Study on mechanical properties of polyethylene with chain branching in atomic scale by molecular dynamics simulation

The effects of length and content of chain branching on the mechanical properties of polyethylene (PE) in atomic scale were examined by molecular dynamics (MD) simulations. Methyl-, ethyl- and butyl-groups were adopted as branched chains to distribute along PE backbones. Plastic flow deformation was captured by providing a uniaxial tensile loading at a given strain rate, which shows the characteristic of rate dependence. Current results are in reasonable agreements with existing experimental data. The statistical results show that the longer length of chain branching induces lower equilibrium density and higher yield strength of branched PE. In addition, higher content of chain branching brings higher equilibrium density and lower yield strength of branched PE. It is assumed that the distribution of dihedral angles influences the deformation of PE definitely. The non-bond interactions contribute to the load-bearing capacity of PE largely. Branched PE shows big differences on mechanical behaviours comparing with the linear one. Chain branching distribution also greatly affects the performance of PE, which needs a further discussion.     

A molecular dynamics investigation on the compression of cross-linked epoxy resins

Molecular dynamics method is employed to simulate the compression deformation of the polymer materials for electronic packaging. The effects of moisture content, conversion degree, strain rate and temperature on the mechanical properties of epoxy resin are investigated. The stress–strain curves, Young's modulus and Poisson ratio are compared with existing experimental data. The results show that mechanical properties of epoxy resin decrease obviously with increasing moisture content and temperature. However, the high cross-linking conversion and strain rate enhance the mechanical properties of resin.     

A novel technique for the study of bacterial cell mechanical properties

A micromanipulation method is described for measuring the bursting forces of bacteria and relating them to cell size. At a compression speed of 6.2 m s^–1, bursting forces of three samples of rapidly growing Staphylococcus epidermis from a batch culture varied from 3 to 34 N with an average value of 13.8 N (standard error 0.8 N). Escherichia coli grown in continuous culture at a specific growth rate of 0.5 h^–1 had bursting forces varying from 1 to 9 N with an average value of 3.6 N (standard error 0.4 N). In squeeze-hold experiments, force relaxation was observed, which was attributed to water loss from the cells, or viscoelasticity, or both. At high compression speed, such as 6.2 m s^–1, this relaxation could be neglected. Micromanipulation strength measurements might be used in studies of cell mechanical disruption and of the dependence of cell strength on cell physiology.     

A comparison of the electromechanical properties of structurally diverse proteins by molecular dynamics simulation

Proteins are subjected to electric fields both within the cell and during routine biochemical analysis. We have used atomistic molecular dynamics simulations to study conformational changes within three structurally diverse proteins subjected to high electric fields. At electric fields in excess of .5?V/nm, major structural changes were observed in all three proteins due to charge redistribution within the biomolecule. However, the electromechanical resilience was found to be highly dependent on the protein secondary structure, with α-helices showing a particularly high susceptibility to deformation by the applied electric field.     

Molecular dynamics simulation studies of mechanical properties of different carbon nanotube systems

Various mechanical properties of single-walled carbon nanotubes (SWCNT) and double-walled carbon nanotubes (DWCNT) are evaluated using molecular dynamics (MD) simulations. A tensioning process was first performed on a SWCNT whose interaction is based on the Brenner’s ‘second generation’ potential under varying length–diameter ratios and strain rates, in order to understand the SWCNT’s behaviour under axial tension. The results showed an increase in the SWCNT’s ultimate tensile strength and a decrease in critical strain given the conditions of increasing strain rate and a decreasing length–diameter ratio. Comparison was done with previous studies on axial tensioning of SWCNT to validate the results obtained from the set-up, based on the general stress–strain relationship and key mechanical properties such as the strain at failure and the Young’s modulus. A DWCNT was then constructed, and Lennard-Jones ‘12-6’ potential was used to describe the energy present between the nanotube layers. Extraction of the inner tube in a DWCNT was performed using two inner wall tubings of different diameters to draw comparison to the energies needed to separate fully the outer and inner tubing. Finally, a bending test was performed on two DWCNTs with different intertube separations. Insights into the entire bending process were obtained through analyses of the variations in the strain energy characteristic of the surface atoms near the bending site, as the DWCNT is gradually bent until failure.     

