Scholars@Duke
Gaurav Arya

Gaurav Arya

Professor in the Thomas Lord Department of Mechanical Engineering and Materials Science
Thomas Lord Department of Mechanical Engineering and Materials Science
gaurav.arya@duke.edu
3383 Fitzpatrick Center (CIEMAS), Duke University, Durham, NC 27708
144 Hudson Hall, Box 90300, Duke University, Durham, NC 27708
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Selected Publications

Piggybacking functionalized DNA nanostructures into live-cell nuclei.

Journal Article Science advances · July 2024 DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches ... Full text Cite

Self-assembly of nanocrystal checkerboard patterns via non-specific interactions.

Journal Article Nature communications · May 2024 Checkerboard lattices-where the resulting structure is open, porous, and highly symmetric-are difficult to create by self-assembly. Synthetic systems that adopt such structures typically rely on shape complementarity and site-specific chemical interactions ... Full text Cite

Mechanism of DNA origami folding elucidated by mesoscopic simulations.

Journal Article Nature communications · April 2024 Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the beh ... Full text Cite

A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids.

Journal Article Angewandte Chemie (International ed. in English) · March 2024 Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay ... Full text Cite

Prediction and Control in DNA Nanotechnology.

Journal Article ACS applied bio materials · February 2024 DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeli ... Full text Cite

Controlling Silicification on DNA Origami with Polynucleotide Brushes.

Journal Article Journal of the American Chemical Society · January 2024 DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However ... Full text Cite

Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets.

Journal Article Current biology : CB · December 2023 Microtubules in cells consist of functionally diverse subpopulations carrying distinct post-translational modifications (PTMs). Akin to the histone code, the tubulin code regulates a myriad of microtubule functions, ranging from intracellular transport to ... Full text Cite

Many-body potential for simulating the self-assembly of polymer-grafted nanoparticles in a polymer matrix

Journal Article npj Computational Materials · December 1, 2023 Many-body interactions between polymer-grafted nanoparticles (NPs) play a key role in promoting their assembly into low-dimensional structures within polymer melts, even when the particles are spherical and isotropically grafted. However, capturing such in ... Full text Cite

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures.

Journal Article Angewandte Chemie (International ed. in English) · November 2023 DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucle ... Full text Cite

Versatile computer-aided design of free-form DNA nanostructures and assemblies.

Journal Article Science advances · July 2023 Featured Publication Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables ... Full text Cite

Steric Communication between Dynamic Components on DNA Nanodevices.

Journal Article ACS nano · May 2023 Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex ... Full text Cite

Thermally reversible pattern formation in arrays of molecular rotors.

Journal Article Nanoscale · May 2023 Control over the mesoscale to microscale patterning of materials is of great interest to the soft matter community. Inspired by DNA origami rotors, we introduce a 2D nearest-neighbor lattice of spinning rotors that exhibit discrete orientational states and ... Full text Cite

Discovery of two-dimensional binary nanoparticle superlattices using global Monte Carlo optimization.

Journal Article Nature communications · December 2022 Featured Publication Binary nanoparticle (NP) superlattices exhibit distinct collective plasmonic, magnetic, optical, and electronic properties. Here, we computationally demonstrate how fluid-fluid interfaces could be used to self-assemble binary systems of NPs into 2D superla ... Full text Cite

Influence of Polymer Characteristics on the Self-Assembly of Polymer-Grafted Metal-Organic Framework Particles.

Journal Article ACS nano · November 2022 Polymer-grafted metal-organic frameworks (MOFs) can combine the properties of MOFs and polymers into a single, matrix-free composite material. Herein, we examine polymer-grafted MOF particles (using UiO-66 as a model system) to examine how the molecular we ... Full text Cite

A bistable and reconfigurable molecular system with encodable bonds.

Journal Article Science advances · November 2022 Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two d ... Full text Cite

Piggybacking functionalized DNA nanostructures into live-cell nuclei.

Journal Article Science advances · July 2024 DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches ... Full text Cite

Self-assembly of nanocrystal checkerboard patterns via non-specific interactions.

Journal Article Nature communications · May 2024 Checkerboard lattices-where the resulting structure is open, porous, and highly symmetric-are difficult to create by self-assembly. Synthetic systems that adopt such structures typically rely on shape complementarity and site-specific chemical interactions ... Full text Cite

Mechanism of DNA origami folding elucidated by mesoscopic simulations.

Journal Article Nature communications · April 2024 Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the beh ... Full text Cite

A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids.

Journal Article Angewandte Chemie (International ed. in English) · March 2024 Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay ... Full text Cite

Prediction and Control in DNA Nanotechnology.

Journal Article ACS applied bio materials · February 2024 DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeli ... Full text Cite

Controlling Silicification on DNA Origami with Polynucleotide Brushes.

Journal Article Journal of the American Chemical Society · January 2024 DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However ... Full text Cite

Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets.

Journal Article Current biology : CB · December 2023 Microtubules in cells consist of functionally diverse subpopulations carrying distinct post-translational modifications (PTMs). Akin to the histone code, the tubulin code regulates a myriad of microtubule functions, ranging from intracellular transport to ... Full text Cite

Many-body potential for simulating the self-assembly of polymer-grafted nanoparticles in a polymer matrix

Journal Article npj Computational Materials · December 1, 2023 Many-body interactions between polymer-grafted nanoparticles (NPs) play a key role in promoting their assembly into low-dimensional structures within polymer melts, even when the particles are spherical and isotropically grafted. However, capturing such in ... Full text Cite

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures.

Journal Article Angewandte Chemie (International ed. in English) · November 2023 DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucle ... Full text Cite

Versatile computer-aided design of free-form DNA nanostructures and assemblies.

Journal Article Science advances · July 2023 Featured Publication Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables ... Full text Cite

Steric Communication between Dynamic Components on DNA Nanodevices.

Journal Article ACS nano · May 2023 Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex ... Full text Cite

Thermally reversible pattern formation in arrays of molecular rotors.

Journal Article Nanoscale · May 2023 Control over the mesoscale to microscale patterning of materials is of great interest to the soft matter community. Inspired by DNA origami rotors, we introduce a 2D nearest-neighbor lattice of spinning rotors that exhibit discrete orientational states and ... Full text Cite

Discovery of two-dimensional binary nanoparticle superlattices using global Monte Carlo optimization.

Journal Article Nature communications · December 2022 Featured Publication Binary nanoparticle (NP) superlattices exhibit distinct collective plasmonic, magnetic, optical, and electronic properties. Here, we computationally demonstrate how fluid-fluid interfaces could be used to self-assemble binary systems of NPs into 2D superla ... Full text Cite

Influence of Polymer Characteristics on the Self-Assembly of Polymer-Grafted Metal-Organic Framework Particles.

Journal Article ACS nano · November 2022 Polymer-grafted metal-organic frameworks (MOFs) can combine the properties of MOFs and polymers into a single, matrix-free composite material. Herein, we examine polymer-grafted MOF particles (using UiO-66 as a model system) to examine how the molecular we ... Full text Cite

A bistable and reconfigurable molecular system with encodable bonds.

Journal Article Science advances · November 2022 Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two d ... Full text Cite

Molecular dynamics of DNA translocation by FtsK.

Journal Article Nucleic acids research · August 2022 The bacterial FtsK motor harvests energy from ATP to translocate double-stranded DNA during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA translocation in FtsK by performing long timescale simulations of its hexameric as ... Full text Cite

Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.

Journal Article Cell Rep · May 24, 2022 Protein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Within its non-proteolytic functions, we showed that K63-linked polyubiquitinated conjugates heavily accumulate in yeast ce ... Full text Link to item Cite

Tunable Orientation and Assembly of Polymer-Grafted Nanocubes at Fluid-Fluid Interfaces.

Journal Article ACS nano · May 2022 Self-assembly of faceted nanoparticles is a promising route for fabricating nanomaterials; however, achieving low-dimensional assemblies of particles with tunable orientations is challenging. Here, we demonstrate that trapping surface-functionalized facete ... Full text Cite

Binding kinetics of harmonically confined random walkers.

