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Graphitic carbon nitride (g-C3N4) is a novel two-dimensional, nitrogen-doped carbon material with various applications in many fields. Recently, g-C3N4 has exhibited excellent ability in separations. In this work, mechanisms of water and ion permeation across nanoporous g-C3N4 membranes with different pore diameters were studied using non-equilibrium molecular dynamics simulations. The water conduction rates derived from our simulations are in good agreement with previous experimental data. Due to the nanoscale confinement, we observe a stacked water cluster structure within the narrowest nanochannel. Similar structures are obscure as the increase of the nanochannel sizes. For desalination purposes, we find that the nanoporous g-C3N4 membrane with the desired opening may completely reject calcium and chloride ions, whereas sieve out monovalent cations with acceptable rejection rates (over 70%). This work provides molecular insight into the mechanism of water and ion transport through nanoporous g-C3N4, which strongly supports that this novel material is a promising candidate for developing selective membrane for water desalination.

Phthalocyanines (Pc) have received considerable attention in the design of photosensitizers for photodynamic therapy (PDT). It is of great interest to design novel Pc-based photosensitizer with improved biological efficiency, which largely relies on the understanding of the interactions of Pc with cell membranes at a molecular level. Here, via all-atom molecular dynamics simulations, we explored the interaction mechanism between a model phospholipid bilayer and three zinc Pc (ZnPc) molecules with different hydrophobicity in nature. We find that the adsorption and insertion behaviors of ZnPc molecules in the model bilayer are different due to the differing hydrophobicity and interaction patterns with phospholipids. Moreover, our simulations demonstrate that the conjunction of a ZnPc skeleton with a cholesterol moiety may reduce the intrinsic molecular rotation of ZnPc in membranes, presumably leading to an increase of the generation efficiency of reactive oxygen species for PDT. The molecular insights obtained here are likely to help improve the rational design of novel photosensitizers with enhanced cellular uptake and photocytotoxic activity.

There is a need for theory on how to group atoms in a molecule to define a coarse-grained (CG) mapping. This article investigates the importance of preserving symmetry of the underlying molecular graph of a given molecule when choosing a CG mapping. 26 CG models of seven alkanes with three different techniques CG techniques were examined. We unexpectedly find preserving symmetry has no consistent effect on CG model accuracy regardless of CG method or comparison metric.

Serine proteases play important roles in numerous physiological and pathophysiological processes. Moreover, serine proteases are classical subjects for studies of catalytic and inhibitory mechanisms of enzymes. Here, we determined the crystal structures of a serine protease, murine plasma kallikrein (mPK), and its complex with a peptidic inhibitor. Although mPK in the complex adopts a canonical protease structure, the apo-mPK exhibits a previously unobserved structural feature: the entrance of the intact S1 pocket is blocked by Glu217. In addition, molecular dynamics simulations and functional assays support the flexibility of Glu217 and suggest that this flexibility plays a role in regulating the activity of serine proteases. Enzymes: EC: 3.4.21.34.

A coarse-grained model-based molecular dynamics simulation was employed to investigate the mechanical properties of NR-graft-rigid-polymer/rigid-polymer systems (N30-g-(R3)6/R10). An external factor (the strain rate) as well as internal factors such as the nonbonding interaction strength, the proportion of rigid polymers, and architecture parameters (the length and number of graft chains in a molecule) were examined for their effect on the tensional behavior of N30-g-(R3)6/R10 systems. Simulation results show that a higher strain rate can promote the enhancement of mechanical performance, such as a higher modulus or yield stress. Moreover, the stress and modulus increase with an increase of the nonbonding interaction strength within rigid polymers or of the rigid polymer proportion in the systems. However, the increasing stress was found to reach a limit with a continuously increasing rigid polymer proportion. On increasing the number of graft chains in a molecule, the stress increases at small strains. However, at large strains, the evident increase in stress was found in systems in which a graft molecule has longer graft chains. In addition, our research shows that N30-g-(R3)6/R10 blends exhibit improved mechanical properties and better compatibilities relative to N30/R10, which is consistent with the experimental results. Lastly, comparisons with experimental observations were also made to ensure the rationality of the simulation results. Overall, bond stretching, bond orientation, and nonbonding interactions were found to be crucial in governing the mechanical properties of the N30-g-(R3)6/R10 systems. These findings may provide important information for further experimental and simulation studies of NR hybrid materials.

