Research Highlight: Systems Biology


*Khammash Group: Dynamical phenomena in biological networks*	*Valentine Group: Force generation and transmission in cellular systems*

The Department of Mechanical Engineering at the University of California, Santa Barbara has emerged as a leader in the field of Systems Biology. Our faculty have deep expertise across many disciplines, spanning most branches of engineering, computer science, physics, applied math and biology. Through collaborative research, we are tackling important problems in biotechnology development, biosystems analysis and medicine using a combination of numerical, computational and experimental approaches. Research areas within the department are broad and multidisciplinary, but fall into three primary categories: biomechanics and biomaterials, biosensors and biomolecular analysis, and computation and modeling of dynamic biological systems.

We are currently hiring in the area of Systems Biology!

For details, please visit: http://me.ucsb.edu/position/mellichamp, or contact Professor Megan Valentine, Search Chair, at sysbio [at] engineering [dot] ucsb [dot] edu

Learn more about Systems Biology in Mechanical Engineering at UCSB:

Research Areas

Biomechanics and Biomaterials
Biosensors and Biomolecular Analysis
Computation and Modeling of Dynamic Biological Systems

News and Recent Awards

Related Institutes and Centers at UCSB

Biomechanics and Biological & Bio-inspired Materials


Molecular Motor Proteins Valentine Group	Actin Cytoskeletal Mechanics McMeeking Group

'Gecko Glue' Turner Group	Mechanics of DNA monolayers Begley Group

By incorporating key concepts from solid mechanics, materials science, and MEMS, we are leading efforts in understanding the activity and regulation of a variety of cellular systems. Recent efforts have focused on force generation in the mitotic spindle, vesicular trafficking in nerve axons and actin stress fiber formation in motile and adherent cells.

Additionally, we are using natural systems to inspire new classes of synthetic materials. Examples include bioinspired wet and dry adhesives and microstructured synthetic abalone shells.

Current Research Efforts in Biomechanics/Biomaterials Research:

Matthew Begley: Investigates connections between molecular and microscale material properties and macroscale behaviors. Current work focuses on how chemical environments affect adhesion, how DNA interacts when adsorbed on surfaces, or how the “brick and mortar” microstructures of synthetic abalone shell can be tailored to optimize strength and toughness.

Robert McMeeking: Applies core concepts from solid mechanics, materials, and structures to understand the mechanical properties of the actin cytoskeleton and mechanotransduction in motile, adherent cells.

Kimberly Turner: Develops MEMS-based biologically inspired reversible adhesives, and flexural plate wave devices with applications in biological sensing.

Megan Valentine: Uses optical traps, magnetic tweezers, advanced fluorescence methods, and traction force microscopy to understand how forces are generated and transmitted in molecular and cellular biological systems. Current work focuses on measuring the biochemical/mechanical properties of single molecules of motor and crosslinking proteins, reconstituted cytoskeletal networks, and intact cells, with an emphasis on understanding the mechanical misregulation that accompanies neurological disorders and cancers.

Biosensors and Biomolecular Analysis


Free-surface microfluidics Meinhart Group	Microfluidic cell sorting Soh Group

Electrokinetic bioseparation in nanofluidics Pennathur Group	Microfluidics for genomic testing Begley Group

Using a wide variety of novel microfluidic and nanofluidic devices, we are pioneering new technologies for sensing, sorting and analyzing biological molecules. These high-throughput technologies are essential to gathering the data required for systems-wide analyses of genomic or proteomic profiles, as well as identifying and characterizing rare but important biological events.

UCSB Engineering is home to world-class facilities in micro- and nano-scale fabrication and analysis, including ~25,000 square feet of clean room space, and core facilities for molecular imaging, protein expression/purification, cell culture, and genomic analysis.

Current Research Efforts in Biosensors/Biomolecular Analysis Research:

Matthew Begley: Development of novel microfluidic devices for genomic testing and DNA-based chemo-mechanical sensors.

Carl Meinhart: Investigates fundamental fluid mechanics problems at the micro-scale and nano-scale, with special emphasis on transport issues in MEMS-based sensors for detection of specific biological molecules.

Sumita Pennathur: Development of novel fabricated nanoscale devices to study biomolecule separation, characterize DNA-based nanostructures, and measure protein kinetics and binding.

H. Tom Soh: Development of innovative analytical biotechnologies for use as molecular diagnostics and therapeutics, with applications to personalized medicine. Current efforts focus on cell sorting, biosensors, and rapid directed evolution.

Computation and Modeling of Dynamic Biological Systems


Chaperone regulation Petzold Group	Noise analysis is gene networks Khammash Group	Microtubule dynamics Atzberger Group

The Mechanical Engineering Department has developed key strengths in the areas of systems, dynamics, control, and computation--all foundational areas for systems biology. These strengths have enabled us to excel in many areas of systems biology, most notably multi-scale stochastic modeling and computation, control and dynamics in biological networks, and robustness analysis of gene regulatory networks.

Current Research Efforts in Computational Modeling of Dynamic Biological Systems:

Paul Atzberger: Development of new computational methods to study stochastic phenomena arising in the biological sciences, physics, and engineering. Specific application areas include: fluctuating hydrodynamics; fluid-structure interaction; soft materials and complex fluids; molecular biology (including motor proteins, microtubules, aptamers); microfluidic and nanofluidic devices.

Mustafa Khammash: Applications of control theory to the quantitative analysis of networks of dynamically interacting biological components, with the goal of reverse engineering these networks to understand how they robustly achieve biological function. Current projects include: Heat-shock response; apoptosis, inflammation, and stress in ischemia; noise analysis of gene networks; calcium homeostasis; pap pili epigenetic switch.

Igor Mezic: Application of dynamical systems theory to complex biological systems, including large-scale networked systems, and the super molecular assembly of proteins.

Jeff Moehlis: Applies dynamical systems techniques to understand the response dynamics of neural populations and the dynamics of natural (schooling fish, flocking birds, etc.) and artificial swarms.

Linda Petzold: Development and analysis of multiscale simulation methods for biochemical networks. Current projects focus on modeling the unfolded protein response in the endoplasmic reticulum, stochastic and deterministic analysis of circadian clocks, spatial stochastic simulation of cellular polarization in yeast mating, and the multiscale computational modeling of metabolic insulin signaling pathways.