Crystalline solid products are around us everywhere – they are central to industrially-relevant production as 70% of the products of the chemical and pharmaceutical industry are sold as solids. A prominent example is an aspirin tablet that we take for a headache. An important part in designing a crystallization process of getting solid materials from liquid solutions is to control the size and shape of the crystals. Fundamental and applied research in this area of crystallization leads to improved process performance with less energy consumption as well as more efficient material utilization.

Such solid-liquid systems are complex and challenging in many ways and fluid flow and particles interact in a variety of fashions. In the lab setup, the evolution of the crystal size and shape distribution is tracked by means of image-based shape estimation. This information is then in turn exploited to obtain the crystallization kinetics that are governing the crystallization process. To incorporate these complexities, the numerical methods have been extended and new tools are developed to simulate crystallization in a better way. Our focus has been on relevant phenomena of crystal growth of multi-faceted crystals as well as on crystal agglomeration with specifically developed model experiments working with selected and well-understood model substances. Experiments and flow field simulations serve to parameterize a coupled population balance equation system. This equation system allows predicting the dynamic evolution of the crystal size and shape distribution. Crystal agglomeration is a major phenomenon of crystal size enlargement. Our research concentrates on the understanding and modeling of this phenomenon.

The crystal growth and agglomeration can be combined where the main control variables are temperature profiles and flow rates. Crystals can be separated by size and withdrawn at a varying crystallizer height. The size separation is again controlled by the flow rates.

Crystallization processes are often modeled in terms of a crystal population instead of considering the behaviour of each individual crystal. Utilising macroscopic conservation laws, one derives a system of coupled equations for the population, a so-called Population Balance System (PBS) that describes an averaged behaviour of the crystals. The crystallization process within a moving incompressible fluid is modeled—the movement is in pipes and/or batch crystallizers. It is assumed that the suspension of the crystals is dilute such that the impact of the crystals on the fluid flow is negligible. Then, the first two conservation laws are the balance of the linear momentum and the conservation of mass for the fluid flow, which are modeled by the incompressible Navier-Stokes equations.

Our study shows that the simulations can indeed be used to model the processes in Fluidized Bed Crystallizers. There is a good agreement between experimental and simulation results. These can be further tested virtually using different operating conditions and settings and this paves the way for cheaper, faster, and informed design and innovation of future fluidized bed crystallizer.

This article is a distilled version of a book chapter: R Ahrens, Z Lakdawala, A Voigt, V Wiedmeyer, V John, Sabine Le Borne, Kai Sundmacher, “Numerical methods for coupled population balance systems applied to the dynamical simulation of crystallisation processes,” in Dynamic Flowsheet Simulation of Solids Processes (2020).

Researchers from the Department of Biology at SBASSE have identified genome-wide transcriptional changes during trophoblast stem cell differentiation, a key event during placental development. This work from Dr. Rahim Ullah’s PhD thesis was carried out under the supervision of Dr. Amir Faisal and has been published in BMC’s Stem Cell Research and Therapy. This multidisciplinary research highlights collaborative efforts between various groups in Biology, including those of Dr. Aziz Mithani and Dr. Muhammad Tariq.

Differentiation of mouse trophoblast stem cells (TSCs) to trophoblast giant cells (TGCs) has been widely used as a model system to study placental development and function. While several differentially expressed genes, including regulators of TSC differentiation, have been identified, a comprehensive analysis of the global expression of genes and splice variants in the two cell types has not been reported.

The paper reports ~7800 differentially expressed genes in TGCs compared to TSCs which include regulators of the cell cycle, apoptosis, cytoskeleton, cell mobility, embryo implantation, metabolism, and various signaling pathways. It shows that several mitotic proteins, including Aurora A kinase, were downregulated in TGCs and that the activity of Aurora A kinase is required for the maintenance of TSCs. The paper also identifies hitherto undiscovered, cell-type-specific alternative splicing events in 31 genes in the two cell types. Finally, we also report 19 novel exons in 12 genes which are expressed in both TSCs and TGCs.

The data reported in this paper point to transcriptional diversity and differential transcriptome in mouse TSCs and TGCs that was not known previously. Differential expression of some of these genes indicates a shift in the functional properties of TGCs as they differentiate from TSCs. Functional validation of these genes will not only enhance our understanding of mammalian development but could also lead to finding ways to treat placental abnormalities and diseases which often lead to premature childbirth.

