John S. Schreck

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All published works

Action	Title	Year	Authors
+ PDF Chat	Improving AI weather prediction models using global mass and energy conservation schemes	2025	Yingkai Sha John S. Schreck William E. Chapman David John Gagne
+ PDF Chat	Community Research Earth Digital Intelligence Twin (CREDIT)	2024	John S. Schreck Yingkai Sha William E. Chapman Dhamma Kimpara Judith Berner Seth McGinnis Arnold Kazadi Nasim Sobhani Ben Kirk David John Gagne
+ PDF Chat	Evidential Deep Learning: Enhancing Predictive Uncertainty Estimation for Earth System Science Applications	2024	John S. Schreck David John Gagne Charles Becker William E. Chapman Kim Elmore Da Fan Gabrielle Gantos Eliot Kim Dhamma Kimpara Thomas P. Martin
+ PDF Chat	Machine Learning and VIIRS Satellite Retrievals for Skillful Fuel Moisture Content Monitoring in Wildfire Management	2023	John S. Schreck William Petzke Pedro A. Jiménez Thomas Brummet Jason C. Knievel Eric P. James Branko Kosović David John Gagne
+	Mimicking non-ideal instrument behavior for hologram processing using neural style translation	2023	John S. Schreck Matthew Hayman Gabrielle Gantos Aaron Bansemer David John Gagne
+ PDF Chat	The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami	2023	Jonathan P. K. Doye Hannah Fowler Domen Prešern Joakim Bohlin Lorenzo Rovigatti Flavio Romano Petr Šulc Chak Kui Wong Ard A. Louis John S. Schreck
+	Mimicking non-ideal instrument behavior for hologram processing using neural style translation	2023	John S. Schreck Matthew Hayman Gabrielle Gantos Aaron Bansemer David John Gagne
+	Machine Learning and VIIRS Satellite Retrievals for Skillful Fuel Moisture Content Monitoring in Wildfire Management	2023	John S. Schreck William Petzke Pedro A. Jiménez Thomas Brummet Jason C. Knievel Eric James Branko Kosović David John Gagne
+	Evidential Deep Learning: Enhancing Predictive Uncertainty Estimation for Earth System Science Applications	2023	John S. Schreck David John Gagne Charles Becker William E. Chapman Kim Elmore Gabrielle Gantos Eliot Kim Dhamma Kimpara Thomas P. Martin María J. Molina
+ PDF Chat	Neural network processing of holographic images	2022	John S. Schreck Gabrielle Gantos Matthew Hayman Aaron Bansemer David John Gagne
+ PDF Chat	Stochastic kinetic study of protein aggregation and molecular crowding effects of <i>Aβ40</i> and <i>Aβ42</i>	2022	John Bridstrup Jian‐Min Yuan John S. Schreck
+	Neural network processing of holographic images	2022	John S. Schreck Gabrielle Gantos Matthew Hayman Aaron Bensemer David John Gagne
+ PDF Chat	Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling	2022	Jonathan P. K. Doye Ard A. Louis John S. Schreck Flavio Romano Ryan M. Harrison Majid Mosayebi Megan C. Engel Thomas E. Ouldridge
+ PDF Chat	Characterizing the free-energy landscapes of DNA origamis	2022	Chak Kui Wong Chuyan Tang John S. Schreck Jonathan P. K. Doye
+	Neural network processing of holographic images	2022	John S. Schreck Gabrielle Gantos Matthew Hayman Aaron Bansemer David John Gagne
+	Stochastic Kinetic Study of Protein Aggregation and Molecular Crowding Effects of Ab40 and Ab42	2022	John Bridstrup Jian‐Min Yuan John S. Schreck
+ PDF Chat	Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling	2021	Jonathan P. K. Doye Ard A. Louis John S. Schreck Flavio Romano Ryan M. Harrison Majid Mosayebi Megan C. Engel Thomas E. Ouldridge
+	Characterizing the free-energy landscapes of DNA origamis	2021	Chak Kui Wong Chuyan Tang John S. Schreck Jonathan P. K. Doye
