Daniel R. Roe, Ph. D. - Related publications

2016- NHLBI National Institues of Health 
molecular dynamics, data analysis, enhanced sampling, implicit solvent models
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Jas GS, Childs EW, Middaugh CR, Kuczera K. Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction. Biomolecules. 11. PMID 34572564 DOI: 10.3390/biom11091351   
2021 Paul A, Samantray S, Anteghini M, Khaled M, Strodel B. Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment. Chemical Science. 12: 6652-6669. PMID 34040740 DOI: 10.1039/d0sc04657d   
2021 Walker CC, Meek GA, Fobe TL, Shirts MR. Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure. Journal of Chemical Theory and Computation. PMID 34495659 DOI: 10.1021/acs.jctc.1c00528   
2021 Li C, Voth GA. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. The Journal of Physical Chemistry. B. PMID 34520198 DOI: 10.1021/acs.jpcb.1c05992   
2021 Wang L, O'Mara ML. Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein. Journal of Chemical Theory and Computation. PMID 34506133 DOI: 10.1021/acs.jctc.1c00414   
2021 Kolimi N, Pabbathi A, Saikia N, Ding F, Sanabria H, Alper J. Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches. The Journal of Physical Chemistry. B. PMID 34506140 DOI: 10.1021/acs.jpcb.1c02424   
2021 Chen H, Yong EH. Energy cost study for controlling complex social networks with conformity behavior. Physical Review. E. 104: 014301. PMID 34412279 DOI: 10.1103/PhysRevE.104.014301   
2021 Peter EK, Manstein DJ, Shea JE, Schug A. CORE-MD II: A fast, adaptive, and accurate enhanced sampling method. The Journal of Chemical Physics. 155: 104114. PMID 34525829 DOI: 10.1063/5.0063664   
2021 Shea-Blymyer C, Roy S, Jantzen B. A General Metric for the Similarity of Both Stochastic and Deterministic System Dynamics. Entropy (Basel, Switzerland). 23. PMID 34573815 DOI: 10.3390/e23091191   
2021 Matsumoto RA, Thompson MW, Vuong VQ, Zhang W, Shinohara Y, van Duin ACT, Kent PRC, Irle S, Egami T, Cummings PT. Investigating the Accuracy of Water Models through the Van Hove Correlation Function. Journal of Chemical Theory and Computation. PMID 34516134 DOI: 10.1021/acs.jctc.1c00637   
2021 Finkelstein J, Smith JS, Mniszewski SM, Barros K, Negre CFA, Rubensson EH, Niklasson AMN. Quantum-Based Molecular Dynamics Simulations Using Tensor Cores. Journal of Chemical Theory and Computation. PMID 34595916 DOI: 10.1021/acs.jctc.1c00726   
2021 Jephthah S, Pesce F, Lindorff-Larsen K, Skepö M. Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. Journal of Chemical Theory and Computation. PMID 34524800 DOI: 10.1021/acs.jctc.1c00408   
2021 Chiangraeng N, Armstrong M, Manokruang K, Lee VS, Jiranusornkul S, Nimmanpipug P. Characteristic Structural Knowledge for Morphological Identification and Classification in Meso-Scale Simulations Using Principal Component Analysis. Polymers. 13. PMID 34451122 DOI: 10.3390/polym13162581   
2021 Singh A, Incardona P, Sbalzarini IF. A C++ expression system for partial differential equations enables generic simulations of biological hydrodynamics. The European Physical Journal. E, Soft Matter. 44: 117. PMID 34554349 DOI: 10.1140/epje/s10189-021-00121-x   
2021 Jiang XZ, Luo KH, Ventikos Y. Understanding the Role of Endothelial Glycocalyx in Mechanotransduction via Computational Simulation: A Mini Review. Frontiers in Cell and Developmental Biology. 9: 732815. PMID 34485313 DOI: 10.3389/fcell.2021.732815   
2021 Hicks A, MacAinsh M, Zhou HX. Removing Thermostat Distortions of Protein Dynamics in Constant-Temperature Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 34464112 DOI: 10.1021/acs.jctc.1c00448   
