Vijay Rajagopal
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View article: Cardiac myofibril networks induce shear stress
Cardiac myofibril networks induce shear stress Open
Myofibril arrangement is critical to cardiac muscle function in health and disease. Historically, analysis of the impact of myofibril organisation on force and cell contraction has relied on the assumption of uniaxial arrays. However, impr…
View article: The Human Cardiac “Age‐OME”: Age‐Specific Changes in Myocardial Molecular Expression
The Human Cardiac “Age‐OME”: Age‐Specific Changes in Myocardial Molecular Expression Open
Ageing is one of the most significant risk factors for heart disease; however, it is still not clear how the human heart changes with age. Taking advantage of a unique set of pre‐mortem, cryopreserved, non‐diseased human hearts, we perform…
View article: Left ventricular myocardial molecular profile of human diabetic ischaemic cardiomyopathy
Left ventricular myocardial molecular profile of human diabetic ischaemic cardiomyopathy Open
View article: Energy-based modelling of single actin filament polymerization using bond graphs
Energy-based modelling of single actin filament polymerization using bond graphs Open
Bond graphs provide an energy-based methodology for modelling complex systems hierarchically; at the moment, the method allows biological systems with both chemical and electrical subsystems to be modelled. Herein, the bond graph approach …
View article: Exploring Design-Based Research as a framework for addressing pedagogical problems faced by higher education
Exploring Design-Based Research as a framework for addressing pedagogical problems faced by higher education Open
Design-Based Research presents a pragmatic approach to addressing both pedagogical problems and innovations within a rigorous framework that aims to build transferable practice. This panel discussion will explore four examples of implement…
View article: Energy-based Modelling of Single Actin Filament Polymerisation Using Bond Graphs
Energy-based Modelling of Single Actin Filament Polymerisation Using Bond Graphs Open
Bond graphs provide an energy-based methodology for modelling complex systems in a hierarchical fashion; at the moment, the method allows biological system with both chemical and electrical subsystems to be modelled. Herein, the bond graph…
View article: Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression
Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression Open
Background DNA replication progression can be affected by the presence of physical barriers like the RNA polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know how transcription influences overall DNA replic…
View article: Design-Based Research
Design-Based Research Open
This concise paper explores how Design-Based Research (DBR) can practically guide pedagogical innovation through collaborative curriculum design. We illustrate this with four short case studies (vignettes) of DBR implemented in different d…
View article: Optimizing coupling layer and superstrate thickness in attachable acoustofluidic devices
Optimizing coupling layer and superstrate thickness in attachable acoustofluidic devices Open
Superstrate-based acoustofluidic devices, where the fluidic elements are reversibly coupled to a transducer rather than bonded to it, offer advantages for cost, interchangeability and preventing contamination between samples. A variety of …
View article: BondGraphs.jl: composable energy-based modelling in systems biology
BondGraphs.jl: composable energy-based modelling in systems biology Open
Summary BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely u…
View article: BondGraphs.jl: Composable energy-based modelling in systems biology
BondGraphs.jl: Composable energy-based modelling in systems biology Open
Summary BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely u…
View article: Frontiers of Mathematical Biology: A workshop honouring Professor Edmund Crampin
Frontiers of Mathematical Biology: A workshop honouring Professor Edmund Crampin Open
• Edmund Crampin was Professor of Systems Biology at the University of Melbourne. He passed away on 15 May 2021. • A workshop in honour of Edmund was held at the University of Melbourne in November 2022. • 11 of his colleagues gave scienti…
View article: InsP3R-RyR channel crosstalk augments sarcoplasmic reticulum Ca2+ release and arrhythmogenic activity in post-MI pig cardiomyocytes
InsP3R-RyR channel crosstalk augments sarcoplasmic reticulum Ca2+ release and arrhythmogenic activity in post-MI pig cardiomyocytes Open
View article: Energy dependence of signalling dynamics and robustness in bacterial two component systems
Energy dependence of signalling dynamics and robustness in bacterial two component systems Open
One of the best known ways bacteria cells understand and respond to the environment are through Two-Component Systems (TCS). These signalling systems are highly diverse in function and can detect a range of physical stimuli including molec…
View article: IP3R activity increases propensity of RyR-mediated sparks by elevating dyadic [Ca2＋]
IP3R activity increases propensity of RyR-mediated sparks by elevating dyadic [Ca2＋] Open
View article: New revelations on the interplay between cardiomyocyte architecture and cardiomyocyte function in growth, health, and disease: a brief introduction