+ PDF Chat	Stochastic Kinetic Treatment of Protein Aggregation and the Effects of Macromolecular Crowding	2021	John Bridstrup John S. Schreck Jesse L. Jorgenson Jian‐Min Yuan
+	Stochastic kinetic treatment of protein aggregation and the effects of macromolecular crowding	2021	John Bridstrup John S. Schreck Jesse L. Jorgenson Jian‐Min Yuan
+	The oxDNA coarse-grained model as a tool to simulate DNA origami	2020	Jonathan P. K. Doye Hannah Fowler Domen Prešern Joakim Bohlin Lorenzo Rovigatti Flavio Romano Petr Šulc Chak Kui Wong Ard A. Louis John S. Schreck
+	Learning retrosynthetic planning through self-play	2019	John S. Schreck Connor W. Coley Kyle J. M. Bishop
+	Learning retrosynthetic planning through self-play	2019	John S. Schreck Connor W. Coley Kyle J. M. Bishop
+ PDF Chat	Coarse-grained modelling of the structural properties of DNA origami	2018	Benedict Snodin John S. Schreck Flavio Romano Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly	2018	Pedro Fonseca Flavio Romano John S. Schreck Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis
+ PDF Chat	Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal	2016	Aleks Reinhardt John S. Schreck Flavio Romano Jonathan P. K. Doye
+ PDF Chat	Introducing improved structural properties and salt dependence into a coarse-grained model of DNA	2015	Benedict Snodin Ferdinando Randisi Majid Mosayebi Petr Šulc John S. Schreck Flavio Romano Thomas E. Ouldridge Roman Tsukanov Eyal Nir Ard A. Louis
+ PDF Chat	DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Petr Šulc Liam P. Shaw Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	Characterizing the bending and flexibility induced by bulges in DNA duplexes	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	Statistical Mechanical Treatments of Protein Amyloid Formation	2013	John S. Schreck Jian‐Min Yuan
+ PDF Chat	A Kinetic Study of Amyloid Formation: Fibril Growth and Length Distributions	2013	John S. Schreck Jian‐Min Yuan
+ PDF Chat	Coarse-graining DNA for simulations of DNA nanotechnology	2013	Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis Flavio Romano Petr Šulc Christian Matek Benedict Snodin Lorenzo Rovigatti John S. Schreck Ryan M. Harrison
+ PDF Chat	A Statistical Mechanical Approach to Protein Aggregation	2012	John S. Schreck Jian‐Min Yuan
+ PDF Chat	A statistical mechanical approach to protein aggregation	2011	John S. Schreck Jian‐Min Yuan
+ PDF Chat	Exactly solvable model for helix-coil-sheet transitions in protein systems	2010	John S. Schreck Jian‐Min Yuan

Common Coauthors

Coauthor	Papers Together
Jonathan P. K. Doye	13
David John Gagne	11
Flavio Romano	11
Ard A. Louis	10
Jian‐Min Yuan	8
Thomas E. Ouldridge	7
Petr Šulc	5
Matthew Hayman	5
Benedict Snodin	5
Gabrielle Gantos	4
Aaron Bansemer	4
Megan C. Engel	4
John Bridstrup	4
William E. Chapman	4
Chak Kui Wong	4
Ryan M. Harrison	3
Gabrielle Gantos	3
Dhamma Kimpara	3
Lorenzo Rovigatti	3
Majid Mosayebi	3
Jesse L. Jorgenson	2
Kim Elmore	2
Kyle J. M. Bishop	2
Pedro A. Jiménez	2
Charles Becker	2
Connor W. Coley	2
Belén Saavedra	2
Thomas P. Martin	2
Justin Willson	2
Branko Kosović	2
Domen Prešern	2
Chuyan Tang	2
Thomas Brummet	2
Jacob Radford	2
Yingkai Sha	2
Erik Poppleton	2
Erik Benson	2
Christopher D. Wirz	2
Joakim Bohlin	2
William Petzke	2
Eliot Kim	2
Jason C. Knievel	2
María J. Molina	2
Michael Matthies	2
Ben Kirk	1
Eyal Nir	1
Ferdinando Randisi	1
Hannah Fowler	1
Pedro Fonseca	1
Nasim Sobhani	1

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+ PDF Chat	Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model	2011	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	10
