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ORCIDDionisios G. Vlachos
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2020 – today
- 2025
[j29]Sashank Kasiraju, Yifan Wang, Saurabh Bhandari, Aayush R. Singh, Dionisios G. Vlachos
:
A Python tool for parameter estimation of "black box" macro- and micro-kinetic models with Bayesian optimization - petBOA. Comput. Phys. Commun. 306: 109358 (2025)- 2024
- [j28]Zhaoxing Wang, Yuqing Luo, Prahalad Srinivasan, Yifan Wang, Tai-Ying Chen, Marianthi G. Ierapetritou, Dionisios G. Vlachos:
Process integration and systems optimization for the hydrodeoxygenation of 5-hydroxymethylfurfural to dimethylfuran. Comput. Chem. Eng. 184: 108644 (2024) - 2023
- [j27]Himaghna Bhattacharjee, Jackson W. Burns, Dionisios G. Vlachos:
AIMSim: An accessible cheminformatics platform for similarity operations on chemicals datasets. Comput. Phys. Commun. 283: 108579 (2023) - [j26]Xue Zong, Jonathan Lym, Dionisios G. Vlachos:
Automated descriptor selection, volcano curve generation, and active site determination using the DescMAP software. Comput. Phys. Commun. 290: 108754 (2023) - [j25]Bharat Medasani, Sashank Kasiraju, Dionisios G. Vlachos:
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. J. Chem. Inf. Model. 63(11): 3377-3391 (2023) - [j24]Siddhant M. Lambor, Sashank Kasiraju, Dionisios G. Vlachos:
CKineticsDB─An Extensible and FAIR Data Management Framework and Datahub for Multiscale Modeling in Heterogeneous Catalysis. J. Chem. Inf. Model. 63(14): 4342-4354 (2023) - [j23]Jackson W. Burns, Kevin A. Spiekermann, Himaghna Bhattacharjee, Dionisios G. Vlachos, William H. Green Jr.:
Machine Learning Validation via Rational Dataset Sampling with astartes. J. Open Source Softw. 8(91): 5996 (2023) - 2022
- [j22]Gerhard R. Wittreich, Dionisios G. Vlachos:
Python Group Additivity (pGrAdd) software for estimating species thermochemical properties. Comput. Phys. Commun. 273: 108277 (2022) - [j21]Yifan Wang, Jake Kalscheur, Elvis Ebikade, Qiang Li, Dionisios G. Vlachos:
LigninGraphs: lignin structure determination with multiscale graph modeling. J. Cheminformatics 14(1): 43 (2022) - [j20]Yue Zhang, Cong Wang, Mya Soukaseum, Dionisios G. Vlachos, Hui Fang:
Unleashing the Power of Knowledge Extraction from Scientific Literature in Catalysis. J. Chem. Inf. Model. 62(14): 3316-3330 (2022) - [j19]Xue Zong, Dionisios G. Vlachos:
Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning. J. Chem. Inf. Model. 62(18): 4361-4368 (2022) - 2021
- [j18]Maximilian Cohen, Dionisios G. Vlachos:
Chemical Kinetics Bayesian Inference Toolbox (CKBIT). Comput. Phys. Commun. 265: 107989 (2021) - [j17]Udit Gupta, Dionisios G. Vlachos:
Learning Chemistry of Complex Reaction Systems via a Python First-Principles Reaction Rule Stencil (pReSt) Generator. J. Chem. Inf. Model. 61(7): 3431-3441 (2021) - [j16]Yifan Wang, Tai-Ying Chen, Dionisios G. Vlachos:
NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering. J. Chem. Inf. Model. 61(11): 5312-5319 (2021) - 2020
- [j15]Jonathan Lym, Gerhard R. Wittreich, Dionisios G. Vlachos:
A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation. Comput. Phys. Commun. 247 (2020) - [j14]Himaghna Bhattacharjee, Dionisios G. Vlachos:
Thermochemical Data Fusion Using Graph Representation Learning. J. Chem. Inf. Model. 60(10): 4673-4683 (2020) - [j13]Udit Gupta, Dionisios G. Vlachos:
Reaction Network Viewer (ReNView): An open-source framework for reaction path visualization of chemical reaction systems. SoftwareX 11: 100442 (2020)
2010 – 2019
- 2014
- [j12]Jacob A. McGill, Babatunde A. Ogunnaike, Dionisios G. Vlachos:
A robust and efficient triangulation-based optimization algorithm for stochastic black-box systems. Comput. Chem. Eng. 60: 143-153 (2014) - 2013
- [j11]Yannis Pantazis, Markos A. Katsoulakis, Dionisios G. Vlachos:
Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory. BMC Bioinform. 14: 311 (2013) - [i1]Yannis Pantazis, Markos A. Katsoulakis, Dionisios G. Vlachos:
Parametric Sensitivity Analysis for Biochemical Reaction Networks based on Pathwise Information Theory. CoRR abs/1304.3962 (2013) - 2012
- [j10]Evangelia Kalligiannaki, Markos A. Katsoulakis, Petr Plechác, Dionisios G. Vlachos:
Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems. J. Comput. Phys. 231(6): 2599-2620 (2012) - [j9]Jacob A. McGill, Babatunde A. Ogunnaike, Dionisios G. Vlachos:
Efficient gradient estimation using finite differencing and likelihood ratios for kinetic Monte Carlo simulations. J. Comput. Phys. 231(21): 7170-7186 (2012) - 2011
- [j8]Michail Stamatakis, Dionisios G. Vlachos:
Equivalence of on-lattice stochastic chemical kinetics with the well-mixed chemical master equation in the limit of fast diffusion. Comput. Chem. Eng. 35(12): 2602-2610 (2011) - [j7]Nasser Mohieddin Abukhdeir, Dionisios G. Vlachos, Markos A. Katsoulakis, Michael Plexousakis:
Long-time integration methods for mesoscopic models of pattern-forming systems. J. Comput. Phys. 230(14): 5704-5715 (2011) - 2010
- [j6]Stuart Collins, Michail Stamatakis, Dionisios G. Vlachos:
Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. BMC Bioinform. 11: 218 (2010) - [c2]Lifan Xu, Michela Taufer, Stuart Collins, Dionisios G. Vlachos:
Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs. IPDPS 2010: 1-9
2000 – 2009
- 2007
- [j5]Asawari Samant, Babatunde A. Ogunnaike, Dionisios G. Vlachos:
A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks. BMC Bioinform. 8 (2007) - 2006
- [j4]Dionisios G. Vlachos, A. B. Mhadeshwar, Niket S. Kaisare:
Hierarchical multiscale model-based design of experiments, catalysts, and reactors for fuel processing. Comput. Chem. Eng. 30(10-12): 1712-1724 (2006) - 2005
- [j3]Abhijit Chatterjee, Kapil Mayawala, Jeremy S. Edwards, Dionisios G. Vlachos:
Time accelerated Monte Carlo simulations of biological networks using the binomial r-leap method. Bioinform. 21(9): 2136-2137 (2005) - [j2]M. A. Snyder, A. Chatterjee, Dionisios G. Vlachos:
Net-event kinetic Monte Carlo for overcoming stiffness in spatially homogeneous and distributed systems. Comput. Chem. Eng. 29(4): 701-712 (2005) - 2001
- [c1]Daniel E. Zak, Francis J. Doyle III, Dionisios G. Vlachos, James S. Schwaber:
Stochastic kinetic analysis of transcriptional feedback models for circadian rhythms. CDC 2001: 849-854
1990 – 1999
- 1997
- [j1]Dionisios G. Vlachos:
Growth of Nanophase Clusters and Potential Energy Minima: Hysteresis, Oscillations, and Phase Transitions. J. Glob. Optim. 11(1): 69-82 (1997)
Coauthor Index
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