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Author Details

Aaron R Dinner
James Franck Institute, Institute for Biophysical Dynamics, University of Chicago
1996
149
44
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36754798Simulating structured fluids with tensorial viscoelasticity.J Chem Phys2023
37693184Motor crosslinking augments elasticity in active nematics.ArXiv2023
37409704Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction.J Chem Phys2023
37307463A unified model for the dynamics of ATP-independent ultrafast contraction.Proc Natl Acad Sci U S A2023
37332834Predicting rare events using neural networks and short-trajectory data.J Comput Phys2023
37259996Understanding the sources of error in MBAR through asymptotic analysis.J Chem Phys2023
36711760Dietary Restriction Impacts Peripheral Circadian Clock Output Important for Longevity in <i>Drosophila</i>.bioRxiv2023
36824805Pervasive, conserved secondary structure in highly charged protein regions.bioRxiv2023
36067319KidA, a multi-PAS domain protein, tunes the period of the cyanobacterial circadian oscillator.Proc Natl Acad Sci U S A2022
36075728Augmented transition path theory for sequences of events.J Chem Phys2022
36179154Thermodynamic Control of Activity Patterns in Cytoskeletal Networks.Phys Rev Lett2022
35868925Computing transition path theory quantities with trajectory stratification.J Chem Phys2022
34355137Error Bounds for Dynamical Spectral Estimation.SIAM J Math Data Sci2021
33603187Spatiotemporal control of liquid crystal structure and dynamics through activity patterning.Nat Mater2021
33908762Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein.J Chem Theory Comput2021
34648712Kinetics of Phenol Escape from the Insulin R<sub>6</sub> Hexamer.J Phys Chem B2021
34584211Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture.Commun Biol2021
34637307Structural Ensemble of the Insulin Monomer.Biochemistry2021
34518221A strong nonequilibrium bound for sorting of cross-linkers on growing biopolymers.Proc Natl Acad Sci U S A2021
34592145Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators.Cell Rep2021
33989373Actin filament alignment causes mechanical hysteresis in cross-linked networks.Soft Matter2021
32559068Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.J Chem Theory Comput2020
34611500Stratification as a general variance reduction method for Markov chain Monte Carlo.SIAM/ASA J Uncertain Quantif2020
32016200Tuning molecular motor transport through cytoskeletal filament network organization.Soft Matter2020
32762843Transient intracellular acidification regulates the core transcriptional heat shock response.Elife2020
32955887Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators.J Phys Chem B2020
32110728Structured silicon for revealing transient and integrated signal transductions in microbial systems.Sci Adv2020
32496641Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock.Mol Syst Biol2020
32515958Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding.J Phys Chem B2020
30904132Transcription factories in Igκ allelic choice and diversity.Adv Immunol2019
31346091Mechanical and kinetic factors drive sorting of F-actin cross-linkers on bundles.Proc Natl Acad Sci U S A2019
31255053Galerkin approximation of dynamical quantities using trajectory data.J Chem Phys2019
30739797Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease.Cell2019
30943415Circadian Clocks Function in Concert with Heat Shock Organizing Protein to Modulate Mutant Huntingtin Aggregation and Toxicity.Cell Rep2019
29535190Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification.Genes Dev2018
34650314Trajectory stratification of stochastic dynamics.SIAM Rev Soc Ind Appl Math2018
30157436Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories.Cell Rep2018
30101659Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data.J Biol Rhythms2018
30204203Nonequilibrium phase diagrams for actomyosin networks.Soft Matter2018
30553248Entropic constraints on the steady-state fitness of competing self-replicators.J Chem Phys2018
30449672Geographically Resolved Rhythms in Twitter Use Reveal Social Pressures on Daily Activity Patterns.Curr Biol2018
30442665Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights.Proc Natl Acad Sci U S A2018
28028226Single-pixel interior filling function approach for detecting and correcting errors in particle tracking.Proc Natl Acad Sci U S A2017
29114058Filament rigidity and connectivity tune the deformation modes of active biopolymer networks.Proc Natl Acad Sci U S A2017
28594651miR-4728-3p Functions as a Tumor Suppressor in Ulcerative Colitis-associated Colorectal Neoplasia Through Regulation of Focal Adhesion Signaling.Inflamm Bowel Dis2017
28802256Stochastic feeding dynamics arise from the need for information and energy.Proc Natl Acad Sci U S A2017
28746855A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks.Biophys J2017
28737755Biphasic growth dynamics control cell division in Caulobacter crescentus.Nat Microbiol2017
28686160The cyanobacterial circadian clock follows midday in vivo and in vitro.Elife2017
26918826Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.J Chem Theory Comput2016
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Collaborators

Martin Karplus
Harvard University
Co-authored papers 14
Jeremy O B Tempkin
University of California san francisco
Co-authored papers 4
Gregory A Voth
Co-authored papers 4
Sean Crosson
Co-authored papers 3
Chuan He
Institute of Hematology, West China Hospital of Sichuan University
Co-authored papers 3
Jack A Gilbert
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 2
Sean M Gibbons
Institute for Systems Biology
Co-authored papers 2
Kevin P White
Co-authored papers 2
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 2
Charles L Brooks
University of Michigan ann arbor
Co-authored papers 1
Vinod Kumar
The University of Queensland
Co-authored papers 1
Mark M Davis
Co-authored papers 1
Michael Feig
Michigan State University
Co-authored papers 1
Lorna J Smith
University of Oxford
Co-authored papers 1
Cecilia Clementi
Co-authored papers 1
Feng Qian
Co-authored papers 1
Eugene I Shakhnovich
Harvard University
Co-authored papers 1
Juan J de Pablo
University of Chicago
Co-authored papers 1
Gajendra S Shekhawat
Co-authored papers 1
Cisca Wijmenga
Co-authored papers 1
Chengqi Yi
Peking University
Co-authored papers 1
Christopher M Dobson
University of Cambridge
Co-authored papers 1
Release 1.2