This workshop aim to bring together researchers from the UK & Pakistan to share research expertise and develop collaborations relevant to enabling a sustainable energy transition in Pakistan.

Eligible candidates should have obtained their PhD no earlier than 2010. Participants must also have a research or academic position (a permanent post, research contract, or fellowship etc.) at a recognised research institution either in the UK or Pakistan. 

Apply before 23rd April, 2021

Learn more: https://bit.ly/3uZyqWL

Dr. Muhammad Shoaib is a clinical turned researcher, who exudes a passion for teaching and research in chromatin biology and proteomics. He is keen on developing new techniques to study how proteins play a part in physiological and pathological cellular processes.

Dr. Shoaib led the Chromatin Biology sub-group which is part of a larger lab at the Biotech Research and Innovation Centre (BRIC) at the University of Denmark, Copenhagen. He was working as Assistant Professor there. In between his PhD from the University of Paris-Sud and his position at the University of Denmark, Shoaib worked as Assistant Professor at the University of Lahore. He steers a group that focuses on chromatin regulation on both the biochemical and genetic mechanisms.

Though Shoaib is a first-rate molecular biologist, he is a clinician by first degree (a dentist). This is a big plus and gives our efforts of translating our research from the benchtop to the bedside a great boost. As our departments develop new strategies for applied research in the areas of health practice, health informatics, design and discovery of drugs and vaccines, systems modeling, anti-resistance drugs for cancer, Hepatitis-C and structural modeling of viruses as well as key questions in developmental biology and genetics, the recruitment of Shoaib will provide an immediate bolus of energy and new ideas.

Three members of the SBASSE faculty have been awarded the inaugural Vice Chancellor’s Award for Teaching Excellence! These awards mark a new beginning in our institutional culture.

Dr. Tariq's inspirational teaching in the lab and classroom, his courses on developmental biology and genetics are the perfect mix of insight, crystal clarity and futurism. For example, see this video in which he describes the marvelous richness of the fruitfly's eye.

Dr. Zubair's immaculate presentations on signal processing are evidenced by the teaching material he has made public for everyone's consumption. One example is his Machine Learning course. For example, see the candeur with which he describes the mathematically complex problem of duality, delving into its geometrical interpretation. 

Finally, Dr. Momin has broken new grounds in defining the EE100 milieu, a course that brings research problems in engineering right to the doorsteps of our freshmen, truly breaking temporal boundaries. His teaching of Signals and Systems bespeaks a solid grip of the student and pedagogical clarity.

On behalf of all students and Faculty, we’d like to extend congratulations to Drs. Muhammad Tariq, Momin Uppal and Zubair Khalid for their well-deserved recognition. 

This course provides a non-specialist introduction to programming in MATLAB. The focus is on developing the thinking process to write simple programs, and the necessary MATLAB tools to implement that.

Title: Matlab for Everyone

Term: Summer I - 2021

Course Outline: Download

Instructor(s): Dr. Safee Ullah Chaudhary

Registration link: Click here

Much like an Agatha Christie novel, mystery shrouded the Department of Biology a few months ago when the incubator in the Plant Growth Rooms refused to maintain its temperature to the set 18˚C and 25˚C. Fearing a fire hazard when the temperature shot up to 56˚C, help was sought from the company that had fitted the incubators in the first place. 

Installed by Force Engineering, the four series of walk-in incubators, barred by heavy steel doors, come equipped with controls for temperature, humidity, and light settings to mimic the conditions necessary for optimum growth and proper circadian rhythms (an internal biological clock tuned to light and dark cycles). While two incubators are reserved for the tiny Drosophila (pronounced Droh-so-filaa) flies buzzing around in their cylindrical food vials, the other two are filled with plant seedlings in plastic pots on racks with fluorescent lighting. These are, of course, the Plant Growth Rooms that harbor various genetic experiments attempting to understand and characterize plant response to an assortment of stress factors. 

Though the Plant Growth Rooms were established several years ago by the pioneering work on plant molecular biology led by Dr. Ahmed Jawaad Afzal, they have just now been continued for use by the newest addition to the Department of Biology - Dr. Khurram Bashir. Unfortunately, it was soon observed that only one outdoor unit was functioning (and that too, barely) while three others had lost utility altogether. Though the indoor units were working, they were unable to maintain the correct levels of temperature and humidity. Further investigation only then revealed the depth of the damage – Extensive fungal contamination on the indoor units, burst pipes and loss of gases had contributed to the malfunction.   

