Jan Michael Carrillo
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janmikel.bsky.social
Jan Michael Carrillo
@janmikel.bsky.social
Those who can, do; those who can't, simulate. *Simulation Scientist*
Steric effects of central dogma processes on the compaction and segregation of bacterial nucleoids
authors.elsevier.com/a/1mBGt_9FM7...
authors.elsevier.com
December 1, 2025 at 4:29 PM
Hydration and Restructuring of Polar Polymer Interfaces: Implications in Antifouling and Responsive Materials | ACS Applied Materials & Interfaces pubs.acs.org/doi/10.1021/...
Hydration and Restructuring of Polar Polymer Interfaces: Implications in Antifouling and Responsive Materials
Manipulating polymer interfaces is crucial for understanding how structure influences function in applications spanning biofouling prevention to energy storage. Moreover, observing how polymers adapt their microscopic structure to changes in their local environment can reveal essential properties that govern their performance in such applications, providing key insights into how to design more effective interfaces. Here, a series of “grafting-from” polymer brushes with side chains varying in charge are probed by sum frequency generation (SFG) and modeled using all-atom molecular dynamics (MD) simulations to elucidate how chemical makeup and charge mediate interfacial restructuring in dry versus hydrated states. Results show that charge, in progressing from nonpolar to cationic to zwitterionic, results in dramatic changes in the interfacial structure and overall hydration. While net neutral systems, regardless of bulk phase polarity, show minimal interfacial water structuring, the cationic species exhibits strong bulk water signals from the surface potential. Meanwhile, the polymer brushes themselves restructure in water differently independent of charge, impacting the functional groups that are presented to the aqueous phase. Nonpolar and cationic species, for instance, undergo a change in alkyl group orientations to accommodate hydrating water molecules, whereas the zwitterionic polymer becomes completely disordered in water. Overall, the structure-based behavior trends presented herein have implications in antifouling applications and responsive material interfaces.
pubs.acs.org
October 31, 2025 at 2:21 PM
Join me in making a gift during WUOT 91.9 FM's Fall Membership Drive. #WUOTmembershipdrive
give.utk.edu/wuot-91-9-fm...
WUOT 91.9 FM Membership Drive
Join me in making a gift during WUOT 91.9 FM's Fall Membership Drive.
give.utk.edu
October 2, 2025 at 2:11 PM
All-Atom Modeling and Simulation of Biopolymer Interface: Dual Role of Antifouling Polymer Brushes | Langmuir pubs.acs.org/doi/10.1021/...
All-Atom Modeling and Simulation of Biopolymer Interface: Dual Role of Antifouling Polymer Brushes
Antifouling polymer brushes are well-known for their exceptional resistance to unwanted protein adsorption. While experimental studies have extensively characterized protein–polymer brush interactions...
pubs.acs.org
September 13, 2025 at 1:18 PM
Enhanced Interfacial Bonding of Graft Copolymers | ACS Applied Materials & Interfaces pubs.acs.org/doi/full/10....
Enhanced Interfacial Bonding of Graft Copolymers
To understand how thermoplastic welding strength can be tuned through chemical modifications and macromolecular topology, we combined coarse-grained molecular dynamics (MD) simulations with experiment...
pubs.acs.org
August 26, 2025 at 5:19 PM
How Topological Polymer Loops on the Nanoparticle Surface Control the Mechanical Properties of Nanocomposites | Macromolecules pubs.acs.org/doi/full/10....
How Topological Polymer Loops on the Nanoparticle Surface Control the Mechanical Properties of Nanocomposites
Carbon black (CB) and silica (SiO2) filled elastomers are known to be the most successful polymer nanocomposites (PNCs) in industry, where “bound rubber (BR)” (i.e., polymer chains that are physically or chemically adsorbed on the nanofiller surface) plays a critical role in their reinforcement. Here, we report a molecular-scale mechanism underlying the “BR-induced reinforcement” by integrating neutron scattering experiments and molecular dynamics simulations. Simplified non-cross-linked SiO2-filled polybutadiene (PB) and CB-filled PB reveal the critical role of topological polymer loops in the BR for the enhanced mechanical performance. The average loop size on the SiO2 surface modified with a silane coupling agent is much smaller than that on the CB surface and the loops on the SiO2 surface are densely formed, preventing interdigitation with the matrix chains. On the other hand, the larger, uncrowded loops formed on the CB surface facilitate the interdigitation with the matrix polymer chains even near the filler surface. In this way, a strong connectivity is established between a matrix and a nanofiller, resulting in an adhesive filler–polymer interface. Our findings shed light on rich and complex physics and materials design problems in PNCs, where the topological polymer structure on the nanofiller surface directly controls the macroscopic mechanical properties.
pubs.acs.org
August 21, 2025 at 3:05 PM
Honored to be a UConn alumnus and to take part in the 60th anniversary of the UConn IMS Polymer Program at the ACS Fall Meeting. It was great to see old friends, colleagues, and mentors.
August 19, 2025 at 6:19 PM
A convergence metric for counting statistics in time-resolved small angle neutron scattering pubs.aip.org/aip/jcp/arti...
A convergence metric for counting statistics in time-resolved small angle neutron scattering
This work introduces a model-independent, dimensionless metric for predicting optimal measurement duration in time-resolved small-angle neutron scattering using
pubs.aip.org
August 15, 2025 at 2:13 PM
Metastable Clusters and Competitive Solvation Tune Ion Pairing at Liquid Interfaces | Journal of the American Chemical Society pubs.acs.org/doi/full/10....
