Category Archives: Job Opportunities

Post-Doc in Qualification of in silico-augmented clinical trial approach @ University of Bologna

Title: Qualification of in silico-augmented clinical trial approach to the efficacy assessment of new tuberculosis therapies in developing countries

Tutor: Prof Marco Viceconti – https://www.unibo.it/sitoweb/marco.viceconti/

Funding source: STriTuVaD project – https://cordis.europa.eu/project/rcn/212940_en.html

To apply: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961

Deadline: 9 January 2019, 12:00 (applications must be sent by post or delivered by hand)

Research Project

In the framework of the STRITUVAD project partner University of Catania is developing a sophisticated simulation of the human immune system that can predict how a patient will respond to the disease activation of the Mycobacterium Tuberculosis bacterium already present in his/her body in term of bacterial spread, as a function of the patient general immune condition, and to the inoculation of specific therapies. The project goal is to refine this model so that it can:

  1. predict with sufficient accuracy the change in bacterial load over time in individual patients treated with different therapies;
  2. generate a cohort of “virtual patients” that well represent the inter-subject variability of all determinants that affect the disease progression and the response to therapy;
  3. develop in collaboration with the University of Sheffield a Bayesian statistical model that combines observational results from a clinical trial to the in silico-predicted response on the virtual patients cohort into an in silico-augmented clinical trial aimed to shorted the duration and the number of physical patients enrolled;
  4. validate the results of the in silico augmented trial to those of a full sized standard clinical trial, so to produce sufficient evidences to qualify the in silico method for studies of future drugs.

Under the guidance of Prof Marco Viceconti, one of the top experts of in silico trials worldwide, the post holder, a post-doctoral researcher with documented experience in modelling and simulation in biomedicine, will conduct the research activities described above in close collaboration with the model developers in Catania, the statistical modelling experts in Sheffield, and the clinical trialists in New Delhi.

The research contract (Assegno di Ricerca), has an annual salary before taxes of € 26,174.00. While the initial contract is for 12 months, if successful the post holder contract will be extended until the end of the project, in July 2022.

The ideal candidate for this position holds a PhD in math, physics, or engineering, documented experience in modelling and simulation in biomedicine, excellent spoken and written English, and one or more of the following skills:

  • Familiarity with the mathematical modelling of the immune system
  • Familiarity with Bayesian statistics and Bayesian modelling
  • Previous experience with biomedical regulatory science
  • Previous experience with verification, validation, and uncertainty quantification of predictive models in biomedicine

If you are interested apply here: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961 or contact me by email for further information.

For original post see:
https://www.unibo.it/sitoweb/marco.viceconti/avvisi/fa93fd8b

Post-doc in Development of an open source software for the multiscale orchestration @ University of Bologna

Title: Development of an open source software for the multiscale orchestration of computational oncology simulations

Tutor: Prof Marco Viceconti – https://www.unibo.it/sitoweb/marco.viceconti/

Funding source: H2020 project PRIMAGE (SC1-PM-16-2017-826494)

To apply: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961

Deadline: 9 January 2019, 12:00 (applications must be sent by post or delivered by hand)

Research Project

In 2017 the European Commission called for proposals on the topic “In-silico trials for developing and assessing biomedical products”; one of the projects funded, PRIMAGE, which will start on December 1st, 2018, aims to develop in silico trials technologies to test the efficacy of new anti-tumour therapies. To predict the response of a new anti-cancer agent over a representative clinical population is a very complex endeavour, which requires a detailed model of the biochemical mechanism of action of the new drug on the cancer cells, another model that describe how this effect modulate the cell-to-cell and the cell-to-tissue interaction and signalling, and another model that can predict the overall growth of the tumour mass over time, its vascularisation, and its cellularity. As each of these models is defined at radically different space-time scales, their coupling is complex and involves an advanced orchestration to build a multiscale simulation.

