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LAMMP Technology Cores

Virtual Photonics Technologies

Selected Publications

"Spatial/Angular Contributon Maps for Improved Adaptive Monte Carlo Algorithms". Carole Hayakawa, Rong Kong and Jerome Spanier. Monte Carlo and Quasi-Monte Carlo Methods 2010, Lecture Notes in Computational Science and Engineering, Springer-Verlag, p. 419-434, 2012.

"Geometric convergence adaptive Monte Carlo algorithms for radiative transport problems based on importance sampling methods". Rong Kong and Jerome Spanier. Nuclear Science and Engineering, Volume 168, Number 3, p. 197-225, 2011.

"Accurate and efficient Monte Carlo solutions to the radiative transport equation in the spatial frequency domain". Adam Gardner, and Venugopalan Vasan. Optics letters, 2011 Jun 15, Volume 36, Issue 12, p.2269-71, 2011.

"Analysis of single Monte Carlo methods for prediction of reflectance from turbid media". Michele Martinelli, Adam Gardner, David Cuccia, Carole Hayakawa, Jerome Spanier, and Vasan Venugopalan. Optics express, 2011 Sep 26, Volume 19, Issue 20, p.19627-42, 2011.

"Electric field Monte Carlo simulations of focal field distributions produced by tightly focused laser beams in tissues. Carole Hayakawa, Eric O. Potma and Vasan Venugopalan.

"Geometric convergence of second generation adaptive Monte Carlo algorithms for general transport problems based on correlated sampling". Rong Kong and Jerome Spanier. International Journal of Pure and Applied Mathematics, Volume 59, Number 4, p. 435-455, 2010.

"Amplitude and phase of tightly focused laser beams in turbid media". Carole Hayakawa, Vasan Venugopalan, Vishnu Krishnamachari, and Eric Potma. Physical review letters, 2009 Jul 24, Volume 103, Issue 4, p.043903, 2009.

"Adaptive Monte Carlo Algorithms Applied to Heterogeneous Transport Problems". Katherine Bhan, Rong Kong and Jerome Spanier. Monte Carlo and Quasi-Monte Carlo Methods 2008, Lecture Notes in Computational Science and Engineering, Springer-Verlag, p. 209-225, 2009.

"A new proof of geometric convergence for general transport problems based on sequential correlated sampling methods". Rong Kong and Jerome Spanier. Journal of Computational Physics, Volume 227, Number 23, p. 9762-9777, 2008.

Selected foundational references:

"Radiative transport in the delta-P1 approximation for semi-infinite turbid media". Inseok Seo, Carole K. Hayakawa and Vasan Venugopalan. Medical Physics, Volume 35, Number 2, p. 681-693, 2008.

"Perturbation and differential Monte Carlo methods for measurement of optical properties in a layered epithelial tissue model". Inseok Seo, Joon You, Carole Hayakawa and Vasan Venugopalan. Journal of Biomedical Optics, Volume 12, Number 1, p. 014030, 2007.

"Coupled forward-adjoint Monte Carlo simulations of radiative transport for the study of optical probe design in heterogeneous tissues". Carole Hayakawa, Jerome Spanier and Vasan Venugopalan. SIAM Journal on Applied Mathematics, Volume 68, Number 1, p. 253-270, 2007.

"Radiative transport in the delta-P1 approximation: accuracy of fluence rate and optical penetration depth predictions in turbid semi-infinite media. Stefan A. Carp, Scott. A. Prahl and Vasan Venugopalan. Journal of Biomedical Engineering, Volume 9, Number 3, p. 632-47, 2004.

"Perturbation Monte Carlo methods to solve inverse photon migration problems in heterogeneous tissues". Carole K. Hayakawa, Jerome Spanier, Fred Bevilacqua, Andy K. Dunn, Joon S. You, Bruce J. Tromberg and Vasan Venugopalan. Optics Letters, Volume 26, Number 17, p. 1335-1337, 2001.
The Virtual Photonics Technology Initiative was established at the Beckman Laser Institute in April 2008 with four primary goals:
  • Design and distribute easy-to-use open-source software tools with graphical-user interfaces that simulate the propagation and distribution of optical radiation in cells and tissues.
  • Supply educational resources that provide the appropriate foundation for the proper usage of these computational tools.
  • Develop improved computational models to simulate and design optical diagnostic, imaging, and therapeutic modalities.
  • Stimulate the formation of an active community of 'experts' in Computational Biophotonics interested in offering their expertise and in developing advanced simulation tools to advance this open-source effort.
Interested users and developers should visit the Virtual Photonics Technologies Website
Virtual Tissue Simulator