When Force Engineering was contacted for the maintenances, the Department of Biology learnt that the company had been disbanded and, thus, had stopped all their services. With great technical expertise needed for this repair job, hope seemed to be a thinning silver line of a very dark cloud. 

Would a fix be found in time?

Then a light bulb went off, and it was decided to procure the same external source that was used for the upkeep of fridges/freezers/cold rooms to restore the walk-in incubators. Bismillah Engineering was therefore put to the task of having the incubators up and running, which they miraculously did in no time. Not only were all four outdoor units now operational but extensive servicing of all components, thorough cleaning of the indoor units, refilling of the gases, and installation of new parts was also provided by them. Additionally, all the tube lights were also replaced with efficient LED lights on the racks and halogen lamps on the ceiling.

Needless to say, the engineers saved a massive expense with their know-how and facilitated in getting the study and research on plants back on track! 

This story has been created by Sitara Hassan who is working as a Research Assistant in the Department of Biology and she is also part of the Carl Sagan Write for Science Centre in the SBASSE's Dean's Office. 

If you ever have had the chance to visit the basement of SBASSE, you may have glanced upon what looks akin to a gleaming white spaceship standing proudly with an air of futuristic appeal. And though the words ‘Nuclear Magnetic Resonance (NMR) Spectrometer’ may seem a mouthful to speak, it is in truth a fundamental piece of technology that is pioneering research and development across a multitude of disciplines.

The NMR Spectrometer Lab at LUMS is a state-of-the-art facility, being the first of its kind in the region, and boasts a miraculous machine capable of probing nuclear spins to determine molecular architecture (imagine an atomic ballet, choreographed by the forces of magnetism). It has not only enabled the instant identification of the structural characteristics of compounds but has also shed light on the vast network of interactions involved at an atomic level. For instance, the discovery of a therapeutic drug extracted from cloves against Dengue virus by students at the Department of Chemistry and Chemical Engineering, or the anti-viral activities of a protein engineered at the Department of Biology last year, is but a small demonstration of the promising potential of employing NMR studies. 

Recently, two undergraduate SBASSE students received the proverbial Golden Ticket to gaining a hands-on experience through a ten-week long NMR Training Internship Program organized by the Department of Biology. Muhammad Azhan (BS Chemistry) and Wahaj Ayub (BS Physics) participated in learning the intricate technicalities of the NMR instrumentation. From sample preparation to data visualization, the apprenticeship was a whirlwind of activities and rigorous training, fostering a proactive involvement by the interns.

The internship was a great way to delve deeper into exploring the specifics of the spectrometer and its associated equipment, ultimately bringing out a practical perspective to theoretical knowledge. During the duration of the training, the students learnt about safety precautions for proper handling of the machine, operated sophisticated software (such as TopSpin), and ran various NMR techniques; (if Heteronuclear Single Quantum Coherence, (HSQC) or Correlation Spectroscopy (COSY) has you scratching your head in confusion, fear not. Such methods simply help to reveal the arrangement of interacting particles – sort of like a Google Map of their location). The two apprentices also expertly calibrated parameters predicted and interpreted spectral data.

For Wahaj, the internship was an exciting prospect of seeing a topic in a Physics course that he had  merely read in passing, come to life before his very eyes. When contacted for a short interview, he also shared how he felt intimidated the first time he saw the gigantic NMR machine – expensive and extremely fragile – but gradually came to appreciate the technology when it would seamlessly react to the input commands. Learning, he exclaims, is especially nice when it is outside of the classroom environment and pressure. Rising to the task of becoming proficient at something new, he is hopeful that similar opportunities would be available for students in the future. He was, however, constantly afraid of breaking one thing or the other. He also highlighted how the biggest challenge for him was navigating through the internship in times of the COVID-19 lockdown, and he is sorry that part of it was left incomplete as they had to cut it short. Wahaj is utterly grateful to Dr. Muhammad Adil Raees (NMR Facility Manager) and wishes to thank him again for the kind help throughout the apprenticeship.

