciences
Abstract

The genetic determinants of fasting glucose (FG) and fasting insulin (FI) have been studied mostly through genome arrays, resulting in over 100 associated variants. We extended this work with high-coverage whole genome sequencing analyses from fifteen cohorts in NHLBI's Trans-Omics for Precision Medicine (TOPMed) program. Over 23,000 non-diabetic individuals from five race-ethnicities/populations (African, Asian, European, Hispanic and Samoan) were included. Eight variants were significantly associated with FG or FI across previously identified regions MTNR1B, G6PC2, GCK, GCKR and FOXA2. We additionally characterize suggestive associations with FG or FI near previously identified SLC30A8, TCF7L2, and ADCY5 regions as well as APOB, PTPRT, and ROBO1. Functional annotation resources including the Diabetes Epigenome Atlas were compiled for each signal (chromatin states, annotation principal components, and others) to elucidate variant-to-function hypotheses. We provide a catalog of nucleotide-resolution genomic variation spanning intergenic and intronic regions creating a foundation for future sequencing-based investigations of glycemic traits.

Published
2022

21. Exploring New Methodological Options: Collaborative Teaching Involving Song, Dance and the Alexander Technique

Author

Kvammen, Anne Cecilie Røsjø, Hagen, Johanne Karen, and Parker, Stephen

Abstract

In an attempt to bridge the gap between the distinct pedagogical strategies often employed in the respective fields of song and dance, this study investigates how collaborative teaching and dialogue can serve as a starting point in finding new teaching and learning methods. This pilot study involving three teacher-researchers and three students aims to show how the practical work of Alexander Technique (AT) applies the theory of embodied cognition and embodied learning in a practical context. Findings suggest that education and learning processes in the field of musical theatre need to have their foundation in the domain of embodied learning. We argue that the dichotomies between mind and body influence methodology and the way we use language; we propose AT as a method to guide collaborative teaching in order to discover how the student learns in an embodied way, implementing principles from AT in the teaching of musical theatre students.

Published
2020

25. Accuracy of hybrid functionals with non-self-consistent Kohn-Sham orbitals for predicting the properties of semiconductors

Author

Skelton, Jonathan M., Gunn, David S. D., Metz, Sebastian, and Parker, Stephen C.

Subjects
Condensed Matter - Materials Science
Abstract

Accurately modeling the electronic structure of materials is a persistent challenge to high-throughput screening. A promising means of balancing accuracy against computational cost are non-self-consistent calculations with hybrid density-functional theory, where the electronic band energies are evaluated using a hybrid functional from orbitals obtained with a less demanding (semi-)local functional. We have quantified the performance of this technique for predicting the physical properties of sixteen tetrahedral semiconductors with bandgaps from 0.2-5.5 eV. Provided the base functional predicts a non-metallic electronic structure, bandgaps within 5 % of the PBE0 and HSE06 gaps can be obtained with an order of magnitude reduction in computing time. The positions of the valence and conduction band extrema and the Fermi level are well reproduced, further enabling calculation of the band dispersion, density of states, and dielectric properties using Fermi's Golden Rule. While the error in the non-self-consistent total energies is ~50 meV atom-1, the energy-volume curves are reproduced accurately enough to obtain the equilibrium volume and bulk modulus with minimal error. We also test the dielectric-dependent scPBE0 functional and obtain bandgaps and dielectric constants to within 2.5 % of the self-consistent results, which amount to a significant improvement over self-consistent PBE0 for a similar computational cost. We identify cases where the non-self-consistent approach is expected to perform poorly, and demonstrate that partial self-consistency provides a practical and efficient workaround. Finally, we perform proof-of-concept calculations on CoO and NiO to demonstrate the applicability of the technique to strongly-correlated open-shell transition-metal oxides., Comment: Manuscript + Supporting Information

