H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

Effect of polar surfaces on organic molecular crystals

NASA Astrophysics Data System (ADS)

Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

PubMed

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Atomistic simulations of bulk, surface and interfacial polymer properties

NASA Astrophysics Data System (ADS)

Natarajan, Upendra

In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

Electrofluorescence polarity in a molecular diode

NASA Astrophysics Data System (ADS)

Petrov, E. G.; Leonov, V. A.; Shevchenko, E. V.

2017-11-01

The kinetic equations describing the transmission of an electron in the molecular compound "electrode 1-molecule-electrode 2" (1M2 system) are derived using the method of a nonequilibrium density matrix. The steady-state transmission regime is considered, for which detailed analysis of the kinetics of electrofluorescence formation in systems with symmetric and asymmetric couplings between the molecule and the electrodes is carried out. It is shown that the optically active state of the molecule is formed as a result of electron hops between the molecule and each of the electrodes, as well as due to inelastic interelectrode tunneling of the electron. The electrofluorescence power for a molecular diode (asymmetric 1M2 system) depends on the polarity of the voltage bias applied to the electrodes. The polarity is explained using a model in which the optically active part of the molecule (chromophore group) is represented by the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Two mechanisms of the emergence of polarity are revealed. One mechanism is associated with nonidentical Stark shifts of the HOMO and LUMO levels relative to the Fermi levels of the electrodes. The second mechanism is associated with the fact that the rates of an electron hopping between HOMO (LUMO) and one of the electrodes are much higher than the rates of such a hopping with the other electrode. The conditions in which each mechanism can be implemented experimentally are indicated.

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

PubMed

Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

2017-03-07

DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

Accelerating molecular Monte Carlo simulations using distance and orientation dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models

PubMed Central

Lettieri, S.; Zuckerman, D.M.

2011-01-01

Typically, the most time consuming part of any atomistic molecular simulation is due to the repeated calculation of distances, energies and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (pre-calculation) of distance and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic – but rigid – benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary (“exact”) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. PMID:22120971

Passing waves from atomistic to continuum

NASA Astrophysics Data System (ADS)

Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

2018-02-01

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

DOE PAGES

Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

2015-01-29

The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations.

PubMed

Ghaemi, Zhaleh; Minozzi, Manuela; Carloni, Paolo; Laio, Alessandro

2012-07-26

Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of paramount importance in drug discovery. We here propose an approach for calculating P based on bias-exchange metadynamics. The approach allows constructing from atomistic simulations a model of permeation taking explicitly into account not only the "trivial" reaction coordinate, the position of the drug along the direction normal to the lipid membrane plane, but also other degrees of freedom, for example, the torsional angles of the permeating molecule, or variables describing its solvation/desolvation. This allows deriving an accurate picture of the permeation process, and constructing a detailed molecular model of the transition state, making a rational control of permeation properties possible. We benchmarked this approach on the permeation of ethanol molecules through a POPC membrane, showing that the value of P calculated with our model agrees with the one calculated by a long unbiased molecular dynamics of the same system.

Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.

2015-08-11

We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We alsomore » consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.« less

Literature review report on atomistic modeling tools for FeCrAl alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Schwen, Daniel; Martinez, Enrique

2015-12-01

This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing formore » better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.« less

First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties

DOE PAGES

von Lilienfeld, O. Anatole

2013-02-26

A well-defined notion of chemical compound space (CCS) is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we give an introduction to an atomistic first principles perspective on CCS. First, CCS is discussed in terms of variational nuclear charges in the context of conceptual density functional and molecular grand-canonical ensemble theory. Thereafter, we revisit the notion of compound pairs, related to each other via “alchemical” interpolations involving fractional nuclear charges in the electronic Hamiltonian. We address Taylor expansions in CCS, property nonlinearity, improved predictions using reference compound pairs, and the ounce-of-gold prizemore » challenge to linearize CCS. Finally, we turn to machine learning of analytical structure property relationships in CCS. Here, these relationships correspond to inferred, rather than derived through variational principle, solutions of the electronic Schrödinger equation.« less

Atomistic polarizable force field for molecular dynamics simulations of azide anion containing ionic liquids and crystals.

NASA Astrophysics Data System (ADS)

Starovoytov, Oleg; Hooper, Justin; Borodin, Oleg; Smith, Grant

2010-03-01

Atomistic polarizable force field has been developed for a number of azide anion containing ionic liquids and crystals. Hybrid Molecular Dynamics/Monte Carlo (MD/MC) simulations were performed on methylguanazinium azide and 1-(2-butynyl)-3-methyl-imidazolium azide crystals, while 1-butyl-2,3-dimethylimidazolium azide and 1-amino-3-methyl-1,2,3-triazolium azide ionic liquids were investigated using MD simulations. Crystal cell parameters and crystal structures of 1-(2-butynyl)-3-methyl-imidazolium azide were found in good agreement with X-ray experimental data. Density and ion transport of 1-butyl-2,3-dimethylimidazolium azide predicted from MD simulations were in good agreement with experiments. Details of the ionic liquid structure and relaxation mechanism will be discussed.

Atomistic Monte Carlo Simulation of Lipid Membranes

PubMed Central

Wüstner, Daniel; Sklenar, Heinz

2014-01-01

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

Atomistic mechanisms of rapid energy transport in light-harvesting molecules

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Koga, Shiro; Akai, Ichiro; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2011-03-01

Synthetic supermolecules such as π-conjugated light-harvesting dendrimers efficiently harvest energy from sunlight, which is of significant importance for the global energy problem. Key to their success is rapid transport of electronic excitation energy from peripheral antennas to photochemical reaction cores, the atomistic mechanisms of which remains elusive. Here, quantum-mechanical molecular dynamics simulation incorporating nonadiabatic electronic transitions reveals the key molecular motion that significantly accelerates the energy transport based on the Dexter mechanism.

Atomistic insights on the nanoscale single grain scratching mechanism of silicon carbide ceramic based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Liu, Yao; Li, Beizhi; Kong, Lingfei

2018-03-01

The precision and crack-free surface of brittle silicon carbide (SiC) ceramic was achieved in the nanoscale ductile grinding. However, the nanoscale scratching mechanism and the root causes of SiC ductile response, especially in the atomistic aspects, have not been fully understood yet. In this study, the SiC atomistic scale scratching mechanism was investigated by single diamond grain scratching simulation based on molecular dynamics. The results indicated that the ductile scratching process of SiC could be achieved in the nanoscale depth of cut through the phase transition to an amorphous structure with few hexagonal diamond structure. Furthermore, the silicon atoms in SiC could penetrate into diamond grain which may cause wear of diamond grain. It was further found out that the chip material in the front of grain flowed along the grain side surface to form the groove protrusion as the scratching speed increases. The higher scratching speed promoted more atoms to transfer into the amorphous structure and reduced the hexagonal diamond and dislocation atoms number, which resulted in higher temperature, smaller scratching force, smaller normal stress, and thinner subsurface damage thickness, due to larger speed impaction causing more bonds broken which makes the SiC more ductile.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

PubMed

van der Vaart, Arjan

2015-05-01

Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Development of Continuum-Atomistic Approach for Modeling Metal Irradiation by Heavy Ions

NASA Astrophysics Data System (ADS)

Batgerel, Balt; Dimova, Stefka; Puzynin, Igor; Puzynina, Taisia; Hristov, Ivan; Hristova, Radoslava; Tukhliev, Zafar; Sharipov, Zarif

2018-02-01

Over the last several decades active research in the field of materials irradiation by high-energy heavy ions has been worked out. The experiments in this area are labor-consuming and expensive. Therefore the improvement of the existing mathematical models and the development of new ones based on the experimental data of interaction of high-energy heavy ions with materials are of interest. Presently, two approaches are used for studying these processes: a thermal spike model and molecular dynamics methods. The combination of these two approaches - the continuous-atomistic model - will give the opportunity to investigate more thoroughly the processes of irradiation of materials by high-energy heavy ions. To solve the equations of the continuous-atomistic model, a software package was developed and the block of molecular dynamics software was tested on the heterogeneous cluster HybriLIT.

Molecular electron recollision dynamics in intense circularly polarized laser pulses

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Yuan, Kai-Jun

2018-04-01

Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

PubMed

May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

2014-02-01

To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

Molecular orbital imaging via above-threshold ionization with circularly polarized pulses.

PubMed

Zhu, Xiaosong; Zhang, Qingbin; Hong, Weiyi; Lu, Peixiang; Xu, Zhizhan

2011-07-18

Above-threshold ionization (ATI) for aligned or orientated linear molecules by circularly polarized laser pulsed is investigated. It is found that the all-round structural information of the molecular orbital is extracted with only one shot by the circularly polarized probe pulse rather than with multi-shot detections in a linearly polarized case. The obtained photoelectron momentum spectrum directly depicts the symmetry and electron distribution of the occupied molecular orbital, which results from the strong sensitivity of the ionization probability to these structural features. Our investigation indicates that the circularly polarized probe scheme would present a simple method to study the angle-dependent ionization and image the occupied electronic orbital.

Simulating complex atomistic processes: On-the-fly kinetic Monte Carlo scheme with selective active volumes

NASA Astrophysics Data System (ADS)

Xu, Haixuan; Osetsky, Yury N.; Stoller, Roger E.

2011-10-01

An accelerated atomistic kinetic Monte Carlo (KMC) approach for evolving complex atomistic structures has been developed. The method incorporates on-the-fly calculations of transition states (TSs) with a scheme for defining active volumes (AVs) in an off-lattice (relaxed) system. In contrast to conventional KMC models that require all reactions to be predetermined, this approach is self-evolving and any physically relevant motion or reaction may occur. Application of this self-evolving atomistic kinetic Monte Carlo (SEAK-MC) approach is illustrated by predicting the evolution of a complex defect configuration obtained in a molecular dynamics (MD) simulation of a displacement cascade in Fe. Over much longer times, it was shown that interstitial clusters interacting with other defects may change their structure, e.g., from glissile to sessile configuration. The direct comparison with MD modeling confirms the atomistic fidelity of the approach, while the longer time simulation demonstrates the unique capability of the model.

Molecular cooperativity and compatibility via full atomistic simulation

NASA Astrophysics Data System (ADS)

Kwan Yang, Kenny

Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

An atomistic model for cross-linked HNBR elastomers used in seals

NASA Astrophysics Data System (ADS)

Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

2015-03-01

Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Coarse graining atomistic simulations of plastically deforming amorphous solids

NASA Astrophysics Data System (ADS)

Hinkle, Adam R.; Rycroft, Chris H.; Shields, Michael D.; Falk, Michael L.

2017-05-01

The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

Anisotropic polarization π -molecular skeleton coupled dynamics in proton-displacive organic ferroelectrics

NASA Astrophysics Data System (ADS)

Fujioka, J.; Horiuchi, S.; Kida, N.; Shimano, R.; Tokura, Y.

2009-09-01

We have investigated the polarization π -molecular skeleton coupled dynamics for the proton-displacive organic ferroelectrics, cocrystal of phenazine with the 2,5-dihalo-3,6-dihydroxy-p-benzoquinones by measurements of the terahertz/infrared spectroscopy. In the course of the ferroelectric-to-paraelectric transition, the ferroelectric soft phonon mode originating from the intermolecular dynamical displacement is observed in the imaginary part of dielectric spectra γ2 , when the electric field of the light (E) is parallel to the spontaneous polarization (P) . The soft phonon mode is isolated from the intramolecular vibrational mode and hence the intramolecular skeleton dynamics is almost decoupled from the polarization fluctuation. In the spectra for E parallel to the hydrogen-bonded supramolecular chain, by contrast, the vibrational mode mainly originating from the oxygen atom motion within the π -molecular plane is anomalously blurred and amalgamated into the polarization relaxation mode concomitantly with the dynamical proton disorder. This indicates that the dynamical disorder of the intramolecular skeleton structure, specifically that of oxygen atom, is strongly enhanced by the proton fluctuation and is significantly coupled to the polarization fluctuation along the hydrogen-bonded supramolecular chain. The results are discussed in terms of the proton-mediated anisotropic polarization π -molecular skeleton interaction, which characterizes these emerging proton-displacive ferroelectrics.

Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

PubMed Central

Buerkle, Marius; Asai, Yoshihiro

2017-01-01

The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations. PMID:28150738

New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2008-01-01

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS

NASA Astrophysics Data System (ADS)

Pavia, F.; Curtin, W. A.

2015-07-01

Deformation and fracture processes in engineering materials often require simultaneous descriptions over a range of length and time scales, with each scale using a different computational technique. Here we present a high-performance parallel 3D computing framework for executing large multiscale studies that couple an atomic domain, modeled using molecular dynamics and a continuum domain, modeled using explicit finite elements. We use the robust Coupled Atomistic/Discrete-Dislocation (CADD) displacement-coupling method, but without the transfer of dislocations between atoms and continuum. The main purpose of the work is to provide a multiscale implementation within an existing large-scale parallel molecular dynamics code (LAMMPS) that enables use of all the tools associated with this popular open-source code, while extending CADD-type coupling to 3D. Validation of the implementation includes the demonstration of (i) stability in finite-temperature dynamics using Langevin dynamics, (ii) elimination of wave reflections due to large dynamic events occurring in the MD region and (iii) the absence of spurious forces acting on dislocations due to the MD/FE coupling, for dislocations further than 10 Å from the coupling boundary. A first non-trivial example application of dislocation glide and bowing around obstacles is shown, for dislocation lengths of ∼50 nm using fewer than 1 000 000 atoms but reproducing results of extremely large atomistic simulations at much lower computational cost.

An Optimization-based Atomistic-to-Continuum Coupling Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell

2014-08-21

In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally,more » we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.« less

Symmetry in circularly polarized molecular high-order harmonic generation with intense bicircular laser pulses

NASA Astrophysics Data System (ADS)

Yuan, Kai-Jun; Bandrauk, André D.

2018-02-01

We present symmetry effects of laser fields and molecular geometries in circularly polarized high-order harmonic generation by bichromatic counter-rotating circularly polarized laser pulses. Simulations are performed on oriented molecules by numerically solving time-dependent Schrödinger equations. We discuss how electron recollision trajectories by the orthogonal laser field polarizations influence the harmonic polarization by using a time-frequency analysis of harmonics. It is found that orientation-dependent asymmetric ionization in linear molecules due to Coulomb potentials gives rise to a dependence of the polarization on the harmonic frequency. Effects of Coriolis forces are also presented on harmonic generation. Electron recollision trajectories illustrate the effects of the relative symmetry of the field and the molecule, thus paving a method for circularly polarized attosecond pulse generation and molecular orbital imaging in more complex systems.

Molecular density functional theory of water including density-polarization coupling.

PubMed

Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

2016-06-22

We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

The notion of a plastic material spin in atomistic simulations

NASA Astrophysics Data System (ADS)

Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

2016-12-01

A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

PubMed

Papaleo, Elena

2015-01-01

In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study.

PubMed

Telesco, Shannon E; Radhakrishnan, Ravi

2009-03-18

HER2 (ErbB2/Neu) is a receptor tyrosine kinase belonging to the epidermal growth factor receptor (EGFR)/ErbB family and is overexpressed in 20-30% of human breast cancers. Although several crystal structures of ErbB kinases have been solved, the precise mechanism of HER2 activation remains unknown, and it has been suggested that HER2 is unique in its requirement for phosphorylation of Y877, a key tyrosine residue located in the activation loop. To elucidate mechanistic details of kinase domain regulation, we performed molecular dynamics simulations of a homology-modeled HER2 kinase structure in active and inactive conformations. Principal component analysis of the atomistic fluctuations reveals a tight coupling between the activation loop and catalytic loop that may contribute to alignment of residues required for catalysis in the active kinase. The free energy perturbation method is also employed to predict a role for phosphorylated Y877 in stabilizing the kinase conformations. Finally, simulation results are presented for a HER2/EGFR heterodimer and reveal that the dimeric interface induces a rearrangement of the alphaC helix toward the active conformation. Elucidation of the molecular regulatory mechanisms in HER2 will help establish structure-function relationships in the wild-type kinase, as well as predict mutations with a propensity for constitutive activation in HER2-mediated cancers.

Atomistic Molecular Dynamics Simulations of Charged Latex Particle Surfaces in Aqueous Solution.

PubMed

Li, Zifeng; Van Dyk, Antony K; Fitzwater, Susan J; Fichthorn, Kristen A; Milner, Scott T

2016-01-19

Charged particles in aqueous suspension form an electrical double layer at their surfaces, which plays a key role in suspension properties. For example, binder particles in latex paint remain suspended in the can because of repulsive forces between overlapping double layers. Existing models of the double layer assume sharp interfaces bearing fixed uniform charge, and so cannot describe aqueous binder particle surfaces, which are soft and diffuse, and bear mobile charge from ionic surfactants as well as grafted multivalent oligomers. To treat this industrially important system, we use atomistic molecular dynamics simulations to investigate a structurally realistic model of commercial binder particle surfaces, informed by extensive characterization of particle synthesis and surface properties. We determine the interfacial profiles of polymer, water, bound and free ions, from which the charge density and electrostatic potential can be calculated. We extend the traditional definitions of the inner and outer Helmholtz planes to our diffuse interfaces. Beyond the Stern layer, the simulated electrostatic potential is well described by the Poisson-Boltzmann equation. The potential at the outer Helmholtz plane compares well to the experimental zeta potential. We compare particle surfaces bearing two types of charge groups, ionic surfactant and multivalent oligomers, with and without added salt. Although the bare charge density of a surface bearing multivalent oligomers is much higher than that of a surfactant-bearing surface at realistic coverage, greater counterion condensation leads to similar zeta potentials for the two systems.

Penetration scaling in atomistic simulations of hypervelocity impact

NASA Astrophysics Data System (ADS)

Ruestes, C. J.; Bringa, E. M.; Fioretti, F.; Higginbotham, A.; Taylor, E. A.; Graham, G.

2011-06-01

We present atomistic molecular dynamics simulations of the impact of copper nano particles at 5 km/s on copper films ranging in thickness from 0.5 to 4 times the projectile diameter. We access both penetration and cratering regimes with final cratering morphologies showing considerable similarity to experimental impacts on both micron and millimeter scales. Both craters and holes are formed from a molten region, with relatively low defect densities remaining after cooling and recrystallisation. Crater diameter and penetration limits are compared to analytical scaling models: in agreement with some models we find the onset of penetration occurs for 1.0 < f/d < 1.5, where f is the film thickness and d is the projectile diameter. However, our results for the hole size agree well with scaling laws based on macroscopic experiments providing enhanced strength of a nano-film that melts completely at the impact region is taken into account. Penetration in films with pre-existing nanocracks is qualitatively similar to penetration in perfect films, including the lack of back-spall. Simulations using ``peridynamics'' are also described and compared to the atomistic simulations. Work supported by PICT2007-PRH, PICT-2008 1325, and SeCTyP.

Robustness of atomistic Gō models in predicting native-like folding intermediates

NASA Astrophysics Data System (ADS)

Estácio, S. G.; Fernandes, C. S.; Krobath, H.; Faísca, P. F. N.; Shakhnovich, E. I.

2012-08-01

Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis.

Understanding the physical metallurgy of the CoCrFeMnNi high-entropy alloy: an atomistic simulation study

NASA Astrophysics Data System (ADS)

Choi, Won-Mi; Jo, Yong Hee; Sohn, Seok Su; Lee, Sunghak; Lee, Byeong-Joo

2018-01-01

Although high-entropy alloys (HEAs) are attracting interest, the physical metallurgical mechanisms related to their properties have mostly not been clarified, and this limits wider industrial applications, in addition to the high alloy costs. We clarify the physical metallurgical reasons for the materials phenomena (sluggish diffusion and micro-twining at cryogenic temperatures) and investigate the effect of individual elements on solid solution hardening for the equiatomic CoCrFeMnNi HEA based on atomistic simulations (Monte Carlo, molecular dynamics and molecular statics). A significant number of stable vacant lattice sites with high migration energy barriers exists and is thought to cause the sluggish diffusion. We predict that the hexagonal close-packed (hcp) structure is more stable than the face-centered cubic (fcc) structure at 0 K, which we propose as the fundamental reason for the micro-twinning at cryogenic temperatures. The alloying effect on the critical resolved shear stress (CRSS) is well predicted by the atomistic simulation, used for a design of non-equiatomic fcc HEAs with improved strength, and is experimentally verified. This study demonstrates the applicability of the proposed atomistic approach combined with a thermodynamic calculation technique to a computational design of advanced HEAs.

Filters for Improvement of Multiscale Data from Atomistic Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, David J.; Reynolds, Daniel R.

Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

Filters for Improvement of Multiscale Data from Atomistic Simulations

DOE PAGES

Gardner, David J.; Reynolds, Daniel R.

2017-01-05

Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang

2016-10-14

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-artmore » molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.« less

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

PubMed

Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

2016-12-01

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

Atomistic observation and simulation analysis of spatio-temporal fluctuations during radiation-induced amorphization.

PubMed

Watanabe, Seiichi; Hoshino, Misaki; Koike, Takuto; Suda, Takanori; Ohnuki, Soumei; Takahashi, Heishichirou; Lam, Nighi Q

2003-01-01

We performed a dynamical-atomistic study of radiation-induced amorphization in the NiTi intermetallic compound using in situ high-resolution high-voltage electron microscopy and molecular dynamics simulations in connection with image simulation. Spatio-temporal fluctuations as non-equilibrium fluctuations in an energy-dissipative system, due to transient atom-cluster formation during amorphization, were revealed by the present spatial autocorrelation analysis.

Laser Polarization Effect on Molecular Harmonic and Elliptically Polarized Attosecond Pulse Generation

NASA Astrophysics Data System (ADS)

Feng, Li-Qiang; Li, Wen-Liang; Liu, Hang

2017-01-01

Molecular harmonic spectra of {{{H}}}2+ driven by the linearly polarized laser pulses with different polarized angles have been theoretically investigated through solving the two-dimensional time-dependent Schrödinger equation. (i) Below-threshold harmonic spectra show a visible enhanced peak around the 7th harmonic (H7), which produces a red-shift phenomenon as the internuclear distance increased. Theoretical analyses show the red-shift enhanced peak is caused by the laser-induced electron transfer between the ground state and the 1st excited state of {{{H}}}2+. (ii) Due to the two-centre interference phenomenon, the above-threshold harmonic spectra exhibit many maxima and minima. (iii) With the introduction of the polarized angle, the anomalous elliptically polarized harmonics can be found. But, with the introduction of the spatial inhomogeneous effect, not only the ellipticities of the harmonics are equal to a stable value of \\varepsilon ˜ 0.1-0.3, but also the harmonic cutoffs are extended. As a result, four super-bandwidths of 407 eV, 310 eV, 389 eV, and 581 eV can be obtained. Time profiles of the harmonic generations have been shown to explain the harmonic characteristics. Finally, a series of elliptically polarized (\\varepsilon ˜ 0.1-0.3) attosecond X-ray pulses with durations from 18as to 25as can be directly produced through Fourier transformation of the spectral continuum. Supported by National Natural Science Foundation of China under Grant No. 11504151, Doctoral Scientific Research Foundation of Liaoning Province under Grant No. 201501123 and Scientific Research Fund of Liaoning Provincial Education Department under Grant No. L2014242

Mitochondrial genetics in Bakers' yeast: a molecular mechanism for recombinational polarity and suppressiveness.

PubMed

Perlman, P S; Birky, C W

1974-11-01

Recombinational polarity and suppressiveness are two well-known but puzzling cytoplasmic genetic phenomena in bakers' yeast, Saccharomyces cerevisiae. Little progress has been made in characterizing the underlying molecular mechanisms of these phenomena. In this paper we describe a molecular model for recombinational polarity that is compatible with the available genetic evidence. The model stresses the role of small deletions and excision/repair processes in otherwise canonical recombinational events. According to the model, both phenomena require recombination and may share mechanistic elements.

Modelling dust polarization observations of molecular clouds through MHD simulations

NASA Astrophysics Data System (ADS)

King, Patrick K.; Fissel, Laura M.; Chen, Che-Yu; Li, Zhi-Yun

2018-03-01

The BLASTPol observations of Vela C have provided the most detailed characterization of the polarization fraction p and dispersion in polarization angles S for a molecular cloud. We compare the observed distributions of p and S with those obtained in synthetic observations of simulations of molecular clouds, assuming homogeneous grain alignment. We find that the orientation of the mean magnetic field relative to the observer has a significant effect on the p and S distributions. These distributions for Vela C are most consistent with synthetic observations where the mean magnetic field is close to the line of sight. Our results point to apparent magnetic disorder in the Vela C molecular cloud, although it can be due to either an inclination effect (i.e. observing close to the mean field direction) or significant field tangling from strong turbulence/low magnetization. The joint correlations of p with column density and of S with column density for the synthetic observations generally agree poorly with the Vela C joint correlations, suggesting that understanding these correlations requires a more sophisticated treatment of grain alignment physics.

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

Cascade Defect Evolution Processes: Comparison of Atomistic Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Haixuan; Stoller, Roger E; Osetskiy, Yury N

2013-11-01

Determining the defect evolution beyond the molecular dynamics (MD) time scale is critical in bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity. In this study, SEAKMC is applied to investigate the cascade defect evolution in bcc iron. First, the evolution of a vacancy rich region is simulated and compared with results obtained using autonomous basin climbing (ABC) +KMC and kinetic activation-relaxation technique (kART) simulations. Previously, it is found the results from kART are orders of magnitude faster than ABC+KMC.more » The results obtained from SEAKMC are similar to kART but the time predicted is about one order of magnitude faster than kART. The fidelity of SEAKMC is confirmed by statistically relevant MD simulations at multiple higher temperatures, which proves that the saddle point sampling is close to complete in SEAKMC. The second is the irradiation-induced formation of C15 Laves phase nano-size defect clusters. In contrast to previous studies, which claim the defects can grow by capturing self-interstitials, we found these highly stable clusters can transform to <111> glissile configuration on a much longer time scale. Finally, cascade-annealing simulations using SEAKMC is compared with traditional object KMC (OKMC) method. SEAKMC predicts substantially fewer surviving defects compared with OKMC. The possible origin of this difference is discussed and a possible way to improve the accuracy of OKMC based on SEAKMC results is outlined. These studies demonstrate the atomistic fidelity of SEAKMC in comparison with other on-the-fly KMC methods and provide new information on long-term defect evolution in iron.« less

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

PubMed

Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

2016-07-20

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.

Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cassidy, Andrew; Jørgensen, Mads R. V.; Rosu-Finsen, Alexander

2016-10-02

It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 10 8 V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization ofmore » a representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.« less

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

PubMed Central

Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

2014-01-01

Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal.

PubMed

Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J; van Duin, Adri C T; Lu, Xiaohua; Gubbins, Keith E

2013-11-21

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O∕H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O∕H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

The Chemistry of Shocked High-energy Materials: Connecting Atomistic Simulations to Experiments

NASA Astrophysics Data System (ADS)

Islam, Md Mahbubul; Strachan, Alejandro

2017-06-01

A comprehensive atomistic-level understanding of the physics and chemistry of shocked high energy (HE) materials is crucial for designing safe and efficient explosives. Advances in the ultrafast spectroscopy and laser shocks enabled the study of shock-induced chemistry at extreme conditions occurring at picosecond timescales. Despite this progress experiments are not without limitations and do not enable a direct characterization of chemical reactions. At the same time, large-scale reactive molecular dynamics (MD) simulations are capable of providing description of the shocked-induced chemistry but the uncertainties resulting from the use of approximate descriptions of atomistic interactions remain poorly quantified. We use ReaxFF MD simulations to investigate the shock and temperature induced chemical decomposition mechanisms of polyvinyl nitrate, RDX, and nitromethane. The effect of various shock pressures on reaction initiation mechanisms is investigated for all three materials. We performed spectral analysis from atomistic velocities at different shock pressures to enable direct comparison with experiments. The simulations predict volume-increasing reactions at the shock-to-detonation transitions and the shock vs. particle velocity data are in good agreement with available experimental data. The ReaxFF MD simulations validated against experiments enabled prediction of reaction kinetics of shocked materials, and interpretation of experimental spectroscopy data via assignment of the spectral peaks to dictate various reaction pathways at extreme conditions.

Communication: Phase diagram of C36 by atomistic molecular dynamics and thermodynamic integration through coexistence regions

NASA Astrophysics Data System (ADS)

Abramo, M. C.; Caccamo, C.; Costa, D.; Munaò, G.

2014-09-01

We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C36. We first show that free energies obtained via thermodynamic integrations along isotherms displaying "van der Waals loops," are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C36, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400-1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C36 fullerite and of its liquid state, at variance with what previously experienced for C60.

Atomistic simulation of hydrophobin HFBII conformation in aqueous and fluorous media and at the water/vacuum interface.

PubMed

Raffaini, Giuseppina; Milani, Roberto; Ganazzoli, Fabio; Resnati, Giuseppe; Metrangolo, Pierangelo

2016-01-01

Hydrophobins are proteins of interest for numerous applications thanks to their unique conformational and surface properties and their ability to self-assemble at interfaces. Here we report fully atomistic molecular mechanics and molecular dynamics results together with circular dichroism experimental data, aimed to study the conformational properties of the hydrophobin HFBII in a fluorinated solvent in comparison with a water solution and/or at an aqueous/vacuum interface. Both the atomistic simulations and the circular dichroism data show the remarkable structural stability of HFBII at all scales in all these environments, with no significant structural change, although a small cavity is formed in the fluorinated solvent. The combination of theoretical calculations and circular dichroism data can describe in detail the protein conformation and flexibility in different solvents and/or at an interface, and constitutes a first step towards the study of their self-assembly. Copyright © 2015 Elsevier Inc. All rights reserved.

Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

NASA Astrophysics Data System (ADS)

Takada, Shoji

Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

2016-01-01

Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

NASA Astrophysics Data System (ADS)

Kushima, A.; Eapen, J.; Li, Ju; Yip, S.; Zhu, T.

2011-08-01

Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.

Molecular orientation in aligned electrospun polyimide nanofibers by polarized FT-IR spectroscopy.

PubMed

Yang, Haoqi; Jiang, Shaohua; Fang, Hong; Hu, Xiaowu; Duan, Gaigai; Hou, Haoqing

2018-07-05

Quantitative explanation on the improved mechanical properties of aligned electrospun polyimide (PI) nanofibers as the increased imidization temperatures is highly required. In this work, polarized FT-IR spectroscopy is applied to solve this problem. Based on the polarized FT-IR spectroscopy and the molecular model in the fibers, the length of the repeat unit of PI molecule, the angle between the fiber axis and the symmetric stretching direction of carbonyl group on the imide ring, and the angle between the PI molecular axis and fiber axis are all investigated. The Mark-Howink equation is used to calculate the number-average molar mass of PI molecules. The orientation states of PI molecules in the electrospun nanofibers are studied from the number-average molar mass of PI molecules and the average fiber diameter. Quantitative analysis of the orientation factor of PI molecules in the electrospun nanofibers is performed by polarized FT-IR spectroscopy. Copyright © 2018 Elsevier B.V. All rights reserved.

A Multiaxial Molecular Ferroelectric with Highest Curie Temperature and Fastest Polarization Switching.

PubMed

Tang, Yuan-Yuan; Li, Peng-Fei; Zhang, Wan-Ying; Ye, Heng-Yun; You, Yu-Meng; Xiong, Ren-Gen

2017-10-04

The classical organic ferroelectric, poly(vinylidene fluoride) (PVDF), has attracted much attention as a promising candidate for data storage applications compatible with all-organic electronics. However, it is the low crystallinity, the large coercive field, and the limited thermal stability of remanent polarization that severely hinder large-scale integration. In light of that, we show a molecular ferroelectric thin film of [Hdabco][ReO 4 ] (dabco = 1,4-diazabicyclo[2.2.2]octane) (1), belonging to another class of typical organic ferroelectrics. Remarkably, it displays not only the highest Curie temperature of 499.6 K but also the fastest polarization switching of 100k Hz among all reported molecular ferroelectrics. Combined with the large remanent polarization values (∼9 μC/cm 2 ), the low coercive voltages (∼10 V), and the unique multiaxial ferroelectric nature, 1 becomes a promising and viable alternative to PVDF for data storage applications in next-generation flexible devices, wearable devices, and bionics.

Atomistic and coarse-grained computer simulations of raft-like lipid mixtures.

PubMed

Pandit, Sagar A; Scott, H Larry

2007-01-01

Computer modeling can provide insights into the existence, structure, size, and thermodynamic stability of localized raft-like regions in membranes. However, the challenges in the construction and simulation of accurate models of heterogeneous membranes are great. The primary obstacle in modeling the lateral organization within a membrane is the relatively slow lateral diffusion rate for lipid molecules. Microsecond or longer time-scales are needed to fully model the formation and stability of a raft in a membra ne. Atomistic simulations currently are not able to reach this scale, but they do provide quantitative information on the intermolecular forces and correlations that are involved in lateral organization. In this chapter, the steps needed to carry out and analyze atomistic simulations of hydrated lipid bilayers having heterogeneous composition are outlined. It is then shown how the data from a molecular dynamics simulation can be used to construct a coarse-grained model for the heterogeneous bilayer that can predict the lateral organization and stability of rafts at up to millisecond time-scales.