Journal Article Physical review. E · April 2022 Diffusion-mediated binding of molecules under the influence of discrete spatially confining potentials is a commonly encountered scenario in systems subjected to explicit fields or implicit fields arising from tethering restraints. Here, we derive analytic ... Full text Cite

Assembly mechanism of surface-functionalized nanocubes.

Journal Article Nanoscale · March 2022 Faceted nanoparticles can be used as building blocks to assemble nanomaterials with exceptional optical and catalytic properties. Recent studies have shown that surface functionalization of such nanoparticles with organic molecules, polymer chains, or DNA ... Full text Cite

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes.

Journal Article Angewandte Chemie (International ed. in English) · October 2021 Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide br ... Full text Cite

Reconfigurable Chirality of DNA-Bridged Nanorod Dimers.

Journal Article ACS nano · August 2021 Featured Publication Gold nanorods assembled in a side-by-side chiral configuration have potential applications in sensing due to their strong chiroptical surface plasmon resonances. Recent experiments have shown that dimers of gold nanorods bridged by double-stranded DNA exhi ... Full text Cite

Microengineered Materials with Self‐Healing Features for Soft Robotics

Journal Article Advanced Intelligent Systems · July 2021 Recent advancements in soft robotics have led to the development of compliant robots that can exhibit complex motions driven by living cells, chemical reactions, or electronics. Further innovations are, however, needed to cr ... Full text Cite

Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor.

Journal Article Nucleic acids research · June 2021 Featured Publication Double-stranded DNA viruses package their genomes into pre-assembled capsids using virally-encoded ASCE ATPase ring motors. We present the first atomic-resolution crystal structure of a multimeric ring form of a viral dsDNA packaging motor, the ATPase of t ... Full text Cite

A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA.

Journal Article Science advances · May 2021 Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible ... Full text Cite

Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · April 2021 Featured Publication Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. H ... Full text Cite

Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units.

Journal Article Journal of the American Chemical Society · February 2021 Dynamic DNA origami has been employed for generating a rich repository of molecular nanomachines that are capable of sensing various cues and changing their conformations accordingly. The common design principle of the existing DNA origami nanomachines is ... Full text Cite

Analytical van der Waals interaction potential for faceted nanoparticles.

Journal Article Nanoscale horizons · December 2020 Featured Publication Our ability to synthesize faceted nanoparticles of tunable shapes and sizes has opened up many intriguing applications of such particles. However, our progress in understanding, modeling, and simulating their collective rheology, phase behavior, and self-a ... Full text Cite

Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.

Journal Article Methods (San Diego, Calif.) · October 2020 Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived f ... Full text Cite

Anharmonic lattice dynamics and superionic transition in AgCrSe 2

Journal Article Proceedings of the National Academy of Sciences · February 25, 2020 Significance Unveiling the unusual atomic dynamics in superionic conductors is critical for the design of energy conversion and storage materials, for example to rationalize their thermal transport pr ... Full text Open Access Cite

Dynamic DNA nanotechnology: Toward functional nanoscale devices

Journal Article Nanoscale Horizons · February 1, 2020 Featured Publication Dynamic DNA nanotechnology involves the creation of nanoscale devices made of DNA whose primary function arises from their ability to undergo controlled motion or reconfiguration. In the past two decades, dynamic DNA nanotechnology has evolved to the point ... Full text Cite

Kinetically assembled binary nanoparticle networks.

Journal Article Nanoscale · February 2020 Embedding percolating networks of nanoparticles (NPs) within polymers is a promising approach for mechanically reinforcing polymers and for introducing novel electronic, transport, and catalytic properties into otherwise inert polymers. While such networks ... Full text Cite

Free energy landscape of salt-actuated reconfigurable DNA nanodevices.

Journal Article Nucleic acids research · January 2020 Achieving rapid, noninvasive actuation of DNA structures is critical to expanding the functionality of DNA nanotechnology. A promising actuation approach involves introducing multiple, short pairs of single-stranded DNA overhangs to components of the struc ... Full text Cite

Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.