Doxorubicin (DOX) is a potent and clinically approved chemotherapeutic agent for cancers. Although human serum albumin (HSA) has been frequently used as a promising drug vehicle for DOX to reduce its doses and toxicities, the pH-dependent binding mechanism of HSA with DOX is still poorly understood. This hampers the rational design of smart HSA-based cancer microenvironment-responsive DOX delivery systems for clinical applications. Here, the molecular interactions of DOX with HSA at various pH levels were systematically investigated using spectroscopic and in silico techniques. Our experiments showed that the binding of DOX to HSA was governed by static quenching mechanism and highly affected by environmental pH. The change of pH altered the conformational states of HSA, which may regulate the binding of DOX onto HSA. In agreement with experimental observations, 1000 ns-long constant-pH molecular dynamics simulations elucidated the structural basis of DOX bound to HSA at different pH. The computational results revealed that the favored binding of DOX at slight alkaline pH may be attributed to the intact structure of HSA and increased intermolecular hydrogen bonding. In contrast, at acidic conditions, the extension of HSA global conformation and drop of local structural identity reduced the number of intermolecular hydrogen bonds. Our study provided novel structural insights into the molecular mechanism of pH-dependent interactions of HSA with DOX, which may be helpful for the design of novel HSA-based microenvironment-responsive drug delivery systems for anticancer therapeutic applications.

The secondary structure content of proteins and their complexes may change significantly on passing from aqueous solution to the gas phase (as in mass spectrometry experiments). In this work, we investigate the impact of hydrophobic residues on the formation of the secondary structure of a real protein complex in the gas phase. We focus on a well-studied protein complex, the amyloid-β (1-40) dimer (2Aβ). Molecular dynamics simulations reproduce the results of ion mobility-mass spectrometry experiments. In addition, a helix (not present in the solution) is identified involving 19FFAED23, consistent with infrared spectroscopy data on an Aβ segment. Our simulations further point to the role of hydrophobic residues in the formation of helical motifs - hydrophobic sidechains "shield" helices from being approached by residues that carry hydrogen bond sites. In particular, two hydrophobic phenylalanine residues, F19 and F20, play an important role for the helix, which is induced in the gas phase in spite of the presence of two carboxyl-containing residues.

In this paper, we study the effects of $\theta ^\prime$-Al$_2$Cu plate-like precipitates on the plasticity of Al-Cu micro-pillars, with a sample size allowing the precipitates to cross the entire micro-pillar. {100}-slip traces are identified for the first time in Al and Al alloys at room temperature. We investigate the underlying mechanisms of this unusual {100}-slip, and show that it operates along the coherent $\theta ^\prime$-Al$_2$Cu precipitate/$\alpha$-Al matrix interface. A combination of molecular dynamics simulations and stress analysis indicates that screw dislocations can cross-slip from the {111} plane onto the {100} $\theta ^\prime$-Al$_2$Cu/$\alpha$-Al interface, then move on it through a kink-pair mechanism, providing a reasonable explanation to the observed {100}-slips. The roles of the $\theta ^\prime$-Al$_2$Cu/$\alpha$-Al matrix interface on the properties of interfacial dislocations are studied within the Peierls-Nabarro framework, showing that the interface can stabilize the {100} screw dislocations from the spreading of the core, and increases the Peierls stress. These results improve our understanding of the mechanical behavior of Al-Cu micro-pillars at room temperature, and imply an enhanced role of interfacial slip in Al-Cu based alloys at elevated temperature in consideration of the underlying kink-pair mechanism., Comment: 24 pages, 10 figures

As a novel two-dimensional material, graphitic carbon nitride (g-C3N4) has proved to be promising for separation membrane. However, the assessment of nanoporous g-C3N4 membrane for efficient desalination process has not been systematically investigated yet. In this work, we designed three g-C3N4 nanopores with different shapes based on the membrane unit structure. The non-equilibrium molecular dynamics simulations were used to study the molecular mechanism of saline water permeation through the nanoporous g-C3N4 membranes. The relationship between water flow rate and external pressure was in good agreement with the classical hydrodynamics. Meanwhile, we observed that the local water diffusion coefficient increased as the enlargement of nanopore sizes, indicating that the nano-effect may also rule the water permeation. For desalination purposes, the designed g-C3N4 nanoporous membrane entirely rejected ions while maintaining a considerable water permeability of 14.9 L/cm2/day/MPa. By analyzing the trajectories of ions passing through the nanopores, we found that the configurational shape could divide one nanopore into several sub-regions, and specific ones may determine the desalination performance of the nanoporous membrane. This work unveils the molecular insights into the desalination process of nanoporous g-C3N4 membrane and further provides useful guidelines for the design of next generation desalination membranes with complex nanopore structures.

