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Bioengineering
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The Power of Models and Simulation Tools in Biomedical and...
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The Power of Models and Simulation Tools in Biomedical and Biochemical Engineering

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biomedical Engineering and Biomaterials".

Deadline for manuscript submissions: 20 June 2025 | Viewed by 3592

Special Issue Editors

Dr. Antonio D’Ambrosio

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Guest Editor
Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Science and Technology for Sustainable Development and One Health, University Campus Bio-Medico of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy
Interests: process simulation; reaction engineering; kinetic modeling; chemical engineering fundamentals; pharmacokinetic modeling
Dr. Nicole Guazzelli

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Guest Editor
Department of Information Engineering, Research Center “E. Piaggio”, School of Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122 Pisa, Italy
Interests: multiscale mechanical; structural computational modeling; multiscale computational fluid-dynamic modeling; bioreactor simulation; in silico-in vitro approaches; high throughput in vitro models design; in vitro-in vivo correlation algorithms; molecular modeling; pharmacokinetic modeling; lung computational modeling
Dr. Leone Mazzeo

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Guest Editor
Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Science and Technology for Sustainable Development and One Health, University Campus Bio-Medico of Rome, Via Alvaro del Portillo, 21, 00128 Rome, Italy
Interests: wastewater treatment; hydrogen production; polyphenol extraction; frugal engineering for medical devices

Special Issue Information

Dear Colleagues,

In recent years, there has been a flourishing of digital tools, which are inevitably affecting the engineering profession as well. It is evident that modeling and simulation instruments are being employed with increasing regularity for the purpose of developing and optimizing devices and processes. This is a matter that cuts across several branches of engineering and therefore requires a multidisciplinary approach. In chemical engineering, the availability of process simulators and equipment models is driving the development of new processes in response to growing health and environmental concerns based on the “one health” paradigm. Concurrently, such instruments can facilitate the optimization of existing processes to align them with new directives and market challenges. This argument may also be applied to the field of biomedical engineering, in which processes and equipment are reimagined as organs and compartments of humans or other living beings.

This Special Issue will focus on the recent developments of models and simulation tools in the fields of biomedical and biochemical engineering.  

The journal will be accepting contributions (both original articles and reviews) mainly centered on the following topics: 

  • Computational simulation of sustainable processes;
  • Bioreactor modeling;
  • Modeling and optimization of the production of biofuels and bio-based products;
  • Bioprocesses intensification;
  • Membranes and biotechnology applications in biochemical and biomedical engineering;
  • Physiologically-based pharmacokinetic (PBPK) models;
  • Artificial organs modeling, simulation and optimization.

Dr. Antonio D’Ambrosio
Dr. Nicole Guazzelli
Dr. Leone Mazzeo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Bioengineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • computational simulation of sustainable processes
  • bioreactor modeling
  • modeling and optimization of the production of biofuels and bio-based products
  • bioprocesses intensification
  • membranes and biotechnology applications in biochemical and biomedical engineering
  • physiologically-based pharmacokinetic (PBPK) models
  • artificial organs modeling, simulation and optimization