Answering the question of how he first came to pursue Chemistry, Muhammad Azhan explained that the concept of ‘Learning Without Borders’ at LUMS, whereby freshmen partake in various SBASSE core courses before declaring their major, lent him exposure to diverse disciplines. Taking a CHEM-101 class by Dr. Habib-ur-Rehman was the turning point in taking up this field in order to unravel the ‘mystery of matter’ and contribute to solving threats of global warming, energy crisis, pollution, and resource scarcity. In his correspondence, he also mentioned that he has been enthralled by the likes of Dr. Muhammad Abdus Salam, Dr. Irshad Hussain and Dr. Basit Yameen for building scientific curiosity and igniting his interest. He found the internship program to be tremendously unique and rewarding, and one that cultivated critical thinking along with inquisitiveness. It also equipped him with the technical expertise that proved immensely valuable in his quest to pursue higher education. He is honored to be part of this enlightening experience. 

When asked if there was anything that could be done to improve the internship, both Wahaj and Azhan believe that the development of a manual or a handout to incorporate all the learning material would help make the initiation process easier for the interns.  

After getting in touch with Dr. Muhammad Adil Raees, the NMR Facility Manager, he gave an account of how his research involves the isolation of natural products from medicinal plants and their structural characterization using both NMR and mass spectroscopic techniques. He further described how a three-month long internship at the NMR facility at the University of Karachi sparked his interest for the first time, and that even after ten years of working with this marvellous machine how each day is replete with the surprise of uncovering the veiled through the eye of the NMR. When questioned about the favorite aspect of his work, he conveyed that it was supervising and supporting the operation of the NMR laboratory as well as aiding students to run experiments with the spectrometer. While working with NMR is technically demanding of expertise, experience, and knowledge for proper upkeep, he proudly exclaimed that they have successfully maintained this facility ever since its induction and strive to continue doing so. In the very near future, he wishes for students and researchers from other institutes to also have the opportunity to inculcate this instrument in their work in order to not only improve the education standards of Pakistan, but to also establish quality research in areas of structural biology, drug discovery, vaccine development, metabolomics, and synthetic chemistry. 

In an interview with Dr. Syed Shahzad-ul-Hussan, an Associate Professor at the Department of Biology and part of the NMR core team, he expressed that he had had a great time supervising the keen interns during their training. He explained that he initially came across the NMR spectroscopy during his MPhil and later during his PhD in Bio-organic Chemistry at the University of Luebeck, Germany, where his advisor encouraged his interest in discovering answers on the atomic level. He fondly remembers how deeply engrossed he was in trying to solve the structure of a protein during his Postdoc, that his supervisor would come in the evening to say, "Go home now!", because 15-16 hours would have passed without Dr. Shahzad noticing. And this is exactly what he loves about his work – discovering the structural basis of a biological process because it gives a real picture. Using the NMR has been such an exceptional experience that it has become an integral part of his career. His research centres around drug discovery against viruses and comprehending the cross talk between viruses and the human immune system to subsequently obtain the necessary information for designing vaccines. He elucidated that NMR spectroscopy is crucial for this in several ways: to identify new molecules from nature as potential antiviral agents, to determine the structure of such compounds, to study the atomic level interactions between the drug and its viral target and then to further optimize their efficacy, and besides this, the structural and dynamic studies of protein and glycans can also aid in answering important biological questions of molecular recognition. 

So, the next time you come across the NMR spectrometer, I hope you find to it to be a glorious example of human ingenuity and innovation; with each piece of data bringing clarity to the jigsaw puzzle of scientific questions and conundrums, and that this remarkable contraption inspires you to join the NMR bandwagon. 

Dr. Shahzad ul Hussan and Dr. Muhammad Afzal from the Department of Biology at SBASSE are working on RNA vaccine of SARS-CoV-2. Dr Afzal as an RNA biologist has established a system of producing linear as well as circular mRNAs. Their laboratory has ability to characterize viral neutralization potential of antibodies produced in the serum (animal or human) in response to RNA vaccine administration. They have established pseudo-virus-based SARS-CoV-2 neutralization assay system and are now trying to make new pseudo-viruses by incorporating sequential modifications related to different viral variants reported in last year and a half.  Moreover, their lab will be able to characterize if the RNA vaccine has been delivered in the cell to produce protein immunogen and if the immunogen is secreted out of cell in the cell culture set up along with evaluating any cytotoxic effects before it could move to animal studies. 

