Campus Map

Tom Matula

Senior Principal Physicist

Affiliate Assistant Professor, Bioengineering and Affiliate Associate Professor, Electrical Engineering






B.S. Physics, California State University at Fresno, 1988

M.S. Physics, Washington State University, 1990

Ph.D. Physics, Washington State University, 1993


Sclerosing Foams Optimized with Ultrasound Preparation

Sclerotherapy is a procedure to treat varicose veins. uWAMIT researchers have discovered that ultrasound applied to therapeutic liquid solutions creates foams with smaller bubbles and a more uniform size distribution than traditional mechanical agitation methods. This technique may yield safer and more effective foam sclerosis treatments.

8 Jul 2016

Ultrasound Contrast Agents (Microbubbles) in the Microvasculature

High-speed images of oscillating micro-bubbles in small blood vessels are imaged to observe how the bubble oscillations might help induce permeation in the endothelium, allowing drugs to be transported across that barrier.

More Info

23 Jan 2013

High-speed images of oscillating micro-bubbles in small blood vessels are imaged to observe how the bubble oscillations might help induce permeation in the endothelium, allowing drugs to be transported across that barrier.

We excise the mesentery, immerse it in a Krebs solution and place it on a microscope. A flash lamp is used to deliver enough light to obtain good images with 50 nsec exposure times. Microbubbles are perfused along with a saline solution. When a vessel is found containing microbubbles, the experiment is triggered, sending a very short ultrasound pulse (1 MHz) towards the tissue sample. 14 images are collected at pre-determined times (usually every 150 or 300 nsec). Quantification of the images gives us information about vessel deformations, bubble oscillations, and registration of the specific locations that are later used to correlate vessel motion with histological observations of vessel damage.


PIXUL: PIXelated ULtrasound Speeds Disease Biomarker Search

More Info

26 Apr 2018

Accurate assessment of chromatin modifications can be used to improve detection and treatment of various diseases. Further, accurate assessment of chromatin modifications can have an important role in designing new drug therapies. This novel technology applies miniature ultrasound transducers to shear chromatin in standard 96-well microplates. PIXUL saves researchers hours of sample preparation time and reduces sample degradation.

Non-invasive Treatment of Abscesses with Ultrasound

Abscesses are walled-off collections of fluid and bacteria within the body. They are common complications of surgery, trauma, and systemic infections. Typical treatment is the surgical placement of a drainage catheter to drain the abscess fluid over several days. Dr. Keith Chan and researchers at APL-UW's Center for Industrial + Medical Ultrasound are exploring how to treat abscesses non-invasively, that is, from outside the body, with high-intensity focused ultrasound (HIFU). This experimental therapy could reduce pain, radiation exposure, antibiotic use, and costs for patients with abscesses. Therapeutic ultrasound could also treat abscesses too small or inaccessible for conventional drainage.

20 Jun 2016

Flow Cytometry Techniques Advance Microbubble Science

Researchers at the Center for Industrial and Medical Ultrasound (CIMU) are measuring the physical properties of ultrasound contrast agents — tiny gas bubbles several microns in diameter used to increase sonogram imaging efficiency in the body. When injected to the general circulation they can act as probes and beacons within the body, and can carry and deploy chemotherapeutic payloads.

CIMU researchers have developed a hybrid instrument that combines an off-the-shelf flow cytometer with an acoustic transducer. The cytometer's laser interrogation counts and measures the bubbles while the acoustic interrogation reveals the bubbles' viscosity and elasticity at megahertz frequencies.

5 Dec 2013

More Videos


2000-present and while at APL-UW

PIXUL-ChIP: Integrated high-throughput sample preparation and analytical platform for epigenetic studies

Bomsztyk, K., D. Mar, Y. Wang, O. Denisenko, C. Ware, C.D. Frazar, A. Blattler, A.D. Maxwell, B.E. MacConaghy, and T.J. Matula, "PIXUL-ChIP: Integrated high-throughput sample preparation and analytical platform for epigenetic studies," Nucleic Acids Res., EOR, doi:10.1093/nar/gkz222, 2019.

More Info

30 Mar 2019

Chromatin immunoprecipitation (ChIP) is the most widely used approach for identification of genome-associated proteins and their modifications. We have previously introduced a microplate-based ChIP platform, Matrix ChIP, where the entire ChIP procedure is done on the same plate without sample transfers. Compared to conventional ChIP protocols, the Matrix ChIP assay is faster and has increased throughput. However, even with microplate ChIP assays, sample preparation and chromatin fragmentation (which is required to map genomic locations) remains a major bottleneck. We have developed a novel technology (termed 'PIXUL') utilizing an array of ultrasound transducers for simultaneous shearing of samples in standard 96-well microplates. We integrated PIXUL with Matrix ChIP ('PIXUL-ChIP'), that allows for fast, reproducible, low-cost and high-throughput sample preparation and ChIP analysis of 96 samples (cell culture or tissues) in one day. Further, we demonstrated that chromatin prepared using PIXUL can be used in an existing ChIP-seq workflow. Thus, the high-throughput capacity of PIXUL-ChIP provides the means to carry out ChIP-qPCR or ChIP-seq experiments involving dozens of samples. Given the complexity of epigenetic processes, the use of PIXUL-ChIP will advance our understanding of these processes in health and disease, as well as facilitate screening of epigenetic drugs.

