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- 2025
- Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics (2025) JOURNAL OF MOLECULAR BIOLOGY. 437(2).
- Myelin sheaths can act as compact temporary oxygen storage units as modeled by an electrical RC circuit model (2025) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 122(20).
- Validation of a coarse-grained Martini 3 model for molecular oxygen (2025) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 21(1). p.428-439
- Drug permeation through phospholipid membranes : predicting exact kinetics via path sampling methodology (2025) CECAM 2025 Workshop : Predicting and understanding drug-target binding kinetics via molecular simulations, Abstracts.
- Protein dynamics and conformational heterogeneity in solution are not well captured by AlphaFold and other computational approaches (2025) ISMB/ECCB 2025, Abstracts.
- Investigating protein flexibility using molecular dynamics simulations of α-1 acid glycoprotein and large-scale normal mode analysis of AlphaFold models (2025)
- 2024
- An exact algorithm to find a maximum weight clique in a weighted undirected graph (2024) SCIENTIFIC REPORTS. 14(1).
- Conformational dynamics of α‐1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and unglycosylated AGP (2024) PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 92(2). p.246-264
- Enhanced molecular docking : novel algorithm for identifying highest weight k-cliques in weighted general and protein-ligand graphs (2024) JOURNAL OF MOLECULAR STRUCTURE. 1304.
- PyRETIS 3 : conquering rare and slow events without boundaries (2024) JOURNAL OF COMPUTATIONAL CHEMISTRY. 45(15). p.1224-1234
- Exact kinetics of drug permeation through phospholipid membranes via path sampling methodology (2024) CECAM 2024 Workshop 'Leveraging Machine Learning for Sampling Rare Events in Biomolecular Systems', Abstracts. p.28-29
- Extending path memory to improve kinetics calculations in rare molecular processes (2024) 2024 FEA Research Symposium, Abstracts.
- From 2D toy systems to real drug molecules : exact permeation kinetics through phospholipid membranes (2024) Workshop : A Time Warp in Digital Chemical Discoveries, Abstracts.
- Advanced molecular dynamics simulation techniques for kinetic analysis of biological systems (2024)
- Investigating the effect of curvature and composition on lipid membrane permeability using molecular dynamics simulations (2024)
- Understanding oxygen 'buffering' by caveolae using coarse-grained molecular dynamics simulations (2024) OXYGEN TRANSPORT TO TISSUE XLV, ISOTT 2023. In Advances in Experimental Medicine and Biology p.271-275
- 2023
- Capric acid and myristic acid permeability enhancers in curved liposome membranes (2023) JOURNAL OF CHEMICAL INFORMATION AND MODELING. 63(21). p.6789-6806
- Defining permeability of curved membranes in molecular dynamics simulations (2023) BIOPHYSICAL JOURNAL. 12(11). p.2082-2091
- Path sampling with memory reduction and replica exchange to reach long permeation timescales (2023) BIOPHYSICAL JOURNAL. 122(14). p.2960-2972
- Understanding the role of caveolae in oxygen buffering : the effect of membrane curvature (2023) Oxygen Transport to Tissue XLIV. In Advances in Experimental Medicine and Biology 1438. p.87-91
- Assessing passive permeability of drug releasing liposomes containing saturated fatty acids with molecular dynamics simulations (2023) GGMM 2023 : Young Modellers Conference, Abstracts. p.60-60
- Exploring caveolae's role in oxygen 'buffering' through coarse-grained molecular dynamics (2023) 2023 FEA Research Symposium, Abstracts.
- Pushing path sampling simulations to longer timescales : reducing memory and introducing replica exchange (2023) Advanced Methods in MD 2023, Abstracts.
- Understanding the mechanism of oxygen 'buffering' by caveolae using coarse grained molecular dynamics (2023) ISOTT 2023, Abstracts.
