arXiv subjects

Shengfeng Cheng

Publications and source records attributed to Shengfeng Cheng.

33 records · Page 2Linked to original sources

arXiv2018

High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics

The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly-bound and loosely-bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.

physics.bio-ph↗

arXiv2018

Stratification in Drying Films Containing Bidisperse Mixtures of Nanoparticles

Large scale molecular dynamics simulations for bidisperse nanoparticle suspensions with an explicit solvent are used to investigate the effects of evaporation rates and volume fractions on the nanoparticle distribution during drying. Our results show that ``small-on-top'' stratification can occur when ${\rm Pe}_sϕ_s \gtrsim c$ with $c\sim 1$, where ${\rm Pe}_s$ is the Péclet number and $ϕ_s$ is the volume fraction of the smaller particles. This threshold of ${\rm Pe}_sϕ_s$ for ``small-on-top'' is larger by a factor of $\simα^2$ than the prediction of the model treating solvent as an implicit viscous background, where $α$ is the size ratio between the large and small particles. Our simulations further show that when the evaporation rate of the solvent is reduced, the ``small-on-top'' stratification can be enhanced, which is not predicted by existing theories. This unexpected behavior is explained with thermophoresis associated with a positive gradient of solvent density caused by evaporative cooling at the liquid-vapor interface. For ultrafast evaporation the gradient is large and drives the nanoparticles toward the liquid/vapor interface. This phoretic effect is stronger for larger nanoparticles and consequently the ``small-on-top'' stratification becomes more distinct when the evaporation rate is slower (but not too slow such that a uniform distribution of nanoparticles in the drying film is produced), as thermophoresis that favors larger particles on the top is mitigated. A similar effect can lead to ``large-on-top'' stratification for ${\rm Pe}_sϕ_s$ above the threshold when ${\rm Pe}_s$ is large but $ϕ_s$ is small. Our results reveal the importance of including the solvent explicitly when modeling evaporation-induced particle separation and organization and point to the important role of density gradients brought about by ultrafast evaporation.

cond-mat.soft↗

arXiv2017

Ordering Nanoparticles with Polymer Brushes

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a single layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. An interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.

cond-mat.soft↗

arXiv2016

Linking microstructural evolution and macro-scale friction behavior in metals

A correlation is established between the macro-scale friction regimes of metals and a transition between two dominant atomistic mechanisms of deformation. Metals tend to exhibit bi-stable friction behavior -- low and converging or high and diverging. These general trends in behavior are shown to be largely explained using a simplified model based on grain size evolution, as a function of contact stress and temperature, and are demonstrated for pure copper and gold. Specifically, the low friction regime is linked to the formation of ultra-nanocrystalline surface films (10 to 20 nm), driving toward shear accommodation by grain boundary sliding. Above a critical combination of stress and temperature -- demonstrated to be a material property -- shear accommodation transitions to dislocation dominated plasticity and high friction. We utilize a combination of experimental and computational methods to develop and validate the proposed structure-property relationship. This quantitative framework provides a shift from phenomenological to mechanistic and predictive fundamental understanding of friction for crystalline materials, including engineering alloys.

cond-mat.mtrl-sci↗

arXiv2016

Nanocapillary adhesion between parallel plates

Molecular dynamics simulations are used to study capillary adhesion from a nanometer scale liquid bridge between two parallel flat solid surfaces. The capillary force and the meniscus shape of the bridge are computed as the separation between the solid surfaces is varied. Macroscopic theory predicts the meniscus shape and the contribution of liquid/vapor interfacial tension to the capillary force quite accurately for separations as small as 2 or 3 molecular diameters (1-2nm). However the total capillary force differs in sign and magnitude from macroscopic theory for separations less than about 5nm (8-10 diameters) because of molecular layering that is not included in macroscopic theory. For these small separations, the pressure tensor in the fluid becomes anisotropic. The components in the plane of the surface vary smoothly and are consistent with theory based on the macroscopic surface tension. Capillary adhesion is affected by only the perpendicular component, which has strong oscillations as the molecular layering changes.

