4.7 Article

Molecular dynamics simulations of the effects of lipid oxidation on the permeability of cell membranes

Related references

Note: Only part of the references are listed.
Article Chemistry, Physical

Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems

Lennard Boeselt et al.

Summary: QM/MM molecular dynamics simulations are computationally expensive due to the need to explicitly treat all valence electrons and perform a self-consistent field procedure. Machine-learned models show promise in reducing the computational cost and improving accuracy.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Materials Science, Multidisciplinary

Artificial Intelligence and QM/MM with a Polarizable Reactive Force Field for Next-Generation Electrocatalysts

Saber Naserifar et al.

Summary: In order to develop high-performance electrocatalysts, the combination of the accurate RexPoN reactive force field and QM enables reactive simulations with QM accuracy in the presence of explicit solvent. By incorporating machine learning to predict the performance of surface sites, it provides an accurate and practical way to design high-performance electrocatalysts.

MATTER (2021)

Article Biochemistry & Molecular Biology

Electropermeabilization does not correlate with plasma membrane lipid oxidation

Olga Michel et al.

BIOELECTROCHEMISTRY (2020)

Article Biochemistry & Molecular Biology

Probing Nanoelectroporation and Resealing of the Cell Membrane by the Entry of Ca2+ and Ba2+ Ions

Wenfei Bo et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Acoustics

New insights on the role of ROS in the mechanisms of sonoporation-mediated gene delivery

Jean-Michel Escoffre et al.

ULTRASONICS SONOCHEMISTRY (2020)

Editorial Material Cell Biology

Igniting the spread of ferroptotic cell death

Andrew J. Davidson et al.

NATURE CELL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

Deep-neural-network solution of the electronic Schrodinger equation

Jan Hermann et al.

NATURE CHEMISTRY (2020)

Review Biophysics

Membrane Electroporation and Electropermeabilization: Mechanisms and Models

Tadej Kotnik et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 48 (2019)

Article Biochemistry & Molecular Biology

Understanding membrane remodelling initiated by photosensitized lipid oxidation

Tayana Mazin Tsubone et al.

BIOPHYSICAL CHEMISTRY (2019)

Article Materials Science, Biomaterials

Development of voltage gated transdermal drug delivery platform to impose synergistic enhancement in skin permeation using electroporation and gold nanoparticle

T. S. Anirudhan et al.

MATERIALS SCIENCE AND ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS (2019)

Article Multidisciplinary Sciences

Unifying machine learning and quantum chemistry with a deep neural network for molecular wavefunctions

K. T. Schuett et al.

NATURE COMMUNICATIONS (2019)

Review Biochemistry & Molecular Biology

A Comprehensive Review on Lipid Oxidation in Meat and Meat Products

Ruben Dominguez et al.

ANTIOXIDANTS (2019)

Review Biochemistry & Molecular Biology

Crashing the computer: apoptosis vs. necroptosis in neuroinflammation

Bradlee L. Heckmann et al.

CELL DEATH AND DIFFERENTIATION (2019)

Article Biotechnology & Applied Microbiology

Noninvasive Gene Electrotransfer in Skin

Lise Pasquet et al.

HUMAN GENE THERAPY METHODS (2019)

Review Chemistry, Multidisciplinary

Mechanisms of Photosensitized Lipid Oxidation and Membrane Permeabilization

Isabel O. L. Bacellar et al.

ACS OMEGA (2019)

Article Biochemistry & Molecular Biology

Investigation of the chemical mechanisms involved in the electropulsation of membranes at the molecular level

Marie Breton et al.

BIOELECTROCHEMISTRY (2018)

Article Chemistry, Physical

Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization

Josef Melcr et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

Article Physics, Applied

Atomic scale understanding of the permeation of plasma species across native and oxidized membranes

Jamoliddin Razzokov et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2018)

Article Multidisciplinary Sciences

Roughness of Transmembrane Helices Reduces Lipid Membrane Dynamics

Marie Olsinova et al.

