Marc R Knecht

University of Miami, كورال غيبلز، فلوريدا, Florida, United States

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Publications (75)440.78 Total impact

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    ABSTRACT: Two-photon initiated photo-isomerization of an azobenzene moiety adsorbed on silver nanoparticles (Ag NPs) is demonstrated. The azobenzene is linked to a materials-binding peptide that brings it into intimate contact with the Ag NP surface, producing a dramatic enhancement of its two-photon absorbance. An integrated modeling approach, combining advanced conformational sampling with Quantum Mechanics/Capacitance Molecular Mechanics and response theory, shows that charge transfer and image charges in the Ag NP generate local fields that enhance two-photon absorption of the cis isomer, but not the trans isomer, of adsorbed molecules. Moreover, dramatic local field enhancement is expected near the localized surface plasmon resonance (LSPR) wavelength, and the LSPR band of the Ag NPs overlaps the azobenzene absorbance that triggers cis to trans switching. As a result, the Ag NPs enable two-photon initiated cis to trans isomerization, but not trans to cis isomerization. Confocal anti-Stokes fluorescence imaging shows that this effect is not due to local heating, while the quadratic dependence of switching rate on laser intensity is consistent with a two-photon process. Highly localized two-photon initiated switching could allow local manipulation near the focal point of a laser within a 3D nanoparticle assembly, which cannot be achieved using linear optical processes.
    Full-text · Article · Jan 2016 · Nanoscale
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    ABSTRACT: Photoresponsive molecules that incorporate peptides capable of material specific recognition provide a basis for biomolecule-mediated control of the nucleation, growth, organization, and activation of hybrid inorganic/organic nanostructures. These hybrid molecules interact with the inorganic surface through multiple noncovalent interactions which allow reconfiguration in response to optical stimuli. Here we quantify the binding of azobenzene-peptide conjugates that exhibit optically triggered cis-trans isomerization on Ag surfaces and compare to their behavior on Au. These results demonstrate differences in binding and switching behavior between the Au and Ag surfaces. These molecules can also produce and stabilize Au and Ag nanoparticles in aqueous media where the biointerface can be reproducibly and reversibly switched by optically-triggered azobenzene isomerization. Comparisons of switching rates and reversibility on the nanoparticles reveal differences that depend upon whether the azobenzene is attached at the peptide N- or C-terminus, its isomerization state, and the nanoparticle composition. Our integrated experimental and computational investigation shows that the number of ligand anchor sites strongly influences the nanoparticle size. As predicted by our molecular simulations, weaker contact between the hybrid biomolecules and the Ag surface, with fewer anchor residues compared with Au, gives rise to differences in switching kinetics on Ag vs. Au. Our findings provide a pathway toward achieving new remotely actuatable nanomaterials for multiple applications from a single system, which remains difficult to achieve using conventional approaches.
    Full-text · Article · Dec 2015 · ACS Applied Materials & Interfaces
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    ABSTRACT: Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.
    No preview · Article · Dec 2015 · Journal of the American Chemical Society
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    ABSTRACT: Bio-inspired approaches for the formation of metallic nanomaterials have been extensively employed for a diverse range of applications including diagnostics and catalysis. These materials can often be used under sustainable conditions; however, it is challenging to control the material size, morphology, and composition simultaneously. Here we have employed the R5 peptide that forms a 3D scaffold to direct the size and linear shape of bimetallic PdAu nanomaterials for catalysis. The materials were prepared at varying Pd:Au ratios to probe optimal compositions to achieve maximal catalytic efficiency. These materials were extensively characterized at the atomic level using transmission electron microscopy, extended X-ray absorption fine structure spectroscopy, and atomic pair distribution function analysis derived from high-energy X-ray diffraction patterns to provide highly resolved structural information. The results confirmed PdAu alloy formation, but also demonstrated that significant surface structural disorder was present. The catalytic activity of the materials was studied for olefin hydrogenation, which demonstrated enhanced reactivity from the bimetallic structures. These results present a pathway to the bio-inspired production of multimetallic materials with enhanced properties, which can be assessed via a suite of characterization methods to fully ascertain structure/function relationships.