Atomistic study of the graphene nanobubbles

NASA Astrophysics Data System (ADS)

Iakovlev, Evgeny; Zhilyaev, Petr; Akhatov, Iskander

2017-11-01

A two-dimensional (2D) heterostructures can be created using 2D crystals stacking method. Substance can be trapped between the layers which leads to formation of the surface nanobubbles. We study nanobubbles trapped between graphene layers with argon atoms inside using molecular dynamics approach. For bubbles with radius in range 7-34 nm the solid close-packed state of argon is found, although according to bulk argon phase diagram the fluid phase must be observed. The universal shape scaling (constant ratio of height to radius), which is found experimentally and proved by the theory of elasticity of membranes, is also observed in our atomistic simulations. An unusual pancake shape (extremely small height to radius ratio) is found for smallest nanobubble with radius 7 nm. The nanobubbles with similar shape were experimentally observed at the interface between water and hydrophobic surface.

Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kibaek; Stewart, D. Scott, E-mail: santc@illinois.edu, E-mail: dss@illinois.edu; Joshi, Kaushik

2016-05-14

We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model ismore » based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J; Praprotnik, Matej

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

PubMed

Yang, Shengfeng; Chen, Youping

2015-03-08

In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

Atomistic simulations of graphite etching at realistic time scales.

PubMed

Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

2017-10-01

Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

PubMed Central

Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

2013-01-01

Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, H. F.; Liu, Z. T.; Fan, C. C.

2016-08-15

By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO{sub 3} thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO{sub 3} and iso-polarity LaAlO{sub 3} substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO{sub 3} (111) substrate was more suitable than Nb-doped SrTiO{sub 3}. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentionsmore » need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO{sub 3} based superlattices.« less

Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Yang, H. F.; Liu, Z. T.; Fan, C. C.; Yao, Q.; Xiang, P.; Zhang, K. L.; Li, M. Y.; Liu, J. S.; Shen, D. W.

2016-08-01

By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO3 thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO3 and iso-polarity LaAlO3 substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO3 (111) substrate was more suitable than Nb-doped SrTiO3. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentions need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO3 based superlattices.

Infrared Polarization of the Molecular Cloud Associated to IRAS 18236-1205

NASA Astrophysics Data System (ADS)

Luna, A.; Retes, R.; Devaraj, R.; Maya, Y. D.; Carrasco, L.

2017-07-01

We present the near-infrared polarization observations towards the star forming molecular cloud associated with the IRAS source 18236-1205, obtained with the near-infrared (NIR) imaging polarimeter POLICAN at the Guillermo Haro Astrophysical Observatory in Cananea, Sonora, México.

Effect of molecular anisotropy on the intensity and degree of polarization of light scattered from model atmospheres

NASA Technical Reports Server (NTRS)

Bahethi, O. P.; Fraser, R. S.

1975-01-01

Computations of the intensity, flux, degree of polarization, and the positions of neutral points are presented for models of the terrestrial gaseous and hazy atmospheres by incorporating the molecular anisotropy due to air in the Rayleigh scattering optical thickness and phase matrix. Molecular anisotropy causes significant changes in the intensity, flux and the degree of polarization of the scattered light. The positions of neutral points do not change significantly. When the Rayleigh scattering optical thickness is kept constant and the molecular anisotropy factor is included only in the Rayleigh phase matrix, the flux does not change and the intensity and positions of neutron points change by a small amount. The changes in the degree of polarization are still significant.

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

PubMed Central

Abriata, Luciano A.; Dal Peraro, Matteo

2015-01-01

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027

A concurrent multiscale micromorphic molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Shaofan, E-mail: shaofan@berkeley.edu; Tong, Qi

2015-04-21

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from firstmore » principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.« less

ALMA’s Polarized View of 10 Protostars in the Perseus Molecular Cloud

NASA Astrophysics Data System (ADS)

Cox, Erin G.; Harris, Robert J.; Looney, Leslie W.; Li, Zhi-Yun; Yang, Haifeng; Tobin, John J.; Stephens, Ian

2018-03-01

We present 870 μm ALMA dust polarization observations of 10 young Class 0/I protostars in the Perseus Molecular Cloud. At ∼0.″35 (80 au) resolution, all of our sources show some degree of polarization, with most (9/10) showing significantly extended emission in the polarized continuum. Each source has incredibly intricate polarization signatures. In particular, all three disk-candidates have polarization vectors roughly along the minor axis, which is indicative of polarization produced by dust scattering. On ∼100 au scales, the polarization is at a relatively low level (≲1%) and is quite ordered. In sources with significant envelope emission, the envelope is typically polarized at a much higher (≳5%) level and has a far more disordered morphology. We compute the cumulative probability distributions for both the small (disk-scale) and large (envelope-scale) polarization percentage. We find that the two are intrinsically different, even after accounting for the different detection thresholds in the high/low surface brightness regions. We perform Kolmogorov–Smirnov and Anderson–Darling tests on the distributions of angle offsets of the polarization from the outflow axis. We find disk-candidate sources are different from the non-disk-candidate sources. We conclude that the polarization on the 100 au scale is consistent with the signature of dust scattering for disk-candidates and that the polarization on the envelope-scale in all sources may come from another mechanism, most likely magnetically aligned grains.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

PubMed Central

Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

2013-01-01

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

PubMed

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Róg, Tomasz; Vattulainen, Ilpo

2017-10-23

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.

doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

PubMed Central

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell–cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS. PMID:28906114

First Observation of the Submillimeter Polarization Spectrum in a Translucent Molecular Cloud

NASA Astrophysics Data System (ADS)

Ashton, Peter C.; Ade, Peter A. R.; Angilè, Francesco E.; Benton, Steven J.; Devlin, Mark J.; Dober, Bradley; Fissel, Laura M.; Fukui, Yasuo; Galitzki, Nicholas; Gandilo, Natalie N.; Klein, Jeffrey; Korotkov, Andrei L.; Li, Zhi-Yun; Martin, Peter G.; Matthews, Tristan G.; Moncelsi, Lorenzo; Nakamura, Fumitaka; Netterfield, Calvin B.; Novak, Giles; Pascale, Enzo; Poidevin, Frédérick; Santos, Fabio P.; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Soler, Juan D.; Thomas, Nicholas E.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

2018-04-01

Polarized emission from aligned dust is a crucial tool for studies of magnetism in the ISM, but a troublesome contaminant for studies of cosmic microwave background polarization. In each case, an understanding of the significance of the polarization signal requires well-calibrated physical models of dust grains. Despite decades of progress in theory and observation, polarized dust models remain largely underconstrained. During its 2012 flight, the balloon-borne telescope BLASTPol obtained simultaneous broadband polarimetric maps of a translucent molecular cloud at 250, 350, and 500 μm. Combining these data with polarimetry from the Planck 850 μm band, we have produced a submillimeter polarization spectrum, the first for a cloud of this type. We find the polarization degree to be largely constant across the four bands. This result introduces a new observable with the potential to place strong empirical constraints on ISM dust polarization models in a previously inaccessible density regime. Compared to models by Draine & Fraisse, our result disfavors two of their models for which all polarization arises due only to aligned silicate grains. By creating simple models for polarized emission in a translucent cloud, we verify that extinction within the cloud should have only a small effect on the polarization spectrum shape, compared to the diffuse ISM. Thus, we expect the measured polarization spectrum to be a valid check on diffuse ISM dust models. The general flatness of the observed polarization spectrum suggests a challenge to models where temperature and alignment degree are strongly correlated across major dust components.

Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoover, W. G.; Hoover, C. G.

1993-08-01

Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

Molecular orientation sensitive second harmonic microscopy by radially and azimuthally polarized light

PubMed Central

Ehmke, Tobias; Nitzsche, Tim Heiko; Knebl, Andreas; Heisterkamp, Alexander

2014-01-01

We demonstrate the possibility to switch the z-polarization component of the illumination in the vicinity of the focus of high-NA objective lenses by applying radially and azimuthally polarized incident light. The influence of the field distribution on nonlinear effects was first investigated by the means of simulations. These were performed for high-NA objective lenses commonly used in nonlinear microscopy. Special attention is paid to the influence of the polarization of the incoming field. For linearly, circularly and radially polarized light a considerable polarization component in z-direction is generated by high NA focusing. Azimuthal polarization is an exceptional case: even for strong focusing no z-component arises. Furthermore, the influence of the input polarization on the intensity contributing to the nonlinear signal generation was computed. No distinct difference between comparable input polarization states was found for chosen thresholds of nonlinear signal generation. Differences in signal generation for radially and azimuthally polarized vortex beams were experimentally evaluated in native collagen tissue (porcine cornea). The findings are in good agreement with the theoretical predictions and display the possibility to probe the molecular orientation along the optical axis of samples with known nonlinear properties. The combination of simulations regarding the nonlinear response of materials and experiments with different sample orientations and present or non present z-polarization could help to increase the understanding of nonlinear signal formation in yet unstudied materials. PMID:25071961

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Atomistic Molecular Dynamics Simulations of Carbon Dioxide Diffusivity in n-Hexane, n-Decane, n-Hexadecane, Cyclohexane, and Squalane.

PubMed

Moultos, Othonas A; Tsimpanogiannis, Ioannis N; Panagiotopoulos, Athanassios Z; Trusler, J P Martin; Economou, Ioannis G

2016-12-22

Atomistic molecular dynamics simulations were carried out to obtain the diffusion coefficients of CO 2 in n-hexane, n-decane, n-hexadecane, cyclohexane, and squalane at temperatures up to 423.15 K and pressures up to 65 MPa. Three popular models were used for the representation of hydrocarbons: the united atom TraPPE (TraPPE-UA), the all-atom OPLS, and an optimized version of OPLS, namely, L-OPLS. All models qualitatively reproduce the pressure dependence of the diffusion coefficient of CO 2 in hydrocarbons measured recently, and L-OPLS was found to be the most accurate. Specifically for n-alkanes, L-OPLS also reproduced the measured viscosities and densities much more accurately than the original OPLS and TraPPE-UA models, indicating that the optimization of the torsional potential is crucial for the accurate description of transport properties of long chain molecules. The three force fields predict different microscopic properties such as the mean square radius of gyration for the n-alkane molecules and pair correlation functions for the CO 2 -n-alkane interactions. CO 2 diffusion coefficients in all hydrocarbons studied are shown to deviate significantly from the Stokes-Einstein behavior.

Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yongfeng Zhang; Paul C Millett; Michael R Tonks

2013-10-01

In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagatingmore » crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.« less

All-atomistic molecular dynamics (AA-MD) studies and pharmacokinetic performance of PAMAM-dendrimer-furosemide delivery systems.

PubMed

Otto, Daniel P; de Villiers, Melgardt M

2018-06-13

Improvement of problematic dissolution and solubility properties of a model drug, furosemide, was investigated for poly(amidoamine) (PAMAM) dendrimer complexes of the drug. Full and half generation dendrimers with amino and ester terminals respectively, were studied. In vitro release performance of these complexes was investigated at drug loads ranging 5-60% using simulated gastric fluids. Full generation dendrimers accommodated higher drug loads, outperformed half-generation complexes, and free drug. Pharmacokinetic studies in rats indicated that the dendrimer complexes markedly improved in the bioavailability of the drug compared to the unformulated drug. The G3.0-PAMAM dendrimer complex showed a two-fold increase in C max and a 1.75-fold increase in AUC over the free drug. Additionally, T max was shortened from approximately 25 to 20 min. One of the first all-atomistic molecular dynamics (AA-MD) simulation studies was performed to evaluate low-generation dendrimer-drug complexes as well as its pharmacokinetic performance. AA-MD provided insight into the intermolecular interactions that take place between the dendrimer and drug. It is suggested that the dendrimer not only encapsulates the drug, but can also orientate the drug in stabilized dispersion to prevent drug clustering which could impact release and bioavailability negatively. AA-MD can be a useful tool to develop dendrimer-based drug delivery systems. Copyright © 2018. Published by Elsevier B.V.

Spin-polarized transport properties of a pyridinium-based molecular spintronics device

NASA Astrophysics Data System (ADS)

Zhang, J.; Xu, B.; Qin, Z.

2018-05-01

By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

Free energy functionals for polarization fluctuations: Pekar factor revisited.

PubMed

Dinpajooh, Mohammadhasan; Newton, Marshall D; Matyushov, Dmitry V

2017-02-14

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces

PubMed Central

Li, Qiang; He, Guo-Wei

2009-01-01

Recent experiments have found that slip length could be as large as on the order of 1 μm for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths, which cannot be obtained by molecular dynamics simulation alone. PMID:19693344

The enhanced spin-polarized transport behaviors through cobalt benzene-porphyrin-benzene molecular junctions: the effect of functional groups

NASA Astrophysics Data System (ADS)

Cheng, Jue-Fei; Zhou, Liping; Wen, Zhongqian; Yan, Qiang; Han, Qin; Gao, Lei

2017-05-01

The modification effects of the groups amino (NH2) and nitro (NO2) on the spin polarized transport properties of the cobalt benzene-porphyrin-benzene (Co-BPB) molecule coupled to gold (Au) nanowire electrodes are investigated by the nonequilibrium Green’s function method combined with the density functional theory. The calculation results show that functional groups can lead to the significant spin-filter effect, enhanced low-bias negative differential resistance (NDR) behavior and novel reverse rectifying effect in Co-BPB molecular junction. The locations and types of functional groups have distinct influences on spin-polarized transport performances. The configuration with NH2 group substituting H atom in central porphyrin ring has larger spin-down current compared to that with NO2 substitution. And Co-BPB molecule junction with NH2 group substituting H atom in side benzene ring shows reverse rectifying effect. Detailed analyses confirm that NH2 and NO2 group substitution change the spin-polarized transferred charge, which makes the highest occupied molecular orbitals (HOMO) of spin-down channel of Co-BPB closer to the Fermi level. And the shift of HOMO strengthens the spin-polarized coupling between the molecular orbitals and the electrodes, leading to the enhanced spin-polarized behavior. Our findings might be useful in the design of multi-functional molecular devices in the future.

Understanding the Interaction of Pluronics L61 and L64 with a DOPC Lipid Bilayer: An Atomistic Molecular Dynamics Study

DOE PAGES

Ileri Ercan, Nazar; Stroeve, Pieter; Tringe, Joseph W.; ...

2016-09-13

In this paper, we investigate the interactions of Pluronics L61 and L64 with a dioleylphosphatidylcholine (DOPC) lipid bilayer by atomistic molecular dynamics simulations using the all-atom OPLS force field. Our results show that the initial configuration of the polymer with respect to the bilayer determines its final conformation within the bilayer. When the polymer is initially placed at the lipid/water interface, we observe partial insertion of the polymer in a U-shaped conformation. On the other hand, when the polymer is centered at the bilayer, it stabilizes to a transmembrane state, which facilitates water transport across the bilayer. We show thatmore » membrane thickness decreases while its fluidity increases in the presence of Pluronics. When the polymer concentration inside the bilayer is high, pore formation is initiated with L64. Finally, our results show good agreement with existing experimental data and reveal that the hydrophilic/lipophilic balance of the polymer plays a critical role in the interaction mechanisms as well as in the dynamics of Pluronics with and within the bilayer.« less

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Modeling the atomistic growth behavior of gold nanoparticles in solution

NASA Astrophysics Data System (ADS)

Turner, C. Heath; Lei, Yu; Bao, Yuping

2016-04-01

The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

Characterization of molecularly imprinted polymers using a new polar solvent titration method.

PubMed

Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

2014-07-01

A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs. Copyright © 2014 John Wiley & Sons, Ltd.

Supramolecular Systems Behavior at the Air-Water Interface. Molecular Dynamic Simulation Study.

NASA Astrophysics Data System (ADS)

Sandoval, C.; Saavedra, M.; Gargallo, L.; Radić, D.

2008-08-01

Atomistic molecular dynamics simulation (MDS) was development to investigate the structural and dynamic properties of a monolayer of supramolecular systems. The simulations were performed at room temperature, on inclusion complexes (ICs) of α-cyclodextrin (CD) with poly(ethylene-oxide)(PEO), poly(ɛ-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF). The simulations were carried out for a surface area of 30Å. The trajectories of the MDS show that the system more stable was IC-PEC, being the less stable IC-PEO. The disordered monolayer for the systems was proved by the orientation correlation function and the radial distribution function between the polar groups of ICs and the water molecules. We found that the system IC-PEC was more stable that the systems IC-PTHF and IC-PEO.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

PubMed

Quevillon, Michael J; Whitmer, Jonathan K

2018-01-02

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

Soil Organic Matter (SOM): Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Amity

Molecular simulation is a powerful tool used to gain an atomistic, molecular, and nanoscale level understanding of the structure, dynamics, and interactions from adsorption on minerals and assembly in aggregates of soil organic matter (SOM). Given the importance of SOM fate and persistence in soils and the current knowledge gaps, applications of atomistic scale simulations to study the complex compounds in SOM and their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types common in soils are few and far between. Here, we describe various molecular simulation methods that are currently inmore » use in various areas and applicable to SOM research, followed by a brief survey of specific applications to SOM research and an illustration with our own recent efforts in this area. We conclude with an outlook and the challenges for future research in this area.« less

First Principles Atomistic Model for Carbon-Doped Boron Suboxide

DTIC Science & Technology

2014-09-01

First Principles Atomistic Model for Carbon-Doped Boron Suboxide by Amol B Rahane, Jennifer S Dunn, and Vijay Kumar ARL-TR-7106...2014 First Principles Atomistic Model for Carbon-Doped Boron Suboxide Amol B Rahane Dr Vijay Kumar Foundation 1969 Sector 4 Gurgaon...5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Amol B Rahane, Jennifer S Dunn, and Vijay Kumar 5d. PROJECT

Intergranular fracture in UO{sub 2}: derivation of traction-separation law from atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Millett, P.C.; Tonks, M.R.

2013-07-01

In this study, the intergranular fracture behavior of UO{sub 2} was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt Σ5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at themore » propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior. (authors)« less

Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

PubMed Central

Gilson, Michael K.

2014-01-01

Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications. PMID:25503996

Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

PubMed

Fenley, Andrew T; Muddana, Hari S; Gilson, Michael K

2014-01-01

Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.

From Atomistic Model to the Peierls-Nabarro Model with {γ} -surface for Dislocations

NASA Astrophysics Data System (ADS)

Luo, Tao; Ming, Pingbing; Xiang, Yang

2018-05-01

The Peierls-Nabarro (PN) model for dislocations is a hybrid model that incorporates the atomistic information of the dislocation core structure into the continuum theory. In this paper, we study the convergence from a full atomistic model to the PN model with {γ} -surface for the dislocation in a bilayer system. We prove that the displacement field and the total energy of the dislocation solution of the PN model are asymptotically close to those of the full atomistic model. Our work can be considered as a generalization of the analysis of the convergence from atomistic model to Cauchy-Born rule for crystals without defects.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

A Configurational-Bias-Monte-Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures Into Atomistic Models.

PubMed

Loeffler, Troy David; Chan, Henry; Narayanan, Badri; Cherukara, Mathew J; Gray, Stephen K; Sankaranarayanan, Subramanian K R S

2018-06-20

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which

Impact of molecular packing on electronic polarization in organic crystals: the case of pentacene vs TIPS-pentacene.

PubMed

Ryno, Sean M; Risko, Chad; Brédas, Jean-Luc

2014-04-30

Polarization energy corresponds to the stabilization of the cation or anion state of an atom or molecule when going from the gas phase to the solid state. The decrease in ionization energy and increase in electron affinity in the solid state are related to the (electronic and nuclear) polarization of the surrounding atoms and molecules in the presence of a charged entity. Here, through a combination of molecular mechanics and quantum mechanics calculations, we evaluate the polarization energies in two prototypical organic semiconductors, pentacene and 6,13-bis(2-(tri-isopropylsilyl)ethynyl)pentacene (TIPS-pentacene). Comparison of the results for the two systems reveals the critical role played by the molecular packing configurations in the determination of the polarization energies and provides physical insight into the experimental data reported by Lichtenberger and co-workers (J. Amer. Chem. Soc. 2010, 132, 580; J. Phys. Chem. C 2010, 114, 13838). Our results underline that the impact of packing configurations, well established in the case of the charge-transport properties, also extends to the polarization properties of π-conjugated materials.

An object oriented Python interface for atomistic simulations

NASA Astrophysics Data System (ADS)

Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

2016-01-01

Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian

2015-12-28

We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, butmore » increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.« less

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

NASA Astrophysics Data System (ADS)

Xiao, HuiFang; Huang, Bin; Yao, Ge; Kang, WenBin; Gong, Sheng; Pan, Hai; Cao, Yi; Wang, Jun; Zhang, Jian; Wang, Wei

2018-03-01

Understanding the processes of protein adsorption/desorption on nanoparticles' surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.

Molecular-level comparison of alkylsilane and polar-embedded reversed-phase liquid chromatography systems.

PubMed

Rafferty, Jake L; Siepmann, J Ilja; Schure, Mark R

2008-08-15

Stationary phases with embedded polar groups possess several advantages over conventional alkylsilane phases, such as reduced peak tailing, enhanced selectivity for specific functional groups, and the ability to use a highly aqueous mobile phase. To gain a deeper understanding of the retentive properties of these reversed-phase packings, molecular simulations were carried out for three different stationary phases in contact with mobile phases of various water/methanol ratios. Two polar-embedded phases were modeled, namely, amide and ether containing, and compared to a conventional octadecylsilane phase. The simulations show that, due to specific hydrogen bond interactions, the polar-embedded phases take up significantly more solvent and are more ordered than their alkyl counterparts. Alkane and alcohol probe solutes indicate that the polar-embedded phases are less retentive than alkyl phases for nonpolar species, whereas polar species are more retained by them due to hydrogen bonding with the embedded groups and the increased amount of solvent within the stationary phase. This leads to a significant reduction of the free-energy barrier for the transfer of polar species from the mobile phase to residual silanols, and this reduced barrier provides a possible explanation for reduced peak tailing.

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

PubMed

Riniker, Sereina

2018-03-26

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

Atomistic and molecular effects in electric double layers at high surface charges

DOE PAGES

Templeton, Jeremy Alan; Lee, Jonathan; Mani, Ali

2015-06-16

Here, the Poisson–Boltzmann theory for electrolytes near a charged surface is known to be invalid due to unaccounted physics associated with high ion concentration regimes. In order to investigate this regime, fluids density functional theory (f-DFT) and molecular dynamics (MD) simulations were used to determine electric surface potential as a function of surface charge. Based on these detailed computations, for electrolytes with nonpolar solvent, the surface potential is shown to depend quadratically on the surface charge in the high charge limit. We demonstrate that modified Poisson–Boltzmann theories can model this limit if they are augmented with atomic packing densities providedmore » by MD. However, when the solvent is a highly polar molecule water an intermediate regime is identified in which a constant capacitance is realized. Simulation results demonstrate the mechanism underlying this regime, and for the salt water system studied here, it persists throughout the range of physically realistic surface charge densities so the potential’s quadratic surface charge dependence is not obtained.« less

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations

PubMed Central

2018-01-01

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure–constant temperature ensemble. These materials exhibit a distinct “smectic” liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications. PMID:29301305

Free energy functionals for polarization fluctuations: Pekar factor revisited

DOE PAGES

Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

2017-02-13

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parametermore » accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found for the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).« less

Free energy functionals for polarization fluctuations: Pekar factor revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parametermore » accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found for the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).« less

Elastic dipoles of point defects from atomistic simulations

NASA Astrophysics Data System (ADS)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

Atomistic Cohesive Zone Models for Interface Decohesion in Metals

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Glaessgen, Edward H.

2009-01-01

Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship characterizing the load transfer across the plane of a growing edge crack is extracted from atomistic simulations for use within a continuum finite element model. The methodology for the atomistic derivation of a cohesive-zone law is presented. This procedure can be implemented to build cohesive-zone finite element models for simulating fracture in nanocrystalline or ultrafine grained materials.

Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

NASA Astrophysics Data System (ADS)

Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

2006-03-01

Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

Atomistic Simulation of Initiation in Hexanitrostilbene

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations

PubMed Central

Hayashi, Shigehiko

2017-01-01

The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown. Here, we report an atomic structure of the IF form predicted by atomic-level molecular dynamics (MD) simulations of the alternating access transition with a recently developed accelerating technique. We successfully obtained a significantly stable IF structure characterized by newly formed well-packed and -organized inter-domain interactions through the accelerated simulations of unprecedentedly large conformational changes of the alternating access without a prior knowledge of the target protein structure. The simulation also shed light on an atomistic mechanism of the strict transport selectivity of adenosine nucleotides over guanosine and inosine ones. Furthermore, the IF structure was shown to bind ATP and BA, and thus revealed their binding mechanisms. The present study proposes a qualitatively novel view of the alternating access of transporters having the unique three-fold symmetry in atomic details and opens the way for rational drug design targeting the transporter in the dynamic functional cycle. PMID:28727843

NGC 7538 IRS. 1. Interaction of a Polarized Dust Spiral and a Molecular Outflow

NASA Astrophysics Data System (ADS)

Wright, M. C. H.; Hull, Charles L. H.; Pillai, Thushara; Zhao, Jun-Hui; Sandell, Göran

2014-12-01

We present dust polarization and CO molecular line images of NGC 7538 IRS 1. We combined data from the Submillimeter Array, the Combined Array for Research in Millimeter-wave Astronomy, and the James Clerk Maxwell Telescope to make images with ~2.''5 resolution at 230 and 345 GHz. The images show a remarkable spiral pattern in both the dust polarization and molecular outflow. These data dramatically illustrate the interplay between a high infall rate onto IRS 1 and a powerful outflow disrupting the dense, clumpy medium surrounding the star. The images of the dust polarization and the CO outflow presented here provide observational evidence for the exchange of energy and angular momentum between the infall and the outflow. The spiral dust pattern, which rotates through over 180° from IRS 1, may be a clumpy filament wound up by conservation of angular momentum in the infalling material. The redshifted CO emission ridge traces the dust spiral closely through the MM dust cores, several of which may contain protostars. We propose that the CO maps the boundary layer where the outflow is ablating gas from the dense gas in the spiral.

Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

DOE PAGES

Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; ...

2017-01-26

When using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. Furthermore, by calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. A comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnonsmore » leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.« less

Fibronectin module FN(III)9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics.

PubMed

Kubiak-Ossowska, Karina; Mulheran, Paul A; Nowak, Wieslaw

2014-08-21

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FN(III)9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (-1e), FN(III)9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN(III)9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FN(III)9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved.

Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

DOE PAGES

Taylor, Christopher D.

2012-01-01

Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies ofmore » the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.« less

Exciton polarization, fine-structure splitting, and the asymmetry of quantum dots under uniaxial stress.

PubMed

Gong, Ming; Zhang, Weiwei; Guo, Guang-Can; He, Lixin

2011-06-03

We derive a general relation between the fine-structure splitting (FSS) and the exciton polarization angle of self-assembled quantum dots under uniaxial stress. We show that the FSS lower bound under external stress can be predicted by the exciton polarization angle and FSS under zero stress. The critical stress can also be determined by monitoring the change in exciton polarization angle. We confirm the theory by performing atomistic pseudopotential calculations for the InAs/GaAs quantum dots. The work provides deep insight into the dot asymmetry and their optical properties and a useful guide in selecting quantum dots with the smallest FSS, which are crucial in entangled photon source applications.

Simulation of dense amorphous polymers by generating representative atomistic models

NASA Astrophysics Data System (ADS)

Curcó, David; Alemán, Carlos

2003-08-01

A method for generating atomistic models of dense amorphous polymers is presented. The generated models can be used as starting structures of Monte Carlo and molecular dynamics simulations, but also are suitable for the direct evaluation physical properties. The method is organized in a two-step procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, an iterative algorithm is applied to relax the nonbonding interactions. In order to check the performance of the method we examined structure-dependent properties for three polymeric systems: polyethyelene (ρ=0.85 g/cm3), poly(L,D-lactic) acid (ρ=1.25 g/cm3), and polyglycolic acid (ρ=1.50 g/cm3). The method successfully generated representative packings for such dense systems using minimum computational resources.

Comparative simulations of microjetting using atomistic and continuous approaches in presence of viscosity and surface tension

NASA Astrophysics Data System (ADS)

Durand, Olivier; Soulard, Laurent; Jaouen, Stephane; Heuze, Olivier; Colombet, Laurent; Cieren, Emmanuel

2017-06-01

We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and they use an equation of state calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of the viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with a very good agreement the distributions, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes exhibit also a similar phenomenology of fragmentation of the metallic liquid sheets ejected.

Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential

NASA Astrophysics Data System (ADS)

Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

2015-12-01

To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are

Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

NASA Technical Reports Server (NTRS)

Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

2006-01-01

A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

Determination of three-dimensional molecular orientation of type-I collagen by circularly-polarized second harmonic generation imaging

NASA Astrophysics Data System (ADS)

Zhuo, Guan-Yu; Hung, Wei-Han; Kao, Fu-Jen

2017-04-01

The content of collagen is up to 30% existing in mammals. It supports the main component of connective tissues such as skin, ligament, and cartilage. Among various types of collagen, type-I collagen is of the most abundance and has been broadly studied due to the importance in bioscience. Second harmonic generation (SHG) microscopy is an effective tool used to study the collagen organization without labeling. In this study, we used circular polarization instead of linear polarization to retrieve three-dimensional (3D) molecular orientation of type-I collagen with only two cross polarized SHG images without acquiring an image stack of varying polarization.

Characterization of Polar, Semi-Polar, and Non-Polar p-n Homo and Hetero-junctions grown by Ammonia Molecular Beam Epitaxy

NASA Astrophysics Data System (ADS)

Hurni, Christophe Antoine

Widespread interest in the group III-Nitrides began with the achievement of p-type conductivity in the early 1990s in Mg-doped GaN films grown by metal organic chemical vapor deposition (MOCVD) by Nakamura et al. Indeed, MOCVD-grown Mg-doped GaN is insulating as-grown, because of the formation of neutral Mg-H complexes. Nakamura et al. showed that a rapid thermal anneal removes the hydrogen and enables p-conductivity. Shortly after this discovery, the first LEDs and lasers were demonstrated by Nakamura et al. The necessary annealing step is problematic for devices which need a buried p-layer, such as hetero-junction bipolar transistors. Ammonia molecular beam epitaxy (NH3-MBE) has a great potential for growing vertical III-Nitrides-based devices, thank to its N-rich growth conditions and all the usual advantages of MBE, which include a low-impurity growth environment, in situ monitoring techniques as well as the ability to grow sharp interfaces. We first investigated the growth of p-GaN by NH3-MBE. We found that the hole concentration strongly depends on the growth temperature. Thanks to comprehensive Hall and transfer length measurements, we found evidences for a compensating donor defects in NH3-MBE-grown Mg-doped GaN films. High-quality p-n junctions with very low reverse current and close to unity ideality factor were also grown and investigated. For the design of heterojunction devices such as laser diodes, light emitting diodes or heterojunction bipolar transistors, hetero-interface's characteristics such as the band offset or interface charges are fundamental. A technique developed by Kroemer et al. uses capacitance-voltage (C-V) profiling to extract band-offsets and charges at a hetero-interface. We applied this technique to the III-Nitrides. We discovered that for the polar III-Nitrides, the technique is not applicable because of the very large polarization charge. We nevertheless successfully measured the polarization charge at the AlGaN/GaN hetero

Stress-dependence of kinetic transitions at atomistic defects

NASA Astrophysics Data System (ADS)

Ball, S. L.; Alexander, K. C.; Schuh, C. A.

2018-01-01

The full second-rank activation volume tensors associated with vacancy migration in FCC copper and HCP titanium as well as transition events in the Σ5 (2 1 0) grain boundary in copper are calculated and analyzed. The full tensorial results quantitatively illustrate how the conventional use of an activation volume scalar in atomistic studies of the kinetic processes of complex defects can miss important stress dependencies, in that neither hydrostatic pressure nor deviatoric stress dependencies can be considered alone as dominating the response. The results speak to the importance of anisotropies in the stress-dependence of atomistic kinetics, including crystal structure anisotropy, elastic anisotropy, and defect structure or migration-path anisotropies.

Atomistic properties of γ uranium.

PubMed

Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

2012-02-22

The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

Atomistic properties of γ uranium

NASA Astrophysics Data System (ADS)

Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

2012-02-01

The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

Atomistic modeling of water diffusion in hydrolytic biomaterials.

PubMed

Gautieri, Alfonso; Mezzanzanica, Andrea; Motta, Alberto; Redealli, Alberto; Vesentini, Simone

2012-04-01

One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.

Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

DOE PAGES

Olson, Derek; Shapeev, Alexander V.; Bochev, Pavel B.; ...

2015-11-16

Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

Electrocaloric effects in the lead-free Ba (Zr ,Ti )O3 relaxor ferroelectric from atomistic simulations

NASA Astrophysics Data System (ADS)

Jiang, Zhijun; Prokhorenko, Sergei; Prosandeev, Sergey; Nahas, Y.; Wang, D.; Íñiguez, Jorge; Defay, E.; Bellaiche, L.

2017-07-01

Atomistic effective Hamiltonian simulations are used to investigate electrocaloric (EC) effects in the lead-free Ba (Zr0.5Ti0.5)O3 (BZT) relaxor ferroelectric. We find that the EC coefficient varies nonmonotonically with the field at any temperature, presenting a maximum that can be traced back to the behavior of BZT's polar nanoregions. We also introduce a simple Landau-based model that reproduces the EC behavior of BZT as a function of field and temperature, and which is directly applicable to other compounds. Finally, we confirm that, for low temperatures (i.e., in nonergodic conditions), the usual indirect approach to measure the EC response provides an estimate that differs quantitatively from a direct evaluation of the field-induced temperature change.

Density functional theory fragment descriptors to quantify the reactivity of a molecular family: application to amino acids.

PubMed

Senet, P; Aparicio, F

2007-04-14

By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a blind test, the method is applied to the lateral chains of the 20 isolated amino acids. One demonstrates that the local softness of the lateral chain is a quantitative measure of the similarity of the amino acids. It predicts the separation of amino acids in different biochemical groups (aliphatic, basic, acidic, sulfur contained, and aromatic). The present approach may find applications in quantitative structure activity relationship methodology.

Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

PubMed

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus

2015-05-01

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

AACSD: An atomistic analyzer for crystal structure and defects

NASA Astrophysics Data System (ADS)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

PubMed

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

Using polarized Raman spectroscopy and the pseudospectral method to characterize molecular structure and function

NASA Astrophysics Data System (ADS)

Weisman, Andrew L.

Electronic structure calculation is an essential approach for determining the structure and function of molecules and is therefore of critical interest to physics, chemistry, and materials science. Of the various algorithms for calculating electronic structure, the pseudospectral method is among the fastest. However, the trade-off for its speed is more up-front programming and testing, and as a result, applications using the pseudospectral method currently lag behind those using other methods. In Part I of this dissertation, we first advance the pseudospectral method by optimizing it for an important application, polarized Raman spectroscopy, which is a well-established tool used to characterize molecular properties. This is an application of particular importance because often the easiest and most economical way to obtain the polarized Raman spectrum of a material is to simulate it; thus, utilization of the pseudospectral method for this purpose will accelerate progress in the determination of molecular properties. We demonstrate that our implementation of Raman spectroscopy using the pseudospectral method results in spectra that are just as accurate as those calculated using the traditional analytic method, and in the process, we derive the most comprehensive formulation to date of polarized Raman intensity formulas, applicable to both crystalline and isotropic systems. Next, we apply our implementation to determine the orientations of crystalline oligothiophenes -- a class of materials important in the field of organic electronics -- achieving excellent agreement with experiment and demonstrating the general utility of polarized Raman spectroscopy for the determination of crystal orientation. In addition, we derive from first-principles a method for using polarized Raman spectra to establish unambiguously whether a uniform region of a material is crystalline or isotropic. Finally, we introduce free, open-source software that allows a user to determine any of a

The molecular orientation of CO on Pd(1 1 1): a polarization-dependent SFG study

NASA Astrophysics Data System (ADS)

Galletto, Paolo; Unterhalt, Holger; Rupprechter, Günther

2003-01-01

The molecular orientation of carbon monoxide adsorbed on Pd(1 1 1) was examined by sum frequency generation (SFG) vibrational spectroscopy utilizing different polarization combinations of the visible and SFG light. This allows to determine the CO tilt angle with respect to the substrate, provided that a proper optical model for the interface can be defined. It is demonstrated that it is essential to invoke the βaac hyperpolarizability into the analysis and that polarization-dependent SFG of CO/Pd(1 1 1) yields information on βaac/ βccc rather than the tilt angle.

Atomistic methodologies for material properties of 2D materials at the nanoscale

NASA Astrophysics Data System (ADS)

Zhang, Zhen

Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our

Molecular frame photoemission by a comb of elliptical high-order harmonics: a sensitive probe of both photodynamics and harmonic complete polarization state.

PubMed

Veyrinas, K; Gruson, V; Weber, S J; Barreau, L; Ruchon, T; Hergott, J-F; Houver, J-C; Lucchese, R R; Salières, P; Dowek, D

2016-12-16

Due to the intimate anisotropic interaction between an XUV light field and a molecule resulting in photoionization (PI), molecular frame photoelectron angular distributions (MFPADs) are most sensitive probes of both electronic/nuclear dynamics and the polarization state of the ionizing light field. Consequently, they encode the complex dipole matrix elements describing the dynamics of the PI transition, as well as the three normalized Stokes parameters s 1 , s 2 , s 3 characterizing the complete polarization state of the light, operating as molecular polarimetry. The remarkable development of advanced light sources delivering attosecond XUV pulses opens the perspective to visualize the primary steps of photochemical dynamics in time-resolved studies, at the natural attosecond to few femtosecond time-scales of electron dynamics and fast nuclear motion. It is thus timely to investigate the feasibility of measurement of MFPADs when PI is induced e.g., by an attosecond pulse train (APT) corresponding to a comb of discrete high-order harmonics. In the work presented here, we report MFPAD studies based on coincident electron-ion 3D momentum imaging in the context of ultrafast molecular dynamics investigated at the PLFA facility (CEA-SLIC), with two perspectives: (i) using APTs generated in atoms/molecules as a source for MFPAD-resolved PI studies, and (ii) taking advantage of molecular polarimetry to perform a complete polarization analysis of the harmonic emission of molecules, a major challenge of high harmonic spectroscopy. Recent results illustrating both aspects are reported for APTs generated in unaligned SF 6 molecules by an elliptically polarized infrared driving field. The observed fingerprints of the elliptically polarized harmonics include the first direct determination of the complete s 1 , s 2 , s 3 Stokes vector, equivalent to (ψ, ε, P), the orientation and the signed ellipticity of the polarization ellipse, and the degree of polarization P. They are

Addressing uncertainty in atomistic machine learning.

PubMed

Peterson, Andrew A; Christensen, Rune; Khorshidi, Alireza

2017-05-10

Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate of the uncertainty when the width is comparable to that in the training data. Intriguingly, we also show that the uncertainty can be localized to specific atoms in the simulation, which may offer hints for the generation of training data to strategically improve the machine-learned representation.

Robust mode space approach for atomistic modeling of realistically large nanowire transistors

NASA Astrophysics Data System (ADS)

Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

2018-01-01

Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Long-time atomistic simulations with the Parallel Replica Dynamics method

NASA Astrophysics Data System (ADS)

Perez, Danny

Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

Atomistic calculations of dislocation core energy in aluminium

DOE PAGES

Zhou, X. W.; Sills, R. B.; Ward, D. K.; ...

2017-02-16

A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin 2β + B·cos 2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

Atomistic calculations of dislocation core energy in aluminium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, X. W.; Sills, R. B.; Ward, D. K.

A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin 2β + B·cos 2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

Atomistic modeling of interphases in spider silk fibers

NASA Astrophysics Data System (ADS)

Fossey, Stephen Andrew

The objective of this work is to create an atomistic model to account for the unusual physical properties of silk fibers. Silk fibers have exceptional mechanical toughness, which makes them of interest as high performance fibers. In order to explain the toughness, a model for the molecular structure based on simple geometric reasoning was formulated. The model consists of very small crystallites, on the order of 5 nm, connected by a noncrystalline interphase. The interphase is a region between the crystalline phase and the amorphous phase, which is defined by the geometry of the system. The interphase is modeled as a very thin (<5 nm) film of noncrystalline polymer constructed using a Monte Carlo, rotational isomeric states approach followed by simulated annealing in order to achieve equilibrium chain configurations and density. No additional assumptions are made about density, orientation, or packing. The mechanical properties of the interphase are calculated using the method of Theodoreau and Suter. Finally, observable properties such as wide angle X-ray scattering and methyl rotation rates are calculated and compared with experimental data available in the literature.

Docking 90Sr radionuclide in cement: An atomistic modeling study

NASA Astrophysics Data System (ADS)

Youssef, Mostafa; Pellenq, Roland J.-M.; Yildiz, Bilge

Cementitious materials are considered to be a waste form for the ultimate disposal of radioactive materials in geological repositories. We investigated by means of atomistic simulations the encapsulation of strontium-90, an important radionuclide, in calcium-silicate-hydrate (C-S-H) and its crystalline analog, the 9 Å-tobermorite. C-S-H is the major binding phase of cement. Strontium was shown to energetically favor substituting calcium in the interlayer sites in C-S-H and 9 Å-tobermorite with the trend more pronounced in the latter. The integrity of the silicate chains in both cementitious waste forms were not affected by strontium substitution within the time span of molecular dynamics simulation. Finally, we observed a limited degradation of the mechanical properties in the strontium-containing cementitious waste form with the increasing strontium concentration. These results suggest the cement hydrate as a good candidate for immobilizing radioactive strontium.

Consistent Temperature Coupling with Thermal Fluctuations of Smooth Particle Hydrodynamics and Molecular Dynamics

PubMed Central

Ganzenmüller, Georg C.; Hiermaier, Stefan; Steinhauser, Martin O.

2012-01-01

We propose a thermodynamically consistent and energy-conserving temperature coupling scheme between the atomistic and the continuum domain. The coupling scheme links the two domains using the DPDE (Dissipative Particle Dynamics at constant Energy) thermostat and is designed to handle strong temperature gradients across the atomistic/continuum domain interface. The fundamentally different definitions of temperature in the continuum and atomistic domain – internal energy and heat capacity versus particle velocity – are accounted for in a straightforward and conceptually intuitive way by the DPDE thermostat. We verify the here-proposed scheme using a fluid, which is simultaneously represented as a continuum using Smooth Particle Hydrodynamics, and as an atomistically resolved liquid using Molecular Dynamics. In the case of equilibrium contact between both domains, we show that the correct microscopic equilibrium properties of the atomistic fluid are obtained. As an example of a strong non-equilibrium situation, we consider the propagation of a steady shock-wave from the continuum domain into the atomistic domain, and show that the coupling scheme conserves both energy and shock-wave dynamics. To demonstrate the applicability of our scheme to real systems, we consider shock loading of a phospholipid bilayer immersed in water in a multi-scale simulation, an interesting topic of biological relevance. PMID:23300586

Nanoscale deicing by molecular dynamics simulation.

PubMed

Xiao, Senbo; He, Jianying; Zhang, Zhiliang

2016-08-14

Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.

Using elaborative interrogation to induce characteristics of polar and nonpolar solvents from animations of their molecular structures

NASA Astrophysics Data System (ADS)

Ems-Wilson, Janice

This study concerned (a) how general chemistry students learn to classify solvent polarity from animated molecules, (b) whether peer interaction increases the number of correct classifications, and (c) whether language, academic ability, logical thinking ability, or prior knowledge interact with rate of learning or posttest performance. Two types of interaction were compared, group discussion and elaborative interrogation. The study rested on three assumptions: (a) animated molecules are appropriate for learning the concept of solvent polarity, (b) question stems and a guided interrogation enhance learning of a visual concept, (c) general chemistry students can induce the concept of solvent polarity from animated molecules when no guiding cues, either visual or verbal, are given. After a review of molecular geometry and bonding theories, students were presented with four trials of ten animated molecular structures. Ten three-to-five minute discussions were distributed among the four trials. Prior to the trials the experimental group received a 45-minute training session on elaborative interrogation; the topic was what happens on the molecular level when a carbonated beverage is opened. The control group received a 45-minute expository lecture on the same carbonated beverage topic. Participants were given a four-part posttest immediately following the trials. Results of the study suggest that most students tend to classify the solvent polarity of animated molecules based on certain structural features using a prototype or feature-frequency categorization strategy. Elaborative interrogation did not show a significant effect on the rate of learning or on the performance of learners on posttest measures of recall and comprehension. The experimental group noted a significantly greater number and range of types of features, and offered higher quality generalizations and explanations of their polarity classification procedure. Finally, the results implied that learning

Protein-Ligand Interaction Detection with a Novel Method of Transient Induced Molecular Electronic Spectroscopy (TIMES): Experimental and Theoretical Studies.

PubMed

Zhang, Tiantian; Wei, Tao; Han, Yuanyuan; Ma, Heng; Samieegohar, Mohammadreza; Chen, Ping-Wei; Lian, Ian; Lo, Yu-Hwa

2016-11-23

Protein-ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein-ligand interactions in relevant physiological conditions. Through experiments and theoretical simulations, we demonstrate that the TIMES technique actually detects protein-ligand binding through signals generated by surface electric polarization. The accuracy and sensitivity of experiments were demonstrated by precise measurements of dissociation constant of lysozyme and N -acetyl-d-glucosamine (NAG) ligand and its trimer, NAG 3 . Computational fluid dynamics (CFD) computation is performed to demonstrate that the surface's electric polarization signal originates from the induced image charges during the transition state of surface mass transport, which is governed by the overall effects of protein concentration, hydraulic forces, and surface fouling due to protein adsorption. Hybrid atomistic molecular dynamics (MD) simulations and free energy computation show that ligand binding affects lysozyme structure and stability, producing different adsorption orientation and surface polarization to give the characteristic TIMES signals. Although the current work is focused on protein-ligand interactions, the TIMES method is a general technique that can be applied to study signals from reactions between many kinds of molecules.

Insulin adsorption on crystalline SiO2: Comparison between polar and nonpolar surfaces using accelerated molecular-dynamics simulations

NASA Astrophysics Data System (ADS)

Nejad, Marjan A.; Mücksch, Christian; Urbassek, Herbert M.

2017-02-01

Adsorption of insulin on polar and nonpolar surfaces of crystalline SiO2 (cristobalite and α -quartz) is studied using molecular dynamics simulation. Acceleration techniques are used in order to sample adsorption phase space efficiently and to identify realistic adsorption conformations. We find major differences between the polar and nonpolar surfaces. Electrostatic interactions govern the adsorption on polar surfaces and can be described by the alignment of the protein dipole with the surface dipole; hence spreading of the protein on the surface is irrelevant. On nonpolar surfaces, on the other hand, van-der-Waals interaction dominates, inducing surface spreading of the protein.

Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation

NASA Astrophysics Data System (ADS)

Wu, Bin; Kerkeni, Boutheïna; Egami, Takeshi; Do, Changwoo; Liu, Yun; Wang, Yongmei; Porcar, Lionel; Hong, Kunlun; Smith, Sean C.; Liu, Emily L.; Smith, Gregory S.; Chen, Wei-Ren

2012-04-01

Based on atomistic molecular dynamics (MD) simulations, the small angle neutron scattering (SANS) intensity behavior of a single generation-4 polyelectrolyte polyamidoamine starburst dendrimer is investigated at different levels of molecular protonation. The SANS form factor, P(Q), and Debye autocorrelation function, γ(r), are calculated from the equilibrium MD trajectory based on a mathematical approach proposed in this work. The consistency found in comparison against previously published experimental findings (W.-R. Chen, L. Porcar, Y. Liu, P. D. Butler, and L. J. Magid, Macromolecules 40, 5887 (2007)) leads to a link between the neutron scattering experiment and MD computation, and fresh perspectives. The simulations enable scattering calculations of not only the hydrocarbons but also the contribution from the scattering length density fluctuations caused by structured, confined water within the dendrimer. Based on our computational results, we explore the validity of using radius of gyration RG for microstructure characterization of a polyelectrolyte dendrimer from the scattering perspective.

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

PubMed Central

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-01-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Polarization recovery through scattering media.

PubMed

de Aguiar, Hilton B; Gigan, Sylvain; Brasselet, Sophie

2017-09-01

The control and use of light polarization in optical sciences and engineering are widespread. Despite remarkable developments in polarization-resolved imaging for life sciences, their transposition to strongly scattering media is currently not possible, because of the inherent depolarization effects arising from multiple scattering. We show an unprecedented phenomenon that opens new possibilities for polarization-resolved microscopy in strongly scattering media: polarization recovery via broadband wavefront shaping. We demonstrate focusing and recovery of the original injected polarization state without using any polarizing optics at the detection. To enable molecular-level structural imaging, an arbitrary rotation of the input polarization does not degrade the quality of the focus. We further exploit the robustness of polarization recovery for structural imaging of biological tissues through scattering media. We retrieve molecular-level organization information of collagen fibers by polarization-resolved second harmonic generation, a topic of wide interest for diagnosis in biomedical optics. Ultimately, the observation of this new phenomenon paves the way for extending current polarization-based methods to strongly scattering environments.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

PubMed Central

Komarov, Pavel V; Khokhlov, Alexei R

2013-01-01

Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

Atomistic characterisation of Li+ mobility and conductivity in Li(7-x)PS(6-x)Ix argyrodites from molecular dynamics simulations, solid-state NMR, and impedance spectroscopy.

PubMed

Pecher, Oliver; Kong, Shiao-Tong; Goebel, Thorsten; Nickel, Vera; Weichert, Katja; Reiner, Christof; Deiseroth, Hans-Jörg; Maier, Joachim; Haarmann, Frank; Zahn, Dirk

2010-07-26

The atomistic mechanisms of Li(+) ion mobility/conductivity in Li(7-x)PS(6-x)I(x) argyrodites are explored from both experimental and theoretical viewpoints. Ionic conductivity in the title compound is associated with a solid-solid phase transition, which was characterised by low-temperature differential scanning calorimetry, (7)Li and (127)I NMR investigations, impedance measurements and molecular dynamics simulations. The NMR signals of both isotopes are dominated by anisotropic interactions at low temperatures. A significant narrowing of the NMR signal indicates a motional averaging of the anisotropic interactions above 177+/-2 K. The activation energy to ionic conductivity was assessed from both impedance spectroscopy and molecular dynamics simulations. The latter revealed that a series of interstitial sites become accessible to the Li(+) ions, whilst the remaining ions stay at their respective sites in the argyrodite lattice. The interstitial positions each correspond to the centres of tetrahedra of S/I atoms, and differ only in terms of their common corners, edges, or faces with adjacent PS(4) tetrahedra. From connectivity analyses and free-energy rankings, a specific tetrahedron is identified as the key restriction to ionic conductivity, and is clearly differentiated from local mobility, which follows a different mechanism with much lower activation energy. Interpolation of the lattice parameters as derived from X-ray diffraction experiments indicates a homogeneity range for Li(7-x)PS(6-x)I(x) with 0.97 < or = x < or = 1.00. Within this range, molecular dynamics simulations predict Li(+) conductivity at ambient conditions to vary considerably.

Morphology dependent near-field response in atomistic plasmonic nanocavities.

PubMed

Chen, Xing; Jensen, Lasse

2018-06-21

In this work we examine how the atomistic morphologies of plasmonic dimers control the near-field response by using an atomistic electrodynamics model. At large separations, the field enhancement in the junction follows a simple inverse power law as a function of the gap separation, which agrees with classical antenna theory. However, when the separations are smaller than 0.8 nm, the so-called quantum size regime, the field enhancement is screened and thus deviates from the simple power law. Our results show that the threshold distance for the deviation depends on the specific morphology of the junction. The near field in the junction can be localized to an area of less than 1 nm2 in the presence of an atomically sharp tip, but the separation distances leading to a large confinement of near field depend strongly on the specific atomistic configuration. More importantly, the highly confined fields lead to large field gradients particularly in a tip-to-surface junction, which indicates that such a plasmonic structure favors observing strong field gradient effects in near-field spectroscopy. We find that for atomically sharp tips the field gradient becomes significant and depends strongly on the local morphology of a tip. We expect our findings to be crucial for understanding the origin of high-resolution near-field spectroscopy and for manipulating optical cavities through atomic structures in the strongly coupled plasmonic systems.

Phase transformations at interfaces: Observations from atomistic modeling

DOE PAGES

Frolov, T.; Asta, M.; Mishin, Y.

2016-10-01

Here, we review the recent progress in theoretical understanding and atomistic computer simulations of phase transformations in materials interfaces, focusing on grain boundaries (GBs) in metallic systems. Recently developed simulation approaches enable the search and structural characterization of GB phases in single-component metals and binary alloys, calculation of thermodynamic properties of individual GB phases, and modeling of the effect of the GB phase transformations on GB kinetics. Atomistic simulations demonstrate that the GB transformations can be induced by varying the temperature, loading the GB with point defects, or varying the amount of solute segregation. The atomic-level understanding obtained from suchmore » simulations can provide input for further development of thermodynamics theories and continuous models of interface phase transformations while simultaneously serving as a testing ground for validation of theories and models. They can also help interpret and guide experimental work in this field.« less

Accurate atomistic first-principles calculations of electronic stopping

DOE PAGES

Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

2015-01-20

In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

Atomistic to continuum modeling of solidification microstructures

DOE PAGES

Karma, Alain; Tourret, Damien

2015-09-26

We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked tomore » experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.« less

Atomistic Conversion Reaction Mechanism of WO 3 in Secondary Ion Batteries of Li, Na, and Ca

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Yang; Gu, Meng; Xiao, Haiyan

2016-04-13

Reversible insertion and extraction of ionic species into a host lattice governs the basic operating principle for both rechargeable battery (such as lithium batteries) and electrochromic devices (such as ANA Boeing 787-8 Dreamliner electrochromic window). Intercalation and/or conversion are two fundamental chemical processes for some materials in response to the ion insertion. The interplay between these two chemical processes has never been established. It is speculated that the conversion reaction is initiated by ion intercalation. However, experimental evidence of intercalation and subsequent conversion remains unexplored. Here, using in situ HRTEM and spectroscopy, we captured the atomistic conversion reaction processes duringmore » lithium, sodium and calcium ion insertion into tungsten trioxide (WO3) single crystal model electrodes. An intercalation step right prior to conversion is explicitly revealed at atomic scale for the first time for these three ion species. Combining nanoscale diffraction and ab initio molecular dynamics simulations, it is found that, beyond intercalation, the inserted ion-oxygen bonding formation destabilized the transition-metal framework which gradually shrunk, distorted and finally collapsed to a pseudo-amorphous structure. This study provides a full atomistic picture on the transition from intercalation to conversion, which is of essential for material applications in both secondary ion batteries and electrochromic devices.« less

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

PubMed Central

Petrov, Drazen; Zagrovic, Bojan

2014-01-01

The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

2014-03-14

A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-bodymore » DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

Atomistic modeling of crystal-to-amorphous transition and associated kinetics in the Ni-Nb system by molecular dynamics simulations.

PubMed

Dai, X D; Li, J H; Liu, B X

2005-03-17

With the aid of ab initio calculations, an n-body potential of the Ni-Nb system is constructed under the Finnis-Sinclair formalism and the constructed potential is capable of not only reproducing some static physical properties but also revealing the atomistic mechanism of crystal-to-amorphous transition and associated kinetics. With application of the constructed potential, molecular dynamics simulations using the solid solution models reveal that the physical origin of crystal-to-amorphous transition is the crystalline lattice collapsing while the solute atoms are exceeding the critical solid solubilities, which are determined to be 19 atom % Ni and 13 atom % Nb for the Nb- and Ni-based solid solutions, respectively. It follows that an intrinsic glass-forming ability of the Ni-Nb system is within 19-87 atom % Ni, which matches well with that observed in ion beam mixing/solid-state reaction experiments. Simulations using the Nb/Ni/Nb (Ni/Nb/Ni) sandwich models indicate that the amorphous layer at the interfaces grows in a layer-by-layer mode and that, upon dissolving solute atoms, the Ni lattice approaches and exceeds its critical solid solubility faster than the Nb lattice, revealing an asymmetric behavior in growth kinetics. Moreover, an energy diagram is obtained by computing the energetic sequence of the Ni(x)Nb(100)(-)(x) alloy in fcc, bcc, and amorphous structures, respectively, over the entire composition range, and the diagram could serve as a guide for predicting the metastable alloy formation in the Ni-Nb system.

The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations.

PubMed

Leung, Yuk Ming; Holdbrook, Daniel A; Piggot, Thomas J; Khalid, Syma

2014-07-15

The multidrug and toxic compound extrusion transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. The substrates transported by these proteins include toxic metabolites and antimicrobial drugs. These proteins contribute to multidrug resistance in both mammalian and bacterial cells and are therefore extremely important from a biomedical perspective. Although specific residues of the protein are known to be responsible for the extrusion of solutes, mechanistic details and indeed structures of all the conformational states remain elusive. Here, we report the first, to our knowledge, simulation study of the recently resolved x-ray structure of the multidrug and toxic compound extrusion transporter, NorM from Neisseria gonorrhoeae (NorM_NG). Multiple, atomistic simulations of the unbound and bound forms of NorM in a phospholipid lipid bilayer allow us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein. In particular, we identify the molecular rearrangements that occur to enable the Na(+) ion to enter the cation-binding cavity even in the presence of a bound drug molecule. These include side chain flipping of a key residue, GLU-261 from pointing toward the central cavity to pointing toward the cation binding side when bound to a Na(+) ion. Our simulations also provide support for cation binding in the drug-bound and apo states of NorM_NG. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Atomistic Molecular Dynamics Simulations of the Electrical Double

NASA Astrophysics Data System (ADS)

Li, Zifeng; Milner, Scott; Fichthorn, Kristen

2015-03-01

The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.

Giant electrocaloric response in the prototypical Pb(Mg,Nb)O3 relaxor ferroelectric from atomistic simulations

NASA Astrophysics Data System (ADS)

Jiang, Zhijun; Nahas, Y.; Prokhorenko, S.; Prosandeev, S.; Wang, D.; Íñiguez, Jorge; Bellaiche, L.

2018-03-01

An atomistic effective Hamiltonian is used to investigate electrocaloric (EC) effects of Pb (Mg1 /3Nb2 /3) O3 relaxor ferroelectrics in its ergodic regime, and subject to electric fields applied along the pseudocubic [111] direction. Such a Hamiltonian qualitatively reproduces (i) the electric field-versus-temperature phase diagram, including the existence of a critical point where first-order and second-order transitions meet each other; and (ii) a giant EC response near such a critical point. It also reveals that such giant response around this critical point is microscopically induced by field-induced percolation of polar nanoregions. Moreover, it is also found that, for any temperature above the critical point, the EC coefficient-versus-electric-field curve adopts a maximum (and thus larger electrocaloric response too), that can be well described by the general Landau-like model proposed by Jiang et al., [Phys. Rev. B 96, 014114 (2017)], 10.1103/PhysRevB.96.014114, and that is further correlated with specific microscopic features related to dipoles lying along different rhombohedral directions. Furthermore, for temperatures being at least 40 K higher than the critical temperature, the (electric field, temperature) line associated with this maximal EC coefficient is below both the Widom line and the line representing percolation of polar nanoregions.

Molecular Packing of Amiphiphiles with Crown Polar Heads at the Air-Water Interface

NASA Astrophysics Data System (ADS)

Larson, K.; Vaknin, D.; Villavicencio, O.; McGrath, D.; Tsukruk, V. V.

2002-03-01

An amphiphilic compound containing a benzyl-15-crown-5 focal point, azobenzene spacer, and a dodecyl tail as a peripheral group has been investigated at the air-water interface. X-ray grazing incident diffraction and reflectivity were preformed on the Langmuir monolayers to elucidate molecular packing and orientation. At high surface pressure, we observed intralayer packing of the alkyl tails with doubling parameters of the conventional orthorhombic unit cell (supercell) and long-range positional ordering. High tilt of the alkyl tails of about 58º from the surface normal was a signature of molecular packing caused by a large mismatch between the cross-sectional areas of the polar heads and the alkyl tail. Higher generation molecules of the same series display straight tail orientation and hexagonal lateral packing.

Atomistic modeling for interfacial properties of Ni-Al-V ternary system

NASA Astrophysics Data System (ADS)

Dong, Wei-ping; Lee, Byeong-Joo; Chen, Zheng

2014-05-01

Interatomic potentials for Ni-Al-V ternary systems have been developed based on the second-nearest-neighbor modified embedded-atom method potential formalism. The potentials can describe various fundamental physical properties of the relevant materials in good agreement with experimental information. The potential is utilized for an atomistic computation of interfacial properties of Ni-Al-V alloys. It is found that vanadium atoms segregate on the γ-fcc/L12 interface and this segregation affects the interfacial properties. The applicability of the atomistic approach to an elaborate alloy design of advanced Ni-based superalloys through the investigation of the effect of alloying elements on interfacial properties is discussed.

Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

NASA Astrophysics Data System (ADS)

Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

2017-10-01

We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

Large-scale atomistic simulations demonstrate dominant alloy disorder effects in GaBixAs1 -x/GaAs multiple quantum wells

NASA Astrophysics Data System (ADS)

Usman, Muhammad

2018-04-01

Bismide semiconductor materials and heterostructures are considered a promising candidate for the design and implementation of photonic, thermoelectric, photovoltaic, and spintronic devices. This work presents a detailed theoretical study of the electronic and optical properties of strongly coupled GaBixAs1 -x /GaAs multiple quantum well (MQW) structures. Based on a systematic set of large-scale atomistic tight-binding calculations, our results reveal that the impact of atomic-scale fluctuations in alloy composition is stronger than the interwell coupling effect, and plays an important role in the electronic and optical properties of the investigated MQW structures. Independent of QW geometry parameters, alloy disorder leads to a strong confinement of charge carriers, a large broadening of the hole energies, and a red-shift in the ground-state transition wavelength. Polarization-resolved optical transition strengths exhibit a striking effect of disorder, where the inhomogeneous broadening could exceed an order of magnitude for MQWs, in comparison to a factor of about 3 for single QWs. The strong influence of alloy disorder effects persists when small variations in the size and composition of MQWs typically expected in a realistic experimental environment are considered. The presented results highlight the limited scope of continuum methods and emphasize on the need for large-scale atomistic approaches to design devices with tailored functionalities based on the novel properties of bismide materials.

Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

PubMed

Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

2016-11-08

Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively 13 C-labeled choline with 29 Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like 1 H- 13 C CP-REDOR (rotational-echo double resonance), 1 H- 13 C HETCOR (heteronuclear correlation), and 1 H- 29 Si- 1 H double CP are employed to determine spatial parameters. The measurement of 29 Si- 13 C internuclear distances for selectively 13 C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

From atomistic interfaces to dendritic patterns

NASA Astrophysics Data System (ADS)

Galenko, P. K.; Alexandrov, D. V.

2018-01-01

Transport processes around phase interfaces, together with thermodynamic properties and kinetic phenomena, control the formation of dendritic patterns. Using the thermodynamic and kinetic data of phase interfaces obtained on the atomic scale, one can analyse the formation of a single dendrite and the growth of a dendritic ensemble. This is the result of recent progress in theoretical methods and computational algorithms calculated using powerful computer clusters. Great benefits can be attained from the development of micro-, meso- and macro-levels of analysis when investigating the dynamics of interfaces, interpreting experimental data and designing the macrostructure of samples. The review and research articles in this theme issue cover the spectrum of scales (from nano- to macro-length scales) in order to exhibit recently developing trends in the theoretical analysis and computational modelling of dendrite pattern formation. Atomistic modelling, the flow effect on interface dynamics, the transition from diffusion-limited to thermally controlled growth existing at a considerable driving force, two-phase (mushy) layer formation, the growth of eutectic dendrites, the formation of a secondary dendritic network due to coalescence, computational methods, including boundary integral and phase-field methods, and experimental tests for theoretical models-all these themes are highlighted in the present issue. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review.

PubMed

Kumar, Rajesh; Parashar, Avinash

2016-01-07

Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.

Primary radiation damage of an FeCr alloy under pressure: Atomistic simulation

NASA Astrophysics Data System (ADS)

Tikhonchev, M. Yu.; Svetukhin, V. V.

2017-05-01

The primary radiation damage of a binary FeCr alloy deformed by applied mechanical loading is studied by an atomistic molecular dynamics simulation. Loading is simulated by specifying an applied pressure of 0.25, 1.0, and 2.5 GPa of both signs. Hydrostatic and uniaxial loading is considered along the [001], [111], [112], and [210] directions. The influence of loading on the energy of point defect formation and the threshold atomic displacement energy in single-component bcc iron is investigated. The 10-keV atomic displacement cascades in a "random" binary Fe-9 at % Cr alloy are simulated at an initial temperature of 300 K. The number of the point defects generated in a cascade is estimated, and the clustering of point defects and the spatial orientation of interstitial configurations are analyzed. Our results agree with the results of other researchers and supplement them.

Effect of the barometric phase transition of a DMPA bilayer on the lipid/water interface. An atomistic description by molecular dynamics simulation.

PubMed

Casares, J J Giner; Camacho, L; Romero, M T Martín; Cascales, J J López

2007-12-13

Understanding the structure and dynamics of phospholipid bilayers is of fundamental relevance in biophysics, biochemistry, and chemical physics. Lipid Langmuir monolayers are used as a model of lipid bilayers, because they are much more easily studied experimentally, although some authors question the validity of this model. With the aim of throwing light on this debate, we used molecular dynamics simulations to obtain an atomistic description of a membrane of dimyristoylphosphatidic acid under different surface pressures. Our results show that at low surface pressure the interdigitation between opposite lipids (that is, back-to-back interactions) controls the system structure. In this setting and due to the absence of this effect in the Langmuir monolayers, the behavior between these two systems differs considerably. However, when the surface pressure increases the lipid interdigitation diminishes and so monolayer and bilayer behavior converges. In this work, four computer simulations were carried out, subjecting the phospholipids to lateral pressures ranging from 0.17 to 40 mN/m. The phospholipids were studied in their charged state because this approach is closer to the experimental situation. Special attention was paid to validating our simulation results by comparison with available experimental data, therebeing in general excellent agreement between experimental and simulation data. In addition, the properties of the lipid/solution interface associated with the lipid barometric phase transition were studied.

Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon

DOE PAGES

Turneaure, Stefan J.; Sinclair, N.; Gupta, Y. M.

2016-07-20

Experimental determination of atomistic mechanisms linking crystal structures during a compression driven solid-solid phase transformation is a long standing and challenging scientific objective. Also, when using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. Furthermore, this approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.

Accurate atomistic potentials and training sets for boron-nitride nanostructures

NASA Astrophysics Data System (ADS)

Tamblyn, Isaac

Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

Sensitivity of Force Fields on Mechanical Properties of Metals Predicted by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Zhang, Yuwen

Increasing number of micro/nanoscale studies for scientific and engineering applications, leads to huge deployment of atomistic simulations such as molecular dynamics and Monte-Carlo simulation. Many complains from users in the simulation community arises for obtaining wrong results notwithstanding of correct simulation procedure and conditions. Improper choice of force field, known as interatomic potential is the likely causes. For the sake of users' assurance, convenience and time saving, several interatomic potentials are evaluated by molecular dynamics. Elastic properties of multiple FCC and BCC pure metallic species are obtained by LAMMPS, using different interatomic potentials designed for pure species and their alloys at different temperatures. The potentials created based on the Embedded Atom Method (EAM), Modified EAM (MEAM) and ReaX force fields, adopted from available open databases. Independent elastic stiffness constants of cubic single crystals for different metals are obtained. The results are compared with the experimental ones available in the literature and deviations for each force field are provided at each temperature. Using current work, users of these force fields can easily judge on the one they are going to designate for their problem.

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision

The NorM MATE Transporter from N. gonorrhoeae: Insights into Drug and Ion Binding from Atomistic Molecular Dynamics Simulations

PubMed Central

Leung, Yuk Ming; Holdbrook, Daniel A.; Piggot, Thomas J.; Khalid, Syma

2014-01-01

The multidrug and toxic compound extrusion transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. The substrates transported by these proteins include toxic metabolites and antimicrobial drugs. These proteins contribute to multidrug resistance in both mammalian and bacterial cells and are therefore extremely important from a biomedical perspective. Although specific residues of the protein are known to be responsible for the extrusion of solutes, mechanistic details and indeed structures of all the conformational states remain elusive. Here, we report the first, to our knowledge, simulation study of the recently resolved x-ray structure of the multidrug and toxic compound extrusion transporter, NorM from Neisseria gonorrhoeae (NorM_NG). Multiple, atomistic simulations of the unbound and bound forms of NorM in a phospholipid lipid bilayer allow us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein. In particular, we identify the molecular rearrangements that occur to enable the Na+ ion to enter the cation-binding cavity even in the presence of a bound drug molecule. These include side chain flipping of a key residue, GLU-261 from pointing toward the central cavity to pointing toward the cation binding side when bound to a Na+ ion. Our simulations also provide support for cation binding in the drug-bound and apo states of NorM_NG. PMID:25028887

Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

PubMed

Tao, Weiwei; Cao, Penghui; Park, Harold S

2018-02-14

The mechanical properties and plastic deformation mechanisms of metal nanowires have been studied intensely for many years. One of the important yet unresolved challenges in this field is to bridge the gap in properties and deformation mechanisms reported for slow strain rate experiments (∼10 -2 s -1 ), and high strain rate molecular dynamics (MD) simulations (∼10 8 s -1 ) such that a complete understanding of strain rate effects on mechanical deformation and plasticity can be obtained. In this work, we use long time scale atomistic modeling based on potential energy surface exploration to elucidate the atomistic mechanisms governing a strain-rate-dependent incipient plasticity and yielding transition for face centered cubic (FCC) copper and silver nanowires. The transition occurs for both metals with both pristine and rough surfaces for all computationally accessible diameters (<10 nm). We find that the yield transition is induced by a transition in the incipient plastic event from Shockley partials nucleated on primary slip systems at MD strain rates to the nucleation of planar defects on non-Schmid slip planes at experimental strain rates, where multiple twin boundaries and planar stacking faults appear in copper and silver, respectively. Finally, we demonstrate that, at experimental strain rates, a ductile-to-brittle transition in failure mode similar to previous experimental studies on bicrystalline silver nanowires is observed, which is driven by differences in dislocation activity and grain boundary mobility as compared to the high strain rate case.

Heterogeneous path ensembles for conformational transitions in semi–atomistic models of adenylate kinase

PubMed Central

Bhatt, Divesh; Zuckerman, Daniel M.

2010-01-01

We performed “weighted ensemble” path–sampling simulations of adenylate kinase, using several semi–atomistic protein models. The models have an all–atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single–processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semi–atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways. PMID:21660120

Characterizing Atomistic Geometries and Potential Functions Using Strain Functionals

NASA Astrophysics Data System (ADS)

Kober, Edward; Mathew, Nithin; Rudin, Sven

2017-06-01

We demonstrate the use of strain tensor functionals for characterizing arbitrarily ordered atomistic structures. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the n-th order moments/derivatives of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. Reducing these metrics to rotational invariant descriptors allows a large number of defect structures to be readily identified and forms the basis of a classification scheme that allows molecular dynamics simulations to be readily analyzed. Applications to the analysis of shock waves impinging on samples of Cu, Ta and Ti will be presented. The method has been extended to vector fields as well, enabling the local stress to be cast in terms of rotationally invariant functions as well. The stress-strain correlations can then be used as the basis for developing and analyzing potential functions.

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

NASA Astrophysics Data System (ADS)

Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

2018-06-01

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems

NASA Technical Reports Server (NTRS)

Jaramillo-Botero, Andres; Goddard, William A, III; Fijany, Amir

1997-01-01

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems,.

Atomistic modeling of carbon Cottrell atmospheres in bcc iron

NASA Astrophysics Data System (ADS)

Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

2013-01-01

Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

Normalized Polarization Ratios for the Analysis of Cell Polarity

PubMed Central

Shimoni, Raz; Pham, Kim; Yassin, Mohammed; Ludford-Menting, Mandy J.; Gu, Min; Russell, Sarah M.

2014-01-01

The quantification and analysis of molecular localization in living cells is increasingly important for elucidating biological pathways, and new methods are rapidly emerging. The quantification of cell polarity has generated much interest recently, and ratiometric analysis of fluorescence microscopy images provides one means to quantify cell polarity. However, detection of fluorescence, and the ratiometric measurement, is likely to be sensitive to acquisition settings and image processing parameters. Using imaging of EGFP-expressing cells and computer simulations of variations in fluorescence ratios, we characterized the dependence of ratiometric measurements on processing parameters. This analysis showed that image settings alter polarization measurements; and that clustered localization is more susceptible to artifacts than homogeneous localization. To correct for such inconsistencies, we developed and validated a method for choosing the most appropriate analysis settings, and for incorporating internal controls to ensure fidelity of polarity measurements. This approach is applicable to testing polarity in all cells where the axis of polarity is known. PMID:24963926

Atomistic Simulation of High-Density Uranium Fuels

DOE PAGES

Garcés, Jorge Eduardo; Bozzolo, Guillermo

2011-01-01

We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

NASA Astrophysics Data System (ADS)

Yinkai Lei

Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

Molecular recognition in chiral smectic liquid crystals: the effect of core-core interactions and chirality transfer on polar order.

PubMed

Lemieux, Robert P

2007-12-01

This critical review focuses on the induction of polar order in smectic liquid crystal phases by dopants with axially chiral cores, and should be of interest to all practitioners of supramolecular chemistry. The variations in polarization power of these dopants with the core structure of the liquid crystal hosts is a manifestation of molecular recognition that reflects the nanosegregation of aromatic cores from paraffinic side-chains in smectic phases, and the collective effect of core-core interactions that enable the propagation of chiral perturbations.

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions

PubMed Central

Kumawat, Amit; Chakrabarty, Suman; Kulkarni, Kiran

2017-01-01

Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of “sub-states” such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound “OFF” state have very similar conformations, whereas the GTP bound “ON” state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the γ-phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors. PMID:28374773

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions

NASA Astrophysics Data System (ADS)

Kumawat, Amit; Chakrabarty, Suman; Kulkarni, Kiran

2017-04-01

Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of “sub-states” such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound “OFF” state have very similar conformations, whereas the GTP bound “ON” state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the γ-phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors.

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

NASA Astrophysics Data System (ADS)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ' Microstructures.

PubMed

Prakash, Aruna; Bitzek, Erik

2017-01-23

Single-crystal Ni-base superalloys, consisting of a two-phase γ / γ ' microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ' phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ / γ ' microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ' particles with planar γ / γ ' interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples-the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE PAGES

Huang, Jing; Mei, Ye; König, Gerhard; ...

2017-01-24

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

PubMed

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jing; Mei, Ye; König, Gerhard

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

Investigation of solvent polarity effect on molecular structure and vibrational spectrum of xanthine with the aid of quantum chemical computations.

PubMed

Polat, Turgay; Yıldırım, Gurcan

2014-04-05

The main scope of this study is to determine the effects of 8 solvents on the geometric structure and vibrational spectra of the title compound, xanthine, by means of the DFT/B3LYP level of theory in the combination with the polarizable conductor continuum model (CPCM) for the first time. After determination of the most-steady state (favored structure) of the xanthine molecule, the role of the solvent polarity on the SCF energy (for the molecule stability), atomic charges (for charge distribution) and dipole moments (for molecular charge transfer) belonging to tautomer is discussed in detail. The results obtained indicate not only the presence of the hydrogen bonding and strong intra-molecular charge transfer (ICT) in the compound but the increment of the molecule stability with the solvent polarity, as well. Moreover, it is noted that the optimized geometric parameters and the theoretical vibrational frequencies are in good agreement with the available experimental results found in the literature. In fact, the correlations between the experimental and theoretical findings for the molecular structures improve with the enhancement of the solvent polarity. At the same time, the dimer forms of the xanthine compound are simulated to describe the effect of intermolecular hydrogen bonding on the molecular geometry and vibrational frequencies. It is found that the CO and NH stretching vibrations shift regularly to lower frequency value with higher IR intensity as the dielectric medium enhances systematically due to the intermolecular NH⋯O hydrogen bonds. Theoretical vibrational spectra are also assigned based on the potential energy distribution (PED) using the VEDA 4 program. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular design and MD simulations of epitaxial superlattice of self-assembling ternary lipid bilayers

NASA Astrophysics Data System (ADS)

Chou, George; Vaughn, Mark; Cheng, K.

2011-10-01

Multicomponent lipid bilayers represent an important model system for studying cell membranes. At present, an ordered multicomponent phospholipid/cholesterol bilayer system involving charged lipid is still not available. Using a lipid superlattice (SL) model, a 13 x 15 x 15 nm^3 ternary phosphatidylcholine/phosphatidylserine/cholesterol bilayer system in water with simultaneous headgroup SL and acyl chain SL at different depths, or epitaxial SL, of the bilayer has been designed with atomistic detail. The arrangements of this epitaxial SL system were optimized by only two molecular parameters, lattice space and rotational angle of the lipids. Using atomistic MD simulations, we demonstrated the stability of the ordered structures for more than 100 ns. A positional restrained system was also used as a control. This system will provide new insights into understanding the nanodomain structures of cell membranes at the molecular level.

Visualizing molecular polar order in tissues via electromechanical coupling

PubMed Central

Denning, Denise; Alilat, Sofiane; Habelitz, Stefan; Fertala, Andrzej; Rodriguez, Brian J.

2015-01-01

Electron microscopy (EM) and atomic force microscopy (AFM) techniques have long been used to characterize collagen fibril ordering and alignment in connective tissues. These techniques, however, are unable to map collagen fibril polarity, i.e., the polar orientation that is directed from the amine to the carboxyl termini. Using a voltage modulated AFM-based technique called piezoresponse force microscopy (PFM), we show it is possible to visualize both the alignment of collagen fibrils within a tissue and the polar orientation of the fibrils with minimal sample preparation. We demonstrate the technique on rat tail tendon and porcine eye tissues in ambient conditions. In each sample, fibrils are arranged into domains whereby neighboring domains exhibit opposite polarizations, which in some cases extend to the individual fibrillar level. Uniform polarity has not been observed in any of the tissues studied. Evidence of anti-parallel ordering of the amine to carboxyl polarity in bundles of fibrils or in individual fibrils is found in all tissues, which has relevance for understanding mechanical and biofunctional properties and the formation of connective tissues. The technique can be applied to any biological material containing piezoelectric biopolymers or polysaccharides. PMID:22985991

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

PubMed

Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

2015-03-05

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

NASA Astrophysics Data System (ADS)

Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

2014-12-01

Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

Atomistic simulation of CO2 solubility in poly(ethylene oxide) oligomers

NASA Astrophysics Data System (ADS)

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2014-06-01

We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henry's constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henry's constant. Dependence of the calculated Henry's constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length.

Efficient Synthesis of Molecular Precursors for Para-Hydrogen-Induced Polarization of Ethyl Acetate-1-(13) C and Beyond.

PubMed

Shchepin, Roman V; Barskiy, Danila A; Coffey, Aaron M; Manzanera Esteve, Isaac V; Chekmenev, Eduard Y

2016-05-10

A scalable and versatile methodology for production of vinylated carboxylic compounds with (13) C isotopic label in C1 position is described. It allowed synthesis of vinyl acetate-1-(13) C, which is a precursor for preparation of (13) C hyperpolarized ethyl acetate-1-(13) C, which provides a convenient vehicle for potential in vivo delivery of hyperpolarized acetate to probe metabolism in living organisms. Kinetics of vinyl acetate molecular hydrogenation and polarization transfer from para-hydrogen to (13) C via magnetic field cycling were investigated. Nascent proton nuclear spin polarization (%PH ) of ca. 3.3 % and carbon-13 polarization (%P13C ) of ca. 1.8 % were achieved in ethyl acetate utilizing 50 % para-hydrogen corresponding to ca. 50 % polarization transfer efficiency. The use of nearly 100% para-hydrogen and the improvements of %PH of para-hydrogen-nascent protons may enable production of (13) C hyperpolarized contrast agents with %P13C of 20-50 % in seconds using this chemistry. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE PAGES

Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

2017-04-26

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shuozhi; Xiong, Liming; Chen, Youping

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Pulsed recording of anisotropy and holographic polarization gratings in azo-polymethacrylates with different molecular architectures

NASA Astrophysics Data System (ADS)

Forcén, Patricia; Oriol, Luis; Sánchez, Carlos; Alcalá, Rafael; Jankova, Katja; Hvilsted, Søren

2008-06-01

Recording of anisotropy and holographic polarization gratings using 532nm, 4ns light pulses has been carried out in thin films of polymers with the same azobenzene content (20wt%) and different molecular architectures. Random and block copolymers comprising azobenzene and methylmethacrylate (MMA) moieties as well as statistical terpolymers with azobenzene, biphenyl, and MMA units have been compared in terms of recording sensitivity and stability upon pulsed excitation. Photoinduced anisotropy just after the pulse was significantly higher in the case of the block copolymers than in the two statistical copolymers. The stability of the recorded anisotropy has also been studied. While a stationary value of the photoinduced anisotropy (approximately 50% of the initial photoinduced value) is reached for the block copolymer, photoinduced anisotropy almost vanished after a few hours in the statistical copolymers. Polarization holographic gratings have been registered using two orthogonally circularly polarized light beams. The results are qualitatively similar to those of photoinduced anisotropy, that is, stability of the registered grating and larger values of diffraction efficiency for the block copolymer as compared with the random copolymers. The recording of holographic gratings with submicron period in films several microns thick, showing both polarization and angular selectivity, has also been demonstrated. Block copolymers showed a lamellar block nanosegregated morphology. The interaction among azo chromophores within the nanosegregated azo blocks seems to be the reason for the stability and the photoresponse enhancement in the block copolymer as compared with the statistical ones.

Atomistic origin of superior performance of ionic liquid electrolytes for Al-ion batteries.

PubMed

Kamath, Ganesh; Narayanan, Badri; Sankaranarayanan, Subramanian K R S

2014-10-14

Encouraged by recent experimental findings, here we report on an in silico investigation to probe the atomistic origin behind the superior performance of ionic liquids (ILs) over traditional carbonate electrolytes for Al-ion batteries. Fundamental insights from computationally derived thermodynamic and kinetic considerations coupled with an atomistic-level description of the solvation dynamics is used to elucidate the performance improvements. The formation of low-stability ion-solvent complexes in ILs facilitates rapid Al-ion solvation-desolvation and translates into favorable transport properties (viscosity and ionic conductivity). Our results offer encouraging prospects for this approach in the a priori prediction of optimal IL formulations for Al-ion batteries.

A molecular dynamics study of polymer/graphene interfacial systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rissanou, Anastassia N.; Harmandaris, Vagelis

2014-05-15

Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

Size effects of 109° domain walls in rhombohedral barium titanate single crystals—A molecular statics analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Endres, Florian, E-mail: florian.endres@ltm.uni-erlangen.de; Steinmann, Paul, E-mail: paul.steinmann@ltm.uni-erlangen.de

2016-01-14

Ferroelectric functional materials are of great interest in science and technology due to their electromechanically coupled material properties. Therefore, ferroelectrics, such as barium titanate, are modeled and simulated at the continuum scale as well as at the atomistic scale. Due to recent advancements in related manufacturing technologies the modeling and simulation of smart materials at the nanometer length scale is getting more important not only to predict but also fundamentally understand the complex material behavior of such materials. In this study, we analyze the size effects of 109° nanodomain walls in ferroelectric barium titanate single crystals in the rhombohedral phasemore » using a recently proposed extended molecular statics algorithm. We study the impact of domain thicknesses on the spontaneous polarization, the coercive field, and the lattice constants. Moreover, we discuss how the electromechanical coupling of an applied electric field and the introduced strain in the converse piezoelectric effect is affected by the thickness of nanodomains.« less

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

PubMed

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity.

PubMed

Anwar-Mohamed, Anwar; Barakat, Khaled H; Bhat, Rakesh; Noskov, Sergei Y; Tyrrell, D Lorne; Tuszynski, Jack A; Houghton, Michael

2014-11-04

Acquired cardiac long QT syndrome (LQTS) is a frequent drug-induced toxic event that is often caused through blocking of the human ether-á-go-go-related (hERG) K(+) ion channel. This has led to the removal of several major drugs post-approval and is a frequent cause of termination of clinical trials. We report here a computational atomistic model derived using long molecular dynamics that allows sensitive prediction of hERG blockage. It identified drug-mediated hERG blocking activity of a test panel of 18 compounds with high sensitivity and specificity and was experimentally validated using hERG binding assays and patch clamp electrophysiological assays. The model discriminates between potent, weak, and non-hERG blockers and is superior to previous computational methods. This computational model serves as a powerful new tool to predict hERG blocking thus rendering drug development safer and more efficient. As an example, we show that a drug that was halted recently in clinical development because of severe cardiotoxicity is a potent inhibitor of hERG in two different biological assays which could have been predicted using our new computational model. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

CHANGE OF MAGNETIC FIELD-GAS ALIGNMENT AT THE GRAVITY-DRIVEN ALFVÉNIC TRANSITION IN MOLECULAR CLOUDS: IMPLICATIONS FOR DUST POLARIZATION OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Che-Yu; King, Patrick K.; Li, Zhi-Yun

Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields, whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in three-dimensional magnetohydrodynamic (MHD) simulations of prestellar core formation in shock-compressed regions within giant molecular clouds. We find that, in the magnetically dominated (sub-Alfvénic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfvénic gas, their elongation becomes preferentially perpendicularmore » to the local magnetic field. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results can be drawn from HROs in projected two-dimensional maps with integrated column densities and synthetic polarized dust emission. We quantitatively analyze our simulated polarization properties, and interpret the reduced polarization fraction at high column densities as the result of increased distortion of magnetic field directions in trans- or super-Alfvénic gas. Furthermore, we introduce measures of the inclination and tangledness of the magnetic field along the line of sight as the controlling factors of the polarization fraction. Observations of the polarization fraction and angle dispersion can therefore be utilized in studying local magnetic field morphology in star-forming regions.« less

Atomistic nucleation sites of Pt nanoparticles on N-doped carbon nanotubes.

PubMed

Sun, Chia-Liang; Pao, Chih-Wen; Tsai, Huang-Ming; Chiou, Jau-Wern; Ray, Sekhar C; Wang, Houng-Wei; Hayashi, Michitoshi; Chen, Li-Chyong; Lin, Hong-Ji; Lee, Jyh-Fu; Chang, Li; Tsai, Min-Hsiung; Chen, Kuei-Hsien; Pong, Way-Faung

2013-08-07

The atomistic nucleation sites of Pt nanoparticles (Pt NPs) on N-doped carbon nanotubes (N-CNTs) were investigated using C and N K-edge and Pt L3-edge X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) spectroscopy. Transmission electron microscopy and XANES/EXAFS results revealed that the self-organized Pt NPs on N-CNTs are uniformly distributed because of the relatively high binding energies of the adsorbed Pt atoms at the imperfect sites. During the atomistic nucleation process of Pt NPs on N-CNTs, stable Pt-C and Pt-N bonds are presumably formed, and charge transfer occurs at the surface/interface of the N-CNTs. The findings in this study were consistent with density functional theory calculations performed using cluster models for the undoped, substitutional-N-doped and pyridine-like-N-doped CNTs.

Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

PubMed Central

Prakash, Aruna; Bitzek, Erik

2017-01-01

Single-crystal Ni-base superalloys, consisting of a two-phase γ/γ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/γ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ′ particles with planar γ/γ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions. PMID:28772453

Molecular Dynamics of Flexible Polar Cations in a Variable Confined Space: Toward Exceptional Two-Step Nonlinear Optical Switches.

PubMed

Xu, Wei-Jian; He, Chun-Ting; Ji, Cheng-Min; Chen, Shao-Li; Huang, Rui-Kang; Lin, Rui-Biao; Xue, Wei; Luo, Jun-Hua; Zhang, Wei-Xiong; Chen, Xiao-Ming

2016-07-01

The changeable molecular dynamics of flexible polar cations in the variable confined space between inorganic chains brings about a new type of two-step nonlinear optical (NLO) switch with genuine "off-on-off" second harmonic generation (SHG) conversion between one NLO-active state and two NLO-inactive states. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

NASA Astrophysics Data System (ADS)

Rezaei Mianroodi, Jaber; Svendsen, Bob

2015-04-01

The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical

Multiscale equation-free algorithms for molecular dynamics

NASA Astrophysics Data System (ADS)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

PubMed Central

2015-01-01

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

DOE PAGES

Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

2014-10-16

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completelymore » avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.« less

[Molecular mechanisms and relationship of M2-polarized macrophages with early response in multiple myeloma].

PubMed

Chen, X Y; Sun, R X; Zhang, W Y; Liu, T; Zheng, Y H; Wu, Y

2017-06-14

Objective: To investigate the relationship between M2-polarized macrophages and early response in multiple myeloma and its molecular mechanism. Methods: Two hundred and forty bone marrow biopsy tissue were collected and M2-polarized macrophages were stained by anti-CD163 monoclonal antibody. In vitro M2-polarized macrophages were derived from human peripheral blood mononuclear cell or THP-1 cells and identified by flow cytometry. Two myeloma cell lines RPMI 8226 and U266 were co-cultured with M2 macrophages using a transwell system. We measured myeloma cells proliferation through CCK-8 method and the pro-inflammatory cytokines expression (TNF-α and IL-6) by ELISA. Real time PCR was applied to measure chemokines (CCL2 and CCL3) , chemokine receptors (CCR2, CCR5) , VEGF and their receptors. In addition, flow cytometry was used to analyze the apoptosis of myeloma cells induced by dexamethasone. Results: ①Patients with high percentage of M2 macrophage involvement in bone marrow showed poorer response (23.9% versus 73.0%, χ (2)=60.31, P <0.001). ② In vitro the proliferation of RPMI 8226 cells ( P =0.005 at 24 h, P =0.020 at 36 h) or U266 myeloma cells ( P = 0.030 at 24h, P =0.020 at 36h) co-cultured with M2-polarized macrophages was higher than control group. ③In vitro the apoptotic rate of RPMI 8226 cells (29.0% versus 71.0%, t =4.97, P =0.008) or U266 myeloma cells (24.9% versus 67.7%, t =6.99, P =0.002) co-cultured with M2-polarized macrophages was lower than control group. ④ In vitro M2-polarized macrophages promoted myeloma cells secreting higher level of IL-6, TNF-α and higher expression of CCL2, CCL3, CCR2, CCR5, VEGFA, VEGFR-1,-2 compared with the non-macrophage co-culture system. Conclusion: M2-polarized macrophages promote myeloma cells proliferation and inhibit apoptosis through a very complex mechanism involving pro-inflammatory cytokines IL-6 and TNF-α, chemokines and related receptors such as CCL2, CCL3, CCR2, CCR3, and VEGF as well as related

Spin-Polarization in Quasi-Magnetic Tunnel Junctions

NASA Astrophysics Data System (ADS)

Xie, Zheng-Wei; Li, Ling

2017-05-01

Spin polarization in ferromagnetic metal/insulator/spin-filter barrier/nonmagnetic metal, referred to as quasi-magnetic tunnel junctions, is studied within the free-electron model. Our results show that large positive or negative spin-polarization can be obtained at high bias in quasi-magnetic tunnel junctions, and within large bias variation regions, the degree of spin-polarization can be linearly tuned by bias. These linear variation regions of spin-polarization with bias are influenced by the barrier thicknesses, barrier heights and molecular fields in the spin-filter (SF) layer. Among them, the variations of thickness and heights of the insulating and SF barrier layers have influence on the value of spin-polarization and the linear variation regions of spin-polarization with bias. However, the variations of molecular field in the SF layer only have influence on the values of the spin-polarization and the influences on the linear variation regions of spin-polarization with bias are slight. Supported by the Key Natural Science Fund of Sichuan Province Education Department under Grant Nos 13ZA0149 and 16ZA0047, and the Construction Plan for Scientific Research Innovation Team of Universities in Sichuan Province under Grant No 12TD008.

Atomistic Model for the Polyamide Formation from β-Lactam Catalyzed by Candida Antarctica Lipase B

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baum, Iris; Elsasser, Brigitta M.; Schwab, Leendert

2011-04-01

Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of {beta}-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly({beta}-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using dockingmore » tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of {beta}-lactam that rationalizes the activation of the monomer, the chain elongation by additional {beta}-lactam molecules, and the termination of the polymer chain. In addition, the processes leading to a premature chain termination are studied. Particularly, the QM/MM calculation enables an atomistic description of all eight steps involved in the catalytic cycle, which features an in situ-generated {beta}-alanine as the elongating monomer and which is compatible with the experimental findings.« less

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding.

PubMed

Tamura, Koichi; Hayashi, Shigehiko

2015-07-14

Molecular functions of proteins are often fulfilled by global conformational changes that couple with local events such as the binding of ligand molecules. High molecular complexity of proteins has, however, been an obstacle to obtain an atomistic view of the global conformational transitions, imposing a limitation on the mechanistic understanding of the functional processes. In this study, we developed a new method of molecular dynamics (MD) simulation called the linear response path following (LRPF) to simulate a protein's global conformational changes upon ligand binding. The method introduces a biasing force based on a linear response theory, which determines a local reaction coordinate in the configuration space that represents linear coupling between local events of ligand binding and global conformational changes and thus provides one with fully atomistic models undergoing large conformational changes without knowledge of a target structure. The overall transition process involving nonlinear conformational changes is simulated through iterative cycles consisting of a biased MD simulation with an updated linear response force and a following unbiased MD simulation for relaxation. We applied the method to the simulation of global conformational changes of the yeast calmodulin N-terminal domain and successfully searched out the end conformation. The atomistically detailed trajectories revealed a sequence of molecular events that properly lead to the global conformational changes and identified key steps of local-global coupling that induce the conformational transitions. The LRPF method provides one with a powerful means to model conformational changes of proteins such as motors and transporters where local-global coupling plays a pivotal role in their functional processes.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

A Molecular Probe for the Detection of Polar Lipids in Live Cells

PubMed Central

Bader, Christie A.; Shandala, Tetyana; Carter, Elizabeth A.; Ivask, Angela; Guinan, Taryn; Hickey, Shane M.; Werrett, Melissa V.; Wright, Phillip J.; Simpson, Peter V.; Stagni, Stefano; Voelcker, Nicolas H.; Lay, Peter A.; Massi, Massimiliano; Brooks, Douglas A.

2016-01-01

Lipids have an important role in many aspects of cell biology, including membrane architecture/compartment formation, intracellular traffic, signalling, hormone regulation, inflammation, energy storage and metabolism. Lipid biology is therefore integrally involved in major human diseases, including metabolic disorders, neurodegenerative diseases, obesity, heart disease, immune disorders and cancers, which commonly display altered lipid transport and metabolism. However, the investigation of these important cellular processes has been limited by the availability of specific tools to visualise lipids in live cells. Here we describe the potential for ReZolve-L1™ to localise to intracellular compartments containing polar lipids, such as for example sphingomyelin and phosphatidylethanolamine. In live Drosophila fat body tissue from third instar larvae, ReZolve-L1™ interacted mainly with lipid droplets, including the core region of these organelles. The presence of polar lipids in the core of these lipid droplets was confirmed by Raman mapping and while this was consistent with the distribution of ReZolve-L1™ it did not exclude that the molecular probe might be detecting other lipid species. In response to complete starvation conditions, ReZolve-L1™ was detected mainly in Atg8-GFP autophagic compartments, and showed reduced staining in the lipid droplets of fat body cells. The induction of autophagy by Tor inhibition also increased ReZolve-L1™ detection in autophagic compartments, whereas Atg9 knock down impaired autophagosome formation and altered the distribution of ReZolve-L1™. Finally, during Drosophila metamorphosis fat body tissues showed increased ReZolve-L1™ staining in autophagic compartments at two hours post puparium formation, when compared to earlier developmental time points. We concluded that ReZolve-L1™ is a new live cell imaging tool, which can be used as an imaging reagent for the detection of polar lipids in different intracellular

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

PubMed Central

Bian, Yunqiang; Tan, Cheng; Wang, Jun; Sheng, Yuebiao; Zhang, Jian; Wang, Wei

2014-01-01

In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes. PMID:24722458

Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting.

PubMed

Goel, Saurav; Luo, Xichun; Reuben, Robert L; Rashid, Waleed Bin

2011-11-11

Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear.

An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era.

PubMed

Spinello, Angelo; Magistrato, Alessandra

2017-08-01

Metallo-drugs have attracted enormous interest for cancer treatment. The achievements of this drug-type are summarized by the success story of cisplatin. That being said, there have been many drawbacks with its clinical use, which prompted decades worth of research efforts to move towards safer and more effective agents, either containing platinum or different metals. Areas covered: In this review, the authors provide an atomistic picture of the molecular mechanisms involving selected metallo-drugs from structural and molecular simulation studies. They also provide an omics perspective, pointing out many unsettled aspects of the most relevant families of metallo-drugs at an epigenetic level. Expert opinion: Molecular simulations are able to provide detailed information at atomistic and temporal (ps) resolutions that are rarely accessible to experiments. The increasing accuracy of computational methods and the growing performance of computational platforms, allow us to mirror wet lab experiments in silico. Consequently, the molecular mechanisms of drugs action/failure can be directly viewed on a computer screen, like a 'computational microscope', allowing us to harness this knowledge for the design of the next-generation of metallo-drugs.

Enhanced calculation of eigen-stress field and elastic energy in atomistic interdiffusion of alloys

NASA Astrophysics Data System (ADS)

Cecilia, José M.; Hernández-Díaz, A. M.; Castrillo, Pedro; Jiménez-Alonso, J. F.

2017-02-01

The structural evolution of alloys is affected by the elastic energy associated to eigen-stress fields. However, efficient calculations of the elastic energy in evolving geometries are actually a great challenge in promising atomistic simulation techniques such as Kinetic Monte Carlo (KMC) methods. In this paper, we report two complementary algorithms to calculate the eigen-stress field by linear superposition (a.k.a. LSA, Lineal Superposition Algorithm) and the elastic energy modification in atomistic interdiffusion of alloys (the Atom Exchange Elastic Energy Evaluation (AE4) Algorithm). LSA is shown to be appropriated for fast incremental stress calculation in highly nanostructured materials, whereas AE4 provides the required input for KMC and, additionally, it can be used to evaluate the accuracy of the eigen-stress field calculated by LSA. Consequently, they are suitable to be used on-the-fly with KMC. Both algorithms are massively parallel by their definition and thus well-suited for their parallelization on modern Graphics Processing Units (GPUs). Our computational studies confirm that we can obtain significant improvements compared to conventional Finite Element Methods, and the utilization of GPUs opens up new possibilities for the development of these methods in atomistic simulation of materials.

Multiscale simulations of defect dipole-enhanced electromechanical coupling at dilute defect concentrations

NASA Astrophysics Data System (ADS)

Liu, Shi; Cohen, R. E.

2017-08-01

The role of defects in solids of mixed ionic-covalent bonds such as ferroelectric oxides is complex. Current understanding of defects on ferroelectric properties at the single-defect level remains mostly at the empirical level, and the detailed atomistic mechanisms for many defect-mediated polarization-switching processes have not been convincingly revealed quantum mechanically. We simulate the polarization-electric field (P-E) and strain-electric field (ɛ-E) hysteresis loops for BaTiO3 in the presence of generic defect dipoles with large-scale molecular dynamics and provide a detailed atomistic picture of the defect dipole-enhanced electromechanical coupling. We develop a general first-principles-based atomistic model, enabling a quantitative understanding of the relationship between macroscopic ferroelectric properties and dipolar impurities of different orientations, concentrations, and dipole moments. We find that the collective orientation of dipolar defects relative to the external field is the key microscopic structure feature that strongly affects materials hardening/softening and electromechanical coupling. We show that a small concentration (≈0.1 at. %) of defect dipoles dramatically improves electromechanical responses. This offers the opportunity to improve the performance of inexpensive polycrystalline ferroelectric ceramics through defect dipole engineering for a range of applications including piezoelectric sensors, actuators, and transducers.

Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

NASA Astrophysics Data System (ADS)

Shadrack Jabes, B.; Krekeler, C.; Klein, R.; Delle Site, L.

2018-05-01

We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

Quasi-Continuum Reduction of Field Theories: A Route to Seamlessly Bridge Quantum and Atomistic Length-Scales with Continuum

DTIC Science & Technology

2016-04-01

AFRL-AFOSR-VA-TR-2016-0145 Quasi-continuum reduction of field theories: A route to seamlessly bridge quantum and atomistic length-scales with...field theories: A route to seamlessly bridge quantum and atomistic length-scales with continuum Principal Investigator: Vikram Gavini Department of...calculations on tens of thousands of atoms, and enable continuing efforts towards a seamless bridging of the quantum and continuum length-scales

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

PubMed

Kang, Myungshim; Chakraborty, Kaushik; Loverde, Sharon M

2018-06-25

We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assembly mechanism from random with ∼0.4 μs molecular dynamics simulations. Furthermore, we also computationally characterize the interfacial structure, directionality of π-π stacking, and water dynamics within several peptide-drug nanotubes with diameters consistent with the reported experimental nanotube diameter. Insight gained should inform the future design of these novel anticancer drug delivery systems.

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2014-03-01

We developed a dual basis approach within the fragment molecular orbital formalism enabling efficient and accurate use of large basis sets. The method was tested on water clusters and polypeptides and applied to perform geometry optimization of chignolin (PDB: 1UAO) in solution at the level of DFT/6-31++G∗∗, obtaining a structure in agreement with experiment (RMSD of 0.4526 Å). The polarization in polypeptides is discussed with a comparison of the α-helix and β-strand.

Envelope molecular-orbital theory of extended systems. I. Electronic states of organic quasilinear nanoheterostructures

NASA Astrophysics Data System (ADS)

Arce, J. C.; Perdomo-Ortiz, A.; Zambrano, M. L.; Mujica-Martínez, C.

2011-03-01

A conceptually appealing and computationally economical course-grained molecular-orbital (MO) theory for extended quasilinear molecular heterostructures is presented. The formalism, which is based on a straightforward adaptation, by including explicitly the vacuum, of the envelope-function approximation widely employed in solid-state physics leads to a mapping of the three-dimensional single-particle eigenvalue equations into simple one-dimensional hole and electron Schrödinger-like equations with piecewise-constant effective potentials and masses. The eigenfunctions of these equations are envelope MO's in which the short-wavelength oscillations present in the full MO's, associated with the atomistic details of the molecular potential, are smoothed out automatically. The approach is illustrated by calculating the envelope MO's of high-lying occupied and low-lying virtual π states in prototypical nanometric heterostructures constituted by oligomers of polyacetylene and polydiacetylene. Comparison with atomistic electronic-structure calculations reveals that the envelope-MO energies agree very well with the energies of the π MO's and that the envelope MO's describe precisely the long-wavelength variations of the π MO's. This envelope MO theory, which is generalizable to extended systems of any dimensionality, is seen to provide a useful tool for the qualitative interpretation and quantitative prediction of the single-particle quantum states in mesoscopic molecular structures and the design of nanometric molecular devices with tailored energy levels and wavefunctions.

[Graviresponse in higher plants and its regulation in molecular bases: relevance to growth and development, and auxin polar transport in etiolated pea seedlings].

PubMed

Ueda, Junichi; Miyamoto, Kensuke

2003-08-01

We review the graviresponse under true and simulated microgravity conditions on a clinostat in higher plants, and its regulation in molecular bases, especially on the aspect of auxin polar transport in etiolated pea (Pisum sativum L. cv. Alaska) seedlings which were the plant materials subjected to STS-95 space experiments. True and simulated microgravity conditions substantially affected growth and development in etiolated pea seedlings, especially the direction of growth of stems and roots, resulting in automorphosis. In etiolated pea seedlings grown in space, epicotyls were the most oriented toward the direction far from the cotyledons, and roots grew toward the aerial space of Plant Growth Chamber. Automorphosis observed in space were well simulated by a clinorotation on a 3-dimensional clinostat and also phenocopied by the application of auxin polar transport inhibitors of 2,3,5-triiodobenzoic acid, N-(1-naphtyl)phthalamic acid and 9-hydroxyfluorene-9-carboxylic acid. Judging from the results described above together with the fact that activities of auxin polar transport in epicotyls of etiolated pea seedlings grown in space substantially were reduced, auxin polar transport seems to be closely related to automorphosis. Strenuous efforts to learn in molecular levels how gravity contributes to the auxin polar transport in etiolated pea epicotyls resulted in successful identification of PsPIN2 and PsAUX1 genes located in plasma membrane which products are considered to be putative efflux and influx carriers of auxin, respectively. Based on the results of expression of PsPIN2 and PsAUX1 genes under various gravistimulations, a possible role of PsPIN2 and PsAUX1 genes for auxin polar transport in etiolated pea seedlings will be discussed.

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

NASA Technical Reports Server (NTRS)

Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

1999-01-01

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

Revised Atomistic Models of the Crystal Structure of C-S-H with high C/S Ratio

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Nicoleau, Luc; Nonat, André; Veryazov, Valera

2016-09-01

The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Computer Science Techniques Applied to Parallel Atomistic Simulation

NASA Astrophysics Data System (ADS)

Nakano, Aiichiro

1998-03-01

Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

Coarse gaining of molecular crystals: limitations imposed by molecular flexibility

NASA Astrophysics Data System (ADS)

Picu, Catalin; Pal, Anirban

Molecular crystals include molecular electronics, energetic materials, pharmaceuticals and some food components. In many of these applications the small scale mechanical behavior of the crystal is important such as for example in energetic materials where detonation is induced by the formation of hot spots which are induced thermomechanically, and in pharmaceuticals where phase stability is critical for the biochemical activity of the drug. Accurate modeling of these processes requires resolving the atomistic scale details of the material. However, the cost of these models is very large due to the complexity of the molecules forming the crystal, and some form of coarse graning is necessary. In this study we identify the limitations imposed by the need to accurately capture molecular flexibility on the development of coarse grained models for the energetic molecular crystal RDX. We define guidelines for the definition of coarse grained models that target elastic and plastic crystal scale properties such as elastic constants, thermal expansion, compressibility, the critical stress for the motion of dislocations (Peierls stress) and the stacking fault energy This work was supported by the ARO through Grant W911NF-09-1-0330 and AFRL through Grant FA8651-16-1-0004.

Spin transport properties of n-polyacene molecules (n = 1–15) connected to Ni surface electrodes: Theoretical analysis

PubMed Central

Caliskan, S.; Laref, A.

2014-01-01

Using non-equilibrium Green function formalism in conjunction with density functional theory, we explore the spin-polarized transport characteristics of several planar n-acene molecules suspended between two semi-infinite Ni electrodes via the thiol group. We examine the spin-dependence transport on Ni-n-acenes-Ni junctions, while the number of fused benzene rings varies between 1 and 15. Intriguingly, the induced magnetic moments of small acene molecules are higher than that of longer acene rings. The augmentation of fused benzene rings affects both the magnetic and transport features, such as the transmission function and conductance owing to their coupling to the Ni surface contacts via the anchoring group. The interplay between the spin-polarized transport properties, structural configuration and molecular electronic is a fortiori essential in these attractive molecular devices. Thus, this can conduct to the engineering of the electron spin transport in atomistic and molecular junctions. These prominent molecules convincingly infer that the molecular spin valves can conduct to thriving molecular devices. PMID:25482076

High molecular weight non-polar hydrocarbons as pure model substances and in motor oil samples can be ionized without fragmentation by atmospheric pressure chemical ionization mass spectrometry.

PubMed

Hourani, Nadim; Kuhnert, Nikolai

2012-10-15

High molecular weight non-polar hydrocarbons are still difficult to detect by mass spectrometry. Although several studies have targeted this problem, lack of good self-ionization has limited the ability of mass spectrometry to examine these hydrocarbons. Failure to control ion generation in the atmospheric pressure chemical ionization (APCI) source hampers the detection of intact stable gas-phase ions of non-polar hydrocarbon in mass spectrometry. Seventeen non-volatile non-polar hydrocarbons, reported to be difficult to ionize, were examined by an optimized APCI methodology using nitrogen as the reagent gas. All these analytes were successfully ionized as abundant and intact stable [M-H](+) ions without the use of any derivatization or adduct chemistry and without significant fragmentation. Application of the method to real-life hydrocarbon mixtures like light shredder waste and car motor oil was demonstrated. Despite numerous reports to the contrary, it is possible to ionize high molecular weight non-polar hydrocarbons by APCI, omitting the use of additives. This finding represents a significant step towards extending the applicability of mass spectrometry to non-polar hydrocarbon analyses in crude oil, petrochemical products, waste or food. Copyright © 2012 John Wiley & Sons, Ltd.

Polarized hydrogen/deuterium molecules

NASA Astrophysics Data System (ADS)

Shestakov, Yu V.; Nikolenko, D. M.; Rachek, I. A.; Sadykov, R. Sh; Toporkov, D. K.; Yurchenko, A. V.; Zevakov, S. A.

2017-12-01

The prototype of a polarized molecular hydrogen/deuterium source which is based on the classical Stern-Gerlach separation scheme has been tested at the Budker Institute of Nuclear Physics (BINP), Novosibirsk. It consists of the circular slit nozzle cooled down to 6.5 K and the two superconducting sextupole magnets. The flux of polarized hydrogen molecules of 3·1012 mol/s was measured for a total gas flow through the nozzle of 5·10-2 Torr·l/s. The obtained results will be used to develop a much more intense source of polarized molecules.

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

PubMed

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

The effect of natural organic matter polarity and molecular weight on NDMA formation from two antibiotics containing dimethylamine functional groups.

PubMed

Leavey-Roback, Shannon L; Krasner, Stuart W; Suffet, Irwin H Mel

2016-12-01

N-nitrosodimethylamine (NDMA) is a disinfection byproduct preferentially formed in chloraminated water. NDMA may be formed from certain chemicals containing dimethylamine (DMA) functional groups. This reaction may be slowed by the presence of natural organic matter (NOM). In this study, NOM fractionated by size or polarity was tested for its ability to slow or impede the formation of NDMA from two DMA-containing precursors, the antibiotics tetracycline and spiramycin. The high molecular weight NOM fractions (>10KDa) were shown to be the most effective in reducing the amount of NDMA formed from the precursor chemicals. The filtrate of a C-18 non-polar cartridge was also effective at reducing NDMA formation from tetracycline (spyramycin not tested). Therefore, polar and charged NOM components may be responsible for the reduction in NDMA formation. A possible mechanism for the reduction of NDMA formation from tetracycline is complexation due to the hydrogen bonding of the DMA functional group on tetracycline to polar phenolic functional groups in the NOM. Copyright © 2016 Elsevier B.V. All rights reserved.

Exploiting molecular dynamics in Nested Sampling simulations of small peptides

NASA Astrophysics Data System (ADS)

Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

2016-04-01

Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

PubMed

Numazawa, Satoshi; Smith, Roger

2011-10-01

Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

Quantifying chain reptation in entangled polymer melts: Topological and dynamical mapping of atomistic simulation results onto the tube model

NASA Astrophysics Data System (ADS)

Stephanou, Pavlos S.; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G.; Kröger, Martin

2010-03-01

The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability ψ(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed ψ(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic

Mapping Cellular Polarity Networks Using Mass Spectrometry-based Strategies.

PubMed

Daulat, Avais M; Puvirajesinghe, Tania M; Camoin, Luc; Borg, Jean-Paul

2018-05-18

Cell polarity is a vital biological process involved in the building, maintenance and normal functioning of tissues in invertebrates and vertebrates. Unsurprisingly, molecular defects affecting polarity organization and functions have a strong impact on tissue homeostasis, embryonic development and adult life, and may directly or indirectly lead to diseases. Genetic studies have demonstrated the causative effect of several polarity genes in diseases; however, much remains to be clarified before a comprehensive view of the molecular organization and regulation of the protein networks associated with polarity proteins is obtained. This challenge can be approached head-on using proteomics to identify protein complexes involved in cell polarity and their modifications in a spatio-temporal manner. We review the fundamental basics of mass spectrometry techniques and provide an in-depth analysis of how mass spectrometry has been instrumental in understanding the complex and dynamic nature of some cell polarity networks at the tissue (apico-basal and planar cell polarities) and cellular (cell migration, ciliogenesis) levels, with the fine dissection of the interconnections between prototypic cell polarity proteins and signal transduction cascades in normal and pathological situations. This review primarily focuses on epithelial structures which are the fundamental building blocks for most metazoan tissues, used as the archetypal model to study cellular polarity. This field offers broad perspectives thanks to the ever-increasing sensitivity of mass spectrometry and its use in combination with recently developed molecular strategies able to probe in situ proteomic networks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Polar and low polar solvents media effect on dipole moments of some diazo Sudan dyes

NASA Astrophysics Data System (ADS)

Zakerhamidi, M. S.; Golghasemi Sorkhabi, Sh.; Shamkhali, A. N.

2014-06-01

Absorption and fluorescence spectra of three Sudan dyes (SudanIII, SudanIV and Sudan black B) were recorded in various solvents with different polarity in the range of 300-800 nm, at room temperature. The solvatochromic method was used to investigate dipole moments of these dyes in ground and excited states, in different media. The solvatochromic behavior of these substances and their solvent-solute interactions were analyzed via solvent polarity parameters. Obtained results express the effects of solvation on tautomerism and molecular configuration (geometry) of Sudan dyes in solvent media with different polarity. Furthermore, analyze of solvent-solute interactions and value of ground and excited states dipole moments suggests different forms of resonance structures for Sudan dyes in polar and low-polar solvents.

Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Adaptive resolution simulation of an atomistic protein in MARTINI water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecularmore » dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.« less

Multiresolution molecular mechanics: Surface effects in nanoscale materials

NASA Astrophysics Data System (ADS)

Yang, Qingcheng; To, Albert C.

2017-05-01

Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), [57]) is applied to capture surface effect for nanosized structures by designing a surface summation rule SRS within the framework of MMM. Combined with previously proposed bulk summation rule SRB, the MMM summation rule SRMMM is completed. SRS and SRB are consistently formed within SRMMM for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to the good performance of SRMMM lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SRS and SRB are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SRMMM accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SRMMM with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SRMMM that is analogous to numerical integration error with quadrature rule in FEM is very small.

Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting

PubMed Central

2011-01-01

Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear. PMID:22078069

Local Polar Fluctuations in Lead Halide Perovskite Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yaffe, Omer; Guo, Yinsheng; Tan, Liang Z.

2017-03-01

Hybrid lead-halide perovskites have emerged as an excellent class of photovoltaic materials. Recent reports suggest that the organic molecular cation is responsible for local polar fluctuations that inhibit carrier recombination. We combine low-frequency Raman scattering with first-principles molecular dynamics (MD) to study the fundamental nature of these local polar fluctuations. Our observations of a strong central peak in the cubic phase of both hybrid (CH3NH3PbBr3) and all-inorganic (CsPbBr3) leadhalide perovskites show that anharmonic, local polar fluctuations are intrinsic to the general lead-halide perovskite structure, and not unique to the dipolar organic cation. MD simulations indicate that head-tohead Cs motion coupledmore » to Br face expansion, occurring on a few hundred femtosecond time scale, drives the local polar fluctuations in CsPbBr3.« less

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials

Atomistic study on the FCC/BCC interface structure with {112}KS orientation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Keonwook; Beyerlein, Irene; Han, Weizhong

2011-09-23

In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.

Atomistic Models of General Anesthetics for Use in in Silico Biological Studies

PubMed Central

2015-01-01

While small molecules have been used to induce anesthesia in a clinical setting for well over a century, a detailed understanding of the molecular mechanism remains elusive. In this study, we utilize ab initio calculations to develop a novel set of CHARMM-compatible parameters for the ubiquitous modern anesthetics desflurane, isoflurane, sevoflurane, and propofol for use in molecular dynamics (MD) simulations. The parameters generated were rigorously tested against known experimental physicochemical properties including dipole moment, density, enthalpy of vaporization, and free energy of solvation. In all cases, the anesthetic parameters were able to reproduce experimental measurements, signifying the robustness and accuracy of the atomistic models developed. The models were then used to study the interaction of anesthetics with the membrane. Calculation of the potential of mean force for inserting the molecules into a POPC bilayer revealed a distinct energetic minimum of 4–5 kcal/mol relative to aqueous solution at the level of the glycerol backbone in the membrane. The location of this minimum within the membrane suggests that anesthetics partition to the membrane prior to binding their ion channel targets, giving context to the Meyer–Overton correlation. Moreover, MD simulations of these drugs in the membrane give rise to computed membrane structural parameters, including atomic distribution, deuterium order parameters, dipole potential, and lateral stress profile, that indicate partitioning of anesthetics into the membrane at the concentration range studied here, which does not appear to perturb the structural integrity of the lipid bilayer. These results signify that an indirect, membrane-mediated mechanism of channel modulation is unlikely. PMID:25303275

Atomistic details of protein dynamics and the role of hydration water

DOE PAGES

Khodadadi, Sheila; Sokolov, Alexei P.

2016-05-04

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

Atomistic details of protein dynamics and the role of hydration water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khodadadi, Sheila; Sokolov, Alexei P.

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

2017-01-01

This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nomura, K; Seymour, R; Wang, W

2009-02-17

A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based onmore » hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).« less

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, JOhn W.; Daw, Murray S.; Bauschlicher, Charles W.

2011-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 are candidate materials for applications in extreme environments because of their high melting point, good mechanical properties and reasonable oxidation resistance. Unlike many ceramics, these materials have high thermal conductivity which can be advantageous, for example, to reduce thermal shock. Recently, we developed Tersoff style interatomic potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current. Results at room temperature and at elevated temperatures will be reported.

Plasma-assisted Molecular Beam Epitaxy of N-polar InAlN-barrier High-electron-mobility Transistors.

PubMed

Hardy, Matthew T; Storm, David F; Katzer, D Scott; Downey, Brian P; Nepal, Neeraj; Meyer, David J

2016-11-24

Plasma-assisted molecular beam epitaxy is well suited for the epitaxial growth of III-nitride thin films and heterostructures with smooth, abrupt interfaces required for high-quality high-electron-mobility transistors (HEMTs). A procedure is presented for the growth of N-polar InAlN HEMTs, including wafer preparation and growth of buffer layers, the InAlN barrier layer, AlN and GaN interlayers and the GaN channel. Critical issues at each step of the process are identified, such as avoiding Ga accumulation in the GaN buffer, the role of temperature on InAlN compositional homogeneity, and the use of Ga flux during the AlN interlayer and the interrupt prior to GaN channel growth. Compositionally homogeneous N-polar InAlN thin films are demonstrated with surface root-mean-squared roughness as low as 0.19 nm and InAlN-based HEMT structures are reported having mobility as high as 1,750 cm 2 /V∙sec for devices with a sheet charge density of 1.7 x 10 13 cm -2 .

Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prezhdo, Oleg V.

2012-03-22

Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results weremore » reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and

Apicobasal polarity of brain endothelial cells

PubMed Central

Worzfeld, Thomas

2015-01-01

Normal brain homeostasis depends on the integrity of the blood–brain barrier that controls the access of nutrients, humoral factors, and immune cells to the CNS. The blood–brain barrier is composed mainly of brain endothelial cells. Forming the interface between two compartments, they are highly polarized. Apical/luminal and basolateral/abluminal membranes differ in their lipid and (glyco-)protein composition, allowing brain endothelial cells to secrete or transport soluble factors in a polarized manner and to maintain blood flow. Here, we summarize the basic concepts of apicobasal cell polarity in brain endothelial cells. To address potential molecular mechanisms underlying apicobasal polarity in brain endothelial cells, we draw on investigations in epithelial cells and discuss how polarity may go awry in neurological diseases. PMID:26661193

Local polar fluctuations in lead halide perovskite crystals

DOE PAGES

Yaffe, Omer; Guo, Yinsheng; Tan, Liang Z.; ...

2017-03-28

Hybrid lead-halide perovskites have emerged as an excellent class of photovoltaic materials. Recent reports suggest that the organic molecular cation is responsible for local polar fluctuations that inhibit carrier recombination. We combine low-frequency Raman scattering with first-principles molecular dynamics (MD) to study the fundamental nature of these local polar fluctuations. Our observations of a strong central peak in the cubic phase of both hybrid (CH 3NH 3PbBr 3) and all-inorganic (CsPbBr 3) lead-halide perovskites show that anharmonic, local polar fluctuations are intrinsic to the general lead-halide perovskite structure, and not unique to the dipolar organic cation. Furthermore, MD simulations indicatemore » that head-to-head Cs motion coupled to Br face expansion, occurring on a few hundred femtosecond time scale, drives the local polar fluctuations in CsPbBr 3.« less

Luminescent N-polar (In,Ga)N/GaN quantum wells achieved by plasma-assisted molecular beam epitaxy at temperatures exceeding 700 °C

NASA Astrophysics Data System (ADS)

Chèze, C.; Feix, F.; Lähnemann, J.; Flissikowski, T.; Kryśko, M.; Wolny, P.; Turski, H.; Skierbiszewski, C.; Brandt, O.

2018-01-01

Previously, we found that N-polar (In,Ga)N/GaN quantum wells prepared on freestanding GaN substrates by plasma-assisted molecular beam epitaxy at conventional growth temperatures of about 650 °C do not exhibit any detectable luminescence even at 10 K. In the present work, we investigate (In,Ga)N/GaN quantum wells grown on Ga- and N-polar GaN substrates at a constant temperature of 730 °C . This exceptionally high temperature results in a vanishing In incorporation for the Ga-polar sample. In contrast, quantum wells with an In content of 20% and abrupt interfaces are formed on N-polar GaN. Moreover, these quantum wells exhibit a spatially uniform green luminescence band up to room temperature, but the intensity of this band is observed to strongly quench with temperature. Temperature-dependent photoluminescence transients show that this thermal quenching is related to a high density of nonradiative Shockley-Read-Hall centers with large capture coefficients for electrons and holes.

Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure.

PubMed

Lee, Tzong-Hsien; Hirst, Daniel J; Kulkarni, Ketav; Del Borgo, Mark P; Aguilar, Marie-Isabel

2018-06-13

The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.

Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

PubMed Central

Bjelkmar, Pär; Niemelä, Perttu S.; Vattulainen, Ilpo; Lindahl, Erik

2009-01-01

Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations. PMID:19229308

Quantum Corrections to the 'Atomistic' MOSFET Simulations

NASA Technical Reports Server (NTRS)

Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

2000-01-01

We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

Inclusion Complexes Behavior at the Air-Water Interface. Molecular Dynamic Simulation Study.

NASA Astrophysics Data System (ADS)

Gargallo, L.; Vargas, D.; Sandoval, C.; Saavedra, M.; Becerra, N.; Leiva, A.; Radić, D.

2008-08-01

The interfacial properties of the inclusion complexes (ICs), obtained from the threading of α-cyclodextrin (α-CD) onto poly(ethylene-oxide)(PEO), poly(ɛ-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF) and their precursor homopolymers (PHPoly), were studied at the air-water interface. The free surface energy was determined by wettability measurements. The experimental behavior of these systems was described by an atomistic molecular dynamics simulation (MDS).

First-principles studies of electrical transport in nanoscale molecular junctions

NASA Astrophysics Data System (ADS)

Neaton, J. B.

2008-03-01

Understanding the conductance of individual molecular junctions is a forefront topic in theoretical nanoscience. The development of a general, efficient atomistic approach for treating an open system out of equilibrium with good accuracy, and then using it to inform experiment, is a significant open challenge in the field. Here I will describe studies where first-principles techniques, based on density functional theory (DFT) and beyond, are used to investigate some of the fundamental issues associated with single-molecule transport measurements. After a brief summary of previous work, a DFT-based scattering-state approach is presented and applied to H2 and amine-Au linked molecular junctions [1], two systems for which there exist reliable data [2]. Similar to most ab initio studies, we rely on a Landauer approach within DFT for junction conductance. Using this framework, which has proven relatively accurate for metallic point contacts, good agreement with experiment is obtained for the H2 conductance. For amine-Au linked junctions, however, the computed conductance is significantly larger than that measured,although structural trends are reproduced by the calculations. To explore this further, we draw on GW calculations of a prototypical metal-molecule contact, benzene on graphite, where interfacial polarization effects are found to drastically modify frontier orbital energies [3]. A physically motivated model self-energy correction is developed from our GW calculations,applied to the amine case, and shown to quantitatively explain the discrepancy with experiment. The importance of many-electron corrections beyond DFT for accurately computing molecular conductance and understanding experiments is thoroughly discussed. [1] S. Y. Quek et al., Nano Lett 7, 3482 (2007); K. H. Khoo et al., submitted (2007). [2] R. Smit et al., Nature 419, 906 (2002); L. Venkataraman et al., Nature 442 ,904 (2006). [3] J. B. Neaton et al., Phys. Rev. Lett. 97, 216405 (2006).

Understanding luminescence properties of grain boundaries in GaN thin films and their atomistic origin

NASA Astrophysics Data System (ADS)

Yoo, Hyobin; Yoon, Sangmoon; Chung, Kunook; Kang, Seoung-Hun; Kwon, Young-Kyun; Yi, Gyu-Chul; Kim, Miyoung

2018-03-01

We report our findings on the optical properties of grain boundaries in GaN films grown on graphene layers and discuss their atomistic origin. We combine electron backscatter diffraction with cathodoluminescence to directly correlate the structural defects with their optical properties, enabling the high-precision local luminescence measurement of the grain boundaries in GaN films. To further understand the atomistic origin of the luminescence properties, we carefully probed atomic core structures of the grain boundaries by exploiting aberration-corrected scanning transmission electron microscopy. The atomic core structures of grain boundaries show different ordering behaviors compared with those observed previously in threading dislocations. Energetics of the grain boundary core structures and their correlation with electronic structures were studied by first principles calculation.

Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

2000-01-01

We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular-dynamics simulation.

PubMed

Ko, Youn Jo; Jo, Won Ho

2010-05-19

Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger, and how the protein brings about the coupled movement of both ions are still unknown. In this work, we use an atomistic molecular dynamics (MD) simulation to demonstrate that a previously unknown secondary water pore is formed inside an Escherichia coli ClC exchanger. The secondary water pore is bifurcated from the chloride ion pathway at E148. From the systematic simulations, we determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore, and that the highly conserved tyrosine residue Y445 functions as a barrier that separates the proton from the chloride ion pathways. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore, and we propose a new mechanism for the coupled transport of chloride ions and protons. It has been reported that several members of ClC proteins are not just channels that simply transport chloride ions across lipid bilayers; rather, they are exchangers that transport both the chloride ion and proton in opposite directions. However, the ion transit pathways and the mechanism of the coupled movement of these two ions have not yet been unveiled. In this article, we report a new finding (to our knowledge) of a water pore inside a prokaryotic ClC protein as revealed by computer simulation. This water pore is bifurcated from the putative chloride ion, and water molecules inside the new pore connect two glutamate residues that are known to be key residues for proton transport. On the basis of our simulation results, we conclude that the water wire that is formed inside the newly found pore acts as a proton pathway, which enables us to

Atomistic insights into deep eutectic electrolytes: the influence of urea on the electrolyte salt LiTFSI in view of electrochemical applications.

PubMed

Lesch, Volker; Heuer, Andreas; Rad, Babak R; Winter, Martin; Smiatek, Jens

2016-10-19

The influence of urea on the conducting salt lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) in terms of lithium ion coordination numbers and lithium ion transport properties is studied via atomistic molecular dynamics simulations. Our results indicate that the presence of urea favors the formation of a deep eutectic electrolyte with pronounced ion conductivities which can be explained by a competition between urea and TFSI in occupying the first coordination shell around lithium ions. All simulation findings verify that high urea concentrations lead to a significant increase of ionic diffusivities and an occurrence of relatively high lithium transference numbers in good agreement with experimental results. The outcomes of our study point at the possible application of deep eutectic electrolytes as ion conducting materials in lithium ion batteries.

Polarized fluorescence in NADH under two-photon excitation with femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Vasyutinskii, O. S.; Smolin, A. G.; Oswald, C.; Gericke, K. H.

2017-04-01

Polarized fluorescence decay in NADH molecules in aqueous solution under two-photon excitation by femtosecond laser pulses has been studied. The excitation was carried out by linear and circularly polarized radiation at four wavelengths: 720, 730, 740, and 750 nm. Time-dependent polarized fluorescence signals were recorded as a function of the excitation light polarization and used for determination of a set of molecular parameters, two lifetimes characterizing the molecular excited states, and the rotation correlation time τrot. The results obtained can be used to create and prove theoretical models describing the intensity and polarization of fluorescence in NADH involved in the regulation of the redox reactions in cells and tissues of living organisms.

Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

NASA Astrophysics Data System (ADS)

Yan, Xin; Gouissem, Afif; Guduru, Pradeep R.; Sharma, Pradeep

2017-10-01

Amorphous lithium-silicon (a-Li-Si), especially in nanostructure form, is an attractive high-capacity anode material for next-generation Li-ion batteries. During cycles of charging and discharging, a-Li-Si undergoes substantive inelastic deformation and exhibits microcracking. The mechanical response to repeated lithiation-delithiation eventually results in the loss of electrical contact and consequent decrease of capacity, thus underscoring the importance of studying the plasticity of a-Li-Si nanostructures. In recent years, a variety of phenomenological continuum theories have been introduced that purport to model plasticity and the electro-chemo-mechanical behavior of a-Li-Si. Unfortunately, the micromechanisms and atomistic considerations underlying plasticity in Li-Si material are not yet fully understood and this impedes the development of physics-based constitutive models. Conventional molecular dynamics, although extensively used to study this material, is grossly inadequate to resolve this matter. As is well known, conventional molecular dynamics simulations can only address phenomena with characteristic time scales of (at most) a microsecond. Accordingly, in such simulations, the mechanical behavior is deduced under conditions of very high strain rates (usually, 108s-1 or even higher). This limitation severely impacts a realistic assessment of rate-dependent effects. In this work, we attempt to circumvent the time-scale bottleneck of conventional molecular dynamics and provide novel insights into the mechanisms underpinning plastic deformation of Li-Si nanostructures. We utilize an approach that allows imposition of slow strain rates and involves the employment of a new and recently developed potential energy surface sampling method—the so-called autonomous basin climbing—to identify the local minima in the potential energy surface. Combined with other techniques, such as nudged elastic band, kinetic Monte Carlo and transition state theory, we assess

Molecular Simulations of Adsorption and Diffusion in Silicalite.

NASA Astrophysics Data System (ADS)

Snurr, Randall Quentin

The adsorption and diffusion of hydrocarbons in the zeolite silicalite have been studied using molecular simulations. The simulations use an atomistic description of zeolite/sorbate interactions and are based on principles of statistical mechanics. Emphasis was placed on developing new simulation techniques to allow complex systems relevant to industrial applications in catalysis and separations processes to be studied. Adsorption isotherms and heats of sorption for methane in silicalite were calculated from grand canonical Monte Carlo (GCMC) simulations and also from molecular dynamics (MD) simulations accompanied by Widom test particle insertions. Good agreement with experimental data from the literature was found. The adsorption thermodynamics of aromatic species in silicalite at low loading was predicted by direct evaluation of the configurational integrals. Good agreement with experiment was obtained for the Henry's constants and the heats of adsorption. Molecules were predicted to be localized in the channel intersections at low loading. At higher loading, conventional GCMC simulations were found to be infeasible. Several variations of the GCMC technique were developed incorporating biased insertion moves. These new techniques are much more efficient than conventional GCMC and allow for the prediction of adsorption isotherms of tightly-fitting aromatic molecules in silicalite. Our simulations when combined with experimental evidence of a phase change in the zeolite structure at intermediate loading provide an explanation of the characteristic steps seen in the experimental isotherms. A hierarchical atomistic/lattice model for studying these systems was also developed. The hierarchical model is more than an order of magnitude more efficient computationally than direct atomistic simulation. Diffusion of benzene in silicalite was studied using transition-state theory (TST). Such an approach overcomes the time-scale limitations of using MD simulations for

Hamiltonian adaptive resolution molecular dynamics simulation of infrared dielectric functions of liquids

NASA Astrophysics Data System (ADS)

Wang, C. C.; Tan, J. Y.; Liu, L. H.