New revelations on the interplay between cardiomyocyte architecture and cardiomyocyte function in growth, health, and disease: a brief introduction Open
View article: CardioVinci: building blocks for virtual cardiac cells using deep learning
CardioVinci: building blocks for virtual cardiac cells using deep learning Open
Advances in electron microscopy (EM) such as electron tomography and focused ion-beam scanning electron microscopy provide unprecedented, three-dimensional views of cardiac ultrastructures within sample volumes ranging from hundreds of nan…
View article: Effects of altered cellular ultrastructure on energy metabolism in diabetic cardiomyopathy: an <i>in silico</i> study
Effects of altered cellular ultrastructure on energy metabolism in diabetic cardiomyopathy: an <i>in silico</i> study Open
Diabetic cardiomyopathy is a leading cause of heart failure in diabetes. At the cellular level, diabetic cardiomyopathy leads to altered mitochondrial energy metabolism and cardiomyocyte ultrastructure. We combined electron microscopy (EM)…
View article: Role of actin filaments and cis binding in cadherin clustering and patterning
Role of actin filaments and cis binding in cadherin clustering and patterning Open
Cadherins build up clusters to maintain intercellular contact through trans and cis (lateral) bindings. Meanwhile, interactions between cadherin and the actin cytoskeleton through cadherin/F-actin linkers can affect cadherin dynamics by co…
View article: Effects of altered cellular ultrastructure on energy metabolism in diabetic cardiomyopathy – an in-silico study
Effects of altered cellular ultrastructure on energy metabolism in diabetic cardiomyopathy – an in-silico study Open
Summary Diabetic cardiomyopathy is a leading cause of heart failure in diabetes. At the cellular level, diabetic cardiomyopathy leads to altered mitochondrial energy metabolism and cardiomyocyte ultrastructure. We combined electron microsc…
View article: The Cell Physiome: What do we need in a computational physiology framework for predicting single cell biology?
The Cell Physiome: What do we need in a computational physiology framework for predicting single cell biology? Open
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a fra…
View article: Paradoxes of Hymenoptera flight muscles, extreme machines
Paradoxes of Hymenoptera flight muscles, extreme machines Open
View article: Cortical tension initiates the positive feedback loop between cadherin and F-actin
Cortical tension initiates the positive feedback loop between cadherin and F-actin Open
View article: Improving student outcomes through transdisciplinary curriculum design in biomedical engineering
Improving student outcomes through transdisciplinary curriculum design in biomedical engineering Open
The boundaries between traditional engineering disciplines are breaking down.It is increasingly important for engineering students to be equipped with the ability to integrate complex concepts across disciplines to tackle real world proble…
View article: Multimodal imaging reveals membrane skeleton reorganisation during reticulocyte maturation and differences in dimple and rim regions of mature erythrocytes
Multimodal imaging reveals membrane skeleton reorganisation during reticulocyte maturation and differences in dimple and rim regions of mature erythrocytes Open
The red blood cell (RBC) is remarkable in its ability to deform as it passages through the vasculature. Its deformability derives from a spectrin-actin protein network that supports the cell membrane and provides strength and flexibility, …
View article: Respiration mask waveguide optimisation for maximised speech intelligibility
Respiration mask waveguide optimisation for maximised speech intelligibility Open
Both the scarcity and environmental impact of disposable face masks, as in the COVID-19 pandemic, have instigated the recent development of reusable masks. Such face masks reduce transmission of infectious agents and particulates, but ofte…
View article: CardioVinci: building blocks for virtual cardiac cells using deep learning
CardioVinci: building blocks for virtual cardiac cells using deep learning Open
Recent advances in high-throughput microscopy imaging have made it easier to acquire large volumes of cell images. Thanks to electron microscopy (EM) imaging, they provide a high-resolution and sufficient field of view that suits imaging l…
View article: A toolbox for generating scalable mitral valve morphometric models
A toolbox for generating scalable mitral valve morphometric models Open
View article: EGFRvIII Promotes Cell Survival during Endoplasmic Reticulum Stress through a Reticulocalbin 1-Dependent Mechanism
EGFRvIII Promotes Cell Survival during Endoplasmic Reticulum Stress through a Reticulocalbin 1-Dependent Mechanism Open
Reticulocalbin 1 (RCN1) is an endoplasmic reticulum (ER)-residing protein, involved in promoting cell survival during pathophysiological conditions that lead to ER stress. However, the key upstream receptor tyrosine kinase that regulates R…
View article: Cortical Tension Initiates the Positive Feedback Loop Between E-cadherin and F-actin
Cortical Tension Initiates the Positive Feedback Loop Between E-cadherin and F-actin Open
Adherens junctions (AJs) physically link two cells at their contact interface via extracellular homophilic interactions between cadherin molecules and intracellular connections between cadherins and the actomyosin cortex. Both cadherin and…