This problem has been approached in different ways in the past by Prof Viceconti’s team and by other research groups, but all solutions so far have been not entirely satisfactory. The main problem is that the software stack to handle this orchestration becomes rapidly very large and complex (thus difficult to maintain), and strongly dependent on implementations of the models being orchestrated; as in most projects these are being developed in parallel, this create some serious difficulties.

In PRIMAGE we intend to tackle a completely different approach loosely inspired by the High Level Architecture approach standardised by IEEE Std 1516-2010, and popular especially in the context of defence research. We intend to develop a very simple and easy to maintain architecture that orchestrate the models by controlling their data flow, centralising in a database all intermediate data objects, so as to explore possible speed-up strategies based on pre-computation, interpolation, and surrogate modelling methods. The result will be an open source software tool that should make much easier for research groups around the world to design and deploy complex multiscale orchestrations, that execute efficiently and flexibly in different execution environments.

Under the guidance of Prof Marco Viceconti, one of the top experts of in silico trials and biomedical multiscale modelling worldwide, the post holder, a researcher with documented experience in software development in Python, will design and develop this orchestration framework, and use it to deploy a large scale multiscale simulation that orchestrate models developed by specialists at partners ANSYS, UNIVERSITY OF SARAGOZA, UNIVERSITY OF SHEFFIELD, and CHEMOTARGETS, which will be tested as in silico trial solution.

The research contract (Assegno di Ricerca), has an annual salary before taxes of € 26,174.00. While the initial contract is for 12 months, if successful the post holder contract will be extended until the end of the project, in November 2022.

The ideal candidate for this position holds a degree in computer science, math, physics, or engineering, documented experience in software development in Python, good spoken and written English, and one or more of the following skills:

  • Familiarity with computational science & engineering software development
  • Familiarity with computational biomedicine software development
  • Previous experience with model orchestration and/or multiscale modelling
  • Previous experience with database software development, NoSQL databases, blockchain public ledgers, surrogate modelling, and/or machine learning
  • Previous experience with Open Source projects management

If you are interested apply here: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961 or contact me by email for further information.

For the original post see:
https://www.unibo.it/sitoweb/marco.viceconti/avvisi/4c20aa93

Communication Officer in Dissemination, communication, and community engagement on in silico medicine @ University of Bologna

In the frame of the Strituvad project we are opening a new position for communication officer.  The position is initially for 12 months, but can be extended for additional two. The gross amount of the research contract (Assegno di Ricerca), contract is € 20.354,99 per annum. The amount is exempt of withholding tax and includes all statutory social security charges the Research Fellow is subject to.

The aim of this research contract is the creation of a community of practice around the emerging applications of the so-called in silico medicine, with particular reference to in silico trials, where modelling and simulation technologies are used for the certification of new drugs or medical devices. Under the guidance of Prof Marco Viceconti one of the top world-wide experts on in silico medicine, the researcher will create the content and manage web sites, social network accounts, e-newsletters, and online communities allowing all those interested in the topic who work in academia, industry, consulting or service firms or in regulatory agencies to exchange good practices on the use of modelling and simulation in medicine. The post is funded by the EU project STRITUVAD, which aims to develop in silico methods to reduce the cost of clinical trials for new therapies for tuberculosis in developing countries where this disease is endemic.

The ideal candidate should have:

  • A Master degree (Laurea Magistrale) or equivalent title in scientific disciplines or Communication Science
  • Excellent knowledge of English language (written and spoken)
  • Priority will be given to candidates with experience in Science Communication, dissemination of research results, networking and community building among scientists, production of press releases

If you are interested apply here: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961 or contact me by email for further information.The deadline is Thursday, January 10th, 2019 or contact me by email for further information.

For original post see:
https://www.unibo.it/sitoweb/marco.viceconti/avvisi/6dcf39bb

Two PhD Positions in Bone Multiscale Mechanics at The City College ofNew York


The Laboratory of Bone Biomechanics headed by Dr.Alessandra Carriero in the Department of Biomedical Engineering at The CityCollege of New York, is offering two PhD Positions in the field of Bone Multiscale Mechanics and Mechanobiology.