The Virtual Tissue Simulator (VTS) is a software library that includes computational algorithms or solvers, spectral data, analysis and optimization tools. The methods to interact with the VTS include a graphical user interface (GUI), software that supports interoperability with MATLAB, and a Monte Carlo Command Line (MCCL) application. All of this software is freely available to the public. The open source codeplex website,, provides a centralized web portal where users can download our entire source code, post comments, questions or requests, access the software documentation, or download packaged modes of interaction. The "Discussions" page provides a forum wherein we field questions with interested users while the "Issue Tracker" page provide a forum whereby users can report software bugs or request additional software features. Our software totals about 75,000 lines of C# code and has been hosted by codeplex since June 2010.

Figure 1: Screenshot of the graphical user interface to the VTS, Fluence/Interrogation Solver Panel.

VTS Documentation

Principal Investigator

Carole Hayakawa, Ph.D.
Dr. Hayakawa is the Resource Director of the Virtual Photonics Technologies Core (VPTC). She serves as the key point of contact for core faculty, users and collaborators in all VPTC activities. Dr. Hayakawa is a Project Scientist in the Department of Chemical Engineering and Materials Science. She is a mathematician who trained with Dr. Jerry Spanier at the Claremont Graduate University in Monte Carlo methods and transport theory. She completed a postdoctoral fellowship with LAMMP co-PI Dr. Venugopalan and was recruited to develop and provide permanent staff support for the Virtual Tissue Simulator. She is the key contact person for our collaboration and service projects. She interacts extensively with LAMMP scientists and collaborators involved in instrumentation and model development to optimize the impact, suitability, and accuracy of the computational methods provided by the VPTC.
Jerome Spanier, Ph.D.
Dr. Spanier is a co-Director of the Virtual Photonics Technologies Core. He is a Researcher (Research Professor) in the Department of Surgery (BLI division). He is a distinguished scientist and mathematician with broad expertise in advanced Monte Carlo methods, transport theory, and computational strategies for modeling physical processes. He is former Dean at Claremont Graduate University (CGU), Joseph H. Pengilly Professor of Mathematics at CGU, and Director and Founder of the CGU Math Clinic. Dr. Spanier provides training and instruction to all LAMMP scientists and collaborators in modeling and computation. He contributes to the development of computation and visualization techniques for the Virtual Photonics Technologies core in collaboration with Drs. Venugopalan and Hayakawa.
Vasan Venugopalan, Sc.D.
Dr. Venugopalan is a co-Director of the Virtual Photonics Technologies Core. He has expertise in laser interactions with bio-materials, thermal-fluid transport, and models of light propagation in cells/tissues. Dr. Venugopalan is Professor in the Department of Chemical Engineering and Materials Science and has joint appointments in the Dept. of Biomedical Engineering and in the School of Medicine in the Department of Surgery, Beckman Division. He was recruited by Dr. Tromberg to join LAMMP in August 1996. He has served as LAMMP Co-Investigator since April 1998, leading the development of new models and methods for probing light-tissue interactions with high temporal and spatial resolution. Dr. Venugopalan is responsible for organizing and directing all scientific, education, and dissemination activities as co-Director of the VPTC. In addition, Dr. Venugopalan collaborates with Drs. Cerussi and Tromberg in the development of Diffuse Optics technologies, and Drs. Potma and Botvinick in advancing LAMMP microbeam and microscopy capabilities.

Research Staff

David Cuccia, Ph.D.
Dr. Cuccia is the chief software architect of the Virtual Tissue Simulator. He is a founder, CTO and acting CEO of Modulated Imaging (MI) Inc., a technology development company housed within the Photonics Incubator at BLI, with a mission to standardize, validate and commercialize BLI related optical and computational technologies. Prior to founding MI Inc., he was an NSF pre-doctoral fellow in Biomedical Engineering at UC Irvine and received his Ph.D. in 2006. He is a co-author of 31 publications, patents, and book chapters in the field of Biomedical Optics, and a co-inventor of the enabling MI technology, spatial frequency domain imaging (SFDI). He has developed a unique skill set in advancing the hardware and software aspects of optical instrument design, development, and production.
Lisa Malenfant, B.Sc.
Ms. Malenfant is the Open Source Project Manager of the Virtual Photonics Technology Core. She joined LAMMP in January 2010 to manage the VPTC open source effort and all websites that provide access to source-code, documentation and discussions. Lisa has a broad spectrum of experiences in all aspects of software development, from project management to hands-on development and has worked on several project teams. Lisa Malenfant was the lead for several projects at both WATG (an architectural firm) and at Epicor (a business software solutions provider). She developed and managed all aspects of these projects from the initial concept and design to the final rollout to the end-users. Her expertise in software development and the extensive consultation and research critical to meet the technical needs of developers and end-users is invaluable for the VPT core.