2021 Singer PM, Parambathu AV, Pinheiro Dos Santos TJ, Liu Y, Alemany LB, Hirasaki GJ, Chapman WG, Asthagiri D. Predicting H NMR relaxation in Gd-aqua using molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. 23: 20974-20984. PMID 34518855 DOI: 10.1039/d1cp03356e   
2021 Rumble CA, Vauthey E. Molecular Dynamics Simulations of Bimolecular Electron Transfer: the Distance-Dependent Electronic Coupling. The Journal of Physical Chemistry. B. PMID 34519508 DOI: 10.1021/acs.jpcb.1c05013   
2021 Ozsipahi M, Akkus Y, Nguyen CT, Beskok A. Energy-Based Interface Detection for Phase Change Processes of Monatomic Fluids in Nanoconfinements. The Journal of Physical Chemistry Letters. 8397-8403. PMID 34435788 DOI: 10.1021/acs.jpclett.1c02517   
2021 Jiang YJ, Ni CY, Zhang Y, Yi Y. Numerical investigation of the plastic deformation behaviour of graded crushed stone. Plos One. 16: e0258113. PMID 34591939 DOI: 10.1371/journal.pone.0258113   
2021 Kogut M, Gong Z, Tang C, Liwo A. Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. Journal of Computational Chemistry. PMID 34402552 DOI: 10.1002/jcc.26736   
2021 Mondal P, Cazade PA, Das AK, Bereau T, Meuwly M. Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer. The Journal of Physical Chemistry. B. PMID 34559531 DOI: 10.1021/acs.jpcb.1c05423   
2021 Cavalcante LSR, Daemen LL, Goldman N, Moulé AJ. Davis Computational Spectroscopy Workflow-From Structure to Spectra. Journal of Chemical Information and Modeling. PMID 34449225 DOI: 10.1021/acs.jcim.1c00688   
2021 Huang CT, Lin TW, Jong WR, Chen SC. A Methodology to Predict and Optimize Ease of Assembly for Injected Parts in a Family-Mold System. Polymers. 13. PMID 34577966 DOI: 10.3390/polym13183065   
2021 Molina A, Kumar S, Karpitschka S, Prakash M. Droplet tilings for rapid exploration of spatially constrained many-body systems. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34417307 DOI: 10.1073/pnas.2020014118   
2021 Mengacci R, Zambella G, Grioli G, Caporale D, Catalano MG, Bicchi A. An Open-Source ROS-Gazebo Toolbox for Simulating Robots With Compliant Actuators. Frontiers in Robotics and Ai. 8: 713083. PMID 34458326 DOI: 10.3389/frobt.2021.713083   
2021 Berthier L. Self-Induced Heterogeneity in Deeply Supercooled Liquids. Physical Review Letters. 127: 088002. PMID 34477435 DOI: 10.1103/PhysRevLett.127.088002   
2021 Washio T, Kanada R, Cui X, Okada JI, Sugiura S, Takada S, Hisada T. Semi-Implicit Time Integration with Hessian Eigenvalue Corrections for a Larger Time Step in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 34351147 DOI: 10.1021/acs.jctc.1c00398   
2021 Li N, Gao Y, Qiu F, Zhu T. Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes. Molecules (Basel, Switzerland). 26. PMID 34500812 DOI: 10.3390/molecules26175379   
2021 Suchý T, Bartoš M, Sedláček R, Šupová M, Žaloudková M, Martynková GS, Foltán R. Various Simulated Body Fluids Lead to Significant Differences in Collagen Tissue Engineering Scaffolds. Materials (Basel, Switzerland). 14. PMID 34442910 DOI: 10.3390/ma14164388   
2021 Richert R, Gabriel JP, Thoms E. Structural Relaxation and Recovery: A Dielectric Approach. The Journal of Physical Chemistry Letters. 8465-8469. PMID 34449235 DOI: 10.1021/acs.jpclett.1c02539   
2021 Nguyen MT, Rousseau R, Paviet PD, Glezakou VA. Actinide Molten Salts: A Machine-Learning Potential Molecular Dynamics Study. Acs Applied Materials & Interfaces. PMID 34494435 DOI: 10.1021/acsami.1c11358   
2021 Li R, Ouyang Q, Cui Y, Jin Y. Preview Control with Dynamic Constraints for Autonomous Vehicles. Sensors (Basel, Switzerland). 21. PMID 34372392 DOI: 10.3390/s21155155   
