Science.gov

Sample records for dynamic molecular interactions

  1. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  2. Theoretical analysis of dynamic processes for interacting molecular motors

    NASA Astrophysics Data System (ADS)

    Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem

    2015-02-01

    Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  3. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro

    2012-01-01

    Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085

  4. Electron-phonon interaction within classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.

    2016-07-01

    We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.

  5. Electron-phonon interaction within classical molecular dynamics

    DOE PAGESBeta

    Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.

    2016-07-14

    Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

  6. Molecular dynamics simulation of complex plasmas: interaction of nonlinear waves

    NASA Astrophysics Data System (ADS)

    Durniak, Celine; Samsonov, Dmitry

    2008-11-01

    Complex plasmas consist of micron sized microspheres immersed into ordinary ion-electron plasmas. They exist in solid, liquid, gaseous states and exhibit a range of dynamic phenomena such as waves, solitons, phase transitions, heat transfer. These phenomena can be modelled in complex plasmas at the microscopic or ``molecular'' scale, which is almost impossible in ordinary solids and liquids. We simulate a monolayer complex plasma consisting of 3000 negatively-charged particles (or grains) with the help of molecular dynamics computer simulations. The equations of grain motion are solved using a 5^th order Runge Kutta method taking into account interaction of every grain with each other via a Yukawa potential. The grains are confined more strongly in the vertical direction than in the horizontal. After seeding the grains randomly the code is run until the equilibrium is reached as the grain kinetics energy reduces due to damping force equal to the neutral friction in the experiments and a monolayer crystal lattice is formed. Then we investigate interactions between nonlinear waves in a monolayer strongly coupled complex plasma moving in three dimensions. Different excitations are applied during a short time symmetrically on both sides of the lattice. Structural properties and nonlinear waves characteristics are examined as the pulses propagate across the complex plasma in opposite directions.

  7. Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions.

    PubMed

    Scholes, Natalie S; Weinzierl, Robert O J

    2016-05-01

    Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators. PMID:27175900

  8. Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions

    PubMed Central

    Scholes, Natalie S.; Weinzierl, Robert O. J.

    2016-01-01

    Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators. PMID:27175900

  9. Understanding Miltefosine-Membrane Interactions Using Molecular Dynamics Simulations.

    PubMed

    de Sá, Matheus Malta; Sresht, Vishnu; Rangel-Yagui, Carlota Oliveira; Blankschtein, Daniel

    2015-04-21

    Coarse-grained molecular dynamics simulations are used to calculate the free energies of transfer of miltefosine, an alkylphosphocholine anticancer agent, from water to lipid bilayers to study its mechanism of interaction with biological membranes. We consider bilayers containing lipids with different degrees of unsaturation: dipalmitoylphosphatidylcholine (DPPC, saturated, containing 0%, 10%, and 30% cholesterol), dioleoylphosphatidylcholine (DOPC, diunsaturated), palmitoyloleoylphosphatidylcholine (POPC, monounsaturated), diarachidonoylphosphatidylcholine (DAPC, polyunsaturated), and dilinoleylphosphatidylcholine (DUPC, polyunsaturated). These free energies, calculated using umbrella sampling, were used to compute the partition coefficients (K) of miltefosine between water and the lipid bilayers. The K values for the bilayers relative to that of pure DPPC were found to be 5.3 (DOPC), 7.0 (POPC), 1.0 (DAPC), 2.2 (DUPC), 14.9 (10% cholesterol), and 76.2 (30% cholesterol). Additionally, we calculated the free energy of formation of miltefosine-cholesterol complexes by pulling the surfactant laterally in the DPPC + 30% cholesterol system. The free energy profile that we obtained provides further evidence that miltefosine tends to associate with cholesterol and has a propensity to partition into lipid rafts. We also quantified the kinetics of the transport of miltefosine through the various bilayers by computing permeance values. The highest permeance was observed in DUPC bilayers (2.28 × 10(-2) m/s) and the lowest permeance in the DPPC bilayer with 30% cholesterol (1.10 × 10(-7) m/s). Our simulation results show that miltefosine does indeed interact with lipid rafts, has a higher permeability in polyunsaturated, loosely organized bilayers, and has higher flip-flop rates in specific regions of cellular membranes. PMID:25819781

  10. Evaluating Molecular Interactions in Polycaprolactone-Biomineralized Hydroxyapatite Nanocomposites using Steered Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Sharma, Anurag; Payne, Scott; Katti, Kalpana S.; Katti, Dinesh R.

    2015-04-01

    An experimental and modeling study of a complex nanoclay-based polymeric scaffold system is presented here. A representative molecular model of polymeric nanocomposite scaffold system for bone tissue engineering applications was developed. Polymeric scaffolds were synthesized using organically modified montmorillonite clay (OMMT) with biomineralized hydroxyapatite and polycaprolactone (OMMT-HAP-PCL). The OMMT-HAP-PCL representative model was constructed and validated using transmission electron microscopy, x-ray diffraction and material density results. We observed strong molecular interactions between OMMT, hydroxyapatite (HAP) and polycaprolactone (PCL) in the OMMT-HAP-PCL system. Attractive and repulsive interactions between PCL and different constituents of OMMT and HAP indicate influence of OMMT-HAP on PCL. Polymeric scaffolds were found to have improved nanomechanical properties as compared to pristine PCL due to the introduction of OMMT-HAP. Stress-strain response for the representative OMMT-HAP-PCL model was evaluated using constant force steered molecular dynamics (SMD) simulations. Two distinct stress-strain responses observed in the system indicate a two-phase nanomechanical behavior of OMMT-HAP-PCL obtained at low and high applied stresses. The results obtained from the MD and SMD simulations provide quantitative understanding of molecular interactions between different constituents of OMMT, HAP and PCL and mechanical response in the OMMT-HAP-PCL system.

  11. Molecular dynamics modeling of a nanomaterials-water surface interaction

    NASA Astrophysics Data System (ADS)

    Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid

    2016-04-01

    In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.

  12. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.

    PubMed

    Zhang, Wenjun; Wang, Ming L; Cranford, Steven W

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  13. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    PubMed Central

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  14. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  15. Molecular dynamics

    SciTech Connect

    Ladd, A.J.C.

    1988-08-01

    The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

  16. Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations.

    PubMed Central

    Shen, L; Bassolino, D; Stouch, T

    1997-01-01

    To probe the fundamentals of membrane/protein interactions, all-atom multi-nanosecond molecular dynamics simulations were conducted on a single transmembrane poly(32)alanine helix in a fully solvated dimyristoyphosphatidylcholine (DMPC) bilayer. The central 12 residues, which interact only with the lipid hydrocarbon chains, maintained a very stable helical structure. Helical regions extended beyond these central 12 residues, but interactions with the lipid fatty-acyl ester linkages, the lipid headgroups, and water molecules made the helix less stable in this region. The C and N termini, exposed largely to water, existed as random coils. As a whole, the helix tilted substantially, from perpendicular to the bilayer plane (0 degree) to a 30 degrees tilt. The helix experienced a bend at its middle, and the two halves of the helix at times assumed substantially different tilts. Frequent hydrogen bonding, of up to 0.7 ns in duration, occurred between peptide and lipid molecules. This resulted in correlated translational diffusion between the helix and a few lipid molecules. Because of the large variation in lipid conformation, the lipid environment of the peptide was not well defined in terms of "annular" lipids and on average consisted of 18 lipid molecules. When compared with a "neat" bilayer without peptide, no significant difference was seen in the bilayer thickness, lipid conformations or diffusion, or headgroup orientation. However, the lipid hydrocarbon chain order parameters showed a significant decrease in order, especially in those methylene groups closest to the headgroup. Images FIGURE 1 FIGURE 14 PMID:9199766

  17. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  18. DyNet: visualization and analysis of dynamic molecular interaction networks

    PubMed Central

    Goenawan, Ivan H.; Lynn, David J.

    2016-01-01

    Summary: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most ‘rewired’ nodes across many network states. Availability and Implementation: DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). Contact: david.lynn@sahmri.com. Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:27153624

  19. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    NASA Astrophysics Data System (ADS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B.

    2015-04-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations.

  20. Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations.

    PubMed

    Hedger, George; Sansom, Mark S P

    2016-10-01

    Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26946244

  1. A molecular dynamics study on slow ion interactions with the polycyclic aromatic hydrocarbon molecule anthracene

    SciTech Connect

    Postma, J.; Hoekstra, R.; Schlathölter, T.; Tielens, A. G. G. M.

    2014-03-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on analytical interaction potentials to model the interaction of low energy hydrogen and helium projectiles with isolated anthracene (C{sub 14}H{sub 10}) molecules. This approach allows for a very detailed investigation of the elastic interaction dynamics on an event by event basis. From the simulation data the threshold projectile kinetic energies above which direct C atom knock out sets in were determined. Anthracene differential energy transfer cross sections and total (dissociation) cross sections were computed for a wide range of projectile kinetic energies. The obtained results are interpreted in the context of PAH destruction in astrophysical environments.

  2. Molecular Dynamics Study on the Biophysical Interactions of Seven Green Tea Catechins with Cell Membranes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular dynamics simulations were performed to study the interactions of bioactive catechins (flavonoids) commonly found in green tea with lipid bilayers, as model for cell membranes. Previously, a number of experimental studies rationalized catechin’s anticarcinogenic, antibacterial, and other be...

  3. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

    PubMed

    Hardy, David J; Wolff, Matthew A; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D

    2016-03-21

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short. PMID:27004867

  4. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.

    2016-03-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.

  5. Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

    NASA Astrophysics Data System (ADS)

    Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

    2007-01-01

    The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are

  6. Multiscale modeling of dislocation-precipitate interactions in Fe: From molecular dynamics to discrete dislocations

    NASA Astrophysics Data System (ADS)

    Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J.

    2016-01-01

    The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2 <111 > {110 } edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.

  7. Multiscale modeling of dislocation-precipitate interactions in Fe: From molecular dynamics to discrete dislocations.

    PubMed

    Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J

    2016-01-01

    The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms. PMID:26871192

  8. Parallel implementation of three-dimensional molecular dynamic simulation for laser-cluster interaction

    SciTech Connect

    Holkundkar, Amol R.

    2013-11-15

    The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.

  9. Molecular mechanics and dynamics studies on the interaction of gallic acid with collagen-like peptides

    NASA Astrophysics Data System (ADS)

    Madhan, B.; Thanikaivelan, P.; Subramanian, V.; Raghava Rao, J.; Unni Nair, Balachandran; Ramasami, T.

    2001-10-01

    Molecular modelling approaches have been used to understand the interaction of collagen-like peptides with gallic acid, which mimic vegetable tanning processes involved in protein stabilization. Several interaction sites have been identified and the binding energies of the complexes have been calculated. The calculated binding energies for various geometries are in the range 6-13 kcal/mol. It is found that some complexes exhibit hydrogen bonding, and electrostatic interaction plays a dominant role in the stabilization of the peptide by gallic acid. The π-OH type of interaction is also observed in the peptide stabilization. Molecular dynamics (MD) simulation for 600 ps revealed the possibility of hydrogen bonding between the collagen-like peptide and gallic acid.

  10. Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties.

    PubMed

    Chakraborty, Chiranjib; Agrawal, Alok

    2013-11-01

    Serum C-reactive protein (CRP) is used as a marker of inflammation in several diseases including autoimmune disease and cardiovascular disease. CRP, a member of the pentraxin family, is comprised of five identical subunits. CRP has diverse ligand-binding properties which depend upon different structural states of CRP. However, little is known about the molecular dynamics and interaction properties of CRP. In this study, we used SAPS, SCRATCH protein predictor, PDBsum, ConSurf, ProtScale, Drawhca, ASAView, SCide and SRide server and performed comprehensive analyses of molecular dynamics, protein-protein and residue-residue interactions of CRP. We used 1GNH.pdb file for the crystal structure of human CRP which generated two pentamers (ABCDE and FGHIJ). The number of residues involved in residue-residue interactions between A-B, B-C, C-D, D-E, F-G, G-H, H-I, I-J, A-E and F-J subunits were 12, 11, 10, 11, 12, 11, 10, 11, 10 and 10, respectively. Fifteen antiparallel β sheets were involved in β-sheet topology, and five β hairpins were involved in forming the secondary structure. Analysis of hydrophobic segment distribution revealed deviations in surface hydrophobicity at different cavities present in CRP. Approximately 33 % of all residues were involved in the stabilization centers. We show that the bioinformatics tools can provide a rapid method to predict molecular dynamics and interaction properties of CRP. Our prediction of molecular dynamics and interaction properties of CRP combined with the modeling data based on the known 3D structure of CRP is helpful in designing stable forms of CRP mutants for structure-function studies of CRP and may facilitate in silico drug design for therapeutic targeting of CRP. PMID:23494263

  11. Computational Analysis of C-Reactive Protein for Assessment of Molecular Dynamics and Interaction Properties

    PubMed Central

    Agrawal, Alok

    2013-01-01

    Serum C-reactive protein (CRP) is used as a marker of inflammation in several diseases including autoimmune disease and cardiovascular disease. CRP, a member of the pentraxin family, is comprised of five identical subunits. CRP has diverse ligand-binding properties which depend upon different structural states of CRP. However, little is known about the molecular dynamics and interaction properties of CRP. In this study, we used SAPS, SCRATCH protein predictor, PDBsum, ConSurf, ProtScale, Drawhca, ASAView, SCide and SRide server and performed comprehensive analyses of molecular dynamics, protein–protein and residue–residue interactions of CRP. We used 1GNH.pdb file for the crystal structure of human CRP which generated two pentamers (ABCDE and FGHIJ). The number of residues involved in residue–residue interactions between A–B, B–C, C–D, D–E, F–G, G–H, H–I, I–J, A–E and F–J subunits were 12, 11, 10, 11, 12, 11, 10, 11, 10 and 10, respectively. Fifteen antiparallel β sheets were involved in β-sheet topology, and five β hairpins were involved in forming the secondary structure. Analysis of hydrophobic segment distribution revealed deviations in surface hydrophobicity at different cavities present in CRP. Approximately 33 % of all residues were involved in the stabilization centers. We show that the bioinformatics tools can provide a rapid method to predict molecular dynamics and interaction properties of CRP. Our prediction of molecular dynamics and interaction properties of CRP combined with the modeling data based on the known 3D structure of CRP is helpful in designing stable forms of CRP mutants for structure–function studies of CRP and may facilitate in silico drug design for therapeutic targeting of CRP. PMID:23494263

  12. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

    PubMed Central

    Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

    2015-01-01

    The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA. PMID:26140374

  13. Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations.

    PubMed

    Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A; Mostofian, Barmak; Kučerka, Norbert; Drazba, Paul; Katsaras, John

    2012-12-27

    Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol's molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup's phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules. PMID:23199292

  14. Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A; Mostofian, Barmak; Kucerka, Norbert; Drazba, Paul; Katsaras, John

    2012-01-01

    Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol s molecular interactions with ether lipids as determined using a combination of small-angle neutron and Xray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

  15. Molecular dynamics simulations of GPCR-cholesterol interaction: An emerging paradigm.

    PubMed

    Sengupta, Durba; Chattopadhyay, Amitabha

    2015-09-01

    G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and represent major targets in the development of novel drug candidates. Membrane cholesterol plays an important role in GPCR structure and function. Molecular dynamics simulations have been successful in exploring the effect of cholesterol on the receptor and a general consensus molecular view is emerging. We review here recent molecular dynamics studies at multiple resolutions highlighting the main features of cholesterol-GPCR interaction. Several cholesterol interaction sites have been identified on the receptor that are reminiscent of nonannular sites. These cholesterol hot-spots are highly dynamic and have a microsecond time scale of exchange with the bulk lipids. A few consensus sites (such as the CRAC site) have been identified that correspond to higher cholesterol interaction. Interestingly, high plasticity is observed in the modes of cholesterol interaction and several sites have been suggested to have high cholesterol occupancy. We therefore believe that these cholesterol hot-spots are indicative of 'high occupancy sites' rather than 'binding sites'. The results suggest that the energy landscape of cholesterol association with GPCRs corresponds to a series of shallow minima interconnected by low barriers. These specific interactions, along with general membrane effects, have been observed to modulate GPCR organization. Membrane cholesterol effects on receptor structure and organization, that in turn influences receptor cross-talk and drug efficacy, represent a new frontier in GPCR research. This article is part of a Special Issue entitled: Lipid-protein interactions. Guest Editors: Amitabha Chattopadhyay and Jean-Marie Ruysschaert. PMID:25817549

  16. NMR and molecular dynamics studies of the interaction of melatonin with calmodulin.

    PubMed

    Turjanski, Adrián G; Estrin, Darío A; Rosenstein, Ruth E; McCormick, John E; Martin, Stephen R; Pastore, Annalisa; Biekofsky, Rodolfo R; Martorana, Vincenzo

    2004-11-01

    Pineal hormone melatonin (N-acetyl-5-methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca(2+) concentration via activation of its G-protein-coupled membrane receptors, or through a direct interaction with calmodulin (CaM). The present work studies the direct interaction of melatonin with intact calcium-saturated CaM both experimentally, by fluorescence and nuclear magnetic resonance spectroscopies, and theoretically, by molecular dynamics simulations. The analysis of the experimental data shows that the interaction is calcium-dependent. The affinity, as obtained from monitoring (15)N and (1)H chemical shift changes for a melatonin titration, is weak (in the millimolar range) and comparable for the N- and C-terminal domains. Partial replacement of diamagnetic Ca(2+) by paramagnetic Tb(3+) allowed the measurement of interdomain NMR pseudocontact shifts and residual dipolar couplings, indicating that each domain movement in the complex is not correlated with the other one. Molecular dynamics simulations allow us to follow the dynamics of melatonin in the binding pocket of CaM. Overall, this study provides an example of how a combination of experimental and theoretical approaches can shed light on a weakly interacting system of biological and pharmacological significance. PMID:15498938

  17. NMR and molecular dynamics studies of the interaction of melatonin with calmodulin

    PubMed Central

    Turjanski, Adrián G.; Estrin, Darío A.; Rosenstein, Ruth E.; McCormick, John E.; Martin, Stephen R.; Pastore, Annalisa; Biekofsky, Rodolfo R.; Martorana, Vincenzo

    2004-01-01

    Pineal hormone melatonin (N-acetyl-5-methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca2+ concentration via activation of its G-protein–coupled membrane receptors, or through a direct interaction with calmodulin (CaM). The present work studies the direct interaction of melatonin with intact calcium-saturated CaM both experimentally, by fluorescence and nuclear magnetic resonance spectroscopies, and theoretically, by molecular dynamics simulations. The analysis of the experimental data shows that the interaction is calcium-dependent. The affinity, as obtained from monitoring 15N and 1H chemical shift changes for a melatonin titration, is weak (in the millimolar range) and comparable for the N- and C-terminal domains. Partial replacement of diamagnetic Ca2+ by paramagnetic Tb3+ allowed the measurement of interdomain NMR pseudocontact shifts and residual dipolar couplings, indicating that each domain movement in the complex is not correlated with the other one. Molecular dynamics simulations allow us to follow the dynamics of melatonin in the binding pocket of CaM. Overall, this study provides an example of how a combination of experimental and theoretical approaches can shed light on a weakly interacting system of biological and pharmacological significance. PMID:15498938

  18. PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts

    NASA Astrophysics Data System (ADS)

    Giorgino, Toni

    2014-03-01

    PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Script development takes place without leaving VMD, thus enabling an incremental try-see-modify development model for molecular metrics.

  19. Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

    NASA Astrophysics Data System (ADS)

    Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

    2012-10-01

    Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

  20. Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

    PubMed

    Ramya, L; Ramakrishnan, Vigneshwar

    2016-07-01

    Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. PMID:27492241

  1. Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

    NASA Astrophysics Data System (ADS)

    Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

    2013-07-01

    This paper extends the image charge solvation model (ICSM) [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated.

  2. Molecular dynamics simulation for ligand-receptor studies. Carbohydrates interactions in aqueous solutions.

    PubMed

    Grigera, J Raul

    2002-01-01

    The review deals with the problem of the study of ligand-receptor interactions and the use of Molecular Dynamics (MD) simulation to approach such a problem. After a short review of the fundamentals of MD we describe the medium in which all biology takes place, water. Emphasis is put on the water models appropriate for simulation of macromolecular systems explicitly including the water molecules. We consider the quality of the water model both in terms of simplicity and performance to describe the liquid water properties. Heavy water, although not a biologically viable medium, is considered since many experiments make use of it as a solvent. Sweetness of carbohydrates is considered as an example of the procedure suitable to characterize active sites on the ligands. Consideration is given to the computation of the binding constants through molecular dynamics. The computation of the Free Energy is described and illustrated. The potentiality of MD for studies of ligand-receptor interactions is limited by the computer resources, for even with large computing facilities the need of relatively long simulation times severely restricts the study of large systems. A method is described in which several shells are treated at different levels of approximation, form mechanical response and mean electrical field to quantum mechanics, through stochastic dynamics and atomic classical MD. The review closes with a brief account of the perspectives of the method. PMID:12052202

  3. Molecular dynamic and docking interaction study of Heterodera glycines serine proteinase with Vigna mungo proteinase inhibitor.

    PubMed

    Prasad, C V S Siva; Gupta, Saurabh; Gaponenko, Alex; Tiwari, Murlidhar

    2013-08-01

    Many plants do produce various defense proteins like proteinase inhibitors (PIs) to protect them against various pests. PIs function as pseudosubstrates of digestive proteinase, which inhibits proteolysis in pests and leads to amino acid deficiency-based mortality. This work reports the structural interaction studies of serine proteinase of Heterodera glycines (SPHG) with Vigna mungo proteinase inhibitor (VMPI). 3D protein structure modeling, validation of SPHG and VMPI, and their putative protein-protein binding sites were predicted. Protein-protein docking followed by molecular dynamic simulation was performed to find the reliable confirmation of SPHG-VMPI complex. Trajectory analysis of each successive conformation concludes better interaction of first loop in comparison with second loop. Lysine residues of first loop were actively participating in complex formation. Overall, this study discloses the structural aspects and interaction mechanisms of VMPI with SPHG, and it would be helpful in the development of pest-resistant genetically modified crops. PMID:23813339

  4. How does the molecular linker in dynamic force spectroscopy affect probing molecular interactions at the single-molecule level?

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Aizawa, Kota; Hanyu, Tatsuya; Hirano, Yuuichi; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-08-01

    Dynamic force spectroscopy (DFS) based on atomic force microscopy, which enables us to obtain information on the interaction potential between molecules such as antigen–antibody complexes at the single-molecule level, is a key technique for advancing molecular science and technology. However, to ensure the reliability of DFS measurement, its basic mechanism must be well understood. We examined the effect of the molecular linker used to fix the target molecule to the atomic force microscope cantilever, i.e., the force direction during measurement, for the first time, which has not been discussed until now despite its importance. The effect on the lifetime and barrier position, which can be obtained by DFS, was found to be ∼10 and ∼50%, respectively, confirming the high potential of DFS.

  5. How does the molecular linker in dynamic force spectroscopy affect probing molecular interactions at the single-molecule level?

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Aizawa, Kota; Hanyu, Tatsuya; Hirano, Yuuichi; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-08-01

    Dynamic force spectroscopy (DFS) based on atomic force microscopy, which enables us to obtain information on the interaction potential between molecules such as antigen-antibody complexes at the single-molecule level, is a key technique for advancing molecular science and technology. However, to ensure the reliability of DFS measurement, its basic mechanism must be well understood. We examined the effect of the molecular linker used to fix the target molecule to the atomic force microscope cantilever, i.e., the force direction during measurement, for the first time, which has not been discussed until now despite its importance. The effect on the lifetime and barrier position, which can be obtained by DFS, was found to be ˜10 and ˜50%, respectively, confirming the high potential of DFS.

  6. Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer

    NASA Astrophysics Data System (ADS)

    Srinivas, Goundla; Klein, Michael L.

    2004-01-01

    The interaction of surfactant diblock poly(ethylene oxide)-poly(ethylethylene) copolymers (PEO-PEE) with a lipid bilayer of dimyristoylphosphatidylcholine has been studied by means of coarse-grain molecular dynamics simulations. The effect of the surfactants on the lipid bilayer was studied over a wide range of diblock copolymer concentrations. The simulations show that the hydrophilic PEO chains adopt different structures at low and high concentrations. In particular, the computed density profiles reveal that the PEO chains extend over a longer range from the bilayer surface, with increasing copolymer concentration. The simulated density profiles are in agreement with the scaling law predictions.

  7. Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides* #

    PubMed Central

    Yu, Hua; Wang, Mao-Jun; Xuan, Nan-Xia; Shang, Zhi-Cai; Wu, Jun

    2015-01-01

    Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues. PMID:26465136

  8. Fluorescence Correlation Spectroscopy Simulations of Photophysical Phenomena and Molecular Interactions: A Molecular Dynamics/Monte Carlo Approach

    PubMed Central

    Dix, James A.; Hom, Erik F. Y.; Verkman, A. S.

    2011-01-01

    Fluorescence correlation spectroscopy (FCS) is being applied increasingly to study diffusion and interactions of fluorescently labeled macromolecules in complex biological systems. Fluctuations in detected fluorescence, δF(t), are expressed as time-correlation functions, G(τ), and photon-count histograms, P(k;ΔT). Here, we developed a generalized simulation approach to compute G(τ) and P(k;ΔT) for complex systems with arbitrary geometry, photophysics, diffusion, and macromolecular interactions. G(τ) and P(k;ΔT) were computed from δF(t) generated by a Brownian dynamics simulation of single-molecule trajectories followed by a Monte Carlo simulation of fluorophore excitation and detection statistics. Simulations were validated by comparing analytical and simulated G(τ) and P(k;ΔT) for diffusion of noninteracting fluorophores in a three-dimensional Gaussian excitation and detection volume. Inclusion of photobleaching and triplet-state relaxation produced significant changes in G(τ) and P(k;ΔT). Simulations of macromolecular interactions and complex diffusion were done, including transient fluorophore binding to an immobile matrix, cross-correlation analysis of interacting fluorophores, and anomalous sub- and superdiffusion. The computational method developed here is generally applicable for simulating FCS measurements on systems complicated by fluorophore interactions or molecular crowding, and experimental protocols for which G(τ) and P(k;ΔT) cannot be computed analytically. PMID:16471761

  9. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions

    NASA Astrophysics Data System (ADS)

    Shao, Qiang; Fan, Yubo; Yang, Lijiang; Qin Gao, Yi

    2012-03-01

    It is well known that alcohols can have strong effects on protein structures. For example, monohydric methanol and ethanol normally denature, whereas polyhydric glycol and glycerol protect, protein structures. In a recent combined theoretical and NMR experimental study, we showed that molecular dynamics simulations can be effectively used to understand the molecular mechanism of methanol denaturing protein. In this study, we used molecular dynamics simulations to investigate how alcohols with varied hydrophobicity and different numbers of hydrophilic groups (hydroxyl groups) exert effects on the structure of the model polypeptide, BBA5. First, we showed that methanol and trifluoroethanol (TFE) but not glycol or glycerol disrupt hydrophobic interactions. The latter two alcohols instead protect the assembly of the α- and β-domains of the polypeptide. Second, all four alcohols were shown to generally increase the stability of secondary structures, as revealed by the increased number of backbone hydrogen bonds formed in alcohol/water solutions compared to that in pure water, although individual hydrogen bonds can be weakened by certain alcohols, such as TFE. The two monohydric alcohols, methanol and TFE, display apparently different sequence-dependence in affecting the backbone hydrogen bond stability: methanol tends to enhance the stability of backbone hydrogen bonds of which the carbonyl groups are from polar residues, whereas TFE tends to stabilize those involving non-polar residues. These results demonstrated that subtle differences in the solution environment could have distinct consequences on protein structures.

  10. Molecular Dynamics Studies of Transportan 10 (Tp10) Interacting with a POPC Lipid Bilayer

    PubMed Central

    Dunkin, Christina M.; Pokorny, Antje; Almeida, Paulo F.; Lee, Hee-Seung

    2011-01-01

    We performed a series of molecular dynamics simulations to study the nature of interactions between transportan 10 (tp10) and a zwitterionic POPC bilayer. Tp10 is an amphipathic cell-penetrating peptide with a net positive charge of +5 and is known to adopt an α-helical secondary structure on the surface of POPC membranes. The study showed that tp10 preferentially binds to the membrane surface with its hydrophobic side facing the hydrophobic lipid core. Such orientation allows Lys residues, with positively charged long side chains, to stay in the polar environment during the insertion process. The simulations revealed that the Lys–phosphate salt bridge is a key factor in determining the orientation of the peptide in the interfacial region as well as in stabilizing the peptide-membrane interaction. The electrostatic attraction between Lys and phosphate groups is also believed to be the main bottleneck for the translocation of tp10 across the membrane. PMID:21194203

  11. Molecular dynamics simulation of interaction of H with vacancy in W

    SciTech Connect

    Li, Xiaochun; Gao, Fei; Lu, Guang-Hong

    2009-09-15

    Molecular dynamics simulations were performed to investigate the interaction between H and vacancy in W using an analytical bond-order potential to describe the interactions between W-W, W-H and H-H. The most stable configuration for H in W is the tetrahedron interstitial site. We calculated the binding energies of an H and a vacancy to an H-vacancy cluster (HnVm) in W, respectively, where n and m ranged from 0 to 10. The binding energy was almost unchanged. The binding energy of a vacancy to H-vacancy cluster is about 0.4eV, which is higher than the binding energy of an H to H-vacancy cluster. Vacancy is much easier to binding with H-vacancy cluster than H. And H is easier to stay in the tetrahedron interstitial site or octahedron interstitial site in bcc W.

  12. Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization.

    PubMed

    Chamachi, Neharika G; Chakrabarty, Suman

    2016-08-01

    The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% β-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present β-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of β-sheet extension) and the G131-V161 H-bond formation. PMID:27390876

  13. Interactions of borneol with DPPC phospholipid membranes: a molecular dynamics simulation study.

    PubMed

    Yin, Qianqian; Shi, Xinyuan; Ding, Haiou; Dai, Xingxing; Wan, Guang; Qiao, Yanjiang

    2014-01-01

    Borneol, known as a "guide" drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol's penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis) to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine) bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol's presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol's penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol. PMID:25383679

  14. Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment.

    PubMed

    Mayes, Heather B; Tian, Jianhui; Nolte, Michael W; Shanks, Brent H; Beckham, Gregg T; Gnanakaran, S; Broadbelt, Linda J

    2014-02-27

    In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose. PMID:24308866

  15. Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields.

    PubMed

    Mangiatordi, Giuseppe Felice; Alberga, Domenico; Siragusa, Lydia; Goracci, Laura; Lattanzi, Gianluca; Nicolotti, Orazio

    2015-07-01

    Neuromyelitis optica (NMO) is a multiple sclerosis-like immunopathology disease affecting optic nerves and the spinal cord. Its pathological hallmark is the deposition of a typical immunoglobulin, called NMO-IgG, against the water channel Aquaporin-4 (AQP4). Preventing NMO-IgG binding would represent a valuable molecular strategy for a focused NMO therapy. The recent observation that aspartate in position 69 (D69) is determinant for the formation of NMO-IgG epitopes prompted us to carry out intensive Molecular Dynamics (MD) studies on a number of single-point AQP4 mutants. Here, we report a domino effect originating from the point mutation at position 69: we find that the side chain of T62 is reoriented far from its expected position leaning on the lumen of the pore. More importantly, the strength of the H-bond interaction between L53 and T56, at the basis of the loop A, is substantially weakened. These events represent important pieces of a clear-cut mechanistic rationale behind the failure of the NMO-IgG binding, while the water channel function as well as the propensity to aggregate into OAPs remains unaltered. The molecular interaction fields (MIF)-based analysis of cavities complemented MD findings indicating a putative binding site comprising the same residues determining epitope reorganization. In this respect, docking studies unveiled an intriguing perspective to address the future design of small drug-like compounds against NMO. In agreement with recent experimental observations, the present study is the first computational attempt to elucidate NMO-IgG binding at the molecular level, as well as a first effort toward a less elusive AQP4 druggability. PMID:25839357

  16. Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

    2015-12-01

    Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle-particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle-particle interaction and high surface diffusion result in the formation of particle-particle bonds of 2 nm TiO2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO2 nanoparticles.

  17. Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations.

    PubMed

    Méndez-Luna, D; Martínez-Archundia, M; Maroun, Rachid C; Ceballos-Reyes, G; Fragoso-Vázquez, M J; González-Juárez, D E; Correa-Basurto, J

    2015-01-01

    The G-protein coupled estrogen receptor 1 GPER/GPR30 is a transmembrane seven-helix (7TM) receptor involved in the growth and proliferation of breast cancer. Due to the absence of a crystal structure of GPER/GPR30, in this work, molecular modeling studies have been carried out to build a three-dimensional structure, which was subsequently refined by molecular dynamics (MD) simulations (up to 120 ns). Furthermore, we explored GPER/GPR30's molecular recognition properties by using reported agonist ligands (G1, estradiol (E2), tamoxifen, and fulvestrant) and the antagonist ligands (G15 and G36) in subsequent docking studies. Our results identified the E2 binding site on GPER/GPR30, as well as other receptor cavities for accepting large volume ligands, through GPER/GPR30 π-π, hydrophobic, and hydrogen bond interactions. Snapshots of the MD trajectory at 14 and 70 ns showed almost identical binding motifs for G1 and G15. It was also observed that C107 interacts with the acetyl oxygen of G1 (at 14 ns) and that at 70 ns the residue E275 interacts with the acetyl group and with the oxygen from the other agonist whereas the isopropyl group of G36 is oriented toward Met141, suggesting that both C107 and E275 could be involved in the protein activation. This contribution suggest that GPER1 has great structural changes which explain its great capacity to accept diverse ligands, and also, the same ligand could be recognized in different binding pose according to GPER structural conformations. PMID:25587872

  18. Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes.

    PubMed

    Chen, Chuanying; Esadze, Alexandre; Zandarashvili, Levani; Nguyen, Dan; Montgomery Pettitt, B; Iwahara, Junji

    2015-07-16

    Intermolecular ion pairs (salt bridges) are crucial for protein-DNA association. For two protein-DNA complexes, we demonstrate that the ion pairs of protein side-chain NH3+ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-μs molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP-SIP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins. PMID:26207171

  19. Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein–DNA Complexes

    PubMed Central

    2015-01-01

    Intermolecular ion pairs (salt bridges) are crucial for protein–DNA association. For two protein–DNA complexes, we demonstrate that the ion pairs of protein side-chain NH3+ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-μs molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP–SIP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins. PMID:26207171

  20. Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis

    PubMed Central

    Wang, Yonghua; Li, Yan; Ma, Zhi; Yang, Wei; Ai, Chunzhi

    2010-01-01

    MicroRNAs (miRNAs) are endogenously produced ∼21-nt riboregulators that associate with Argonaute (Ago) proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target) and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1) three important (PAZ, Mid and PIWI) domains exist in Argonaute which define the global dynamics of the protein; 2) the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3) it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5′-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg2+) plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA). Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago. PMID:20686687

  1. Distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of three distal mutants.

    PubMed Central

    Jewsbury, P; Kitagawa, T

    1995-01-01

    Six 90-ps molecular dynamics trajectories, two for each of three distal mutants of sperm whale carbonmonoxy myoglobin, are reported; solvent waters within 16 A of the active site have been included. In both His64GIn trajectories, the distal side chain remains part of the heme pocket, forming a "closed" conformation similar to that of the wild type 64N delta H tautomer. Despite a connectivity more closely resembling the N epsilon H histidine tautomer, close interactions with the carbonyl ligand similar to those observed for the wild type 64N epsilon H tautomer are prevented in this mutant by repulsive interactions between the carbonyl O and the 64O epsilon. The aliphatic distal side chain of the His64Leu mutant shows little interaction with the carbonyl ligand in either His64Leu trajectory. Solvent water molecules move into and out of the active site in the His64Gly mutant trajectories; during all the other carbonmonoxy myoglobin trajectories, including the wild type distal tautomers considered in an earlier work, solvent molecules rarely encroach closer than 6 A of the active site. These results are consistent with a recent structural interpretation of the wild type infrared spectrum, and the current reinterpretation that the distal-ligand interaction in carbonmonoxy myoglobin is largely electrostatic, not steric, in nature. Images FIGURE 5 FIGURE 7 PMID:7787018

  2. Molecular dynamics of interactions of rice with rice blast and sheath blight pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In an effort to develop the molecular strategies to control rice (Oryzae sativa) diseases, molecular interactions of rice with rice blast [Magnaporthe oryzae, formerly (Magnaporthe grisea] and sheath blight (Rhizoctonia solani) fungi were analyzed. The interaction of rice with M. oryzae follows a b...

  3. Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes

    PubMed Central

    Olausson, Bjoern E.S.; Grossfield, Alan; Pitman, Michael C.; Brown, Michael F.; Feller, Scott E.; Vogel, Alexander

    2012-01-01

    We present a detailed analysis of the behavior of the highly flexible post-translational lipid modifications of rhodopsin from multiple-microsecond all-atom molecular dynamics simulations. Rhodopsin was studied in a realistic membrane environment that includes cholesterol, as well as saturated and polyunsaturated lipids with phosphocholine and phosphoethanolamine headgroups. The simulation reveals striking differences between the palmitoylations at Cys322 and Cys323 as well as between the palmitoyl chains and the neighboring lipids. Notably the palmitoyl group at Cys322 shows considerably greater contact with helix H1 of rhodopsin, yielding frequent chain upturns with longer reorientational correlation times, and relatively low order parameters. While the palmitoylation at Cys323 makes fewer protein contacts and has increased order compared to Cys322, it nevertheless exhibits greater flexibility with smaller order parameters than the stearoyl chains of the surrounding lipids. The dynamical structure of the palmitoylations—as well as their extensive fluctuations—suggests a complex function for the post-translational modifications in rhodopsin and potentially other G protein-coupled receptors, going beyond their role as membrane anchoring elements. Rather, we propose that the palmitoylation at Cys323 has a potential role as a lipid anchor, whereas the palmitoyl-protein interaction observed for Cys322 suggests a more specific interaction that affects the stability of the dark state of rhodopsin. PMID:22280374

  4. Molecular Dynamics Study of the Interactions Between Minerals and Gas Hydrate Species

    NASA Astrophysics Data System (ADS)

    Kvamme, B.; Leirvik, K. N.; Olsen, R.; Kuznetsova, T.

    2014-12-01

    The need for knowledge on gas hydrate "host" and "guest" interactions with reservoir rocks comes from the two folded exploitation of gas hydrates. On one hand natural gas hydrates represent an immense energy source, on the other hand carbon sequestration in the form of CO2 hydrates represents a long-term storage of carbon dioxide. Whether one's goal is to extract methane from natural gas hydrates or store carbon dioxide in the form of hydrates, it requires an understanding of the complex phenomena involving coupled dynamics of hydrates and hydrate stability in porous media. Hydrates can never attach directly to solid mineral surfaces because of the incompatibility of charges between the mineral surfaces and the hydrates. However, adsorption of water and carbon dioxide on mineral surfaces may favor heterogeneous nucleation of hydrate in the immediate vicinity. Different surfaces have their own specific adsorption preferences and corresponding adsorption thermodynamics. We have selected calcite, a common mineral found in porous media. Using molecular dynamics we have initially focused on the water interface in order to evaluate the "host" interactions towards the surface. We also aimed at evaluating the model before including guest molecules.

  5. Structure and Dynamics of Antifreeze Protein--Model Membrane Interactions: A Combined Spectroscopic and Molecular Dynamics Study.

    PubMed

    Kar, Rajiv K; Mroue, Kamal H; Kumar, Dinesh; Tejo, Bimo A; Bhunia, Anirban

    2016-02-11

    Antifreeze proteins (AFPs) are the key biomolecules that enable species to survive under subzero temperature conditions. The physiologically relevant activities of AFPs are based on the adsorption to ice crystals, followed by the inhibition of subsequent crystal layer growth of ice, routed with depression in freezing point in a noncolligative manner. The functional attributes governing the mechanism by which AFPs inhibit freezing of body fluids in bacteria, fungi, plants, and fishes are mainly attributed to their adsorption onto the surface of ice within the physiological system. Importantly, AFPs are also known for their application in cryopreservation of biological samples that might be related to membrane interaction. To date, there is a paucity of information detailing the interaction of AFPs with membrane structures. Here, we focus on elucidating the biophysical properties of the interactions between AFPs and micelle models that mimic the membrane system. Micelle model systems of zwitterionic DPC and negatively charged SDS were utilized in this study, against which a significant interaction is experienced by two AFP molecules, namely, Peptide 1m and wfAFP (the popular AFP sourced from winter flounder). Using low- and high-resolution biophysical characterization techniques, such as circular dichroism (CD) and NMR spectroscopy, a strong evidence for the interactions of these AFPs with the membrane models is revealed in detail and is corroborated by in-depth residue-specific information derived from molecular dynamics simulation. Altogether, these results not only strengthen the fact that AFPs interact actively with membrane systems, but also demonstrate that membrane-associated AFPs are dynamic and capable of adopting a number of conformations rendering fluidity to the system. PMID:26785292

  6. CF interaction with Si(1 0 0)-(2 × 1): Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Gou, F.; Gleeson, M. A.; Kleyn, A. W.

    2007-01-01

    In this study, the interaction of CF with the clean Si(1 0 0)-(2 × 1) surface at normal incidence and room temperature was investigated using molecular dynamics simulation. Incident energies of 2, 12 and 50 eV were simulated. C atoms, arising from dissociation, preferentially react with Si to form Si-C bonds. A Si xC yF z interfacial layer is formed, but no etching is observed. The interfacial layer thickness increases with increasing incident energy, mainly through enhanced penetration of the silicon lattice. Silicon carbide and fluorosilyl species are formed at 50 eV, which is in good agreement with available experimental data. The level of agreement between the simulated and experimental results is discussed.

  7. Shock wave interactions with nano-structured materials: a molecular dynamics approach

    NASA Astrophysics Data System (ADS)

    Al-Qananwah, A. K.; Koplik, J.; Andreopoulos, Y.

    2013-02-01

    Porous materials have long been known to be effective in blast mitigation strategies. Nano-structured materials appear to have an even greater potential for blast mitigation because of their high surface-to-volume ratio, a geometric factor which substantially attenuates shock wave propagation. A molecular dynamics approach was used to explore the effects of this remarkable property on the behavior of traveling shocks impacting on solid materials. The computational setup included a moving piston, a gas region, and a target solid wall with and without a porous structure. The materials involved were represented by realistic interaction potentials. The results indicate that the presence of a nano-porous material layer in front of the target wall reduced the stress magnitude and the energy deposited inside the solid by about 30 %, while at the same time substantially decreasing the loading rate.

  8. Characterization of monobody scaffold interactions with ligand via force spectroscopy and steered molecular dynamics.

    PubMed

    Cheung, Luthur Siu-Lun; Shea, Daniel J; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos

    2015-01-01

    Monobodies are antibody alternatives derived from fibronectin that are thermodynamically stable, small in size, and can be produced in bacterial systems. Monobodies have been engineered to bind a wide variety of target proteins with high affinity and specificity. Using alanine-scanning mutagenesis simulations, we identified two scaffold residues that are critical to the binding interaction between the monobody YS1 and its ligand, maltose-binding protein (MBP). Steered molecular dynamics (SMD) simulations predicted that the E47A and R33A mutations in the YS1 scaffold substantially destabilize the YS1-MBP interface by reducing the bond rupture force and the lifetime of single hydrogen bonds. SMD simulations further indicated that the R33A mutation weakens the hydrogen binding between all scaffold residues and MBP and not just between R33 and MBP. We validated the simulation data and characterized the effects of mutations on YS1-MBP binding by using single-molecule force spectroscopy and surface plasmon resonance. We propose that interfacial stability resulting from R33 of YS1 stacking with R344 of MBP synergistically stabilizes both its own bond and the interacting scaffold residues of YS1. Our integrated approach improves our understanding of the monobody scaffold interactions with a target, thus providing guidance for the improved engineering of monobodies. PMID:25650239

  9. Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Cheung, Luthur Siu-Lun; Shea, Daniel J.; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos

    2015-02-01

    Monobodies are antibody alternatives derived from fibronectin that are thermodynamically stable, small in size, and can be produced in bacterial systems. Monobodies have been engineered to bind a wide variety of target proteins with high affinity and specificity. Using alanine-scanning mutagenesis simulations, we identified two scaffold residues that are critical to the binding interaction between the monobody YS1 and its ligand, maltose-binding protein (MBP). Steered molecular dynamics (SMD) simulations predicted that the E47A and R33A mutations in the YS1 scaffold substantially destabilize the YS1-MBP interface by reducing the bond rupture force and the lifetime of single hydrogen bonds. SMD simulations further indicated that the R33A mutation weakens the hydrogen binding between all scaffold residues and MBP and not just between R33 and MBP. We validated the simulation data and characterized the effects of mutations on YS1-MBP binding by using single-molecule force spectroscopy and surface plasmon resonance. We propose that interfacial stability resulting from R33 of YS1 stacking with R344 of MBP synergistically stabilizes both its own bond and the interacting scaffold residues of YS1. Our integrated approach improves our understanding of the monobody scaffold interactions with a target, thus providing guidance for the improved engineering of monobodies.

  10. Molecular Dynamics Simulation of Shock Waves Interacting with Nano-structures

    NASA Astrophysics Data System (ADS)

    Alqananwah, Ahmad; Koplik, Joel; Andreopoulos, Yiannis

    2009-11-01

    Typical theoretical treatments of shock wave interactions are based on a continuum approach, which cannot resolve the spatial variations in solids with nano-scale porous structure. To investigate such interactions we have developed a molecular dynamics simulation model, based on Lennard-Jones interactions. A piston, modeled as a uni-directional repulsive force field translating at a prescribed velocity, impinges on a region of gas which is compressed to form a shock, which in turn is driven against an atomistic solid wall. Periodic boundary conditions are used in the directions orthogonal to the piston motion, and we have considered solids based on either atoms tethered to lattice sites by stiff springs, or on embedded atom potentials. Velocity, temperature and stress fields are computed locally in both gas and solid regions, and displacements within the solid are interpreted in terms of its elastic constants. In this talk we present preliminary results, and the longer-term goal of this work is to understand energy transport and absorption in porous materials.

  11. A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

    PubMed

    Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon

    2014-01-01

    With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude. PMID:25340458

  12. Capsaicin interaction with TRPV1 channels in a lipid bilayer: molecular dynamics simulation.

    PubMed

    Hanson, Sonya M; Newstead, Simon; Swartz, Kenton J; Sansom, Mark S P

    2015-03-24

    Transient receptor potential vanilloid subtype 1 (TRPV1) is a heat-sensitive ion channel also involved in pain sensation, and is the receptor for capsaicin, the active ingredient of hot chili peppers. The recent structures of TRPV1 revealed putative ligand density within the S1 to S4 voltage-sensor-like domain of the protein. However, questions remain regarding the dynamic role of the lipid bilayer in ligand binding to TRPV1. Molecular dynamics simulations were used to explore behavior of capsaicin in a 1-palmitoyl-2-oleoyl phosphatidylcholine bilayer and with the target S1-S4 transmembrane helices of TRPV1. Equilibrium simulations reveal a preferred interfacial localization for capsaicin. We also observed a capsaicin molecule flipping from the extracellular to the intracellular leaflet, and subsequently able to access the intracellular TRPV1 binding site. Calculation of the potential of mean force (i.e., free energy profile) of capsaicin along the bilayer normal confirms that it prefers an interfacial localization. The free energy profile indicates that there is a nontrivial but surmountable barrier to the flipping of capsaicin between opposing leaflets of the bilayer. Molecular dynamics of the S1-S4 transmembrane helices of the TRPV1 in a lipid bilayer confirm that Y511, known to be crucial to capsaicin binding, has a distribution along the bilayer normal similar to that of the aromatic group of capsaicin. Simulations were conducted of the TRPV1 S1-S4 transmembrane helices in the presence of capsaicin placed in the aqueous phase, in the lipid, or docked to the protein. No stable interaction between ligand and protein was seen for simulations initiated with capsaicin in the bilayer. However, interactions were seen between TRPV1 and capsaicin starting from the cytosolic aqueous phase, and capsaicin remained stable in the majority of simulations from the docked pose. We discuss the significance of capsaicin flipping from the extracellular to the intracellular

  13. Molecular Dynamics Simulations of Amyloid β-Peptide (1-42): Tetramer Formation and Membrane Interactions.

    PubMed

    Brown, Anne M; Bevan, David R

    2016-09-01

    The aggregation cascade and peptide-membrane interactions of the amyloid β-peptide (Aβ) have been implicated as toxic events in the development and progression of Alzheimer's disease. Aβ42 forms oligomers and ultimately plaques, and it has been hypothesized that these oligomeric species are the main toxic species contributing to neuronal cell death. To better understand oligomerization events and subsequent oligomer-membrane interactions of Aβ42, we performed atomistic molecular-dynamics (MD) simulations to characterize both interpeptide interactions and perturbation of model membranes by the peptides. MD simulations were utilized to first show the formation of a tetramer unit by four separate Aβ42 peptides. Aβ42 tetramers adopted an oblate ellipsoid shape and showed a significant increase in β-strand formation in the final tetramer unit relative to the monomers, indicative of on-pathway events for fibril formation. The Aβ42 tetramer unit that formed in the initial simulations was used in subsequent MD simulations in the presence of a pure POPC or cholesterol-rich raft model membrane. Tetramer-membrane simulations resulted in elongation of the tetramer in the presence of both model membranes, with tetramer-raft interactions giving rise to the rearrangement of key hydrophobic regions in the tetramer and the formation of a more rod-like structure indicative of a fibril-seeding aggregate. Membrane perturbation by the tetramer was manifested in the form of more ordered, rigid membranes, with the pure POPC being affected to a greater extent than the raft membrane. These results provide critical atomistic insight into the aggregation pathway of Aβ42 and a putative toxic mechanism in the pathogenesis of Alzheimer's disease. PMID:27602722

  14. Interaction of dislocations with carbides in BCC Fe studied by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Granberg, F.; Terentyev, D.; Nordlund, K.

    2015-05-01

    In this study, the atomic processes involving the interaction of an edge dislocation with carbide precipitates in an iron matrix are investigated by molecular dynamics, utilizing two interatomic potentials (Hepburn, 2008 and Henriksson, 2013). The carbides investigated were Fe3 C and M23C6, where M was either Fe or Cr. The results from spherical precipitates were compared with rod shaped obstacles, to investigate the effect of climb in the unpinning process and the stress related to this process. The rod simulations showed a higher unpinning stress for all investigated sizes and temperatures, which indicates that climb will play a role in the unpinning phenomenon. The results showed, as previous studies, a decrease of the unpinning stress with increasing temperature and that a larger obstacle yields a higher unpinning stress. The Orowan process of dislocation unpinning was observed with both potentials as an increase in the needed unpinning stress in consecutive interactions with the same obstacle. The results showed that the structure of the obstacle does not affect the unpinning stress, as much as temperature, for obstacles ⩾ 2 nm. Comparison of obstacles with the same structure but with different composition, Fe23C6 and Cr23C6, showed that the small shearable chromium carbides were stronger than the corresponding iron carbides, pointing to the importance of the chemical composition of the carbide.

  15. Interaction of the Disaccharide Trehalose with a Phospholipid Bilayer: A Molecular Dynamics Study

    PubMed Central

    Pereira, Cristina S.; Lins, Roberto D.; Chandrasekhar, Indira; Freitas, Luiz Carlos G.; Hünenberger, Philippe H.

    2004-01-01

    The disaccharide trehalose is well known for its bioprotective properties. Produced in large amounts during stress periods in the life of organisms able to survive potentially damaging conditions, trehalose plays its protective role by stabilizing biostructures such as proteins and lipid membranes. In this study, molecular dynamics simulations are used to investigate the interaction of trehalose with a phospholipid bilayer at atomistic resolution. Simulations of the bilayer in the absence and in the presence of trehalose at two different concentrations (1 or 2 molal) are carried out at 325 K and 475 K. The results show that trehalose is able to minimize the disruptive effect of the elevated temperature and stabilize the bilayer structure. At both temperature, trehalose is found to interact directly with the bilayer through hydrogen bonds. However, the water molecules at the bilayer surface are not completely replaced. At high temperature, the protective effect of trehalose is correlated with a significant increase in the number of trehalose-bilayer hydrogen bonds, predominantly through an increase in the number of trehalose molecules bridging three or more lipid molecules. PMID:15041666

  16. Three-Dimensional FRET Reconstruction Microscopy for Analysis of Dynamic Molecular Interactions in Live Cells

    PubMed Central

    Hoppe, Adam D.; Shorte, Spencer L.; Swanson, Joel A.; Heintzmann, Rainer

    2008-01-01

    Analysis of cellular pathways requires concentration measurements of dynamically interacting molecules within the three-dimensional (3D) space of single living cells. Förster resonance energy transfer (FRET) microscopy from widefield, from confocal, and potentially from superresolution microscopes can access this information; however, these measurements are distorted by the inherent 3D blurring of optical imaging, spectral overlap of fluorophores, and detection noise. We propose a mathematical model of these processes and demonstrate, through simulation, how these distortions limit the dynamic range and sensitivity of conventional FRET microscopy. Using this model, we devise and validate a new approach (called 3D-FRET stoichiometry reconstruction, 3DFSR) for reconstructing 3D distributions of bound and free fluorescent molecules. Previous attempts to reconstruct 3D-FRET data relied on sequential spectral unmixing and deconvolution, a process that corrupts the detection statistics. We demonstrate that 3DFSR is superior to these approaches since it simultaneously models spectral mixing, optical blurring, and detection noise. To achieve the full potential of this technique, we developed an instrument capable of acquiring 3D-FRET data rapidly and sensitively from single living cells. Compared with conventional FRET microscopy, our 3D-FRET reconstruction technique and new instrumentation provides orders of magnitude gains in both sensitivity and accuracy wherein sustained high-resolution four-dimensional (x,y,z,t) imaging of molecular interactions inside living cells was achieved. These results verify previous observations that Cdc42 signaling is localized to the advancing margins of forming phagosomes in macrophages. PMID:18339754

  17. Molecular Dynamics Study of Interaction between Acrylamide Copolymers and Alumina Crystal

    NASA Astrophysics Data System (ADS)

    Wang, Feng-he; Wang, Feng-yun; Gong, Xue-dong

    2012-10-01

    Four acrylamide polymer flocculants, anionic polyacrylamide P(AA-co-AM), cationic polyacrylamide P(DMB-co-AM), nonionic polyacrylamide P(AM), and hydrophobical polyacrylamide P(OA-co-AM) have been prepared by copolymerizing with acrylic acid, cationic monomer dimethylethyl (acryloxyethyl) ammonium bromide (DMB) and hydrophobical monomer octadecyl acrylate with acrylamide. The interactions between the flocculants with the (012) surface of alumina crystal (Al2O3) have been simulated by molecular dynamics method. All the polymers can bind tightly with Al2O3 crystal, the interaction between the O of polymers and Al of the (012) surface of Al2O3 is significantly strong. The order of binding energy is as follows: P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), implying a better flocculation performance of P(DMB-co-AM) than the others. Analysis indicates that binding energy is mainly determined by Coulomb interaction. Bonds are found between the O atoms of the polymers and the Al atoms of Al2O3. The polymers' structures deform when they combine with Al2O3 crystal, but the deformation energies are low and far less than non-bonding energies. Flocculation experiments in suspension medium of 1%Kaolin show a transmittancy of 90.8% for 6 mg/L P(DMB-co-AM) and 73.0% for P(AM). The sequence of flocculation performance of four polymers is P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), which is in excellent agreement with the simulation results of binding energy.

  18. Estimation of the mutual orientation and intermolecular interaction of C12Ex from molecular dynamics simulations.

    PubMed

    Velinova, Maria; Tsoneva, Yana; Ivanova, Anela; Tadjer, Alia

    2012-04-26

    Nonionic surfactants, such as poly(ethylene glycol) alkyl ethers (abbreviated as CyEx) show a rich phase behavior in aqueous solution, i.e., they form micellar, lamellar, cubic, and so forth phases depending on experimental parameters such as the hydrophobic and hydrophilic chain lengths, temperature, or concentration. The aim of the present study is to determine the nature of the preaggregates, which are inferred to exist before the actual self-assembly process in aqueous solution, and to assess the aptitude to their formation. The target molecules are C12E3, C12E4 and C12E5, surfactants of moderate water solubility. Coarse-grained and all-atom molecular dynamics simulations (NPT/293 K) of two molecules of each species with explicit water in periodic boundary conditions are carried out to estimate the mutual orientation and the interaction between the surfactants in their dimers. The force fields are MARTINI and Amber99, the latter with self-derived parameters for the ether groups. The change in the orientation and distance between the molecules in the dimers are discussed based on different structural parameters. In addition, the interaction between the surfactants is evaluated from quantum chemistry calculations in terms of binding energy for the average structures from the cluster analysis. The solvent-solute interaction is quantified by the mean number of hydrogen bonds formed between them. On the basis of combined analysis, a series of different structures for subsequent study of the possible self-assembly patterns of C12E3, C12E4, and C12E5 is outlined. PMID:22448734

  19. Molecular dynamics investigation of the interaction of dislocations with carbides in BCC Fe

    NASA Astrophysics Data System (ADS)

    Granberg, F.; Terentyev, D.; Nordlund, K.

    2015-06-01

    Different types of carbides are present in many steels used as structural materials. To safely use steel in demanding environments, like nuclear power plants, it is important to know how defects will affect the mechanical properties of the material. In this study, the effect of carbide precipitates on the edge dislocation movement is investigated. Three different types of carbides were investigated by means of molecular dynamics, with a Tersoff-like bond order interatomic potential by Henriksson et al. The obstacles were 4 nm in diameter and were of Fe3C- (cementite-), Fe23C6- and Cr23C6-type. The critical unpinning stress was calculated for each type at different temperatures, to get the temperature-dependent obstacle strength. The results showed a decreasing critical stress with increasing temperature, consistent with previous studies. The critical unpinning stress was seen to be dependent on the type of carbide, but the differences were small. A difference was also observed between the obstacles with the same structure, but with different composition. This study shows the relation between the existing Cr23C6 carbide and the experimentally non-existing Fe23C6 carbide, which needs to be used as a model system for investigations with interatomic potentials not able to describe the interaction of Cr in the Fe-C-system. We found the difference to be a between 7% and 10% higher critical unpinning stress for the chromium carbide, than for the iron carbide of the same type.

  20. Dynamic, mechanistic, molecular-level modelling of cyanobacteria: Anabaena and nitrogen interaction.

    PubMed

    Hellweger, Ferdi L; Fredrick, Neil D; McCarthy, Mark J; Gardner, Wayne S; Wilhelm, Steven W; Paerl, Hans W

    2016-09-01

    Phytoplankton (eutrophication, biogeochemical) models are important tools for ecosystem research and management, but they generally have not been updated to include modern biology. Here, we present a dynamic, mechanistic, molecular-level (i.e. gene, transcript, protein, metabolite) model of Anabaena - nitrogen interaction. The model was developed using the pattern-oriented approach to model definition and parameterization of complex agent-based models. It simulates individual filaments, each with individual cells, each with genes that are expressed to yield transcripts and proteins. Cells metabolize various forms of N, grow and divide, and differentiate heterocysts when fixed N is depleted. The model is informed by observations from 269 laboratory experiments from 55 papers published from 1942 to 2014. Within this database, we identified 331 emerging patterns, and, excluding inconsistencies in observations, the model reproduces 94% of them. To explore a practical application, we used the model to simulate nutrient reduction scenarios for a hypothetical lake. For a 50% N only loading reduction, the model predicts that N fixation increases, but this fixed N does not compensate for the loading reduction, and the chlorophyll a concentration decreases substantially (by 33%). When N is reduced along with P, the model predicts an additional 8% reduction (compared to P only). PMID:27059435

  1. Electrostatic unfolding and interactions of albumin driven by pH changes: a molecular dynamics study.

    PubMed

    Baler, K; Martin, O A; Carignano, M A; Ameer, G A; Vila, J A; Szleifer, I

    2014-01-30

    A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation. PMID:24393011

  2. Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study

    PubMed Central

    2015-01-01

    A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation. PMID:24393011

  3. Interactions of fatty acids with phosphatidylethanolamine membranes: X-ray diffraction and molecular dynamics studies

    PubMed Central

    Cordomí, Arnau; Prades, Jesús; Frau, Juan; Vögler, Oliver; Funari, Sérgio S.; Perez, Juan J.; Escribá, Pablo V.; Barceló, Francisca

    2010-01-01

    An experimental and theoretical study on 1,2-dielaidoyl-sn-glycero-3-phosphoethanolamine (DEPE) membranes containing fatty acids (FAs) was performed by means of X-ray diffraction analysis and molecular dynamics (MD) simulations. The study was aimed at understanding the interactions of several structurally related FAs with biomembranes, which is necessary for further rational lipid drug design in membrane-lipid therapy. The main effect of FAs was to promote the formation of a HII phase, despite a stabilization of the coexisting Lα + HII phases. Derivatives of OA exhibited a specific density profile in the direction perpendicular to the bilayer that reflects differences in the relative localization of the carboxylate group within the polar region of the membrane as well as in the degree of membrane penetration of the FA acyl chain. Hydroxyl and methyl substituents at carbon-2 in the FA acyl chain were identified as effective modulators of the position of carboxylate group in the lipid bilayer. Our data highlight the specific potential of each FA in modulating the membrane structure properties. PMID:19965616

  4. Binding interaction of SGLT with sugar and thiosugar by the molecular dynamics simulation.

    PubMed

    Tamura, Yunoshin; Miyagawa, Hiroh; Yoshida, Tatsusada; Chuman, Hiroshi

    2015-11-01

    The human sodium-glucose co-transporter 2 (hSGLT2) is a transporter responsible for reabsorption of glucose in the proximal convoluted tubule of the kidney. hSGLT2 inhibitors, including luseogliflozin, have been developed as drugs for type 2 diabetes mellitus. Only luseogliflozin contains a thiosugar ring in its chemical structure, while other hSGLT2 inhibitors contain glucose rings. Consequently, we focused on the binding interactions of hSGLT2 with sugars and thiosugars. We first revealed that the binding affinities of thiosugars are stronger than those of sugars through molecular dynamics simulations of Vibrio parahaemolyticus, sodium-galactose co-transporter, and human hSGLT2. We then demonstrated that Na(+) dissociates from the protein to the cytoplasmic solution more slowly in the thiosugar system than in the sugar system. These differences between sugars and thiosugars are discussed on the basis of the different binding modes due to the atom at the 5-position of the sugar and thiosugar rings. Finally, as a result of Na(+) dissociation, we suggest that the dissociation of thiosugars is slower than that of sugars. PMID:26260238

  5. Interactions of sarin with polyelectrolyte membranes: a molecular dynamics simulation study.

    PubMed

    Lee, Ming-Tsung; Vishnyakov, Aleksey; Gor, Gennady Yu; Neimark, Alexander V

    2013-01-10

    Nanostructured polyelectrolyte membranes (PEMs), which are widely used as permselective diffusion barriers in fuel cell technologies and electrochemical processing, are considered as protective membranes suitable for blocking warfare toxins, including water-soluble nerve agents such as sarin. In this article, we examine the mechanisms of sorption and diffusion of sarin in hydrated PEMs by means of atomistic molecular dynamics simulations. Three PEMs are considered: Nafion, sulfonated polystyrene (sPS) that forms the hydrophilic subphase of segregated sPS-polyolefin block copolymers, and random sPS-polyethylene copolymer. We found that sarin concentrates at the interface between the hydrophilic and hydrophobic subphases of hydrated Nafion acting as a surfactant. In hydrated sPS, where the scale of water-polymer segregation is much smaller (1-2 nm), sarin also interacts favorably with hydrophobic and hydrophilic components. Water diffusion slows as the sarin content increases despite the overall increase in solvent content, which suggests that sarin and water have somewhat different pathways through the segregated membrane. Upon replacement of counterions of monovalent potassium with those of divalent calcium, sarin diffusion slows but remains substantial in all ionomers considered, especially at high sarin concentrations. The behavior of sarin is similar to that of its common simulant, dimethyl methylphosphonate. PMID:23205740

  6. Molecular Dynamics Simulations of the Interactions Between Tungsten Dust and Beryllium Plasma-Facing Material

    NASA Astrophysics Data System (ADS)

    Niu, Guojian; Li, Xiaochun; Xu, Qian; Yang, Zhongshi; Luo, Guangnan

    2015-12-01

    In the present research, molecular dynamics simulation is applied to study the interactions between tungsten dusts and a beryllium plasma-facing material surface. Calculation results show that it is quite difficult for nanometer-size dust particles to damage the plasma-facing material surface, which is different from the micrometer-size ones. The reason may be the size difference between dust and crystal grains. The depth of dust penetration into plasma-facing materials is closely related to the incident velocity, and the impacting angle also plays an important role. Dust and material surface damage is also investigated. Results show that both incident velocity and angle can significantly influence the damage. supported by the National Magnetic Confinement Fusion Science Program of China (Nos. 2013GB105001, 2013GB105002, and 2015GB109001), National Natural Science Foundation of China (Nos. 11205198, 11305213 and 11405201), as well as Technological Development Grant of Hefei Science Center of CAS (No. 2014TDG-HSC003)

  7. Interaction of Curcumin with PEO-PPO-PEO block copolymers: a molecular dynamics study.

    PubMed

    Samanta, Susruta; Roccatano, Danilo

    2013-03-21

    Curcumin, a naturally occurring drug molecule, has been extensively investigated for its various potential usages in medicine. Its water insolubility and high metabolism rate require the use of drug delivery systems to make it effective in the human body. Among various types of nanocarriers, block copolymer based ones are the most effective. These polymers are broadly used as drug-delivery systems, but the nature of this process is poorly understood. In this paper, we propose a molecular dynamics simulation study of the interaction of Curcumin with block copolymer based on polyethylene oxide (PEO) and polypropylene oxide (PPO). The study has been conducted considering the smallest PEO and PPO oligomers and multiple chains of the block copolymer Pluronic P85. Our study shows that the more hydrophobic 1,2-dimethoxypropane (DMP) molecules and PPO block preferentially coat the Curcumin molecule. In the case of the Pluronic P85, simulation shows formation of a drug-polymer aggregate within 50 ns. This process leaves exposed the PEO part of the polymers, resulting in better solvation and stability of the drug in water. PMID:23441964

  8. Visualization for Molecular Dynamics Simulation of Gas and Metal Surface Interaction

    NASA Astrophysics Data System (ADS)

    Puzyrkov, D.; Polyakov, S.; Podryga, V.

    2016-02-01

    The development of methods, algorithms and applications for visualization of molecular dynamics simulation outputs is discussed. The visual analysis of the results of such calculations is a complex and actual problem especially in case of the large scale simulations. To solve this challenging task it is necessary to decide on: 1) what data parameters to render, 2) what type of visualization to choose, 3) what development tools to use. In the present work an attempt to answer these questions was made. For visualization it was offered to draw particles in the corresponding 3D coordinates and also their velocity vectors, trajectories and volume density in the form of isosurfaces or fog. We tested the way of post-processing and visualization based on the Python language with use of additional libraries. Also parallel software was developed that allows processing large volumes of data in the 3D regions of the examined system. This software gives the opportunity to achieve desired results that are obtained in parallel with the calculations, and at the end to collect discrete received frames into a video file. The software package "Enthought Mayavi2" was used as the tool for visualization. This visualization application gave us the opportunity to study the interaction of a gas with a metal surface and to closely observe the adsorption effect.