cond-mat.soft↗

arXiv2016

Dispersing Nanoparticles in a Polymer Film via Solvent Evaporation

Large scale molecular dynamics simulations are used to study the dispersion of nanoparticles (NPs) in a polymer film during solvent evaporation. As the solvent evaporates, a dense polymer-rich skin layer forms at the liquid/vapor interface, which is either NP rich or poor depending on the strength of the NP/polymer interaction. When the NPs are strongly wet by the polymer, the NPs accumulate at the interface and form layers. However when the NPs are only partially wet by the polymer, most NPs are uniformly distributed in the bulk of the polymer film with the dense skin layer serving as a barrier to prevent the NPs from moving to the interface. Our results point to a possible route to employ less favorable NP/polymer interactions and fast solvent evaporation to uniformly disperse NPs in a polymer film, contrary to the common belief that strong NP/polymer attractions are needed to make NPs well dispersed in polymer nanocomposites.

cond-mat.soft↗

arXiv2014

Capillary Adhesion at the Nanometer Scale

Molecular dynamics simulations are used to study the capillary adhesion from a nonvolatile liquid meniscus between a spherical tip and a flat substrate. The atomic structure of the tip, the tip radius, the contact angles of the liquid on the two surfaces, and the volume of the liquid bridge are varied. The capillary force between the tip and substrate is calculated as a function of their separation h. The force agrees with continuum predictions for h down to ~ 5 to 10nm. At smaller h, the force tends to be less attractive than predicted and has strong oscillations. This oscillatory component of the capillary force is completely missed in the continuum theory, which only includes contributions from the surface tension around the circumference of the meniscus and the pressure difference over the cross section of the meniscus. The oscillation is found to be due to molecular layering of the liquid confined in the narrow gap between the tip and substrate. This effect is most pronounced for large tip radii and/or smooth surfaces. The other two components considered by the continuum theory are also identified. The surface tension term, as well as the meniscus shape, is accurately described by the continuum prediction for h down to ~ 1nm, but the capillary pressure term is always more positive than the corresponding continuum result. This shift in the capillary pressure reduces the average adhesion by a factor as large as 2 from its continuum value and is found to be due to an anisotropy in the pressure tensor. The cross-sectional component is consistent with the capillary pressure predicted by the continuum theory (i.e., the Young-Laplace equation), but the normal pressure that determines the capillary force is always more positive than the continuum counterpart.

cond-mat.soft↗

arXiv2013

Self-assembly of Chiral Tubules

The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter 8, 5666-5678 (2012)]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ the lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch and protofilament number observed in microtubule assembly.

cond-mat.soft↗

arXiv2013

Molecular Dynamics Simulations of Evaporation-Induced Nanoparticle Assembly

While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present large scale molecular dynamics simulations of the evaporation-induced assembly of nanoparticles suspended in a liquid that evaporates in a controlled fashion. The quality of the nanoparticle crystal formed just below the liquid/vapor interface is found to be better at relatively slower evaporation rates, as less defects and grain boundaries appear. This trend is understood as the result of the competition between the accumulation and diffusion times of nanoparticles at the liquid/vapor interface. When the former is smaller, nanoparticles are deposited so fast at the interface that they do not have sufficient time to arrange through diffusion, which leads to the prevalence of defects and grain boundaries. Our results have important implications in understanding assembly of nanoparticles and colloids in non-equilibrium liquid environments.

cond-mat.soft↗

arXiv2012

Structure and Diffusion of Nanoparticle Monolayers Floating at Liquid/Vapor Interfaces: A Molecular Dynamics Study

Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles diffusing on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by linear homopolymers, are studied. The organization and diffusion of the nanoparticles are analyzed as the nanoparticle density and the contact angle between the nanoparticles and liquid are varied. When the interaction between the nanoparticles and liquid is reduced the contact angle increases and the nanoparticles ride higher on the liquid surface, which enables them to diffuse faster. In this case the short range order is also reduced as seen in the pair correlation function. For the polymeric liquids, the out-of-layer fluctuation is suppressed and the short range order is slightly enhanced. However, the diffusion becomes much slower and the mean square displacement even shows sub-linear time dependence at large times. The relation between diffusion coefficient and viscosity is found to deviate from that in bulk diffusion. Results are compared to simulations of the identical nanoparticles in 2-dimensions.