Journal Article Journal of molecular biology · November 2019 Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. M ... Full text Cite

Orientational phase behavior of polymer-grafted nanocubes.

Journal Article Nanoscale · August 2019 Surface functionalization of nanoparticles with polymer grafts was recently shown to be a viable strategy for controlling the relative orientation of shaped nanoparticles in their higher-order assemblies. In this study, we investigated in silico the orient ... Full text Cite

Interfacial Assembly of Tunable Anisotropic Nanoparticle Architectures.

Journal Article ACS nano · April 2019 Featured Publication We propose a strategy for assembling spherical nanoparticles (NPs) into anisotropic architectures in a polymer matrix. The approach takes advantage of the interfacial tension between two mutually immiscible polymers forming a bilayer and differences in the ... Full text Cite

One-Dimensional Anomalous Diffusion of Gold Nanoparticles in a Polymer Melt.

Journal Article Physical review letters · March 2019 We investigated the dynamics of polymer-grafted gold nanoparticles loaded into polymer melts using x-ray photon correlation spectroscopy. For low molecular weight host matrix polymer chains, normal isotropic diffusion of the gold nanoparticles is observed. ... Full text Cite

Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor.

Journal Article Nucleic acids research · February 2019 ASCE ATPases include ring-translocases such as cellular helicases and viral DNA packaging motors (terminases). These motors have conserved Walker A and B motifs that bind Mg2+-ATP and a catalytic carboxylate that activates water for hydrolysis. Here we dem ... Full text Cite

Nanofiber-Based Total Internal Reflection Microscopy for Characterizing Colloidal Systems at the Microscale

Journal Article Journal of Physical Chemistry C · September 27, 2018 Bulk colloidal interactions are dictated by the physical properties of individual particles dispersed in solution. However, for many applications it remains challenging to predict system-level colloidal behavior. Comprehensive characterization typically re ... Full text Cite

Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices.

Journal Article ACS nano · September 2018 The ability to design and control DNA nanodevices with programmed conformational changes has established a foundation for molecular-scale robotics with applications in nanomanufacturing, drug delivery, and controlling enzymatic reactions. The most commonly ... Full text Cite

Colloidal Plasmonic Nanocomposites: From Fabrication to Optical Function.

Journal Article Chemical reviews · March 2018 Plasmonic nanostructures are extensively used building blocks for engineering optical materials and device architectures. Plasmonic nanocomposites (pNCs) are an emerging class of materials that integrate these nanostructures into hierarchical and often mul ... Full text Cite

Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α.

Journal Article Nature communications · January 2018 Featured Publication The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics ... Full text Cite

Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations.

Journal Article ACS nano · May 2017 Featured Publication Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. H ... Full text Cite

Anisotropic Three-Particle Interactions between Spherical Polymer-Grafted Nanoparticles in a Polymer Matrix

Journal Article Macromolecules · February 14, 2017 Spherical nanoparticles (NPs) uniformly grafted with polymer chains have recently been shown to assemble into anisotropic phases like strings and sheets. Here we investigated the underlying basis for anisotropic interactions between polymer-grafted NPs in ... Full text Cite

Modelling the morphology and thermomechanical behaviour of low-bandgap conjugated polymers and bulk heterojunction films

Journal Article Energy & Environmental Science · 2017 Schematic diagram showing the information flow from molecular structure, to atomistic model, to a slice of the solid morphology under mechanical deformation and the stress–strain response. ... Full text Cite

Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments

Journal Article Molecular Simulation · September 1, 2016 Single-molecule force spectroscopy is a powerful experimental technique for probing intermolecular forces and conformational transitions of individual molecules. This technique involves measuring the mechanical response of a molecule subjected to a constan ... Full text Cite

Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases.