Understanding interaction and dynamics of water molecules in the epoxy via molecular dynamics simulation

The robust structural integrity of the epoxy plays an important role in ensuring the long-term service life of its applications, which is affected by the absorbed moisture. In order to understand the mechanism of the moisture effect, the knowledge of the interaction and dynamics of the water molecules inside the epoxy is of great interest. Molecular dynamics simulation is used in this work to investigate the structure and bonding behaviour of the water molecules in the highly cross-linked epoxy network. When the moisture concentration is low, the water molecules are well dispersed in the cross-linked structure and located in the vicinity of the epoxy functional groups, which predominantly form the hydrogen bond (H-bond) with the epoxy network, resulting in the low water mobility in the epoxy. At the high concentration, the water favourably forms the large cluster due to the predominant water–water H-bond interaction, and the water molecules diffuse primarily inside the cluster, which leads to the high water mobility and the accelerated H-bond dynamics. The variation of the bonding behaviour and dynamics of the water molecules reported here could be exploited to understand the material change and predict the long-term performance of the epoxy-based products during the intended service life.     

Interfacial adhesion properties of graphene sheet on nanoscale corrugated surface: a molecular dynamics simulation study

Adhesive contacts between graphene sheet (GS) and corrugated substrates made of an ordered array of atomic pillars with variable geometries were investigated by molecular dynamics simulations. Depending on the height and interval distance of the pillars, GS can conformably coat the surface, partially adhere, or remain flat on top of the pillars. The relationship between the geometries of the pillar and the final adhesion configurations of GS was partially established. A critical adsorption energy was determined to achieve stable adsorption configuration of GS on corrugated substrates made of ordered pillar arrays. Besides the geometries of pillars, the effects of initial coating angle of GS were also considered as an important factor that affects the final adsorption configuration. We observed two interesting morphologies of GS, ‘I shape’ and ‘L shape’, which were determined by the initial coating angles.     

The role of chromium and nickel on the thermal and mechanical properties of FeNiCr austenitic stainless steels under high pressure and temperature: a molecular dynamics study

The effect of Cr and Ni content on thermo-mechanical properties of FeNiCr austenitic stainless steel under ambient and high pressure and temperature were investigated by MD simulations. The FCC structure was selected as optimum structure for FeNiCr system based on obtained MD results from Bonny EAM potential and valid experimental results. The structural and mechanical properties of pure Fe, Ni, and Cr were also estimated based on this potential, indicating good agreement with experimental results. These properties were computed for four experimental case studies which showed less than 10% error. Moreover, the elastic constants of the Fe–(8–18)Ni–(18–25)Cr systems were estimated. Results showed that bulk modulus increases by increasing the Ni and Cr contents, which can be connected to the changes in bonding electrons. The thermal properties of FeNiCr were calculated in ambient and high pressure. Although thermo-mechanical properties confirm good agreement with experimental results at the ambient condition, however, they indicate that FeNiCr Bonny potential is not applicable at high pressure. In order to tackle this issue, a hybrid potential was used at high Pressure/Temperature. The results illustrate enhanced mechanical properties, increase of melting point and reduction of LTE in high pressure and deteriorated mechanical properties at high temperature.     

Structural modeling and molecular dynamics simulation of the actin filament

Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.     

Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation

An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ～1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen–phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.     

Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: An investigation by steered molecular dynamics simulation

Like the muscle protein Titin, proteins of the ubiquitin family exhibit a parallel strand arrangement, but otherwise having a distinctly different fold and not involved in an obvious load‐bearing function, exhibit high resistance to mechanical unfolding. We have applied all‐atom molecular dynamics simulation technique in implicit solvent to present a deep insight into the force‐induced unfolding pathway of three proteins—ubiquitin, NEDD8, and SUMO‐2—all having almost similar structural features. Two intermediates evolve in the unfolding pathway of each of the three proteins. The first intermediate, which has already been identified in case of ubiquitin by earlier simulation results, is similar for ubiquitin and NEDD8, but different in SUMO‐2. We have found a new intermediate with β3–β4 hairpin and some residual α‐helical character; and this intermediate is common for all the three proteins. Thus, proteins of the ubiquitin family pass through a well‐defined conformation in their force‐induced unfolding pathway. Reason behind the higher mechanical stability of the proteins with parallel strand structures like Titin has also been identified. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study

