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May 30, 2017
Rachael Mansbach wins 2017 Christopher J. Wormald Prize in Thermodynamics
Rachael has been selected as the 2017 recipient of the Christopher J. Wormald Prize in Thermodynamics. This award is associated with the Thermodynamics 2017 conference to be held 5-8 September in Edinburgh, Scotland, and recognizes excellence in thermodynamics research conducted by an outstanding graduate student as part of their PhD studies. Rachael will deliver an invited talk on her work at the 2017 Thermodynamics conference. Well done, Rachael!
May 22, 2017
Greg Hart awarded Blue Waters allocation
Greg awarded a 50,000 node-hours Blue Waters exploratory allowance for his proposal "In Silico Hepatitis C Vaccine Design". This high-performance computational resource will enable in silico screening of HCV immunogens to rationally design vaccines to both cripple viral fitness and block escape. Congratulations, Greg!
March 29, 2017
Rachael Mansbach wins a 2017-18 Blue Waters Graduate Fellowship
Rachael's was selected for a 2017-18 Blue Waters Graduate Fellowship. This award provides RA support, travel funds, and 50,000 node hours of computation on the Blue Waters supercomputer. Rachael will use her fellowship to understand and engineer self-assembling pi-conjugated oligopeptides using classical and quantum simulations. Congratulations, Rachael!
March 5, 2017
Prof. Ferguson named on List of Excellent Teachers for Fall 2016
Prof. Ferguson was named on the Fall 2016 List of Teachers Ranked as Excellent by their Students, ranked as "Outstanding" (top 10%) as the instructor of MSE 404 Computational Materials Science and Engineering (MICRO) / (MACRO).
Feb 10, 2017
Rachael Mansbach's paper on coarse-grained simulation of self-assembling π-conjugated peptides published in J. Phys. Chem. B
Rachael's paper "Coarse-grained molecular simulation of the hierarchical self-assembly of π-conjugated optoelectronic peptides" has been published in J. Phys. Chem. B (http://dx.doi.org/10.1021/acs.jpcb.6b10165). This work supported by DOE/BES describes the development of a coarse-grained molecular model for a prototypical π-conjugated oligopeptide Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) comprising two symmetric peptide wings and an OPV3 (distyrylbenzene) aromatic core. Our efficient coarse-grained model enables us to directly simulate the self-assembly of hundreds of molecules over hundreds of nanoseconds to resolve a hierarchical assembly process in which peptides form into short stacks with aligned aromatic cores, followed by ellipsoidal aggregates, and finally a fractal network of dimensionality ~1.5. We also demonstrate that aggregation is effectively irreversible and well modeled by a Smoluchowski coagulation process. By parameterizing the coagulation kernel against our simulation data, we predict the aggregation kinetics at arbitrarily long length and time scales. Congratulations, Rachael!
Feb 3, 2017
Prof. Ferguson wins 2017 Dean's Award for Excellence in Research
Prof. Ferguson was awarded a College of Engineering Dean's Award for Excellence in Research that recognizes research achievements by Illinois engineering faculty over the past year. He will be recognized at the Engineering Faculty Awards Ceremony on April 24, 2017 from 6 to 8 p.m. in the NCSA Auditorium.
Jan 23, 2017
Prof. Ferguson gives an invited talk at the 3rd Annual Scottish Chemistry Symposium
Prof. Ferguson delivered a talk "Finding folding funnels frae following FRET fluorescence" at the 3rd Annual Scottish Chemistry Symposium at Northwestern University. This symposium brings together Scottish chemists from the UK and US, and is organized around the annual Burns Night celebration on Jan 25 celebrating the life and work of the Scottish national poet Robert Burns. This year's wonderful event and Burns Supper were graciously organized and hosted by Professor Sir Fraser Stoddart the 2016 Nobel Chemistry laureate. It was remarkable to see the impact of Scottish chemists in so many diverse fields, and a first for many in delivering a scientific seminar in traditional Scottish dress!
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3rd Scottish Chemistry Symposium, Northwestern University, 23 January 2017
(back row) Steve Whitelam, Bruce Gibb, Tom Muir, Eric Anslyn, Bruce Turnbull
(middle row) Stuart Rowan, Douglas Philp, Jon Sessler, Sir Fraser Stoddart, David Fulton, Eleanor Campbell
(front row) Andy Ferguson, Ross Forgan, Paul McGonigal

Jan 23, 2017
Jiang Wang selected for UIUC Physics Graduate Travel Award
Jiang was selected for a UIUC Department of Physics Graduate Student Travel Award to partially support his attendance at the APS March Meeting 13-17 March 2017 in New Orleans, LA where he will deliver a talk in Session S40: Physics of Ring Polymers. Jiang’s talk is entitled "Analysis of the morphology, stability, and folding pathways of ring polymers with supramolecular topological constraints using molecular simulation and nonlinear manifold learning", concerning the coupled use of machine learning and molecular simulation to probe the fundamental physics of interlocking ring polymers. Well done, Jiang!
Jan 9, 2017
Greg Hart selected for Global Young Scientists Summit 2017
Greg was selected as an invitee of the Global Young Scientists Summit (GYSS) held at the Singapore University of Technology and Design during 15-17 January 2017. Organized by the National Research Foundation Singapore, this event hosts 250 outstanding PhDs and post-doctoral fellows under the age of 35, who will interact with one another and 20 distinguished scientific speakers including Nobel Laureates, Fields Medallists, Millennium Technology Prize winners, and Turing Award winners. Congratulations to Greg, and best wishes for a terrific trip!