Dr. Carriero’s research focuses on providing a comprehensiveunderstanding of bone mechanics and adaptation in healthy, aging and disease so to aid in the development of new treatment strategies for bone frailty and deformities.  Dr. Carriero’s lab uses mechanical engineering methods, material science approaches, high-resolution imaging, clinical data and biological analysis to reveal how mechanical forces influence bone growth, maintenance and function. Bone fragility is a very common but yet not well understood. Understanding the mechanisms of bone failure in frailty has potential to make a significant positive impact on the quality of life of people worldwide, while delivering economic benefits to our society.

Position 1: This research will contribute to understanding the effect of aging and disease on the composition, structure and mechanical properties of bone along its hierarchy and its impact on whole bone fracture toughness. The specific aims of this PhD project are to 1) develop novel high-resolution imaging acquisition and analysis for bone composition and structure, while simultaneously conduct fracture mechanics tests in healthy, disease and treated bone; (2) assess local bone measurements with biomarkers and compare these to the structure/compositon and mechanics of bone; (3) develop new multiscale modeling approaches to evaluate fracture resistance in brittle bones and treatments.


Position 2: This research will contribute to understanding of hearing loss in osteogenesis imperfecta (or brittle bone disease). The specific aims of this PhD project are to 1) develop novel high-resolution imaging acquisition analysis for cochlea micromechanics; (2) assess bone and soft tissue structure, composition and mechanics; (3) develop modeling approaches to evaluate cochlea mechanics in healthy, disease and treated conditions.

Both positions will be based at at The City College of New York, where the candidates will be enrolled in the Doctorate Program in Biomedical Engineering, and research will be conducted in collaboration with other instistutions in US and UK, particularly Hospital for Special Surgery, Northwestern University, Imperial College and the Diamond Light Source.

The successful candidate holds or will soon receive a Master’s or an equivalent Degree in Biomedical Engineering, Mechanical Engineering, Physics, or Materials Science. A high motivation to work in a pioneering research environment at the interface between engineering, science and medicine is essential as well as the enthusiasm to work in an international and multidisciplinary team. Availability to travel and work with animals is required. Good knowledge of English (oral and written) is essential. Experience in one or more of the following is desirable: biomedical research, mechanical testing, experimental testing of bone, imaging acquisition, imaging processing, computational modeling techniques.

We look forward to receiving your application including a motivation letter, CV, university transcripts and names and contact details of three references. Applications must be submitted both via email to acarriero@ccny.cuny.edu and through our website at CCNY https://www.ccny.cuny.edu/bme/grad by January 15. For international students, GRE and/or TOEFL can be submitted by March 1 2019. While there is no minimum score for the GRE and/or TOEFL, it is however expected that the scores demonstrate aptitute for graduate research. The positions are available immediately and will last until filled.

For further information about the positions, please contact Dr. Alessandra Carriero at acarriero@ccny.cuny.edu.

PhD opportunity in respiratory biomechanics in Sheffield

PhD opportunity in respiratory biomechanics in collaboration with industry and the UK National Health Service. Supervisors: Dr Alberto Marzo and Prof Jim Wild at the University of Sheffield, United Kingdom. Deadline: 15 Jan 2019.

Asthma is a chronic disease that affects 5.4M sufferers in the UK alone. Control of the disease can be achieved by administrating drugs (bronchodilators) using pressurised Metered Dose inhalers, often enhanced by the combined use of asthma spacer devices. These devices are mostly effective in children but their design is old, cumbersome and difficult to use, which leads to a low treatment intake with increased risk of serious complications.