Journal Article Journal of biomolecular structure & dynamics · May 2016 Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between bindi ... Full text Cite

Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations

Journal Article Macromolecules · April 26, 2016 The ability to predict the mechanical properties of organic semiconductors is of critical importance for roll-to-roll production and thermomechanical reliability of organic electronic devices. Here, we describe the use of coarse-grained molecular dynamics ... Full text Cite

Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes

Journal Article Physical Review E · March 10, 2016 The nucleosome represents the basic unit of eukaryotic genome organization, and its conformational fluctuations play a crucial role in various cellular processes. Here we provide insights into the flipping transition of a nucleosome by computing its free-e ... Full text Cite

Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites

Journal Article Physical Review E · February 18, 2016 Understanding how nanoparticles (NPs) diffuse, stick, and assemble into larger structures within polymers is key to the design and fabrication of NP-polymer composites. Here we describe an approach for inferring the dynamic parameters of NP assembly from s ... Full text Cite

Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals.

Journal Article Nano letters · February 2016 This article describes an effect based on the wetting transparency of graphene; the morphology of a metallic film (≤20 nm) when deposited on graphene by evaporation depends strongly on the identity of the substrate supporting the graphene. This control per ... Full text Open Access Cite

Quantification of DNA cleavage specificity in Hi-C experiments.

Journal Article Nucleic acids research · January 2016 Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonucleas ... Full text Open Access Cite

Molecular mechanical properties of short-sequence peptide enzyme mimics.

Journal Article Journal of biomolecular structure & dynamics · January 2016 While considerable attempts have been made to recreate the high turnover rates of enzymes using synthetic enzyme mimics, most have failed and only a few have produced minimal reaction rates that can barely be considered catalytic. One particular approach w ... Full text Cite

Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions.

Journal Article Nano letters · November 2015 The bottom-up fabrication of ordered and oriented colloidal nanoparticle assemblies is critical for engineering functional nanomaterials beyond conventional polymer-particle composites. Here, we probe the influence of polymer surface ligands on the self-or ... Full text Cite

Micromotor-based on-off fluorescence detection of sarin and soman simulants

Journal Article Chemical Communications · July 18, 2015 Self-propelled micromotor-based fluorescent "On-Off" detection of nerve agents is described. The motion-based assay utilizes Si/Pt Janus micromotors coated with fluoresceinamine toward real-time "on-the-fly" field detection of sarin and soman simulants. ... Full text Cite

Molecular Dynamics (MD) and Coarse Grain Simulation of High Strain-Rate Elastomeric Polymers (HSREP): Molecular and Coarse-Grained Methods for Microstructure-Property Relations in HSREP

Chapter · July 1, 2015 In this unique book, Elastomeric Polymers with High Rate Sensitivity, Dr. Roshdy Barsoum and expert contributors bring together the cutting-edge testing methodologies, material properties, and critical design data for engineers seeking to ... ... Cite

Automated quantitative image analysis of nanoparticle assembly

Journal Article Nanoscale · June 7, 2015 The ability to characterize higher-order structures formed by nanoparticle (NP) assembly is critical for predicting and engineering the properties of advanced nanocomposite materials. Here we develop a quantitative image analysis software to characterize k ... Full text Cite

Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations

Journal Article Macromolecules · February 24, 2015 To provide insights into how polymer-grafted nanoparticles (NPs) enhance the viscoelastic properties of polymers, we have computed the frequency-dependent storage and loss modulus of coarse-grained models of polymer nanocomposites by means of molecular dyn ... Full text Cite

Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains.

Journal Article Journal of physics. Condensed matter : an Institute of Physics journal · February 2015 The estimation of contact probabilities (CP) from conformations of simulated bead-chain polymer models is a key step in methods that aim to elucidate the spatial organization of chromatin from analysis of experimentally determined contacts between differen ... Full text Cite

Biomimetic Material-Assisted Delivery of Human Embryonic Stem Cell Derivatives for Enhanced In Vivo Survival and Engraftment.

Journal Article ACS Biomater Sci Eng · January 12, 2015 The ability of human embryonic stem cells (hESCs) and their derivatives to differentiate and contribute to tissue repair has enormous potential to treat various debilitating diseases. However, improving the in vivo viability and function of the transplante ... Full text Link to item Cite

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

Journal Article Journal of molecular biology · December 2014 Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA ... Full text Cite

Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes.