In this work, we investigate how nanoporous hexagonal boron nitride (hBN) membrane can achieve efficient water/ion separation using molecular dynamics simulations. In particular, it is interesting to figure out the transport mechanisms through slit-like orifices with different edge patterns, namely armchair, B-edged, and N-edged. It is observed that the water and ion conduction rates are sensitive to the edge patterns, which is attributed to the intriguing electrostatic interactions between hBN and solution particles. The armchair nanoslits barely discriminate ion from water molecules, whereas the nanoslits edged with zigzag patterns collaboratively impede ion permeation and allow fast water conduction. Our simulations not only support that hBN is a promising candidate for the development of permeable membrane for water desalination but also highlight the importance of nanoslit edge pattern. Together, this work will be helpful for the design of permeable membrane in the future.

The aggregation behavior of sodium bis-(2-ethylhexyl)-sulfosuccinate (AOT) at the air/water interface in the absence and presence of inorganic salts was investigated by molecular dynamics simulation. Both monovalent and divalent ions were studied, such as LiCl, NaCl, KCl, MgCl2 and CaCl2. It has been proved that these inorganic ions have great influence on the structure of the AOT monolayer and water molecules around its headgroup. In the presence of inorganic salts, AOT molecules are relatively ordered at the interface and water around the headgroups of AOT shows a lower diffusion coefficient compared with the situation without inorganic salts. All the counterions are prone to move toward the headgroups and locate at the interface. Divalent ions have a strong interaction with AOT, thus they affect the aggregation behavior of AOT remarkably.

In recent years native mass spectrometry has been increasingly employed to study protein structure. As such a thorough understanding of the effect of the gas-phase on protein structure is becoming increasingly important. We show how a combination of top-down ETD and ion mobility can be used to probe the gas-phase structure of heterogeneous protein ensembles. By applying collisional activation to the non-covalently bound ETD products after IM separation, the peptide fragments can be released while maintaining the conformational information of the protein ion. We studied the unknown gas-phase structures of the measles virus (MeV) phosphoprotein X domain (P XD), which shows a wide range of different conformations in the gas-phase. We then generated structural models by state-of-the-art gas-phase steered molecular dynamics, which we verified using restraints from ion mobility and the fragment patterns observed. Our findings illustrate the applicability of ETD for obtaining conformational specific structural information on heterogeneous protein ensembles. All rights reserved. No reuse allowed without permission. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint. http://dx.

Photodynamic therapy (PDT) is a noninvasive and effective approach in clinical cancer treatments. Boron-dipyrromethene (BODIPY)-based derivatives have emerged as novel and promising photosensitizers (PSs) in PDT, attributed to their strong near-infrared singlet oxygen luminescence emissions and high photostabilities. However, the binding mechanism of BODIPY derivatives to proteins, key for their therapeutic and biomedical applications is still poorly understood. Here, we investigated the molecular interactions of two 2, 6-diiodo-BODIPY derivatives with human serum albumin (HSA) using combined experimental and computational techniques. Our spectroscopic results showed that both BODIPY derivatives formed stable complexes with HSA. Strikingly, the BODIPY/HSA complexes exhibited notably enhanced water solubility and singlet oxygen generation efficiency with respect to the BODIPY alone. Furthermore, molecular docking, molecular dynamics simulations, and binding free energy calculations provided the structural and energetic insights into the binding mechanism of BODIPY-based derivatives to HSA. Our work demonstrated that conjugation of BODIPYs with HSA may be a promising strategy to enhance the performance of BODIPY-based PSs, and the combination of computational and experimental techniques is expected to play key roles in the design and development of novel PSs with improved bioavailability and biocompatibility for cancer therapeutic applications.