cond-mat.soft↗

arXiv2012

Self-assembly of artificial microtubules

Understanding the complex self-assembly of biomacromolecules is a major outstanding question. Microtubules are one example of a biopolymer that possesses characteristics quite distinct from standard synthetic polymers that are derived from its hierarchical structure. In order to understand how to design and build artificial polymers that possess features similar to those of microtubules, we have initially studied the self-assembly of model monomers into a tubule geometry. Our model monomer has a wedge shape with lateral and vertical binding sites that are designed to form tubules. We used molecular dynamics simulations to study the assembly process for a range of binding site interaction strengths. In addition to determining the optimal regime for obtaining tubules, we have calculated a diagram of the structures that form over a wide range of interaction strengths. Unexpectedly, we find that the helical tubules form, even though the monomer geometry is designed for nonhelical tubules. We present the detailed dynamics of the tubule self-assembly process and show that the interaction strengths must be in a limited range to allow rearrangement within clusters. We extended previous theoretical methods to treat our system and to calculate the boundaries between different structures in the diagram.

cond-mat.soft↗

arXiv2011

Evaporation of Lennard-Jones Fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature $T/T_c$, where $T_c$ is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.

cond-mat.soft↗

arXiv2011

Mechanical response of a self avoiding membrane: fold collisions and the birth of conical singularities

An elastic membrane that is forced to reside in a container smaller than its natural size will deform and, upon further volume reduction, eventually crumple. The crumpled state is characterized by the localization of energy in a complex network of highly deformed crescent-like regions joined by line ridges. Previous studies have focused on the onset of the crumpled state by analyzing the mechanical response and stability of a conical dislocation, while others have simulated the highly packed regime neglecting the importance of the connectivity of the membrane. Here we show, through a combination of experiments, numerical simulations, and analytic approach, that the emergence of new regions of high stretching is a generic outcome when a self avoiding membrane is subject to a severe geometrical constraint. We demonstrate that, at moderate packing fraction, interlayer interactions produce a response equivalent to the one of a thicker membrane that has the shape of the deformed one. Evidence is found that friction plays a key role stabilizing the folded structures.

cond-mat.mtrl-sci↗

arXiv2010

Defining Contact at the Atomic Scale

Molecular dynamics simulations are used to study different definitions of contact at the atomic scale. The roles of temperature, adhesive interactions and atomic structure are studied for simple geometries. An elastic, crystalline substrate contacts a rigid, atomically flat surface or a spherical tip. The rigid surface is formed from a commensurate or incommensurate crystal or an amorphous solid. Spherical tips are made by bending crystalline planes or removing material outside a sphere. In continuum theory the fraction of atomically flat surfaces that is in contact rises sharply from zero to unity when a load is applied. This simple behavior is surprisingly difficult to reproduce with atomic scale definitions of contact. Due to thermal fluctuations, the number of atoms making contact at any instant rises linearly with load over a wide range of loads. Pressures comparable to the ideal hardness are needed to achieve full contact at typical temperatures. A simple harmonic mean-field theory provides a quantitative description of this behavior and explains why the instantaneous forces on atoms have a universal exponential form. Contact areas are also obtained by counting the number of atoms with a time-averaged repulsive force. For adhesive interactions, the resulting area is nearly independent of temperature and averaging interval, but usually rises from zero to unity over a range of pressures that is comparable to the ideal hardness. The only exception is the case of two identical commensurate surfaces. For nonadhesive surfaces, the mean pressure is repulsive if there is any contact during the averaging interval $Δt$. The associated area is very sensitive to $Δt$ and grows monotonically. Similar complications are encountered in defining contact areas for spherical tips.

cond-mat.mtrl-sci↗

arXiv2009

Contact and Friction of Nano-Asperities: Effects of Adsorbed Monolayers

Molecular dynamics simulations are used to study contact between a rigid, nonadhesive, spherical tip with radius of order 30nm and a flat elastic substrate covered with a fluid monolayer of adsorbed chain molecules. Previous studies of bare surfaces showed that the atomic scale deviations from a sphere that are present on any tip constructed from discrete atoms lead to significant deviations from continuum theory and dramatic variability in friction forces. Introducing an adsorbed monolayer leads to larger deviations from continuum theory, but decreases the variations between tips with different atomic structure. Although the film is fluid, it remains in the contact and behaves qualitatively like a thin elastic coating except for certain tips at high loads. Measures of the contact area based on the moments or outer limits of the pressure distribution and on counting contacting atoms are compared. The number of tip atoms making contact in a time interval grows as a power of the interval when the film is present and logarithmically with the interval for bare surfaces. Friction is measured by displacing the tip at a constant velocity or pulling the tip with a spring. Both static and kinetic friction rise linearly with load at small loads. Transitions in the state of the film lead to nonlinear behavior at large loads. The friction is less clearly correlated with contact area than load.

cond-mat.mtrl-sci↗