Molecular Dynamics Predictions Research Articles

Potential Implications for Designing Drugs Against the Brown Spider Venom Phospholipase-D.

Loxoscelism refers to the clinical symptoms that develop after brown spider bites. Brown spider venoms contain several phospholipase-D isoforms, which are the main toxins responsible for both the cutaneous and systemic effects of loxoscelism. Understanding of the phospholipase-D catalytic mechanism is crucial for the development of specific treatment that could reverse the toxic effects caused by the spider bite. Based on enzymatic, biological, structural, and thermodynamic tests, we show some features suitable for designing drugs against loxoscelism. Firstly, through molecular docking and molecular dynamics predictions, we found three different molecules (Suramin, Vu0155056, and Vu0359595) that were able to bind the enzyme's catalytic site and interact with catalytically important residues (His12 or His47) and with the Mg2+ co-factor. The binding promoted a decrease in the recombinant brown spider venom phospholipase-D (LiRecDT1) enzymatic activity. Furthermore, the presence of the inhibitors reduced the hemolytic, dermonecrotic, and inflammatory activities of the venom toxin in biological assays. Altogether, these results indicate the mode of action of three different LiRecDT1 inhibitors, which were able to prevent the venom toxic effects. This strengthen the idea of the importance of designing a specific drug to treat the serious clinical symptoms caused by the brown spider bite, a public health problem in several parts of the world, and until now without specific treatment. J. Cell. Biochem. 118: 726-738, 2017. © 2016 Wiley Periodicals, Inc.

Ab Initio Force Fields for Imidazolium-Based Ionic Liquids.

We develop ab initio force fields for alkylimidazolium-based ionic liquids (ILs) that predict the density, heats of vaporization, diffusion, and conductivity that are in semiquantitative agreement with experimental data. These predictions are useful in light of the scarcity of and sometimes inconsistency in experimental heats of vaporization and diffusion coefficients. We illuminate physical trends in the liquid cohesive energy with cation chain length and anion. These trends are different than those based on the experimental heats of vaporization. Molecular dynamics prediction of the room temperature dynamics of such ILs is more difficult than is generally realized in the literature due to large statistical uncertainties and sensitivity to subtle force field details. We believe that our developed force fields will be useful for correctly determining the physics responsible for the structure/property relationships in neat ILs.

Effect of nanostructures on heat transfer coefficient of an evaporating meniscus

The effect of nanostructures on heat transfer coefficient of an evaporating meniscus in thin film evaporation and nucleate boiling is investigated using combined modeling and molecular dynamics (MD) simulations. The model is developed accounting for the evaporation kinetics, disjoining pressure, conduction resistance, and Kapitza resistance of an evaporating meniscus on a nanostructured surface. The model is then verified using MD simulations for a water–gold system with square nanostructures of varying depth and film thickness. Good agreement is obtained between MD results and model predictions. The results show the existence of a critical film thickness on the order of a few nanometers where the heat transfer coefficient reaches its maximum. For a film thickness below this critical value, the evaporation resistance dominates and the heat transfer coefficient increases with film thickness but decreases with nanostructure depth due to the enhanced disjoining pressure. However, for a film thickness greater than the critical value, the conduction resistance dominates and the heat transfer coefficient decreases with film thickness but increases with nanostructure depth. In addition, both critical film thickness and maximum heat transfer coefficient increase with the roughness ratio of the nanostructure, mainly due to the reduction in Kapitza resistance.

Continuum and molecular-dynamics simulation of nanodroplet collisions.

