Philip Pearce

Office: 2-179
Department of Mathematics
Massachusetts Institute of Technology
77 Massachusetts Avenue
Cambridge, MA 02139-4307


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Research Interests


Current/Previous Projects and Publications

Learning dynamical information from static protein and sequencing data (MIT Applied Mathematics Instructorship):

Protein folding and microbial evolution belong to the large class of physical, chemical and biological processes that can be described as diffusive exploration of an effective high-dimensional energy landscape. Recent advances in electronic and optical data acquisition technologies have been accompanied by substantial progress in the development of mathematical dimensionality reduction techniques for complex systems. By contrast, the reliable reconstruction of relevant dynamical information from static ensemble data, as provided by modern sequencing protocols and similar instantaneous sampling methods, still poses major challenges. In this project, we introduce a generic computational framework to reconstruct low-dimensional dynamical transition networks from high-dimensional static samples. We demonstrate the broad applicability of the underlying concepts by successfully predicting protein folding transitions and HIV evolution pathways. In collaboration with the groups of Jörn Dunkel and Halim Kusumaatmaja.

Physical determinants of bacterial biofilm architectures (MIT Applied Mathematics Instructorship):

In many situations bacteria aggregate to form biofilms: dense, surface-associated, three-dimensional structures populated by cells embedded in matrix. Biofilm architectures are sculpted by mechanical processes including cell growth, cell-cell interactions and external forces. In this project, using single-cell live imaging in combination with simulations, we characterize the cell-cell interactions that generate Vibrio cholerae biofilm morphologies. Fluid shear is shown to affect biofilm shape through the growth rate and orientation of cells, despite spatial differences in shear stress being balanced by cell-cell adhesion. Our results demonstrate the importance of cell dynamics mediated by adhesion proteins and matrix generation in determining the global architecture of biofilm structures. In collaboration with the groups of Jörn Dunkel and Knut Drescher.

Blood flow and solute transport in the placenta (EPSRC Doctoral Prize Fellowship):

Throughout the mammalian species, solute exchange takes place in complex microvascular networks. In recent years, multi-scale models have proved successful in investigating the structure-function relationship of such networks in specific contexts. However, general methods for incorporating experimental data on complex, heterogeneous capillary networks into whole-organ multi-scale models remain under-developed. In this project we introduce a theoretical framework, tested against image-based computations, for quantifying the transport capacity of feto-placental capillary networks using experimental data. We find that solute transfer can be described using a near-universal physical scaling based on two non-dimensional parameters (the diffusive capacity and a Damköhler number), which can be extracted from microscopy images via standard computational and image-analysis tools. In collaboration with Oliver Jensen, Igor Chernyavsky and others.

Propagation and stability of flames in inhomogeneous mixtures (EPSRC Doctoral Training Award):

In many practical situations involving a propagating flame, inhomogeneities are present in the mixture through which the flame propagates. These inhomogeneities can be caused by fluctuations or stratifications in the temperature, the composition or the flow field. In this project the effect of inhomogeneities on laminar flames is modelled, including premixed flames and triple flames, through the numerical and asymptotic solution of the coupled equations for temperature, mass fractions and flow. In collaboration with Joel Daou.

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