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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…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…
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…
Biomedical signals carry signature rhythms of complex physiological processes that control our daily bodily activity. The properties of these rhythms indicate the nature of interaction dynamics among physiological processes that maintain a…
The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted…