Rachael Mansbach

Rachael Mansbach
Concordia University Montreal

Doctor of Philosophy

About

32
Publications
5,368
Reads
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707
Citations
Citations since 2016
27 Research Items
687 Citations
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2016201720182019202020212022050100150
Introduction
I am an Assistant Professor of Physics at Concordia University in Montreal. I have a great love of proteins and computational biophysics, as well as deep learning and mapping out interpretable search spaces for therapeutics design. I'm always on the look out for collaborators!
Additional affiliations
September 2015 - May 2016
University of Illinois, Urbana-Champaign
Position
  • Computational Teaching Assistant
Description
  • I designed and supervised computational modules for integration into different courses, and also lectured, covered office hours, and graded homework assignments
January 2014 - present
University of Illinois, Urbana-Champaign
Position
  • PhD Student
Description
  • I perform computational research on self-assembling peptides with interesting optoelectronic properties--essentially biological nanowires.
September 2012 - May 2014
University of Illinois, Urbana-Champaign
Position
  • Research Assistant
Description
  • I led discussion sections to cement concepts and teach problem-solving strategies, gave short lectures on physical concepts, graded quizzes, and proctored examinations.
Education
September 2007 - June 2011
Swarthmore College
Field of study
  • Physics

Publications

Publications (32)
Preprint
Full-text available
Short, cysteine-rich peptides can exist in stable or metastable structural ensembles due to the number of possible patterns of formation of their disulfide bonds. One interesting subset of this peptide group is the conotoxins, which are produced by aquatic snails in the family Conidae . The μ conotoxins, which are antagonists and blockers of the vo...
Preprint
Full-text available
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to dissect and understand the structure and dynamics of this complex pathogen. The Spike glycoprotein of SARS-CoV-2 has received special attention as it is the means by which the virus enters the human host cells. The N-terminal domain (NTD) is one of the targeted r...
Article
Full-text available
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike...
Article
Full-text available
The COVID-19 (coronavirus disease 2019) pandemic underwent a rapid transition with the emergence of a dominant viral variant (from the “D-form” to the “G-form”) that carried an amino acid substitution D614G in its “Spike” protein. The G-form is more infectious in vitro and is associated with increased viral loads in the upper airways. To gain insig...
Preprint
Full-text available
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike...
Article
The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, are responsible for their function and malfunction. Misfolding of α-synuclein can lead to neurodegenerative diseases, and the ability to study their conformations and those of other intrinsically disordered proteins under varying physiological conditions can be c...
Article
Full-text available
Efflux pump avoidance and inhibition are desired properties for the optimization of antibacterial activities against Gram-negative bacteria. However, molecular and physicochemical interactions defining the interface between compounds and efflux pumps remain poorly understood. We identified properties that correlate with efflux avoidance and inhibit...
Preprint
The COVID-19 pandemic underwent a rapid transition with the emergence of a SARS-CoV-2 variant that carried the amino acid substitution D614G in the Spike protein that became globally prevalent. The G-form is both more infectious in vitro and associated with increased viral loads in infected people. To gain insight into the mechanism underlying thes...
Article
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present pro...
Article
Full-text available
Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural c...
Article
Full-text available
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water soluble and biocompatible substra...
Preprint
Full-text available
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from $\pi$-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water soluble and biocompatible sub...
Preprint
Full-text available
Many toxins are short, cysteine-rich peptides that are of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. To perform initial candidate identification for design of a drug impacting a particular receptor...
Preprint
Full-text available
Gram-negative bacteria are a serious health concern due to the strong multidrug resistance that they display, partly due to the presence of a permeability barrier comprising two membranes with active efflux. New approaches are urgently needed to design antibiotics effective against these pathogens. In this work, we present a novel topological fragm...
Preprint
Full-text available
Gram-negative bacteria are a serious health concern due to the strong multidrug resistance that they display, partly due to the presence of a permeability barrier comprising two membranes with active efflux. New approaches are urgently needed to design antibiotics effective against these pathogens. In this work, we present a novel topological fragm...
Article
Full-text available
Syk/Zap70 family kinases are essential for signaling via multichain immune-recognition receptors such as the tetrameric (αβγ2) FcεRI. Syk activation is generally attributed to cis binding of its tandem SH2 domains to dual phosphotyrosines within FcεRIγ-ITAMs (immunoreceptor tyrosine-based activation motifs). However, the mechanistic details of Syk...
Article
Marine cone snails are carnivorous gastropods that use peptide toxins called conopeptides both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variations both...
Preprint
Full-text available
Marine cone snails are carnivorous gastropods that use paralytic peptide toxins called conotoxins both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variati...
Article
Self-assembling peptides containing aromatic groups are an attractive target for bioelectronic materials design due to their ease of manufacture, biocompatibility, aqueous solubility, and chemical tunability. Microscopic understanding of the properties that control assembly is a prerequisite for rational design. In this work, we study the assembly...
Article
Full-text available
Synthetic polypeptides have received increasing attention due to their ability to form higher ordered structures similar to proteins. The control over their secondary structures, which enables dynamic conformational changes, is primarily accomplished by tuning the side-chain hydrophobic or ionic interactions. Herein we report a strategy to modulate...
Article
Self-assembled nanoaggregates of π-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups that make them attractive candidates for the fabrication of bioelectronic materials. We present a computational and theoretical study to resolve the microscopic effects of pH and flow on the non-...
Article
Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a...
Article
Computational competencies such as the use of modeling and simulation tools are a new core literacy that students in Materials Science and Engineering must develop. To develop this literacy among our students, the Department of Materials Science and Engineering at the University of Illinois at Urbana Champaign is synthesizing computational tools an...
Article
Significance We developed antimicrobial polypeptides (AMPs) with unprecedented radial amphiphilicity. Unlike typical AMPs characterized by facial amphiphilicity or biomimetic antimicrobial polymers with randomly distributed charged and hydrophobic groups, this class of AMPs is made up of homo-polypeptides that feature a radially amphiphilic (RA) st...
Article
The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energ...
Article
Full-text available
Current modularity-based community detection methods show decreased performance as relational networks become increasingly noisy. These methods also yield a large number of diverse community structures as solutions, which is prob-lematic for applications that impose constraints on the accept-able solutions or in cases where the user is focused on s...
Article
Full-text available
The Self-organizing Distinctive State Abstraction (SODA) algorithm was im-plemented on a new task. The original SODA algorithm was used in order to learn a navigation task, but the intent of this paper was to investigate whether the SODA algorithm was generalizable to a new task and to the real world. This paper inves-tigates whether the SODA algor...

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Projects

Projects (3)
Project
Certain families of peptides possess, due to their pi-conjugation, optoelectronic properties that are desirable for applications such as organic photovoltaic cells, organic field-effect transistors, and organic light-emitting diodes. I am using a coarse-rained model to investigate the self-assembly properties of one such peptide, a symmetric peptide with a pi-conjugated distyrylbenzene core that experimentally displays triggerable assembly in low pH solution.