2018-05-01

Hamiltonian adaptive resolution scheme (H-AdResS), which allows to simulate materials by treating different domains of the system at different levels of resolution, is a recently proposed atomistic/coarse-grained multiscale model. In this work, a scheme to calculate the dielectric functions of liquids on account of H-AdResS is presented. In the proposed H-AdResS dielectric-function calculation scheme (DielectFunctCalS), the corrected molecular dipole moments are calculated by multiplying molecular dipole moment by the weighting fraction of the molecular mapping point. As the widths of all-atom and hybrid regions show different degrees of influence on the dielectric functions, a prefactor is multiplied to eliminate the effects of all-atom and hybrid region widths. Since one goal of using the H-AdResS method is to reduce computational costs, widths of the all-atom region and the hybrid region can be reduced considering that the coarse-grained simulation is much more timesaving compared to atomistic simulation. Liquid water and ethanol are taken as test cases to validate the DielectFunctCalS. The H-AdResS DielectFunctCalS results are in good agreement with all-atom molecular dynamics simulations. The accuracy of the H-AdResS results, together with all-atom molecular dynamics results, depends heavily on the choice of the force field and force field parameters. The H-AdResS DielectFunctCalS allows us to calculate the dielectric functions of macromolecule systems with high efficiency and makes the dielectric function calculations of large biomolecular systems possible.

Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N.; Harrabi, K.

2015-07-14

Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect onmore » the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.« less

Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding

NASA Astrophysics Data System (ADS)

Xu, Yun; Chen, Jun

2015-02-01

The energy flux integral criterion based on atomistic potentials within the framework of hyperelasticity-plasticity is proposed for dynamic adiabatic shear banding (ASB). System Helmholtz energy decomposition reveals that the dynamic influence on the integral path dependence is originated from the volumetric strain energy and partial deviatoric strain energy, and the plastic influence only from the rest part of deviatoric strain energy. The concept of critical shear banding energy is suggested for describing the initiation of ASB, which consists of the dynamic recrystallization (DRX) threshold energy and the thermal softening energy. The criterion directly relates energy flux to the basic physical processes that induce shear instability such as dislocation nucleations and multiplications, without introducing ad-hoc parameters in empirical constitutive models. It reduces to the classical path independent J-integral for quasi-static loading and elastic solids. The atomistic-to-continuum multiscale coupling method is used to simulate the initiation of ASB. Atomic configurations indicate that DRX induced microstructural softening may be essential to the dynamic shear localization and hence the initiation of ASB.

Molecular dynamics simulations of substitutional diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

2016-12-18

In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less

3d visualization of atomistic simulations on every desktop

NASA Astrophysics Data System (ADS)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-08-01

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

Dynamic Nuclear Polarization NMR in Human Cells Using Fluorescent Polarizing Agents.

PubMed

Albert, Brice J; Gao, Chukun; Sesti, Erika L; Saliba, Edward P; Alaniva, Nicholas; Scott, Faith J; Sigurdsson, Snorri Th; Barnes, Alexander B

2018-06-20

Solid-state nuclear magnetic resonance (NMR) enables atomic resolution characterization of molecular structure and dynamics within complex heterogeneous samples, but it is typically insensitive. Dynamic nuclear polarization (DNP) increases NMR signal intensity by orders of magnitude and can be performed in combination with magic angle spinning (MAS) for sensitive, high-resolution spectroscopy. Here we report MAS DNP experiments, for the first time, within intact human cells with >40-fold DNP enhancement and a sample temperature below 6 K. In addition to cryogenic MAS results below 6 K, we also show in-cell DNP enhancements of 57-fold at 90 K. In-cell DNP is demonstrated using biradicals and sterically-shielded monoradicals as polarizing agents. A novel trimodal polarizing agent is introduced for DNP, which contains a nitroxide biradical, a targeting peptide for cell penetration, and a fluorophore for subcellular localization with confocal microscopy. The fluorescent polarizing agent provides in-cell DNP enhancements of 63-fold at a concentration of 2.7 mM. These experiments pave the way for structural characterization of biomolecules in an endogenous cellular context.

p/n-Polarity of thiophene oligomers in photovoltaic cells: role of molecular vs. supramolecular properties.

PubMed

Ghosh, Tanwistha; Gopal, Anesh; Saeki, Akinori; Seki, Shu; Nair, Vijayakumar C

2015-04-28

Molecular and supramolecular properties play key roles in the optoelectronic properties and photovoltaic performances of organic materials. In the present work, we show how small changes in the molecular structure affect such properties, which in turn control the intrinsic and fundamental properties such as the p/n-polarity of organic semiconductors in bulk-heterojunction solar cells. Herein, we designed and synthesized two acceptor-donor-acceptor type semiconducting thiophene oligomers end-functionalized with oxazolone/isoxazolone derivatives (OT1 and OT2 respectively). The HOMO-LUMO energy levels of both derivatives were found to be positioned in such a way that they can act as electron acceptors to P3HT and electron donors to PCBM. However, OT1 functions as a donor (with PCBM) and OT2 as an acceptor (with P3HT) in BHJ photovoltaic cells, and their reverse roles results in either no or poor performance of the cells. Detailed studies using UV-vis absorption and fluorescence spectroscopy, time-correlated single photon counting, UV-photoelectron spectroscopy, density functional theory calculations, X-ray diffraction, and thermal gravimetric analysis proved that both molecular and supramolecular properties contributed equally but in a contrasting manner to the abovementioned observation. The obtained results were further validated by flash-photolysis time-resolved microwave conductivity studies which showed an excellent correlation between the structure, property, and device performances of the materials.

A Comparative Study of Molecular Structure, pKa, Lipophilicity, Solubility, Absorption and Polar Surface Area of Some Antiplatelet Drugs.

PubMed

Remko, Milan; Remková, Anna; Broer, Ria

2016-03-19

Theoretical chemistry methods have been used to study the molecular properties of antiplatelet agents (ticlopidine, clopidogrel, prasugrel, elinogrel, ticagrelor and cangrelor) and several thiol-containing active metabolites. The geometries and energies of most stable conformers of these drugs have been computed at the Becke3LYP/6-311++G(d,p) level of density functional theory. Computed dissociation constants show that the active metabolites of prodrugs (ticlopidine, clopidogrel and prasugrel) and drugs elinogrel and cangrelor are completely ionized at pH 7.4. Both ticagrelor and its active metabolite are present at pH = 7.4 in neutral undissociated form. The thienopyridine prodrugs ticlopidine, clopidogrel and prasugrel are lipophilic and insoluble in water. Their lipophilicity is very high (about 2.5-3.5 logP values). The polar surface area, with regard to the structurally-heterogeneous character of these antiplatelet drugs, is from very large interval of values of 3-255 Ų. Thienopyridine prodrugs, like ticlopidine, clopidogrel and prasugrel, with the lowest polar surface area (PSA) values, exhibit the largest absorption. A high value of polar surface area (PSA) of cangrelor (255 Ų) results in substantial worsening of the absorption in comparison with thienopyridine drugs.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

PubMed

Pluhackova, Kristyna; Wassenaar, Tsjerk A; Kirsch, Sonja; Böckmann, Rainer A

2015-03-26

A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding to neutral membranes is shown to be dominated by initial binding of the positively charged N-terminus to the phospholipid headgroup region, followed by membrane surface-aligned insertion of the peptide at the interface between the hydrophobic core of the membrane and its polar headgroup region. Both coarse-grained and atomistic simulations confirm a before hypothesized snorkeling of lysine side chains for the membrane-bound state of the peptide K. Cholesterol was found to be enriched in peptide vicinity, which is probably of importance for the mechanism of membrane fusion. The applied sequential multiscale method, using coarse-grained simulations for the slow adsorption process of peptides to membranes followed by backward transformation to atomistic detail and subsequent atomistic simulations of the preformed peptide-lipid complexes, is shown to be a versatile approach to study the interactions of peptides or proteins with biomembranes.

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

Quinuclidinium salt ferroelectric thin-film with duodecuple-rotational polarization-directions

NASA Astrophysics Data System (ADS)

You, Yu-Meng; Tang, Yuan-Yuan; Li, Peng-Fei; Zhang, Han-Yue; Zhang, Wan-Ying; Zhang, Yi; Ye, Heng-Yun; Nakamura, Takayoshi; Xiong, Ren-Gen

2017-04-01

Ferroelectric thin-films are highly desirable for their applications on energy conversion, data storage and so on. Molecular ferroelectrics had been expected to be a better candidate compared to conventional ferroelectric ceramics, due to its simple and low-cost film-processability. However, most molecular ferroelectrics are mono-polar-axial, and the polar axes of the entire thin-film must be well oriented to a specific direction to realize the macroscopic ferroelectricity. To align the polar axes, an orientation-controlled single-crystalline thin-film growth method must be employed, which is complicated, high-cost and is extremely substrate-dependent. In this work, we discover a new molecular ferroelectric of quinuclidinium periodate, which possesses six-fold rotational polar axes. The multi-axes nature allows the thin-film of quinuclidinium periodate to be simply prepared on various substrates including flexible polymer, transparent glasses and amorphous metal plates, without considering the crystallinity and crystal orientation. With those benefits and excellent ferroelectric properties, quinuclidinium periodate shows great potential in applications like wearable devices, flexible materials, bio-machines and so on.

Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

PubMed Central

Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

2015-01-01

We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling. PMID:25637963

Atomistic investigation on the detachment of oil molecules from defective alumina surface

NASA Astrophysics Data System (ADS)

Xie, W. K.; Sun, Y. Z.; Liu, H. T.

2017-12-01

The mechanism of oil detachment from defective alumina surface in aqueous solution was investigated via atomistic molecular dynamics (MD) simulations. Special attention was focused on the effect of surface defect on the oil detachment. Our simulation results suggest that compared with perfect Al2O3 surface, defective substrate surface provides much more sites for the adsorption of oil molecules, thus it has higher oil adsorption energy. However, higher oil-solid adsorption energy does not mean that oil contaminants are much more difficult to be detached. It is found that surface defect could induce the spontaneous imbibition of water molecules, effectively promoting the detachment of oil molecules. Thus, compared with perfect alumina surface, the detachment of oil molecules from defective alumina surface tends to be much easier. Moreover, surface defect could lead to the oil residues inside surface defect. In water solution, the entire detachment process of oil molecules on defective surface consists of following stages, including the early detachment of oil molecules inside surface defect induced by capillary-driven spontaneous imbibition of water molecules, the following conformational change of oil molecules on topmost surface and the final migration of detached oil molecules from solid surface. These findings may help to sufficiently enrich the removal mechanism of oil molecules adhered onto defective solid surface.

Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations.

PubMed

Rydzewski, J; Nowak, W

2017-08-10

Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

NASA Astrophysics Data System (ADS)

Chung, Pil Seung; Song, Wonyup; Biegler, Lorenz T.; Jhon, Myung S.

2017-05-01

During the operation of hard disk drive (HDD), the perfluoropolyether (PFPE) lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic) and loss (viscous) moduli (G' and G″) by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

The effects of polar excipients transcutol and dexpanthenol on molecular mobility, permeability, and electrical impedance of the skin barrier.

PubMed

Björklund, Sebastian; Pham, Quoc Dat; Jensen, Louise Bastholm; Knudsen, Nina Østergaard; Nielsen, Lars Dencker; Ekelund, Katarina; Ruzgas, Tautgirdas; Engblom, Johan; Sparr, Emma

2016-10-01

In the development of transdermal and topical products it is important to understand how formulation ingredients interact with the molecular components of the upper layer of the skin, the stratum corneum (SC), and thereby influence its macroscopic barrier properties. The aim here was to investigate the effect of two commonly used excipients, transcutol and dexpanthenol, on the molecular as well as the macroscopic properties of the skin membrane. Polarization transfer solid-state NMR methods were combined with steady-state flux and impedance spectroscopy measurements to investigate how these common excipients influence the molecular components of SC and its barrier function at strictly controlled hydration conditions in vitro with excised porcine skin. The NMR results provide completely new molecular insight into how transcutol and dexpanthenol affect specific molecular segments of both SC lipids and proteins. The presence of transcutol or dexpanthenol in the formulation at fixed water activity results in increased effective skin permeability of the model drug metronidazole. Finally, impedance spectroscopy data show clear changes of the effective skin capacitance after treatment with transcutol or dexpanthenol. Based on the complementary data, we are able to draw direct links between effects on the molecular properties and on the macroscopic barrier function of the skin barrier under treatment with formulations containing transcutol or dexpanthenol. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular Memory of Morphologies by Septins during Neuron Generation Allows Early Polarity Inheritance.

PubMed

Boubakar, Leila; Falk, Julien; Ducuing, Hugo; Thoinet, Karine; Reynaud, Florie; Derrington, Edmund; Castellani, Valérie

2017-08-16

Transmission of polarity established early during cell lineage history is emerging as a key process guiding cell differentiation. Highly polarized neurons provide a fascinating model to study inheritance of polarity over cell generations and across morphological transitions. Neural crest cells (NCCs) migrate to the dorsal root ganglia to generate neurons directly or after cell divisions in situ. Using live imaging of vertebrate embryo slices, we found that bipolar NCC progenitors lose their polarity, retracting their processes to round for division, but generate neurons with bipolar morphology by emitting processes from the same locations as the progenitor. Monitoring the dynamics of Septins, which play key roles in yeast polarity, indicates that Septin 7 tags process sites for re-initiation of process growth following mitosis. Interfering with Septins blocks this mechanism. Thus, Septins store polarity features during mitotic rounding so that daughters can reconstitute the initial progenitor polarity. Copyright © 2017 Elsevier Inc. All rights reserved.

Assessing the fracture strength of geological and related materials via an atomistically based J-integral

NASA Astrophysics Data System (ADS)

Jones, R. E.; Criscenti, L. J.; Rimsza, J.

2016-12-01

Predicting fracture initiation and propagation in low-permeability geomaterials is a critical yet un- solved problem crucial to assessing shale caprocks at carbon dioxide sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-geomaterial interfaces play a major role in subcritical crack growth by weakening the material and altering crack nu- cleation and growth rates. Engineering the subsurface fracture environment, however, has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We have developed a fundamental atomic-level understanding of the chemical-mechanical mecha- nisms that control subcritical cracks through coarse-graining data from reactive molecular simulations. Previous studies of fracture at the atomic level have typically been limited to producing stress-strain curves, quantifying either the system-level stress or energy at which fracture propagation occurs. As such, these curves are neither characteristic of nor insightful regarding fracture features local to the crack tip. In contrast, configurational forces, such as the J-integral, are specific to the crack in that they measure the energy available to move the crack and truly quantify fracture resistance. By development and use of field estimators consistent with the continuum conservation properties we are able to connect the data produced by atomistic simulation to the continuum-level theory of fracture mechanics and thus inform engineering decisions. In order to trust this connection we have performed theoretical consistency tests and validation with experimental data. Although we have targeted geomaterials, this capability can have direct impact on other unsolved technological problems such as predicting the corrosion and embrittlement of metals and ceramics. Sandia National

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Brodeck, M.; Alvarez, F.; Arbe, A.; Juranyi, F.; Unruh, T.; Holderer, O.; Colmenero, J.; Richter, D.

2009-03-01

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below ≈0.6 Å-1. We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments.

PubMed

Brodeck, M; Alvarez, F; Arbe, A; Juranyi, F; Unruh, T; Holderer, O; Colmenero, J; Richter, D

2009-03-07

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

2006-01-01

A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

First principles molecular dynamics of molten NaI: Structure, self-diffusion, polarization effects, and charge transfer

NASA Astrophysics Data System (ADS)

Galamba, N.; Costa Cabral, B. J.

2007-09-01

The structure and self-diffusion of NaI and NaCl at temperatures close to their melting points are studied by first principles Hellmann-Feynman molecular dynamics (HFMD). The results are compared with classical MD using rigid-ion (RI) and shell-model (ShM) interionic potentials. HFMD for NaCl was reported before at a higher temperature [N. Galamba and B. J. Costa Cabral, J. Chem. Phys. 126, 124502 (2007)]. The main differences between the structures predicted by HFMD and RI MD for NaI concern the cation-cation and the anion-cation pair correlation functions. A ShM which allows only for the polarization of I- reproduces the main features of the HFMD structure of NaI. The inclusion of polarization effects for both ionic species leads to a more structured ionic liquid, although a good agreement with HFMD is also observed. HFMD Green-Kubo self-diffusion coefficients are larger than those obtained from RI and ShM simulations. A qualitative study of charge transfer in molten NaI and NaCl was also carried out with the Hirshfeld charge partitioning method. Charge transfer in molten NaI is comparable to that in NaCl, and results for NaCl at two temperatures support the view that the magnitude of charge transfer is weakly state dependent for ionic systems. Finally, Hirshfeld charge distributions indicate that differences between RI and HFMD results are mainly related to polarization effects, while the influence of charge transfer fluctuations is minimal for these systems.

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

NASA Astrophysics Data System (ADS)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic

Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics

NASA Astrophysics Data System (ADS)

Puzyrkov, Dmitry; Polyakov, Sergey; Podryga, Viktoriia; Markizov, Sergey

2018-02-01

At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.

Quantum mechanical modeling the emission pattern and polarization of nanoscale light emitting diodes.

PubMed

Wang, Rulin; Zhang, Yu; Bi, Fuzhen; Frauenheim, Thomas; Chen, GuanHua; Yam, ChiYung

2016-07-21

Understanding of the electroluminescence (EL) mechanism in optoelectronic devices is imperative for further optimization of their efficiency and effectiveness. Here, a quantum mechanical approach is formulated for modeling the EL processes in nanoscale light emitting diodes (LED). Based on non-equilibrium Green's function quantum transport equations, interactions with the electromagnetic vacuum environment are included to describe electrically driven light emission in the devices. The presented framework is illustrated by numerical simulations of a silicon nanowire LED device. EL spectra of the nanowire device under different bias voltages are obtained and, more importantly, the radiation pattern and polarization of optical emission can be determined using the current approach. This work is an important step forward towards atomistic quantum mechanical modeling of the electrically induced optical response in nanoscale systems.

Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate.

PubMed

Zanuy, David; Hamley, Ian W; Alemán, Carlos

2011-07-21

The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helical-like arrangements. Furthermore, calculations indicate that backbone···side chain interactions involving the N-H of the amide groups and the π clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand, MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

PubMed

Nagata, Yuki

2010-02-01

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

Experimentally driven atomistic model of 1,2 polybutadiene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gkourmpis, Thomas, E-mail: thomas.gkourmpis@borealisgroup.com; Mitchell, Geoffrey R.; Centre for Rapid and Sustainable Product Development, Institute Polytechnic Leiria, Marinha Grande

2014-02-07

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for themore » models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.« less

Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains

NASA Astrophysics Data System (ADS)

Chugunov, Anton O.; Volynsky, Pavel E.; Krylov, Nikolay A.; Nolde, Dmitry E.; Efremov, Roman G.

2016-09-01

Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed “iris-like” symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.

Atomistic nature in band-to-band tunneling in two-dimensional silicon pn tunnel diodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tabe, Michiharu, E-mail: tabe.michiharu@shizuoka.ac.jp; Tan, Hoang Nhat; Mizuno, Takeshi

We study low-temperature transport properties of two-dimensional (2D) Si tunnel diodes, or Si Esaki diodes, with a lateral layout. In ordinary Si Esaki diodes, interband tunneling current is severely limited because of the law of momentum conservation, while nanoscale Esaki diodes may behave differently due to the dopants in the narrow depletion region, by atomistic effects which release such current limitation. In thin-Si lateral highly doped pn diodes, we find clear signatures of interband tunneling between 2D-subbands involving phonon assistance. More importantly, the tunneling current is sharply enhanced in a narrow voltage range by resonance via a pair of amore » donor- and an acceptor-atom in the pn junction region. Such atomistic behavior is recognized as a general feature showing up only in nanoscale tunnel diodes. In particular, a donor-acceptor pair with deeper ground-state energies is likely to be responsible for such a sharply enhanced current peak, tunable by external biases.« less

A Comparative Study of Molecular Structure, pKa, Lipophilicity, Solubility, Absorption and Polar Surface Area of Some Antiplatelet Drugs

PubMed Central

Remko, Milan; Remková, Anna; Broer, Ria

2016-01-01

Theoretical chemistry methods have been used to study the molecular properties of antiplatelet agents (ticlopidine, clopidogrel, prasugrel, elinogrel, ticagrelor and cangrelor) and several thiol-containing active metabolites. The geometries and energies of most stable conformers of these drugs have been computed at the Becke3LYP/6-311++G(d,p) level of density functional theory. Computed dissociation constants show that the active metabolites of prodrugs (ticlopidine, clopidogrel and prasugrel) and drugs elinogrel and cangrelor are completely ionized at pH 7.4. Both ticagrelor and its active metabolite are present at pH = 7.4 in neutral undissociated form. The thienopyridine prodrugs ticlopidine, clopidogrel and prasugrel are lipophilic and insoluble in water. Their lipophilicity is very high (about 2.5–3.5 logP values). The polar surface area, with regard to the structurally-heterogeneous character of these antiplatelet drugs, is from very large interval of values of 3–255 Å2. Thienopyridine prodrugs, like ticlopidine, clopidogrel and prasugrel, with the lowest polar surface area (PSA) values, exhibit the largest absorption. A high value of polar surface area (PSA) of cangrelor (255 Å2) results in substantial worsening of the absorption in comparison with thienopyridine drugs. PMID:27007371

Random Dopant Induced Threshold Voltage Lowering and Fluctuations in Sub-0.1 (micron)meter MOSFET's: A 3-D 'Atomistic' Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen

1998-01-01

A three-dimensional (3-D) "atomistic" simulation study of random dopant induced threshold voltage lowering and fluctuations in sub-0.1 microns MOSFET's is presented. For the first time a systematic analysis of random dopant effects down to an individual dopant level was carried out in 3-D on a scale sufficient to provide quantitative statistical predictions. Efficient algorithms based on a single multigrid solution of the Poisson equation followed by the solution of a simplified current continuity equation are used in the simulations. The effects of various MOSFET design parameters, including the channel length and width, oxide thickness and channel doping, on the threshold voltage lowering and fluctuations are studied using typical samples of 200 atomistically different MOSFET's. The atomistic results for the threshold voltage fluctuations were compared with two analytical models based on dopant number fluctuations. Although the analytical models predict the general trends in the threshold voltage fluctuations, they fail to describe quantitatively the magnitude of the fluctuations. The distribution of the atomistically calculated threshold voltage and its correlation with the number of dopants in the channel of the MOSFET's was analyzed based on a sample of 2500 microscopically different devices. The detailed analysis shows that the threshold voltage fluctuations are determined not only by the fluctuation in the dopant number, but also in the dopant position.

Atomistic and Ab Initio Calculations or Ternary II-IV-V2 Semiconductors

DTIC Science & Technology

1999-12-07

consisting of two- and three-body terms is developed reproducing crystal lattice constants, elastic and dielectric constants very well. The calculated...the lattice . This difference may well be due to defect-induced lattice distortion which plays a key role in stabilizing the hole states in the... lattice . 15. SUBJECT TERMS Chalcopyrites, Defects, Atomistic and AB Initio Calculations 16. SECURITY CLASSIFICATION OF: a. REPORT u b. ABSTRACT U

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

PubMed

Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V

2014-08-06

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

Do embryonic polar bodies commit suicide?

PubMed

Fabian, Dušan; Čikoš, Štefan; Rehák, Pavol; Koppel, Juraj

2014-02-01

The extrusion and elimination of unnecessary gametic/embryonic material is one of the key events that determines the success of further development in all living organisms. Oocytes produce the first polar body to fulfill the maturation process just before ovulation, and release the second polar body immediately after fertilization. The aim of this study was to compile a physiological overview of elimination of polar bodies during early preimplantation development in mice. Our results show that three-quarters of the first polar bodies were lost even at the zygotic stage; the 4-cell stage embryos contained only one (second) polar body, and the elimination of second polar bodies proceeded continuously during later development. Both first and second polar bodies showed several typical features of apoptosis: phosphatidylserine redistribution (observed for the first time in the first polar body), specific DNA degradation, condensed nuclear morphology, and inability to exclude cationic dye from the nucleus during the terminal stage of the apoptotic process. Caspase-3 activity was recorded only in the second polar body. From the morphological point of view, mouse polar bodies acted very similarly to damaged embryonic cells which have lost contact with their neighboring blastomeres. In conclusion, polar bodies possess all the molecular equipment necessary for triggering and executing an active suicide process. Furthermore, similarly as in dying embryonic cells, stressing external conditions (culture in vitro) might accelerate and increase the incidence of apoptotic elimination of the polar bodies in embryos.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Brennan, John

2015-06-01

Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

NASA Astrophysics Data System (ADS)

Pan, Xiaoliang; Schwartz, Steven

2015-03-01

It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

NASA Astrophysics Data System (ADS)

Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

2010-03-01

It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field.

PubMed

Duan, Rui; Lazim, Raudah; Zhang, Dawei

2015-09-30

Human immunodeficiency virus (HIV)-1 protease is one of the most promising drug target commonly utilized to combat Acquired Immune Deficiency Syndrome (AIDS). However, with the emergence of drug resistance arising from mutations, the efficiency of protease inhibitors (PIs) as a viable treatment for AIDS has been greatly reduced. I50V mutation as one of the most significant mutations occurring in HIV-1 protease will be investigated in this study. Molecular dynamics (MD) simulation was utilized to examine the effect of I50V mutation on the binding of two PIs namely indinavir and amprenavir to HIV-1 protease. Prior to the simulations conducted, the electron density distributions of the PI and each residue in HIV-1 protease are derived by combining quantum fragmentation approach molecular fractionation with conjugate caps and Poisson-Boltzmann solvation model based on polarized protein-specific charge scheme. The atomic charges of the binding complex are subsequently fitted using delta restrained electrostatic potential (delta-RESP) method to overcome the poor charge determination of buried atom. This way, both intraprotease polarization and the polarization between protease and the PI are incorporated into partial atomic charges. Through this study, the mutation-induced affinity variations were calculated and significant agreement between experiments and MD simulations conducted was observed for both HIV-1 protease-drug complexes. In addition, the mechanism governing the decrease in the binding affinity of PI in the presence of I50V mutation was also explored to provide insights pertaining to the design of the next generation of anti-HIV drugs. © 2015 Wiley Periodicals, Inc.

Highly Polarized Fluorescent Illumination Using Liquid Crystal Phase.

PubMed

Gim, Min-Jun; Turlapati, Srikanth; Debnath, Somen; Rao, Nandiraju V S; Yoon, Dong Ki

2016-02-10

Liquid crystal (LC) materials are currently the dominant electronic materials in display technology because of the ease of control of molecular orientation using an electric field. However, this technology requires the fabrication of two polarizers to create operational displays, reducing light transmission efficiency below 10%. It is therefore desirable to develop new technologies to enhance the light efficiency while maintaining or improving other properties such as the modulation speed of the molecular orientation. Here we report a uniaxial-oriented B7 smectic liquid crystalline film, using fluorescent bent-core LC molecules, a chemically modified substrate, and an in-plane electric field. A LC droplet under homeotropic boundary conditions of air/LC as well as LC/substrate exhibits large focal conic like optical textures. The in-plane electric field induced uniaxial orientation of the LC molecules, in which molecular polar directors are aligned in the direction of the electric field. This highly oriented LC film exhibits linearly polarized luminescence and microsecond time-scale modulation characteristics. The resultant device is both cheap and easy to fabricate and thus has great potential for electro-optic applications, including LC displays, bioimaging systems, and optical communications.

Polarization-resolved SHG microscopy in cardiac hypertrophy study (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wang, Zhonghai; Yuan, Cai; Shao, Yonghong; Bradshaw, Amy D.; Borg, Thomas K.; Gao, Bruce Z.

2017-02-01

Cardiac hypertrophy, a process initiated by mechanical alterations, is hypothesized to cause long-term molecular-level alteration in the sarcomere lattice, which is the main force-generating component in the heart muscle. This molecular-level alteration is beyond the resolving capacity of common light microscopy. Second harmonic generation (SHG) microscopy has unique capability for visualizing ordered molecular structures in biological tissues without labeling. Combined with polarization imaging technique, SHG microscopy is able to extract structural details of myosin at the molecular level so as to reveal molecular-level alterations that occur during hypertrophy. The myosin filaments are believed to possess C6 symmetry; thus, the nonlinear polarization response relationship between generated second harmonic light I^2ωand incident fundamental light I^ω is determined by nonlinear coefficients, χ_15, χ_31 and χ_33. χ_31/χ_15 is believed to be an indicator of the molecular symmetry of myosin filament, whileχ_33/χ_15represents the intramyosin orientation angle of the double helix. By changing the polarization of the incident light and evaluating the corresponding SHG signals, the molecular structure of the myosin, reflected by the χ coefficients, can be revealed. With this method, we studied the structural properties of heart tissues in different conditions, including those in normal, physiologically hypertrophic (heart tissue from postpartum female rats), and pathologically hypertrophic (heart tissue from transverse-aorta constricted rats) conditions. We found that ratios of χ_31/χ_15 showed no significant difference between heart tissues from different conditions; their values were all close to 1, which demonstrated that Kleinman symmetry held for all conditions. Ratios of χ_33/χ_15 from physiologically or pathologically hypertrophic heart tissues were raised and showed significant difference from those from normal heart tissues, which indicated that

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE PAGES

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov; ...

2017-12-08

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2018-04-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2017-12-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

NASA Astrophysics Data System (ADS)

De Simone, Alfonso; Derreumaux, Philippe

2010-04-01

The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

Circularly polarized attosecond pulse generation and applications to ultrafast magnetism

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Guo, Jing; Yuan, Kai-Jun

2017-12-01

Attosecond science is a growing new field of research and potential applications which relies on the development of attosecond light sources. Achievements in the generation and application of attosecond pulses enable to investigate electron dynamics in the nonlinear nonperturbative regime of laser-matter interactions on the electron’s natural time scale, the attosecond. In this review, we describe the generation of circularly polarized attosecond pulses and their applications to induce attosecond magnetic fields, new tools for ultrafast magnetism. Simulations are performed on aligned one-electron molecular ions by using nonperturbative nonlinear solutions of the time-dependent Schrödinger equation. We discuss how bichromatic circularly polarized laser pulses with co-rotating or counter-rotating components induce electron-parent ion recollisions, thus producing circularly polarized high-order harmonic generation, the source of circularly polarized attosecond pulses. Ultrafast quantum electron currents created by the generated attosecond pulses give rise to attosecond magnetic field pulses. The results provide a guiding principle for producing circularly polarized attosecond pulses and ultrafast magnetic fields in complex molecular systems for future research in ultrafast magneto-optics.

Polar order in nanostructured organic materials

NASA Astrophysics Data System (ADS)

Sayar, M.; Olvera de la Cruz, M.; Stupp, S. I.

2003-02-01

Achiral multi-block liquid crystals are not expected to form polar domains. Recently, however, films of nanoaggregates formed by multi-block rodcoil molecules were identified as the first example of achiral single-component materials with macroscopic polar properties. By solving an Ising-like model with dipolar and asymmetric short-range interactions, we show here that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a approx 8 nm), leading to a reduction in the repulsive dipolar interactions which oppose polar order within layers. In finite-thickness films of nanostructures, this effect enables the formation of polar domains. We compute exactly the energies of the possible structures consistent with the experiments as a function of film thickness at zero temperature (T). We also provide Monte Carlo simulations at non-zero T for a disordered hexagonal lattice that resembles the smectic-like packing in these nanofilms.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Effect of substrate orientation on CdS homoepitaxy by molecular dynamics

DOE PAGES

Almeida, S.; Chavez, J. J.; Zhou, X. W.; ...

2016-02-10

CdS homoepitaxy growth was performed by molecular dynamics using different substrate orientations and structures in order to analyze the CdS crystallinity. As anticipated from thermodynamics of homoepitaxy, highly crystalline films with only point defects were obtained on substrates with rectangular surface geometries, including View the MathML source[112¯] zinc blende (ZB), [101¯0] wurtzite (WZ), [112¯0] WZ, [110][110] ZB, [010][010] ZB, and View the MathML source[1101110] ZB. In contrast, films grown on substrates with hexagonal surface geometries, corresponding to the [0001][0001] WZ and [111][111] ZB growth directions, showed structures with a large number of defects including; anti-sites, vacancies, stacking faults, twinning, andmore » polytypism. WZ and ZB transitions and grain boundaries are identified using a lattice identification algorithm and represented graphically in a structural map. A dislocation analysis was performed to detect, identify, and quantify linear defects within the atomistic data. Systematic simulations using different temperatures, deposition rates, and substrate polarities were perform to analyze the trends of dislocation densities on [0001][0001] WZ direction and showed persistent polytypism. As a result, the polytypism observed in the films grown on the substrates with hexagonal surface geometry is attributed to the similar formation energies of the WZ and ZB phases.« less

Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van de Put, Maarten L., E-mail: maarten.vandeput@uantwerpen.be; Magnus, Wim; imec, B-3001 Heverlee

A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases inmore » current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.« less

Polar Nature of Biomimetic Fluorapatite/Gelatin Composites: A Comparison of Bipolar Objects and the Polar State of Natural Tissue.

PubMed

Burgener, Matthias; Putzeys, Tristan; Gashti, Mazeyar Parvinzadeh; Busch, Susanne; Aboulfadl, Hanane; Wübbenhorst, Michael; Kniep, Rüdiger; Hulliger, Jürg

2015-09-14

The correspondence of the state of alignment of macromolecules in biomimetic materials and natural tissues is demonstrated by investigating a mechanism of electrical polarity formation: An in vitro grown biomimetic FAp/gelatin composite is investigated for its polar properties by second harmonic (SHGM) and scanning pyroelectric microscopy (SPEM). Hexagonal prismatic seed crystals formed in gelatin gels represent a monodomain polar state, due to aligned mineralized gelatin molecules. Later growth stages, showing dumbbell morphologies, develop into a bipolar state because of surface recognition by gelatin functionality: A reversal of the polar alignment of macromolecules, thus, takes place close to that basal plane of the seed. In natural hard tissues (teeth and bone investigated by SPEM) and the biomimetic FAp/gelatin composite, we find a surprising analogy in view of growth-induced states of polarity: The development of polarity in vivo and in vitro can be explained by a Markov-type mechanism of molecular recognition during the attachment of macromolecules.