- 2022
- Counting permeant crossings to assess the effect of membrane curvature and composition on the permeability rate (2022) BIOPHYSICAL JOURNAL. 121(3). p.71a-72a
- Dissecting conformational dynamics of α-1 acid glycoprotein (AGP) : a study of glycosylated and un-glycosylated mutants (2022) Faculty of Engineering and Architecture Research Symposium 2022 (FEARS 2022), Abstracts.
- Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants (2022) OncoPoint Symposium, 8th, Abstracts.
- Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants (2022) BACR Annual meeting 2022 : Tumour plasticity and heterogeneity during cancer progression, Abstracts.
- Effect of membrane curvature and lipid composition on membrane permeability in liposomal drug delivery (2022) CRF-ChemCYS 2022, Abstracts.
- Investigating membrane curvature and composition effect on membrane permeability by counting permeant crossings (2022) Molecular Simulation 2022 : present, past and future, Abstracts.
- Investigating the caveolin protein role in mitochondrial oxygen consumption (2022) Faculty of Engineering and Architecture Research Symposium 2022 (FEARS 2022), Abstracts.
- Investigation of the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein using Replica Exchange Transition Interface Sampling (2022) Faculty of Engineering and Architecture Research Symposium 2022 (FEARS 2022), Abstracts.
- Mechanism of oxygen 'buffering' by caveolae (2022) ISOTT 2022, Abstracts.
- Replica Exchange Transition Interface Sampling to investigate the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein (2022) Computational Chemistry Gordon Research Conference : Multiscale Modeling of Complex Systems : Methods and Applications, Abstracts.
- Replica exchange transition interface sampling to simulate the kinetics of molecular transport through membranes (2022) ACS Spring 2022, Abstracts.
- Understanding membrane permeability of drug releasing liposomes from molecular dynamics simulations : effect of curvature and composition (2022) OncoPoint Symposium, 8th, Abstracts.
- Oxygen storage in stacked phospholipid membranes under an oxygen gradient as a model for myelin sheaths (2022) Oxygen Transport to Tissue XLIII. In Advances in Experimental Medicine and Biology 1395. p.301-307
- 2021
- Permeation rates of oxygen through a lipid bilayer using replica exchange transition interface sampling (2021) JOURNAL OF PHYSICAL CHEMISTRY B. 125(1). p.193-201
- Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility–diffusion model (2021) JOURNAL OF CHEMICAL PHYSICS. 154(5).
- Exact non-Markovian permeability from rare event simulations (2021) PHYSICAL REVIEW RESEARCH. 3(3).
- Computational tools for protein-ligand binding kinetics in personalized medicine (2021) OncoDot.3 symposium, Abstracts.
- Inhomogeneous solubility-diffusion model gives insight in efficacy of counting crossings method to calculate the membrane permeability (2021) BIOPHYSICAL JOURNAL. 120(3). p.80A-80A
- Oxygen permeation pathways through phospholipid membranes in the liquid ordered and liquid disordered phases (2021) ISOTT 2021, meeting of the International Society on Oxygen Transport to Tissue, Abstracts.
- Path sampling methodology for membrane permeability simulations (2021) 2021 ISQBP President's Meeting, Abstracts.
- Path sampling methods for protein-ligand binding kinetics (2021) 2021 ISQBP President's Meeting, Abstracts.
- Bringing hidden variables into the open unveils a barrier for lipid insertion into membranes (2021) BIOPHYSICAL JOURNAL. 120(17). p.3542-3543
- 2020
- Membrane permeability of small molecules from unbiased molecular dynamics simulations (2020) JOURNAL OF CHEMICAL PHYSICS. 153(12).
- Assessing counting method efficacy in cell membrane permeability calculations (2020) 19th National Day on Biomedical Engineering, Abstracts.
- 2019
- Permeability of membranes in the liquid ordered and liquid disordered phases (2019) NATURE COMMUNICATIONS. 10.