BF Bio, a leading biotechnology and pharmaceutical company, is interested to sign an MoU with LUMS to get support for the development of mRNA-based vaccine for COVID-19. 

Watch more on this subject, here: 

Supervisor: Dr. Ammar Ahmed Khan at the Department of Physics 

Energizing solar cell technology 

How strange does ‘flowing crystals’ sound? It seems at the heart of key scientific discoveries lie nature’s most well-kept secrets, tied up nicely with a bow of non-intuition; such is the existence of DLC i.e., discotic liquid crystals. Supervised by Dr. Ammar Ahmed Khan, Ms. Qurat ul Ain has worked with a next generation of materials that are more potent in catching and harnessing light to be converted into electricity, compared to contemporary technology. This leap of faith can be summed up into three words: perovskite solar cells.

Investigating the Role of Proteins in Disease and their Treatment with Drugs

Supervisor: Dr. Safee Ullah Chaudhry at the Department of Biology 

Uncovering protein structures

Trillions of cells need a multi-trillion economy of well-kept proteins, safe metabolic environments, and reliable understanding of their complex interactions with drugs. Ms. Kanzal Iman, under supervision of Dr. Safee Ullah Chaudhry, proposes to uncover the structure of these important proteins, through developing better computer programs that do the heavy lifting by bypassing less efficient ways current software applications have in place. In other words, her project aims to develop software that works smarter, rather than harder. This will potentially unlock ways in understanding disease prevalence and eventually the drug interactions involved in treatment.

Designing the Cellular Core for Ultra-Low Latency Communication-based Applications

Supervisor: Dr. Zafar Ayyub Qazi at the Department of Computer Science 

Cellular without speed limits 

Can research rid the world of lag in communication technology? Mukhtiar Ahmad may have an answer! Supervised by Dr. Zafar Ayyub Qazi, Mr. Mukhtiar is working on thinking about cellular network systems from the ground up that can provide extremely low latency, enabling wide scale prevalence of mind-blowing technologies that may have a groundbreaking impact on many fields, ranging from medical science to online gaming. These applications require higher reliability and ultra-low latency, in the order of 10 ms. Mr. Mukhtiar Ahmad aims to re-design the cellular networks to support low latency communication-based applications.

Noninvasive Blood Glucose Monitoring System using Single Wavelength NIR Spectrometry

Supervisor: Dr. Wala Saadeh at the Department of Electrical Engineering 

The future of monitoring diabetes

Imagine measuring blood sugar levels without pricking any part of the skin. Ms. Aminah Hina’s project is all about developing a non-invasive blood glucose monitoring system. Although the product idea itself isn’t new. The market is saturated with portable gluco-meters and few companies even offer wireless blood glucose monitoring support. However, the caviat is their price – these devices are expensive! Ms. Aminah Hina, along with Dr. Wala Saadeh, propose a cheaper alternate. Pakistan is amongst the list of countries with highest prevalence of diabetes. Approximately 19 million Pakistanis have been diagnosed with diabetes in the year 2020. The research project of Ms. Aminah is poised to address this large fraction of Pakistani adults as well as some fraction of the Pakistani youth that suffers from both sub-types of the disease. 

Evaluation of Protective Immune Response Induced by Pneumococcal Conjugate Vaccines (PCV-10) in Individuals with Type 2 diabetes

Supervisor: Dr. Shaper Mirza at the Department of Biology 

Easy breathing for diabetics 

Diabetes is bad enough. Patients suffering this terrible illness have an additional risk of running into frequent respiratory tract infections. Since the immune response of the body is already attenuated in diabetics, the risk posed by additional infections is much greater than in healthy individuals. This is exactly where Mr. Izaz Ahmad’s proposal sprouts hope. Izaz Ahmad is studying the effects of a potent vaccine made for the bacterial culprit responsible for such respiratory disease – bacteria Streptococcus pneumoniae. His study will measure impact of the body’s immune response to PCV10 (the vaccine under investigation) in individuals with type 2-diabetes and figure out whether these responses are comparable between individuals with and without type 2-diabetes. The study will be the first to demonstrate efficacy and immunogenicity of pneumococcal conjugate vaccine in those with type 2-daibetes in Pakistani population. 

Read more about these awards here: https://sbasse.lums.edu.pk/syed-babar-ali-research-awards-sbasse#link-d