A5069981197- Nanopore and Nanochannel Transport Studies
- Protein Structure and Dynamics
- Spectroscopy and Quantum Chemical Studies
- Lipid Membrane Structure and Behavior
- Graphene research and applications
- Fuel Cells and Related Materials
- Microfluidic and Capillary Electrophoresis Applications
- Supramolecular Self-Assembly in Materials
- Ion channel regulation and function
- Gold and Silver Nanoparticles Synthesis and Applications
- Electrostatics and Colloid Interactions
- Dendrimers and Hyperbranched Polymers
- Carbon Nanotubes in Composites
- Nanocluster Synthesis and Applications
- RNA Interference and Gene Delivery
- Ion-surface interactions and analysis
- Advanced biosensing and bioanalysis techniques
- Metal and Thin Film Mechanics
- Membrane-based Ion Separation Techniques
- Peptidase Inhibition and Analysis
- Nanoparticle-Based Drug Delivery
- Cancer Immunotherapy and Biomarkers
- Microfluidic and Bio-sensing Technologies
- Cancer Research and Treatments
- Algal biology and biofuel production
Kansas State University
2016-2025
United States Department of State
2018-2022
University of Kansas
2018
Manhattan High School
2016
University of Illinois Urbana-Champaign
2007-2015
Université de Lorraine
2013-2015
Centre National de la Recherche Scientifique
2013-2015
Research Complex at Harwell
2014
Rutherford Appleton Laboratory
2014
Universidad Andrés Bello
2013
In the host of numerical schemes devised to calculate free energy differences by way geometric transformations, adaptive biasing force algorithm has emerged as a promising route map complex free-energy landscapes. It relies upon simple concept that simulation progresses, continuously updated is added equations motion, such in long-time limit it yields Hamiltonian devoid an average acting along transition coordinate interest. This means sampling proceeds uniformly on flat surface, thus...
Using all-atom molecular dynamics and atomic-resolution Brownian dynamics, we simulate the translocation of single-stranded DNA through graphene nanopores characterize ionic current blockades produced by nucleotides. We find that transport single strands may occur in nucleotide steps. For certain pore geometries, hydrophobic interactions with membrane lead to a dramatic reduction conformational fluctuations nucleotides nanopores. Furthermore, show different are, general, indicative type, but...
Predicting the rate of nonfacilitated permeation solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with inhomogeneous solubility-diffusion model, which requires calculation potential mean force position-dependent diffusivity solute along transmembrane axis. In this paper, we assess efficiency accuracy several methods for permeability a model DMPC bilayer urea, benzoic acid, codeine....
Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis arises from the reorientation bases in nanopore constriction. Such results detectable changes electrostatic potential at electrodes capacitor and drift strand under an oscillating transmembrane bias. A strategy is suggested for sequencing using electric field alternates periodically time.
Computational techniques have the potential to accelerate design and optimization of nanomaterials for applications such as drug delivery contaminant removal; however, success requires reliable models nanomaterial surfaces well accurate descriptions their interactions with relevant solutes. In present work, we evaluate ability selected naked hydroxylated carbon nanotubes predict adsorption equilibrium constants about 30 small aromatic compounds a variety functional groups. The determined...
It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results such measurements and improve sequence detection method, we have developed computational approach that both atomic-scale accuracy efficiency required predict sequence-specific differences nanopore current. In our Brownian dynamics interaction between ions is described...
PAMAM dendrimers have been widely studied as a novel means for controlled drug delivery; however, computational study of dendrimer-drug complexation is made difficult by the conformational flexibility and nonspecific nature interactions. Conventional protocols studying binding designed primarily protein substrates, and, therefore, there need to establish new deal with unique aspects dendrimers. In this work, we generate cavities in generation-5 polyamidoamine (PAMAM) at selected distances...
The extraction of membrane proteins from their native environment by detergents is central to biophysical characterization. Recent studies have emphasized that may perturb the structure locally and modify dynamics proteins. However, it remains challenging determine whether these perturbations are negligible or could be responsible for misfolded conformations, altering protein's function. In this work, we propose an original strategy combining functional molecular simulations address...