Substrate phosphorylation by cAMP-dependent-protein kinase A (protein kinase A, PKA) has been studied extensively. Phosphoryl transfer was found to be fast, whereas ADP release was found to be the slow, rate-limiting step. There is also evidence that ADP release may be preceded by a partially rate-limiting conformational change. However, the atomic details of the conformational change and the mode of ADP release are difficult to obtain experimentally. In this work, we studied ADP release from PKA by carrying out molecular dynamics simulations with different pulling forces applied to the ligand. The detailed ADP release pathway and the associated conformational changes were analyzed. The ADP release process was found to involve a swinging motion with the phosphate of ADP anchored to the Gly-rich loop, so that the more buried adenine base and ribose ring came out before the phosphate. In contrast to the common belief that a hinge-bending motion was responsible for the opening of the ligand-binding cleft, our simulations showed that the small lobe exhibited a large amplitude "rocking" motion when the ligand came out. The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process.     

A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties

Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Ku?erka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (D_B), hydrophobic thickness (D_C), and lipid volume (V_L). The only minor discrepancy between simulation and experiment is a measure of (D_B − D_HH) / 2 where D_HH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures.     

Molecular docking and molecular dynamics simulation approaches for identifying new lead compounds as potential AChE inhibitors

To provide hints for the design of novel acetylcholinesterase (AChE) inhibitors with higher potency and specificity, the binding modes of the (RS, S)-17b and (RS, R)-17b enantiomers on AChE were chosen to investigate by molecular docking and molecular dynamics simulation. The results show that the binding modes of (RS, S)-17b and (RS, R)-17b are clearly different from each other. In particular, the (RS, S)-17b and (RS, R)-17b enantiomers tend to be planar and bend conformations to interact with AChE, respectively. Furthermore, based on the binding mode on AChE and structure modification of (RS, S)-17b, two novel inhibitors (1 and 2) with higher inhibitory activity were designed. Our design strategy suggests that the number of N and O atoms should be increased, the 5, 6-dimethoxy should be transformed into ring and the indanone moiety should be ring-opening, which would result in generating potent and selective AChE inhibitors.     

Interaction of human SRY protein with DNA: A molecular dynamics study

Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG–DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein–DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG–DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417–433, 1998. © 1998 Wiley-Liss, Inc.     

A coarse grained molecular dynamics study on the structure and stability of small-sized liposomes

The dependence of geometric structure and thermal stability of liposomes on their component phospholipid molecules and distribution of molecules in the inner and the outer layers of the liposome is investigated by conducting molecular simulations in explicit water for the eight types of liposomes constructed from different phospholipids. Using molecular mechanics structure-relaxation based on the coarse grained (CG) model, stable structures of the solvated liposomes are obtained. In addition, the molecular dynamics (MD) simulations based on the CG model are carried out at 310 and 360 K for elucidating the change in structure of the solvated liposomes. The MD simulations reveal that liposomes having the same number of lipids (SNL) in both the inner and the outer layers keep their spherical structures even at 360 K. In particular, the SNLs composed of palmitoyloleoyl-phosphatidyl-ethanolamine1 or dimyristoylglycero-phosphatidyl-choline lipid exhibit a compact spherical shape. In contrast, liposomes having the same density of lipids in the inner and the outer layers cannot keep their spherical shapes at 360 K. The obtained results contribute toward developing novel liposomes with enhanced thermal stability.     

Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study

The nature of binding of specially designed charge transfer (CT) fluorophore at the hydrophobic protein interior of human serum albumin (HSA) has been explored by massive blue-shift (82 nm) of the polarity sensitive probe emission accompanying increase in emission intensity, fluorescence anisotropy, red edge excitation shift, and average fluorescence lifetimes. Thermal unfolding of the intramolecular CT probe bound HSA produces almost opposite spectral changes. The spectral responses of the molecule reveal that it can be used as an extrinsic fluorescent reporter for similar biological systems. Circular dichrosim spectra, molecular docking, and molecular dynamics simulation studies scrutinize this binding process and stability of the protein probe complex more closely.     

