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ABSTRACT: The kinetics and thermodynamics of structural transformations under pressure depend strongly on particle size due to the influence of surface free energy. By suitable design of surface structure, composition, and passivation it is possible, in principle, to prepare nanocrystals in structures inaccessible to bulk materials. However, few realizations of such extreme size-dependent behavior exist. Here, we show with molecular dynamics computer simulation that in a model of CdSe/ZnS core/shell nanocrystals the core high-pressure structure can be made metastable under ambient conditions by tuning the thickness of the shell. In nanocrystals with thick shells, we furthermore observe a wurtzite to NiAs transformation, which does not occur in the pure bulk materials. These phenomena are linked to a fundamental change in the atomistic transformation mechanism from heterogeneous nucleation at the surface to homogeneous nucleation in the crystal core.
Nano Letters 07/2012; · 13.20 Impact Factor
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ABSTRACT: Cryptic allosteric sites--transient pockets in a folded protein that are invisible to conventional experiments but can alter enzymatic activity via allosteric communication with the active site--are a promising opportunity for facilitating drug design by greatly expanding the repertoire of available drug targets. Unfortunately, identifying these sites is difficult, typically requiring resource-intensive screening of large libraries of small molecules. Here, we demonstrate that Markov state models built from extensive computer simulations (totaling hundreds of microseconds of dynamics) can identify prospective cryptic sites from the equilibrium fluctuations of three medically relevant proteins--β-lactamase, interleukin-2, and RNase H--even in the absence of any ligand. As in previous studies, our methods reveal a surprising variety of conformations--including bound-like configurations--that implies a role for conformational selection in ligand binding. Moreover, our analyses lead to a number of unique insights. First, direct comparison of simulations with and without the ligand reveals that there is still an important role for an induced fit during ligand binding to cryptic sites and suggests new conformations for docking. Second, correlations between amino acid sidechains can convey allosteric signals even in the absence of substantial backbone motions. Most importantly, our extensive sampling reveals a multitude of potential cryptic sites--consisting of transient pockets coupled to the active site--even in a single protein. Based on these observations, we propose that cryptic allosteric sites may be even more ubiquitous than previously thought and that our methods should be a valuable means of guiding the search for such sites.
Proceedings of the National Academy of Sciences 07/2012; 109(29):11681-6. · 9.68 Impact Factor
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ABSTRACT: A set of interatomic pair potentials is developed for CdS and ZnS crystals. We show that a simple energy function, which has been used to describe the properties of CdSe [E. Rabani, J. Chem. Phys. 116, 258 (2002)], can be parametrized to accurately describe the lattice and elastic constants, and phonon dispersion relations of bulk CdS and ZnS in the wurtzite and rocksalt crystal structures. The predicted coexistence pressure of the wurtzite and rocksalt structures as well as the equation of state are in good agreement with experimental observations. These new pair potentials enable the study of a wide range of processes in bulk and nanocrystalline II-VI semiconductor materials.
The Journal of chemical physics 06/2012; 136(23):234111. · 3.09 Impact Factor
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ABSTRACT: The adsorption behavior of ions at liquid-vapor interfaces exhibits several
unexpected yet generic features. In particular, energy and entropy are both
minimum when the solute resides near the surface, for a variety of ions in a
range of polar solvents, contrary to predictions of classical theories.
Motivated by this generality, and by the simple physical ingredients implicated
by computational studies, we have examined interfacial solvation in highly
schematic models, which resolve only coarse fluctuations in solvent density and
cohesive energy. Here we show that even such lattice gas models recapitulate
surprising thermodynamic trends observed in detailed simulations and
experiments. Attention is focused on the case of two dimensions, for which
approximate energy and entropy profiles can be calculated analytically.
Simulations and theoretical analysis of the lattice gas highlight the role of
capillary wave-like fluctuations in mediating adsorption. They further point to
ranges of temperature and solute-solvent interaction strength where surface
propensity is expected to be strongest.
05/2012;
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ABSTRACT: Direct imaging of nanoparticle solutions by liquid phase transmission electron microscopy has enabled unique in situ studies of nanoparticle motion and growth. In the present work, we report on real-time formation of two-dimensional nanoparticle arrays in the very low diffusive limit, where nanoparticles are mainly driven by capillary forces and solvent fluctuations. We find that superlattice formation appears to be segregated into multiple regimes. Initially, the solvent front drags the nanoparticles, condensing them into an amorphous agglomerate. Subsequently, the nanoparticle crystallization into an array is driven by local fluctuations. Following the crystallization event, superlattice growth can also occur via the addition of individual nanoparticles drawn from outlying regions by different solvent fronts. The dragging mechanism is consistent with simulations based on a coarse-grained lattice gas model at the same limit.
ACS Nano 03/2012; 6(3):2078-85. · 10.77 Impact Factor
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ABSTRACT: Mechanical cues affect many important biological processes in metazoan cells, such as migration, proliferation, and differentiation. Such cues are thought to be detected by specialized mechanosensing molecules linked to the cytoskeleton, an intracellular network of protein filaments that provide mechanical rigidity to the cell and drive cellular shape change. The most abundant such filament, actin, forms branched networks nucleated by the actin-related protein (Arp) 2/3 complex that support or induce membrane protrusions and display adaptive behavior in response to compressive forces. Here we show that filamentous actin serves in a mechanosensitive capacity itself, by biasing the location of actin branch nucleation in response to filament bending. Using an in vitro assay to measure branching from curved sections of immobilized actin filaments, we observed preferential branch formation by the Arp2/3 complex on the convex face of the curved filament. To explain this behavior, we propose a fluctuation gating model in which filament binding or branch nucleation by Arp2/3 occur only when a sufficiently large, transient, local curvature fluctuation causes a favorable conformational change in the filament, and we show with Monte Carlo simulations that this model can quantitatively account for our experimental data. We also show how the branching bias can reinforce actin networks in response to compressive forces. These results demonstrate how filament curvature can alter the interaction of cytoskeletal filaments with regulatory proteins, suggesting that direct mechanotransduction by actin may serve as a general mechanism for organizing the cytoskeleton in response to force.
Proceedings of the National Academy of Sciences 02/2012; 109(8):2913-8. · 9.68 Impact Factor
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ABSTRACT: The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1-10 basepair (bp) scale, which holds particular interest in biological contexts. Here, we examine a class of microscopic models which allow for disruption of base pairing (i.e., a "melt" or "kink", generically an "excitation") and consequently enhanced local flexibility. We first analyze the effect on the excitation free energy of integrating out the spatial degrees of freedom in a wormlike chain. Based on this analysis, we present a formulation of these models that ensures consistency with the well-established thermodynamics of melting in long chains. Using a new method to calculate cyclization statistics of short chains from enhanced-sampling Monte Carlo simulations, we compute J-factors of a meltable wormlike chain over a broad range of chain lengths, including very short molecules (30 bp) that have not yet been explored experimentally. For chains longer than about 120 bp, including most molecules studied to date in the laboratory, we find that melting excitations have little impact on cyclization kinetics. Strong signatures of melting, which might be resolved within typical experimental scatter, emerge only for shorter chains.
The Journal of chemical physics 01/2012; 136(4):045102. · 3.09 Impact Factor
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ABSTRACT: Adsorption of aqueous thiocyanate ions from bulk solution to the liquid/vapor interface was measured as a function of temperature by resonant UV second harmonic generation spectroscopy. The resulting adsorption enthalpy and entropy changes of this prototypical chaotrope were both determined to be negative. This surprising result is supported by molecular simulations, which clarify the microscopic origins of observed thermodynamic changes. Calculations reveal energetic influences of adsorbed ions on their surroundings to be remarkably local. Negative adsorption enthalpies thus reflect a simple repartitioning of solvent density among surface, bulk, and coordination regions. A different, and much less spatially local, mechanism underlies the concomitant loss of entropy. Simulations indicate that ions at the interface can significantly bias surface height fluctuations even several molecular diameters away, imposing restrictions consistent with the scale of measured and computed adsorption entropies. Based on these results, we expect an ion's position in the Hofmeister lyotropic series to be determined by a combination of driving forces associated with the pinning of capillary waves and with a competition between ion hydration energy and the neat liquid's surface tension.
Proceedings of the National Academy of Sciences 01/2012; 109(3):701-5. · 9.68 Impact Factor
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ABSTRACT: Understanding how polyhedra pack into extended arrangements is integral to the design and discovery of crystalline materials at all length scales. Much progress has been made in enumerating and characterizing the packing of polyhedral shapes, and the self-assembly of polyhedral nanocrystals into ordered superstructures. However, directing the self-assembly of polyhedral nanocrystals into densest packings requires precise control of particle shape, polydispersity, interactions and driving forces. Here we show with experiment and computer simulation that a range of nanoscale Ag polyhedra can self-assemble into their conjectured densest packings. When passivated with adsorbing polymer, the polyhedra behave as quasi-hard particles and assemble into millimetre-sized three-dimensional supercrystals by sedimentation. We also show, by inducing depletion attraction through excess polymer in solution, that octahedra form an exotic superstructure with complex helical motifs rather than the densest Minkowski lattice. Such large-scale Ag supercrystals may facilitate the design of scalable three-dimensional plasmonic metamaterials for sensing, nanophotonics and photocatalysis.
