Simulating realistic membrane shapes

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity

(2021) Kristyna Pluhackova et al.   BMC BIOLOGY

Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus

(2021) Martín Soñora et al.   Journal of Chemical Information and Modeling

Protein-dependent membrane remodeling in mitochondrial morphology and clathrin-mediated endocytosis

(2021) Daryna Tarasenko et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations

(2021) Semen Yesylevskyy et al.   Journal of Chemical Theory and Computation

FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes

(2021) Marc Siggel et al.   Journal of Physical Chemistry Letters

Curvature-regulated lipid membrane softening of nano-vesicles

(2021) Choon-Peng Chng et al.   Extreme Mechanics Letters

An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

(2020) Christopher T. Lee et al.   BIOPHYSICAL JOURNAL

Molecular Simulation of Mechanical Properties and Membrane Activities of the ESCRT-III Complexes

(2020) Taraknath Mandal et al.   BIOPHYSICAL JOURNAL

To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes

(2020) Damien Jefferies et al.   JOURNAL OF MOLECULAR BIOLOGY

Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

(2020) Carsten F. E. Schroer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulation of subcellular structures

(2020) Syma Khalid et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dual Resolution Membrane Simulations Using Virtual Sites

(2020) Yang Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission

(2020) Thomas G. Flower et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Backmapping triangulated surfaces to coarse-grained membrane models

(2020) Weria Pezeshkian et al.   Nature Communications

A molecular view on the escape of lipoplexed DNA from the endosome

(2020) Bart MH Bruininks et al.   eLife

Capturing biologically complex tissue-specific membranes at different levels of compositional complexity

(2020) Helgi I Ingólfsson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models

(2020) Mohsen Sadeghi et al.   Nature Communications

Active particles induce large shape deformations in giant lipid vesicles

(2020) Hanumantha Rao Vutukuri et al.   NATURE

Coarse-Grained Simulations Suggest the Epsin N-Terminal Homology Domain Can Sense Membrane Curvature without Its Terminal Amphipathic Helix

(2020) Alexis Belessiotis-Richards et al.   ACS Nano

Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins

(2020) Zack Jarin et al.   BIOPHYSICAL JOURNAL

Diffusion on Membrane Domes, Tubes, and Pearling Structures

(2020) Rossana Rojas Molina et al.   BIOPHYSICAL JOURNAL

Simulations of Proposed Mechanisms of FtsZ-Driven Cell Constriction

(2020) Lam T. Nguyen et al.   JOURNAL OF BACTERIOLOGY

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

(2019) Giray Enkavi et al.   CHEMICAL REVIEWS

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

(2019) Alison N. Leonard et al.   CHEMICAL REVIEWS

Bilayer membranes with frequent flip-flops have tensionless leaflets

(2019) Markus Sakari Miettinen et al.   NANO LETTERS

Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy

(2019) Ramachandra M. Bhaskara et al.   Nature Communications

MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes

(2019) Harsh Bhatia et al.   Journal of Chemical Theory and Computation

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

(2019) Abhishek Singharoy et al.   CELL

Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations

(2019) Benjamin Bouvier   Journal of Chemical Theory and Computation

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

(2019) Giacomo Fiorin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

(2019) Grzegorz Nawrocki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shape transition from elliptical to cylindrical membrane tubes induced by chiral crescent-shaped protein rods

(2019) Hiroshi Noguchi   Scientific Reports

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

(2019) Semen Yesylevskyy et al.   Scientific Reports

Spontaneous Curvature, Differential Stress, and Bending Modulus of Asymmetric Lipid Membranes

(2019) Amirali Hossein et al.   BIOPHYSICAL JOURNAL

Mitochondrial morphology provides a mechanism for energy buffering at synapses

(2019) Guadalupe C. Garcia et al.   Scientific Reports

Organizing membrane-curving proteins: the emerging dynamical picture

(2018) Mijo Simunovic et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

­­Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force­

(2018) Claudio Anselmi et al.   JOURNAL OF GENERAL PHYSIOLOGY

The 2018 biomembrane curvature and remodeling roadmap

(2018) Patricia Bassereau et al.   JOURNAL OF PHYSICS D-APPLIED PHYSICS

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

(2018) N Ramakrishnan et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Curvature-Mediated Assembly of Janus Nanoparticles on Membrane Vesicles

(2018) Amir Houshang Bahrami et al.   NANO LETTERS

The glycolipid GM1 reshapes asymmetric biomembranes and giant vesicles by curvature generation

(2018) Raktim Dasgupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins

(2018) Matthieu Chavent et al.   Nature Communications

Acyl chain asymmetry and polyunsaturation of brain phospholipids facilitate membrane vesiculation without leakage

(2018) Marco M Manni et al.   eLife

Accurate in silico modeling of asymmetric bilayers based on biophysical principles

(2018) Milka Doktorova et al.   BIOPHYSICAL JOURNAL

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

Reactive molecular dynamics: From small molecules to proteins

(2018) Markus Meuwly   Wiley Interdisciplinary Reviews-Computational Molecular Science

BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition

(2018) Kevin J. Boyd et al.   Journal of Chemical Theory and Computation

The role of scaffold reshaping and disassembly in dynamin driven membrane fission

(2018) Martina Pannuzzo et al.   eLife

It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli

(2017) Pin-Chia Hsu et al.   Journal of Physical Chemistry Letters

Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

(2017) Ricardo de Oliveira dos Santos Soares et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

t-SNARE Transmembrane Domain Clustering Modulates Lipid Organization and Membrane Curvature

(2017) Satyan Sharma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics

(2017) Masashi Tachikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The influence of solid scaffolds on flat and curved lipid membranes

(2017) D. H. de Jong et al.   AIP Advances

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes

(2017) Anna L. Duncan et al.   Scientific Reports

Computational virology: From the inside out

(2016) Tyler Reddy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Nonadditive Compositional Curvature Energetics of Lipid Bilayers

(2016) A. J. Sodt et al.   PHYSICAL REVIEW LETTERS

Membrane invagination induced by Shiga toxin B-subunit: from molecular structure to tube formation

(2016) W. Pezeshkian et al.   Soft Matter

Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations

(2016) Jan K. Marzinek et al.   STRUCTURE

The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation

(2016) Julian Weichsel et al.   PLoS Computational Biology

Organelle morphogenesis by active membrane remodeling

(2015) N. Ramakrishnan et al.   Soft Matter

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

(2014) Heidi Koldsø et al.   PLoS Computational Biology

Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles

(2011) H. Jelger Risselada et al.   PHYSICAL REVIEW LETTERS