Molecular Modeling

Molecular Modeling

TR&D1:  Molecular modeling and simulations: Bridging molecular and cellular scales Vision. There is a growing need to understand molecular events at…

Cell Modeling

Cell Modeling

TR&D2: Cell modeling, with an emphasis on developing tools to handle spatial and molecular complexity inherent to neuronal signal transmission.…

Image Processing & Analysis

Image Processing & Analysis

TR&D3: Image processing and analysis, with an emphasis on analysis of cell and tissue organization in support of modeling Microscope…

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Research Highlights


Tools for determining the spatial relationships

An important task for understanding how cells are organized is determining which components have spatial patterns that are related to each other. Read more


4d rtd

Pipeline for creation of spatiotemporal maps

Using a combination of diffeomorphic methods and improved cell segmentation, we developed a CellOrganizer pipeline for use in DPB4 to construct models of the 4D distributions of actin and 8 of its regulators during the response of T cells to antigen presentation. Read more


Multi-scale Hybrid Methodology

The hybrid methodology, coMD, that we have recently developed [1] has been recently extended to construct the energy landscape near the functional states of LeuT (Fig 1) [2]. This is the first energy landscape constructed for this NSS family member.  Read more


Insights into the cooperative dynamics of AMPAR

Comparative analysis of AMPAR and NMDAR dynamics reveals striking similarities, opening the way to designing new modulators of allosteric interactions. Read more

Improved Sampling of Cell-Scale Models using the WE Strategy

The WE strategy for orchestrating a large set of parallel simulations has now been extended to spatially resolved cell-scale systems. The WESTPA implementation of WE has been used to control MCell simulations, including models built using a BioNetGen-CellOrganizer pipeline for situating complex biochemistry within spatially realistic cell models. Read more

Mouse visual cortex
Anatomy and Function of an Excitatory Network in the Visual Cortex

MMBioS researcher Greg Hood’s collaboration with Wei-Chung Allen Lee of Harvard University and R. Clay Reid of the Allen Institute for Brain Science concerning the reconstruction of an excitatory nerve-cell network in the mouse brain cortex at a subcellular level using the AlignTK software has been published in Nature. Read more


Molecular Mechanism of Dopamine Transport by hDAT

Dopamine transporters (DATs) control neurotransmitter dopamine (DA) homeostasis by reuptake of excess DA, assisted by sodium and chloride ions. The recent resolution of DAT structure (dDAT) from Drosophila permits us for the first time to directly view the sequence of events involved in DA reuptake in human DAT (hDAT). Read more

figure good 170Synaptic Facilitation Revealed

An investigation of several mechanisms of short-term facilitation at the frog neuromuscular junction concludes that the presence of a second class of calcium sensor proteins distinct from synaptotagmin can explain known properties of facilitation.  Read more


langmead2 200Sparse Graphical Models of Protein:Protein Interactions

DgSpi is a new method for learning and using graphical models that explicitly represent the amino acid basis for interaction specificity and extend earlier classification-oriented approaches to predict ΔG of binding.  Read more


Picture1 180Advancing Parallel Bio-simulations

A new non-Markovian analysis can eliminate bias in estimates of long-timescale behavior, such as the mean first-passage time for the dissociation of methane molecules in explicit solvent. Read more