Whether we investigate the growth and interactions of an entire population, the evolution of DNA sequences, the inheritance of traits, or the spread of disease, biological systems are marked by change and adaptation [1]. It is often said that biology is going to be the science of the 21st century as physics was the science of the 20th [3,4]. Computers, and computer science ideas and techniques, are of course an important part of all these scientific and engineering activities [4].
Indeed this represents the challenges in biological modeling compared to traditional branches such as physics. In general the adaptations and changes are much faster than physical systems, what makes the modeling and analysis in most of the cases a formidable task.
When I first read a biology textbook, it was like reading a thriller. Every page brought a new shock. As a physicist, I was used to studying matter that obeys precise mathematical laws. But cells are matter that dances. Structures spontaneously assemble, perform elaborate biochemical functions, and vanish effortlessly when their work is done. Molecules encode and process information virtually without errors, despite the fact that they are under strong thermal noise and embedded in a dense molecular soup. The main message is that biological systems contain an inherent simplicity [3] .
In the pharmaceutical industry, the incorporation of the disciplines of pharmacokinetics, pharmacodynamics, and drug metabolism (PK/PD/DM) into various drug development processes has been recognized to be extremely important for appropriate compound selection and optimization [2].
 |
| Conerstones of my research |
1. Introduction
The first year was dedicated
to: 1) achieving the minimal requirements in terms of credits; 2) gathering the
maximum amount of knowledge. The academic activities was divided into
mathematical and biomedical; and master-level disciplines, summer schools,
readings, and short courses. The activities was either suggested by the
advisors, prof. Palumbo and prof. Manes, or chosen by me. Some of the
disciplines was followed on the hope to increase my theoretical background.
2.
Master-level disciplines
- Controllo Ottimo. Prof E De Santis (UAQ): in theory important for
optimum regimen design in medical treatments. As result, a talk in the
IASI-CNR in June and a paper in the Symposium SIMPEP 2014.
- Farmacologia Speciale. Prof. R, Maggio (UAQ): this theory supposes to
support me next year, drug regimen design. As result, a talk given in the
department of Medicine (UAQ) and an awarded paper in SIMPEP
3.
Summer Schools
- Mathematical Models and Methods for
Living Systems: it was a
one-intensive week of studies, see http://web.math.unifi.it/users/cime/. Presentation of talk: On the mathematical modeling in gene expression
estimation: an initial discussion on PBM and BM;
- Systems
Biology and
Systems Medicine: precision
Biotechnology
and Therapies: this was a one-intensive week
of studies and computer simulations, tutorial and lessons. See: http://ucbf.lakecomoschool.org/.
Presentation of poster: On the mathematical modeling in gene expression
estimation: an initial discussion on PBM and BM;
4.
Short courses
- Software
Architecture:
theory of how to design better software;
- Convergence theory for observers: Necessary, and Sufficient
conditions: theory on the design of state reconstruction systems;
- Others: other courses were followed in the hope
to find insights and methodologies.
5.
Main references used
- S Lenhart, J T Workman, Optimal Control Applied
to biological models, Chapman & Hall/ CRC, Mathematical and
Computational Biology Series, 2007;
- Sara E Rosenbaum, basic pharmacokinetics and
pharmacodynamics: an integrated textbook and computer simulations, John
Wiley & Sons, 2011.
6.
Most significant publications
- JG Pires, R Maggio, C Manes, P Palumbo, On the
importance of pharmacokinetics and pharmacodynamics in engineering
sciences as an inter- and multidisciplinary field: an introductory
analysis. SIMPEP 2014,
- JG Pires, C Manes, P Palumbo, On the importance
of optimal control theory in engineering sciences as a complementary and
supplementary methodology to Operations Research: a case-study analysis.
SIMPEP 2014,
1. Introduction
The year of 2015, second year of the PhD
pathway of the abovementioned student, was agreed to be dedicated to researches
on the IASI-CNR (Gemelli Ospedale)[1].
The researches will consist of reading literatures and testing models published
or propose new ones. The main topics is what we have called "The Big
Glucose Model," which boils down to an attempt to enhance already existing
mathematical and computational models for studying glucose control, in general
the models are based just on insulin, the idea is to gather several different
models based on other hormones or bio- molecules considered significant on the
alteration of glucose levels in the human blood.
2. Courses to enroll
- Identificazione dei Modelli e Analisi dei Dati: this is based on state space models;
- Complementi di Automatica: this is based on kalman filter models and parameter stimation;
3. References
The references were not defined
yet, it will be taken from an archive offered by De Gaetano, from the IASI-CNR Gemelli Ospedale.
A starting point could be:
- P. Palumbo, S. Ditlevsen, A. Bertuzzi, A. De Gaetano, Mathematical modeling of the glucose-insulin system: A review, Mathematical Bioscience, 2013;
- Ludovic J. Chassin, Malgorzata E. Wilinska, Roman Hovorka. Evaluation of glucose controllers in virtual environment: methodology and sample application, Artificial Intelligence in Medicine (2004) 32, 171—181
4. Final Remarks
Unfortunately a precise agenda for next year is complex,
once it depends on my response to the project proposed by Andrea De Gaetano and
the success on the research. In the first year I have finished all the
prerequisites - two master-level disciplines and 18 credits of ad hoc activities - for avoiding
conflicts with this part of my academic cycle.
5. Extra
One paper partially accepted: Biologia Sistêmica: um novo paradigma para as ciências biológicas e
exatas “ou” Biologia Sistêmica e Inteligência Computacional. One paper
invited to a journal, and three textbooks proposed to publish under invitation.
[1] CNR-IASI - Laboratorio di Biomatematica, UCSC – Largo
A. Gemelli 8, 00168, Roma , Italy
Suggestion: Access the video from Youbube, then you will see a set of correlated videos, which can be very helpful. See scheme below.
 |
| Accessing Youtube from the current blog |
