No Arabic abstract
A molecular dynamics simulation is performed to investigate spatial scale of low energy excitation (LEE) in a single linear chain of united atoms. The self part of the dynamic structure function, $S_mathrm{S}(q,omega)$, is obtained in a wide range in frequency space ($omega$) and reciprocal space ($q$). A broad peak corresponding to the LEE is detected at $omega/2pi=2.5 times 10^{11} mathrm{s^{-1}}$ ($equiv omega_{mathrm{LEE}}/2pi$) on the contour maps of $S_mathrm{S}(q,omega)$, near and below the glass transition temperature ($T_{mathrm{g}}$=230 K). The $S_mathrm{S}(q,omega_{mathrm{LEE}})$ is symmetric around a maximum along the logarithm of $q$. The inverse of $q_{mathrm{max}}$, giving the maximum position of $S_mathrm{S}(q,omega_{mathrm{LEE}})$, depends on temperature as $2pi/q_{mathrm{max}}sim T^{0.52}$ for $60 mathrm{K}<T<T_{mathrm{g}}$ and $2pi/q_{mathrm{max}}sim T^{0.97}$ for $T_{mathrm{g}}<T<600 mathrm{K}$, which is the spatial scale of the motion corresponding to the LEE at low temperatures. Based on a Gaussian approximation for the displacements of monomer groups which give rise to the motion relevant to the LEE, it is found that the number of monomers contained in a group is about 6.
Oriented block copolymers exhibit a buckling instability when submitted to a tensile test perpendicular to the lamellae direction. In this paper we study this behavior using a coarse grained molecular dynamics simulation approach. Coarse grained models of lamellar copolymers with alternate glassy rubbery layers are generated using the Radical Like Polymerization method, and their mechanical response is studied. For large enough systems, uniaxial tensile tests perpendicular to the direction of the lamellae reveal the occurrence of the buckling instability at low strain. The results that emerge from molecular simulation are compared to an elastic theory of the buckling instability introduced by Read and coworkers. At high strain rates, significant differences are observed between elastic theory and simulation results for the buckling strain and the buckling wavelength. We explain this difference by the strain rate dependence of the mechanical response. A simple model that takes into account the influence of the strain rate in the mechanical response is presented to rationalize the results at low and moderate strain rates. At very high strain rates, cavitation takes place in the rubbery phase of the sample and limits the validity of the approach.
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain terminator [phthalic anhydride (PA)], and a branching agent [tris[4-(4-aminophenoxy)phenyl] ethane (TAPE)]. An atomistic model is first built for the branched polyetherimide. A systematic protocol based on chemistry-informed grouping of atoms, derivation of bond and angle interactions by direct Boltzmann inversion, and parameterization of nonbonded interactions by potential of mean force (PMF) calculations via gas-phase MD simulations of atomic group pairs, is used to construct the coarse-grained model. A six-pair geometry, with one atomic group at the center and six replicates of the other atomic group placed surrounding the central group in a NaCl structure, has been demonstrated to significantly speed up the PMF calculations and partially capture the many-body aspect of the PMFs. Furthermore, we propose a correction term to the PMFs that can make the resulting coarse-grained model transferable temperature-wise, by enabling the model to capture the thermal expansion property of the polymer. The coarse-grained model has been applied to explore the mechanical, structural, and rheological properties of the branched polyetherimide.
Metallic thin-walled round tubes are widely used as energy absorption elements. However, lateral splash of the round tubes under impact loadings reduces the energy absorption efficiency and may cause secondary damages. Therefore, it is necessary to assemble and fasten round tubes together by boundary constraints and/or fasteners between tubes, which increases the time and labor cost and affects the mechanical performance of round tubes. In an effort to break through this limitation, a novel self-locked energy-absorbing system has been proposed in this paper. The proposed system is made up of thin-walled tubes with dumbbell-shaped cross section, which are specially designed to interlock with each other and thus provide lateral constraint under impact loadings. Both finite element simulations and impact experiment demonstrated that without boundary constraints or fasteners between tubes, the proposed self-locked energy-absorbing system can still effectively attenuate impact loads while the round tube systems fail to carry load due to the lateral splashing of tubes. Furthermore, the optimal geometric design for a single dumbbell-shaped tube and the optimal stacking arrangement for the system are discussed, and a general guideline on the structural design of the proposed self-locked energy absorbing system is provided.
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology in the folding process. Our calculations show that sites contributing to phenotypic resistance of FDA-approved drugs are among the most sensitive positions for the stability of partially folded states and should play a relevant role in the folding process. Furthermore, associations between amino acid sites mutating under drug treatment are shown to be statistically correlated. The striking correlation between clinical data and our calculations suggest a novel approach to the design of drugs tailored to bind regions crucial not only for protein function but also for folding.
The processability and optoelectronic properties of organic semiconductors can be tuned and manipulated via chemical design. The substitution of the alkyl side chains by oligoethers has recently been successful for applications such as bioelectronic sensors and photocatalytic water-splitting. The carbon-oxygen bond in oligoethers is likely to render the system softer and more prone to dynamical disorder that can be detrimental to charge transport for example. We use neutron spectroscopy, X-Ray diffraction (XRD), differential scanning calorimetry (DSC) and polarized optical microscopy to study the effect of the substitution of n-hexyl (Hex) by triethylene glycol (TEG) on the structural dynamics of two organic semiconductors: a phenylene-bithiophene-phenylene (PTTP) molecule and a fluorene-co-dibenzothiophene (FS) polymer. Counterintuitively, inelastic neutron scattering (INS) reveals a softening of the modes of PTTP and FS with Hex side chains, pointing towards an increased dynamical disorder in these systems. However, T-dependent X-Ray and neutron diffraction, INS and DSC evidence an extra reversible transition close to room temperature (RT) for PTTP with TEG side chains. The observed transition, not accompanied by a change in birefringence, can also be observed by quasi-elastic neutron scattering. A fastening of the TEG side chains dynamics is observed in the case of PTTP and not FS. We therefore assign this transition to the melt of the TEG side chains which are promoting dynamical order at RT, but if crystallising, may introduce an extra reversible structural transition above RT leading to thermal instabilities. A deeper understanding of side chain polarity and structural dynamics can help guide materials design and navigate the intricate balance between electronic charge transport and aqueous swelling, sought for a number of emerging organic electronic and bioelectronic applications.