Journal Article Nucleic acids research · September 2014 Torsionally stressed DNA plays a critical role in genome organization and regulation. While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organizati ... Full text Open Access Cite

Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.

Journal Article Nature communications · June 2014 How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by ... Full text Open Access Cite

Simultaneous iterative boltzmann inversion for coarse-graining of polyurea

Journal Article Macromolecules · May 27, 2014 Polyurea is an alternating copolymer with excellent viscoelastic properties for dissipating shock and impact loads; however, a molecular-level understanding of how its chemistry relates to its performance remains elusive. While molecular dynamics simulatio ... Full text Cite

Evolutionary dynamics and information hierarchies in biological systems.

Journal Article Annals of the New York Academy of Sciences · December 2013 The study of evolution has entered a revolutionary new era, where quantitative and predictive methods are transforming the traditionally qualitative and retrospective approaches of the past. Genomic sequencing and modern computational techniques are permit ... Full text Cite

Recovering ensembles of chromatin conformations from contact probabilities.

Journal Article Nucleic acids research · January 2013 The 3D higher order organization of chromatin within the nucleus of eukaryotic cells has so far remained elusive. A wealth of relevant information, however, is increasingly becoming available from chromosome conformation capture (3C) and related experiment ... Full text Open Access Cite

Lattice animal model of chromosome organization

Journal Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics · July 12, 2012 Polymer models tied together by constraints of looping and confinement have been used to explain many of the observed organizational characteristics of interphase chromosomes. Here we introduce a simple lattice animal representation of interphase chromosom ... Full text Cite

Self-orienting nanocubes for the assembly of plasmonic nanojunctions.

Journal Article Nature nanotechnology · June 2012 Plasmonic hot spots are formed when metal surfaces with high curvature are separated by nanoscale gaps and an electromagnetic field is localized within the gaps. These hot spots are responsible for phenomena such as subwavelength focusing, surface-enhanced ... Full text Cite

Viscoelastic properties and shock response of coarse-grained models of multiblock versus diblock copolymers: Insights into dissipative properties of polyurea

Journal Article Macromolecules · April 10, 2012 We compare and contrast the microstructure, viscoelastic properties, and shock response of coarse-grained models of multiblock copolymer and diblock copolymers using molecular dynamics simulations. This study is motivated by the excellent dissipative and s ... Full text Cite

Rapid self-healing hydrogels.

Journal Article Proc Natl Acad Sci U S A · March 20, 2012 Synthetic materials that are capable of autonomous healing upon damage are being developed at a rapid pace because of their many potential applications. Despite these advancements, achieving self-healing in permanently cross-linked hydrogels has remained e ... Full text Link to item Cite

Computational prediction of efficient splice sites for trans-splicing ribozymes.

Journal Article RNA (New York, N.Y.) · March 2012 Group I introns have been engineered into trans-splicing ribozymes capable of replacing the 3'-terminal portion of an external mRNA with their own 3'-exon. Although this design makes trans-splicing ribozymes potentially useful for therapeutic application, ... Full text Cite

Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation.

Journal Article Biomaterials · May 2011 The effective utilization of stem cells in regenerative medicine critically relies upon our understanding of the intricate interactions between cells and their extracellular environment. While bulk mechanical and chemical properties of the matrix have been ... Full text Link to item Cite

Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations.

Journal Article BMC biophysics · April 2011 Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulati ... Full text Cite

Influence of pulling handles and device stiffness in single-molecule force spectroscopy.

Journal Article Physical chemistry chemical physics : PCCP · February 2011 In single-molecule force spectroscopy, individual molecules and complexes are often stretched by pulling devices via intervening molecular handles. Accurate interpretation of measurements from such experiments in terms of the underlying energy landscape, d ... Full text Cite

Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation.

