Yusheng Feng, Ph.D
Computational Bioengineering and Nanomechanics Lab
SiViRT Computation Center
External Advisory Board Review Meeting
March 5th, 2010
Real time can refer to events simulated by a
computer at the same speed that they would
occur in real life.
real-time computing (RTC), or "reactive
computing", is the study of hard ware and
software systems that are subject to a “real-
time constraint” – i.e. operational deadlines
from event to system response.
Research and Real-time
Yusheng Feng, Ph.D Gerald Dodd III, M.D
UTSA (Team Lead) UC Denver
and Real-time Cellular Control
Allan Coop, Ph.D Hugo Cornelis, Ph.D
Unmanned Aerial Vehicle
(UVA) and Real-Time Flight
C-J Qian, Ph.D
Why we are here?
Where we were?
Where we are?
Where we are going?
SiViRT = Si + Vi + RT
• Real-Time Computing
• Uncertainty Quantification
Research and Real Time
Diagnosis Immuno- Prognosis
And Thermo- And
Planning And Prediction
Medical Imaging and data processing
Mathematical Modeling of Laser-Tissue Interaction
Bioheat transfer in tissue and cellular response
Mesh generation and numerical simulation
Cell Damage and tissue Characterization
Inverse problem and parallel computing
Treatment planning and outcome prediction
Real-time surgical monitoring and control
Application of nano-technology with laser therapy
Model validation: in vitro and in vivo experimentation
MRTI-Guided Laser Surgery RT Control
980-nm Diode Laser finite
Imaging process (co-
lofting) and mesh generation.
Bio-Heat Transfer Model
Laser Tissue Interaction Model
Nanoshell Model and Effective Tissue
Cell Damage Model
Heat Shock Protein Models
Ablation: With enough photon energy,
laser can be used to ionize molecules in
biological tissue. There exists a threshold
at which the absorbed energy is high
enough to cause decomposition of tissue.
Diffusion Theory Monte Carlo Method
– Beer-Lambert’s law – Easy to implement
– Inexpensive – Very expensive
– Less accurate – Not suitable for
Cell Damage and Heat Shock Protein
Damage can be determined by
ln Co C A e dt
Heat shock proteins (HSP) assist in
refolding and repairing other Green Fluorescence HSP27
Red Fluorescence HSP70
denatured proteins, and facilitating
synthesis of new proteins in response
HSP Empirical Model: >1).
H(t,T) Aexp( t t )
Major Problems with Arrhenius Law
for Tissue Damage
May need two sets of
Ea / RT
C(T,t) e At e
Cannot predict “shoulder”
T=46oC Model parameters are
extremely large and very
sensitive to measurement
It is not so clear what is
the biophysical and
physiological meaning of
Heating Time (min)
Results for Human Prostate PC3 Cells
E / RT
T=56oC At e
Arrhenius Model C(T,t) e
( H T S ) /T
New Model* e
C (T , t ) ( H T S ) /T
* Feng, Oden, and Rylander, “A Two State model for cell damage: Theory and
its validation in vitro” J. Biomech Eng., 2008
Biological Quantities of Interest
How to measure effectiveness of Cancer
Cell Damage Fraction Index.
How to quantify cancer recurrence?
Heat Shock Protein Expression.
Control parameter: Temperature.
Objective of Optimization
Nonlinear Transient Bio-Heat Transfer Equation
Heterogeneous and nonlinear thermal
properties: ki(x, t, T), wi(x, t, T)
Heterogeneous tissue optical properties:
a(x), s(x), …
Laser parameters: , P, location, …
Note: A domain was ki(x, t, T)
wi(x, t, T)
discretized into 3700
elements to characterize
One master processor
One communication processor
Optimization processors: 60
Calibration Processors: 60 190 CPU
Visualization Processors: 70
Simulation/real time ratio is 10:1
(e.g. 1 sec ~ 10 sec real time)
Typical laser surgery time is 3 ~ 5 min.
Processors numbers and allocation is
Imaged guided real time predictive control
Capability to characterize heterogeneous and
nonlinear tissue properties on the fly
Feasibility demonstrated in canine
Computational framework can be
generalized to other applications
And Real-Time Cellular Control
Developing neurological pathways of
computational models and real systems
CBI Simulator Framework
CBI Simulator Framework (Cont’d)
Software & Hardware Validation
We have designed and implemented a RTXI plugin module that controls the
magnitude of a single channel conductance.
The conductance magnitude is read from a pre-generated data file.
The standard model of conductance in an equivalent circuit is used to
calculate the magnitude of current injected into a real cell (Iinj) based on
the supplied conductance value (g), the recorded membrane potential (Vm)
and channel current reversal potential (Er) of a real cell.
UAV and Real-Time
CJ Qian, Ph.D.
Two major research directions
Research team on UAV: Hardware
(undergraduate students), control
algorithms (graduate students)
Research team on real-time estimation and
control over the network
Development of fast convergent estimators/controllers with
applications to real-time estimation and control of PVTOL
Fast convergence of our estimated states (dashed)
to the real states(solid)
Unified Real-Time Computational
Integrated SW/HW Control System
Questions and Comments?