The extent to which the continuum treatment holds in binary droplet collisions is examined in the present work by using a continuum-based implicit surface capturing strategy (volume-of-fluid coupled to Navier-Stokes) and a molecular dynamics methodology. The droplet pairs are arranged in a head-on-collision configuration with an initial separation distance of 5.3 nm and a velocity of 3 ms^{-1}. The size of droplets ranges from 10-50nm. Inspecting the results, the collision process can be described as consisting of two periods: a preimpact phase that ends with the initial contact of both droplets, and a postimpact phase characterized by the merging, deformation, and coalescence of the droplets. The largest difference between the continuum and molecular dynamics (MD) predictions is observed in the preimpact period, where the continuum-based viscous and pressure drag forces significantly overestimate the MD predictions. Due to large value of Knudsen number in the gas (Kn_{gas}=1.972), this behavior is expected. Besides the differences between continuum and MD, it is also observed that the continuum simulations do not converge for the set of grid sizes considered. This is shown to be directly related to the initial velocity profile and the minute size of the nanodroplets. For instance, for micrometer-size droplets, this numerical sensitivity is not an issue. During the postimpact period, both MD and continuum-based simulations are strikingly similar, with only a moderate difference in the peak kinetic energy recorded during the collision process. With values for the Knudsen number in the liquid (Kn_{liquid}=0.01 for D=36nm) much closer to the continuum regime, this behavior is expected. The 50 nm droplet case is sufficiently large to be predicted reasonably well with the continuum treatment. However, for droplets smaller than approximately 36 nm, the departure from continuum behavior becomes noticeably pronounced, and becomes drastically different for the 10 nm droplets.

Molecular dynamics prediction and experimental evidence for density of normal and metastable liquid zirconium

The density of normal and metastable undercooled liquid zirconium was predicted by performing molecular dynamics calculation with a system consisting of 4000 atoms and measured by electrostatic levitation experiments. The results show that the density increases linearly with the descending of temperature, including a maximum undercooling of 928K. The density is 6.00gcm−3 at the melting temperature, which agrees well with the experimental result of 6.06gcm−3. Furthermore, the atomic number is increased to 32,000 on the basis of 4000 atoms and there appears only 0.02% difference. Besides, the pair distribution function was applied to display the atomic structure, which indicates the liquid structure change occurs at the first neighbor distance.

Molecular Dynamics Simulations of Small Clusters and Liquid Hydrogen Sulfide at Different Thermodynamic Conditions.

A new force field for the intermolecular H2S-H2S interaction has been used to study the most relevant properties of the hydrogen sulfide system from gaseous to liquid phases by means of molecular dynamics (MD) simulations. In order to check the validity of the interaction formulation, ab initio CCSD(T)/aug-cc-pVTZ calculations, including the counterpoise correction on the H2S, (H2S)2, and (H2S)3 structures optimized at the MP2/aug-cc-pVDZ level, have been performed. The (H2S)2,3 systems have been characterized by performing NVE MD simulations at decreasing values of the temperature, while the liquid sulfide behavior has been investigated considering a NpT ensemble of 512 molecules at several thermodynamic states, defined by different pressure and temperature values. Additional calculations using an ensemble of 2197 molecules at two different temperatures have been performed to investigate the liquid/vapor interface of the system. The S-S, S-H, and H-H radial distribution functions and the coordination number, calculated at the same conditions used in X-ray and neutron diffraction experiments, and the evaluated thermodynamic and structural properties have been compared successfully with experimental data, thus confirming the reliability of the force field formulation and of the MD predictions.

Editorial: In silico Modeling of Brain Receptors for Antidepressants, Psychostimulants, and Other CNS-Active Drugs.

Editorial: In silico Modeling of Brain Receptors for Antidepressants, Psychostimulants, and Other CNS-Active Drugs.

A Multiscale Model for the Quasi-Static Thermo-Plastic Behavior of Highly Cross-Linked Glassy Polymers

We present experimentally validated molecular dynamics predictions of the quasi-static yield and postyield behavior for a highly cross-linked epoxy polymer under general stress states and for different temperatures. In addition, a hierarchical multiscale model is presented where the nanoscale simulations obtained from molecular dynamics were homogenized to a continuum thermoplastic constitutive model for the epoxy that can be used to describe the macroscopic behavior of the material. Three major conclusions were achieved: (1) the yield surfaces generated from the nanoscale model for different temperatures agree well with the paraboloid yield criterion, supporting previous macroscopic experimental observations; (2) rescaling of the entire yield surfaces to the quasi-static case is possible by considering Argon’s theoretical predictions for pure compression of the polymer at absolute zero temperature; (3) nanoscale simulations can be used for an experimentally free calibration of macroscopic continuum models, opening new avenues for the design of materials and structures through multiscale simulations that provide structure–property–performance relationships.