    No preview · Article · Oct 2015 · ACS Nano
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    ABSTRACT: Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins ( SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.
    No preview · Article · Sep 2015 · IEEE/ACM Transactions on Computational Biology and Bioinformatics
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    ABSTRACT: C-C coupling reactions are of great importance in the synthesis of numerous organic compounds, where Pd nanoparticle catalyzed systems represent new materials to efficiently drive these reactions. Despite their pervasive utility, the catalytic mechanism of these particle-based reactions remains highly contested. Herein we present evidence of an atom leaching mechanism for Stille coupling under aqueous conditions using peptide-capped Pd nanoparticles. EXAFS analysis revealed Pd coordination changes in the nanoparticle consistent with Pd atom abstraction, where sizing analysis by SAXS confirmed particle size changes associated with a leaching process. It is likely that recently discovered highly disordered surface Pd atoms are the favored catalytic active sites and are leached during oxidative addition, resulting in smaller particles. Probing the mechanism of nanoparticle-driven C-C coupling reactions through structural analyses provides fundamental information concerning these active sites and their reactivity at the atomic-scale, which can be used to improve catalytic performance to meet important sustainability goals.
    Full-text · Article · Jul 2015 · Chemical Science
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    ABSTRACT: Bio-molecular non-covalent interactions provide a powerful platform for material-specific self-organization in aqueous media. Here, we introduce a strategy that integrates a synthetic optically-responsive motif with a materials-binding peptide to enable remote actuation. Specifically, we linked a photoswitchable azobenzene moiety to either terminus of a Au-binding peptide. We employed these hybrid molecules as capping agents for synthesis of Au nanoparticles. Integrated experiments and molecular simulations showed that the hybrid molecules maintained both of their functions, i.e. binding to Au and optically-triggered reconfiguration. The azobenzene unit was optically switched reversibly between trans and cis states while adsorbed on the particle surface. Upon switching, the conformation of the peptide component of the molecule also changed. This highlights the interplay between the surface adsorption and conformational switching that will be pivotal to the creation of actuatable nanoparticle bio-interfaces, and paves way toward multifunctional peptide hybrids that can produce stimuli responsive nanoassemblies.
    Full-text · Article · Jul 2015 · Nanoscale
  • Dennis B. Pacardo · Marc R. Knecht

    No preview · Article · Jun 2015 · ChemInform
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    ABSTRACT: We report a synthetic approach to form octahedral Cu2O microcrystals with a tunable edge length and demonstrate their use as catalysts for the photodegradation of aromatic organic compounds. In this particular study, the effects of the Cu2+ and reductant concentrations and stoichiometric ratios were carefully examined to identify their roles in controlling the final material composition and size under sustainable reaction conditions. Varying the ratio and concentrations of Cu2+ and reductant added during the synthesis determined the final morphology and composition of the structures. Octahedral particles were prepared at selected ratios of Cu2+:glucose that demonstrated a range of photocatalytic reactivity. The results indicate that material composition, surface area, and substrate charge effects play important roles in controlling the overall reaction rate. Additionally, analysis of the post-reacted materials revealed photocorrosion was inhibited and that surface etching had preferentially occurred at the particle edges during the reaction, suggesting that the reaction predominately occurred at these interfaces. Such results advance the understanding of how size and composition affect the surface interface and catalytic functionality of materials.
    No preview · Article · May 2015 · ACS Applied Materials & Interfaces
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    ABSTRACT: Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information correlating peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach was used to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through the rational tailoring of peptide sequences.