Development and assessment of atomistic models for predicting static friction coefficients

NASA Astrophysics Data System (ADS)

Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

2016-08-01

The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

Atomistic simulation and XAS investigation of Mn induced defects in Bi{sub 12}TiO{sub 20}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezende, Marcos V dos S.; Santos, Denise J.; Jackson, Robert A.

2016-06-15

This work reports an investigation of the valence and site occupancy of Mn dopants in Bi{sub 12}TiO{sub 20} (BTO: Mn) host using X-ray Absorption (XAS) and atomistic simulation techniques based on energy minimisation. X-ray Absorption Near Edge Structure (XANES) at the Mn K-edges gave typical results for Mn ions with mixed valences of 3+ and 4+. Extended X-ray Absorption Fine Structure (EXAFS) results indicated that Mn ions are probably substituted at Ti sites. Atomistic simulation was performed assuming the incorporation of Mn{sup 2+}, Mn{sup 3+} and Mn{sup 4+} ions at either Bi{sup 3+} or Ti{sup 4+} sites, and the resultsmore » were compared to XANES and EXAFS measurements. Electrical conductivity for pure and doped samples was used to evaluate the consistency of the proposed model. - Graphical abstract: The structure of Bi{sub 12}TiO{sub 20} (BTO). Display Omitted - Highlights: • Pure and Mn-doped Bi{sub 12}TiO{sub 20} samples were studied by experimental techniques combined with atomistic simulation. • Good agreement between experimental and simulation results was obtained. • XANES results suggest a mixture of 3+ and 4+ valences for Mn, occupying the Ti4+ site in both cases. • Charge compensation by holes is most energetically favoured, explaining the enhancement observed in AC dark conductivity.« less

Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation

PubMed Central

Ramirez, Samuel A.; Elston, Timothy C.

2018-01-01

Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our

Polarized x-ray excitation for scatter reduction in x-ray fluorescence computed tomography.

PubMed

Vernekohl, Don; Tzoumas, Stratis; Zhao, Wei; Xing, Lei

2018-05-25

X-ray fluorescence computer tomography (XFCT) is a new molecular imaging modality which uses x-ray excitation to stimulate the emission of fluorescent photons in high atomic number contrast agents. Scatter contamination is one of the main challenges in XFCT imaging which limits the molecular sensitivity. When polarized x rays are used, it is possible to reduce the scatter contamination significantly by placing detectors perpendicular to the polarization direction. This study quantifies scatter contamination for polarized and unpolarized x-ray excitation and determines the advantages of scatter reduction. The amount of scatter in preclinical XFCT is quantified in Monte Carlo simulations. The fluorescent x rays are emitted isotropically, while scattered x rays propagate in polarization direction. The magnitude of scatter contamination is studied in XFCT simulations of a mouse phantom. In this study, the contrast agent gold is examined as an example, but a scatter reduction from polarized excitation is also expected for other elements. The scatter reduction capability is examined for different polarization intensities with a monoenergetic x-ray excitation energy of 82 keV. The study evaluates two different geometrical shapes of CZT detectors which are modeled with an energy resolution of 1 keV FWHM at an x-ray energy of 80 keV. Benefits of a detector placement perpendicular to the polarization direction are shown in iterative and analytic image reconstruction including scatter correction. The contrast to noise ratio (CNR) and the normalized mean square error (NMSE) are analyzed and compared for the reconstructed images. A substantial scatter reduction for common detector sizes was achieved for 100% and 80% linear polarization while lower polarization intensities provide a decreased scatter reduction. By placing the detector perpendicular to the polarization direction, a scatter reduction by factor up to 5.5 can be achieved for common detector sizes. The image

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast

Fabrication of lateral lattice-polarity-inverted GaN heterostructure

NASA Astrophysics Data System (ADS)

Katayama, Ryuji; Kuge, Yoshihiro; Kondo, Takashi; Onabe, Kentaro

2007-04-01

Fabrication of the lateral polarity-inverted GaN heterostructure on sapphire (0 0 0 1) using a radio-frequency plasma enhanced molecular beam epitaxy is demonstrated. Its microscopic properties, which are closely related to the local polarity distribution, such as surface potentials, piezoelectric polarizations and residual carrier concentrations were investigated by Kelvin force microscopy and micro-Raman scattering. The successful inversion from Ga-polarity to N-polarity of GaN in a specific domain and its higher crystal perfection had been confirmed clearly by these microscopic analyses. The results were also fairly consistent with that of KOH etching experiments, which suggest the applicability of these processes to the fabrication of photonic nanostructures composed of nitride semiconductors.

Microwave-mediated magneto-optical trap for polar molecules

NASA Astrophysics Data System (ADS)

Dizhou, Xie; Wenhao, Bu; Bo, Yan

2016-05-01

Realizing a molecular magneto-optical trap has been a dream for cold molecular physicists for a long time. However, due to the complex energy levels and the small effective Lande g-factor of the excited states, the traditional magneto-optical trap (MOT) scheme does not work very well for polar molecules. One way to overcome this problem is the switching MOT, which requires very fast switching of both the magnetic field and the laser polarizations. Switching laser polarizations is relatively easy, but fast switching of the magnetic field is experimentally challenging. Here we propose an alternative approach, the microwave-mediated MOT, which requires a slight change of the current experimental setup to solve the problem. We calculate the MOT force and compare it with the traditional MOT and the switching MOT scheme. The results show that we can operate a good MOT with this simple setup. Project supported by the Fundamental Research Funds for the Central Universities of China.

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase.

PubMed

van der Kamp, Marc W; Perruccio, Francesca; Mulholland, Adrian J

2007-11-15

Citrate synthase is an archetypal carbon-carbon bond forming enzyme. It promotes the conversion of oxaloacetate (OAA) to citrate by catalyzing the deprotonation (enolization) of acetyl-CoA, followed by nucleophilic attack of the enolate form of this substrate on OAA to form a citryl-CoA intermediate and subsequent hydrolysis. OAA is strongly bound to the active site and its alpha-carbonyl group is polarized. This polarization has been demonstrated spectroscopically, [(Kurz et al., Biochemistry 1985;24:452-457; Kurz and Drysdale, Biochemistry 1987;26:2623-2627)] and has been suggested to be an important catalytic strategy. Substrate polarization is believed to be important in many enzymes. The first step, formation of the acetyl-CoA enolate intermediate, is thought to be rate-limiting in the mesophilic (pig/chicken) enzyme. We have examined the effects of substrate polarization on this key step using quantum mechanical/molecular mechanical (QM/MM) methods. Free energy profiles have been calculated by AM1/CHARMM27 umbrella sampling molecular dynamics (MD) simulations, together with potential energy profiles. To study the influence of OAA polarization, profiles were calculated with different polarization of the OAA alpha-carbonyl group. The results indicate that OAA polarization influences catalysis only marginally but has a larger effect on intermediate stabilization. Different levels of treatment of OAA are compared (MM or QM), and its polarization in the protein and in water analyzed at the B3LYP/6-31+G(d)/CHARMM27 level. Analysis of stabilization by individual residues shows that the enzyme mainly stabilizes the enolate intermediate (not the transition state) through electrostatic (including hydrogen bond) interactions: these contribute much more than polarization of OAA. (c) 2007 Wiley-Liss, Inc.

Polarization of Rayleigh scattered Lyα in active galactic nuclei

NASA Astrophysics Data System (ADS)

Chang, Seok-Jun; Lee, Hee-Won; Yang, Yujin

2017-02-01

The unification scheme of active galactic nuclei invokes an optically thick molecular torus component hiding the broad emission line region. Assuming the presence of a thick neutral component in the molecular torus characterized by a H I column density >1022 cm-2, we propose that far-UV radiation around Lyα can be significantly polarized through Rayleigh scattering. Adopting a Monte Carlo technique, we compute polarization of Rayleigh scattered radiation near Lyα in a thick neutral region in the shape of a slab and a cylindrical shell. It is found that radiation near Lyα Rayleigh reflected from a very thick slab can be significantly polarized in a fairly large range of wavelength Δλ ˜ 50 Å exhibiting a flux profile similar to the incident one. Rayleigh transmitted radiation in a slab is characterized by the central dip with a complicated polarization behaviour. The optically thick part near Lyα centre is polarized in the direction perpendicular to the slab normal, which is in contrast to weakly polarized wing parts in the direction parallel to the slab normal. A similar polarization flip phenomenon is also found in the case of a tall cylindrical shell, in which the spatial diffusion along the vertical direction near the inner cylinder wall for core photons leads to a tendency of the electric field aligned to the direction perpendicular to the vertical axis. Observational implications are briefly discussed including spectropolarimetry of the quasar PG 1630+377 by Koratkar et al. in 1990 where Lyα is strongly polarized with no other emission lines polarized.

Theoretical and experimental examination of SFG polarization analysis at acetonitrile-water solution surfaces.

PubMed

Saito, Kengo; Peng, Qiling; Qiao, Lin; Wang, Lin; Joutsuka, Tatsuya; Ishiyama, Tatsuya; Ye, Shen; Morita, Akihiro

2017-03-29

Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through a combination of various types of polarization. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurements and molecular dynamics (MD) simulations of acetonitrile/water solutions. The present SFG experiment and MD simulations yield quite consistent results on the ratios of χ (2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculations. The reasons for discrepancy are examined in terms of three issues; (i) anisotropy of the Raman tensor, (ii) cross-correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In methyl CH stretching, the anisotropy of Raman tensor cannot be estimated from the simple bond polarizability model. The neglect of the orientational distribution is shown to systematically underestimate the tilt angle of acetonitrile. Further refined use of polarization analysis in collaboration with MD simulations should be proposed.

Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

NASA Astrophysics Data System (ADS)

Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

2018-04-01

Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

Slush-like polar structures in single-crystal relaxors

NASA Astrophysics Data System (ADS)

Takenaka, Hiroyuki; Grinberg, Ilya; Liu, Shi; Rappe, Andrew M.

2017-06-01

Despite more than 50 years of investigation, it is still unclear how the underlying structure of relaxor ferroelectrics gives rise to their defining properties, such as ultrahigh piezoelectric coefficients, high permittivity over a broad temperature range, diffuse phase transitions, strong frequency dependence in dielectric response, and phonon anomalies. The model of polar nanoregions inside a non-polar matrix has been widely used to describe the structure of relaxor ferroelectrics. However, the lack of precise knowledge about the shapes, growth and dipole patterns of polar nanoregions has led to the characterization of relaxors as “hopeless messes”, and no predictive model for relaxor behaviour is currently available. Here we use molecular dynamics simulations of the prototypical Pb(Mg1/3,Nb2/3)O3-PbTiO3 relaxor material to examine its structure and the spatial and temporal polarization correlations. Our simulations show that the unusual properties of relaxors stem from the presence of a multi-domain state with extremely small domain sizes (2-10 nanometres), and no non-polar matrix, owing to the local dynamics. We find that polar structures in the multi-domain state in relaxors are analogous to those of the slush state of water. The multi-domain structure of relaxors that is revealed by our molecular dynamics simulations is consistent with recent experimental diffuse scattering results and indicates that relaxors have a high density of low-angle domain walls. This insight explains the recently discovered classes of relaxors that cannot be described by the polar nanoregion model, and provides guidance for the design and synthesis of new relaxor materials.

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

PubMed

Tiwary, Pratyush

2017-12-07

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during dissociation and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the dissociation process. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacokinetics. An improved understanding of biotin-streptavidin dissociation dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

NASA Astrophysics Data System (ADS)

Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

2017-10-01

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces.

PubMed

Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

2017-10-28

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

PubMed

Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

2015-04-14

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

Combined Atomistic Molecular Calculations and Experimental Investigations for the Architecture, Screening, Optimization, and Characterization of Pyrazinamide Containing Oral Film Formulations for Tuberculosis Management.

PubMed

Adeleke, Oluwatoyin A; Monama, Nkwe O; Tsai, Pei-Chin; Sithole, Happy M; Michniak-Kohn, Bozena B

2016-02-01

semicrystalline in nature and displayed a dual phased ex vivo mucosal permeation pattern. In silico and in vitro physicomechanical quantities revealed OF 2's flexibility, robustness, and compressibility. OF 2 was most stable under controlled environmental humidity, pressure, and temperature conditions in silico and in vitro. OF 2 was potentially non-cytotoxic and biocompatible. Succinctly, this work demonstrated the applicability of a combination of atomistic molecular mechanics and dynamics calculations as well as experimental analyses to the fabrication, screening, optimization, and characterization of drug formulations. Lastly, the fabricated OF 2 formulation can function as a potential alternative for the effective loading and delivery of PYZ.

Atomistic Modeling of RuAl and (RuNi) Al Alloys

NASA Technical Reports Server (NTRS)

Gargano, Pablo; Mosca, Hugo; Bozzolo, Guillermo; Noebe, Ronald D.; Gray, Hugh R. (Technical Monitor)

2002-01-01

Atomistic modeling of RuAl and RuAlNi alloys, using the BFS (Bozzolo-Ferrante-Smith) method for alloys is performed. The lattice parameter and energy of formation of B2 RuAl as a function of stoichiometry and the lattice parameter of (Ru(sub 50-x)Ni(sub x)Al(sub 50)) alloys as a function of Ni concentration are computed. BFS based Monte Carlo simulations indicate that compositions close to Ru25Ni25Al50 are single phase with no obvious evidence of a miscibility gap and separation of the individual B2 phases.

Rigorous theory of molecular orientational nonlinear optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwak, Chong Hoon, E-mail: chkwak@ynu.ac.kr; Kim, Gun Yeup

2015-01-15

Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecularmore » hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented.« less

Semiconductor Seeded Nanorods with Graded Composition Exhibiting High Quantum-Yield, High Polarization, and Minimal Blinking.

PubMed

Hadar, Ido; Philbin, John P; Panfil, Yossef E; Neyshtadt, Shany; Lieberman, Itai; Eshet, Hagai; Lazar, Sorin; Rabani, Eran; Banin, Uri

2017-04-12

Seeded semiconductor nanorods represent a unique family of quantum confined materials that manifest characteristics of mixed dimensionality. They show polarized emission with high quantum yield and fluorescence switching under an electric field, features that are desirable for use in display technologies and other optical applications. So far, their robust synthesis has been limited mainly to CdSe/CdS heterostructures, thereby constraining the spectral tunability to the red region of the visible spectrum. Herein we present a novel synthesis of CdSe/Cd 1-x Zn x S seeded nanorods with a radially graded composition that show bright and highly polarized green emission with minimal intermittency, as confirmed by ensemble and single nanorods optical measurements. Atomistic pseudopotential simulations elucidate the importance of the Zn atoms within the nanorod structure, in particular the effect of the graded composition. Thus, the controlled addition of Zn influences and improves the nanorods' optoelectronic performance by providing an additional handle to manipulate the degree confinement beyond the common size control approach. These nanorods may be utilized in applications that require the generation of a full, rich spectrum such as energy-efficient displays and lighting.

Rotation Detection Using the Precession of Molecular Electric Dipole Moment

NASA Astrophysics Data System (ADS)

Ke, Yi; Deng, Xiao-Bing; Hu, Zhong-Kun

2017-11-01

We present a method to detect the rotation by using the precession of molecular electric dipole moment in a static electric field. The molecular electric dipole moments are polarized under the static electric field and a nonzero electric polarization vector emerges in the molecular gas. A resonant radio-frequency pulse electric field is applied to realize a 90° flip of the electric polarization vector of a particular rotational state. After the pulse electric field, the electric polarization vector precesses under the static electric field. The rotation induces a shift in the precession frequency which is measured to deduce the angular velocity of the rotation. The fundamental sensitivity limit of this method is estimated. This work is only a proposal and does not involve experimental results.

Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells.

PubMed

Recouvreux, Pierre; Sokolowski, Thomas R; Grammoustianou, Aristea; ten Wolde, Pieter Rein; Dogterom, Marileen

2016-02-16

Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

PubMed Central

Yang, Shengfeng; Chen, Youping

2015-01-01

In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

Coherent manipulation of non-thermal spin order in optical nuclear polarization experiments

NASA Astrophysics Data System (ADS)

Buntkowsky, Gerd; Ivanov, Konstantin L.; Zimmermann, Herbert; Vieth, Hans-Martin

2017-03-01

Time resolved measurements of Optical Nuclear Polarization (ONP) have been performed on hyperpolarized triplet states in molecular crystals created by light excitation. Transfer of the initial electron polarization to nuclear spins has been studied in the presence of radiofrequency excitation; the experiments have been performed with different pulse sequences using different doped molecular systems. The experimental results clearly demonstrate the dominant role of coherent mechanisms of spin order transfer, which manifest themselves in well pronounced oscillations. These oscillations are of two types, precessions and nutations, having characteristic frequencies, which are the same for the different molecular systems and the pulse sequences applied. Hence, precessions and nutations constitute a general feature of polarization transfer in ONP experiments. In general, coherent manipulation of spin order transfer creates a powerful resource for improving the performance of the ONP method, which paves the way to strong signal enhancement in nuclear magnetic resonance.

Reaction pathways in atomistic models of thin film growth

NASA Astrophysics Data System (ADS)

Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.

2017-10-01

The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.

Natural Product Molecular Fossils.

PubMed

Falk, Heinz; Wolkenstein, Klaus

The natural products synthesized by organisms that were living a long time ago gave rise to their molecular fossils. These can consist of either the original unchanged compounds or they may undergo peripheral transformations in which their skeletons remain intact. In cases when molecular fossils can be traced to their organismic source, they are termed "geological biomarkers".This contribution describes apolar and polar molecular fossils and, in particular biomarkers, along the lines usually followed in organic chemistry textbooks, and points to their bioprecursors when available. Thus, the apolar compounds are divided in linear and branched alkanes followed by alicyclic compounds and aromatic and heterocyclic molecules, and, in particular, the geoporphyrins. The polar molecular fossils contain as functional groups or constituent units ethers, alcohols, phenols, carbonyl groups, flavonoids, quinones, and acids, or are polymers like kerogen, amber, melanin, proteins, or nucleic acids. The final sections discuss the methodology used and the fundamental processes encountered by the biomolecules described, including diagenesis, catagenesis, and metagenesis.

Investigating molecular crowding within nuclear pores using polarization-PALM

PubMed Central

Fu, Guo; Tu, Li-Chun; Zilman, Anton

2017-01-01

The key component of the nuclear pore complex (NPC) controlling permeability, selectivity, and the speed of nucleocytoplasmic transport is an assembly of natively unfolded polypeptides, which contain phenylalanine-glycine (FG) binding sites for nuclear transport receptors. The architecture and dynamics of the FG-network have been refractory to characterization due to the paucity of experimental methods able to probe the mobility and density of the FG-polypeptides and embedded macromolecules within intact NPCs. Combining fluorescence polarization, super-resolution microscopy, and mathematical analyses, we examined the rotational mobility of fluorescent probes at various locations within the FG-network under different conditions. We demonstrate that polarization PALM (p-PALM) provides a rich source of information about low rotational mobilities that are inaccessible with bulk fluorescence anisotropy approaches, and anticipate that p-PALM is well-suited to explore numerous crowded cellular environments. In total, our findings indicate that the NPC’s internal organization consists of multiple dynamic environments with different local properties. PMID:28949296

Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

PubMed

Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

2016-10-15

Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Fmoc-RGDS based fibrils: atomistic details of their hierarchical assembly.

PubMed

Zanuy, David; Poater, Jordi; Solà, Miquel; Hamley, Ian W; Alemán, Carlos

2016-01-14

We describe the 3D supramolecular structure of Fmoc-RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively. For this purpose, we performed atomistic all-atom molecular dynamics simulations of a wide variety of packing modes derived from both parallel and antiparallel β-sheet configurations. The proposed model, which closely resembles the cross-β core structure of amyloids, is stabilized by π-π stacking interactions between hydrophobic Fmoc groups. More specifically, in this organization, the Fmoc-groups of β-strands belonging to the same β-sheet form columns of π-stacked aromatic rings arranged in a parallel fashion. Eight of such columns pack laterally forming a compact and dense hydrophobic core, in which two central columns are surrounded by three adjacent columns on each side. In addition to such Fmoc···Fmoc interactions, the hierarchical assembly of the constituent β-strands involves a rich variety of intra- and inter-strand interactions. Accordingly, hydrogen bonding, salt bridges and π-π stacking interactions coexist in the highly ordered packing network proposed for the Fmoc-RGDS amphiphile. Quantum mechanical calculations, which have been performed to quantify the above referred interactions, confirm the decisive role played by the π-π stacking interactions between the rings of the Fmoc groups, even though both inter-strand and intra-strand hydrogen bonds and salt bridges also play a non-negligible role. Overall, these results provide a solid reference to complement the available experimental data, which are not precise enough to determine the fibril structure, and reconcile previous independent observations.

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Electrical Deflection of Polar Liquid Streams: A Misunderstood Demonstration

NASA Astrophysics Data System (ADS)

Ziaei-Moayyed, Maryam; Goodman, Edward; Williams, Peter

2000-11-01

The electrical deflection of polar liquid streams, commonly used as a textbook illustration of the behavior of polar molecules, is shown to be due to the formation of electrically charged droplets in the polar liquid stream, induced by a nearby charged object, rather than any force exerted on molecular dipoles. Streams of water and polar organic liquids could be deflected in a uniform electric field, which could not have exerted any force on dipolar species. Water and polar organic liquid streams formed within a grounded, electrically screened region could not be deflected after exiting the screened region, demonstrating that there is no electrical force on uncharged polar liquid droplets. Induced charging was observed also in insulating polar organic liquids and is suggested to be due to ionic impurities. A weak deflection of a stream of a nonpolar liquid (tetrachloroethylene) was also observed, indicating that such impurity effects are quite general, even in nonpolar liquids.

Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guin, Laurent; Department of Mechanical Engineering, Columbia University, New York, New York 10027; Raphanel, Jean L.

2016-06-28

Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagationmore » which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.« less

Departure of microscopic friction from macroscopic drag in molecular fluid dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanasaki, Itsuo; Fujiwara, Daiki; Kawano, Satoyuki, E-mail: kawano@me.es.osaka-u.ac.jp

2016-03-07

Friction coefficient of the Langevin equation and drag of spherical macroscopic objects in steady flow at low Reynolds numbers are usually regarded as equivalent. We show that the microscopic friction can be different from the macroscopic drag when the mass is taken into account for particles with comparable scale to the surrounding fluid molecules. We illustrate it numerically by molecular dynamics simulation of chloride ion in water. Friction variation by the atomistic mass effect beyond the Langevin regime can be of use in the drag reduction technology as well as the electro or thermophoresis.

Attosecond polarization control in atomic RABBITT-like experiments assisted by a circularly polarized laser

NASA Astrophysics Data System (ADS)

Boll, D. I. R.; Fojón, O. A.

2017-12-01

We study theoretically the single ionization of noble gas atoms by the combined action of an attosecond pulse train with linear polarization and an assistant laser field with circular polarization. We employ a non-perturbative model that under certain approximations gives closed-form expressions for the angular distributions of photoelectrons. Interestingly, our model allow us to interpret these angular distributions as two-centre interferences where the orientation and the modulus of the separation vector between the virtual emitters is governed by the assistant laser field. Additionally, we show that such a configuration of light fields is similar to the polarization control technique, where both the attosecond pulse train and the assistant laser field have linear polarizations whose relative orientation may be controlled. Moreover, in order to compare our results with the available experimental data, we obtain analytical expressions for the cross sections integrated over the photoelectron emission angles. By means of these expressions, we define the ‘magic time’ as the delay for which the total cross sections for atomic targets exhibit the same functional form as the one of the monochromatic photoionization of diatomic molecular targets.

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neilson, James R.; McQueen, Tyrel M.

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE PAGES

Neilson, James R.; McQueen, Tyrel M.

2015-09-20

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

Atomistic Simulations of Graphene Growth: From Kinetics to Mechanism.

PubMed

Qiu, Zongyang; Li, Pai; Li, Zhenyu; Yang, Jinlong

2018-03-20

Epitaxial growth is a promising strategy to produce high-quality graphene samples. At the same time, this method has great flexibility for industrial scale-up. To optimize growth protocols, it is essential to understand the underlying growth mechanisms. This is, however, very challenging, as the growth process is complicated and involves many elementary steps. Experimentally, atomic-scale in situ characterization methods are generally not feasible at the high temperature of graphene growth. Therefore, kinetics is the main experimental information to study growth mechanisms. Theoretically, first-principles calculations routinely provide atomic structures and energetics but have a stringent limit on the accessible spatial and time scales. Such gap between experiment and theory can be bridged by atomistic simulations using first-principles atomic details as input and providing the overall growth kinetics, which can be directly compared with experiment, as output. Typically, system-specific approximations should be applied to make such simulations computationally feasible. By feeding kinetic Monte Carlo (kMC) simulations with first-principles parameters, we can directly simulate the graphene growth process and thus understand the growth mechanisms. Our simulations suggest that the carbon dimer is the dominant feeding species in the epitaxial growth of graphene on both Cu(111) and Cu(100) surfaces, which enables us to understand why the reaction is diffusion limited on Cu(111) but attachment limited on Cu(100). When hydrogen is explicitly considered in the simulation, the central role hydrogen plays in graphene growth is revealed, which solves the long-standing puzzle into why H 2 should be fed in the chemical vapor deposition of graphene. The simulation results can be directly compared with the experimental kinetic data, if available. Our kMC simulations reproduce the experimentally observed quintic-like behavior of graphene growth on Ir(111). By checking the

Shared antigenicity between the polar filaments of myxosporeans and other Cnidaria.

PubMed

Ringuette, Maurice J; Koehler, Anne; Desser, Sherwin S

2011-02-01

Nematocysts containing coiled polar filaments are a distinguishing feature of members of the phylum Cnidaria. As a first step to characterizing the molecular structure of polar filaments, a polyclonal antiserum was raised in rabbits against a cyanogen bromide-resistant protein extract of mature cysts containing spores of Myxobolus pendula. The antiserum reacted only with proteins associated with extruded polar filaments. Western blot and whole-mount immunohistochemical analyses indicated a conservation of polar filament epitopes between M. pendula and 2 related cnidarians, i.e., the anthozoan, Nematostella vectensis, and the hydrozoan, Hydra vulgaris. This conservation of polar filament epitopes lends further support to a shared affinity between Myxozoa and cnidarians.

Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.

PubMed

Tavernelli, Ivano

2015-03-17

Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular

Molecular Origins of Mesoscale Ordering in a Metalloamphiphile Phase

PubMed Central

2015-01-01

Controlling the assembly of soft and deformable molecular aggregates into mesoscale structures is essential for understanding and developing a broad range of processes including rare earth extraction and cleaning of water, as well as for developing materials with unique properties. By combined synchrotron small- and wide-angle X-ray scattering with large-scale atomistic molecular dynamics simulations we analyze here a metalloamphiphile–oil solution that organizes on multiple length scales. The molecules associate into aggregates, and aggregates flocculate into meso-ordered phases. Our study demonstrates that dipolar interactions, centered on the amphiphile headgroup, bridge ionic aggregate cores and drive aggregate flocculation. By identifying specific intermolecular interactions that drive mesoscale ordering in solution, we bridge two different length scales that are classically addressed separately. Our results highlight the importance of individual intermolecular interactions in driving mesoscale ordering. PMID:27163014

Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields.

PubMed

Pandey, Poonam; Mallajosyula, Sairam S

2016-07-14

Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.

Combining configurational energies and forces for molecular force field optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

2017-07-21

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Mono- and polynucleation, atomistic growth, and crystal phase of III-V nanowires under varying group V flow

NASA Astrophysics Data System (ADS)

Dubrovskii, V. G.

2015-05-01

We present a refined model for the vapor-liquid-solid growth and crystal structure of Au-catalyzed III-V nanowires, which revisits several assumptions used so far and is capable of describing the transition from mononuclear to polynuclear regime and ultimately to regular atomistic growth. We construct the crystal phase diagrams and calculate the wurtzite percentages, elongation rates, critical sizes, and polynucleation thresholds of Au-catalyzed GaAs nanowires depending on the As flow. We find a non-monotonic dependence of the crystal phase on the group V flow, with the zincblende structure being preferred at low and high group V flows and the wurtzite structure forming at intermediate group V flows. This correlates with most of the available experimental data. Finally, we discuss the atomistic growth picture which yields zincblende crystal structure and should be very advantageous for fabrication of ternary III-V nanowires with well-controlled composition and heterointerfaces.

Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

NASA Astrophysics Data System (ADS)

HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

2016-04-01

Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

Automated Algorithms for Quantum-Level Accuracy in Atomistic Simulations: LDRD Final Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Aidan Patrick; Schultz, Peter Andrew; Crozier, Paul

2014-09-01

This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projectedmore » on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel

Dielectric properties of crystalline organic molecular films in the limit of zero overlap

DOE Office of Scientific and Technical Information (OSTI.GOV)

D’Avino, Gabriele, E-mail: gabriele.davino@gmail.com; Vanzo, Davide; Soos, Zoltán G., E-mail: soos@princeton.edu

2016-01-21

We present the calculation of the static dielectric susceptibility tensor and dipole field sums in thin molecular films in the well-defined limit of zero intermolecular overlap. Microelectrostatic and charge redistribution approaches are applied to study the evolution of dielectric properties from one to a few molecular layers in films of different conjugated molecules with organic electronics applications. Because of the conditional convergence of dipolar interactions, dipole fields depend on the shape of the sample and different values are found in the middle layer of a thick film and in the bulk. The shape dependence is eliminated when depolarization is takenmore » into account, and the dielectric tensor of molecular films converges to the bulk limit within a few molecular layers. We quantify the magnitude of surface effects and interpret general trends among different systems in terms of molecular properties, such as shape, polarizability anisotropy, and supramolecular organization. A connection between atomistic models for molecular dielectrics and simpler theories for polarizable atomic lattices is also provided.« less

Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized System Dynamics

NASA Astrophysics Data System (ADS)

Ho, Phay; Knight, Christopher; Bostedt, Christoph; Young, Linda; Tegze, Miklos; Faigel, Gyula

2016-05-01

We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

Molecular dynamics simulation of metal nanoislands growth

NASA Astrophysics Data System (ADS)

Kapralov, N. V.; Babich, E. S.; Redkov, A. V.

2017-11-01

We present the atomistic model and the simulation of a self-assembled growth of a silver nanoisland film and small groups of nanoislands on a glass substrate after thermal poling of the glass with a profiled electrode. The calculations were performed in molecular dynamics simulator LAMMPS taking into account the diffusion of the metal atoms towards and along the glass surface and their clustering. Lennard-Jones potential was used to describe metal-metal and metal-glass interaction. The potential parameters were determined to provide qualitative coincidence of the simulated configurations of the metal nanostructures and the experimental ones, such as an isolated nanoisland, a pair and a set of three nanoislands and a “plasmonic molecule”.

Two Arabidopsis AGC kinases are critical for the polarized growth of pollen tubes

USDA-ARS?s Scientific Manuscript database

Reproduction of flowering plants requires the growth of pollen tubes to deliver immotile sperm for fertilization. Pollen tube growth resembles that of polarized metazoan cells, in that some molecular mechanisms underlying cell polarization and growth are evolutionarily conserved, including the funct...

Bulk viscosity of molecular fluids

NASA Astrophysics Data System (ADS)

Jaeger, Frederike; Matar, Omar K.; Müller, Erich A.

2018-05-01

The bulk viscosity of molecular models of gases and liquids is determined by molecular simulations as a combination of a dilute gas contribution, arising due to the relaxation of internal degrees of freedom, and a configurational contribution, due to the presence of intermolecular interactions. The dilute gas contribution is evaluated using experimental data for the relaxation times of vibrational and rotational degrees of freedom. The configurational part is calculated using Green-Kubo relations for the fluctuations of the pressure tensor obtained from equilibrium microcanonical molecular dynamics simulations. As a benchmark, the Lennard-Jones fluid is studied. Both atomistic and coarse-grained force fields for water, CO2, and n-decane are considered and tested for their accuracy, and where possible, compared to experimental data. The dilute gas contribution to the bulk viscosity is seen to be significant only in the cases when intramolecular relaxation times are in the μs range, and for low vibrational wave numbers (<1000 cm-1); This explains the abnormally high values of bulk viscosity reported for CO2. In all other cases studied, the dilute gas contribution is negligible and the configurational contribution dominates the overall behavior. In particular, the configurational term is responsible for the enhancement of the bulk viscosity near the critical point.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2011-02-28

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

A Statistical Approach for the Concurrent Coupling of Molecular Dynamics and Finite Element Methods

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2007-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, increasing the size of the MD domain quickly presents intractable computational demands. A robust approach to surmount this computational limitation has been to unite continuum modeling procedures such as the finite element method (FEM) with MD analyses thereby reducing the region of atomic scale refinement. The challenging problem is to seamlessly connect the two inherently different simulation techniques at their interface. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the typical boundary value problem used to define a coupled domain. The method uses statistical averaging of the atomistic MD domain to provide displacement interface boundary conditions to the surrounding continuum FEM region, which, in return, generates interface reaction forces applied as piecewise constant traction boundary conditions to the MD domain. The two systems are computationally disconnected and communicate only through a continuous update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM) as opposed to a direct coupling method where interface atoms and FEM nodes are individually related. The methodology is inherently applicable to three-dimensional domains, avoids discretization of the continuum model down to atomic scales, and permits arbitrary temperatures to be applied.

