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Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
Cell membranes interact via anchored receptor and ligand molecules. Central questions on cell adhesion concern the binding affinity of these membrane-anchored molecules, the mechanisms leading to the receptor-ligand domains observed during…
The multi-cellular hydrodynamic interactions play a critical role in the phenomenology of blood flow in the microcirculation. A fast algorithm has been developed to simulate large numbers of cells modeled as elastic thin membranes. For red…
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. In this work, we introduce a new,…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
Inhibiting a signalling pathway concerns controlling the cellular processes of a cancer cell's viability, cell division, and death. Assay protocols created to see if the molecular structures of the drugs being tested have the desired…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…
Recent studies have highlighted intracellular viscosity as a key biomechanical property with potential as a biomarker for cancer cell metastasis. In the context of cellular mechanobiology, magnetic rotational spectroscopy (MRS), which…
Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance,…
Studying cell morphology changes in time is critical to understanding cell migration mechanisms. In this work, we present a deep learning-based workflow to segment cancer cells embedded in 3D collagen matrices and imaged with phase-contrast…
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations provide a rigorous physical basis for studying these dynamics,…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
Soft interfaces formed by lipid membranes are fundamental to living cells, synthetic cells, and membrane-based soft materials. However, a quantitative framework linking molecular organization with nonlinear interfacial mechanics remains…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Skin dynamics contributes to the enriched realism of human body models in rendered scenes. Traditional methods rely on physics-based simulations to accurately reproduce the dynamic behavior of soft tissues. Due to the model complexity and…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…