Themengebiete für Studien- & Abschlussarbeiten

KIT – University of the State of Baden-Wuerttemberg and

National Research Center of the Helmholtz Association

Institute of Process Engineering in Life Sciences

Section IV: Biomelecular Separation Engineering

www.kit.edu

Themengebiete für Studien- & Abschlussarbeiten

Doktoranden des MAB

Institute of Process Engineering in Life Sciences

Section IV: Biomolecular Separation Engineering

2

Allgemeines

Die folgende Übersicht dient dazu, Interessenten von Studien- bzw.

Abschlussarbeiten (BA, MA) einen Überblick über die Arbeitsgebiete

am Institut für „Molekulare Aufarbeitung von Bioprodukten“ zu geben.

Interessenten mit konkreten Themenwünschen können sich direkt bei

den jeweiligen Doktoranden melden oder allgemein bei David Grijalva

([email protected]).

Themengebiete für Bachelor- und Masterarbeiten13.08.2021

3 13.08.2021 Themengebiete für Bachelor- und Masterarbeiten

Angela Valentic

PhD project started 09/2019

Tasks: Analytical development + method development

Disassembly

and effect of

host cell nucleic

acids

Reassembly in

the presence of

nucleic acids

VLPVLP loaded

with RNA

Analytics:

- qPCR

- cGE

- SLS, DLS

- RP-/SEC- UHPLC

- Spectroscopic methods

Experimental:

- Process development + characterization of process

parameters by common and nucleic acid specific

analytical tools

- VLP production by cultivation in E.coli and purification by

e.g. precipitation, chromatography methods and UF/DF

@ThermoFisher@Wyatt @ThermoFisher

Changes in dispersity, structure and phase behaviour of

virus-like particles (VLPs) in the presence of nucleic acids

Motivation: Virus-like particles as carrier system for gene therapy

4

© ThermoFisher

Background

Carrier systems with nucleic acid cargo are

used for targeted delivery in the field of gene

therapy.

Robust production, purification and formula-

tion processes are required to ensure their

product quality attributes. Therefore, Process

Analytical Technology (PAT) is applied to

monitor process parameters by in-line, on-line

or off-line measurements.

13.08.2021 Themengebiete für Bachelor- und Masterarbeiten

Annabelle Dietrich

Process development, analytical development and PAT implementation

for carrier systems with nucleic acid cargo.

© Spectrum Labs

Materials & Methods

Experiments- Process & analytical development

- Ultra-/Diafiltration (UF/DF)

- …

- PAT Implementation

Analytics - Spectroscopic methods (UV/Vis, Raman)

- Light Scattering

- RP-/SEC- UHPLC

- …

Tools- Matlab © Malvern

Virus-like particle (VLP)

Lipid-nanoparticle (LNP)

© TECAN

5

Christina Wegner – Protein Crystallization

Purification of biopharmaceuticals by protein crystallization is an attractive alternative to

chromatography. Up to now, laborious, empirical screenings are the core approach for

process development of crystallization processes. The combination of high throughput

screenings (HTS), spectroscopy, rheometry and elaborate data analysis can overcome

these limitations.


PredictionPhase behaviour

On-line

analytics

HT screening

Purity

Yield

𝑐𝑝𝑟𝑜𝑡𝑒𝑖𝑛

Spectroscopy

𝑐𝑝𝑟𝑜𝑡𝑒𝑖𝑛

𝑐𝑐𝑜𝑛𝑡𝑎𝑚𝑖𝑛𝑎𝑛𝑡

Rheometry

𝜔𝐶𝑂

𝐺′

𝐺′′

Current projects:

- Process Analytical Technology (PAT) of solid and liquid

phase in lab-scale selective crystallization processes

- Prediction of crystallization behavior by protein-protein

interaction analysis

- Selective precipitation process development with

HTS of proteins in harvest broth

Methods:

- Spectroscopic methods (UV/Vis, Raman)