To explore the effect of surfactant structure and concentration on the dispersibility of SWNTs in aqueous solutions, the molecular dynamics (MD) simulation was employed to investigate the interactions between the single-walled carbon nanotubes (SWNTs) and four surfactants with and without conjugated structure in water. It is confirmed that surfactants with conjugated structure have a stronger interaction with the SWNT. Aggregate morphologies of surfactants with conjugated structure are different from those without conjugated structure. Multi-layers are prone to form in the former system and the latter one appears semi-micelles on the surface of SWNT. Furthermore, the structures of water and counterion layers around the headgroups are also affected by surfactant structure and concentration. All these changes could present the dispersing ability of surfactants for SWNTs and instruct their applications.

In this study, the binding of hemoglobin (Hb) with three benzimidazole-biphenyl derivatives (telmisartan (TST), candesartan (CST), and DB921) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. Results demonstrate that the three drugs locate in the cavities formed by α1, α2, and β2 subunits. The average gyration radii are estimated and consistent with available experimental results. The binding free energies suggest that the binding site of CST/Hb is more stable than those of TST/Hb and DB921/Hb. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of CST/Hb or DB921/Hb while the van der Waals interactions contribute largely to stabilization of the binding site of TST/Hb. The key residues stabilizing the binding sites of TST/Hb, CST/Hb, and DB921/Hb are identified based on the residue decomposition analysis. The probability densities of salt bridge distances demonstrate that there still exist the four salt bridges between α1 and α2 subunits of Hb in presence of these drugs.

Since cyclodextrins (CDs) were discovered to be an excellent reagent to disperse carbon nanotubes (CNTs), they were used for the construction of CD/CNT based electrodes. Therefore, it is crucial to investigate the interactions between CDs and CNTs for their applications. Herein, β-cyclodextrin (β-CD) and their four derivatives, 2-O-(2-hydroxypropyl)-β-cyclodextrin (2-HP-β-CD), 6-O-(2-hydroxypropyl)-β-cyclodextrin (6-HP-β-CD), 2-O-(2-hydroxybutyl)-β-cyclodextrin (2-HB-β-CD) and 6-O-(2-hydroxybutyl)-β-cyclodextrin (6-HB-β-CD), were employed to investigate the interactions with single-walled carbon nanotubes (SWNTs) both in anhydrous and aqueous conditions by molecular dynamics simulation. The results showed that the interactions between SWNTs and CDs were strongly influenced by the structures of CDs such as substituted group and position. The attractive interactions between SWNTs and CDs monotonically increased with the radius of SWNT. Van der Waals attraction was the dominating force for CDs wrapped onto the surface of the nanotube ropes. Therefore, the results could provide a fundament for the choice of CDs in their further applications.

The main component of senile plaques found in AD brain is amyloid beta-peptide (A beta), and the neurotoxicity and aggregation of A beta are associated with the formation of beta-sheet structure. Experimentally, beta sheet breaker (BSB) peptide fragment Leu-Pro-Phe-Phe-Asp (LPFFD) can combine with A beta, which can inhibit the aggregation of A beta. In order to explore why LPFFD can inhibit the formation of beta-sheet conformation of A beta at atomic level, first, molecular docking is performed to obtain the binding sites of LPFFD on the A beta(1-42) (LPFFD/A beta(1-42)), which is taken as the initial conformation for MD simulations. Then, MD simulations on LPFFD/A beta(1-42) in water are carried out. The results demonstrate that LPFFD can inhibit the conformational transition from alpha-helix to beta-sheet structure for the C-terminus of A beta(1-42), which may be attributed to the hydrophobicity decreasing of C-terminus residues of A beta(1-42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFD.

The dispersion effect of carbon nanotubes (CNTs) in aqueous solutions by a silicon surfactant (ethoxy modified trisiloxane, named Ag-64) was investigated in detail using experimental method and molecular dynamics simulation. The Si–O–Si chain of silicon surfactant was flexible due to long Si–C bond and it could easily wrap onto the surface of CNTs through hydrophobic and other intermolecular interactions. The hydrophilic part of PEO provided the CNTs dispersed in the aqueous solution and prevented CNTs from aggregating in water through steric stabilization. It was found that Ag-64 could disperse CNTs with different diameters and it was an effective dispersing agent. The results of molecular dynamics simulation indicated that Ag-64 molecules could wrap onto the surface of CNTs leading to steric stabilization so that it could well disperse CNTs, and Van der Waals attraction was the dominating force of Ag-64 adsorbing onto CNTs. Our study may provide experimental and theoretical basis for using silicon surfactants to disperse CNTs, which can open the avenue of new applications for silicon surfactants.