Postdoctoral Scholars

Adam Gardner, Ph.D.
Dr. Gardner is a Postdoctoral Researcher in the Beckman Laser Institute and Department of Chemical Engineering and Materials Science. Dr. Gardner has broad expertise in the development of analytical, numerical and Monte Carlo methods for analysis and solution of the Radiative Transport Equation. He spearheads the development of the analytical SHEFN framework for the solution of the radiative transport equation on mesoscopic scales. These methods are being applied in a collaborative project with Profs. Richards-Kortum (Rice University) and Sokolov (MD Anderson Cancer Center), to model the efficacy of nanoparticles to provide enhanced diagnostic contrast in epithelial tissues.
Janaka Ranasinghesagara, Ph.D.
Dr. Ranasinghesagara is a Postdoctoral Fellow in the Beckman Laser Institute and the Department of Chemical Engineering and Materials Science. His research interests focus on modeling and analyzing mechanisms of light propagation in various biological tissues and cells. He has experience in electromagnetic wave propagation, Monte Carlo methods, advanced computation, simulation and wide-field optical scattering experiments. He earned his Ph.D. in Biological Engineering from the University of Missouri for his work on light propagation in fibrous tissues and skeletal muscles. Before joining LAMMP in September 2010, he had worked in the University of Alberta to apply his expertise to solve problems in photoacoustic microscopy. Currently, he is spearheading the Huygens Fresnel electric-field Monte Carlo (HF-EMC) project under the joint direction of LAMMP co-Investigators Profs. Vasan Venugopalan and Eric Potma.

Graduate Students

Jennifer Nguyen, M.S.
Ms. Nguyen is a doctoral candidate in the Department of Biomedical Engineering and is advised by VPTC co-Directors Profs. Spanier and Venugopalan. Ms. Nguyen focuses on the development of perturbation and differential Monte Carlo methods to solve forward and inverse problems involving measurements of polarized light. She is currently working with Drs. Spanier and Hayakawa in a collaborative project with Dr. Judith y Mourant (Los Alamos National Lab) to apply these methods for non-invasive optical characterization of tissue morphology that occurs during precancerous transformations within cervical epithelia. Jennifer will play a leading role in the development of the MCADE research initiative within VPTC. That research is the primary focus of her doctoral dissertation.

48-node compute cluster

Our compute server is housed and maintained free of charge by UC Irvine's Office of Information Technology (OIT) as part of the Broadcom Distributed Unified Cluster (BDUC), free of charge. This server contains 48 AMD compute nodes, with 256 GB of RAM, and 6 hot swap 3GB each SATA drives in RAID 6 mode, providing 12 TB of redundant, on board, data storage. This compute server enables simultaneous long running Monte Carlo simulations, for example, and simulations that require large amounts of memory. Further, the use of the Sun Grid Engine (SGE) of the BDUC system enables the staging of simulation jobs to maximize compute resources and efficiency.

8-quad core compute cluster

We house a large computer tower locally in our labs. This system contains 8 quad core Intel Xeon X5550 processors with 24 GB of RAM, and 2 Fermi NVidia GPUs. This system has duel boot capabilities for both Windows 7 and Linux Red Hat. Thus, this system allows for the development of algorithms across OS platforms and for GPU related tasks.

24TB storage server

Our storage server is housed in the UC Irvine Health Sciences server room. This storage utility contains 24 1TB SATA disk drives with an onboard Intel processor operating on a solid-state drive. This device allows for the storage of vast amounts of data produced from data intense Monte Carlo (MC) simulations, for example, and the onboard processor provides for simple processing of these databases. This storage utility enables the VPTC to save important simulation data for later.

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  • Hanna Kim
    Resource Coordinator

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