Tag: chemical and biomolecular engineering

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Ravi Radhakrishnan Adapts Multiscale Modeling Course

 

Ravi Radhakrishnan, PhD

Ravi Radhakrishnan, Professor and Chair of the Department of Bioengineering and Professor in Chemical and Biomolecular Engineering, is among the many faculty who quickly adapted their courses to an online format in the wake of the COVID-19 pandemic. Now, a recent publication in the American Institute of Chemical Engineers (AIChE) Journal reflects one of these revamped courses. The course BE 559: “Multiscale Modeling of Chemical and Biological Systems” provides theoretical, conceptual, and hands-on modeling experience on three different length and time scales: (1) electronic structure (A, ps); (2) molecular mechanics (100A, ns); and (3) deterministic and stochastic approaches for microscale systems (um, sec). During the course, students gained hands-on experience in running codes on real applications together with the following theoretical formalisms: molecular dynamics, Monte Carlo, free energy methods, deterministic and stochastic modeling. The transition to the online format was greatly facilitated by a grant from the Extreme Science and Engineering Discovery Environment (XSEDE) which provided cloud and supercomputing resources to the students facilitating the computational laboratory experience. Radhakrishnan’s article, “A survey of multiscale modeling: Foundations, historical milestones, current status, and future prospects,” reviews the foundations, historical developments, and current paradigms in multiscale modeling (MSM).

Radhakrishnan aspires to modernize computational science, integrating Multiscale Modeling and Data Science for Biological and Biomedical Science & Engineering. His team does so by integrating multiphysics modeling, computing, data science to tackle applications. The integrative approach is pictorially depicted here in terms of modeling different length and timescales using techniques such as molecular dynamics of atomistic systems, Brownian dynamics of coarse-grained systems, and field equations governing continuum scales of macroscopic systems.

Read the full article in the AIChE Journal: https://doi.org/10.1002/aic.17026

Funding source: National Institutes of Health, Grant/Award Number: CA227550

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BE Seminar: “Stem Cell Fate is a Touchy Subject” (Quinton Smith, MIT)

The first lecture in the Fall 2020 Penn Bioengineering Seminar Series will be held Thursday, September 10th. All seminars this semester will be held virtually on Zoom.

Quinton Smith, PhD

Speaker: Quinton Smith, Ph.D.
Postdoctoral Fellow
Laboratory for Multiscale Regenerative Technologies
Massachusetts Institute of Technology

Date: Thursday, September 10, 2020
Time: 3:00-4:00 pm
Zoom – check email for link or contact ksas@seas.upenn.edu

Title: “Stem Cell Fate is a Touchy Subject”

Abstract:

The success of regenerative cell therapy relies on the integration of a functional vascular system within the redeveloping tissue, to mediate the exchange of oxygen, nutrients and waste. Although the advent of human induced pluripotent stem cells (hiPSCs) has accelerated progress towards this goal, owing to their potential to generate clinically relevant scales of patient-specific cells, techniques to drive their specification mainly rely on chemical cues. In this seminar, I will discuss engineering strategies to control the complex stem cell extracellular milieu, emphasizing the importance of mechanical cues during hiPSC development, specification and downstream functionality as it relates to vascular differentiation.

Bio:

Quinton Smith received his PhD in Chemical and Biomolecular Engineering from Johns Hopkins University in 2017 after completing his bachelor’s degree in Chemical Engineering from the University of New Mexico. As a graduate student under the guidance of Dr. Sharon Gerecht, Quinton implemented various engineering tools to explore the roles of physical and chemical cues on stem cell lineage specification and downstream maturation. Dr. Smith is currently a postdoctoral fellow under the mentorship of Dr. Sangeeta Bhatia at MIT’s Koch Institute for Integrative Cancer Research, where he is investigating the role biliary epithelium in liver regeneration. Dr. Smith’s predoctoral work was supported by an NIH/NHLBI F-31 and NSF Graduate Research Fellowship. He is a recipient of the 2017 Siebel Scholar award, and most recently joined the class of 2018 HHMI Hanna Gray Fellows.

See the full list of upcoming Penn Bioengineering fall seminars here.

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Bomyi Lim Receives KIChE President Young Investigator

Bomyi Lim, Ph.D.

Bomyi Lim, Assistant Professor in the Department of Chemical Biomolecular Engineering, has been selected by the U.S. Chapter of the Korean Institute of Chemical Engineers (KIChE) as the recipient of the KIChE President Young Investigator Award. As a recipient of this Award, Lim will be invited to present a research talk at the KIChE Open Forum during the AIChE Conference.

KIChE is an organization that aims “to promote constructive and mutually beneficial interactions among Korean Chemical Engineers in the U.S. and facilitate international collaboration between engineers in the U.S. and Korea.”

Read more on the Penn Engineering blog. Dr. Lim is a member of the Department of Bioengineering Graduate Group.

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Daniel A. Hammer and Miriam Wattenbarger to Offer Summer Course on COVID-19

Daniel A. Hammer and Miriam Wattenbarger

As researchers hunt for a solution to the coronavirus outbreak, Daniel A. Hammer, Alfred G. and Meta A. Ennis Professor in Bioengineering and in Chemical and Biomolecular Engineering (CBE), is bringing lessons from the fight for a vaccine to the classroom.

Hammer will offer a course on COVID-19 and the coronavirus pandemic during Penn’s Summer II session, which will be held online this year. The course will be co-taught with Miriam Wattenbarger, senior lecturer in CBE.