Dec 6, 2016
Bryce Thurston passes prelim exam
Bryce Thurston successfully passed his Physics prelim exam. Well done, Bryce!
Oct 15, 2016
Ferguson and Wong publish PNAS paper on machine learning discovery and design of membrane active peptides
In a PNAS paper published online today "Mapping membrane activity in undiscovered peptide sequence space using machine learning" (http://dx.doi.org/10.1073/pnas.1609893113) Prof. Ferguson and Ben Fulan (Math, UIUC) report a support vector classifier as a new machine learning tool to efficiently screen peptide sequence space for membrane active peptides. Working in collaboration with Prof. Gerard Wong (BioE, UCLA) and his student Ernest Lee, experimental tests of peptides computationally designed using this approach validate that the classifier can discover new membrane active peptides, and also identify membrane activity in diverse and unexpected peptide families including neuropeptides, viral fusion proteins, topogenic peptides, and amyloids. This tool has implications for the rational design of peptides with diverse biomedical applications, including immunotherapy, intracellular drug delivery, broad-spectrum membrane-active antimicrobials, and nucleic acid transfection. The UIUC CoE press release is available here.
Oct 25, 2016
Prof. Ferguson wins AIChE CoMSEF Young Investigator Award
Prof. Ferguson is the recipient of the 2016 Young Investigator Award for Modeling and Simulation, from the Computational Molecular Science and Engineering Forum (CoMSEF) of the American Institute of Chemical Engineers (AIChE). The award recognizes outstanding research in computational molecular science and engineering by researchers within seven years of completion of their highest degree, and was awarded to Prof. Ferguson for his development and application of statistical thermodynamics and machine learning to computational immunology and vaccine design. Prof. Ferguson will receive the award and deliver an invited talk at the AIChE Annual Meeting in San Francisco in November. The UIUC CoE press release is available here.
August 14, 2016
Prof. Ferguson named on List of Excellent Teachers for Spring 2016
Prof. Ferguson was named on the Spring 2016 List of Teachers Ranked as Excellent by their Students, ranked as "Outstanding" (top 10%) as the instructor of MSE 458 Polymer Physical Chemistry.
Aug 10, 2016
Jiang Wang's paper on mesoscale modeling of asphaltene aggregation published in J. Phys. Chem. B
Jiang's paper "Mesoscale simulation of asphaltene aggregation" has been published in J. Phys. Chem. B (http://dx.doi.org/10.1021/acs.jpcb.6b05925). Asphaltenes constitute a heavy aromatic crude oil fraction with a propensity to aggregate and precipitate out of solution during petroleum processing. This paper describes the construction of a coarse-grained model for asphaltene parameterized directly against all-atom calculations, and the use of this model to probe the self-assembly of hundreds of asphlatenes over microsecond time scales. These calculations provide molecular level support for the proposed Yen-Mullins hierarchy for assembly into nanoaggregates, clusters, and finally a porous percolating network with fractal dimension of ~2. Congratulations to Jiang!
Aug 1, 2016
Andy Long's paper on machine learning and design of digital colloid information storage elements published in Soft Matter
Andy's paper "Nonlinear machine learning and design of reconfigurable digital colloids" in collaboration with Eric Jankowski (Boise State) and Carolyn Phillips (Neurensic Inc.) has been published in Soft Matter (http://dx.doi.org/10.1039/C6SM01156J). So-called "digital colloids" -- a cluster of freely rotating “halo” particles tethered to the surface of a central particle -- present a novel ultra-high density soft memory storage substrate in which information is encoded in the arrangement of halo particles around the central colloid. Information is written by reconfiguring the halo particle arrangement, and information read by interrogating the particular rotationally distinguishable halo particle state. A digital colloid comprising 6 halo particles can store an estimated 1.1 TB/g (1.4 TB/cm3). Using diffusion map nonlinear manifold learning to discover the low dimensional free energy surface governing the halo particle collective reconfigurations and mean first passage time calculations to define interconversion rates between states, we characterized the thermodynamics, morphology, and kinetics of the structural information storage process. Using this framework we designed a digital colloid with particular central to halo particle diameter to trade off the competing design criteria of memory addressability and volatility. Well done, Andy!
June 28, 2016
Rachael Mansbach presents educational innovation paper at the 2016 ASEE Annual Conference and Exposition
Rachael presents a conference paper "Computational Modules for the MatSE Undergraduate Curriculum" in the T308-Computers in Education Division Poster Session at the 2016 ASEE Annual Conference & Exposition in New Orleans. The paper concerns the development and deployment of computational modules, educational practices, and a community of practice within the Materials Science and Engineering undergraduate curriculum developed by a faculty team and supported by Rachael in her role as a computational TA. This work was supported by a Strategic Instructional Innovations Program (SIIP) award from the University of Illinois College of Engineering, and an NSF CAREER Award (Grant No. DMR-1350008) to Prof. Ferguson.
May 5, 2016
Rachael Mansbach wins a 2016-17 CSE Graduate Fellowship
Rachael's proposal "Mesoscale Molecular Simulations of Self-Assembling Organic Electronic Nanowires" was selected for a 2016-17 Computational Science and Engineering Graduate Fellowship. This award provides RA support, conference travel funds, and access to CSE and NCSA high performance computing facilities. Well done to Rachael on another great award!