Comparative investigation of a newly optimized modified embedded atom method potential with other potentials for silicon

Genetic algorithm (GA) is used to optimize the parameter set of the second nearest-neighbor modified embedded atom method (2NN MEAM) interatomic potential for silicon (Si). The optimization is carried out by tuning the parameters to match a set of physical properties including elastic constants, point defect formation energy, phase transformation, surface formation/relaxation and stacking faults. Besides the physical properties for optimization, other molecular dynamics (MD) predictions such as surface reconstruction, point defect diffusion, dislocations and thermal properties are also calculated to test the robustness of the new potential. Another purpose of this work is to compare various physical properties of available MEAM potentials for Si (and Tersoff and SW where necessary). It is shown that the new potential gives a better description in surface, stacking fault and dislocation. Finally, extensive discussion is given to specify the applicability of this potential and the validity of the potentials on fracture simulation.

Molecular Dynamics Simulations of CO2/Water/Quartz Interfacial Properties: Impact of CO2 Dissolution in Water.

The safe trapping of carbon dioxide (CO2) in deep saline aquifers is one of the major concerns of CO2 sequestration. The amount of capillary trapping is dominated by the capillary pressure of water and CO2 inside the reservoir, which in turn is controlled by the interfacial tension (IFT) and the contact angle (CA) of CO2/water/rock systems. The measurement of IFT and CA could be very challenging at reservoir conditions, especially in the presence of toxic cocontaminants. Thus, the ability to accurately predict these interfacial properties at reservoir conditions is very advantageous. Although the majority of existing molecular dynamics (MD) studies of CO2/water/mineral systems were able to capture the trends in IFT and CA variations with pressure and temperature, their predictions often deviated from experimental data, possibly due to erroneous models and/or overlooked chemical reactions. The objective of this study was to improve the MD predictions of IFT and CA of CO2/water/quartz systems at various pressure and temperature conditions by (i) considering the chemical reactions between CO2 and water and (ii) using a new molecular model for α-quartz surface. The results showed that the presence of carbonic acid at the CO2/water interface improved the predictions of IFT, especially at low temperature and high pressure where more CO2 dissolution occurs. On the other hand, the effect on CA was minor. The slight decrease in CA observed across the pressure range investigated could be attributed to an increase in the total number of H-bonds between fluid molecules and quartz surface.

Model of Meniscus Shape and Disjoining Pressure of Thin Liquid Films on Nanostructured Surfaces with Electrostatic Interactions

The effect of electrostatic interactions on the stability of thin liquid films on nanostructured surfaces is important in lubrication, wetting, and phase change but is poorly understood. In this study, a general, closed-form model is developed to account for both the effects of electrostatic and van der Waals interactions on meniscus shape and disjoining pressure for thin liquid films on nanostructured surfaces based on the minimization of free energy, the Derjaguin approximation, and the disjoining pressure theory for flat surfaces. The model is verified using the molecular dynamics (MD) simulations for a water–alumina system with both triangular and square nanostructures of varying depth and film thickness. Good agreement is obtained between MD results and model predictions, demonstrating the robustness of the analytical model. The results show that the electrostatic interactions enhance the disjoining pressure, thereby making the meniscus more conformal to the nanostructured surfaces. In addition, the electrostatic disjoining pressure is shown to increase with the nanostructure depth but decrease with the thin film thickness.

Vibrational mismatch of metal leads controls thermal conductance of self-assembled monolayer junctions.

We present measurements of the thermal conductance of self-assembled monolayer (SAM) junctions formed between metal leads (Au, Ag, Pt, and Pd) with mismatched phonon spectra. The thermal conductance obtained from frequency domain thermoreflectance experiments is 65 ± 7 MW/m(2) K for matched Au-alkanedithiol-Au junctions, while the mismatched Au-alkanedithiol-Pd junctions yield a thermal conductance of 36 ± 3 MW/m(2) K. The experimental observation that junction thermal conductance (per molecule) decreases as the mismatch between the lead vibrational spectra increases, paired with results from molecular dynamics (MD) simulations, suggest that phonons scatter elastically at the metal-SAM interfaces. Furthermore, we resolve a known discrepancy between measurements and MD predictions of SAM thermal conductance by using a contact mechanics model to predict 54 ± 15% areal contact in the Au-alkanedithiol-Au experimental junction. This incomplete contact obscures the actual junction thermal conductance of 115 ± 22 MW/m(2) K, which is comparable to that of metal-dielectric interfaces.

Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and (13)C NMR Spectroscopy.

The diffusion coefficients of carbon dioxide (CO2) and ethanol (EtOH) in carbonated hydroalcoholic solutions and Champagne wines are evaluated as a function of temperature by classical molecular dynamics (MD) simulations and (13)C NMR spectroscopy measurements. The excellent agreement between theoretical and experimental diffusion coefficients suggest that ethanol is the main molecule, apart from water, responsible for the value of the CO2 diffusion coefficients in typical Champagne wines, a result that could likely be extended to most sparkling wines with alike ethanol concentrations. CO2 and EtOH hydrodynamical radii deduced from viscometry measurements by applying the Stokes-Einstein relationship are found to be mostly constant and in close agreement with MD predictions. The reliability of our approach should be of interest to physical chemists aiming to model transport phenomena in supersaturated aqueous solutions or water/alcohol mixtures.

Large permeabilities of hourglass nanopores: from hydrodynamics to single file transport.

In fluid transport across nanopores, there is a fundamental dissipation that arises from the connection between the pore and the macroscopic reservoirs. This entrance effect can hinder the whole transport in certain situations, for short pores and/or highly slipping channels. In this paper, we explore the hydrodynamic permeability of hourglass shape nanopores using molecular dynamics (MD) simulations, with the central pore size ranging from several nanometers down to a few Angströms. Surprisingly, we find a very good agreement between MD results and continuum hydrodynamic predictions, even for the smallest systems undergoing single file transport of water. An optimum of permeability is found for an opening angle around 5°, in agreement with continuum predictions, yielding a permeability five times larger than for a straight nanotube. Moreover, we find that the permeability of hourglass shape nanopores is even larger than single nanopores pierced in a molecular thin graphene sheet. This suggests that designing the geometry of nanopores may help considerably increasing the macroscopic permeability of membranes.

P.3.d.050 Assessment of personal and social functioning and caregiver burden in schizophrenics treated with paliperidone palmitate long acting injectable, followed up for 1 year

Aquaporin-4 (AQP4) is the CNS water channel organized into well-ordered protein aggregates called Orthogonal Arrays of Particles (OAPs). Neuromyelitis Optica (NMO) is an autoimmune disease caused by anti-OAP autoantibodies (AQP4-IgG). Molecular Dynamics (MD) simulations have identified an H-bond between L53 and T56 as the key for AQP4 epitope and therefore of potential interest for drug design in NMO field.In the present study, we have experimentally tested this MD-prediction using the classic mutagenesis approach. We substituted T56 with V56 and tested this mutant for AQP4 aggregates and AQP4-IgG binding. gSTED super-resolution microscopy showed that the mutation does not affect AQP4 aggregate dimension; immunofluorescence and cytofluorimetric analysis demonstrated its unaltered AQP4-IgG binding, therefore invalidating the MD-prediction.We later investigated whether AQP4, expressed in Sf9 insect and HEK-293F cells, is able to correctly aggregate before and after the purification steps usually applied to obtain AQP4 crystal. The results demonstrated that AQP4-IgG recognizes AQP4 expressed in Sf9 and HEK-293F cells by immunofluorescence even though BN-PAGE analysis showed that AQP4 forms smaller aggregates when expressed in insect cells compared to mammalian cell lines. Notably, after AQP4 purification, from both insect and HEK-293F cells, no aggregates are detectable by BN-PAGE and AQP4-IgG binding is impaired in sandwich ELISA assays.All together these results indicate that 1) the MD prediction under analysis is not supported by experimental data and 2) the procedure to obtain AQP4 crystals might affect its native architecture and, as a consequence, MD simulations. In conclusion, given the complex nature of the AQP4 epitope, MD might not be the suitable for molecular medicine advances in NMO.

Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111).

Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the range 0.2-0.3 eV due to ehp excitation, which should be possible to observe. The average non-adiabatic energy losses for non-penetrative scattering exceed the adiabatic losses to phonons by 0.9-1.0 eV. This suggests that for scattering of hyperthermal H-atoms from coinage metals the dominant energy dissipation channel should be to ehp excitation. These predictions can be tested by experiments that combine techniques for generating H-atom beams that are well resolved in translational energy and for detecting the scattered atoms with high energy-resolution.

Selection of Arginine-Rich Anti-Gold Antibodies Engineered for Plasmonic Colloid Self-Assembly

Antibodies are affinity proteins with a wide spectrum of applications in analytical and therapeutic biology. Proteins showing specific recognition for a chosen molecular target can be isolated and their encoding sequence identified in vitro from a large and diverse library by phage display selection. In this work, we show that this standard biochemical technique rapidly yields a collection of antibody protein binders for an inorganic target of major technological importance: crystalline metallic gold surfaces. 21 distinct anti-gold antibody proteins emerged from a large random library of antibodies and were sequenced. The systematic statistical analysis of all the protein sequences reveals a strong occurrence of arginine in anti-gold antibodies, which corroborates recent molecular dynamics predictions on the crucial role of arginine in protein/gold interactions. Once tethered to small gold nanoparticles using histidine tag chemistry, the selected antibodies could drive the self-assembly of the colloids onto the surface of single crystalline gold platelets as a first step towards programmable protein-driven construction of complex plasmonic architectures. Electrodynamic simulations based on the Green Dyadic Method suggest that the antibody-driven assembly demonstrated here could be exploited to significantly modify the plasmonic modal properties of the gold platelets. Our work shows that molecular biology tools can be used to design the interaction between fully folded proteins and inorganic surfaces with potential applications in the bottom-up construction of plasmonic hybrid nanomaterials.

Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans.

Gox2253 from Gluconobacter oxydans belongs to the short-chain dehydrogenases/reductases family, and catalyzes the reduction of heptanal, octanal, nonanal, and decanal with NADPH. To develop a robust working platform to engineer novel G. oxydans oxidoreductases with designed coenzyme preference, we adopted a structure based rational design strategy using computational predictions that considers the number of hydrogen bonds formed between enzyme and docked coenzyme. We report the crystal structure of Gox2253 at 2.6 Å resolution, ternary models of Gox2253 mutants in complex with NADH/short-chain aldehydes, and propose a structural mechanism of substrate selection. Molecular dynamics simulation shows that hydrogen bonds could form between 2'-hydroxyl group in the adenosine moiety of NADH and the side chain of Gox2253 mutant after arginine at position 42 is replaced with tyrosine or lysine. Consistent with the molecular dynamics prediction, Gox2253-R42Y/K mutants can use both NADH and NADPH as a coenzyme. Hence, the strategies here could provide a practical platform to engineer coenzyme selectivity for any given oxidoreductase and could serve as an additional consideration to engineer substrate-binding pockets.

CABS-flex predictions of protein flexibility compared with NMR ensembles.

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles.Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes.Availability and implementation: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex.Contact: sekmi@chem.uw.edu.plSupplementary information: Supplementary data are available at Bioinformatics online.

Influence of waviness and curliness of fibres on mechanical properties of composites

Polymeric composite materials reinforced by curved cylindrical inclusions of very high aspect ratio are studied for their elastic stiffness. The waviness and curliness of the fibres are described by sinusoidal and helical models with different amplitudes and spiral radii, respectively. Effects are investigated in detail by finite element-based homogenisation methods, analytical models and molecular dynamics simulations. Within the finite element models two types of discretisation are considered for the fibres, using continuum solid and beam elements, respectively. Periodic boundary conditions or a special set of mixed boundary conditions are applied for approximating the effective elastic properties. The analytical investigations use a mean-field approximation in which inhomogeneities are split into unconnected segments of appropriate orientation, the elasticity tensor being calculated with a Mori–Tanaka method. It is shown that both curved fibre geometries, sinusoidal and helical, significantly reduce the longitudinal elastic stiffness of the composite. Beam element-based fibre models and analytical solutions give low and high estimates, respectively, for the elastic constants. The continuum mechanical results are found to be in good agreement with the molecular dynamics predictions.