Related papers: Data-driven modelling of biological multi-scale pr…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
This paper presents a comprehensive survey of various established mathematical models pertaining to Somitogenesis, a biological process. The study begins by revisiting and replicating the findings from prominent research papers in this…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
We propose a multiscale approach for predicting quantities in dynamical systems which is explicitly structured to extract information in both fine-to-coarse and coarse-to-fine directions. We envision this method being generally applicable…
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…
In this short note, we discuss the basic approach to computational modeling of dynamical systems. If a dynamical system contains multiple time scales, ranging from very fast to slow, computational solution of the dynamical system can be…
Neural activity fluctuates over a wide range of timescales within and across brain areas. Experimental observations suggest that diverse neural timescales reflect information in dynamic environments. However, how timescales are defined and…
Mathematical oncology provides unique and invaluable insights into tumour growth on both the microscopic and macroscopic levels. This review presents state-of-the-art modelling techniques and focuses on their role in understanding…
This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
The importance of molecular-scale forces in sculpting biological form and function has been acknowledged for more than a century. Accounting for forces in biology is a problem that lies at the intersection of soft condensed matter physics,…
The modeling of complex systems such as ecological or socio-economic systems can be very challenging. Although various modeling approaches exist, they are generally not compatible and mutually consistent, and empirical data often do not…
Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
Multi-scale structures are prevalent in both natural and artificial systems, as they can handle increasing complexity. Several terms are employed almost interchangeably across various application domains to refer to the multi-scale concept…