April 29, 2016
Greg Hart and Jiang Wang pass their prelim exams
Two passes in one day. Greg and Jiang both pass their prelim exams with flying colors. All that now stands between them and their PhDs is this thing called a thesis. Well done, Greg and Jiang!
April 1, 2016
Andy Long wins runner-up in 2016 MRS Spring Best Poster Competition
Andy wins runner-up in the Best Poster Competition for his submission "Learning the 'Write Mechanism' For Digital Colloids" in Session MD1.3: Poster Session I: Materials, Interfaces and Devices by Design I at 2016 MRS Spring. Congratulations to Andy!
March 22, 2016
Bryce Thurston's paper "Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides" published in Molecular Simulation
Bryce's article "Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides" has been published in Molecular Simulation (http://dx.doi.org/10.1080/08927022.2015.1125997). This work applies a combination of atomistic molecular dynamics, coarse-grained molecular simulation, and Markov state models to unravel the structure, driving forces, and dynamics for the self-assembly of synthetic oligopeptides possessing aromatic cores into optically and electronically active nanoaggregates. Congratulations to Bryce on his new publication!
March 21, 2016
Jiang Wang's study "Nonlinear reconstruction of single-molecule free-energy surfaces from univariate time series" out in Physical Review E
Jiang's paper "Nonlinear reconstruction of single-molecule free-energy surfaces from univariate time series" has been published in Physical Review E (http://link.aps.org/doi/10.1103/PhysRevE.93.032412). This paper describes a new approach integrating statistical mechanics, dynamical systems theory, and nonlinear dimensionality reduction to reconstruct single molecule folding funnels from univariate experimentally measurable observables. In molecular dynamics of the collapse of a hydrophobic polymer chain, we demonstrate that the single-molecule free energy landscape recovered by our approach from a knowledge of only the head-to-tail distance of the chain is topologically and geometrically identical to that computed from knowing all of the atomic coordinates. Our approach lays the foundations to reconstruct protein folding funnels directly from single-molecule measurements such as single molecule FRET. Big congratulations to Jiang on his new publication!

Read the UofI press release here and see the news coverage of our work here.
March 6, 2016
Prof. Ferguson named on List of Excellent Teachers for Fall 2015
Prof. Ferguson was named on the Fall 2015 List of Teachers Ranked as Excellent by their Students, ranked as "Outstanding" (top 10%) as the instructor of MSE 498AF Computational Materials Science and Engineering.
February 9, 2016
Andy Long to give a talk and a poster at 2016 MRS Spring Meeting
Andy Long has had two abstracts accepted for the 2016 MRS Spring Meeting, March 28 - April 1 in Phoenix, AZ. Both of Andy's presentations will be on March 29 in Symposium MD1—Materials, Interfaces and Devices by Design. He will give a talk on his collaborative work with the Granick Lab entitled "Mixing Machine Learning with Experiment: Learning Assembly Mechanisms from Particle Tracking Data" in Session MD1.2: Machine Learning with Experimental Data and Synthesis Control, and a poster on his work in collaboration with Carolyn Phillips (Argonne) and Eric Jankowski (Boise State) titled "Learning the 'Write Mechanism' For Digital Colloids" in Session MD1.3: Poster Session I: Materials, Interfaces and Devices by Design I. Well done to Andy!
January 20, 2016
Rachael selected for NC State "Building Future Faculty" program
Rachael accepted for the Building Future Faculty Program 20 March - April 2, 2016 at NC State. This two day all-expenses paid workshop supports doctoral students and post-doctoral scholars who are interested in pursuing academic careers and who are committed to promoting diversity in higher education. Participants attend sessions describing life as a faculty member at a research extensive university, expectations of new faculty, and resources available to faculty for help with research and teaching. Congratulations to Rachael!
January 1, 2016
Greg, Bryce, Jiang, and Rachael to give talks at the 2016 APS March Meeting
Greg, Bryce, Jiang, and Rachael have all had abstracts accepted to deliver oral presentations at the 2016 APS March Meeting, March 14-18 in Baltimore, MD,. Greg will discuss his work on the rational design of hepatitis C immunogens using empirical spin glass models and population dynamics simulations in Session H35: Population and Evolutionary Dynamics III (http://meetings.aps.org/Meeting/MAR16/Session/H35.13). Bryce will discuss his work on the computational and theoretical modeling of the morphology, thermodynamics, and kinetics of early stage assembly of π-conjugated peptides in Session P34: Biopolymers and Biohybrid Polymers - Assembly and Thermodynamics (http://meetings.aps.org/Meeting/MAR16/Session/P34.1). Jiang will talk about mesoscale modeling of asphalt aggregation and morphology in Session C36: Soft Colloids: From Single Particle Properties to Bulk Phase Behavior and Dynamics (http://meetings.aps.org/Meeting/MAR16/Session/C36.12). Rachael will speak on her simulation and numerical modeling of optoelectronic peptide assembly in Session F42: Polymer Assembly I (http://meetings.aps.org/Meeting/MAR16/Session/F42.3). Congratulations to Greg, Jiang, and Rachael!
November 24, 2015
Greg Hart's paper "Empirical fitness models for hepatitis C virus immunogen design" published in Physical Biology
Greg's article "Empirical fitness models for hepatitis C virus immunogen design" has been published in Physical Biology (http://dx.doi.org/10.1088/1478-3975/12/6/066006). This work describes the translation of hepatitis C virus sequence databases into empirical "fitness landscapes" describing the replicative fitness of the virus as a function of its amino acid sequence, and the use of these landscapes for the rational design of potent antiviral vaccine immunogens. By identifying how to hit the virus where it hurts, these empirical landscapes have allowed us to narrow the search space for optimal immunogen candidates by over five orders of magnitude, guiding and accelerating experimental vaccine development efforts. Congratulations to Greg on his new publication!