Using modelling and experimental approaches, the project will investigate the link between spacer design, patient-specific respiratory system anatomy, and drug delivery. The aim is to ultimately develop a computational framework for the identification of effective and personalised devices that are easy to use, portable, discrete, attractive to the younger population, cost effective, easy to manufacture, disposable and with low environmental impact.

The project is in collaboration with ELAROS (NHS spin-off company), the Sheffield Pulmonary Vascular Disease Unit (national NHS referral centre for Clinical Pulmonary Imaging) and the Sheffield Children’s Hospital.

Supporting figure for PhD project description

Figure 1. CFD analysis of drug particles distribution in a typical asthma spacer (left). Comparison of CFD vs MRI data in central airways (right).

Applicants for the post must have (or be expected to attain) a first-class or upper second class degree in an engineering discipline. An aerospace/mechanical engineering background would be an advantage, as would experience of computational fluid dynamics, aerodynamics, or image-based computer modelling.

Please note, this position is only open to UK and EU citizens with 3 or more years residency.

This studentship covers the cost of tuition fees and provides an annual tax-free stipend at the standard UK research rate (£14,777 in 2018/19).

For further information about this project please contact Dr Alberto Marzo.

To apply please use our standard on-line PhD application form and indicate on your form that you are replying to this advert or email me-pgadmit@sheffield.ac.uk for further guidance on applying.

Closing date: 15th January 2019

More info at:

https://www.sheffield.ac.uk/mecheng/phd/phd-studentships/improving-design-medical-devices-asthmatic

PhD position in spinal implant design

This PhD project will focus on materials development and implant design for spinal fusion. Numerical models will be used to design and structurally optimize a bioactive, osteoinductive spinal fusion device based on a combination of ceramics and metals. 3D printing will be used to produce prototypes for initial mechanical evaluation of the developed implants in an ex vivo model, guided by standards on intervertebral devices. The project will be performed mainly at Uppsala University, and in collaboration with OssDsign AB. Main supervision will be undertaken by Prof. Cecilia Persson (UU), with co-supervision from Prof. Per Isaksson (Solid mechanics, UU) and Dr Kajsa Björklund (OssDsign AB). The position is part of a large EU-funded Marie Sklodowska Curie Innovative Training Network, NU-SPINE (nu-spine.eu) and includes secondments at OssDsign AB, Sweden (PM10-12) and University of Leeds, UK (PM20-23).

More details: https://www.uu.se/en/about-uu/join-us/details/?positionId=239509

PhD student_CADENCE / Catalytic Dual‐Function Devices Against Cancer (H2020 nº GA 742684)


  • ORGANISATION/COMPANY: UNIVERSIDAD DE ZARAGOZA
  • RESEARCH FIELD: Computational modeling
  • RESEARCHER PROFILE: First Stage Researcher (R1)
  • APPLICATION DEADLINE (PROVISIONAL): 30/10/2018 17:00 – Europe/Madrid
  • LOCATION: Spain › Zaragoza
  • TYPE OF CONTRACT: Temporary
  • JOB STATUS: Full-time
  • HOURS PER WEEK: 37.5
  • EU RESEARCH FRAMEWORK PROGRAMME: H2020 / ERC
  • REFERENCE NUMBER: 742684

– Development of reaction-diffusion equations to simulate the behavior and activation of nanoparticles.

– Numerical development of glucose transport models.

– Simulation of tumour behaviour and experimental validation with in-vitro and in-vivo experiments.

– Numerical implementation of simulation of poroelastic behavior of tumor spheroids.

– Elaboration of summary reports and presentations (English preferentially).

– Preparation of scientific works and periodic reports.

– International mobility for collaboration in different research tasks.