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

18 pages, 4448 KiB  
Article
Six-Month Patency of Long Carotid Bypass Grafts Constructed with In-Body Tissue Architecture-Induced Small-Diameter Biotubes in a Goat Model
by Kazuki Mori, Tadashi Umeno, Takayuki Kawashima, Takashi Shuto, Ryosuke Iwai, Lupeng Teng, Tsutomu Tajikawa, Yasuhide Nakayama and Shinji Miyamoto
Bioengineering 2025, 12(3), 260; https://doi.org/10.3390/bioengineering12030260 - 5 Mar 2025
Viewed by 656
Abstract
This study investigated the long-term patency of regenerative Biotube grafts and discusses their feasibility as an alternative to autologous vein grafts for peripheral artery disease. Six Biotubes with a diameter of 4 mm were autologously fabricated in recipients using in vivo tissue engineering [...] Read more.
This study investigated the long-term patency of regenerative Biotube grafts and discusses their feasibility as an alternative to autologous vein grafts for peripheral artery disease. Six Biotubes with a diameter of 4 mm were autologously fabricated in recipients using in vivo tissue engineering (in-body tissue architecture) technology and implanted as carotid artery bypass grafts in a goat model. All six grafts remained patent at 6 months despite exceeding 10 cm in length, demonstrating their biocompatibility and durability. Histological analysis revealed neointima formation, endothelialization, and minimal inflammation. However, in one goat, a graft developed stenosis, while another showed dilatation. These findings demonstrate the use of Biotubes as a viable option for peripheral vascular reconstruction as tissue-engineered vascular grafts. However, further optimization is needed to address emerging issues with their use, such as stenosis and aneurysm formation, to improve long-term patency. Full article
(This article belongs to the Special Issue The Power of Models and Simulation Tools in Biomedical and Biochemical Engineering)
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15 pages, 2822 KiB  
Article
Comparison of Machine Learning Algorithms and Hybrid Computational Intelligence Algorithms for Rehabilitation Classification and Prognosis in Reverse Total Shoulder Arthroplasty
by Sotiria Vrouva, George A. Koumantakis, Varvara Sopidou, Petros I. Tatsios, Christos Raptis and Adam Adamopoulos
Bioengineering 2025, 12(2), 150; https://doi.org/10.3390/bioengineering12020150 - 5 Feb 2025
Viewed by 618
Abstract
Despite the increasing application of machine learning and computational intelligence algorithms in medicine and physiotherapy, accurate classification and prognosis algorithms for postoperative patients in the rehabilitation phase are still lacking. The present study was carried out in two phases. In Phase I, classification [...] Read more.
Despite the increasing application of machine learning and computational intelligence algorithms in medicine and physiotherapy, accurate classification and prognosis algorithms for postoperative patients in the rehabilitation phase are still lacking. The present study was carried out in two phases. In Phase I, classification performance of simple machine learning algorithms applied on data of patients suffering of reverse total shoulder arthroplasty (RTSA), examining algorithms’ classification accuracy and patients’ rehabilitation prognosis. In Phase II, hybrid computational intelligence algorithms were developed and applied in order to search for the minimum possible training set that achieves the maximum classification and prognostic performance. The data included features like age and gender, passive range of available motion of all movements (preoperative and postoperative), visual analog pain scale (preoperative and postoperative), and total rehabilitation time. In Phase I, K-nearest neighbors (ΚΝΝ) classification algorithm and K-means clustering algorithm (GAKmeans) were applied. Also, a genetic algorithm (GA)-based clustering algorithm (GAClust) was also applied. To achieve 100% performance on the test set, KNN used 80% of the data in the training set, whereas K-means and GAClust used 90% and 53.3%, respectively. In Phase II, additional computational intelligence algorithms were developed, namely, GAKNN (Genetic Algorithm K-nearest neighbors), GAKmeans, and GA2Clust (genetic algorithm-based clustering algorithm 2), for genetic algorithm optimization of the training set. Genetic algorithm optimization of the training set using hybrid algorithms in Phase II resulted in 100% performance on the test set by using only 35% of the available data for training. The proposed hybrid algorithms can reliably be used for patients’ rehabilitation prognosis. Full article
(This article belongs to the Special Issue The Power of Models and Simulation Tools in Biomedical and Biochemical Engineering)
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Figure 1

27 pages, 4692 KiB  
Article
Predicting the Impact of Polysulfone Dialyzers and Binder Dialysate Flow Rate on Bilirubin Removal
by Alexander Novokhodko, Nanye Du, Shaohang Hao, Ziyuan Wang, Zhiquan Shu, Suhail Ahmad and Dayong Gao
Bioengineering 2024, 11(12), 1262; https://doi.org/10.3390/bioengineering11121262 - 12 Dec 2024
Viewed by 1270
Abstract
Liver failure is the 12th leading cause of death worldwide. Protein-bound toxins such as bilirubin are responsible for many complications of the disease. Binder dialysis systems use albumin or another binding molecule in dialysate and detoxifying sorbent columns to remove these toxins. Systems [...] Read more.
Liver failure is the 12th leading cause of death worldwide. Protein-bound toxins such as bilirubin are responsible for many complications of the disease. Binder dialysis systems use albumin or another binding molecule in dialysate and detoxifying sorbent columns to remove these toxins. Systems like the molecular adsorbent recirculating system and BioLogic-DT have existed since the 1990s, but survival benefits in randomized controlled trials have not been consistent. New binder dialysis systems, including open albumin dialysis and the Advanced Multi-Organ Replacement system, are being developed. Optimal conditions for binder dialysis have not been established. We developed and validated a computational model of bound solute dialysis. It predicted the impact of changing between two test setups using different polysulfone dialyzers (F3 and F6HPS). We then predicted the impact of varying the dialysate flow rate on toxin removal. We found that bilirubin removal declines with dialysate flow rate. This can be explained through a linear decline in free bilirubin membrane permeability. Our model quantifies this decline through a single parameter (polysulfone dialyzers). Validation for additional dialyzers and flow rates will be needed. This model will benefit clinical trials by predicting optimal dialyzer and flow rate conditions. Accounting for toxin adsorption onto the dialyzer membrane may improve results further. Full article
(This article belongs to the Special Issue The Power of Models and Simulation Tools in Biomedical and Biochemical Engineering)
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