The course, “Biotechnology, Immunology, and COVID-19,” will culminate with a case study of the coronavirus pandemic including the types of drugs proposed and their mechanism of action, as well as the process of vaccine development.

“Obviously, the pandemic has been a life-altering event, causing an immense dislocation for everyone in our community, especially the students. Between me and Miriam, who has been trumpeting the importance of vaccines for some time in her graduate-level CBE courses, we have the expertise to inform students about this disease and how we might combat it,” says Hammer.

For more than ten years, Wattenbarger has run courses and labs focused on drug delivery and biotechnology, key elements of the vaccine development process.

“I invite both researchers and industry speakers to meet with my students,” Wattenbarger says, “so that they learn the crucial role engineers play in both vaccine development and manufacturing.”

Beyond studying the interactions between the immune system and viruses — including HIV, influenza, adenovirus and coronavirus — students will cover a variety of biotechnological techniques relevant to tracking and defending against them, including recombinant DNA technology, polymerase chain reaction, DNA sequencing, gene therapy, CRISPR-Cas9 editing, drug discovery, small molecule inhibitors, vaccines and the clinical trial process.

Students will also learn the mathematical principles used to quantify biomolecular interactions, as well as those found behind simple epidemiological models and methods for making and purifying drugs and vaccines.

“We all have to contribute in the ways that we can. Having taught biotechnology to freshmen for the past decade, this is something that I can do that can both inform and build community,” says Hammer. “Never has it been more important to have an informed and scientifically literate community that can fight this or any future pandemic.”

Originally posted on the Penn Engineering blog. Media contact Evan Lerner. For more on BE’s COVID-19 projects, read our recent blog post.

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Penn Bioengineering Former Postdoc Whelton Miller Appointed Assistant Professor Loyola University

 

Whelton Miller, Ph.D.

The Department of Bioengineering is proud to congratulate Whelton Miller, Ph.D., a former BE Postdoctoral Fellow, on his appointment as an Assistant Professor in the Department of Medicine in the Health Sciences Division at Loyola University. Miller’s appointment began in January 2020.

Miller received his B.S. in Biochemistry in 2001 from the University of Delaware where he worked under the supervision of Dr. Douglass F. Taber. After graduation, he worked in industry as a synthetic organic chemist for a pharmaceutical company. After three years of industry experience, he returned to academia to complete a Ph.D. in Theoretical/Computational Chemistry from the University of the Sciences in Philadelphia in 2012.

After graduate school, he was given a unique opportunity through Penn’s Postdoctoral Opportunities in Research and Teaching (PennPORT) program, an NIH-sponsored, Institutional Research and Academic Career Development Award (IRACDA) postdoctoral fellowship. In addition to Miller’s responsibilities through the PennPORT program, he served on the Biomedical Postdoctoral Council (BPC), as well as chair of the Engineering PostDoc Association (EpoD). He has worked closely with the Physician Scientist Training Program (PSTP) as a mentor to a high school student, as well as a program guest speaker. This allowed Miller to be a Postdoctoral Research Fellow in the Department of Bioengineering at Penn in the Radhakrishnan Lab – led by BE Department Chair Ravi Radhakrishnan – which focuses on the interface between chemical physics and molecular biology.

Miller has also gained experience in various affiliated appointments, serving as an Assistant Professor in the Department of Chemistry and Physics at Lincoln University (2015-2019), and is currently an Adjunct Assistant Professor in the Department of Chemical and Biomolecular Engineering (CBE) at Penn and an Adjunct Professor in Biomedical Engineering at the University of Ghana in Accra.

Miller joined Loyola University in Chicago, IL in the summer of 2019. Now in his new faculty position, Miller continues to work on collaborative research projects and include colleagues at Instituto Tecnológico de Santo Domingo, the University of Pennsylvania, Lincoln University, University of Ghana, and the University of the Sciences. His current research involves using computational chemistry techniques for theoretical design and study of organometallic and inorganic compounds, protein ligand interactions, and structural electronic effects. His goal is to employ several computational techniques to understand, as well as predict, molecular interactions, such as protein-ligand interactions and protein-protein interactions. Miller says he is always looking forward to more opportunities for minority student development and enrichment in the STEM-related disciplines. Congratulations, Dr. Miller!

 

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Ravi Radhakrishnan Named Chair of the Department of Bioengineering

The Department of Bioengineering would like to congratulate and welcome our new Chair, Dr. Ravi Radhakrishnan! Read the post below, originally posted on the Penn Engineering blog, and visit the Radhakrishnan Lab’s website for more information on his research.

Ravi Radhakrishnan, Ph.D.

Ravi Radhakrishnan has been named Chair of the Department of Bioengineering.

Radhakrishnan holds joint appointments in the Department of Bioengineering and the Department of Chemical and Biomolecular Engineering. He is a founding member and the current Director of the Penn Institute for Computational Science, as well as a member of the Penn Physical Sciences in Oncology Center, Institute for Translational Medicine and Therapeutics, and several graduate groups, including Materials Science and Engineering, Genomics and Computational Biology, and Biochemistry and Molecular Biophysics.

In addition to these roles at Penn, Radhakrishnan holds many editorial board positions in the research community, including Nature Publishing’s Scientific Reports.

Beyond being a passionate teacher and advocate for his students, Radhakrishnan’s research interests lie at the interface of chemical physics and molecular biology. His lab’s goal is to provide molecular level and mechanistic characterization of biomolecular and cellular systems and formulate quantitatively accurate microscopic models for predicting the interactions of various therapeutic agents with innate biochemical signaling mechanisms.