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Conformational dynamics of α‐1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and unglycosylated AGP
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PyRETIS 3: Conquering rare and slow events without boundaries
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- Journal Article
- A1
- open access
Defining permeability of curved membranes in molecular dynamics simulations
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Capric acid and myristic acid permeability enhancers in curved liposome membranes
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- Conference Paper
- C3
- open access
Understanding the mechanism of oxygen 'buffering' by caveolae using coarse grained molecular dynamics
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- Conference Paper
- C3
- open access
Assessing passive permeability of drug releasing liposomes containing saturated fatty acids with molecular dynamics simulations
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- Journal Article
- A1
- open access
Path sampling with memory reduction and replica exchange to reach long permeation timescales
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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 -
Exploring caveolae's role in oxygen 'buffering' through coarse-grained molecular dynamics
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Pushing path sampling simulations to longer timescales : reducing memory and introducing replica exchange
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- Conference Paper
- C3
- open access
Counting permeant crossings to assess the effect of membrane curvature and composition on the permeability rate
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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 -
- Conference Paper
- C3
- open access
Investigating membrane curvature and composition effect on membrane permeability by counting permeant crossings
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- Conference Paper
- C3
- open access
Dissecting conformational dynamics of α-1 acid glycoprotein (AGP) : a study of glycosylated and un-glycosylated mutants
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- Conference Paper
- C3
- open access
Investigating the caveolin protein role in mitochondrial oxygen consumption
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- Conference Paper
- C3
- open access
Investigation of the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein using Replica Exchange Transition Interface Sampling
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Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants
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- Conference Paper
- C3
- open access
Replica Exchange Transition Interface Sampling to investigate the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein
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- Conference Paper
- C3
- open access
Effect of membrane curvature and lipid composition on membrane permeability in liposomal drug delivery
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- Conference Paper
- C3
- open access
Mechanism of oxygen 'buffering' by caveolae
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Understanding membrane permeability of drug releasing liposomes from molecular dynamics simulations : effect of curvature and composition
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Replica exchange transition interface sampling to simulate the kinetics of molecular transport through membranes
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Permeation rates of oxygen through a lipid bilayer using replica exchange transition interface sampling
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- Journal Article
- A1
- open access
Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility–diffusion model
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Bringing hidden variables into the open unveils a barrier for lipid insertion into membranes
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Oxygen permeation pathways through phospholipid membranes in the liquid ordered and liquid disordered phases
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- Journal Article
- A2
- open access
Exact non-Markovian permeability from rare event simulations
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Inhomogeneous solubility-diffusion model gives insight in efficacy of counting crossings method to calculate the membrane permeability
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- Conference Paper
- C3
- open access
Computational tools for protein-ligand binding kinetics in personalized medicine
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Path sampling methodology for membrane permeability simulations
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- Conference Paper
- C3
- open access
Path sampling methods for protein-ligand binding kinetics
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- Journal Article
- A1
- open access
Membrane permeability of small molecules from unbiased molecular dynamics simulations
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Assessing counting method efficacy in cell membrane permeability calculations
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- Journal Article
- A1
- open access
Permeability of membranes in the liquid ordered and liquid disordered phases
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- Journal Article
- A1
- open access
Membrane permeability: characteristic times and lengths for oxygen, and a simulation-based test of the inhomogeneous solubility-diffusion model
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Effect of chain unsaturation and temperature on oxygen diffusion through lipid membranes from simulations
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- Journal Article
- A1
- open access
The importance of cell shape sampling to accurately predict flexibility in metal-organic frameworks
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Correction to “Shape-Selective Diffusion of Olefins in 8-Ring Solid Acid Microporous Zeolites”
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Position-dependent diffusion tensors in anisotropic media from simulation : oxygen transport in and through membranes
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Discovery of mycobacterium tuberculosis InhA inhibitors by binding sites comparison and ligands prediction
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- Journal Article
- A1
- open access
Water coordination and dehydration processes in defective UiO-66 type metal organic frameworks
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- Journal Article
- A1
- open access
Semi-analytical mean-field model for predicting breathing in metal–organic frameworks
