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- 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
- Understanding membrane permeability of drug releasing liposomes from molecular dynamics simulations : effect of curvature and composition (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)
- INVESTIGATING MEMBRANE CURVATURE AND COMPOSITION EFFECT ON MEMBRANE PERMEABILITY BY COUNTING PERMEANT CROSSINGS (2022)
- 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