Publications by authors named "John Royer"

16 Publications

  • Page 1 of 1

Soft matter science and the COVID-19 pandemic.

Soft Matter 2020 Sep;16(36):8310-8324

Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.

Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids complexed to proteins surrounded by a protein-studded lipid bilayer shell. A dominant route for transmission is via air-borne aerosols and droplets. Viral interaction with polymeric body fluids, particularly mucus, and cell membranes controls their infectivity, while their interaction with skin and artificial surfaces underpins cleaning and disinfection and the efficacy of masks and other personal protective equipment. The global response to COVID-19 has highlighted gaps in the soft matter knowledge base. We survey these gaps, especially as pertaining to the transmission of the disease, and suggest questions that can (and need to) be tackled, both in response to COVID-19 and to better prepare for future viral pandemics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d0sm01223hDOI Listing
September 2020

Rhodoxanthin synthase from honeysuckle; a membrane diiron enzyme catalyzes the multistep conversation of β-carotene to rhodoxanthin.

Sci Adv 2020 Apr 22;6(17):eaay9226. Epub 2020 Apr 22.

DSM Nutritional Products, 60 Westview St, Lexington, MA 02421, USA.

Rhodoxanthin is a vibrant red carotenoid found across the plant kingdom and in certain birds and fish. It is a member of the atypical retro class of carotenoids, which contain an additional double bond and a concerted shift of the conjugated double bonds relative to the more widely occurring carotenoid pigments, and whose biosynthetic origins have long remained elusive. Here, we identify LHRS ( hydroxylase rhodoxanthin synthase), a variant β-carotene hydroxylase (BCH)-type integral membrane diiron enzyme that mediates the conversion of β-carotene into rhodoxanthin. We identify residues that are critical to rhodoxanthin formation by LHRS. Substitution of only three residues converts a typical BCH into a multifunctional enzyme that mediates a multistep pathway from β-carotene to rhodoxanthin via a series of distinct oxidation steps in which the product of each step becomes the substrate for the next catalytic cycle. We propose a biosynthetic pathway from β-carotene to rhodoxanthin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/sciadv.aay9226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176425PMC
April 2020

Liquid Migration in Shear Thickening Suspensions Flowing through Constrictions.

Phys Rev Lett 2019 Sep;123(12):128002

SUPA and School of Physics and Astronomy, The University of Edinburgh, King's Buildings, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.

Dense suspensions often become more dilute as they move downstream through a constriction. We find that as a shear-thickening suspension is extruded through a narrow die and undergoes such liquid migration, the extrudate maintains a steady concentration ϕ_{out}^{LM}, independent of time or initial concentration. At low volumetric flow rate Q, ϕ_{out}^{LM} is a universal function of Q/r_{d}^{3}, a characteristic shear rate in the die of radius r_{d}, and coincides with the critical input concentration for the onset of LM, ϕ_{in}^{crit}. We predict this function by coupling the Wyart-Cates model for shear thickening and the "suspension balance model" for solvent permeation through particles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.123.128002DOI Listing
September 2019

Rheological Behavior and in Situ Confocal Imaging of Bijels Made by Mixing.

Langmuir 2019 Aug 12;35(33):10927-10936. Epub 2019 Aug 12.

School of Physics and Astronomy , University of Edinburgh , James Clerk Maxwell Building, Peter Guthrie Tait Road , Edinburgh EH9 3FD , U.K.

Bijels (bicontinuous interfacially jammed emulsion gels) have the potential to be useful in many different applications due to their internal connectivity and the possibility of efficient mass transport through the channels. Recently, new methods of making the bijel have been proposed, which simplify the fabrication process, making commercial application more realistic. Here, we study the flow properties of bijels prepared by mixing alone using oscillatory rheology combined with confocal microscopy and also squeezing flow experiments. We found that the bijel undergoes a two-step yielding process where the first step corresponds to the fluidizing of the interface, allowing the motion of the structure, and the second step corresponds to the breaking of the structure. In the squeeze flow experiments, the yield stress of the bijel is observed to show a power law dependence on squeezing speed. However, when stress in excess of yield stress is plotted against shear rate, all the different squeeze flow data show a superposition.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.langmuir.9b00636DOI Listing
August 2019

Rheological Signature of Frictional Interactions in Shear Thickening Suspensions.