Aβ(1–40) and Aβ(1–42) are the two predominant forms of amyloid β-peptide (Aβ) in the plaques found in the brains of Alzheimer’s patients. They possess identical amino acid sequence except that the latter has additional two residues (Ile and Ala) at the end of C-terminus, but the latter is more prone to aggregate and neurotoxic than the former. In order to explore the reason why Aβ(1–42) has more unfolded C-terminus than Aβ(1–40) in water, we employ molecular dynamics simulation technology to investigate their different conformational behaviors in water and methanol. Results reveal that the N-terminal parts of both peptides exhibit similar structural changes, but the secondary structures of their C-terminal parts are different. In water and methanol, the C-terminus of Aβ(1–42) mainly adopts β-sheet structure, while some residues in the C-terminus of Aβ(1–40) still keep initial helix structures, no β-sheet structure is observed. The primary mechanism of different conformational behaviors of Aβ(1–40) and Aβ(1–42) in the solvents is analyzed and discussed based on the results of MD simulations.

Amyloid β-peptide (Aβ) is the major component of plaques found in the brains of Alzheimer’s patients. Among its two predominate forms − Aβ(1–40) and Aβ(1–42), the latter possesses stronger aggregation and deposition propensity than the former. To explore the conformational preference of Aβ(1–42) in different solvents, molecular dynamics (MD) simulations are performed to investigate its secondary structures in the following four solvents: hexafluoroisopropanol (HFIP), 2,2,2-trifluoroethanol (TFE), water, and dimethyl sulfoxide (DMSO). Structural analyses demonstrate that there are two stable helix regions of Aβ(1–42) in HFIP and TFE, supporting the idea that they act as helix-promoting solvents. In aqueous solution, α-helix to β-sheet conformational transition is observed in the C-terminal domain of Aβ(1–42). However, in pure DMSO, the unfolding of C-terminal region occurs, but no β-sheet structure is observed. The primary mechanism of conformational behaviors of Aβ(1–42) in the four solvents mentioned above is analyzed and discussed based on the results of MD simulations.

Fullerene and its derivatives show promising prospects for applications in a vast array of biological systems. A key aspect concerning their biomedical applications is how they interact with proteins from molecular levels, which is still poorly understood. In the current study, we investigated the structural and thermodynamic basis of the interactions between two pharmacologically relevant fullerene derivatives and human serum albumin (HSA) using molecular docking, molecular dynamics simulations, and binding free energy calculations. Our results demonstrate that fullerenes steadily bind with HSA at the interfacial cavity formed by subdomains IIA and IIIA. In agreement with available experimental data, our simulations show that the global structure of HSA becomes more compact in the presence of fullerene, while local structural dynamics of the binding cavity behaves diversely depending on the chemical properties of bound fullerenes. Binding free energy calculations confirmed that the interactions between fullerenes and HSA are dominantly stabilized by van der Waals forces and they further allowed the identification of key residues involved in fullerene binding. The structural and energetic insights obtained from this work may help for the development of fullerene-based drug delivery devices and therapeutic agents with improved biological profile.

Boron cluster ion implantation is a potential technology for shallow junction formation in integrated circuits manufacture. A molecular dynamic method for cluster implantation simulation, aiming at microelectronics application, is presented in this paper. Accurate geometric structures of boron clusters are described by the model, and the H atoms in clusters are included. A potential function taking the form of combining the ZBL and the SW potentials is presented here to model interaction among the atoms in the boron cluster. The impact of these models on cluster implantation simulation is investigated. There are notable impact on dopant distribution and amount of implantation defects with consideration of these models. The simulation on the distributions of B and H are verified by SIMS data.

Pre-amorphization implantation has been applied as a shallow junction technology. Roughness at amorphous/crystalline (a/c) interface should be controlled to improve junction characteristics. To understand and model a/c interface roughness, molecular dynamic method is applied in simulating pre-amorphization implantation. A method to reproduce roughness at a/c interface by molecular dynamic simulation is presented. A model of interface roughness is presented. Si and Ge implantation from 2-20keV at a dose of 1x10^1^5cm^-^2 is simulated. The depth of a/c interface is reproduced. Experimental results of a/c interface roughness are successfully simulated. The interface roughness is well reproduced and interpreted by the model presented.