Journal Article Physical chemistry chemical physics : PCCP · February 2011 The H4 histone tail plays a critical role in chromatin folding and regulation--it mediates strong interactions with the acidic patch of proximal nucleosomes and its acetylation at lysine 16 (K16) leads to partial unfolding of chromatin. The molecular mecha ... Full text Cite

Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture.

Journal Article Adv Funct Mater · January 7, 2011 Hydrogels have numerous biomedical applications including synthetic matrices for cell culture and tissue engineering. Here we report the development of hydrogel based multifunctional matrices that not only provide three-dimensional structural support to th ... Full text Link to item Cite

Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells.

Journal Article Biomacromolecules · December 13, 2010 Heparin and heparan sulfate mediated basic fibroblast growth factor (bFGF) signaling plays an important role in skeletal muscle homeostasis by maintaining a balance between proliferation and differentiation of muscle progenitor cells. In this study we inve ... Full text Link to item Cite

Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids.

Journal Article The journal of physical chemistry. B · December 2010 We report here the effects of chain stiffness and surface attachment on the effective interactions between polyelectrolyte-grafted colloidal particles in monovalent salt obtained using Monte Carlo simulations. Our approach involves computation of the dista ... Full text Cite

Twist propagation in dinucleosome arrays.

Journal Article Biophysical journal · November 2010 We present a Monte Carlo simulation study of the distribution and propagation of twist from one DNA linker to another for a two-nucleosome array subjected to externally applied twist. A mesoscopic model of the array that incorporates nucleosome geometry al ... Full text Cite

A structural perspective on the where, how, why, and what of nucleosome positioning.

Journal Article Journal of biomolecular structure & dynamics · June 2010 The DNA in eukaryotic chromatin is packed by histones into arrays of repeating units called nucleosomes. Each nucleosome contains a nucleosome core, where the DNA is wrapped around a histone octamer, and a stretch of relatively unconstrained DNA called the ... Full text Cite

Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements

Journal Article Physical Review Letters · March 12, 2010 Single-molecule force spectroscopy provides a powerful approach for investigating molecular transitions along specific reaction coordinates. Here, we present a general analytical model for extracting the intrinsic rates and activation free energies from fo ... Full text Cite

Biophysics of knotting.

Journal Article Annual review of biophysics · January 2010 Knots appear in a wide variety of biophysical systems, ranging from biopolymers, such as DNA and proteins, to macroscopic objects, such as umbilical cords and catheters. Although significant advancements have been made in the mathematical theory of knots a ... Full text Cite

Energetic and entropic forces governing the attraction between polyelectrolyte-grafted colloids.

Journal Article The journal of physical chemistry. B · December 2009 The energetic and entropic interactions governing the attraction between like-charged colloidal particles grafted with oppositely charged polyelectrolyte chains in a monovalent electrolyte are investigated computationally. We employ coarse-grained models o ... Full text Cite

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2009 The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Car ... Full text Cite

A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.

Journal Article The journal of physical chemistry. A · April 2009 To elucidate the role of the histone tails in chromatin compaction and in higher-order folding of chromatin under physiological conditions, we extend a mesoscale model of chromatin (Arya, Zhang, and Schlick. Biophys. J. 2006, 91, 133; Arya and Schlick. Pro ... Full text Cite

Monte Carlo simulation and molecular theory of tethered polyelectrolytes.

Journal Article The Journal of chemical physics · June 2007 We investigate the structure of end-tethered polyelectrolytes using Monte Carlo simulations and molecular theory. In the Monte Carlo calculations we explicitly take into account counterions and polymer configurations and calculate electrostatic interaction ... Full text Cite

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo.

Journal Article The Journal of chemical physics · January 2007 We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other M ... Full text Cite

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2006 The role of each histone tail in regulating chromatin structure is elucidated by using a coarse-grained model of an oligonucleosome incorporating flexible histone tails that reproduces the conformational and dynamical properties of chromatin. Specifically, ... Full text Cite

Flexible histone tails in a new mesoscopic oligonucleosome model.