- Variable path length UV/Vis spectroscopy

- High frequency rheometry

- Multivariate data analysis in Matlab

- Analytical chromatography

- Pipetting roboter, automated screenings …

© Formulatrix

ddw-online.com

Dionex

Matlab


David Grijalva – 3D Bioprinting

Background:Automated, reproducible manufacturing and analysis of

complex structures with biomaterials containing viable

cells

© T

eca

n

© A

nto

n-P

aa

rAnalytics:- Rheometry

- Flow cytometry

- Microscopy

- UV/Vis spectroscopy

Experimental:- Evaluation of biomaterials for 3D printing

applications

- Characterisation cell metabolic activities

© M

ilte

nyiB

iote

c

© Z

eis

s

7

Dennis Weber

Themengebiete für Bachelor- und Masterarbeiten13.08.2021

PROTEIN STABILITY IN FREEZE-THAW OPERATIONS

Material & Methods

Experiments

• µL- and mL cryodevices

• Robotic liquid handling station

Analytics

• SLS, DLS

• Melting temperature

• FT-IR

• …

CFD simulations

Background

Freezing and thawing are necessary

process units during the production of

biopharmaceuticals.

During the freezing process, freeze

concentration might occur. This may

lead to:

• Protein aggregation

• Surface denaturation

• pH denaturation

• Cold denaturation

• …

It is the aim of my thesis to evaluate the

protein stability during freezing/thawing.

ice

T / °

Cr / m

© T

ecan

© G

rant

© M

alv

ern

8 Themengebiete für Bachelor- und Masterarbeiten13.08.2021

Synthesis of Hybrid Nanoparticles via Aerosol Thiol-ene Photopolymerization

Gold Nanoparticle

HS

HS SH

3-functional ene

Aerosol

DropletsSpray SolutionPolymer

Nanoparticles

Atomization

Bio-agent

BioconjugationPhotoreaction

Bioconjugated

Nanoparticles

Narmin Suvarli

Legend:HS

HS SH

3-functional thiol Photoinitiator

Photothermal

therapy

Imaging

and Diagnostics

Pro

cess

Ap

pli

cati

on

s

• Cancer Screening and

treatment

• Drug delivery

• Encapsulation into hydrogels

for enzymatic reactions

Cancer tumor

Horizon 2020

Marie Sklodowska-Curie Actions

Innovative training network


Nils Hillebrandt

Entwicklung eines hochdurchsatzfähigen Hochfrequenz-Rheometers zur Analyse der viskoelastischen Eigenschaften hochkonzentrierter Proteinlösungen [1]

[1] Kooperation mit dem Institut für Automation und angewandte Informatik (IAI), Ansprechpartner: Prof. Dr. Christian Pylatiuk

[2] Schermeyer et al. (2016). Squeeze flow rheometry as a novel tool for the characterization of highly concentrated protein solutions.

Biotechnology and Bioengineering, 113(3), 576–587. https://doi.org/10.1002/bit.25834

Ziel

Korrelation viskoelastischer

Eigenschaften mit der Lösungsstabilität

von Proteinlösungen [2]

Aufgaben

Evaluierung und konzeptionelle

Optimierung von

Messaufbau/Konstruktion

Design und Implementierung der

Automatisierungs- und

Temperierungseinheit

Techniken/Arbeitsbereiche

Ansteuerung von

piezokeramischen Aktoren und

Sensoren

Schwingungsanalyse

Programmierung mit MATLAB

Ansteuerung der peripheren

Bauteile (Pumpen, Peltier-

Element, Temperatur-

Controller

Kooperation%20mit%20dem%20Institut%20für%20Automation%20und%20angewandte%20Informatik%20(IAI),%20Ansprechpartner:%20Christian%20Pylatiuk

https://doi.org/10.1002/bit.25834


Advancingultra- and

diafiltration

Online-Monitoring

ModelingHigh-

Throughput

Source:

https://www.sartorius.com/en/products/

process-filtration-purification/process-

filtration-hardware/crossflow-holders-

systems/crossflow-systems/ambr-

crossflow

Source: https://gosilico.com/

In collaboration with

Source:

http://spectrumlabs.com/filtration/K

R2System.html

Nils Hillebrandt


Sandra Haas

Development and establishment of bioinks made of specially developed

elastic proteins for 3D printing of high-performance materials

Theoretical backgroundElastic materials are mostly petroleum-based and not biodegradable. The goal of my work is the use of biotechnologically

produced, elastin-like proteins (ELP) to produce highly elastic, 3D-printed hydrogels. Therefore, it is necessary to develop an

understanding of the factors influencing the later mechanical properties of the resulting hydrogels.

Ink developmentElastin-like proteins (ELP) 3D-Printing

• Development of protein analytics

• Optimisation of downstream processes

• Formulation of bioinks (model proteins and ELPs)

• Characterisation of formulated bioinks and hydrogels

• 3D printing using different techniques

(Stereolithography, Extrusion)


Background:Automated, reproducible

manufacturing and analysis of

complex structures with biomaterials

containing viable cells

© T

eca

n

© A

nto

n-P

aa

r

Analytics and tools:- Rheometry

- Microscopy

- Image processing

- Matlab

Experimental:- Printing optimisation of biomaterials

- Development of standardised analytical

methods

Svenja Strauß – 3D Bioprinting

13

Process modeling and control• PAT tools in combination with mechanistic

models for all steps in the conjugation workflow

• Model-predictive control of conjugation reaction

Experimental Methods:▪ Kinetics determination▪ Analytics: RP-HPLC▪ UV-Vis spectroscopy

CFD-based reactor modeling▪ Scale-down reactor modeling

▪ Hydrodynamics-guided process scale-up for ADC reaction

▪ Full-3D conjugation reaction model

Simulation Methods:▪ 0D-Simulations with MATLAB®▪ CFD Simulation with Ansys Fluent®


Jan WeggenAdvanced methodologies for modelling antibody-drug conjugation

Background: ADC production comprise a set of stirred tank operations, coupled with UF/DFfor buffer exchange and at least one chromatographic step. To increase processunderstanding, enable trouble shooting and ease process characterization as well as scalebridging, a set-up such as a ‘Digital Twin’ is developed.

Antibody-Drug Conjugate (ADCs):

© W

ater

s co

rpo

rati

on

© D

ion

ex

Conjugation

HIC

UF/DF

#Digital Twin

𝑓(𝑥)


Robin Schiemer

Artificial Intelligence for Bioprocess Development

Artificial Intelligence (AI) and Machine Learning (ML) methods provide powerful toolboxes for advanced data analytics with the increasing computation power

enabling the use of these algorithms in all sorts of sciences. In bioprocesses, process variables are monitored by in-line or off-line measurements which carry

information about the progress of the process. Spectroscopic sensors such as UV/VIS, FTIR or Raman sensors were shown to be reliable sources of process

information concerning the concentration of the contained species, excipient concentrations or structural conformations of the components. Parallely,

mechanistic models were established for various unit operations to save experimental time and costs and considerably increase process understanding. AI/ML

methods can help to create hybrid modeling strategies where real-time process information is combined with model predictions to successfully implement

efficient and precise process control.

Process

Sensor

Data Science

Mechanistic Modeling

capturereal-time information

extract patterns& makeprediction

use process knowledge

makeprediction

model-basedcontrol

Materials & Methods

Process Analytical Technologies (PAT) and mechanistic models are

applied to improve gene therapy process development and enable

model-predictive control of monoclonal antibody purification processes.

Experimental:

» Chromatography et al.

» Spectroscopy (UV/VIS, FTIR, Raman)

» Light Scattering (Zetasizer, MALS, RI)

» Analytics (HPLC, qPCR, ..)

Computational:

» Data Science (Python, TensorFlow)

» Process automation (MATLAB)

» Mechanistic modeling (ChromX)

Documents

Themengebiete für Studien- & Abschlussarbeiten