Phys Rev Lett 2016 May 5;116(18):188301. Epub 2016 May 5.

Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.

Colloidal shear thickening presents a significant challenge because the macroscopic rheology becomes increasingly controlled by the microscopic details of short ranged particle interactions in the shear thickening regime. Our measurements here of the first normal stress difference over a wide range of particle volume fractions elucidate the relative contributions from hydrodynamic lubrication and frictional contact forces, which have been debated. At moderate volume fractions we find N_{1}<0, consistent with hydrodynamic models; however, at higher volume fractions and shear stresses these models break down and we instead observe dilation (N_{1}>0), indicating frictional contact networks. Remarkably, there is no signature of this transition in the viscosity; instead, this change in the sign of N_{1} occurs while the shear thickening remains continuous. These results suggest a scenario where shear thickening is driven primarily by the formation of frictional contacts, with hydrodynamic forces playing a supporting role at lower concentrations. Motivated by this picture, we introduce a simple model that combines these frictional and hydrodynamic contributions and accurately fits the measured viscosity over a wide range of particle volume fractions and shear stress.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.116.188301DOI Listing
May 2016

Rheology and dynamics of colloidal superballs.

Soft Matter 2015 Jul;11(28):5656-65

Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.

Recent advances in colloidal synthesis make it possible to generate a wide array of precisely controlled, non-spherical particles. This provides a unique opportunity to probe the role that particle shape plays in the dynamics of colloidal suspensions, particularly at higher volume fractions, where particle interactions are important. We examine the role of particle shape by characterizing both the bulk rheology and micro-scale diffusion in a suspension of pseudo-cubic silica superballs. Working with these well-characterized shaped colloids, we can disentangle shape effects in the hydrodynamics of isolated particles from shape-mediated particle interactions. We find that the hydrodynamic properties of isolated superballs are marginally different from comparably sized hard spheres. However, shape-mediated interactions modify the suspension microstructure, leading to significant differences in the self-diffusion of the superballs. While this excluded volume interaction can be captured with a rescaling of the superball volume fraction, we observe qualitative differences in the shear thickening behavior of moderately concentrated superball suspensions that defy simple rescaling onto hard sphere results. This study helps to define the unknowns associated with the effects of shape on the rheology and dynamics of colloidal solutions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/c5sm00729aDOI Listing
July 2015

Precisely cyclic sand: self-organization of periodically sheared frictional grains.

Proc Natl Acad Sci U S A 2015 Jan 23;112(1):49-53. Epub 2014 Dec 23.

Center for Soft Matter Research and Department of Physics, New York University, New York, NY 10003; and.

The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain-friction space that shows chaotic dispersion, crystal formation, vortex patterns, and most unusually a disordered phase in which each particle precisely retraces its unique path. However, the system is not reversible. Rather, the trajectory of each particle, and the entire frictional, many-degrees-of-freedom system, organizes itself into a limit cycle absorbing state. Of particular note is that fact that the cyclic states are spatially disordered, whereas the ordered states are chaotic.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1413468112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291669PMC
January 2015

Cinnamate-based DNA photolithography.

Nat Mater 2013 Aug 19;12(8):747-53. Epub 2013 May 19.

Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, New York 10003, USA.