Nature Material 11/2011; 11(2):131-7. · 32.84 Impact Factor
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ABSTRACT: Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations.
PLoS Computational Biology 09/2011; 7(9):e1002168. · 5.22 Impact Factor
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ABSTRACT: When deposited from an evaporating solution onto a substrate, even nondescript nanoparticles can organize into intricate spatial patterns. Here we show that a simple but long-ranged anisotropy in nanoparticles' interactions can greatly enrich this scenario. In experiments with colloidal Co nanocrystals, which bear a substantial magnetic dipole, we observe assemblies quite distinct from those formed by nonmagnetic particles. Reflecting the strongly nonequilibrium nature of this process, nanocrystal aggregates also differ substantially from expected low-energy arrangements. Using coarse-grained computer simulations of dipolar nanoparticles, we have identified several dynamical mechanisms from which such unusual morphologies can arise. For particles with modest dipole moments, transient connections between growing domains frustrate phase separation into sparse and dense regions on the substrate. Characteristic length scales of the resulting cellular networks depend non-monotonically on the depth of quenches we use to mimic the effects of solvent evaporation. For particles with strong dipole moments, chain-like aggregates formed at early times serve as the agents of assembly at larger scales. Their effective interactions drive the formation of layered loop structures similar to those observed in experiments.
Journal of the American Chemical Society 02/2011; 133(4):838-48. · 9.91 Impact Factor
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ABSTRACT: The propensity of a peptide chain for adopting helical secondary structure can be modulated not only through the solvation properties of its side chains but also through their size and shape. Here we examine a coarse-grained model for dendronized polypeptides that focuses on the susceptibility of α-helical structure to the steric strain exerted by hydrophilic pendant groups. Undecorated molecules exhibit a pronounced transition from random coil to helix upon cooling [J. P. Kemp and J. Z. Y. Chen, Biomacromolecules 2, 389 (2001)]. As gauged by specific heat and by order parameters characterizing helicity at several length scales, this transition is quite robust to the introduction of first- and second-generation dendron side chains. More highly branched side chains, however, reduce the entropy of compact states so severely that helical ordering is undetectable over the entire temperature range accessible to our importance sampling methods. Consistent with experimental observations for side chains comparable to those of our model in volume-excluding size and shape, we find the backbone of these third-generation molecules to assume a distended rodlike state that is both stiff and achiral.
The Journal of chemical physics 10/2010; 133(14):145102. · 3.09 Impact Factor
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ABSTRACT: Recent experiments [J. van Mameren, Proc. Natl. Acad. Sci. U.S.A. 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed that this observation rules out the existence of an elongated, hybridized form of DNA (S-DNA). Here, we argue that the S-DNA picture is consistent with the observation of unpeeling during overstretching. We demonstrate that assuming the existence of S-DNA does not imply DNA overstretching to consist of the complete or near-complete conversion of the molecule from B to S form. Instead, this assumption implies in general a more complex dynamic coexistence of hybridized and unhybridized forms of DNA. We argue that such coexistence can rationalize several recent experimental observations.
Physical Review E 08/2010; 82(2 Pt 1):021907. · 2.26 Impact Factor
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ABSTRACT: We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each approximately 25 nm(2) patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic association, multiparticle interactions suppress the exposure of each sphere's equator to its implicit solvent surroundings. The requirement of high equatorial density stabilizes two-dimensional structures without necessitating crystalline order, allowing us to match both the elasticity and fluidity of natural lipid membranes. We illustrate the model's versatility and realism by characterizing a membrane's response to a prodding nanorod.
The Journal of chemical physics 04/2010; 132(15):154107. · 3.09 Impact Factor
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ABSTRACT: Self-assembling, light harvesting arrays of organic chromophores can be templated using the tobacco mosaic virus coat protein (TMVP). The efficiency of energy transfer within systems containing a high ratio of donors to acceptors shows a strong dependence on the TMVP assembly state. Rod and disk assemblies derived from a single stock of chromophore-labeled protein exhibit drastically different levels of energy transfer, with rods significantly outperforming disks. The origin of the superior transfer efficiency was probed through the controlled introduction of photoinactive conjugates into the assemblies. The efficiency of the rods showed a linear dependence on the proportion of deactivated chromophores, suggesting the availability of redundant energy transfer pathways that can circumvent defect sites. Similar disk-based systems were markedly less efficient at all defect levels. To examine these differences further, the brightness of donor-only systems was measured as a function of defect incorporation. In rod assemblies, the photophysical properties of the donor chromophores showed a significant dependence on the number of defects. These differences can be partly attributed to vertical energy transfer events in rods that occur more rapidly than the horizontal transfers in disks. Using these geometries and the previously measured energy transfer rates, computational models were developed to understand this behavior in more detail and to guide the optimization of future systems. These simulations have revealed that significant differences in excited state dissipation rates likely also contribute to the greater efficiency of the rods and that statistical variations in the assembly process play a more minor role.
