A5046797476- Spectroscopy and Quantum Chemical Studies
- Advanced Thermodynamics and Statistical Mechanics
- Advanced Chemical Physics Studies
- stochastic dynamics and bifurcation
- Protein Structure and Dynamics
- Quantum chaos and dynamical systems
- Material Dynamics and Properties
- Nonlinear Dynamics and Pattern Formation
- Lipid Membrane Structure and Behavior
- Phase Equilibria and Thermodynamics
- Gold and Silver Nanoparticles Synthesis and Applications
- Machine Learning in Materials Science
- Quantum, superfluid, helium dynamics
- Pickering emulsions and particle stabilization
- Advanced biosensing and bioanalysis techniques
- Theoretical and Computational Physics
- Photochemistry and Electron Transfer Studies
- Career Development and Diversity
- Force Microscopy Techniques and Applications
- Polymer Surface Interaction Studies
- Advanced Memory and Neural Computing
- Mentoring and Academic Development
- Diffusion and Search Dynamics
- Molecular Junctions and Nanostructures
- Computational Drug Discovery Methods
Johns Hopkins University
2016-2025
St. Johns Hospital
2025
École Polytechnique Fédérale de Lausanne
2021
Istituto di Matematica Applicata e Tecnologie Informatiche
2021
Universidad Autónoma Metropolitana
2021
University of Baltimore
2017-2020
Georgia Institute of Technology
2008-2018
University of Pennsylvania
1995-2017
University of Massachusetts Amherst
2017
American Institute of Physics
2017
We report a solution NMR-based analysis of (16-mercaptohexadecyl)trimethylammonium bromide (MTAB) self-assembled monolayers on colloidal gold nanospheres (AuNSs) with diameters from 1.2 to 25 nm and nanorods (AuNRs) aspect ratios 1.4 3.9. The chemical shift the proton signals solvent-exposed headgroups bound ligands suggests that are saturated ligand shell as sizes nanoparticles increase beyond ∼10 nm. Quantitative NMR shows density MTAB-AuNSs is size-dependent. Ligand ranges ∼3 molecules...
A statistical distribution of state-specific unimolecular decay rates is derived (within the framework random matrix theory) that determined completely by transition state properties potential energy surface. It includes standard χ-square distributions as a special case. Model calculations are presented to show extent which it can differ from distribution, and specific application made rate data for D2CO→D2+CO.
Neuropeptide Y (NPY) has been found to adopt two stable conformations in vivo: (1) a monomeric form called the PP-fold which polyproline tail is folded onto an α-helix via β-turn and (2) dimeric of unfolded proteins α-helices interact with each other side chains. The transition pathway rates between remain unknown are important nature binding protein. Toward addressing this question, present work suggests that unfolding too slow play role NPY unless receptor catalyzes it do so. Specifically,...
The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] a landmark article demonstrating the efficacy combining steered molecular dynamics Jarzynski's nonequilibrium relation. In this study, recently developed adaptive (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, R. Hernandez, J. Theory Comput. 6, 3026 (2010)] is used to reproduce PMF unraveling averaging over fewer trajectories. efficiency...
Thermalized chemical reactions driven under dynamical load are characteristic of activated dynamics for arbitrary nonautonomous systems. Recent generalizations transition state theory to obtain formally exact rates have required the construction a time-dependent trajectory. Here, we show that Lagrangian descriptors can be used this structure directly. By developing phase space separatrix is void recrossings, these constructs allow principal criterion in implementation modern rate theories...
For assistance in the design of next generation nanomaterials that are functional and have minimal health safety concerns, it is imperative to establish causality, rather than correlations, how properties determine biological environmental outcomes. Due vast space available complexity nano/bio interfaces, theoretical computational studies expected play a major role this context. In minireview, we highlight opportunities pressing challenges for chemistry approaches explore relevant...
Carbon dots (CDs) have attracted great attention in a range of applications due to their bright photoluminescence, high photostability, and good biocompatibility. However, it is challenging design CDs with specific emission properties because the syntheses involve many parameters, not clear how each parameter influences CD properties. To help bridge this gap, machine learning, specifically an artificial neural network, employed work characterize impact synthesis parameters on make...
Abstract Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application functional nanomaterials design. However, multiple non-specific binding sites intrinsic surface QDs have prevented fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework selectively attach spatially addressable on 3D wireframe DNA origami scaffolds using interfacial control QD surface....
Seed-mediated synthesis strategies, in which small gold nanoparticle precursors are added to a growth solution initiate heterogeneous nucleation, among the most prevalent, simple, and productive methodologies for generating well-defined colloidal anisotropic nanostructures. However, size, structure, chemical properties of seeds remain poorly understood, partially explains lack mechanistic understanding many particle reactions. Here, we identify majority component seed as an atomically...
The nonequilibrium stretching of decaalanine in vacuum using steered molecular dynamics and Jarzynski's relation led to the landmark determination its potential mean force by Park Schulten (Chem. Phys. 2004). In so doing, relative thermodynamics hydrogen-bond contacts entropy chain were quantified through reversible work, (PMF). A recently developed adaptive algorithm (Ozer et al. J. Chem. Theory Comput. 2010) has now made it possible determine thermodynamics, PMF, a model solvent TIP3P...
Phase space contours (shown in color) constructed using the method of Lagrangian descriptors resolve separatrices governing state transitions on reaction-path potential energy surface white) for field-induced ketene isomerization.
Carbon dots (CDs) are emerging as the material of choice in a range applications due to their excellent photoluminescence properties, ease preparation from inexpensive precursors, and low toxicity. However, precise nature mechanism for fluorescence is still under debate, several molecular fluorophores have been reported. In this work, new blue fluorophore, 5-oxopyrrolidine-3-carboxylic acid, was discovered carbon synthesized most commonly used precursors: citric acid urea. The product alone...
We present a general scheme for converting coarse-grained models into Dissipative Particle Dynamics (DPD) models. build the corresponding DPD by analogy with de novo coarse-graining suggested Groot and Warren (J. Chem. Phys., 1997). Electrostatic interactions between charged particles are represented though addition of long-range Slater Coulomb potential as González-Melchor et al. 2006). The construction is illustrated MARTINI various proteins representation, but it not restricted to usual...
Transition state theory overestimates reaction rates in solution because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing time-dependent surface free of such recrossings presence noise. The no-recrossing limit transition thus becomes generally available description reactions fluctuating environment.
We investigated the photoinduced one-electron oxidation of a series DNA oligomers having covalently linked anthraquinone group (AQ) and containing [(A)(n)GG](m) or [(T)(n)GG](m) segments. These have m GG steps, where = 4 6, separated by (A)(n) (T)(n) segments, n 1-7 for set 1-5 set. Irradiation with UV light that is absorbed AQ causes injection radical cation into DNA. The migrates through DNA, causing chemical reaction, primarily at leads to strand cleavage after piperidine treatment....
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding ligand binding. However, the calculated averages are generally dominated by "rare events" from ensemble of nonequilibrium trajectories. The recently proposed adaptive steered ASMD, introduced a new idea selecting important events eliminating non-contributing...
Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD) advantage by limiting spread trajectories staged approach. The contraction end each stage can be performed taking structure whose nonequilibrium work is closest Jarzynski average (in naive ASMD) or relaxing under no-work condition...
The minimum contour in the forward Lagrangian descriptor overlaps invariant manifold (in green) dividing reactant and product regions.
The persistence of a transition state structure in systems driven by time-dependent environments allows the application modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this is problematic has been limited built on series expansion about saddle point. Recently, it shown that obtain formally exact rates for reactions thermal environments, trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven R....