Read the UofI press release here.
November 16, 2015
Rachael Mansbach passes prelim exam
Rachael Mansbach successfully passed her Physics prelim exam and is now ABD. Big congratulations to Rachael!
October 28, 2015
Greg Hart featured as a 2015-16 CSE Fellow
Greg Hart was featured as one of the 2015-16 Computational Science and Engineering (CSE) Graduate Fellows in his new CSE Fellow page and a very cool video interview. Great work, Greg!
October 12, 2015
Rachael Mansbach's paper "Helical antimicrobial polypeptides with radial amphiphilicity" published in PNAS
In a joint publication with the labs of Prof. JJ Cheng (MatSE, UIUC) and Prof. Gerard Wong (BioE, UCLA), Rachael and Prof. Ferguson have published a paper in PNAS on the design and characterization of novel antimicrobial peptides possessing unique radial amphiphilicity entitled "Helical antimicrobial peptides with radial amphiphilicity". Rachael and Prof. Ferguson led the molecular modeling effort to quantify the radially amphiphilic structure and charge distribution in atomistic detail. The structure of the peptides with a hydrophobic core and cationic shell enables them to efficiently bind to bacterial membranes while decreasing non-specific interactions with eukaryotes. In addition to possessing native antimicrobial properties, they are also effective adjuvants that increase permeation and activity of commercial antibiotics by one to two orders of magnitude. The radially amphiphilic design may present a useful platform for the treatment of drug-resistant bacteria. Read the UofI press release here.
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September 14, 2015
Bridgette Lafaye invited speaker at Undergraduate Women in Physical Sciences (WoPhyS) conference at U. Nebraska - Lincoln
Bridgette Lafaye has been invited by the organizing committee to present her work on biomolecular simulation of ultrashort amphiphilic peptide self-assembly at the Undergraduate Women in Physical Sciences (WoPhyS) conference at U. Nebraska - Lincoln, Oct 15-17, 2015. She will give a talk titled "Self-assembly of biomineralization scaffolds from ultrashort peptide amphiphiles". Big congratulations to Bridgette!
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September 1, 2015
Wei Chen joins Ferguson Lab
Wei Chen (Physics; B.S., Nanjing University) joins the Ferguson Lab. Wei is integrating nonlinear machine learning with biased sampling to develop accelerated sampling algorithms for bimolecular simulation.
August 26, 2015
Prof. Ferguson named on List of Excellent Teachers for Spring 2015
Prof. Ferguson was named on the Spring 2015 List of Teachers Ranked as Excellent by their Students, ranked as "Outstanding" (top 10%) as the instructor of MSE 458 Polymer Physical Chemistry.
August 25, 2015
Rachael Mansbach's JCP article ranked as one of the most read Biological Molecules and Networks articles of the year
Rachael's article describing the use of nonlinear machine learning to connect molecular chemistry and experimental conditions to microscopic single-molecule behavior has been rated as one of the most read Biological Molecules and Networks articles of the year in the Journal of Chemical Physics (http://dx.doi.org/10.1063/1.4914144). Big congratulations to Rachael on her achievement!
August 24, 2015
Andy Long publishes article on machine learning of nonequilibrium materials assembly landscapes from experimental particle tracking data
In a collaboration with Prof. Steve Granick and his student Jie Zhang, Andy Long and Prof. Ferguson published an article in Soft Matter (http://dx.doi.org/10.1039/C5SM01981H) in which we apply nonlinear machine learning to experimental particle tracking data of the nonequilibrium assembly of Janus colloids to infer the low-dimensional assembly landscapes mapping the morphology, stability, and assembly pathways of accessible aggregates as a function of experimental conditions. To the best of our knowledge, this represents the first time that collective order parameters and assembly landscapes have been inferred directly from experimental data, furnishing new understanding of the underlying physics and informing rational engineering of experimental conditions to drive assembly along desired aggregation pathways. Congratulations to Jie and Andy on a great paper and a really fun collaboration!
July 22, 2015
Prof. Ferguson named Fall 2015 American Chemical Society OpenEye Outstanding Junior Faculty Awardee
Prof. Ferguson was named as one of four Fall 2015 OpenEye Outstanding Junior Faculty awardees by the Computers in Chemistry Division (COMP) of the American Chemical Society. This work recognizes Prof. Ferguson's work in the computational design of hepatitis C virus vaccines. Prof. Ferguson will present his work and receive a prize and award certificate at the Fall 2015 ACS Meeting in Boston, MA.
May 7, 2015
Greg Hart wins a 2015-16 Computational Science and Engineering Graduate Fellowship
Greg Hart was renewed as a Computational Science and Engineering Graduate Fellow for a second year. This renewal recognizes Greg's excellent progress over the past year in his research on host-pathogen dynamics of hepatitis C virus infection, and provides RA support, conference travel funds, and access to CSE and NCSA high performance computing facilities. Big congratulations to Greg!
May 4, 2015
Haotian Jiang joins Ferguson Lab as a Summer 2015 NCSA SPIN intern
Haotian was selected to perform a summer research internship in the Ferguson Lab as part of the competitive NCSA SPIN (Students Pushing Innovation) Program. Haotian will work with Prof. Ferguson to develop machine learning algorithms to predict and design antimicrobial peptides.