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- Journal Article
- A1
- open access
A comparison of barostats for the mechanical characterization of metal-organic frameworks
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- Journal Article
- A1
- open access
Shape-selective diffusion of olefins in 8-ring solid acid microporous zeolites
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- Journal Article
- A1
- open access
Mechanical properties from periodic plane wave quantum mechanical codes: the challenge of the flexible nanoporous MIL-47(V) framework
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- Conference Paper
- P1
- open access
Normal mode analysis of macromolecular systems with the mobile block Hessian method
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- Conference Paper
- C3
- open access
Exploring new frontiers in modeling complex zeolite-catalyzed reactions using advanced molecular dynamics techniques
(2015) -
- Journal Article
- A1
- open access
Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics
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Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics
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Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
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Tailoring metal-organic frameworks for adsorption applications
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- Conference Paper
- C3
- open access
New quasi-1D materials: DFT-study of breathing metal-organic frameworks
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Critical analysis of the accuracy of models predicting or extracting liquid structure information
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On the thermodynamics of framework breathing: a free energy model for gas adsorption in MIL-53
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- Conference Paper
- C3
- open access
Oxygen diffusion water, alkanes, and lipid bilayers
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Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining
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- Conference Paper
- C3
- open access
Empty host breathing profiles of MIL-53 type frameworks with various cations at the nodal points
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- Journal Article
- A1
- open access
Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system
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- Journal Article
- A1
- open access
Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids : application to methanol
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Thermodynamics of 'breathing' of metal-organic frameworks: free energy model for adsorption induced transitions
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- Conference Paper
- C3
- open access
Implosion-based mapping procedure between all-atom and coarse-grained normal modes
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Free energy profile of 'breathing' flexible porous frameworks
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Introducing BSSE as an extra energy term in molecular dynamics
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First principle kinetic studies of zeolite-catalyzed methylation reactions
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Efficient calculation of QM/MM frequencies with the mobile block hessian
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Normal mode analysis in zeolites: toward an efficient calculation of adsorption entropies
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- Conference Paper
- C3
- open access
A theoretical and experimental spectroscopy study on methanol and ethanol conversion over H-SAPO-34
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- Journal Article
- A1
- open access
Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34
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- Conference Paper
- C3
- open access
Monte Carlo simulations to understand 'breathing' phenomenon of metal organic frameworks
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Understanding framework flexibility by Monte Carlo simulation
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Advanced normal mode analysis for multi-scale modeling
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Comparative study of various normal mode analysis techniques based on partial Hessians
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TAMkin : a versatile package for vibrational analysis and chemical kinetics
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- Conference Paper
- C3
- open access
Efficient calculation of QM/MM frequencies with the Mobile Block Hessian
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Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach
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Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules
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- Conference Paper
- C1
- open access
Normal mode analysis of macromolecular systems with the Mobile Block Hessian method
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- Conference Paper
- C3
- open access
The evaluation of the QM/MM full Hessian and some applications
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- Conference Paper
- C3
- open access
Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method
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The evaluation of QM/MM full Hessian and some applications
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- PhD Thesis
- open access
Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian Method
(2009) -
- Conference Paper
- C3
- open access
Normal modes in partially optimized molecular systems: the Mobile Block Hessian (MBH) approach
(2008) -
- Conference Paper
- C3
- open access
On the development of a partial vibrational analysis within a QM/MM approach
(2008) -
- Conference Paper
- C3
- open access
An efficient approach for the calculation of frequencies in macromolecules
(2008) -
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit
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Calculating reaction rates with partial Hessians: Validation of the mobile block Hessian approach
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MFI fingerprint: How pentasil-induced IR bands shift during zeolite nanogrowth
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Vibrational modes in partially optimized molecular systems
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Cartesian formulation of the mobile block Hessian approach to vibrational analysis in partially optimized systems
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- Journal Article
- A1
- open access
Role of mean free path in spatial phase correlation and nodal screening