412 research outputs found
A Ca puff model based on integrodifferential equations
The calcium (Ca) signalling system is important for many cellular
processes within the human body. Signals are transmitted within the cell by
releasing Ca from the endoplasmic reticulum (ER) into the cytosol via
clusters of Ca channels. Mathematical models of Ca release via
inositol 1,4,5-trisphosphate receptors (IPR) help with understanding
underlying Ca dynamics but data-driven modelling of stochastic Ca
release events, known as Ca puffs, is a difficult challenge.
Parameterising Markov models for representing the IPR with steady-state
single channel data obtained at fixed combinations of the ligands Ca and
inositol-trisphosphate (IP) has previously been demonstrated to be
insufficient. However, by extending an IPR model based on steady-state
data with an integral term that incorporates the delayed response of the
channel to varying Ca concentrations we succeed in generating realistic
Ca puffs. By interpreting the integral term as a weighted average of
Ca concentrations that extend over a time interval of length into
the past we conclude that the IPR requires a certain amount of memory of
past ligand concentrations.Comment: 31 pages, 8 figures, 1 tabl
Computational Explorations in Biomedicine: Unraveling Molecular Dynamics for Cancer, Drug Delivery, and Biomolecular Insights using LAMMPS Simulations
With the rapid advancement of computational techniques, Molecular Dynamics
(MD) simulations have emerged as powerful tools in biomedical research,
enabling in-depth investigations of biological systems at the atomic level.
Among the diverse range of simulation software available, LAMMPS (Large-scale
Atomic/Molecular Massively Parallel Simulator) has gained significant
recognition for its versatility, scalability, and extensive range of
functionalities. This literature review aims to provide a comprehensive
overview of the utilization of LAMMPS in the field of biomedical applications.
This review begins by outlining the fundamental principles of MD simulations
and highlighting the unique features of LAMMPS that make it suitable for
biomedical research. Subsequently, a survey of the literature is conducted to
identify key studies that have employed LAMMPS in various biomedical contexts,
such as protein folding, drug design, biomaterials, and cellular processes. The
reviewed studies demonstrate the remarkable contributions of LAMMPS in
understanding the behavior of biological macromolecules, investigating
drug-protein interactions, elucidating the mechanical properties of
biomaterials, and studying cellular processes at the molecular level.
Additionally, this review explores the integration of LAMMPS with other
computational tools and experimental techniques, showcasing its potential for
synergistic investigations that bridge the gap between theory and experiment.
Moreover, this review discusses the challenges and limitations associated with
using LAMMPS in biomedical simulations, including the parameterization of force
fields, system size limitations, and computational efficiency. Strategies
employed by researchers to mitigate these challenges are presented, along with
potential future directions for enhancing LAMMPS capabilities in the biomedical
field.Comment: 39 pages- 10 figure
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