April 21, 2015
Andy Long passes prelim exam
Andy Long successfully passed his MatSE prelim exam! All that now remains is to complete and write a PhD dissertation... :) Big congratulations to Andy!
April 15, 2015
Rachael Mansbach selected as College of Engineering Mavis Future Faculty Fellow
Rachael was selected by the College of Engineering as a Mavis Future Faculty Fellow (MF3) for 2015-16. This highly competitive program is designed to prepare PhD candidates for academic careers, training the next generation of great science and engineering faculty. The program prepares students through workshops, instruction, and capstone professional development activities in research, teaching, and mentoring. Way to go, Rachael!
April 3, 2015
Prof. Ferguson named 2015-16 NCSA Faculty Fellow
Prof. Ferguson was named as a 2015-16 Faculty Fellow of the National Center for Supercomputing Applications. This fellowship will support Prof. Ferguson's research into in silico hepatitis C vaccine design, enabling collaborative interactions with NCSA personnel to help accelerate and refactor our code base, and providing access to high performance cyberinfrastructure to perform computational vaccine design.
March 12, 2015
Rachael Mansbach publishes paper on the structural mechanism of the helix-coil transition in alpha-helical peptides with antimicrobial activity in the Journal of Chemical Physics
By developing a sophistication of the diffusion map nonlinear manifold learning approach, Rachael and Prof. Ferguson have quantitatively connected the molecular chemistry and experimental conditions to microscopic molecular behavior. In a manuscript published in JCP (http://dx.doi.org/10.1063/1.4914144) Rachael has exposed the molecular mechanism by which decreasing side chain length destabilizes the alpha-helical form of synthetic antimicrobial peptides, bringing new microscopic understanding to this fascinating class of peptides. We are now woking with JJ Cheng's lab to guide the rational design of cell penetrating peptides with tailored stability capable of triggered drug release upon passing through the microbial membrane. Congratulations to Rachael!
March 10, 2015
Lectures for Prof. Ferguson's class MSE 498AF - Computational Science and Engineering hosted on YouTube and nanoHUB
The lectures for Prof. Ferguson's new course MSE 498AF - Computational Materials Science and Engineering have been uploaded to YouTube and nanoHUB to allow for wide dissemination and access to this educational content. This course is designed to provide hands-on immersive training in the computational materials science and engineering methods and packages: (i) Density Functional Theory (DFT) w/ Quantuum Espresso, (ii) Molecular Dynamics (MD) w/ LAMMPS, (iii) Finite Element Method (FEM) w/ OOF2, and (iv) CALculation of PHAse Diagrams w/ Thermo-Calc.
March 10, 2015
Greg Hart publishes paper on the HIV "viral error catastrophe" in Physical Review E
Greg and Prof. Ferguson have provided the first computational confirmation of the viral "error catastrophe" over a realistic viral fitness landscape in a paper published in Phys. Rev. E (http://journals.aps.org/pre/abstract/10.1103/PhysRevE.91.032705). Using a landscape for the HIV protein p6 inferred from clinical sequence databases, the error catastrophe -- the lethal accumulation of mutations in the viral population -- is manifested as a first order phase transition between a high-fitness population containing only a small number of mutant strains, and a low-fitness, highly-diverse ensemble. This work provides support for the viability of treating HIV with mutagenic drugs to induce the error catastrophe and cripple viral fitness, and also reveals particular mutations that can induce the catastrophe as new potential targets for antiviral drugs. Congratulations to Greg!
March 8, 2015
Prof. Ferguson named on List of Excellent Teachers for Fall 2014
Prof. Ferguson was named on the Fall 2014 List of Teachers Ranked as Excellent by their Students as the instructor of MSE 498AF - Computational Materials Science and Engineering.
March 5, 2015
Bridgette Lafaye joins Ferguson Lab
Bridgette Lafaye (MatSE, freshman) joins the Ferguson Lab as an undergraduate researcher. Bridgette will be employing coarse-grained molecular dynamics to simulate the self-assembly of ultrashort amphiphilic peptides into mesoscale aggregates with biosilification activity.
February 19, 2015
Prof. Ferguson AIChE nominee for DiscoverE "New Faces of Engineering" award
Prof. Ferguson is one of four AIChE nominees for the DiscoverE (formerly National Engineers Week Foundation) 2015 "New Faces of Engineering" award. This award recognizes the outstanding talents, skills and abilities the next generation of engineering leaders have shown on projects that significantly impact public welfare or further professional development and growth.
February 6, 2015
Deepak Mani joins Ferguson Lab
Deepak Mani (MatSE, sophomore) joins the Ferguson Lab as an undergraduate researcher. Deepak will be using all-atom molecular dynamics simulations to study the stability, morphology, and pH response of engineered radially-amphiphilic peptides with antimicrobial activity.
January 9, 2015
Prof. Ferguson receives IPAM 2015 Machine Learning for Many-Particle Systems travel award
Prof. Ferguson wins travel award to attend the IPAM workshop on Machine Learning for Many-Particle Systems at UCLA 23-27 Feb 2015 (http://www.ipam.ucla.edu/programs/workshops/machine-learning-for-many-particle-systems/). This workshop will address the reaches and limitations of ML as applied to many-particle systems and highlight examples where physical models can be successfully combined with ML algorithms.