The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model

Abstract

The capacity of silencing genes makes small interfering RNA (siRNA) becomes potential candidates for curing many fatal diseases. Due to the low stability and delivery efficiency of siRNA, the design of amphiphilic carrier for siRNA delivery is vital for the practical gene therapy. In the present work, we explored how the complexation and dissociation of siRNA with poly (maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine (PMAL), which is a recent synthesised amphiphilic polymer and can be used in delivery of siRNAs and proteins, using traditional molecular dynamics simulations, together with steered molecular dynamics simulations. It was shown that the complexation of siRNA with PMALs can spontaneously occur, no matter what unit number of PMAL is. PMALs of different unit numbers form micelle-like structures and interact with siRNA surface. With the increase of unit number, PMAL becomes more flexible and interacts with siRNA from attachment to entanglement. The dissociation of PMAL from siRNA is an energy-consuming process. The free energy difference increases with the unit number of PMAL. The free energy for dissociation involves both the stretch of PMAL and the separation of PMAL from siRNA. Therefore, an optimal unit number of PMAL is critical for the delivery efficiency of siRNA when PMAL is used as carrier. In present work, when the radius of gyration of PMAL approaches to that of siRNA, PMAL gives a favoured both complexation and dissociation between siRNA and PMAL. Finally, we propose the mechanism of complexation and dissociation of PMAL with siRNA. The above simulation established a molecular insight of the interaction between siRNA and PMAL and was helpful for the design and applications of new PMAL-based polymers as siRNA delivery carriers.     

A molecular dynamics simulation study of segment B1 of protein G

The immunoglobulin binding protein, segment B1 of protein G, has been studied experimentally as a paradigm for protein folding. This protein consists of 56 residues, includes both β sheet and α helix and contains neither disulfide bonds nor proline residues. We report an all-atom molecular dynamics study of the native manifold of the protein in explicit solvent. A 2-ns simulation starting from the nuclear magnetic resonance (NMR) structure and a 1-ns control simulation starting from the x-ray structure were performed. The difference between average structures calculated over the equilibrium portion of trajectories is smaller than the difference between their starting conformations. These simulation averages are structurally similar to the x-ray structure and differ in systematic ways from the NMR-determined structure. Partitioning of the fluctuations into fast (<20 ps) and slow (<20 ps) components indicates that the β sheet displays greater long-time mobility than does the α helix. Clore and Gronenborn [J. Mol. Biol. 223:853–856, 1992] detected two long-residence water molecules by NMR in a solution structure of segment B1 of protein G. Both molecules were found in the fully exposed regions and were proposed to be stabilized by bifurcated hydrogen bonds to the protein backbone. One of these long-residence water molecules, found near an exposed loop region, is identified in both of our simulations, and is seen to be involved in the formation of a stable water-mediated hydrogen bond bridge. The second water molecule, located near the middle of the α helix, is not seen with an exceptional residence time in either as a result of the conformation being closer to the x-ray structure in this region of the protein. Proteins 29:193–202, 1997. © 1997 Wiley-Liss, Inc.     

Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study

We study the unfolding of a parallel G-quadruplex from human telomeric DNA by mechanical stretching using steered molecular dynamics (MD) simulation. We find that the force curves and unfolding processes strongly depend on the pulling sites. With pulling sites located on the sugar-phosphate backbone, the force-extension curve shows a single peak and the unfolding proceeds sequentially. Pulling sites located on the terminal nucleobases lead to a force-extension curve with two peaks and the unfolding is more cooperative. Simulations of the refolding of partially unfolded quadruplexes show very different behavior for the two different pulling modalities. In particular, starting from an unfolded state prepared by nucleobase pulling leads to a long-lived intermediate state whose existence is also corroborated by the free energy profile computed with the Jarzynski equation. Based on this observation, we propose a novel folding pathway for parallel G-quadruplexes with the human telomere sequence.