Inactivation of planktonic Escherichia coli by focused 1-MHz ultrasound pulses with shocks: Efficacy and kinetics upon volume scale-up

Brayman, A.A., B.E. MacConaghy, Y.-N. Wang, K.T. Chan, W.L. Monsky, V.P. Chernikov, S.V. Buravkov, V.A. Khokhlova, and T.J. Matula, "Inactivation of planktonic Escherichia coli by focused 1-MHz ultrasound pulses with shocks: Efficacy and kinetics upon volume scale-up," Ultrasound Med. Biol., 44, 1996-2008, doi:10.1016/j.ultrasmedbio.2018.05.010, 2018.

More Info

1 Sep 2018

This study addresses inactivation of E. coli in either 5- or 10-mL volumes, which were 50- to 100-fold greater than used in an earlier study (Brayman et al. 2017). Cells were treated with 1-MHz pulsed high-intensity focused ultrasound (10 cycles, 2-kHz repetition frequency, +65/–12.8 MPa focal pressures). The surviving fraction was assessed by coliform assay, and inactivation demonstrated curvilinear kinetics. The reduction of surviving fraction to 50% required 2.5 or 6 min in 5- or 10-mL samples, respectively. Exposure of 5 mL for 20 min reduced the surviving fraction to ~1%; a similar exposure of 10-mL samples reduced the surviving fraction to ~10%. Surviving cells from 5-min exposures appeared normal under light microscopy, with minimal debris; after 20 min, debris dominated. Transmission electron microscopy images of insonated samples showed some undamaged cells, a few damaged but largely intact cells and comminuted debris. Cellular damage associated with substantive but incomplete levels of inactivation can be variable, ranging from membrane holes tens of nanometers in diameter to nearly complete comminution.

Ultrasound-based cell sorting with microbubbles: A feasibility study

Matula, T.J. O.A. Sapozhnikov, L.A. Ostrovsky, A.A. Brayan, J. Kucewicz, B.E. MacConaghy, and D. De Raad, "Ultrasound-based cell sorting with microbubbles: A feasibility study," J. Acoust. Soc. Am., 144, doi:10.1121/1.5044405, 2018.

More Info

1 Jul 2018

The isolation and sorting of cells is an important process in research and hospital labs. Most large research and commercial labs incorporate fluorescently or magnetically labeled antibodies adherent to cell surface antigens for cell identification and separation. In this paper, a process is described that merges biochemical labeling with ultrasound-based separation. Instead of lasers and fluorophore tags, or magnets and magnetic particle tags, the technique uses ultrasound and microbubble tags. Streptavidin-labeled microbubbles were mixed with a human acute lymphoblastic leukemia cell line, CCL 119, conjugated with biotinylated anti-CD7 antibodies. Tagged cells were forced under ultrasound, and their displacement and velocity quantified. Differential displacement in a flow stream was quantified against erythrocytes, which showed almost no displacement under ultrasound. A model for the acoustic radiation force on the conjugated pairs compares favorably with observations. This technology may improve on current time-consuming and costly purification procedures.

More Publications


Systems, Devices, and Methods for Separating, Concentrating, and/or Differentiating Between Cells from a Cell Sample

Embodiments are generally related to differentiating and/or separating portions of a sample that are of interest from the remainder of the sample. Embodiments may be directed towards separating cells of interest from a cell sample. In some embodiments, acoustic impedances of the cells of interest may be modified. For example, the acoustic properties of the cells of interest may be modified by attaching bubbles to the cells of interest. The cell sample may then be subjected to an acoustic wave. The cells of interest may be differentiated and/or separated from the remainder of the sample based on relative displacements and/or volumetric changes experienced by the cells of interest in response thereto. The cells of interest may be separated using a standing wave and sorted into separate channels of a flow cell. Optionally, the cells may be interrogated by a light source and differentiated by signals generated in response thereto.

Patent Number: 9,645,080

Tom Matula, Andrew Brayman, Oleg Sapozhnikov, Brian MacConaghy, Jarred Swalwell, Camilo Perez


9 May 2017

Dynamic Characterization of Particles with Flow Cytometry

Patent Number: 8,264,683

Tom Matula, Jarred Swalwell

More Info


11 Sep 2012

Flow cytometry concepts are modified to enable dynamic characterizations of particles to be obtained using optical scattering data. Particles in flow will be introduced into a sample volume. Light scattered by a particle in the sample volume is collected and analyzed. What differentiates the concepts disclosed herein from conventional flow cytometry is the use of an acoustic source that is disposed to direct acoustic energy into the sample volume. As the particle passes through the sample volume, it responds to the acoustic energy, causing changes in the light scattered by the particle. Those changes, which are not measured during conventional flow cytometry, can be analyzed to determine additional physical properties of the particle.

Method of Selective Foaming for Porous Polymeric Material

Patent Number: 8,247,464

Wei Li, Hai Wang, Vipin Kumar, Tom Matula

More Info


21 Aug 2012

A selective high intensity ultrasonic foaming technique is described to fabricate porous polymers for biomedical applications. Process variables, including ultrasound power, scanning speed, and gas concentration have an affect on pore size. Pore size can be controlled with the scanning speed of the ultrasound insonation and interconnected porous structures could be obtained using a partially saturated polymers. A gas concentration range of 3-5% by weight creates interconnected open-celled porous structures. The selective high intensity ultrasonic foaming method can be used on biocompatible polymers so as not to introduce any organic solvents. The method has use in cell related biomedical applications such as studying cell growth behaviors by providing a porous environment with varying topological features.

More Inventions

Acoustics Air-Sea Interaction & Remote Sensing Center for Environmental & Information Systems Center for Industrial & Medical Ultrasound Electronic & Photonic Systems Ocean Engineering Ocean Physics Polar Science Center