Journal of the American Chemical Society 04/2010; 132(17):6068-74. · 9.91 Impact Factor
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ABSTRACT: The self-assembly of nanocrystals enables new classes of materials whose properties are controlled by the periodicities of the assembly, as well as by the size, shape, and composition of the nanocrystals. While self-assembly of spherical nanoparticles has advanced significantly in the past decade, assembly of rod-shaped nanocrystals has seen limited progress due to the requirement of orientational order. Here, the parameters relevant to self-assembly are systematically quantified using a combination of diffraction and theoretical modeling; these highlight the importance of kinetics on orientational order. Through drying-mediated self-assembly, we achieve unprecedented control over orientational order (up to 96% vertically oriented rods on 1 cm(2) areas) on a wide range of substrates (ITO, PEDOT:PSS, Si(3)N(4)). This opens new avenues for nanocrystal-based devices competitive with thin film devices, as problems of granularity can be tackled through crystallographic orientational control over macroscopic areas.
Nano Letters 12/2009; 10(1):195-201. · 13.20 Impact Factor
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ABSTRACT: We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle x-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble fluorescence resonance energy transfer) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs are consistent with a simple wormlike chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 basepairs) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.
Biophysical Journal 10/2009; 97(5):1408-17. · 3.65 Impact Factor
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ABSTRACT: Contrary to the expectations from classic theories of ion solvation, spectroscopy and computer simulations of the liquid-vapor interface of aqueous electrolyte solutions suggest that ions little larger than a water molecule can prefer to reside near the liquid's surface. Here we advance the view that such affinity originates in a competition between strong opposing forces, primarily due to volume exclusion and dielectric polarization, that are common to all dense polar liquids. We present evidence for this generic mechanism from computer simulations of (i) water and (ii) a Stockmayer fluid near its triple point. In both cases, we show that strong surface enhancement of small ions, obtained by tuning solutes' size and charge, can be accentuated or suppressed by modest changes in either of those parameters. Statistics of solvent polarization, when the ion is held at and above the Gibbs dividing surface, highlight a basic deficiency in conventional models of dielectric response, namely, the neglect of interfacial flexibility. By distorting the solution's boundary, an ion experiences fluctuations in electrostatic potential and in electric field whose magnitudes attenuate much more gradually (as the ion is removed from the liquid phase) than for a quiescent planar interface. As one consequence, the collective responses that determine free energies of solvation can resolve very differently in nonuniform environments than in bulk. We show that this persistence of electric-field fluctuations additionally shapes the sensitivity of solute distributions to ion polarizability.
Proceedings of the National Academy of Sciences 09/2009; 106(36):15125-30. · 9.68 Impact Factor
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ABSTRACT: Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of homogeneous deformations, whose magnitudes can be severely restricted by its stiffest parts. Here we present a Monte Carlo algorithm designed to circumvent this difficulty, which can be prohibitive in many systems of modern interest. By deforming randomly selected subvolumes alone, it naturally distributes the amplitude of spontaneous elastic fluctuations according to intrinsic heterogeneity. We describe in detail implementations of such "slice moves" that are consistent with detailed balance. Their practical application is illustrated for crystals of two-dimensional hard disks and random networks of cross-linked polymers.
The Journal of chemical physics 06/2009; 130(19):194706. · 3.09 Impact Factor
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ABSTRACT: Second-order vibrational spectroscopies successfully isolate signals from interfaces, but they report on intermolecular structure in a complicated and indirect way. Here, we adapt a perspective on vibrational response developed for bulk spectroscopies to explore the microscopic fluctuations to which sum frequency generation (SFG), a popular surface-specific measurement, is most sensitive. We focus exclusively on inhomogeneous broadening of spectral susceptibilities for OH stretching of HOD as a dilute solute in D(2)O. Exploiting a simple connection between vibrational frequency shifts and an electric field variable, we identify several functions of molecular orientation whose averages govern SFG. The frequency dependence of these quantities is well captured by a pair of averages, involving alignment of OH and OD bonds with the surface normal at corresponding values of the electric field. The approximate form we obtain for SFG susceptibility highlights a dramatic sensitivity to the way a simulated liquid slab is partitioned for calculating second-order response.
The Journal of Physical Chemistry B 05/2009; 113(13):4065-74. · 3.70 Impact Factor