    No preview · Article · Apr 2015 · ACS Nano
  • Beverly D Briggs · Yue Li · Mark T Swihart · Marc R Knecht
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    ABSTRACT: The use of peptides as capping ligands for materials synthesis has been widely explored. The ambient conditions of bio-inspired syntheses using molecules such as peptides represent an attractive route for controlling the morphology and activity of nanomaterials. Although various reductants can be used in such syntheses, no comprehensive comparison of the same bio-based ligand with different reductants has been reported. In this contribution, peptides AuBP1, AuBP2 and Pd4 are used in the synthesis of Au nanoparticles. The reductant strength is varied by using three different reducing agents: NaBH4, hydrazine, and ascorbic acid. These changes in reductant produce significant morphological differences in the final particles. The weakest reductant, ascorbic acid, yields large, globular nanoparticles with rough surfaces, while the strongest reductant, NaBH4, yields small, spherical and smooth nanomaterials. Studies of 4-nitrophenol reduction using the Au nanoparticles as catalysts reveal a decrease in activation energy for the large, globular, rough materials relative to the small, spherical, smooth materials. These studies demonstrate that modifying the reductant is a simple way to control the activity of peptide-capped nanoparticles.
    No preview · Article · Apr 2015 · ACS Applied Materials & Interfaces
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    ABSTRACT: Controllable 3D assembly of multicomponent inorganic nanomaterials by precisely positioning two or more types of nanoparticles to modulate their interactions and achieve multifunctionality remains a major challenge. The diverse chemical and structural features of biomolecules can generate the compositionally specific organic/inorganic interactions needed to create such assemblies. Toward this aim, we studied the materials-specific binding of peptides selected based upon affinity for Ag (AgBP1 and AgBP2) and Au (AuBP1 and AuBP2) surfaces, combining experimental binding measurements, advanced molecular simulation, and nanomaterial synthesis. This reveals, for the first time, different modes of binding on the chemically similar Au and Ag surfaces. Molecular simulations showed flatter configurations on Au and a greater variety of 3D adsorbed conformations on Ag, reflecting primarily enthalpically driven binding on Au and entropically driven binding on Ag. This may arise from differences in the interfacial solvent structure. On Au, direct interaction of peptide residues with the metal surface is dominant, while on Ag, solvent-mediated interactions are more important. Experimentally, AgBP1 is found to be selective for Ag over Au, while the other sequences have strong and comparable affinities for both surfaces, despite differences in binding modes. Finally, we show for the first time the impact of these differences on peptide mediated synthesis of nanoparticles, leading to significant variation in particle morphology, size, and aggregation state. Because the degree of contact with the metal surface affects the peptides ability to cap the nanoparticles and thereby control growth and aggregation, the peptides with the least direct contact (AgBP1 and AgBP2 on Ag) produced relatively polydispersed and aggregated nanoparticles. Overall, we show that thermodynamically different binding modes at metallic interfaces can enable selective binding on very similar inorganic surfaces and can provide control over nanoparticle nucleation and growth. This supports the promise of bionanocombinatoric approaches that rely upon materials recognition.
    No preview · Article · Sep 2014 · Chemistry of Materials
  • Beverly D. Briggs · Ryan T. Pekarek · Marc R. Knecht
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    ABSTRACT: Carbon carbon (C-C) coupling reactions are ubiquitously used for the generation of advanced chemical species; however, this reactivity remains inefficient and energy intensive. Transitioning such systems toward more sustainable and green conditions would be ideal where Pd nanoparticles represent unique catalysts to achieve this goal. In this contribution, we demonstrate the use of peptide-capped Pd nanoparticles as catalysts for driving Suzuki C-C coupling, focusing specifically on the effects of the transmetalation step in controlling the reactivity. These materials achieved C-C bond formation in water at room temperature using low Pd loadings. Coupling across a variety of mono- and disubstituted substrates was studied, where the reactivity was dependent upon the halogen moiety. Furthermore, studies of the reaction conditions revealed a strong sensitivity to the base identity, suggesting that competing transmetalation pathways and reaction equilibrium effects lead to variations in Suzuki coupling yields. Based on these results, and in comparison to the Stille coupling reactivity of the same materials, it is suggested that the transmetalation step is important in controlling the overall C-C coupling process. This evidence is significant for nanocatalysts to optimize reactivity under sustainable conditions.