January 6, 2015
Andy Long wins Outstanding Student Presenter Award at MRS Fall Meeting
Andy Long wins the Outstanding Student Presenter Award for Symposium SS (Informatics and Genomics for Materials Development) at the 2014 MRS Fall Meeting for his talk "Accelerated Sampling of Self-Assembly Systems Using Machine Learning" (http://www.matse.illinois.edu/newsfeed/010915grads-MRS.html). Congratulations, Andy!
January 1, 2015
Rachael wins the FGSA Travel Award for Excellence in Graduate Research
Rachael wins the APS Forum on Graduate Student Affairs (FGSA) Travel Award for Excellence in Graduate Research (http://www.aps.org/units/fgsa/activities/travelgrants.cfm)! This award recognizes graduate students who demonstrate great potential and have made noteworthy progress in their academic careers. The award partially covers travel expenses to attend a scientific conference or workshop that Rachael will use to support her travel to present her work on the use of machine learning to quantify the impact of molecular environment and chemistry upon single molecule free energy landscapes at the APS March Meeting (http://meeting.aps.org/Meeting/MAR15/Session/T26.15). Congratulations to Rachael!
January 1, 2015
Greg, Jiang, and Rachael to give talks at the 2015 APS March Meeting
Greg, Jiang, and Rachael have all had abstracts accepted to deliver oral presentations at the 2015 APS March Meeting in San Antonio, TX. Greg will discuss his work on the use of empirical fitness landscapes for the rational design of hepatitis C immunogens in Session Q47: Physics of Bacteria and Viruses (http://meeting.aps.org/Meeting/MAR15/Session/Q47.1). Jiang will talk about his recently completed work on the inference of of single molecule folding landscapes from simulated smFRET data in Session Q42: Focus Session: Theory and Simulation of Macromolecules I (http://meeting.aps.org/Meeting/MAR15/Session/Q42.6). Rachael will speak on her applications of machine learning to quantify the impact of molecular environment and chemistry upon single molecule free energy landscapes in Session T26: Computational Applications and Methods I (http://meeting.aps.org/Meeting/MAR15/Session/T26.15). Congratulations to Greg, Jiang, and Rachael!
December 1, 2014
Andy Long places 3rd in MRS Fall Meeting Hackathon
Andy Long and teammate Ioan Magdau (University of Edinburgh) placed third in the Materials Hackathon (MatHack) at the 2014 MRS Fall Meeting, creating in 24h a working code for materials machine learning (http://www.mrs.org/fall-2014-materials-hackathon/). Congratulations, Andy!
November 16-21, 2014
Prof. Ferguson delivers talk and chairs session at AIChE 2014 Annual Meeting in Atlanta, GA
Prof. Ferguson will deliver a talk "Computational Design of Hepatitis C Vaccines" in the Multiscale Systems Biology session (3:15-5:30 pm, Mon 11/17, 214 Hilton Atlanta) at the AIChE Annual Meeting. Along with Prof. Sapna Sarupria (Clemson), he will chair the session Thermodynamics of Biomolecular Folding and Assembly (12:30-2:15 pm, Thu 11/20, Crystal Ballroom B/E, Hilton Atlanta).
November 10, 2014
Prof. Ferguson invited to talk at GradSWE Lunch Series on "Working Across Disciplines"
Along with Prof. Scott White (AE, UIUC) Prof. Ferguson will talk to the Graduate Society of Women Engineers about his experience and advice for interdisciplinary work in science and engineering.
October 28, 2014
"Investigating the optimal size of anticancer nanomedicine" published in PNAS
A joint publication between senior authors Profs. A.L. Ferguson, W.G. Helferich, T.M. Fan, and J. Cheng "Investigating the optimal size of anticancer nanomedicine" appears in the 28 Oct issue of PNAS. Prof. Ferguson led the development of simple ODE models of the trafficking and retention of nanoparticles into multicellular tumor spheroids to predict an optimal nanoparticle size of 50 nm, in excellent agreement with experimental work led by the other senior authors. This particle size represents an optimal trade-off between rapid permeation into tumor tissue and long retention times, providing deep and enduring accumulation of the anticancer payload within tumor tissue. These predictive models are of great value in exposing the mechanisms of nanoparticle trafficking and guiding the rational engineering and design of new nanomedicines.
September 26, 2014
Andy Long accepted to deliver oral presentation at 2014 MRS in Boston
Andy will deliver a contributed oral presentation at the 2014 MRS Fall Meeting - Program SS: Informatics and Genomics for Materials Development November 30 - December 5 2014 in Boston, MA. He will discuss his recent work on the use of nonlinear machine learning techniques to infer self-assembly pathways and mechanisms from molecular simulations and experimental 4D particle tracking data in a talk entitled "Accelerated Sampling of Self-Assembly Systems Using Machine Learning".
August 10, 2014
Prof. Ferguson named on List of Excellent Teachers for Spring 2014
Prof. Ferguson was named on the Spring 2014 List of Teachers Ranked as Excellent by their Students as the instructor of MSE 458 - Polymer Physical Chemistry.
August 7, 2014
Prof. Ferguson featured in "Inside Illinois" as I-Promise faculty mentor
Prof. Ferguson's work as a faculty mentor in the Illinois Promise program was featured in an article in Inside Illinois 34 (3) (Aug 7, 2014). The Illinois Promise (I-Promise) program provides full scholarships to high-achieving first generation college students from Illinois, and offers voluntary peer or adult mentoring with a program alum or member of the Illinois community to support the transition to college and promote academic and personal success. Illinois faculty, staff, or retirees interested in serving as I-Promise mentors should contact the program director Susan Gershenfeld (sgershen@illinois.edu).