  9. Nature of protein-CO2 interactions as elucidated via molecular dynamics.

    PubMed

    Drummond, Michael L; Wilson, Angela K; Cundari, Thomas R

    2012-09-27

    Rising global temperatures require innovative measures to reduce atmospheric concentrations of CO(2). The most successful carbon capture technology on Earth is the enzymatic capture of CO(2) and its sequestration in the form of glucose. Efforts to improve upon or mimic this naturally occurring process will require a rich understanding of protein-CO(2) interactions. Toward that end, extensive all-atom molecular dynamics (MD) simulations were performed on the CO(2)-utilizing enzyme phosphoenolpyruvate carboxykinase (PEPCK). Preliminary simulations were performed using implicit and explicit solvent models, which yielded similar results: arginine, lysine, tyrosine, and asparagine enhance the ability of a protein to bind carbon dioxide. Extensive explicit solvent simulations were performed for both wild-type PEPCK and five single-point PEPCK mutants, revealing three prevalent channels by which CO(2) enters (or exits) the active site cleft, as well as a fourth channel (observed only once), the existence of which can be rationalized in terms of the position of a key Arg residue. The strongest CO(2) binding sites in these simulations consist of appropriately positioned hydrogen bond donors and acceptors. Interactions between CO(2) and both Mn(2+) and Mg(2+) present in PEPCK are minimal due to the stable protein- and solvent-based coordination environments of these cations. His 232, suggested by X-ray crystallography as being a potential important CO(2) binding site, is indeed found to be particularly "CO(2)-philic" in these simulations. Finally, a recent mechanism, proposed on the basis of X-ray crystallography, for PEPCK active site lid closure is discussed in light of the MD trajectories. Overall, the results of this work will prove useful not only to scientists investigating PEPCK, but also to groups seeking to develop an environmentally benign, protein-based carbon capture, sequestration, and utilization system. PMID:22882078

  10. A spectroscopic and molecular dynamic approach on the interaction between ionic liquid type gemini surfactant and human serum albumin.

    PubMed

    Maurya, Jitendra Kumar; Mir, Muzaffar Ul Hassan; Maurya, Neha; Dohare, Neeraj; Ali, Anwar; Patel, Rajan

    2016-10-01

    The interactions of imidazolium bashed ionic liquid-type cationic gemini surfactant ([C12-4-C12im]Br2) with HSA were studied by fluorescence, time-resolved fluorescence, UV-visible, circular dichroism, molecular docking and molecular dynamic simulation methods. The results showed that the [C12-4-C12im]Br2 quenched the fluorescence of HSA through dynamic quenching mechanism as confirmed by time-resolved spectroscopy. The Stern-Volmer quenching constant (Ksv) and relevant thermodynamic parameters such as enthalpy change (ΔH), Gibbs free energy change (ΔG) and entropy change (ΔS) for interaction system were calculated at different temperatures. The results revealed that hydrophobic forces played a major role in the interactions process. The results of synchronous fluorescence, UV-visible and CD spectra demonstrated that the binding of [C12-4-C12im]Br2 with HSA induces conformational changes in HSA. Inquisitively, the molecular dynamics study contribute towards understanding the effect of binding of [C12-4-C12im]Br2 on HSA to interpret the conformational change in HSA upon binding in aqueous solution. Moreover, the molecular modelling results show the possible binding sites in the interaction system. PMID:26473302

  11. Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.

    PubMed

    Czeleń, Przemysław; Czyżnikowska, Żaneta

    2016-06-01

    In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein-ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component. PMID:27154340

  12. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.

    PubMed

    Pruitt, Spencer R; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, Mark S

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Møller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed. PMID:26913837

  13. Coarse-grained molecular dynamics simulations of depletion-induced interactions for soft matter systems

    SciTech Connect

    Shendruk, Tyler N.; Bertrand, Martin; Harden, James L.; Slater, Gary W.; Haan, Hendrick W. de

    2014-12-28

    Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.

  14. Theory of polymer-nanopore interactions refined using molecular dynamics simulations.

    PubMed

    Balijepalli, Arvind; Robertson, Joseph W F; Reiner, Joseph E; Kasianowicz, John J; Pastor, Richard W

    2013-05-01

    Molecular dynamics simulations were used to refine a theoretical model that describes the interaction of single polyethylene glycol (PEG) molecules with α-hemolysin (αHL) nanopores. The simulations support the underlying assumptions of the model, that PEG decreases the pore conductance by binding cations (which reduces the number of mobile ions in the pore) and by volume exclusion, and provide bounds for fits to new experimental data. Estimation of cation binding indicates that four monomers coordinate a single K(+) in a crown-ether-like structure, with, on average, 1.5 cations bound to a PEG 29-mer at a bulk electrolyte concentration of 4 M KCl. Additionally, PEG is more cylindrical and has a larger cross-section area in the pore than in solution, although its volume is similar. Two key experimental quantities of PEG are described by the model: the ratio of single channel current in the presence of PEG to that in the polymer's absence (blockade depth) and the mean residence time of PEG in the pore. The refined theoretical model is simultaneously fit to the experimentally determined current blockade depth and the mean residence times for PEGs with 15 to 45 monomers, at applied transmembrane potentials of -40 to -80 mV and for three electrolyte concentrations. The model estimates the free energy of the PEG-cation complexes to be -5.3 kBT. Finally the entropic penalty of confining PEG to the pore is found to be inversely proportional to the electrolyte concentration. PMID:23590258

  15. Coarse-grained molecular dynamics simulations of depletion-induced interactions for soft matter systems

    NASA Astrophysics Data System (ADS)

    Shendruk, Tyler N.; Bertrand, Martin; Harden, James L.; Slater, Gary W.; de Haan, Hendrick W.

    2014-12-01

    Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.

  16. Interactions of anesthetics with the water-hexane interface. A molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Chipot, C.; Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles characterizing the transfer of nine solutes across the liquid-vapor interfaces of water and hexane and across the water-hexane interface were calculated from molecular dynamics simulations. Among the solutes were n-butane and three of its halogenated derivatives, as well as three halogenated cyclobutanes. The two remaining molecules, dichlorodifluoromethane and 1,2-dichloroperfluoroethane, belong to series of halo-substituted methanes and ethanes, described in previous studies (J. Chem. Phys. 1996, 104, 3760; Chem. Phys. 1996, 204, 337). Each series of molecules contains structurally similar compounds that differ greatly in anesthetic potency. The accuracy of the simulations was tested by comparing the calculated and the experimental free energies of solvation of all nine compounds in water and in hexane. In addition. the calculated and the measured surface excess concentrations of n-butane at the water liquid-vapor interface were compared. In all cases, good agreement with experimental results was found. At the water-hexane interface, the free energy profiles for polar molecules exhibited significant interfacial minima, whereas the profiles for nonpolar molecules did not. The existence of these minima was interpreted in terms of a balance between the free energy contribution arising from solute-solvent interactions and the work to form a cavity that accommodates the solute. These two contributions change monotonically, but oppositely, across the interface. The interfacial solubilities of the solutes, obtained from the free energy profiles, correlate very well with their anesthetic potencies. This is the case even when the Meyer-Overton hypothesis, which predicts a correlation between anesthetic potency and solubility in oil, fails.

  17. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  18. Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

    PubMed Central

    Etheve, Loïc; Martin, Juliette; Lavery, Richard

    2016-01-01

    Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein–DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex. PMID:26721385

  19. Cyto•IQ: an adaptive cytometer for extracting the noisy dynamics of molecular interactions in live cells

    NASA Astrophysics Data System (ADS)

    Ball, David A.; Moody, Stephen E.; Peccoud, Jean

    2010-02-01

    We have developed a fundamentally new type of cytometer to track the statistics of dynamic molecular interactions in hundreds of individual live cells within a single experiment. This entirely new high-throughput experimental system, which we have named Cyto•IQ, reports statistical, rather than image-based data for a large cellular population. Like a flow cytometer, Cyto•IQ rapidly measures several fluorescent probes in a large population of cells to yield a reduced statistical model that is matched to the experimental goals set by the user. However, Cyto•IQ moves beyond flow cytometry by tracking multiple probes in individual cells over time. Using adaptive learning algorithms, we process data in real time to maximize the convergence of the statistical model parameter estimators. Software controlling Cyto•IQ integrates existing open source applications to interface hardware components, process images, and adapt the data acquisition strategy based on previously acquired data. These innovations allow the study of larger populations of cells, and molecular interactions with more complex dynamics, than is possible with traditional microscope-based approaches. Cyto•IQ supports research to characterize the noisy dynamics of molecular interactions controlling biological processes.

  20. The Dynamics of Molecular Interactions and Chemical Reactions at Metal Surfaces: Testing the Foundations of Theory

    NASA Astrophysics Data System (ADS)

    Golibrzuch, Kai; Bartels, Nils; Auerbach, Daniel J.; Wodtke, Alec M.

    2015-04-01

    We review studies of molecular interactions and chemical reactions at metal surfaces, emphasizing progress toward a predictive theory of surface chemistry and catalysis. For chemistry at metal surfaces, a small number of central approximations are typically made: (a) the Born-Oppenheimer approximation of electronic adiabaticity, (b) the use of density functional theory at the generalized gradient approximation level, (c) the classical approximation for nuclear motion, and (d) various reduced-dimensionality approximations. Together, these approximations constitute a provisional model for surface chemical reactivity. We review work on some carefully studied examples of molecules interacting at metal surfaces that probe the validity of various aspects of the provisional model.

  1. The dynamics of molecular interactions and chemical reactions at metal surfaces: testing the foundations of theory.

    PubMed

    Golibrzuch, Kai; Bartels, Nils; Auerbach, Daniel J; Wodtke, Alec M

    2015-04-01

    We review studies of molecular interactions and chemical reactions at metal surfaces, emphasizing progress toward a predictive theory of surface chemistry and catalysis. For chemistry at metal surfaces, a small number of central approximations are typically made: (a) the Born-Oppenheimer approximation of electronic adiabaticity, (b) the use of density functional theory at the generalized gradient approximation level, (c) the classical approximation for nuclear motion, and (d) various reduced-dimensionality approximations. Together, these approximations constitute a provisional model for surface chemical reactivity. We review work on some carefully studied examples of molecules interacting at metal surfaces that probe the validity of various aspects of the provisional model. PMID:25580627

  2. Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene.

    PubMed

    Cleland, Dougal; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A; McCluskey, Adam

    2014-02-01

    The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer-template (FM-T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with trimethylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2.8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the π-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to π-π stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level

  3. Relevant interactions of antimicrobial iron chelators and membrane models revealed by nuclear magnetic resonance and molecular dynamics simulations.