The molecular dynamics (MD) method, with David Cai’s electronic stopping power model applied, is successfully applied to simulate implantation into HfO2. For the first time, a reliable fitting value of the single electron radius in the electronic stopping power model is given for boron, arsenic and phosphorus implantation into HfO2. Excellent agreement between simulation results and SIMS data has been obtained over the energy range of 3–40 keV using the derived fitting value. Our simulation results are found to be in better agreement with the SIMS data than those obtained by means of the traditional simulator TSUPREM4.

In this letter, atomistic-level models and simulations of unipolar TiO2 RRAM are addressed. A dynamic model of SET/RESET is developed based on recent experimental findings, which attributes SET to oxygen vacancy (VO) drift and Ti4O7 conductive filament (CF) growth, while RESET is explained by the melting of Ti4O7 CF and subsequent (VO) diffusion and recombination. Based on the model, electro-thermal and molecular dynamics simulations are carried out to reproduce the complete switching cycle at an atomistic level.

Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information., Author Summary Electrospray ionization (ESI) mass spectrometry (MS) plays a pivotal role in proteomics and structural biology. The applications of ESI-MS to protein complexes make use of the assumption that the vaporization of protein complexes into the gas phase (as occurs during ESI-MS) preserves the structural determinants of the complexes that are observed in water. We used computational methods to investigate this key issue by studying the gaseous structure of a pharmacologically relevant protein complex. The complex in the gas phase differs in a subtle yet significant way from the solution structure. This finding is likely of general relevance for protein-protein complexes. Hence, our work implies that the assumption used in proteomic studies, i.e. that in the gas phase non-covalent complexes generally preserve the representative structural determinants observed in the aqueous phase, needs to be reconsidered. Therefore we suggest that the analysis of complexes should be performed on an individual base rather than by generalized principles.

The properties of adsorbed monolayers of three hydrocarbon surfactants with the same hydrophobic tail, sodium dodecyl sulfate (SDS), dodecyltrimethylammonium bromide (DTAB) and octaethylene glycol dodecyl ether (C(12)E(8)) at the air/water surface in the absence and presence of a dimethylsiloxane ethoxylate-propoxylate (DSEP) were studied via molecular dynamics simulations to compare the effect of the headgroups on the aggregation behaviors of surfactant mixtures. The structures and dynamical properties of the monolayers were greatly affected after adding DSEP. In the presence of DSEP, SDS monolayer was better ordered and more compact, whereas C(12)E(8) monolayer was relatively disordered. Some DTAB molecules immerged into water, and the others adsorbed at the surface were in less compact but well-ordered arrangement. The reason for the appearance of different types of monolayers was also discussed, with the goal of providing a theoretical approach for their further applications.

The aggregation behaviors of sodium deoxycholate (NaDC) at the air/water surface were investigated via surface tension and oscillating bubble measurements in the absence and presence of three alkaline amino acids, namely, L-Lysine (L-Lys), L-Arginine (L-Arg), and L-Histidine (L-His). The results of surface tension measurements show that NaDC has a lower ability to reduce the surface tension of water, because NaDC molecules orient at the surface in an oblique direction and tend to aggregate together, which is approved by molecular dynamics (MD) simulation. L-Lys is the most efficient of the three amino acids in reducing the critical aggregation concentration (cac) of NaDC in aqueous solution. The influence of amino acids on the dilational rheological properties of NaDC was studied using the drop shape analysis method in the frequency range from 0.02 to 0.5 Hz. The results reveal that the absolute modulus passes through a maximum value with increasing NaDC concentration. The addition of amino acids increases the absolute modulus of NaDC, and the maximum value is observed at much lower concentration. From the perspective of structures of amino acids, the performance of L-Arg is similar to that of L-His, and both of them bring out a smaller effect on the absolute modulus than that of L-Lys. From the above results, it may be presumed that electrostatic and hydrophobic effects are important impetus during the interaction between amino acids and NaDC at the air/water surface. Hydrogen bonding is so ubiquitous in the system that the difference of hydrogen bonding between NaDC and amino acid is ignored.