July 1, 2014
Greg Hart accepted to deliver oral presentation at IOP "Physics Meets Biology"
Greg will deliver a contributed oral presentation at the Institute of Physics "Physics Meets Biology" conference September 3-5 2014 at Oxford University, Oxford, UK. He will discuss his recent work on the inverse inference of empirical fitness landscapes for hepatitis C virus and their use in rational vaccine design in a talk entitled "Inferring Fitness Models from Sequence Databases for Rational Hepatitis C Immunogen Design".
June 17, 2014
Prof. Ferguson invited speaker at the 2014 MWTCC
Prof. Ferguson delivered a presentation at the 2014 Midwest Theoretical Chemistry Conference at Northwestern University on the application of physical chemical models and statistical mechanics in modeling Hepatitis C virus fitness landscapes, systematically identifying viral vulnerabilities, and the computational design of T-cell vaccines.
June 9, 2014
Prof. Ferguson wins ACS Petroleum Research Fund - Doctoral New Investigator Award
Prof. Ferguson is delighted to receive the American Chemical Society Petroleum Research Fund Doctoral New Investigator Award for his proposal entitled "Mesoscale Simulation and Machine Learning of Asphaltene Aggregation". We are excited to embark upon an investigation of the mesoscale clustering, thermodynamics, and assembly pathways of asphaltenes, to help understand the fundamental aggregation and flocculation behaviors of these compounds.
June 1, 2014
Rachael Mansbach joins the Ferguson Lab
Rachael Mansbach (Physics; B.S., Swarthmore) formally joins the Ferguson Lab. Rachael is investigating nonlinear machine learning models of the impact of molecular chemistry and environmental conditions on the structure and thermodynamics of polymers and peptides, and studying coarse-grained models of the assembly of synthetic peptides into clusters and ribbons.
May 8, 2014
Greg Hart wins a 2014-15 Computational Science and Engineering Graduate Fellowship
Greg Hart has been awarded a competitive graduate fellowship by the University of Illinois Computational Science and Engineering program to study the host-pathogen dynamics of hepatitis C virus infection. This award provides RA support, conference travel funds, and access to CSE and NCSA high performance computing facilities. Congratulations to Greg!
May 6, 2014
Sam Kaufman wins a 2014 Computational Science and Engineering Summer Research Internship
Sam Kaufman (MatSE, sophomore) has been awarded a 2014 Computational Science and Engineering Summer Research Internship. This award is given to exceptional undergraduate students participating in the CSE Certificate Option to conduct graduate-level research with a University of Illinois faculty member. Sam will join the Ferguson Lab this summer to work with Prof. Ferguson and Greg Hart in developing population dynamics simulations of the mutational evolution of hepatitis C virus over empirical viral fitness landscapes. Congratulations, Sam!
March 24, 2014
Andy Long publishes paper on nonlinear learning of self-assembly landscapes and mechanisms in the Journal of Physical Chemistry B
Andy Long and Prof. Ferguson have published a paper in J. Phys. Chem. B in which they describe the development and validation of a new many-body machine learning algorithm capable of systematically discovering low-dimensional free energy landscapes and assembly mechanisms by data mining molecular assembly trajectories (http://dx.doi.org/10.1021/jp500350b). Andy has validated this methodology in simulations of patchy colloid assembly as an experimentally realizable system as a simple model of viral capsid assembly. His approach resolves competing assembly pathways to reveal the microscopic mechanisms driving self-assembly, providing deep insight to guide the rational design of self-assembling building blocks. We are currently working with Steve Granick to apply our technology to experimental particle tracking trajectories. Congratulations to Andy!
March 19, 2014
Jiang Wang and Prof. Ferguson named on List of Excellent Teachers for Fall 2013
Prof. Ferguson and Jiang Wang were named in the Fall 2013 List of Teachers Ranked Excellent by Their Students, Jiang as a TA for PHYS 212: Electricity and Magnetism, and Prof. Ferguson as the instructor of the new course he developed MSE 498 AF: Computational Materials Science and Engineering.
March 4, 2014
Prof. Ferguson receives NSF CAREER Award
Prof. Ferguson has received a National Science Foundation (NSF) CAREER Award for his proposal "Teaching Machines to Design Self-Assembling Materials." We are very excited to embark on a five year program of work establishing nonlinear machine learning tools to understand and design self-assembling biomaterials.
November 4, 2013
Prof. Ferguson wins the 2013 IChemE North America “Young Chemical Engineer of the Year”
Prof. Ferguson was honored to receive this award for his work in the development of statistical mechanical models of viral fitness for rational vaccine design. He was presented with this award at a ceremony on Nov 4 at the AIChE Annual Meeting in San Francisco. The press release is available here.

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November 4-7, 2013
Prof. Ferguson delivers two talks at AIChE 2013 in San Francisco
Prof. Ferguson presents two talks at the AIChE Annual Meeting. In “Multiscale Systems Biology” he described the development of HIV and HCV fitness landscapes, including some of Greg’s recent and exciting results. In “Computational Studies of Self-Assembly I” he presented Andrew’s beautiful work on the development of a new machine learning algorithm to infer self-assembly mechanisms and kinetic free energy landscapes.
September 20, 2013
Jiang Wang joins the Ferguson Lab
Jiang Wang (Physics; B.S., University of Science and Technology China) joins the Ferguson Lab to conduct his PhD research. Jiang is investigating the recovery of single molecule free energy landscapes from low-dimensional time series using dynamical systems theory and machine learning.