Published
2020

27. An immunomodulating peptide to counteract solar radiation-induced immunosuppression and DNA damage

Author

Agrez, Michael, Rybchyn, Mark Stephen, De Silva, Warusavithana Gunawardena Manori, Mason, Rebecca Sara, Chandler, Christopher, Piva, Terrence J., Thurecht, Kristofer, Fletcher, Nicholas, Liu, Feifei, Subramaniam, Gayathri, Howard, Christopher B., Blyth, Benjamin, Parker, Stephen, Turner, Darryl, Rzepecka, Justyna, Knox, Gavin, Nika, Anastasia, Hall, Andrew, Gooding, Hayley, and Gallagher, Laura

Published
2023
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42. The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits

Author

Abecasis, Gonçalo, Akolkar, Beena, Alexander, Benjamin R., Allred, Nicholette D., Altshuler, David, Below, Jennifer E., Bergman, Richard, Beulens, Joline W.J., Blangero, John, Boehnke, Michael, Bokvist, Krister, Bottinger, Erwin, Boughton, Andrew P., Bowden, Donald, Brosnan, M. Julia, Brown, Christopher, Bruskiewicz, Kenneth, Burtt, Noël P., Carmichael, Mary, Caulkins, Lizz, Cebola, Inês, Chambers, John, Ida Chen, Yii-Der, Cherkas, Andriy, Chu, Audrey Y., Clark, Christopher, Claussnitzer, Melina, Costanzo, Maria C., Cox, Nancy J., Hoed, Marcel den, Dong, Duc, Duby, Marc, Duggirala, Ravindranath, Dupuis, Josée, Elders, Petra J.M., Engreitz, Jesse M., Fauman, Eric, Ferrer, Jorge, Flannick, Jason, Flicek, Paul, Flickinger, Matthew, Florez, Jose C., Fox, Caroline S., Frayling, Timothy M., Frazer, Kelly A., Gaulton, Kyle J., Gilbert, Clint, Gloyn, Anna L., Green, Todd, Hanis, Craig L., Hanson, Robert, Hattersley, Andrew T., Hoang, Quy, Im, Hae Kyung, Iqbal, Sidra, Jacobs, Suzanne B.R., Jang, Dong-Keun, Jordan, Tad, Kamphaus, Tania, Karpe, Fredrik, Keane, Thomas M., Kim, Seung K., Kluge, Alexandria, Koesterer, Ryan, Kudtarkar, Parul, Lage, Kasper, Lange, Leslie A., Lazar, Mitchell, Lehman, Donna, Liu, Ching-Ti, Loos, Ruth J.F., Ma, Ronald Ching-wan, MacDonald, Patrick, Massung, Jeffrey, Maurano, Matthew T., McCarthy, Mark I., McVean, Gil, Meigs, James B., Mercader, Josep M., Miller, Melissa R., Mitchell, Braxton, Mohlke, Karen L., Morabito, Samuel, Morgan, Claire, Mullican, Shannon, Narendra, Sharvari, Ng, Maggie C.Y., Nguyen, Lynette, Palmer, Colin N.A., Parker, Stephen C.J., Parrado, Antonio, Parsa, Afshin, Pawlyk, Aaron C., Pearson, Ewan R., Plump, Andrew, Province, Michael, Quertermous, Thomas, Redline, Susan, Reilly, Dermot F., Ren, Bing, Rich, Stephen S., Richards, J. Brent, Rotter, Jerome I., Ruebenacker, Oliver, Ruetten, Hartmut, Salem, Rany M., Sander, Maike, Sanders, Michael, Sanghera, Dharambir, Scott, Laura J., Sengupta, Sebanti, Siedzik, David, Sim, Xueling, Singh, Preeti, Sladek, Robert, Small, Kerrin, Smith, Philip, Stein, Peter, Spalding, Dylan, Stringham, Heather M., Sun, Ying, Susztak, Katalin, ’t Hart, Leen M., Taliun, Daniel, Taylor, Kent, Thomas, Melissa K., Todd, Jennifer A., Udler, Miriam S., Voight, Benjamin, von Grotthuss, Marcin, Wan, Andre, Welch, Ryan P., Wholley, David, Yuksel, Kaan, Zaghloul, Norann A., Jang, Dongkeun, Moriondo, Annie, Nguyen, Trang, Smadbeck, Patrick, Brandes, MacKenzie, Dornbos, Peter, Huellas-Bruskiewicz, Kenneth C., Ji, Yue, McMahon, Aoife C., Fauman, Eric B., Kamphaus, Tania Nayak, and Abecasis, Gonçalo R.