Offer requirements

  • REQUIRED EDUCATION LEVEL

Computer Science or Applied Mathematics : Master Degree or equivalent

OR

Mechanical, Biomedical or Chemical Engineering: Master Degree or equivalent

Specific skill requirements

– Programming (C++, C and Python)

– Data analysis and representation (Paraview, matplotlib, MatLab)

– Basic knowledge of the mechanical and chemical bases of biological processes

– Basic knowledge as user of Finite Element softwares (Abaqus, Ansys, Comsol)

How to apply:

CV submission or further inquiries to Dr. Jose M. García Aznar (jmgaraz@unizar.es)

Provisional Deadline: December 23th 2018

PhD in Multiscale simulations for translational explorations of emphysema

POSITION DESCRIPTION

-Research Project / Research Group Description:

The proposed PhD will involve the Biomechanics and Mechanobiology, the Image analysis and the machine learning laboratories of the BCN MedTech research unit at the University Pompeu Fabra (UPF). BCN MedTech focuses on biomedical integrative research, including mathematical and computational models, algorithms and systems for computer-aided diagnosis and treatment of health problems. It has 60 full time researchers and belongs to the Department of Information and Communication Technologies, awarded with the prestigious label of Unit of Excellence through the Spanish Maria de Maeztu Strategic Research Program.
The project focusses on multiscale modelling and simulations to identify early biomarker candidates in emphysema. Emphysema is the most harming form of chronic obstructive pulmonary diseases (COPD) and its current diagnostic is usually confirmed at a relatively advanced stage of disease progression, through computed tomography image analyses. In order to cope with this limitation and support the early prevention of emphysema progression, we propose a multiscale modelling approach that combines image analysis, tissue finite element modelling and cell-cytokines agent-based modelling. Such approach has already allowed successful simulation of emphysema progression, as a response to cigarette smoking [1]. The proposed PhD will push forward this research towards the use of disease mechanism models for the identification of early emphysema biomarkers.

-Job position description:

Specifically, the work will include
• The development and implementation of advanced constitutive equations for the lung parenchyma
• The systematic evaluation of computational networks to simulate the dynamics of the biological processes that control the turnover of parenchyma macromolecules
• The meta-analysis of patient data and multiscale simulation results
The grant is supported by a European Marie Sklodowska-Curie co-fund and provides a competitive gross annual salary of 34.800 € during a period of three years to attract young talents. This salary is supplemented by a research allowance of 3.564 € per year, and a PhD award of 7.500 € will be granted if the PhD thesis is submitted within 6 months after the end of the fellowship.

The successful candidate will work in the Poble Nou Campus of UPF, in the beautiful town of Barcelona, in collaboration with the Barcelona Super Computing center for the multiscale simulations, and with ISGlobal for epidemiological data.

Applicants are expected to have a bachelor’s and master’s degrees in biomedical engineering, physics, applied mathematics or any related fields. They should be motivated to work in an international environment and have good communication skills. Experience in Python programming is welcome and proficient English is mandatory.

– Deadline for application: February 6th 2019

Apply here: https://www.lacaixafellowships.org/index.aspx

For any inquiry, please contact Dr Jerome Noailly: Jerome.noailly@upf.edu

PhD Position in Implant Biomechanics @ Karl Landsteiner University of Health Sciences, Krems, AT

 The Karl Landsteiner University of Health Sciences (KL) is part of an academic and research community located at the Campus Krems, and includes a network of comprising teaching hospitals in St. Pölten, Krems and Tulln. The university offers degree programs in Human Medicine, Psychotherapy, Counselling Sciences and Psychology and are tailored to the requirements of the Bologna model, opening the door to new, cutting-edge health professions. KL is committed to raising its profile in specific areas of biomedicine, biomedical engineering, and biopsychosocial sciences by entering into strategic academic and research partnerships with other institutions. 

Starting at November 2018, the department of anatomy and biomechanics (division of biomechanics, Prof. Pahr, Dr. Reisinger) offers a research position, which is limited to the duration of three years: Research Assistant m/f (Pre Doc, 30 h)  Your responsibilities:  • Participation in the funded research project “A morphology based failure criterion for implanted bone screws”  • In more detail: using of micro CT imaging, biomechanical testing, continuum mechanics, and 3d-printing  • Programming of evaluation- and analysis scripts  • Assistance in teaching in the fields of mathematics, physics, informatics and biomedical engineering  • Engagement in other research projects 
Your profile:  • Degree in civil or mechanical engineering, biomedical engineering, technical physics, or similar fields  • Basic knowledge in programming, biomechanics, imaging (CT), experimental material characterization  • Good English skills  • The willingness to support teaching, experience is of advantage  • Self-responsible and reliable working approach  • Interest on scientific working and writing a dissertation  • Friendly and team oriented personality 
Your perspective:  • You can expect a challenging job in an internationally recognized and highly motivated team  • Achieve the academic degree of a PhD (Dr. techn.), issued from the TU Vienna. 
The Karl Landsteiner University of Health Sciences is dedicated to achieving a balanced mix of male and female academic and non-academic staff. Consequently, applications from female candidates are particularly welcome.  The minimum gross salary for this position is € 2.112,40 (30 h). 
Applications should include a motivation letter, curriculum vitae, and credentials and should be mailed by 17.10.2018 to Ms. Christina Schwaiger of the Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, 3500 Krems, Austria (bewerbung@kl.ac.at). 

PhD Position at Insigneo, Sheffield

PhD position (Closing date: 30th January 2019)

Validation of a micro-finite-element model for contact-induced stresses at bone joints

Supervisor: Dr Pinaki Bhattacharya

Are you a bright, enthusiastic and self-motivated student interested in a PhD in biomechanics? A position is now available at the Integrated Musculo-Skeletal Biomechanics (IMSB) group in the Department of Mechanical Engineering at the University of Sheffield.

The IMSB group is part of the Insigneo Institute for in silico Medicine and possesses extensive experience in the development of computer simulations to better understand the biomechanics of the musculoskeletal system. In addition, this PhD project will profit from world-class collaborations at ETH Zürich (Switzerland) and KU Leuven (Belgium).

Research context

Figure 1. Stresses inside the femoral head induced by contact at the hip-joint

Contact occurs everywhere in musculoskeletal biomechanics, most notably at bone joints, where contact-induced stresses determine both fracture risk and joint disease progression.

Micro-finite-element (uFE) models – supported by specialised, highly-efficient, parallelized solvers (e.g. ParOSol) – can potentially predict contact-induced stresses with high accuracy using a recently-introduced contact formulation (SS-SC). Yet this opportunity to make an important technological breakthrough still needs to be realised.

The PhD project will involve:

  • Enriching an existing uFE solver by implementing the SS-SC formulation;
  • Analysing contact-induced stresses in the wrist joint using the enriched solver;
  • Performing cadaver experiments to validate uFE model predictions.

You should expect to undertake research stays at both collaborating universities (ETH Zürich and KU Leuven) for training purposes.

Candidate Profile

The successful candidate should have or be expected to obtain a 1st class or a good 2.1 degree in mechanical engineering, bioengineering, computer science, physics, applied mathematics or a related discipline.

Experience in programming languages (e.g. C, C++, Matlab, Python) is essential. Exposure to high-performance computing or previous knowledge of finite-element analysis and/or experimental testing is highly desirable.

Funding and Duration

A three-year studentship funded by the Department of Mechanical Engineering is available for UK and EU applicants. The studentship covers the cost of tuition fees and provides an annual tax-free stipend at the standard UK research rate.

How to apply

Link: https://www.sheffield.ac.uk/mecheng/phd/phd-studentships/model-contact-induced-stresses

For further information about this project, please contact Dr Pinaki Bhattacharya, with “VOXCON PhD studentship” in the title, at p.bhattacharya@sheffield.ac.uk

To apply, please use our standard on-line PhD application form, including your CV and two references, and indicate on your form that you are replying to this advert. For further guidance on applying, please email me-pgadmit@sheffield.ac.uk