    No preview · Article · Aug 2014 · The Journal of Physical Chemistry C
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    ABSTRACT: Peptide-driven nanomaterials synthesis and assembly has become a significant research thrust due to the capability to generate a range of multifunctional materials with high spatial precision and tunable properties. Despite the extensive amount of available literature, the majority of studies report the use of free peptides to drive synthesis and assembly. Such strategies are not an entirely accurate representation of nature, as many materials binding peptides found in biological systems are sterically constrained to a larger biological motif. Herein we report the synthesis of catalytic Pd nanomaterials using constrained peptides covalently attached to the surface of small, water-soluble dendrimers. Using the R5 peptide conjugated to polyamidoamine dendrimer as a bioconjugate, Pd nanomaterials were generated that displayed altered morphologies compared to nanomaterials templated with free R5. It was discovered that the peptide surface density on the dendrimer affected the resulting nanoscale morphology. Furthermore, the catalytic activities of Pd materials templated with R5/dendrimer are higher as compared to the R5-templated Pd materials for the hydrogenation of allyl alcohol, with an average increase in turnover frequency of ∼1500 mol product (mol Pd × h)−1. Small angle X-ray scattering analysis and dynamic light scattering indicate that Pd derived from R5/dendrimer templates remained less aggregated in solution and displayed more available reactive Pd surface area. Such morphological changes in solution are attributed to the constrained peptide binding motifs, which altered the Pd morphology and subsequent properties. Moreover, the results of this study suggest that constrained materials binding peptide systems can be employed as a means to alter morphology and improve resulting properties.
    No preview · Article · Jul 2014 · Chemistry of Materials
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    ABSTRACT: Adsorption of small biomolecules onto the surface of nanoparticles offers a novel route to the generation of nanoparticle assemblies with predictable architectures. Previously, ligand exchange experiments on citrate-capped gold nanoparticles with the amino acid arginine were reported to support linear nanoparticle assemblies. Here, we use a combination of atomistic modelling with experimental characterization to explore aspects of the assembly hypothesis for these systems. Using molecular simulation, we probe the structural and energetic characteristics of arginine overlayers on the Au(111) surface under aqueous conditions, at both low and high coverage regimes. In the low density regime, the arginines lie flat on the surface. At constant composition, these overlayers are found to be lower in energy than the densely-packed films, although the latter case appears kinetically stable when arginine is adsorbed via the zwitterion group, exposing the charged guanidinium group to the solvent. Our findings suggest that zwitterion-zwitterion hydrogen-bonding at the gold surface, and minimization of the electrostatic repulsion between adjacent guanidinium groups, play key roles in determining arginine overlayer stability at the aqueous gold interface. Ligand-exchange experiments of citrate-capped gold nanoparticles with arginine derivatives agmatine and N-methyl-L-arginine reveal that modification at the guanidinium group significantly diminishes the propensity for linear assembly of the nanoparticles.
    No preview · Article · Jun 2014 · ACS Applied Materials & Interfaces
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    ABSTRACT: Biomimetic nanotechnologies that use peptides to guide the growth and assembly of nanostructures offer new avenues for the creation of functional nanomaterials and manipulation of their physicochemical properties. However, the impacts of peptide sequence and binding motif upon the surface characteristics and physicochemical properties of nanoparticles remain poorly understood. The configurations of the biomolecules are expected to be extremely important for directing the synthesis and achieving desired material functionality, and these binding motifs will vary with the peptide sequence. Here, we have prepared a series of Au nanoparticles capped with a variety of materials-directing peptides with known affinity for metal surfaces. These nanomaterials were characterized by UV-vis and circular dichroism spectroscopies, transmission electron microscopy, and ζ-potential measurement. Then their catalytic activity for 4-nitrophenol reduction was analyzed. The results indicate that substantially different Au-peptide interfaces are generated using different peptide sequences, even when these sequences have similar binding affinity. This is consistent with recent work showing that Au-peptide binding affinity can have varying entropic and enthalpic contributions, with enthalpically- and entropically-driven binders exhibiting quite different ensembles of configurations on the Au surface. The catalytic activity, as reflected by the measured activation energy, did not correlate with the particle size or with the binding affinity of the peptides, suggesting that the reactivity of these materials is governed by the more subtle details of the conformation of the bound peptide and on the nanoparticle surface reconstruction as dictated by the peptide structure. Such variations in both nanoparticle surface reconstruction and peptide configuration could potentially be used to program specific functionality into the peptide-capped nanomaterials.