2021 Scalliet C, Guiselin B, Berthier L. Excess wings and asymmetric relaxation spectra in a facilitated trap model. The Journal of Chemical Physics. 155: 064505. PMID 34391365 DOI: 10.1063/5.0060408   
2021 Kubincová A, Riniker S, Hünenberger PH. Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. The Journal of Chemical Physics. 155: 094107. PMID 34496576 DOI: 10.1063/5.0057384   
2021 Sanzaro S, Bongiorno C, Badalà P, Bassi A, Deretzis I, Enachescu M, Franco G, Fisicaro G, Vasquez P, Alberti A, La Magna A. Simulations of the Ultra-Fast Kinetics in Ni-Si-C Ternary Systems under Laser Irradiation. Materials (Basel, Switzerland). 14. PMID 34443290 DOI: 10.3390/ma14164769   
2021 Nino DF, Milstein JN. Estimating the Dynamic Range of Quantitative Single-Molecule Localization Microscopy. Biophysical Journal. PMID 34437847 DOI: 10.1016/j.bpj.2021.08.024   
2021 Zobel JP, González L. The Quest to Simulate Excited-State Dynamics of Transition Metal Complexes. Jacs Au. 1: 1116-1140. PMID 34467353 DOI: 10.1021/jacsau.1c00252   
2021 Edwards BJ, Nafar Sefiddashti MH, Khomami B. A method for calculating the nonequilibrium entropy of a flowing polymer melt via atomistic simulation. The Journal of Chemical Physics. 155: 111101. PMID 34551537 DOI: 10.1063/5.0056547   
2021 Fang J, Hu L, Dong J, Li H, Wang H, Zhao H, Zhang Y, Liu M. Predicting scalar coupling constants by graph angle-attention neural network. Scientific Reports. 11: 18686. PMID 34548513 DOI: 10.1038/s41598-021-97146-1   
2021 Gupta A, Rajaram SS, Thompson GB, Tucker GJ. Improved computational method to generate properly equilibrated atomistic microstructures. Methodsx. 8: 101217. PMID 34434740 DOI: 10.1016/j.mex.2021.101217   
2021 Wang A, Zhang Z, Lei X, Xia Y, Sun L. All-Weather Thermal Simulation Methods for Concrete Maglev Bridge Based on Structural and Meteorological Monitoring Data. Sensors (Basel, Switzerland). 21. PMID 34502680 DOI: 10.3390/s21175789   
2021 Knudsen PA, Niss K, Bailey NP. Quantifying dynamical and structural invariance in a simple molten salt model. The Journal of Chemical Physics. 155: 054506. PMID 34364358 DOI: 10.1063/5.0055794   
2021 Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, et al. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of Chemical Theory and Computation. PMID 34551262 DOI: 10.1021/acs.jctc.1c00571   
2021 Fujimoto K, Nagai T, Yamaguchi T. Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation. Journal of Computational Chemistry. PMID 34406659 DOI: 10.1002/jcc.26742   
2021 Lai YC. Finding nonlinear system equations and complex network structures from data: A sparse optimization approach. Chaos (Woodbury, N.Y.). 31: 082101. PMID 34470223 DOI: 10.1063/5.0062042   
2021 Fischer M. Revisiting the Structure of Calcined and Hydrated AlPO-11 with DFT-Based Molecular Dynamics Simulations. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 34314095 DOI: 10.1002/cphc.202100486   
2021 Pieroni C, Agostini F. Nonadiabatic Dynamics with Coupled Trajectories. Journal of Chemical Theory and Computation. 17: 5969-5991. PMID 34506154 DOI: 10.1021/acs.jctc.1c00438   
2021 Chen X, Zhang X, Chen L, Guo Y, Zhu F. A Curve-Shaped Beam Bistable Piezoelectric Energy Harvester with Variable Potential Well: Modeling and Numerical Simulation. Micromachines. 12. PMID 34442617 DOI: 10.3390/mi12080995   
2021 Caracas R, Kobsch A, Solomatova NV, Li Z, Soubiran F, Hernandez JA. Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package. Journal of Visualized Experiments : Jove. PMID 34605802 DOI: 10.3791/61534