Published
2023
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43. An introduction to classical molecular dynamics simulation for experimental scattering users

Author

McCluskey, Andrew R., Grant, James, Symington, Adam R., Snow, Tim, Doutch, James, Morgan, Benjamin J., Parker, Stephen C., and Edler, Karen J.

Subjects
Condensed Matter - Statistical Mechanics
Abstract

Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a "black box" analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data., Comment: Electronic Supplementary Information (ESI) available: All analysis/plotting scripts and figure files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at \url{https://github.com/arm61/sim_and_scat_paper} (DOI: 10.5281/zenodo.2556826) under a CC BY-SA 4.0 license

Published
2019
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44. Assessing molecular simulation for the analysis of lipid monolayer reflectometry

Author

McCluskey, Andrew R., Grant, James, Smith, Andrew J., Rawle, Jonathan L., Barlow, David J., Lawrence, M. Jayne, Parker, Stephen C., and Edler, Karen J.

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This work presents the first direct comparison between the reflectometry profiles obtained from different all-atom and coarse-grained molecular dynamics simulations. These are compared with a traditional model layer structure analysis method to determine the minimum simulation resolution required to accurately reproduce experimental data. We find that systematic limits reduce the efficacy of the MARTINI potential model, while the Berger united-atom and Slipids all-atom potential models agree similarly well with the experimental data. The model layer structure gives the best agreement, however, the higher resolution simulation-dependent methods produce an agreement that is comparable. Finally, we use the atomistic simulation to advise on possible improvements that may be offered to the model layer structures, creating a more realistic monolayer model., Comment: Electronic Supplementary Information (ESI) available: All analysis/plotting scripts and figure files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at \url{https://github.com/arm61/sim_vs_trad} (DOI: 10.5281/zenodo.2600729) under a CC BY-SA 4.0 license

Published
2019
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45. Loci for insulin processing and secretion provide insight into type 2 diabetes risk

Author

Broadaway, K. Alaine, Yin, Xianyong, Williamson, Alice, Parsons, Victoria A., Wilson, Emma P., Moxley, Anne H., Vadlamudi, Swarooparani, Varshney, Arushi, Jackson, Anne U., Ahuja, Vasudha, Bornstein, Stefan R., Corbin, Laura J., Delgado, Graciela E., Dwivedi, Om P., Fernandes Silva, Lilian, Frayling, Timothy M., Grallert, Harald, Gustafsson, Stefan, Hakaste, Liisa, Hammar, Ulf, Herder, Christian, Herrmann, Sandra, Højlund, Kurt, Hughes, David A., Kleber, Marcus E., Lindgren, Cecilia M., Liu, Ching-Ti, Luan, Jian’an, Malmberg, Anni, Moissl, Angela P., Morris, Andrew P., Perakakis, Nikolaos, Peters, Annette, Petrie, John R., Roden, Michael, Schwarz, Peter E.H., Sharma, Sapna, Silveira, Angela, Strawbridge, Rona J., Tuomi, Tiinamaija, Wood, Andrew R., Wu, Peitao, Zethelius, Björn, Baldassarre, Damiano, Eriksson, Johan G., Fall, Tove, Florez, Jose C., Fritsche, Andreas, Gigante, Bruna, Hamsten, Anders, Kajantie, Eero, Laakso, Markku, Lahti, Jari, Lawlor, Deborah A., Lind, Lars, März, Winfried, Meigs, James B., Sundström, Johan, Timpson, Nicholas J., Wagner, Robert, Walker, Mark, Wareham, Nicholas J., Watkins, Hugh, Barroso, Inês, O’Rahilly, Stephen, Grarup, Niels, Parker, Stephen CJ., Boehnke, Michael, Langenberg, Claudia, Wheeler, Eleanor, and Mohlke, Karen L.

