Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

N Ramakrishnan, PBS Kumar, R Radhakrishnan - Physics reports, 2014 - Elsevier
Biological membranes constitute boundaries of cells and cell organelles. These membranes
are soft fluid interfaces whose thermodynamic states are dictated by bending moduli …

Systems biology and physical biology of clathrin-mediated endocytosis

V Ramanan, NJ Agrawal, J Liu, S Engles… - Integrative …, 2011 - academic.oup.com
In this review, we describe the application of experimental data and modeling of intracellular
endocytic trafficking mechanisms with a focus on the process of clathrin-mediated …

Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis

NJ Agrawal, J Nukpezah… - PLoS computational …, 2010 - journals.plos.org
In eukaryotic cells, the internalization of extracellular cargo via the endocytic machinery is an
important regulatory process required for many essential cellular functions. The role of …

The role of glycocalyx in nanocarrier-cell adhesion investigated using a thermodynamic model and Monte Carlo simulations

NJ Agrawal, R Radhakrishnan - The Journal of Physical Chemistry …, 2007 - ACS Publications
We present an equilibrium model for quantifying the effect of glycocalyx in mediating the
interaction of functionalized nanocarriers with endothelial cells. In this model, nanocarrier …

Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers

RW Tourdot, N Ramakrishnan, R Radhakrishnan - Physical Review E, 2014 - APS
Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and
Exo70, are known to reshape cell membranes, and this remodeling event is essential for key …

Nanocarrier hydrodynamics and binding in targeted drug delivery: challenges in numerical modeling and experimental validation

PS Ayyaswamy, V Muzykantov… - Journal of …, 2013 - asmedigitalcollection.asme.org
This review discusses current progress and future challenges in the numerical modeling of
targeted drug delivery using functionalized nanocarriers (NC). Antibody coated nanocarriers …

Multiscale computational models in physical systems biology of intracellular trafficking

RW Tourdot, RP Bradley, N Ramakrishnan… - IET systems …, 2014 - Wiley Online Library
In intracellular trafficking, a definitive understanding of the interplay between protein binding
and membrane morphology remains incomplete. The authors describe a computational …

A multiscale computational approach to dissect early events in the Erb family receptor mediated activation, differential signaling, and relevance to oncogenic …

Y Liu, J Purvis, A Shih, J Weinstein, N Agrawal… - Annals of biomedical …, 2007 - Springer
We describe a hierarchical multiscale computational approach based on molecular
dynamics simulations, free energy-based molecular docking simulations, deterministic …

Mesoscale simulations of curvature-inducing protein partitioning on lipid bilayer membranes in the presence of mean curvature fields

J Liu, R Tourdot, V Ramanan, NJ Agrawal… - Molecular …, 2012 - Taylor & Francis
The membrane-surface migration of curvature-inducing proteins in response to membrane
curvature gradients has been investigated using Monte Carlo simulations of a curvilinear …

Nonaxisymmetric shapes of biological membranes from locally induced curvature

YAD Omar, A Sahu, RA Sauer, KK Mandadapu - Biophysical journal, 2020 - cell.com
In various biological processes such as endocytosis and caveolae formation, the cell
membrane is locally deformed into curved morphologies. Previous models to study …