ISCIENCE (2018)

Article Biochemistry & Molecular Biology

Preferential hydrolysis of truncated oxidized glycerophospholipids by lysosomal phospholipase A2

Akira Abe et al.

JOURNAL OF LIPID RESEARCH (2017)

Article Chemistry, Organic

Lipid Peroxidation: Kinetics, Mechanisms, and Products

Zosia A. M. Zielinski et al.

JOURNAL OF ORGANIC CHEMISTRY (2017)

Review Biochemistry & Molecular Biology

Membrane Oxidation in Cell Delivery and Cell Killing Applications

Ting-Yi Wang et al.

ACS CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Lipid peroxidation in cell death

Michael M. Gaschler et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2017)

Article Biochemistry & Molecular Biology

A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields

Maura Casciola et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2016)

Review Biochemistry & Molecular Biology

Ferroptosis: process and function

Y. Xie et al.

CELL DEATH AND DIFFERENTIATION (2016)

Article Multidisciplinary Sciences

Peroxidation of polyunsaturated fatty acids by lipoxygenases drives ferroptosis

Wan Seok Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Chemistry, Multidisciplinary

Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress

Jonas Van der Paal et al.

CHEMICAL SCIENCE (2016)

Article Biochemistry & Molecular Biology

Effect of Pulsed Electric Field on Membrane Lipids and Oxidative Injury of Salmonella typhimurium

Ou Yun et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2016)

Article Biochemistry & Molecular Biology

Critical role of peroxiredoxin 6 in the repair of peroxidized cell membranes following oxidative stress

Haitao Li et al.

FREE RADICAL BIOLOGY AND MEDICINE (2015)

Article Biochemistry & Molecular Biology

Optimization of the Electroformation of Giant Unilamellar Vesicles (GUVs) with Unsaturated Phospholipids

Marie Breton et al.

JOURNAL OF MEMBRANE BIOLOGY (2015)

Article Chemistry, Physical

Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids

Phansiri Boonnoy et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2015)

Review Medicine, General & Internal

Photodynamic Therapy: Current Status and Future Directions

Ludmil Benov

MEDICAL PRINCIPLES AND PRACTICE (2015)

Review Chemistry, Multidisciplinary

The Structural Role of Cholesterol in Cell Membranes: From Condensed Bilayers to Lipid Rafts

Martin R. Krause et al.

ACCOUNTS OF CHEMICAL RESEARCH (2014)

Review Engineering, Biomedical

Electroporation-Based Technologies for Medicine: Principles, Applications, and Challenges

Martin L. Yarmush et al.

ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 16 (2014)

Article Biochemistry & Molecular Biology

The dynamics of giant unilamellar vesicle oxidation probed by morphological transitions

Shalene Sankhagowit et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2014)

Article Biochemistry & Molecular Biology

Reactive oxygen species at phospholipid bilayers: Distribution, mobility and permeation

Rodrigo M. Cordeiro

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2014)

Article Biophysics

Ion-Induced Defect Permeation of Lipid Membranes

Igor Vorobyov et al.

BIOPHYSICAL JOURNAL (2014)

Article Biophysics

Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

W. F. Drew Bennett et al.

BIOPHYSICAL JOURNAL (2014)

Article Chemistry, Physical

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations

Michel A. Cuendet et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Lipid Peroxidation in Membranes: The Peroxyl Radical Does Not Float

Julian Garrec et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)

Article Chemistry, Physical

Lipid oxidation induces structural changes in biomimetic membranes

Georges Weber et al.

SOFT MATTER (2014)

Article Biochemistry & Molecular Biology

Nanosecond pulsed electric field stimulation of reactive oxygen species in human pancreatic cancer cells is Ca2+-dependent

Richard Nuccitelli et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2013)

Article Agriculture, Multidisciplinary

Effect of electroporation on viability and bioconversion of isoflavones in mannitol-soymilk fermented by lactobacilli and bifidobacteria

Siok-Koon Yeo et al.

JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE (2013)

Article Cell Biology

Bactericidal Antibiotics Induce Mitochondrial Dysfunction and Oxidative Damage in Mammalian Cells

Sameer Kalghatgi et al.