September 3, 2013
Prof. Ferguson becomes ChBE faculty affiliate
Prof. Ferguson has become a faculty affiliate with the Department of Chemical and Biomolecular Engineering at UIUC.
September 1, 2013
UIUC / Hopkins DOE Award to study self-assembling peptides
In a collaborative DOE Award, Prof. Ferguson will join J.D. Tovar and Howard Katz at Johns Hopkins in the integrated computational/experimental study of self-assembling peptides into biocompatible conductive wires for energy applications.
August 27, 2013
Prof. Ferguson teaches a new MatSE course:
MSE 498 AF - Computational Materials Science and Engineering
Prof Ferguson will teach a new computational materials course that he developed in conjunction with Profs. Trinkle & Bellon. Designed to familiarize students with materials software packages through hands-on experience, this class will expose students to DFT calculations (Quantum Espresso), molecular simulation (Gromacs), finite element calculations (OOF2), and phase equilibria (Thermo-Calc).
August 26, 2013
Alex Trick joins the Ferguson Lab
Alex (MatSE sophomore) will be pursuing independent study in the Ferguson Lab exploring the computational design of mutant lasso peptides as "molecular thermometers".
August 20, 2013
Greg Hart, Bryce Thurston, and Prof. Ferguson named on List of Excellent Teachers for Spring 2013
Prof. Ferguson makes the Spring 2013 List of Teachers Ranked as Excellent by their Students as the instructor of MSE 458 - Polymer Physical Chemistry. Greg Hart and Bryce Thurston were ranked on the same list as "Outstanding" (top 10%) for their TA performance in PHYS 213: Thermal Physics / PHYS 214: Quantum Physics. Congratulations to Bryce and Greg!
May 28 - August 3, 2013
“Passionate on Parallel” REU Students join Ferguson Lab
POP REU students Ali Hajimirza (U. Oklahoma, CS) and Abhijit Pujare (Yale, EE/CS) join the Ferguson Lab for the summer to develop parallelized implementations of nonlinear graph matching algorithms.
May 15, 2013
Bryce Thurston III joins the Ferguson Lab
Bryce Thurston (Physics; B.S., Colorado School of Mines) joins the Ferguson Lab to complete his PhD research. Bryce is studying the hierarchical self-assembly of organic electronics using molecular dynamics simulations at multiple resolutions.
May 12, 2013
Jingtian Hu graduates from UIUC MatSE!
After performing some beautiful work in developing a new graph matching algorithm based on nonlinear machine learning of graph topologies, Jingtian Hu has graduated from UIUC MSE and will be heading to Northwestern University to pursue a PhD in Materials Science and Engineering. Congratulations to Jingtian!
March 1, 2013
Profs. Ferguson & DeVille win UIUC IMSE Small Grant
Prof. Ferguson and Prof. R.E. Lee DeVille are awarded seed funding from the UIUC Initiative for Mathematical Sciences and Engineering to support their work on the nonlinear inference of protein folding landscapes form low-dimensional experimental time series.
February 20, 2012
Prof. Ferguson delivers the UIUC CSE Seminar
Prof. Ferguson describes the coupling of machine learning tools and statistical thermodynamics theory to infer protein folding pathways and viral fitness landscapes.
January 23, 2013
Shao Mei joins the Ferguson Lab
Shao (MatSE junior) will be pursuing his UG thesis in the Ferguson Lab working on an experimental/computational collaboration with Prof. JJ Cheng on positively charged helical peptides.
November 28, 2012
Prof. Ferguson delivers the UIUC Physics Colloquium
Prof. Ferguson describes the coupling of machine learning tools and statistical thermodynamics theory to infer protein folding pathways and viral fitness landscapes.
October 24, 2012
Greg Hart joins the Ferguson Lab
Greg Hart (Physics; B.S., BYU Physics) joins the Ferguson Lab to pursue PhD research. Greg will be working on the development of data driven models of viral fitness, and their incorporation into predator-prey population dynamics models of host-pathogen interaction.
August 27, 2012
Jingtian Hu and Peter Zhou join the Ferguson Lab
Jingtian (MatSE senior) and Peter (MatSE junior) will be pursuing their UG theses in the Ferguson Lab. Jingtian is working on a new nonlinear algorithm for graph matching, and Peter is developing a new tool to accelerate biomolecular simulation.
August 27, 2012
Andrew Long joins the Ferguson Lab
Andrew Long (MatSE; M.S., CMU) officially joins the Ferguson Laboratory to pursue PhD research. Andrew will be investigating the application of nonlinear machine learning to collective self-assembly phenomena.
June 7, 2012
Prof. Ferguson wins AIDS Vaccine 2012 Conference Scholarship
Prof. Ferguson was selected to receive a conference scholarship to present his work on HIV viral fitness landscapes and computational immunogen design at AIDS Vaccine 2012, September 9-12 in Boston, MA.
May 16, 2012
Prof. Ferguson becomes CSE faculty affiliate
Prof. Ferguson has become a faculty affiliate with the UIUC Computational Science and Engineering Program.
April 15, 2012
Ferguson Lab Opens for Business
Professor Andrew L. Ferguson commences his appointment in the Department of Materials Science and Engineering at the University of Illinois at Urbana-Champaign. The interdisciplinary computational and theoretical Ferguson Lab opens for business, and is currently recruiting talented graduate students for multiple research openings.