As demonstrated by means of DNA nanoconstructs, as well as DNA functionalization of nanoparticles and micrometre-scale colloids, complex self-assembly processes require components to associate with particular partners in a programmable fashion. In many cases the reversibility of the interactions between complementary DNA sequences is an advantage. However, permanently bonding some or all of the complementary pairs may allow for flexibility in design and construction. Here, we show that the substitution of a cinnamate group for a pair of complementary bases provides an efficient, addressable, ultraviolet light-based method to bond complementary DNA covalently. To show the potential of this approach, we wrote micrometre-scale patterns on a surface using ultraviolet light and demonstrated the reversible attachment of conjugated DNA and DNA-coated colloids. Our strategy enables both functional DNA photolithography and multistep, specific binding in self-assembly processes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmat3645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722280PMC
August 2013

Droplet and cluster formation in freely falling granular streams.

Phys Rev E Stat Nonlin Soft Matter Phys 2011 May 12;83(5 Pt 1):051302. Epub 2011 May 12.

Department of Physics, University of Chicago, Chicago, Illinois 60637, USA.

Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream's macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gaslike jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.83.051302DOI Listing
May 2011

Rupture and clustering in granular streams.

Chaos 2009 Dec;19(4):041103

The University of Chicago, Chicago, Illinois 60637, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.3211191DOI Listing
December 2009

High-speed tracking of rupture and clustering in freely falling granular streams.

Nature 2009 Jun;459(7250):1110-3

James Franck Institute and Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA.

Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven Plateau-Rayleigh instability. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains, even though flows of macroscopic particles are considered to lack surface tension. Recent studies on freely falling granular streams tracked fluctuations in the stream profile, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force microscopy to measure grain-grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that of ordinary liquids. We find that the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature08115DOI Listing
June 2009

Birth and growth of a granular jet.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Jul 18;78(1 Pt 1):011305. Epub 2008 Jul 18.

James Franck Institute and Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA.

The interaction between fine grains and the surrounding interstitial gas in a granular bed can lead to qualitatively new phenomena not captured in a simple, single-fluid model of granular flows. This is demonstrated by the granular jet formed by the impact of a solid sphere into a bed of loose, fine sand. Unlike jets formed by impact in fluids, this jet is actually composed of two separate components, an initial thin jet formed by the collapse of the cavity left by the impacting object stacked on top of a second, thicker jet which depends strongly on the ambient gas pressure. This complex structure is the result of an interplay between ambient gas, bed particles, and impacting sphere. Here we present the results of systematic experiments that combine measurements of the jet above the surface varying the release height, sphere diameter, container size, and bed material with x-ray radiography below the surface to connect the changing response of the bed to the changing structure of the jet. We find that the interstitial gas trapped by the low permeability of a fine-grained bed plays two distinct roles in the formation of the jet. First, gas trapped and compressed between grains prevents compaction, causing the bed to flow like an incompressible fluid and allowing the impacting object to sink deep into the bed. Second, the jet is initiated by the gravity driven collapse of the cavity left by the impacting object. If the cavity is large enough, gas trapped and compressed by the collapsing cavity can amplify the jet by directly pushing bed material upwards and creating the thick jet. As a consequence of these two factors, when the ambient gas pressure is decreased, there is a crossover from a nearly incompressible, fluidlike response of the bed to a highly compressible, dissipative response. Compaction of the bed at reduced pressure reduces the final depth of the impacting object, resulting in a smaller cavity and in the demise of the thick jet.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.78.011305DOI Listing
July 2008

Gas-mediated impact dynamics in fine-grained granular materials.

Phys Rev Lett 2007 Jul 20;99(3):038003. Epub 2007 Jul 20.

James Franck Institute and Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA.

Noncohesive granular media exhibit complex responses to sudden impact that often differ from those of ordinary solids and liquids. We investigate how this response is mediated by the presence of interstitial gas between the grains. Using high-speed x-ray radiography we track the motion of a steel sphere through the interior of a bed of fine, loose granular material. We find a crossover from nearly incompressible, fluidlike behavior at atmospheric pressure to a highly compressible, dissipative response once most of the gas is evacuated. We discuss these results in light of recent proposals for the drag force in granular media.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.99.038003DOI Listing
July 2007

Wave-number selection by target patterns and sidewalls in Rayleigh-Bénard convection.