Human P450 protein CYP2C9 is one of the major drug-metabolizing isomers, contributing to the oxidation of 16% of the drugs currently in clinical use. To examine the interaction mechanisms between CYP2C9 and proton pump inhibitions (PPIs), we used molecular docking and molecular dynamics (MD) simulation methods to investigate the conformations and interactions around the binding sites of PPIs/CYPP2C9. Results from molecular docking and MD simulations demonstrate that nine PPIs adopt two different conformations (extended and U-bend structures) at the binding sites and position themselves far above the heme of 2C9. The presence of PPIs changes the secondary structures and residue flexibilities of 2C9. Interestingly, at the binding sites of all PPI–CYP2C9 complexes except for Lan/CYP2C9, there are hydrogen-bonding networks made of PPIs, water molecules, and some residues of 2C9. Moreover, there are strong hydrophobic interactions at all binding sites for PPIs/2C9, which indicate that electrostatic interactions and hydrophobic interactions appear to be important for stabilizing the binding sites of most PPIs/2C9. However, in the case of Lan/2C9, the hydrophobic interactions are more important than the electrostatic interactions for stabilizing the binding site. In addition, an interesting conformational conversion from extended to U-bend structures was observed for pantoprazole, which is attributed to an H-bond interaction in the binding pocket, an internal π–π stacking interaction, and an internal electrostatic interaction of pantoprazole.

Switching processes of carbon-based resistive memory cells are simulated on a fully atomistic level by the molecular dynamics (MD) method and the Extended-Huckel-Theory-based Non Equilibrium Green's Function (EHT-NEGF) method. Graphitic filament breakage and re-growth are found to be responsible for the switching of resistance of carbon-based memory. Key parameters that affect the switching speed of a memory cell are studied and trade-off between speed and power is discussed.

A molecular dynamic method for cluster implantation simulation which is a potential technology for shallow junction formation in integrated circuits manufacture, aimed at microelectronics application, is presented in this paper. Accurate geometric structures of boron clusters including H atoms are described by the model. A potential function taking a form of combining the ZBL and the SW potentials is applied to model interaction among the atoms in the boron cluster. Simulations of B monomer, B 10 H 14 and B 18 H 22 are performed. The distributions of both B and H in monomer and cluster implantation are verified by SIMS data. It is notable that with the cluster model presented, the simulation can reproduce the difference of monomer and cluster implantation very well.

Atomistic modeling has been applied in studying and simulating the advanced junction technologies. We present in this paper the application of molecular dynamics method in simulation of amorphization ion implantation and that of kinetic Monte Carlo method in simulation of annealing. Roughness at amorphous/crystal (a/c) interface is interpreted as transition field and related to the steepness of defects profile. The dissipation of Si extended defects are simulated for both 40kev and 5kev Si implantation. Evolution of extended defects for low energy implantation is well simulated. The simulation indicates that at the initial stage of annealing, the density of extended defects should be larger than that predicted by +1 model.

A new damage model for ion implantation simulation based on molecular dynamic method is introduced in this paper. The model not only describes the formation of point defects but also describe the effect of amorphous pockets. The new model is successfully incorporated into the simulator LEACS (Ran Yajun et al., 2000). Pre-amorphization implantation (PAI) (A. Al-Bayati et al., 2000) with Sb is simulated. The simulation shows obviously better agreement with the RBS results than that achieved with point defects only. The simulation with new damage model can simulate the dose effect in implantation of impurities. Simulations As of and B into single-crystal silicon at 3 kev agree with experimental data.

A new method for the acceleration of MD (molecular dynamics) simulation of ion implantation into crystalline targets is presented, named REACE (Rare Event Algorithm with Cascade Effect). This method can speed up the MD simulation of ion implantation with cascade processes. As a result, the time required to perform a simulation with high precision and dose effect is drastically reduced. And many details producing statistical noise in the simulation are simulated in the REACE and help it to be more reasonable and reliable.

Porous low-k materials with low dielectric constant and reasonable mechanicalal property are demanded urgently for microelectronic applications. In this paper, we proposed a pure classic Molecular Dynamics based simulation method to create atomic models for amorphous dielectrics. Elaborately generating an initial guess for the Molecular Dynamics relaxation allows the structure to contain several hundreds of atoms and realizes pores and special local features at one time. Both mechanical and dielectric properties can be obtained within the classic Molecular Dynamics framework. This method has been applied to the modeling of the microstructure of SiO2 system as an example. In a 360-atom SiO2 system, we can modify the size of the pores inside the dielectrics. The calculated properties are consistent with the experimental results.