Metastable Clusters and Competitive Solvation Tune Ion Pairing at Liquid Interfaces
The balance of hydrophobic and hydrophilic interactions underlies emergent phenomena in complex multicomponent chemical systems. Here, we show that a supposedly ‘non–interacting’ nonpolar phase can be used to competitively solvate amphiphilic molecules at an oil/aqueous interface. This solvation, as probed by surface specific nonlinear spectroscopy and simulations, results in a molecularly thin corrugated phase boundary featuring metastable assemblies that alter the hydrogen bonding networks of water and the apparent ‘hard/soft’ descriptors used to describe ionic interactions. We show that competitive solvation enhances amphiphile mobility, opening up otherwise energetically inaccessible complexes that transiently interact with aqueous phase ions. These transient species impact ensemble binding affinities and may represent the molecular agents responsible for aspects of ionic transport and function. The result of this work highlights how seemingly unrelated nonpolar interactions feedback onto aqueous phase chemical phenomena, providing a pathway to tune phase separation and self-assembly to access new reaction pathways using interfaces for a range of chemical and biological systems.
pubs.acs.org
August 15, 2025 at 2:12 PM
Watch how a polyelectrolyte chain behaves under shear flow—featuring its characteristic tumbling motion.
pubs.acs.org/doi/10.1021/...
June 18, 2025 at 2:17 AM
It’s been a tough time lately, but I wanted to share something positive—my paper has officially been accepted for publication! Feeling thankful.
June 14, 2025 at 3:37 AM
RIP Pope Francis — his Jesuit heart shaped a papacy rooted in compassion, justice, and humility. He stood with the least of us, embraced migrants, and gave voice to the voiceless. May he rest in peace. #RIPPopeFrancis
April 22, 2025 at 12:03 AM
It's hard being a dormant native speaker in a multilingual context, characterized by limited or no active use of my first language, regular use of a secondary language at home, and predominant use of a third, societally dominant language in public or institutional settings.
April 14, 2025 at 12:53 PM
ACS Spring 2025, San Diego CA. I'm going to present my work on lipid bilayers under an oscillating electric field
March 24, 2025 at 1:24 AM
Rubenstein asks Colby a question during Colby's invited talk on polyelectrolytes. #APS2025
March 19, 2025 at 6:30 AM
Our collaborative work on characterizing the deformation of semiflexible polymer chains.
doi.org/10.1063/5.02...
A discretized representation for Monte Carlo simulation of deformed semiflexible chains
In this study, we present a novel orientation discretization approach based on the rhombic triacontahedron for Monte Carlo simulations of semiflexible polymer c
doi.org
December 13, 2024 at 4:10 PM
Check out our latest collaborative work on vitrimers, which involves polymer synthesis, characterization, and computations! pubs.acs.org/doi/10.1021/...
Source of Processable Vitrimer Viscosities: Swap Frequencies and Steric Factors
Vitrimers exhibit high, processable viscosities, where other polymers do not, and are among the most promising polymers for closed-loop material circularity. We sought to investigate the underlying chemical kinetic factors that result in high viscosities for vitrimers, which are crucial to designing vitrimers with tunable viscosity. To interrogate these factors, we achieved the first simulated predictions of real vitrimer viscosities, using a novel kinetic Monte Carlo molecular dynamics method, overcoming the time and length scale gaps to predict experimental bulk viscosities. The vitrimer architecture investigated is based on poly(dimethylsiloxane) chains and vinylogous urethane bond swaps. We probed the effects of the extent of free swapping groups, %F, the activation energy, EA, and the steric factor, ρ. The steric factor is related to the intrinsic reaction probability for molecules with sufficient energy. All three factors were found to be significant, but the role of ρ was found to be the biggest and also the most underappreciated. The results show that the inclusion of accurate ρ is of critical importance for viscosity predictions, with the evidence suggesting that the typical assumption of ρ = 1 is not valid for vitrimers and that, indeed, very low steric factors are present in bond-swap vitrimers such that values of ρ < 10–10 may be typical. This greatly influences the bond exchange rates and, ultimately, the viscosities. Recognition of this result is necessary for the prediction of vitrimer viscosities from molecular simulations and to make vitrimers by design from molecular dynamics. We also investigated the effects that EA, ρ, and the number of free swapping groups have upon vitreous range temperatures, TV, with respect to achieving a specific viscosity (ηV = 1 × 108 Pa·s), as well as for a commonly reported higher viscosity extrapolation (ηV = 1 × 1012 Pa·s). The evidence suggests that vitrimers may follow universal curves for EA vs TV, as a function of ρ. This study achieves the first of these comparisons of molecular simulations to experiments and reveals critical insights toward creating vitrimers by design, while providing a route for the prediction of TV from kinetic Monte Carlo molecular dynamics simulations.
pubs.acs.org
December 3, 2024 at 5:25 PM
Final home game of the season. Go vols! 🍊
November 25, 2024 at 3:48 AM
Any soft matter researchers here?
November 13, 2024 at 6:19 PM
Molecular dynamics simulation of a salt-free polyelectrolyte solution under shear: 2D small-angle scattering spectrum in the flow-gradient plane.
November 13, 2024 at 6:00 PM