A5028183845- Surfactants and Colloidal Systems
- Pickering emulsions and particle stabilization
- Lipid Membrane Structure and Behavior
- Material Dynamics and Properties
- Molecular Junctions and Nanostructures
- Force Microscopy Techniques and Applications
- Machine Learning in Materials Science
- Block Copolymer Self-Assembly
- Advancements in Transdermal Drug Delivery
- Scientific Computing and Data Management
- Protein Structure and Dynamics
- Distributed and Parallel Computing Systems
- Phase Equilibria and Thermodynamics
- Lubricants and Their Additives
- Enzyme Structure and Function
- Diatoms and Algae Research
- Theoretical and Computational Physics
- Advanced Polymer Synthesis and Characterization
- Lattice Boltzmann Simulation Studies
- Supramolecular Self-Assembly in Materials
- Mesoporous Materials and Catalysis
- Polymer Surface Interaction Studies
- Electrostatics and Colloid Interactions
- Microfluidic and Bio-sensing Technologies
- Micro and Nano Robotics
Vanderbilt University
2014-2024
Memorial Sloan Kettering Cancer Center
2023-2024
University of Colorado Boulder
2023
Tri-Institutional PhD Program in Chemical Biology
2023
University of Montana
2023
University of California, San Diego
2023
Open Geospatial Consortium
2023
Open Molecular Software Foundation
2023
University of California, Berkeley
2023
New York University
2023
In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used derive coarse-grained potentials. It shown that inclusion of target data from multiple states yields a less state-dependent potential, and thus better suited simulate systems over range thermodynamic than IBI method. The forces algorithm sample regions potential phase space match radial distribution function at state points, producing derived more representative underlying interactions....
The surprising recent discoveries of quasicrystals and their approximants in soft-matter systems poses the intriguing possibility that these structures can be realized a broad range nanoscale microscale assemblies. It has been theorized are largely entropically stabilized, but thermodynamic mechanism underlying formation remains elusive. Here, we use computer simulation free-energy calculations to demonstrate simple design heuristic for assembling systems. Our study builds on previous...
A generalized and extensible machine-learned molecular mechanics force field trained on over 1.1 million QC data applicable for drug discovery applications. Figure reproduced from the arXiv:201001196 preprint under arXiv non-exclusive license.
Ceramides are known to be a key component of the stratum corneum, outermost protective layer skin that controls barrier function. In this work, molecular dynamics simulations used examine behavior ceramide bilayers, focusing on nonhydroxy sphingosine (NS) and phytosphingosine (NP) ceramides. Here, we propose modified version CHARMM force field for simulation, which is directly compared more commonly GROMOS-based Berger (Biophys. J. 1997, 72, 2002–2013); while both fields shown closely match...
We perform Brownian dynamics simulations on model 3-D systems of mono-tethered nanospheres (TNS) to study the equilibrium morphologies formed by their self-assembly in a selective solvent. predict that contrast flexible amphiphiles are locally ordered and there is an increase local order with concentration or relative nanoparticle diameter. present temperature vs phase diagram for system TNS propose dimensionless scaling factor F(v) (headgroup volume/tether volume) allows comparison between...
We present results of simulations that predict the phases formed by self-assembly model nanospheres functionalized with a single polymer ``tether,'' including double gyroid, perforated lamella, and crystalline bilayer phases. show microphase separation immiscible tethers causes confinement nanoparticles, which promotes local icosahedral packing in turn stabilizes gyroid. new metric for determining arrangement particles based on spherical harmonic ``fingerprints,'' we use to quantify extent ordering.
We report the results from a computational study of self-assembly amphiphilic ditethered nanospheres using molecular simulation. As function interaction strength and directionality tether−tether interactions, we predict formation four highly ordered phases not previously reported for nanoparticle systems. find double diamond structure comprised zinc blende (binary diamond) arrangement spherical micelles with complementary network nanoparticles (ZnS/D), phase alternating in NaCl simple cubic...
All data and codes are distributed via GitHub Appendix S1: Supporting Information Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by authors. Any queries (other than missing content) should be directed to corresponding author article.
We use Brownian dynamics (BD), molecular dynamics, and dissipative particle to study the phase behavior of diblock copolymer melts determine if hydrodynamics is required in formation phases with greater than one-dimensional periodicity. present a diagram for copolymers predicted by BD provide relationship between inverse dimensionless temperature epsilon/k(B)T Flory-Huggins chi parameter, allowing quantitative comparison methods mean field predictions. Our results concerning are good...
Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior properties of condensed matter systems. While standard for characterizing structure exist, they insufficient treating problems in emerging field nano microscale self-assembly, where structures encountered may be complex unusual. The computer science "shape matching" offers a robust solution this problem by defining diverse methods quantifying similarity...
Systems composed of soft matter (e.g. liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science engineering, but molecular simulations such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a system involves multiple steps, which have traditionally been performed by researchers 'bespoke' fashion, resulting many published...
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface systems is indispensable for biomolecular simulation computer-aided drug design. Here, we introduce a generalized machine-learned MM field, \texttt{espaloma-0.3}, an end-to-end differentiable framework using graph neural networks to overcome limitations traditional rule-based methods. Trained in single GPU-day fit large diverse quantum...
Recent simulations predict that aggregating nanospheres functionalized with polymer "tethers" can self-assemble to form the double gyroid (DG) phase seen in block copolymer and surfactant systems. Within struts of gyroid, nanoparticles pack icosahedral motifs, stabilizing a small region diagram. Here, we study impact nanoparticle size polydispersity on stability phase. We show for low amounts energy is lowered. A large amount raises system, disrupts packing, eventually destabilizes gyroid....
Interfacial properties of n-alkylsilane monolayers on silica have been investigated with molecular dynamics simulations using both reactive and classical (i.e., nonreactive) force fields. A synthesis mimetic simulation (SMS) procedure the field ReaxFF has developed to mimic experimental processing silicon wafers involved in preparation alkylsilane monolayers; SMS procedure, amorphous surfaces are generated exposed hydrogen peroxide (H2O2) create a hydroxide surface layer. Alkylsilane then...
We demonstrate how the recently developed Python-based Molecular Simulation and Design Framework (MoSDeF) can be used to perform molecular dynamics screening of functionalized monolayer films, focusing on tribological effectiveness. MoSDeF is an open-source package that allows for programmatic construction parametrization soft matter systems enables TRUE (transferable, reproducible, usable by others, extensible) simulations. The MoSDeF-enabled identifies several film chemistries...
We study fluidic assembly and packing of spherical particles in rectilinear microchannels that are terminated by a flow constriction. First, we introduce method for active the confined triggering local constriction fluid channel using partially closed membrane valve. This microfluidic valve allows active, on-demand particle as opposed to previous passive methods based on terminal channels weirs. Second, three-dimensional against weir microchannels. The packings result achiral chains with...
We present results of Brownian dynamics simulations tethered nanospheres and nanorods. Immiscibility between tether nanoparticle facilitates microphase separation into the bicontinuous, double gyroid structure (first reported by Iacovella et al. [Phys. Rev. E 75, 040801(R) (2007)] Horsch [J. Chem. Phys. 125, 184903 (2006)], respectively). demonstrate ability these nanoparticles to adopt distinct, minimal energy local packings, in which form icosahedral-like clusters nanorods splayed...
We report a novel atomistic model of carbide-derived carbons (CDCs), which are nanoporous with high specific surface areas, synthesis-dependent degrees graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, catalytic supports. materials heterogenous, non-ideal structures include important parameters that govern their performance. Therefore, realistic the...