+ PDF Chat	DNA Nanotweezers Studied with a Coarse-Grained Model of DNA	2010	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	8
+ PDF Chat	Coarse-grained simulations of DNA overstretching	2013	Flavio Romano Debayan Chakraborty Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis	8
+ PDF Chat	Introducing improved structural properties and salt dependence into a coarse-grained model of DNA	2015	Benedict Snodin Ferdinando Randisi Majid Mosayebi Petr Šulc John S. Schreck Flavio Romano Thomas E. Ouldridge Roman Tsukanov Eyal Nir Ard A. Louis	7
+ PDF Chat	DNA hybridization kinetics: zippering, internal displacement and sequence dependence	2013	Thomas E. Ouldridge Petr Šulc Flavio Romano Jonathan P. K. Doye Ard A. Louis	7
+ PDF Chat	Sequence-dependent thermodynamics of a coarse-grained DNA model	2012	Petr Šulc Flavio Romano Thomas E. Ouldridge Lorenzo Rovigatti Jonathan P. K. Doye Ard A. Louis	7
+ PDF Chat	Coarse-graining DNA for simulations of DNA nanotechnology	2013	Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis Flavio Romano Petr Šulc Christian Matek Benedict Snodin Lorenzo Rovigatti John S. Schreck Ryan M. Harrison	7
+ PDF Chat	Simulating a burnt-bridges DNA motor with a coarse-grained DNA model	2013	Petr Šulc Thomas E. Ouldridge Flavio Romano Jonathan P. K. Doye Ard A. Louis	5
+ PDF Chat	The role of collective motion in examples of coarsening and self-assembly	2008	Stephen Whitelam Edward H. Feng Michael F. Hagan Phillip L. Geissler	5
+ PDF Chat	A comparison between parallelization approaches in molecular dynamics simulations on GPUs	2014	Lorenzo Rovigatti Petr Šulc István Z. Reguly Flavio Romano	5
+ PDF Chat	Coarse-grained modelling of the structural properties of DNA origami	2018	Benedict Snodin John S. Schreck Flavio Romano Ard A. Louis Jonathan P. K. Doye	4
+ PDF Chat	The effect of topology on the structure and free energy landscape of DNA kissing complexes	2012	Flavio Romano Alexander Hudson Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis	4
+	Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"	2015	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	4
+	Exact stochastic simulation of coupled chemical reactions	1977	Daniel T. Gillespie	4
+ PDF Chat	The Role of Loop Stacking in the Dynamics of DNA Hairpin Formation	2014	Majid Mosayebi Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	3
+ PDF Chat	A Kinetic Study of Amyloid Formation: Fibril Growth and Length Distributions	2013	John S. Schreck Jian‐Min Yuan	3
+ PDF Chat	Self-assembly of protein amyloids: A competition between amorphous and ordered aggregation	2009	Chiu Fan Lee	3
+ PDF Chat	What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils?	2011	Jeremy D. Schmit Kingshuk Ghosh Ken A. Dill	3
+ PDF Chat	Molecular engineering of chiral colloidal liquid crystals using DNA origami	2017	Mahsa Siavashpouri Christian Wachauf Mark J. Zakhary Florian Praetorius Hendrik Dietz Zvonimir Dogic	3
+ PDF Chat	Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors	2015	Majid Mosayebi Ard A. Louis Jonathan P. K. Doye Thomas E. Ouldridge	3
+ PDF Chat	Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model	2019	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	3
+ PDF Chat	Characterizing the bending and flexibility induced by bulges in DNA duplexes	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Ard A. Louis Jonathan P. K. Doye	3
+ PDF Chat	DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Petr Šulc Liam P. Shaw Ard A. Louis Jonathan P. K. Doye	3
+ PDF Chat	A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality	2010	Alex Morriss-Andrews Jörg Rottler Steven S. Plotkin	3