Journal Article Biophysical journal · July 2006 We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by h ... Full text Cite

Impact of branching on the phase behavior of polymers

Journal Article Macromolecules · December 13, 2005 We have studied the effect of branching on the solution phase behavior of branched homopolymers using grand canonical Monte Carlo (GCMC) simulations in conjunction with multihistogram reweighting and finite-size scaling analysis. The critical temperature ( ... Full text Cite

Shear ordering in thin films of spherical block copolymer.

Journal Article Langmuir : the ACS journal of surfaces and colloids · November 2005 We have investigated shear-induced alignment of a bilayer of spherical diblock copolymer micelles within thin films using molecular dynamics simulations at two different levels of coarse-graining. At the microscopic level, the copolymers are modeled as bea ... Full text Cite

Log-rolling micelles in sheared amphiphilic thin films.

Journal Article Physical review letters · October 2005 Using molecular dynamics simulations, we show that sheared solutions of cylindrical micelle-forming amphiphiles behave very differently under extreme confinement as compared to the bulk. When confined to ultrathin films, the self-assembled cylindrical mice ... Full text Cite

Molecular modeling of shear-induced alignment of cylindrical micelles

Journal Article Computer Physics Communications · July 1, 2005 This paper presents results from Monte Carlo (MC) and molecular dynamics (MD) simulations on the shear-induced long-ranged alignment of cylindrical micelles in thin films. The surfactant is represented on a lattice and the shear flow is simulated via incor ... Full text Cite

Phase transitions of confined lattice homopolymers

Journal Article Journal of Physical Chemistry B · May 27, 2004 The effect of confinement on the phase behavior of lattice homopolymers has been studied using grand canonical Monte Carlo simulations in conjunction with multihistogram reweighting. The scaling of critical parameters and chain dimensions with chain length ... Full text Cite

Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films

Journal Article Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics · January 1, 2004 The behavior of confined cylindrical micelle-forming surfactants under the influence of shear has been investigated using Monte Carlo simulations. The surfactants are modeled as coarse-grained lattice polymers, while the Monte Carlo shear flow is implement ... Full text Cite

Knudsen diffusivity of a hard sphere in a rough slit pore

Journal Article Physical Review Letters · July 11, 2003 Studying the diffusion of gases within nanopores is an area of intense research due to the practical importance of diffusion in the areas of catalysis and separations, as well as the emerging interest in diffusion in carbon nanotubes. In the large Knudsen ... Full text Cite

Molecular simulations of knudsen wall-slip: Effect of wall morphology

Journal Article Molecular Simulation · January 1, 2003 This work involves a molecular simulation study of the phenomena of wall slip occurring in rarefied gases flowing through micro- and nano-channels. A simulation strategy that mimics a scattering experiment is developed in order to compute the tangential mo ... Full text Cite

Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: Applications

Journal Article Fluid Phase Equilibria · July 15, 2002 The pressure-enthalpy driven molecular dynamics technique, developed in a companion paper [1], is used to compute various thermodynamic properties for the Lennard-Jones (LJ) fluid. These properties include the vapor-liquid coexistence curve, the critical p ... Full text Cite

A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials

Journal Article Journal of Chemical Physics · November 1, 2001 Three different molecular dynamics methods (EMD, EF-NEMD, and DCV-GCMD) were compared for the calculation of nonequilibrium transport coefficients in microporous materials. Two different pore systems were examined: An idealized pore of varying pore diamete ... Full text Cite

Effect of the surface energy barrier on sorbate diffusion in A1PO4-5

Journal Article Journal of Physical Chemistry B · April 12, 2001 The importance of pore exit effects on the diffusion of molecules in AlPO4-5 pores is evaluated using two molecular modeling techniques. In the first approach, a dual control volume grand canonical molecular dynamics technique is used to obtain molecular f ... Full text Cite

Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation

Journal Article Journal of Chemical Physics · August 8, 2000 A technique to determine shear viscosity of Newtonian fluids using molecular dynamics simulation is presented. This technique requires thermostated simulation box and decaying coarse-grain Gaussian velocity profile. The method requires short simulation tim ... Full text Cite