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Sep 24;70(3 Pt 2):036313. Epub 2004 Sep 24.

Department of Physics and iQUEST, University of California, Santa Barbara, California 93106, USA.

We present experimental results for patterns of Rayleigh-Bénard convection in a cylindrical container with static sidewall forcing. The fluid used was methanol, with a Prandlt number sigma=7.17 , and the aspect ratio was Gamma identical withR/d approximately 19 ( R is the radius and d the thickness of the fluid layer). In the presence of a small heat input along the sidewall, a sudden jump of the temperature difference DeltaT from below to slightly above a critical value Delta T(c) produced a stable pattern of concentric rolls (a target pattern) with the central roll (the umbilicus) at the center of the cell. A quasistatic increase of epsilon identical withDeltaT/Delta T(c) -1 beyond epsilon(1,c) approximately 0.8 caused the umbilicus of the pattern to move off center. As observed by others, a further quasistatic increase of epsilon up to epsilon=15.6 caused a sequence of transitions at epsilon(i,b) ,i=1,...,8 , each associated with the loss of one convection roll at the umbilicus. Each loss of a roll was preceded by the displacement of the umbilicus away from the center of the cell. After each transition the umbilicus moved back toward but never quite reached the center. With decreasing epsilon new rolls formed at the umbilicus when epsilon was reduced below epsilon(i,a) < epsilon(i,b) . When decreasing epsilon , large umbilicus displacements did not occur. In addition to quantitative measurements of the umbilicus displacement, we determined and analyzed the entire wave-director field of each image. The wave numbers varied in the axial direction, with minima at the umbilicus and at the cell wall and a maximum at a radial position close to 2Gamma/3 . The wave numbers at the maximum showed hysteretic jumps at epsilon(i,b) and epsilon(i,a) , but on average agreed well with the theoretical predictions for the wave numbers selected in the far field of an infinitely extended target pattern. To our knowledge there is as yet no prediction for the wave number selected by the umbilicus itself, or by the cell wall of the finite experimental system.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.70.036313DOI Listing
September 2004

Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains.

Nat Biotechnol 2003 Feb 21;21(2):150-6. Epub 2003 Jan 21.

Microbia, Inc., 320 Bent Street, Cambridge, MA 02141, USA.

We describe a method to decipher the complex inter-relationships between metabolite production trends and gene expression events, and show how information gleaned from such studies can be applied to yield improved production strains. Genomic fragment microarrays were constructed for the Aspergillus terreus genome, and transcriptional profiles were generated from strains engineered to produce varying amounts of the medically significant natural product lovastatin. Metabolite detection methods were employed to quantify the polyketide-derived secondary metabolites lovastatin and (+)-geodin in broths from fermentations of the same strains. Association analysis of the resulting transcriptional and metabolic data sets provides mechanistic insight into the genetic and physiological control of lovastatin and (+)-geodin biosynthesis, and identifies novel components involved in the production of (+)-geodin, as well as other secondary metabolites. Furthermore, this analysis identifies specific tools, including promoters for reporter-based selection systems, that we employed to improve lovastatin production by A. terreus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt781DOI Listing
February 2003

Interrelationship of Xylanase Induction and Cellulase Induction of Trichoderma longibrachiatum.

Appl Environ Microbiol 1990 Aug;56(8):2535-2539

College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210.

Xylose oligomers rapidly induced xylanase activity of Trichoderma longibrachiatum, whereas induction was delayed in the presence of glucose. Cellobiose, cellopentaose, and xylobiose did not induce detectable levels of cellulase activity. However, mixtures of xylobiose with cellobiose or cellopentaose rapidly induced cellulase activity. In addition, mixtures of xylobiose with cellopentaose or cellobiose induced xylanase activity more effectively than xylobiose alone. Both xylanase and cellulase activity were detected after a lag period in the presence of lactose.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC184761PMC
http://dx.doi.org/10.1128/AEM.56.8.2535-2539.1990DOI Listing
August 1990