Growth of non-polar and semi-polar gallium nitride with plasma assisted molecular beam epitaxy: Relatonships between film microstructure, reciprocal lattice and transport properties

NASA Astrophysics Data System (ADS)

McLaurin, Melvin Barker

2007-12-01

The group-III nitrides exhibit significant spontaneous and piezoelectric polarization parallel to the [0001] direction, which are manifested as sheet charges at heterointerfaces. While polarization can be used to engineer the band-structure of a device, internal electric fields generated by polarization discontinuities can also have a number of negative consequences for the performance and design of structures utilizing heterojunctions. The most direct route to polarization free group-III nitride devices is growth on either one of the "non-polar" prismatic faces of the crystal (m-plane (1010) or a-plane (1120)) where the [0001] direction lies in the plane of any heterointerfaces. This dissertation focuses on the growth of non-polar and semi-polar GaN by MBE and on how the dominant feature of the defect structure of non-polar and semi-polar films, basal plane stacking faults, determines the properties of the reciprocal lattice and electrical transport of the films. The first part is a survey of the MBE growth of the two non-polar planes (10 10) and (1120) and three semi-polar planes (1011), (1013) and {11 22} investigated in this work. The relationship between basal plane stacking faults and broadening of the reciprocal lattice is discussed and measured with X-ray diffraction using a lateral-variant of the Williamson-Hall analysis. The electrical properties of m-plane films are investigated using Hall-effect and TLM measurements. Anisotropic mobilities were observed for both electrons and holes along with record p-type conductivities and hole concentrations. By comparison to both inversion-domain free c-plane films and stacking-fault-free free-standing m-plane GaN wafers it was determined that basal plane stacking faults were the source of both the enhanced p-type conductivity and the anisotropic carrier mobilities. Finally, we propose a possible source of anisotropic mobilities and enhanced p-type conduction in faulted films is proposed. Basal plane stacking faults

3D Cloud Radiative Effects on Polarized Reflectances

NASA Astrophysics Data System (ADS)

Cornet, C.; Matar, C.; C-Labonnote, L.; Szczap, F.; Waquet, F.; Parol, F.; Riedi, J.

2017-12-01

by the molecular signal at the shortest wavelength. At the satellite scale (few kilometers), depending on the wavelength and the molecular contribution, the absolute polarized signal may be increased or decreased in the forward scattering direction and is decreased in the cloudbow directions because of the plan-parallel biases.

Cell polarity proteins and spermatogenesis.

PubMed

Gao, Ying; Xiao, Xiang; Lui, Wing-Yee; Lee, Will M; Mruk, Dolores; Cheng, C Yan

2016-11-01

When the cross-section of a seminiferous tubule from an adult rat testes is examined microscopically, Sertoli cells and germ cells in the seminiferous epithelium are notably polarized cells. For instance, Sertoli cell nuclei are found near the basement membrane. On the other hand, tight junction (TJ), basal ectoplasmic specialization (basal ES, a testis-specific actin-rich anchoring junction), gap junction (GJ) and desmosome that constitute the blood-testis barrier (BTB) are also located near the basement membrane. The BTB, in turn, divides the epithelium into the basal and the adluminal (apical) compartments. Within the epithelium, undifferentiated spermatogonia and preleptotene spermatocytes restrictively reside in the basal compartment whereas spermatocytes and post-meiotic spermatids reside in the adluminal compartment. Furthermore, the heads of elongating/elongated spermatids point toward the basement membrane with their elongating tails toward the tubule lumen. However, the involvement of polarity proteins in this unique cellular organization, in particular the underlying molecular mechanism(s) by which polarity proteins confer cellular polarity in the seminiferous epithelium is virtually unknown until recent years. Herein, we discuss latest findings regarding the role of different polarity protein complexes or modules and how these protein complexes are working in concert to modulate Sertoli cell and spermatid polarity. These findings also illustrate polarity proteins exert their effects through the actin-based cytoskeleton mediated by actin binding and regulatory proteins, which in turn modulate adhesion protein complexes at the cell-cell interface since TJ, basal ES and GJ utilize F-actin for attachment. We also propose a hypothetical model which illustrates the antagonistic effects of these polarity proteins. This in turn provides a unique mechanism to modulate junction remodeling in the testis to support germ cell transport across the epithelium in

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear.

PubMed

Lindqvist, Charlotte; Schuster, Stephan C; Sun, Yazhou; Talbot, Sandra L; Qi, Ji; Ratan, Aakrosh; Tomsho, Lynn P; Kasson, Lindsay; Zeyl, Eve; Aars, Jon; Miller, Webb; Ingólfsson, Olafur; Bachmann, Lutz; Wiig, Oystein

2010-03-16

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

PubMed Central

Lindqvist, Charlotte; Schuster, Stephan C.; Sun, Yazhou; Talbot, Sandra L.; Qi, Ji; Ratan, Aakrosh; Tomsho, Lynn P.; Kasson, Lindsay; Zeyl, Eve; Aars, Jon; Miller, Webb; Ingólfsson, Ólafur; Bachmann, Lutz; Wiig, Øystein

2010-01-01

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage. PMID:20194737

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

USGS Publications Warehouse

Lindqvist, Charlotte; Schuster, Stephan C.; Sun, Yazhou; Talbot, Sandra L.; Qi, Ji; Ratan, Aakrosh; Tomsho, Lynn P.; Kasson, Lindsay; Zeyl, Eve; Aars, Jon; Miller, Webb; Ingólfsson, Ólafur; Bachmann, Lutz; Wiig, Øystein

2010-01-01

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

Tuning spin-polarized transport in organic semiconductors

NASA Astrophysics Data System (ADS)

Mattana, Richard; Galbiati, Marta; Delprat, Sophie; Tatay, Sergio; Deranlot, Cyrile; Seneor, Pierre; Petroff, Frederic

Molecular spintronics is an emerging research field at the frontier between organic chemistry and the spintronics. Compared to traditional inorganic materials molecules are flexible and can be easily tailored by chemical synthesis. Due to their theoretically expected very long spin lifetime, they were first only seen as the ultimate media for spintronics devices. It was recently that new spintronics tailoring could arise from the chemical versatility brought by molecules. The hybridization between a ferromagnet and molecules induces a spin dependent broadening and energy shifting of the molecular orbitals leading to an induced spin polarization on the first molecular layer. This spin dependent hybridization can be used to tailor the spin dependent transport in organic spintronics devices. We have studied vertical Co/Alq3/Co organic spin valves. The negative magnetoresistance observed is the signature of different coupling strengths at the top and bottom interfaces. We have then inserted an inorganic tunnel barrier at the bottom interface in order to suppress the spin-dependent hybridization. In this case we restore a positive magnetoresistance. This demonstrates that at the bottom Co/Alq3 interface a stronger coupling occurs which induces an inversion of the spin polarization.

The GTP-bound and Sumoylated Form of the rab17 Small Molecular Weight GTPase Selectively Binds Syntaxin 2 in Polarized Hepatic WIF-B Cells*

PubMed Central

Striz, Anneliese C.; Tuma, Pamela L.

2016-01-01

A major focus for our laboratory is identifying the molecules and mechanisms that regulate polarized apical protein sorting in hepatocytes, the major epithelial cells of the liver. These trafficking pathways are regulated, in part, by small molecular weight rab GTPases. We chose to investigate rab17, whose expression is restricted to polarized epithelial cells, is enriched in liver, and has been implicated in regulating basolateral to apical transcytosis. To initiate our studies, we generated three recombinant adenoviruses expressing wild type, constitutively active (GTP bound), or dominant-negative (GDP bound) rab17. Immunoblotting revealed rab17 immunoreactive species at 25 kDa (the predicted rab17 molecular mass) and 40 kDa. We determined that mono-sumoylation of the 25-kDa rab17 is responsible for the shift in molecular mass, and that rab17 prenylation is required for sumoylation. We further determined that sumoylation selectively promotes interactions with syntaxin 2 (but not syntaxins 3 or 4) and that these interactions are nucleotide dependent. Furthermore, a K68R-mutated rab17 led to the redistribution of syntaxin 2 and 5′ nucleotidase from the apical membrane to subapical puncta, whereas multidrug resistance protein 2 distributions were not changed. Together these data are consistent with the proposed role of rab17 in vesicle fusion with the apical plasma membrane and further implicate sumoylation as an important mediator of protein-protein interactions. The selectivity in syntaxin binding and apical protein redistribution further suggests that rab17 and syntaxin 2 mediate fusion of transcytotic vesicles at the apical surface. PMID:26957544

Efficient room-temperature source of polarized single photons

DOEpatents

Lukishova, Svetlana G.; Boyd, Robert W.; Stroud, Carlos R.

2007-08-07

An efficient technique for producing deterministically polarized single photons uses liquid-crystal hosts of either monomeric or oligomeric/polymeric form to preferentially align the single emitters for maximum excitation efficiency. Deterministic molecular alignment also provides deterministically polarized output photons; using planar-aligned cholesteric liquid crystal hosts as 1-D photonic-band-gap microcavities tunable to the emitter fluorescence band to increase source efficiency, using liquid crystal technology to prevent emitter bleaching. Emitters comprise soluble dyes, inorganic nanocrystals or trivalent rare-earth chelates.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Exp6-polar thermodynamics of dense supercritical water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bastea, S; Fried, L E

2007-12-13

We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, based on ideas originally applied to dipolar hard spheres, performs very well when tested against molecular dynamics simulations. Comparisons of the model predictions with experimental data available for supercritical water yield excellent agreement for the shock Hugoniot, isotherms and sound speeds, and are also quite good for the self-diffusion constant and relative dielectric constant. We expect the present approach to be also useful for other small polar moleculesmore » and their mixtures.« less

Functional fixedness and functional reduction as common sense reasonings in chemical equilibrium and in geometry and polarity of molecules

NASA Astrophysics Data System (ADS)

Furió, C.; Calatayud, M. L.; Bárcenas, S. L.; Padilla, O. M.

2000-09-01

Many of the learning difficulties in the specific domain of chemistry are found not only in the ideas already possessed by students but in the strategic and procedural knowledge that is characteristic of everyday thinking. These defects in procedural knowledge have been described as functional fixedness and functional reduction. This article assesses the procedural difficulties of students (grade 12 and first and third year of university) based on common sense reasoning in two areas of chemistry: chemical equilibrium and geometry and polarity of molecules. In the first area, the theme of external factors affecting equilibria (temperature and concentration change) was selected because the explanations given by the students could be analyzed easily. The existence of a functional fixedness where Le Chatelier's principle was almost exclusively applied by rote could be observed, with this being the cause of the incorrect responses given to the proposed items. Functional fixedness of the Lewis structure also led to an incorrect prediction of molecular geometry. When molecular geometry was correctly determined by the students, it seemed that other methodological or procedural difficulties appeared when the task was to determine molecular polarity. The students showed a tendency, in many cases, to reduce the factors affecting molecular polarity in two possible ways: (a) assuming that polarity depends only on shape (geometric functional reduction) or (b) assuming that molecular polarity depends only on the polarity of bonds (bonding functional reduction).

Protein displacements under external forces: An atomistic Langevin dynamics approach.

PubMed

Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

2009-02-28

We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

Emergence of linear elasticity from the atomistic description of matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cakir, Abdullah, E-mail: acakir@ntu.edu.sg; Pica Ciamarra, Massimo; Dipartimento di Scienze Fisiche, CNR–SPIN, Università di Napoli Federico II, I-80126 Napoli

2016-08-07

We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of themore » fluctuations of the local elastic constants close to the jamming transition.« less

Polarization retention in ultra-thin barium titanate films on Ge(001)

NASA Astrophysics Data System (ADS)

Cho, Yujin; Ponath, Patrick; Zheng, Lu; Hatanpaa, Benjamin; Lai, Keji; Demkov, Alexander A.; Downer, Michael C.

2018-04-01

We investigate polarization retention in 10 to 19 nm thick ferroelectric BaTiO3 (BTO) grown on Ge(001) by molecular beam epitaxy. The out-of-plane direction and reversibility of electric polarization were confirmed using piezoresponse force microscopy. After reverse-poling selected regions of the BTO films to a value P with a biased atomic-force microscope tip, we monitored relaxation of their net polarization for as long as several weeks using optical second-harmonic generation microscopy. All films retained reversed polarization throughout the observation period. 10 nm-thick BTO films relaxed monotonically to a saturation value of 0.9 P after 27 days and 19 nm films to 0.75 P after 24 h. Polarization dynamics are discussed in the context of a 1D polarization relaxation/kinetics model.

Extending atomistic simulation timescale in solid/liquid systems: crystal growth from solution by a parallel-replica dynamics and continuum hybrid method.

PubMed

Lu, Chun-Yaung; Voter, Arthur F; Perez, Danny

2014-01-28

Deposition of solid material from solution is ubiquitous in nature. However, due to the inherent complexity of such systems, this process is comparatively much less understood than deposition from a gas or vacuum. Further, the accurate atomistic modeling of such systems is computationally expensive, therefore leaving many intriguing long-timescale phenomena out of reach. We present an atomistic/continuum hybrid method for extending the simulation timescales of dynamics at solid/liquid interfaces. We demonstrate the method by simulating the deposition of Ag on Ag (001) from solution with a significant speedup over standard MD. The results reveal specific features of diffusive deposition dynamics, such as a dramatic increase in the roughness of the film.

Structural Insights into the Atomistic Mechanisms of Action of Small Molecule Inhibitors Targeting the KCa3.1 Channel Pore

PubMed Central

Nguyen, Hai M.; Singh, Vikrant; Pressly, Brandon; Jenkins, David Paul

2017-01-01

The intermediate-conductance Ca2+-activated K+ channel (KCa3.1) constitutes an attractive pharmacological target for immunosuppression, fibroproliferative disorders, atherosclerosis, and stroke. However, there currently is no available crystal structure of this medically relevant channel that could be used for structure-assisted drug design. Using the Rosetta molecular modeling suite we generated a molecular model of the KCa3.1 pore and tested the model by first confirming previously mapped binding sites and visualizing the mechanism of TRAM-34 (1-[(2-chlorophenyl)diphenylmethyl]-1H-pyrazole), senicapoc (2,2-bis-(4-fluorophenyl)-2-phenylacetamide), and NS6180 (4-[[3-(trifluoromethyl)phenyl]methyl]-2H-1,4-benzothiazin-3(4H)-one) inhibition at the atomistic level. All three compounds block ion conduction directly by fully or partially occupying the site that would normally be occupied by K+ before it enters the selectivity filter. We then challenged the model to predict the receptor sites and mechanisms of action of the dihydropyridine nifedipine and an isosteric 4-phenyl-pyran. Rosetta predicted receptor sites for nifedipine in the fenestration region and for the 4-phenyl-pyran in the pore lumen, which could both be confirmed by site-directed mutagenesis and electrophysiology. While nifedipine is thus not a pore blocker and might be stabilizing the channel in a nonconducting conformation or interfere with gating, the 4-phenyl-pyran was found to be a classical pore blocker that directly inhibits ion conduction similar to the triarylmethanes TRAM-34 and senicapoc. The Rosetta KCa3.1 pore model explains the mechanism of action of several KCa3.1 blockers at the molecular level and could be used for structure-assisted drug design. PMID:28126850

Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry.

PubMed

Ruiz, Luis; Benjamin, Ari; Sullivan, Matthew; Keten, Sinan

2015-05-07

We use atomistic nonequilibrium molecular dynamics simulations to demonstrate how specific ionic flux in peptide nanotubes can be regulated by tailoring the lumen chemistry through single amino acid substitutions. By varying the size and polarity of the functional group inserted into the nanotube interior, we are able to adjust the Na(+) flux by over an order of magnitude. Cl(-) is consistently denied passage. Bulky, nonpolar groups encourage interactions between the Na(+) and the peptide backbone carbonyl groups, disrupting the Na(+) solvation shell and slowing the transport of Na(+). Small groups have the opposite effect and accelerate flow. These results suggest that relative ion flux and selectivity can be precisely regulated in subnanometer pores by molecularly defining the lumen according to biological principles.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

PubMed

Šponer, Jiří; Bussi, Giovanni; Krepl, Miroslav; Banáš, Pavel; Bottaro, Sandro; Cunha, Richard A; Gil-Ley, Alejandro; Pinamonti, Giovanni; Poblete, Simón; Jurečka, Petr; Walter, Nils G; Otyepka, Michal

2018-04-25

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

PubMed Central

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

Atomistic Design of Favored Compositions for Synthesizing the Al-Ni-Y Metallic Glasses

PubMed Central

Wang, Q.; Li, J. H.; Liu, J. B.; Liu, B. X.

2015-01-01

For a ternary alloy system promising for obtaining the so-called bulk metallic glasses (BMGs), the first priority issue is to predict the favored compositions, which could then serve as guidance for the appropriate alloy design. Taking the Al-Ni-Y system as an example, here we show an atomistic approach, which is developed based on a recently constructed and proven realistic interatomic potential of the system. Applying the Al-Ni-Y potential, series simulations not only clarify the glass formation mechanism, but also predict in the composition triangle, a hexagonal region, in which a disordered state, i.e., the glassy phase, is favored energetically. The predicted region is defined as glass formation region (GFR) for the ternary alloy system. Moreover, the approach is able to calculate an amorphization driving force (ADF) for each possible glassy alloy located within the GFR. The calculations predict an optimized sub-region nearby a stoichiometry of Al80Ni5Y15, implying that the Al-Ni-Y metallic glasses designed in the sub-region could be the most stable. Interestingly, the atomistic predictions are supported by experimental results observed in the Al-Ni-Y system. In addition, structural origin underlying the stability of the Al-Ni-Y metallic glasses is also discussed in terms of a hybrid packing mode in the medium-range scale. PMID:26592568

Atomistic Design of Favored Compositions for Synthesizing the Al-Ni-Y Metallic Glasses

NASA Astrophysics Data System (ADS)

Wang, Q.; Li, J. H.; Liu, J. B.; Liu, B. X.

2015-11-01

For a ternary alloy system promising for obtaining the so-called bulk metallic glasses (BMGs), the first priority issue is to predict the favored compositions, which could then serve as guidance for the appropriate alloy design. Taking the Al-Ni-Y system as an example, here we show an atomistic approach, which is developed based on a recently constructed and proven realistic interatomic potential of the system. Applying the Al-Ni-Y potential, series simulations not only clarify the glass formation mechanism, but also predict in the composition triangle, a hexagonal region, in which a disordered state, i.e., the glassy phase, is favored energetically. The predicted region is defined as glass formation region (GFR) for the ternary alloy system. Moreover, the approach is able to calculate an amorphization driving force (ADF) for each possible glassy alloy located within the GFR. The calculations predict an optimized sub-region nearby a stoichiometry of Al80Ni5Y15, implying that the Al-Ni-Y metallic glasses designed in the sub-region could be the most stable. Interestingly, the atomistic predictions are supported by experimental results observed in the Al-Ni-Y system. In addition, structural origin underlying the stability of the Al-Ni-Y metallic glasses is also discussed in terms of a hybrid packing mode in the medium-range scale.

Redox reactions with empirical potentials: atomistic battery discharge simulations.

PubMed

Dapp, Wolf B; Müser, Martin H

2013-08-14

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

Optically-pumped spin-exchange polarized electron source

NASA Astrophysics Data System (ADS)

Pirbhai, Munir Hussein

Polarized electron beams are an indispensable probe of spin-dependent phenomena in fields of atomic and molecular physics, magnetism and biophysics. While their uses have become widespread, the standard source based on negative electron affinity gallium arsenide (GaAs) remains technically complicated. This has hindered progress on many experiments involving spin-polarized electrons, especially those using target gas loads, which tend to adversely affect the performance of GaAs sources. A robust system based on an alternative way to make polarized electron beams has been devised in this study, which builds on previous work done in our lab. It involves spin-exchange collisions between free, unpolarized electrons and oriented rubidium atoms in the presence of a quenching gas. This system has less stringent vacuum requirements than those of GaAs sources, and is capable of operating in background pressures of ~1mTorr. Beams with ~24% polarization and 4μA of current have been recorded, which is comparable to the performance obtained with the earlier version built in our lab. The present system is however not as unstable as in the previous work, and has the potential to be developed into a "turn-key" source of polarized electron beams. It has also allowed us to undertake a study to find factors which affect the beam polarization in this scheme of producing polarized electrons. Such knowledge will help us to design better optically-pumped spin-exchange polarized electron sources.

Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations

NASA Astrophysics Data System (ADS)

Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

2017-04-01

Zircon is an essential mineral that is used in the U-Pb dating. Moreover, zircon is highly resistant to radioactive exposure. It is of great interest in solving both fundamental and applied problems associated with the isolation of high-level radioactive waste. There is significant progress in forecasting of the most energetically favorable crystal structures at the present time. Unfortunately, the theoretical forecast of crystal morphology at high technological level is under-explored nowadays, though the estimation of crystal equilibrium habit is extremely important in studying the physical and chemical properties of new materials. For the first time, the thesis about relation of the equilibrium shape of a crystal with its crystal structure was put forward in the works by O.Brave. According to it, the idealized habit is determined in the simplest case by a correspondence with the reticular densities Rhkl of individual faces. This approach, along with all subsequent corrections, does not take into account the nature of atoms and the specific features of the chemical bond in crystals. The atomistic calculations of crystal surfaces are commonly performed using the energetic characteristics of faces, namely, the surface energy (Esurf), which is a measure of the thermodynamic stability of the crystal face. The stable crystal faces are characterized by small positive values of Esurf. As we know from our previous research (Gromalova et al.,2015) one of the constitutive factors affecting the value of the surface energy in calculations is a choice of potentials model. In this regard, we studied several sets of parameters of atomistic interatomic potentials optimized previously. As the first test model («Zircon 1») were used sets of interatomic potentials of interaction Zr-O, Si-O and O-O in the form of Buckingham potentials. To improve playback properties of zircon additionally used Morse potential for a couple of Zr-Si, as well as the three-particle angular harmonic

Polarization-controlled optimal scatter suppression in transient absorption spectroscopy

PubMed Central

Malý, Pavel; Ravensbergen, Janneke; Kennis, John T. M.; van Grondelle, Rienk; Croce, Roberta; Mančal, Tomáš; van Oort, Bart

2017-01-01

Ultrafast transient absorption spectroscopy is a powerful technique to study fast photo-induced processes, such as electron, proton and energy transfer, isomerization and molecular dynamics, in a diverse range of samples, including solid state materials and proteins. Many such experiments suffer from signal distortion by scattered excitation light, in particular close to the excitation (pump) frequency. Scattered light can be effectively suppressed by a polarizer oriented perpendicular to the excitation polarization and positioned behind the sample in the optical path of the probe beam. However, this introduces anisotropic polarization contributions into the recorded signal. We present an approach based on setting specific polarizations of the pump and probe pulses, combined with a polarizer behind the sample. Together, this controls the signal-to-scatter ratio (SSR), while maintaining isotropic signal. We present SSR for the full range of polarizations and analytically derive the optimal configuration at angles of 40.5° between probe and pump and of 66.9° between polarizer and pump polarizations. This improves SSR by (or compared to polarizer parallel to probe). The calculations are validated by transient absorption experiments on the common fluorescent dye Rhodamine B. This approach provides a simple method to considerably improve the SSR in transient absorption spectroscopy. PMID:28262765

Rheology of wormlike micellar fluids from Brownian and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Padding, J. T.; Boek, E. S.; Briels, W. J.

2005-11-01

There is a great need for understanding the link between the detailed chemistry of surfactants, forming wormlike micelles, and their macroscopic rheological properties. In this paper we show how this link may be explored through particle simulations. First we review an existing bead-spring model. We find that shear flow enhances the formation of rings at the expense of linear chains. The shear viscosity of this model is dominated by solvent contributions, however, and the link with the chemistry of the surfactants is missing. We introduce a more realistic Brownian dynamics model, the parameters of which are measured from atomistic molecular dynamics simulations.

Molecular mechanics of mineralized collagen fibrils in bone

PubMed Central

Nair, Arun K.; Gautieri, Alfonso; Chang, Shu-Wei; Buehler, Markus J.

2013-01-01

Bone is a natural composite of collagen protein and the mineral hydroxyapatite. The structure of bone is known to be important to its load-bearing characteristics, but relatively little is known about this structure or the mechanism that govern deformation at the molecular scale. Here we perform full-atomistic calculations of the three-dimensional molecular structure of a mineralized collagen protein matrix to try to better understand its mechanical characteristics under tensile loading at various mineral densities. We find that as the mineral density increases, the tensile modulus of the network increases monotonically and well beyond that of pure collagen fibrils. Our results suggest that the mineral crystals within this network bears up to four times the stress of the collagen fibrils, whereas the collagen is predominantly responsible for the material’s deformation response. These findings reveal the mechanism by which bone is able to achieve superior energy dissipation and fracture resistance characteristics beyond its individual constituents. PMID:23591891

Polarization anisotropy in fiber-optic second harmonic generation microscopy.

PubMed

Fu, Ling; Gu, Min

2008-03-31

We report the investigation and implementation of a compact second harmonic generation microscope that uses a single-mode fiber coupler and a double-clad photonic crystal fiber. Second harmonic polarization anisotropy through the fiber-optic microscope systems is quantitatively measured with KTP microcrystals, fish scale and rat tail tendon. It is demonstrated that the polarized second harmonic signals can be excited and collected through the single-mode fiber coupler to analyze the molecular orientations of structural proteins. It has been discovered that a double-clad photonic crystal fiber can preserve the linear polarization in the core, although a depolarization effect is observed in the inner cladding region. The feasibility of polarization anisotropy measurements in fiber-optic second harmonic generation microscopy will benefit the in vivo study of collagen-related diseases with a compact imaging probe.

Binding of polarity-sensitive hydrophobic ligands to erythroid and nonerythroid spectrin: fluorescence and molecular modeling studies.

PubMed

Patra, Malay; Mitra, Madhurima; Chakrabarti, Abhijit; Mukhopadhyay, Chaitali

2014-01-01

We have used three polarity-sensitive fluorescence probes, 6-propionyl 2-(N,N-dimethyl-amino) naphthalene (Prodan), pyrene and 8-anilino 1-naphthalene sulphonic acid, to study their binding with erythroid and nonerythroid spectrin, using fluorescence spectroscopy. We have found that both bind to prodan and pyrene with high affinities with apparent dissociation constants (Kd) of .50 and .17 μM, for prodan, and .04 and .02 μM, for pyrene, respectively. The most striking aspect of these bindings have been that the binding stoichiometry have been equal to 1 in erythroid spectrin, both in dimeric and tetrameric form, and in tetrameric nonerythroid spectrin. From an estimate of apparent dielectric constants, the polarity of the binding site in both erythroid and nonerythroid forms have been found to be extremely hydrophobic. Thermodynamic parameters associated with such binding revealed that the binding is favored by positive change in entropy. Molecular docking studies alone indicate that both prodan and pyrene bind to the four major structural domains, following the order in the strength of binding to the Ankyrin binding domain > SH3 domain > Self-association domain > N-terminal domain of α-spectrin of both forms of spectrin. The binding experiments, particularly with the tetrameric nonerythroid spectrin, however, indicate more toward the self association domain in offering the unique binding site, since the binding stoichiometry have been 1 in all forms of dimeric and tetrameric spectrin, so far studied by us. Further studies are needed to characterize the hydrophobic binding sites in both forms of spectrin.

Separation of polar gases from nonpolar gases

DOEpatents

Kulprathipanja, S.

1986-08-19

The separation of polar gases from nonpolar gases may be effected by passing a mixture of nonpolar gases over the face of a multicomponent membrane at separation conditions. The multicomponent membrane which is used to effect the separation will comprise a mixture of a glycol plasticizer having a molecular weight of from about 200 to about 600 and an organic polymer cast on a porous support. The porous support is pretreated prior to casting of the mixture thereon by contact with a polyhydric alcohol whereby the pores of the support are altered, thus adding to the increased permeability of the polar gas.

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles.

PubMed

Yuan, Fang; Larson, Ronald G

2015-09-24

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments. PMID:28666087

Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy.

PubMed

Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R

2014-04-01

Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

Atomistic models of vacancy-mediated diffusion in silicon

NASA Astrophysics Data System (ADS)

Dunham, Scott T.; Wu, Can Dong

1995-08-01

Vacancy-mediated diffusion of dopants in silicon is investigated using Monte Carlo simulations of hopping diffusion, as well as analytic approximations based on atomistic considerations. Dopant/vacancy interaction potentials are assumed to extend out to third-nearest neighbor distances, as required for pair diffusion theories. Analysis focusing on the third-nearest neighbor sites as bridging configurations for uncorrelated hops leads to an improved analytic model for vacancy-mediated dopant diffusion. The Monte Carlo simulations of vacancy motion on a doped silicon lattice verify the analytic results for moderate doping levels. For very high doping (≳2×1020 cm-3) the simulations show a very rapid increase in pair diffusivity due to interactions of vacancies with more than one dopant atom. This behavior has previously been observed experimentally for group IV and V atoms in silicon [Nylandsted Larsen et al., J. Appl. Phys. 73, 691 (1993)], and the simulations predict both the point of onset and doping dependence of the experimentally observed diffusivity enhancement.

Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations.

PubMed

Nguyen, Phuong H; Sterpone, Fabio; Campanera, Josep M; Nasica-Labouze, Jessica; Derreumaux, Philippe

2016-06-15

The A2V mutation was reported to protect from Alzheimer's disease in its heterozygous form and cause an early Alzheimer's disease type dementia in its homozygous form. Experiments showed that the aggregation rate follows the order A2V > WT (wild-type) > A2V-WT. To understand the impact of this mutation, we carried out replica exchange molecular dynamics simulations of Aβ1-40 WT-A2V and A2V-A2V dimers and compared to the WT dimer. Our atomistic simulations reveal that the mean secondary structure remains constant, but there are substantial differences in the intramolecular and intermolecular conformations upon single and double A2V mutation. Upon single mutation, the intrinsic disorder is reduced, the intermolecular potential energies are reduced, the population of intramolecular three-stranded β-sheets is increased, and the number of all α dimer topologies is decreased. Taken together, these results offer an explanation for the reduced aggregation rate of the Aβ1-40 A2V-WT peptides and the protective effect of A2V in heterozygotes.

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Saether, E.; Glaessgen, E.H.; Yamakov, V.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Interplay of dust alignment, grain growth, and magnetic fields in polarization: lessons from the emission-to-extinction ratio

NASA Astrophysics Data System (ADS)

Fanciullo, L.; Guillet, V.; Boulanger, F.; Jones, A. P.

2017-06-01

Context. Polarized extinction and emission from dust in the interstellar medium (ISM) are hard to interpret, as their dependence on dust optical properties, grain alignment, and magnetic field orientation is complex. This is particularly true in molecular clouds. The aforementioned phenomena are usually considered independently in polarization studies, while it is likely that they all contribute and their effects have yet to be disentangled. Aims: The data available today are not yet used to their full potential. The combination of emission and extinction, in particular, provides information not available from either of them alone. We combine data from the scientific literature on polarized dust extinction with Planck data on polarized emission, and we use them to constrain the possible variations in dust and environmental conditions inside molecular clouds, and especially translucent lines of sight, taking the magnetic field orientation into account. Methods: We focused on the dependence between λmax (the wavelength of maximum polarization in extinction) and other observables such as the extinction polarization, the emission polarization, and the ratio between the two. We set out to reproduce these correlations using Monte Carlo simulations in which we varied the relevant quantities in a dust model, which are grain alignment, size distribution, and magnetic field orientation, to mimic the diverse conditions that are expected inside molecular clouds. Results: None of the quantities we chose can explain the observational data on their own: the best results are obtained when all quantities vary significantly across and within clouds. However, some of the data, most notably the stars with a low ratio of polarization in emission to polarization in extinction, are not reproduced by our simulation. Conclusions: Our results suggest not only that dust evolution is necessary to explain polarization in molecular clouds, but that a simple change in size distribution is not

Thermodynamics of adaptive molecular resolution.

PubMed

Delgado-Buscalioni, R

2016-11-13

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U (1) -U (0) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as 'real' thermodynamic variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Thermodynamics of adaptive molecular resolution

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, R.

2016-11-01

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U(1)-U(0). The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al., J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as `real' thermodynamic variables. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Application of bi-Helmholtz nonlocal elasticity and molecular simulations to the dynamical response of carbon nanotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koutsoumaris, C. Chr.; Tsamasphyros, G. J.; Vogiatzis, G. G.

2015-12-31

The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains anmore » open (albeit well-posed) problem.« less

Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

PubMed

Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

2016-01-01

Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

Cracking and adhesion at small scales: atomistic and continuum studies of flaw tolerant nanostructures

NASA Astrophysics Data System (ADS)

Buehler, Markus J.; Yao, Haimin; Gao, Huajian; Ji, Baohua