Search Results - "Schreck, John"

Understanding DNA interactions in crowded environments with a coarse-grained model by Hong, Fan, Schreck, John S, Šulc, Petr

“…Abstract Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and…”
Get full text

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection by Di Gioacchino, Andrea, Procyk, Jonah, Molari, Marco, Schreck, John S, Zhou, Yu, Liu, Yan, Monasson, Rémi, Cocco, Simona, Sulc, Petr

“…Selection protocols such as SELEX, where molecules are selected over multiple rounds for their ability to bind to a target of interest, are popular methods for…”
Get full text

Mimicking non-ideal instrument behavior for hologram processing using neural style translation by Schreck, John S, Hayman, Matthew, Gantos, Gabrielle, Bansemer, Aaron, Gagne, David John

“…Holographic cloud probes provide unprecedented information on cloud particle density, size and position. Each laser shot captures particles within a large…”
Get full text

Investigating the Effects of Molecular Crowding on the Kinetics of Protein Aggregation by Schreck, John S, Bridstrup, John, Yuan, Jian-Min

“…The thermodynamics and kinetics of protein folding and protein aggregation in vivo are of great importance in numerous scientific areas including fundamental…”
Get full text

Learning Retrosynthetic Planning through Simulated Experience by Schreck, John S, Coley, Connor W, Bishop, Kyle J. M

“…The problem of retrosynthetic planning can be framed as a one-player game, in which the chemist (or a computer program) works backward from a molecular target…”
Get full text

Coarse-grained modelling of the structural properties of DNA origami by Snodin, Benedict E K, Schreck, John S, Romano, Flavio, Louis, Ard A, Doye, Jonathan P K

“…Abstract We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on…”
Get full text

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA by Snodin, Benedict E K, Randisi, Ferdinando, Mosayebi, Majid, Šulc, Petr, Schreck, John S, Romano, Flavio, Ouldridge, Thomas E, Tsukanov, Roman, Nir, Eyal, Louis, Ard A, Doye, Jonathan P K

“…We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and…”
Get more information

A Kinetic Study of Amyloid Formation: Fibril Growth and Length Distributions by Schreck, John S., Yuan, Jian-Min

“…We propose a kinetic model for the self-aggregation by amyloid proteins. By extending several well-known models for protein aggregation, the time evolution of…”
Get full text

Stochastic Kinetic Treatment of Protein Aggregation and the Effects of Macromolecular Crowding by Bridstrup, John, Schreck, John S, Jorgenson, Jesse L, Yuan, Jian-Min

“…Investigation of protein self-assembly processes is important for understanding the growth processes of functional proteins as well as disease-causing…”
Get full text

Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model by Sharma, Rahul, Schreck, John S, Romano, Flavio, Louis, Ard A, Doye, Jonathan P. K

“…As detailed structural characterizations of large complex DNA nanostructures are hard to obtain experimentally, particularly if they have substantial…”
Get full text

Characterizing the free-energy landscapes of DNA origamis by Wong, Chak Kui, Tang, Chuyan, Schreck, John S, Doye, Jonathan P K

“…We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes…”
Get more information

Neural Network Emulation of the Formation of Organic Aerosols Based on the Explicit GECKO‐A Chemistry Model by Schreck, John S., Becker, Charles, Gagne, David John, Lawrence, Keely, Wang, Siyuan, Mouchel‐Vallon, Camille, Choi, Jinkyul, Hodzic, Alma

“…Secondary organic aerosols (SOA) are formed from oxidation of hundreds of volatile organic compounds (VOCs) emitted from anthropogenic and natural sources…”
Get full text

Coarse-graining DNA for simulations of DNA nanotechnology by Doye, Jonathan P K, Ouldridge, Thomas E, Louis, Ard A, Romano, Flavio, Šulc, Petr, Matek, Christian, Snodin, Benedict E K, Rovigatti, Lorenzo, Schreck, John S, Harrison, Ryan M, Smith, William P J

“…To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different…”
Get more information

Design principles for rapid folding of knotted DNA nanostructures by Kočar, Vid, Schreck, John S., Čeru, Slavko, Gradišar, Helena, Bašić, Nino, Pisanski, Tomaž, Doye, Jonathan P. K., Jerala, Roman

“…Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is…”
Get full text

DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size by Khara, Dinesh C, Schreck, John S, Tomov, Toma E, Berger, Yaron, Ouldridge, Thomas E, Doye, Jonathan P K, Nir, Eyal

“…Abstract We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal…”
Get full text

Stochastic kinetic study of protein aggregation and molecular crowding effects of Aβ40 and Aβ42 by Bridstrup, John, Yuan, Jian‐Min, Schreck, John S.

“…Two isoforms of β‐amyloid peptides, Aβ40 and Aβ42, differ from each other only in the last two amino acids, IA, at the end of Aβ42. They, however, differ…”
Get full text

Machine Learning and VIIRS Satellite Retrievals for Skillful Fuel Moisture Content Monitoring in Wildfire Management by Schreck, John S., Petzke, William, Jiménez, Pedro A., Brummet, Thomas, Knievel, Jason C., James, Eric, Kosović, Branko, Gagne, David John

“…Monitoring the fuel moisture content (FMC) of 10 h dead vegetation is crucial for managing and mitigating the impact of wildland fires. The combination of in…”
Get full text

Neural network processing of holographic images by Schreck, John S, Gantos, Gabrielle, Hayman, Matthew, Bansemer, Aaron, Gagne, David John

“…HOLODEC, an airborne cloud particle imager, captures holographic images of a fixed volume of cloud to characterize the types and sizes of cloud particles, such…”
Get full text

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly by Fonseca, Pedro, Romano, Flavio, Schreck, John S, Ouldridge, Thomas E, Doye, Jonathan P K, Louis, Ard A

“…Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed…”
Get more information

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization by Schreck, John S, Ouldridge, Thomas E, Romano, Flavio, Šulc, Petr, Shaw, Liam P, Louis, Ard A, Doye, Jonathan P K

“…The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how…”
Get full text