    Preview · Article · Feb 2014 · Nanoscale
  • Dennis B. Pacardo · Eric Ardman · Marc R. Knecht
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    ABSTRACT: Advancing catalytic processes toward sustainable conditions is necessary to maintain current production levels in light of dwindling natural resources. Nanomaterial-based catalysts have been suggested as a possible route to achieve this goal; however, the effects of particle structure on the reaction remain unclear. Furthermore, for each reaction, different substrates are likely to be used that vary the molecular size, functional group composition, and reactive moiety site that could significantly alter the reactivity of nanomaterial-based catalysts. In this contribution, we have studied the effects of the molecular substrate structure on the reactivity of peptide-templated Pd nanomaterials with selectable morphologies. In this regard, spherical, ribbon-like, and networked metallic nanomaterials were studied that demonstrated significant degrees of reactivity of olefin hydrogenation using the substrates that varied the molecular size and reactive group position. The results demonstrated that substrate isomerization, rather than molecular structure, plays a significant role in attenuating the reactivity of the materials. Furthermore, the Pd structures demonstrated the ability to drive multistep reactivity for the complete hydrogenation of substrates with multiple reactive groups. Such results advance the structure/function relationship of nanocatalysis that could be important in addressing future sustainability goals.
    No preview · Article · Jan 2014 · The Journal of Physical Chemistry C
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    ABSTRACT: Transitioning energy-intensive and environmentally intensive processes toward sustainable conditions is necessary in light of the current global condition. To this end, photocatalytic processes represent new approaches for H2 generation; however, their application toward tandem catalytic reactivity remains challenging. Here, we demonstrate that metal oxide materials decorated with noble metal nanoparticles advance visible light photocatalytic activity toward new reactions not typically driven by light. For this, Pd nanoparticles were deposited onto Cu2O cubes to generate a composite structure. Once characterized, their hydrodehalogenation activity was studied via the reductive dechlorination of polychlorinated biphenyls. To this end, tandem catalytic reactivity was observed with H2 generation via H2O reduction at the Cu2O surface, followed by dehalogenation at the Pd using the in situ generated H2. Such results present methods to achieve sustainable catalytic technologies by advancing photocatalytic approaches toward new reaction systems.
    Full-text · Article · Jan 2014 · Journal of the American Chemical Society
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    ABSTRACT: Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.
    No preview · Article · Oct 2013 · ACS Nano
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    ABSTRACT: With the rapid development of bionanotechnology, there has been a growing interest recently in identifying the affinity classes of the inorganic materials binding peptide sequences. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on our new amino acid transition matrix, and then the probability of test sequences belonging to a specific affinity class is calculated through solving an objective function. In addition, the objective function is solved through iterative propagation of probability estimates among sequences and sequence clusters. Experimental results on a real inorganic material binding sequence dataset show that the proposed framework is highly effective on identifying the affinity classes of inorganic material binding sequences.
    No preview · Conference Paper · Sep 2013

Publication Stats

2k Citations
440.78 Total Impact Points


  • 2011-2015
    • University of Miami
      • Department of Chemistry
      كورال غيبلز، فلوريدا, Florida, United States
  • 2008-2011
    • University of Kentucky
      • Department of Chemistry
      Lexington, Kentucky, United States
  • 2006-2009
    • University of Texas at Austin
      • • Department of Chemistry and Biochemistry
      • • Center for Nano- and Molecular Science and Technology
      Austin, Texas, United States
    • Texas A&M University
      • Department of Chemistry
      College Station, Texas, United States
  • 2003-2005
    • Vanderbilt University
      • Department of Chemistry
      Нашвилл, Michigan, United States