Developing tools, techniques, algorithms, and mathematical theory to integrate modeling and simulation from the micro to the macro-scale is important in biocomputing. This session aims to foster the interactive environment for researchers working across different scales of biological problems, so that more collaborations and activities to bridge multi-scales will be initiated. The overall focus of our session is on challenges to be overcome in computational approaches to multiscale modeling in biology, with a specific focus on mechanistic (i.e. biophysics-based) patient-specific modeling crossing different scales from proteins, cells, tissues, organs, up to the whole-organism level.

Since the last few decades, novel diagnostic and therapeutic medical technologies have been developed. This resulted in an increasing knowledge of pathophysiology from gene to organ systems. Together with ever increasing computer power, it is becoming feasible to design biophysically detailed multi-scale patient-specific models to guide and predict the response to therapy in many aspects of medicine. Modeling from a biophysical base would not only provide predictions of specific therapies or surgical interventions, but also insight into the degree of success or failure. To rely on the predictive capabilities of these types of models, efficient methods and computational tools are of the utmost importance.

Session topics

We cordially invite submissions of papers or abstracts that will address physics-based modeling activities focused on encompassing at least two levels of physiology. Submission topics can include, but are not limited to:

   Multiscale methods

• Methods for making the connection between continuum macroscale models and discrete molecular phenomena

• Model reduction and systems identification for multiscale dynamical systems

• Algorithmic tools for multi-scale modeling systems using optimization and simulation in time and space

• Mesoscale methods to bridge microscales and macroscales

• Multi-level finite element methods 

• From genotype to phenotype

• Molecular biology of ion channels and transporters

• Excitation-contraction coupling and mechanoelectric feedback in normal and diseased cells

• Mechanotransduction

• Dynamic simulation of neuromuscular systems

   Patient-specific modeling

• Real-time patient-specific modeling during surgery

• Pharmacological (toxicological) effects on physiologic function

• Acquisition of patient-specific material properties

• Automation of patient-specific modeling

Session chairs

Roy Kerckhoffs

University of California San Diego