- 2018
- Effect of chain unsaturation and temperature on oxygen diffusion through lipid membranes from simulations (2018) ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY. 1072. p.399-404
- Membrane permeability: characteristic times and lengths for oxygen, and a simulation-based test of the inhomogeneous solubility-diffusion model (2018) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 14(7). p.3811-3824
- The importance of cell shape sampling to accurately predict flexibility in metal-organic frameworks (2018) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 14(3). p.1186-1197
- 2017
- Position-dependent diffusion tensors in anisotropic media from simulation : oxygen transport in and through membranes (2017) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 13(6). p.2962-2976
- Correction to “Shape-Selective Diffusion of Olefins in 8-Ring Solid Acid Microporous Zeolites” (2017) JOURNAL OF PHYSICAL CHEMISTRY C. 121(10). p.5854-5854
- 2016
- Discovery of mycobacterium tuberculosis InhA inhibitors by binding sites comparison and ligands prediction (2016) JOURNAL OF MEDICINAL CHEMISTRY. 59(24). p.11069-11078
- Water coordination and dehydration processes in defective UiO-66 type metal organic frameworks (2016) CRYSTENGCOMM. 18(37). p.7056-7069
- 2015
- A comparison of barostats for the mechanical characterization of metal-organic frameworks (2015) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 11(12). p.5583-5597
- Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics (2015) CHEMISTRY-A EUROPEAN JOURNAL. 21(26). p.9385-9396
- Mechanical properties from periodic plane wave quantum mechanical codes: the challenge of the flexible nanoporous MIL-47(V) framework (2015) JOURNAL OF PHYSICAL CHEMISTRY C. 119(41). p.23752-23766
- Semi-analytical mean-field model for predicting breathing in metal–organic frameworks (2015) MOLECULAR SIMULATION. 41(16-17). p.1311-1328
- Shape-selective diffusion of olefins in 8-ring solid acid microporous zeolites (2015) JOURNAL OF PHYSICAL CHEMISTRY C. 119(41). p.23721-23734
- Exploring new frontiers in modeling complex zeolite-catalyzed reactions using advanced molecular dynamics techniques (2015)
- Normal mode analysis of macromolecular systems with the mobile block Hessian method (2015) AIP Conference Proceedings. In AIP Conference Proceedings 1642. p.559-562
- 2014
- Advances in molecular quantum chemistry contained in the Q-Chem 4 program package (2014) MOLECULAR PHYSICS. 113(2). p.184-215
- Critical analysis of the accuracy of models predicting or extracting liquid structure information (2014) JOURNAL OF PHYSICAL CHEMISTRY B. 118(9). p.2451-2470
- Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics (2014) JOURNAL OF CHEMICAL PHYSICS. 140(13).
- New quasi-1D materials: DFT-study of breathing metal-organic frameworks (2014) IAP P7/05 Annual meeting, Abstracts.
- Tailoring metal-organic frameworks for adsorption applications (2014) E-MRS spring meeting, Abstracts.
- 2013
- On the thermodynamics of framework breathing: a free energy model for gas adsorption in MIL-53 (2013) JOURNAL OF PHYSICAL CHEMISTRY C. 117(22). p.11540-11554
- Oxygen diffusion water, alkanes, and lipid bilayers (2013) 245th ACS National Meeting and Exposition, Abstracts.
- 2012
- Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids : application to methanol (2012) JOURNAL OF CHEMICAL PHYSICS. 137(10).
- Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining (2012) JOURNAL OF COMPUTATIONAL CHEMISTRY. 33(28). p.2250-2275
- Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system (2012) THEORETICAL CHEMISTRY ACCOUNTS. 131(7).
- Empty host breathing profiles of MIL-53 type frameworks with various cations at the nodal points (2012) Metal-Organic Frameworks and Open Framework Compounds, 3rd International conference, Abstracts.
- Free energy profile of 'breathing' flexible porous frameworks (2012) Challenges in Density Matrix and Density Functional Theory, Abstracts. p.P13-P13
- Implosion-based mapping procedure between all-atom and coarse-grained normal modes (2012) ISQBP President's Meeting. p.9-9
- Thermodynamics of 'breathing' of metal-organic frameworks: free energy model for adsorption induced transitions (2012) 14th International Conference on Theoretical Aspects of Catalysis, Book of abstracts. p.169-170
- 2011
- Efficient calculation of QM/MM frequencies with the mobile block hessian (2011) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 7(2). p.496-514
- Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34 (2011) CATALYSIS TODAY. 177(1). p.12-24
- First principle kinetic studies of zeolite-catalyzed methylation reactions (2011) JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 133(4). p.888-899
- Normal mode analysis in zeolites: toward an efficient calculation of adsorption entropies (2011) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 7(4). p.1090-1101
- A theoretical and experimental spectroscopy study on methanol and ethanol conversion over H-SAPO-34 (2011) 5th International FEZA conference : abstracts. p.623-624
- Advanced normal mode analysis for multi-scale modeling (2011) ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 241.
- Introducing BSSE as an extra energy term in molecular dynamics (2011) Interuniversity Attraction Pole IAP P6/27 FS2 Annual Network Meeting, Abstracts. p.WP3/8-WP3/8
- Monte Carlo simulations to understand 'breathing' phenomenon of metal organic frameworks (2011) Ninth triennial congress of the World Association of Theoretical and Computational Chemists, WATOC 2011. p.269-269
- Understanding framework flexibility by Monte Carlo simulation (2011) ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 241.
- 2010
- Comparative study of various normal mode analysis techniques based on partial Hessians (2010) JOURNAL OF COMPUTATIONAL CHEMISTRY. 31(5). p.994-1007
- TAMkin : a versatile package for vibrational analysis and chemical kinetics (2010) JOURNAL OF CHEMICAL INFORMATION AND MODELING. 50(9). p.1736-1750
- Efficient calculation of QM/MM frequencies with the Mobile Block Hessian (2010) Computational chemistry, Gordon Research Conference, Abstracts.
- 2009
- Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules (2009) Journal of Chemical Theory and Computation. 5(5). p.1203-1215
- Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach (2009) JOURNAL OF CHEMICAL PHYSICS. 130(8).
- Normal mode analysis of macromolecular systems with the Mobile Block Hessian method (2009) Proceedings ICCMSE 2009.
- Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method (2009) Abstracts 7th Canadian Computational Chemistry Conference.
- The evaluation of QM/MM full Hessian and some applications (2009) ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 238.
- The evaluation of the QM/MM full Hessian and some applications (2009) ACS National Meeting, 238th, Abstracts. p.345-345
- Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian Method (2009)
- 2008
- Calculating reaction rates with partial Hessians: Validation of the mobile block Hessian approach (2008) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 4(4). p.614-625
- MFI fingerprint: How pentasil-induced IR bands shift during zeolite nanogrowth (2008) JOURNAL OF PHYSICAL CHEMISTRY C. 112(25). p.9186-9191
- Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit (2008) Journal of Chemical Physics. 129(21).
- An efficient approach for the calculation of frequencies in macromolecules (2008)
- Normal modes in partially optimized molecular systems: the Mobile Block Hessian (MBH) approach (2008)
- On the development of a partial vibrational analysis within a QM/MM approach (2008)
- 2007
- Cartesian formulation of the mobile block Hessian approach to vibrational analysis in partially optimized systems (2007) JOURNAL OF CHEMICAL PHYSICS. 127(16).
- Vibrational modes in partially optimized molecular systems (2007) JOURNAL OF CHEMICAL PHYSICS. 126(22).
- 2006
- Role of mean free path in spatial phase correlation and nodal screening (2006) EUROPHYSICS LETTERS. 74(6). p.999-1005