SCIENCE TRANSLATIONAL MEDICINE (2013)

Article Biochemistry & Molecular Biology

Oxidative effects of nanosecond pulsed electric field exposure in cells and cell-free media

Olga N. Pakhomova et al.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2012)

Article Biochemistry & Molecular Biology

Nanosecond pulsed electric fields (nsPEFs) activate intrinsic caspase-dependent and caspase-independent cell death in Jurkat cells

Wei Ren et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2012)

Review Biochemistry & Molecular Biology

Biophysics of lipid bilayers containing oxidatively modified phospholipids: Insights from fluorescence and EPR experiments and from MD simulations

Piotr Jurkiewicz et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2012)

Review Biochemistry & Molecular Biology

Chemistry of phospholipid oxidation

Ana Reis et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2012)

Article Chemistry, Physical

Heating and flooding: A unified approach for rapid generation of free energy surfaces

Ming Chen et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

Article Biochemistry & Molecular Biology

Plasma membrane permeabilization by trains of ultrashort electric pulses

Bennett L. Ibey et al.

BIOELECTROCHEMISTRY (2010)

Article Biochemical Research Methods

The current-voltage relation for electropores with conductivity gradients

Jianbo Li et al.

BIOMICROFLUIDICS (2010)

Article Biochemistry & Molecular Biology

Life Cycle of an Electropore: Field-Dependent and Field-Independent Steps in Pore Creation and Annihilation

Zachary A. Levine et al.

JOURNAL OF MEMBRANE BIOLOGY (2010)

Article Chemistry, Physical

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Jeffery B. Klauda et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Biochemistry & Molecular Biology

Lipid nanopores can form a stable, ion channel-like conduction pathway in cell membrane

Andrei G. Pakhomov et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2009)

Article Biophysics

Giant Vesicles under Oxidative Stress Induced by a Membrane-Anchored Photosensitizer

Karin A. Riske et al.

BIOPHYSICAL JOURNAL (2009)

Article Computer Science, Interdisciplinary Applications

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

Massimiliano Bonomi et al.

COMPUTER PHYSICS COMMUNICATIONS (2009)

Article Chemistry, Multidisciplinary

Lateral Diffusion of Membrane Proteins

Sivaramakrishnan Ramadurai et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Article Multidisciplinary Sciences

Electroporating Fields Target Oxidatively Damaged Areas in the Cell Membrane

P. Thomas Vernier et al.

PLOS ONE (2009)

Article Chemistry, Physical

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Berk Hess et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Multidisciplinary Sciences

Protein area occupancy at the center of the red blood cell membrane

Allison D. Dupuy et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biophysics

Effect of lipid peroxidation on the properties of lipid bilayers: A molecular dynamics study

Jirasak Wong-Ekkabut et al.

BIOPHYSICAL JOURNAL (2007)

Article Biochemistry & Molecular Biology

Membrane permeabilization and cell damage by ultrashort electric field shocks

Andrei G. Pakhomov et al.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2007)

Review Biochemistry & Molecular Biology

Oxidized phospholipids: From molecular properties to disease

Gilbert O. Fruhwirth et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2007)

Article Engineering, Biomedical

Peroxidation of polyunsaturated phosphatidyl-choline lipids during electroformation

Yong Zhou et al.

BIOMATERIALS (2007)

Article Biochemistry & Molecular Biology

Electroporation in dense cell suspension - Theoretical and experimental analysis of ion diffusion and cell permeabilization

Mojca Pavlin et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2007)

Article Ophthalmology

(R)-α-lipoic acid protects retinal pigment epithelial cells from oxidative damage

LA Voloboueva et al.

INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE (2005)

Article Biochemistry & Molecular Biology

What's so special about cholesterol?

OG Mouritsen et al.

LIPIDS (2004)

Article Chemistry, Multidisciplinary

Influence of cholesterol and water content on phospholipid lateral diffusion in bilayers

A Filippov et al.

LANGMUIR (2003)