+	Fully Convolutional Networks for Semantic Segmentation	2016	Evan Shelhamer Jonathan Long Trevor Darrell	3
+ PDF Chat	Extracting bulk properties of self-assembling systems from small simulations	2010	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	3
+ PDF Chat	DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism	2012	Christian Matek Thomas E. Ouldridge Adam Levy Jonathan P. K. Doye Ard A. Louis	3
+ PDF Chat	Forward flux sampling for rare event simulations	2009	Rosalind J. Allen Chantal Valeriani Pieter Rein ten Wolde	3
+ PDF Chat	Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly	2018	Pedro Fonseca Flavio Romano John S. Schreck Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis	2
+ PDF Chat	A statistical mechanical approach to protein aggregation	2011	John S. Schreck Jian‐Min Yuan	2
+ PDF Chat	Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles	2007	Stephen Whitelam Phillip L. Geissler	2
+ PDF Chat	Monodisperse self-assembly in a model with protein-like interactions	2009	Alex W. Wilber Jonathan P. K. Doye Ard A. Louis Anna Lewis	2
+ PDF Chat	Exactly solvable model for helix-coil-sheet transitions in protein systems	2010	John S. Schreck Jian‐Min Yuan	2
+ PDF Chat	DNA brick self-assembly with an off-lattice potential	2016	Aleks Reinhardt Daan Frenkel	2
+ PDF Chat	A nucleotide-level coarse-grained model of RNA	2014	Petr Šulc Flavio Romano Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis	2
+ PDF Chat	Stochastic lag time in nucleated linear self-assembly	2016	Nitin Tiwari Paul van der Schoot	2
+ PDF Chat	LinkNet: Exploiting encoder representations for efficient semantic segmentation	2017	Abhishek Chaurasia Eugenio Culurciello	2
+ PDF Chat	Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures	2020	Hemani Chhabra Garima Mishra Yijing Cao Domen Prešern Enrico Skoruppa Maxime M. C. Tortora Jonathan P. K. Doye	2
+ PDF Chat	Tversky Loss Function for Image Segmentation Using 3D Fully Convolutional Deep Networks	2017	Seyed Sadegh Mohseni Salehi Deniz Erdoğmuş Ali Gholipour	2
+ PDF Chat	Equilibrium mechanisms of self-limiting assembly	2021	Michael F. Hagan Gregory M. Grason	2
+ PDF Chat	You Only Look Once: Unified, Real-Time Object Detection	2016	Joseph Redmon Santosh Divvala Ross Girshick Ali Farhadi	2
+ PDF Chat	Pyramid Scene Parsing Network	2017	Hengshuang Zhao Jianping Shi Xiaojuan Qi Xiaogang Wang Jiaya Jia	2
+ PDF Chat	DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response	2012	Anton Kuzyk Robert Schreiber Zhiyuan Fan Günther Pardatscher Eva-Maria Roller Alexander Högele Friedrich C. Simmel Alexander O. Govorov Tim Liedl	2
+ PDF Chat	Densely Connected Convolutional Networks	2017	Gao Huang Zhuang Liu Laurens van der Maaten Kilian Q. Weinberger	2
+ PDF Chat	Coarse-Grained Simulations of RNA and DNA Duplexes	2013	Tristan Cragnolini Philippe Derreumaux Samuela Pasquali	2
+ PDF Chat	Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation	2018	Liang-Chieh Chen Yukun Zhu George Papandreou Florian Schroff Hartwig Adam	2
+ PDF Chat	Deep Residual Learning for Image Recognition	2016	Kaiming He Xiangyu Zhang Shaoqing Ren Jian Sun	2
+ PDF Chat	Simplified Exactly Solvable Model for<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>β</mml:mi></mml:math>-Amyloid Aggregation	2010	Marco Zamparo Antonio Trovato Amos Maritan	2
+ PDF Chat	Inherent Variability in the Kinetics of Autocatalytic Protein Self-Assembly	2014	Juraj Szavits-Nossan Kym Eden Ryan J. Morris Cait E. MacPhee M. R. Evans Rosalind J. Allen	2
+ PDF Chat	Modeling DNA structure, elasticity, and deformations at the base-pair level	2003	Boris Mergell Mohammad Reza Ejtehadi Ralf Everaers	2