Calculating transition rates and other kinetic quantities from molecular simulations requires knowledge not only of the free energy along relevant coordinate but also diffusivity as a function that coordinate. A variety methods are currently used to map free-energy landscape in simulations; however, simultaneous calculation position-dependent is complicated by biasing forces applied with many these methods. Here, we describe method calculate diffusivities including known time-dependent...
From the most powerful supercomputers to multicore desktops and laptops, parallel computing architectures have been in mainstream for some time. However, numerical schemes calculating free energies molecular systems that directly leverage this hardware paradigm, usually taking form of multiple-replica strategies, are just now on cusp becoming standard practice. Here, we present a modification popular dynamics program NAMD is envisioned facilitate use strategies improve ergodic sampling...
Abstract Within the solubility–diffusion model of passive membrane permeation small molecules, translocation permeant across biological is traditionally assumed to obey Smoluchowski diffusion equation, which germane for classical on an inhomogeneous free-energy and diffusivity landscape. This however, cannot accommodate subdiffusive regimes, have long been recognized in lipid bilayer dynamics, notably lateral individual lipids. Through extensive biased unbiased molecular dynamics...
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) has been recognized as an important activator of certain transient receptor potential (TRP) channels. More specifically, TRPV1 is a pain activated by wide range stimuli. However, whether or not PI(4,5)P2 agonist remains open to debate. Utilizing combined approach mutagenesis and molecular modeling, we identified binding site located between the TRP box S4-S5 linker. At this site, interacts with amino acid residues Arg-575 Arg-579 in linker...
Hydration layers are formed on hydrophilic crystalline surfaces immersed in water.
It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using nanopore, smaller in diameter than the double helix, solid-state membrane. By applying an electric force larger threshold for stretching, dsDNA can be impelled through pore. Once current blockade associated with translocating detected, field pore switched interval less translocation time value below stretching. According molecular dynamics (MD) simulations, this leaves stretched...
Calculations of lipid bilayer permeabilities from first principles, using molecular simulations, would be valuable to rapidly assess the bioavailability drug candidates, as well decipher, at atomic level, mechanisms that underlie translocation permeants. The most common theoretical approach, solubility-diffusion model, requires determination free energy and diffusivity functions position permeant. Quantitative predictions permeability have, however, been stymied by acute difficulties in...
We investigated two critical aspects of rose Bengal (RB) photosensitized protein cross-linking that may underlie recently developed medical applications. Our studies focused on the binding RB to collagen by physical interaction and effect this certain amino acids photochemistry. Molecular dynamics simulations free-energy calculation techniques, complemented with isothermal titration calorimetry, provided insight into between a collagen-like peptide (CLP) at atomic level. Electrostatic...
We studied the interaction of four new pentapeptides with spherical silver nanoparticles. Our findings indicate that combination thiol in Cys and amines Lys/Arg residues is critical to providing stable protection for surface. Molecular simulation reveals atomic scale interactions underlie observed stabilizing effect these peptides, while yielding qualitative agreement experiment ranking affinity
Adsorption of organic molecules from aqueous solution to the surface carbon nanotubes or graphene is an important process in many applications these materials. Here we use molecular dynamics simulation, supplemented by analytical chemistry, explore detail adsorption thermodynamics a diverse set aromatic compounds on graphenic materials, elucidating effects solvent, coverage, curvature, defects, and functionalization hydroxy groups. We decompose free energies into entropic enthalpic...
Ultrasound has emerged as a promising means to effect controlled delivery of therapeutic agents through cell membranes. One possible mechanism that explains the enhanced permeability lipid bilayers is fast contraction cavitation bubbles produced on membrane surface, thereby generating large impulses, which, in turn, enhance bilayer small molecules. In present contribution, we investigate collapse different diameters, using atomistic and coarse-grained molecular dynamics simulations calculate...