Published
2023
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46. Bayesian determination of the effect of a deep eutectic solvent on the structure of lipid monolayers

Author

McCluskey, Andrew R., Sanchez-Fernandez, Adrian, Edler, Karen J., Parker, Stephen C., Jackson, Andrew J., Campbell, Richard A., and Arnold, Tom

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

In this work, we present the first example of the self-assembly of phospholipid monolayers at the interface between air and an ionic solvent. Deep eutectic solvents are a novel class of environmentally friendly non-aqueous room temperature liquids with tunable properties, that have wide ranging potential applications and are capable of promoting the self-assembly of surfactant molecules. We use a chemically-consistent Bayesian modelling of X-ray and neutron reflectometry measurements to show that these monolayers broadly behave as they do on water. This method allows for the monolayer structure to be determined, alongside the molecular volumes of the individual monolayer components without the need for water-specific constraints to be introduced. Furthermore, using this method we are able to better understand the correlations present between parameters in the analytical model. This example of a non-aqueous phospholipid monolayer has important implications for the potential uses of these solvents and for our understanding of how biomolecules behave in the absence of water., Comment: Electronic Supplementary Information (ESI) available: All analysis/plotting scripts and figures files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at https://github.com/arm61/lipids_at_airdes (DOI: 10.5281/zenodo.2577796) under a CC-BY-SA 4.0 license

Published
2018
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47. Particle Morphology and Lithium Segregation to Surfaces of the Li$_7$La$_3$Zr$_2$O$_{12}$ Solid Electrolyte

Author

Canepa, Pieremanuele, Dawson, James A., Gautam, Gopalakrishnan Sai, Statham, Joel M., Parker, Stephen C., and Islam, M. Saiful

Subjects
Condensed Matter - Materials Science
Abstract

Solid electrolytes for solid-state Li-ion batteries are stimulating considerable interest for next-generation energy storage applications. The Li$_7$La$_3$Zr$_2$O$_{12}$ garnet-type solid electrolyte has received appreciable attention as a result of its high ionic conductivity. However, several challenges for the successful application of solid-state devices based on Li$_7$La$_3$Zr$_2$O$_{12}$ remain, such as dendrite formation and maintaining physical contact at interfaces over many Li intercalation/extraction cycles. Here, we apply first-principles density functional theory to provide insights into the Li$_7$La$_3$Zr$_2$O$_{12}$ particle morphology under various physical and chemical conditions. Our findings indicate Li segregation at the surfaces, suggesting Li-rich grain boundaries at typical synthesis and sintering conditions. On the basis of our results, we propose practical strategies to curb Li segregation at the Li$_7$La$_3$Zr$_2$O$_{12}$ interfaces. This approach can be extended to other Li-ion conductors for the design of practical energy storage devices.

Published
2018
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48. DL_MONTE: A multipurpose code for Monte Carlo simulation

Author

Brukhno, Andrey V., Grant, James, Underwood, Tom L., Stratford, Kevin, Parker, Stephen C., Purton, John A., and Wilding, Nigel B.

Subjects
Physics - Computational Physics
Abstract

DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation. Here we provide an overview of DL_MONTE, focusing on key features recently added to the package. These include the ability to treat systems confined to a planar pore (i.e. `slit' or `slab' boundary conditions); the lattice-switch Monte Carlo (LSMC) method for evaluating precise free energy differences between competing polymorphs; various commonly-used methods for evaluating free energy profiles along transition pathways (including umbrella sampling, Wang-Landau and transition matrix); and a supplementary Python toolkit for simulation management and application of the histogram reweighting analysis method. We provide two `real world' examples to elucidate the use of these methods in DL_MONTE. In particular, we apply umbrella sampling to calculate the free energy profile associated with the translocation of a lipid through a bilayer. Moreover we employ LSMC to examine the thermodynamic stability of two plastic crystal phases of water at high pressure. Beyond this, we provide instructions on how to access DL_MONTE, and point to additional information valuable to existing and prospective users.

Published
2018

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