Experimental and Computafional biomedicine

Министерство образования 
и науки Российской Федерации 
Уральский федеральный  
университет  
имени первого Президента  
России Б. Н. Ельцина  
 
 
 
 
 
 
 
 
 
 
 
 
EXPERIMENTAL 
AND COMPUTATIONAL  
BIOMEDICINE 
 
Russian Conference with 
International Participation 
 
in memory of Professor 
 Vladimir S. Markhasin 
 
Научное издание 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Екатеринбург 
Издательство  
Уральского университета 
2016 

УДК 612.089(063) 
ББК 51я43 
        Е97 
 
Все права на размножение и распространение  
в любой форме остаются за разработчиком. 
 
 
 
EXPERIMENTAL AND COMPUTATIONAL BIOMEDICINE : Russian 
Conference with International Participation in memory of Professor 
Vladimir S. Markhasin [Электронный ресурс]. – Екатеринбург : 
Изд‐во Урал. ун‐та, 2016. 
 
ISBN 978‐5‐7996‐1739‐4 
 
Сборник содержит тезисы докладов, представленных на российской конферен‐
ции с международным участием «Экспериментальная и компьютерная биомедици‐
на», посвященной памяти члена‐корреспондента РАН В. С. Мархасина (г. Екатерин‐
бург, 10‒12 апреля 2016 г.). Основной целью конференции является обсуждение 
современного состояния экспериментальных и теоретических исследований в обла‐
сти биомедицины. 
Сборник предназначен для ученых, преподавателей, студентов и аспирантов 
биологического и медицинского профиля. 
 
The volume contains the presentations that were made during Russian conference 
with international participation "Experimental and Computational Biomedicine" dedicated 
to corresponding member of RAS V.S. Markhasin (Ekaterinburg, April 10‒12, 2016). The 
main purpose of the conference is the discussion of the current state of experimental and 
theoretical research in biomedicine. 
For a wide range of scientists, as well as for lecturers, students of the biological and 
medical high schools. 

УДК 612.089(063)
ББК 51я43

Электронное научное издание 
 
Формат 60 × 84 1/8. Гарнитура Calibri. Усл. печ. л. 9,0. 
 
Издательство Уральского университета 
620000, Екатеринбург, ул. Тургенева, 4 
Тел.: +7 (343) 350‐56‐64, 350‐90‐13 
Факс: +7 (343) 358‐93‐06 
E‐mail: press‐urfu@mail.ru 
 
ISBN 978‐5‐7996‐1739‐4 
                                                        © Уральский федеральный университет, 2016 

 

Contents 

Plenary lectures ................................................................................................ 10 

Experimental and computational models in cardiovascular physiology and 
cardiology ........................................................................................................ 15 

Biomechanics. Experimental and mathematical models ................................... 30 

Electrophysiology. Experimental and computational models. Clinical studies .. 40 

Experimental and computational models in immunology ................................. 45 

Molecular basis of biological motility ............................................................... 49 

Medical bioinformatics ..................................................................................... 54 

Translational medicine. From basic science to clinical practice ......................... 58 

Medical chemistry ............................................................................................ 64 

Biomedical technology ..................................................................................... 69 

Author index .................................................................................................... 75 

 

 

Plenary lectures 

10 
 

Plenary lectures 
 

Non‐Markovian random walks and anomalous transport in biology 

Fedotov S. 

The University of Manchester 

sergei.fedotov@gmail.com

What is anomalous transport? It is a widespread natural phenomenon. Examples 
include movement of proteins on cell membranes, motor‐protein mediated active transport 
inside cells, transport of signalling molecules in the dendrites, bacterial motility, animals and 
human migration. Anomalous transport cannot be described by standard tools like advection‐
diffusion equations. Instead it requires the use of linear fractional partial differential equations 
involving fractional derivatives of non‐integer order. The question arises as to how to extend 
these equations for the nonlinear case involving transport with adhesion, non‐linear crowding 
and biochemical reactions. The talk is concerned with new nonlinear and non‐Markovian 
random walk models developed in the recent years. We present the nonlinear fractional 
equations and show how to apply these equations to the anomalous chemotaxis, morphogen 
gradient formation and intracellular superdiffusion. 
 

Multiscale modelling in vascular disease 
Hoekstra A. 

University of Amsterdam 
A.G.Hoekstra@uva.nl

I will introduce our ongoing work on the Virtual Artery, a multiscale model for 
Vascular Disease. Both the arterial wall and blood are modelled on the cell level and tissue 
level, and are all coupled together into a tightly coupled multiscale model, which in turn is 
coupled to whole body models for blood flow. I will show examples of applying the Virtual 
Artery in modelling thrombosis in intracranial aneurisms and in modelling in‐stent restenosis in 
stented coronary arteries. 
 

Systems biology of the heart: why bother? 
Kohl P.

Research Centre for Cardiovascular Medicine, University of Freiburg 

p.kohl@imperial.ac.uk

 Systems Biology has moved from a theoretical idea, or rather a disparate set of 
ideas, to a mainstream feature of research activities and funding priorities. Institutes, 
departments and centres of various flavours of Systems Biology have sprung up all over the 
world. An internet search will now produce more than 60 million hits (compared to <6 million 
in 2010). Out of PubMed’s 8,700 entries with “Systems Biology” in either title or abstract, only 
2 (two) papers are pre‐2000, while more than two thirds were published since 2010. Still, 
there seem to be more questions than answers when one discusses the topc: What is systems 
biology? How does it differ from classic biomedical research? Do we need it? What is the role 
of computer models in this context? Can they be relied on? Can computer simulations replace 
experiments on biological samples, including living animals? When will we have an all‐inclusive 
model of a real patient? This lecture will attempt to address the above questions, using 
illustrations from heart research. Aims: provide conceptual background, introduce definitions, 
provide examples of the systems research approach to integration and reduction of data 

Plenary lectures 

11 
 

related to cardiac structure and function – with the aim of turning data into information. 
Objective: highlight the need for multi‐level (ion channel to ECG) and multi‐type (e.g. 
experimental and theoretical) model systems, for quantitative projection between basic 
science and clinical relevance. Take home message: it is hoped that at the end of the lecture, 
we will be able to explain ‘systems biology’ as an approach, define the term ‘model’, and 
illustrate the concepts associated with these terms on one or two examples. Further reading: 
Combining wet and dry research: http://www.ncbi.nlm.nih.gov/pubmed/23334215 Systems 
biology: an approach: http://www.ncbi.nlm.nih.gov/pubmed/20531468 

 

On the regulation of virus infection fates 
Meyerhans A. 

Pompeu Fabra University 

andreas.meyerhans@upf.edu

Viral infections can be fundamentally categorized as acute or persistent according 
to their temporal relationships with their hosts. In an acute infection, virus‐specific T‐cells 
become activated, proliferate, and differentiate into effector T‐cells, allowing the virus 
elimination within a few weeks. By contrast, persistent infections, such as the caused by HIV 
and HCV, are not resolved and develop when T‐cells become exhausted, i.e. differentiate into 
a state with poor effector function to avoid immunopathology. In my presentation I will 
describe ongoing work of my group that aims (i) to understand the mechanisms of how 
exhaustion is established and (ii) to identify strategies of immune interventions for shifting the 
dynamic equilibrium between virus expansion and immune control. 
 
Systems approach to studying mechanisms of ventricular fibrillation 

using anatomically accurate modeling 
Panfilov A.V., Dierckx H., Kazbanov I., Vandersickel N. 

Ghent University 

alexander.panfilov@ugent.be

We report on the development of anatomically accurate model of ventricles of the 
human heart. The model integrates our knowledge from a single cell to the whole organ and 
allows us to study mechanisms of cardiac arrhythmias in the human heart, where 
experimental interventions are very limited. We will present and discuss our recent research 
using this model. It includes studies of ventricular fibrillation during global ischaemia and 
quantification of the relative contributions of the hypoxia, acidosis and hyperkalemia on the 
changes in the fibrillation frequency and complexity. We have also studied arrhythmias which 
occur as a result of early after depolarizations (EADs). EADs occur in many forms of genetic 
defects such as the long QT syndrome or under the action of pharmacological agents as a 
result of cardiotoxicity. We also present our studies on the arrhythmias which occur due to 
fibrosis of cardiac tissue. We discuss importance of heterogeneity for the onset of the 
arrhythmias and recently found effect of attraction of sources of arrhythmia to the regions 
with a high degree of fibrosis. Finally we discuss possibilities of application of our approaches 
to clinic.