    PubMed

    Coimbra, João T S; Moniz, Tânia; Brás, Natércia F; Ivanova, Galya; Fernandes, Pedro A; Ramos, Maria J; Rangel, Maria

    2014-12-18

    The dynamics and interaction of 3-hydroxy-4-pyridinone fluorescent iron chelators, exhibiting antimicrobial properties, with biological membranes were evaluated through NMR and molecular dynamics simulations. Both NMR and MD simulation results support a strong interaction of the chelators with the lipid bilayers that seems to be strengthened for the rhodamine containing compounds, in particular for compounds that include ethyl groups and a thiourea link. For the latter type of compounds the interaction reaches the hydrophobic core of the lipid bilayer. The molecular docking and MD simulations performed for the potential interaction of the chelators with DC-SIGN receptors provide valuable information regarding the cellular uptake of these compounds since the results show that the fluorophore fragment of the molecular framework is essential for an efficient binding. Putting together our previous and present results, we put forward the hypothesis that all the studied fluorescent chelators have access to the cell, their uptake occurs through different pathways and their permeation properties correlate with a better access to the cell and its compartments and, consequently, with the chelators antimicrobial properties. PMID:25482538

  4. Modulation of amphotericin B membrane interaction by cholesterol and ergosterol--a molecular dynamics study.

    PubMed

    Czub, Jacek; Baginski, Maciej

    2006-08-24

    Amphotericin B (AmB) is a well-known polyene macrolide antibiotic used to treat systemic fungal infections. According to a well-documented hypothesis, molecules of AmB form ionic membrane channels that are responsible for chemotherapeutic action. These channels disturb the barrier function of the cell membrane which, in consequence, leads to cell death. The presence of sterols in the cell membrane is necessary for full manifestation of the antibiotic's ionophoric activity, at least in vivo. Ergosterol-containing fungal membranes are targeted more efficiently by AmB than mammalian membranes containing cholesterol. However, a similar level of disturbance of fungal and mammalian membranes is responsible for serious toxicity of the antibiotic. Due to the importance of AmB and lack of better antifungal alternatives, the search for new less toxic derivatives of this antibiotic still continues. Therefore, studies of the AmB-membrane interaction are very important. The present work constitutes a continuation of a broad program of study on AmB mode of action in our group. In particular, molecular dynamics simulations of AmB monomers inside the bilayers of three different compositions (pure dimiristoylphosphatidylcholine (DMPC) and DMPC bilayer containing approximately 25 mol % of cholesterol or ergosterol) were carried out. In general, analysis of generated trajectories resulted in identifying many significant differences in the behavior of AmB monomers depending on the membrane environment. In particular, it was established that the antibiotic increases the internal order of DMPC bilayer containing 25 mol % of cholesterol, while it has no effect on the order of the bilayer with the same amount of ergosterol. Performed calculations also revealed that relatively rigid and elongated AmB molecules exhibit higher affinity toward the sterol-containing lo phases and, therefore, may be cumulated in ordered membrane domains (e.g., lipid rafts). Since the partition coefficient

  5. Accelerated molecular dynamics methods

    SciTech Connect

    Perez, Danny

    2011-01-04

    The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

  6. Small molecule interactions with lipid bilayers: a molecular dynamics study of chlorhexidine

    NASA Astrophysics Data System (ADS)

    van Oosten, Brad; Marquardt, Drew; Sternin, Edward; Harroun, Thad

    2013-03-01

    Chlorhexidine presents an interesting modelling challenge with a hydrophobic hexane connecting two biguanides (arginine analogues) and two aromatic rings. We conducted molecular dynamic simulations using the GROMACS simulation software to reproduce the experimental environment of chlorhexidine in a 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) bilayer to produce atomic-level information. We constructed an all-atom force field of chlorhexidine from the CHARMM36 force field using well established parameters of certain amino acids. Partial charges were treated differently, which were calculated using GAUSSIAN software. We will compare and contrast the results of our model to that of our neutron scattering experiments previously done in our lab.

  7. Molecular docking and dynamics simulations on the interaction of cationic porphyrin-anthraquinone hybrids with DNA G-quadruplexes.

    PubMed

    Arba, Muhammad; Kartasasmita, Rahmana E; Tjahjono, Daryono H

    2016-01-01

    A series of cationic porphyrin-anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction. PMID:25808513

  8. Precritical State Transition Dynamics in the Attractor Landscape of a Molecular Interaction Network Underlying Colorectal Tumorigenesis

    PubMed Central

    Cho, Kwang-Hyun

    2015-01-01

    From the perspective of systems science, tumorigenesis can be hypothesized as a critical transition (an abrupt shift from one state to another) between proliferative and apoptotic attractors on the state space of a molecular interaction network, for which an attractor is defined as a stable state to which all initial states ultimately converge, and the region of convergence is called the basin of attraction. Before the critical transition, a cellular state might transit between the basin of attraction for an apoptotic attractor and that for a proliferative attractor due to the noise induced by the inherent stochasticity in molecular interactions. Such a flickering state transition (state transition between the basins of attraction for alternative attractors from the impact of noise) would become more frequent as the cellular state approaches near the boundary of the basin of attraction, which can increase the variation in the estimate of the respective basin size. To investigate this for colorectal tumorigenesis, we have constructed a stochastic Boolean network model of the molecular interaction network that contains an important set of proteins known to be involved in cancer. In particular, we considered 100 representative sequences of 20 gene mutations that drive colorectal tumorigenesis. We investigated the appearance of cancerous cells by examining the basin size of apoptotic, quiescent, and proliferative attractors along with the sequential accumulation of gene mutations during colorectal tumorigenesis. We introduced a measure to detect the flickering state transition as the variation in the estimate of the basin sizes for three-phenotype attractors from the impact of noise. Interestingly, we found that this measure abruptly increases before a cell becomes cancerous during colorectal tumorigenesis in most of the gene mutation sequences under a certain level of stochastic noise. This suggests that a frequent flickering state transition can be a precritical

  9. The effect of stacking fault energy on interactions between an edge dislocation and a spherical void by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Asari, K.; Hetland, O. S.; Fujita, S.; Itakura, M.; Okita, T.

    2013-11-01

    Molecular dynamics simulations were conducted using a set of six interatomic potentials for FCC metals that differed only in stacking fault energy (SFE), to clarify the effect of SFE on interactions between a dissociated edge dislocation and a void. There are two different types of interaction mechanism: separate depinning of the individual partial dislocations and almost simultaneous depinning of the combined partial dislocations. The interaction mechanism depends on both the SFE and void size, and changes the absolute value of the critical resolved shear stress (CRSS) and its dependence on the SFE. In the separate depinning case, the CRSS is relatively low and is almost independent of the SFE, while in the simultaneous case, the CRSS is increases with SFE. The void size for which the change in interaction mechanism occurs increases with decreasing SFE.

  10. Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.

    PubMed

    Salmon, Loïc; Ahlstrom, Logan S; Horowitz, Scott; Dickson, Alex; Brooks, Charles L; Bardwell, James C A

    2016-08-10

    Chaperones maintain a healthy proteome by preventing aggregation and by aiding in protein folding. Precisely how chaperones influence the conformational properties of their substrates, however, remains unclear. To achieve a detailed description of dynamic chaperone-substrate interactions, we fused site-specific NMR information with coarse-grained simulations. Our model system is the binding and folding of a chaperone substrate, immunity protein 7 (Im7), with the chaperone Spy. We first used an automated procedure in which NMR chemical shifts inform the construction of system-specific force fields that describe each partner individually. The models of the two binding partners are then combined to perform simulations on the chaperone-substrate complex. The binding simulations show excellent agreement with experimental data from multiple biophysical measurements. Upon binding, Im7 interacts with a mixture of hydrophobic and hydrophilic residues on Spy's surface, causing conformational exchange within Im7 to slow down as Im7 folds. Meanwhile, the motion of Spy's flexible loop region increases, allowing for better interaction with different substrate conformations, and helping offset losses in Im7 conformational dynamics that occur upon binding and folding. Spy then preferentially releases Im7 into a well-folded state. Our strategy has enabled a residue-level description of a dynamic chaperone-substrate interaction, improving our understanding of how chaperones facilitate substrate folding. More broadly, we validate our approach using two other binding partners, showing that this approach provides a general platform from which to investigate other flexible biomolecular complexes through the integration of NMR data with efficient computational models. PMID:27415450

  11. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    DOE PAGESBeta

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

  12. Molecular dynamics simulations of formamide interaction with hydrocyanic acid on a catalytic surface TiO2

    NASA Astrophysics Data System (ADS)

    Artoshina, O. V.; Vorob'eva, M. Yu.; Dushanov, E. B.; Kholmurodov, Kh. T.

    2014-06-01

    The behavior of water—formamide and hydrocyanic acid—formamide solutions on an anatase surface have been studied using molecular dynamics (MD) simulation method. The interaction activation energies have been estimated for the temperature range from 250 up to 400 K. The diffusion coefficients and structural radial distribution functions have been calculated for the formamide, water and hydrocyanic acid on an anatase surface. The calculated activation energies of the water—formamide—anatase and hydrocyanic acid—formamide—anatase systems were analyzed and compared. A comparative analysis of the systems under investigation was performed and a possible correlation between the obtained MD results and the molecular mechanism involving the formamide's interaction with dioxide titan adsorbing surface were discussed.

  13. Inelastic Neutron Scattering and Molecular Dynamics Determination of the Interaction Potential in Liquid CD{sub 4}

    SciTech Connect

    Guarini, E.; Barocchi, F.

    2007-10-19

    Anisotropic interactions of liquid CD{sub 4} are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,{omega}) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results.

  14. Multiscale reactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-12-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

  15. Multiscale reactive molecular dynamics

    PubMed Central

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-01-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062

  16. Unveiling the complex network of interactions in Ionic Liquids: a combined EXAFS and Molecular Dynamics approach

    NASA Astrophysics Data System (ADS)

    Serva, A.; Migliorati, V.; Lapi, A.; D'Angelo, P.

    2016-05-01

    The structural properties of geminal dicationic ionic liquids ([Cn (mim)2]Br2)/water mixtures have been investigated by means of extended X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. This synergic approach allowed us to assess the reliability of the MD results and to provide accurate structural information about the first coordination shell of the Br- ion. We found that the local environment around the anion changes as a function of the water concentration, while it is the same independently from the length of the bridge-alkyl chain. Moreover, as regards the long-range structural organization, no tail-tail aggregation occurs with increasing alkyl chain length.

  17. Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations.

    PubMed

    Hu, Guodong; Xu, Shicai; Wang, Jihua

    2015-12-01

    Inhibition of p53-MDM2 interaction by small molecules is considered to be a promising approach to re-activate wild-type p53 for tumor suppression. Several inhibitors of the MDM2-p53 interaction were designed and studied by the experimental methods and the molecular dynamics simulation. However, the unbinding mechanism was still unclear. The steered molecular dynamics simulations combined with Brownian dynamics fluctuation-dissipation theorem were employed to obtain the free-energy landscape of unbinding between MDM2 and their four ligands. It was shown that compounds 4 and 8 dissociate faster than compounds 5 and 7. The absolute binding free energies for these four ligands are in close agreement with experimental results. The open movement of helix II and helix IV in the MDM2 protein-binding pocket upon unbinding is also consistent with experimental MDM2-unbound conformation. We further found that different binding mechanisms among different ligands are associated with H-bond with Lys51 and Glu25. These mechanistic results may be useful for improving ligand design. PMID:26032728

  18. Interaction between Pin1 and its natural product inhibitor epigallocatechin-3-gallate by spectroscopy and molecular dynamics simulations.

    PubMed

    Xi, Lei; Wang, Yu; He, Qing; Zhang, Qingyan; Du, Linfang

    2016-12-01

    The binding of epigallocatechin-3-gallate (EGCG) to wild type Pin1 in solution was studied by spectroscopic methods and molecular dynamics simulations in this research to explore the binding mode and inhibition mechanism. The binding constants and number of binding sites per Pin1 for EGCG were calculated through the Stern-Volmer equation. The values of binding free energy and thermodynamic parameters were calculated and indicated that hydrogen bonds, electrostatic interaction and Van der Waals interaction played the major role in the binding process. The alterations of Pin1 secondary structure in the presence of EGCG were confirmed by far-UV circular dichroism spectra. The binding model at atomic-level revealed that EGCG was bound to the Glu12, Lys13, Arg14, Met15 and Arg17 in WW domain. Furthermore, EGCG could also interact with Arg69, Asp112, Cys113 and Ser114 in PPIase domain. PMID:27372509

  19. Atomic & Molecular Interactions

    SciTech Connect

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  20. Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

    PubMed Central

    Wang, Feng; Stuart, Steven J.; Latour, Robert A.

    2009-01-01

    The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized surface is of fundamental importance for a broad range of applications in biotechnology. The adsorption free energy for these types of interactions can be determined from a molecular dynamics simulation using the partitioning between adsorbed and nonadsorbed states, provided that sufficient sampling of both states is obtained. However, if interactions between the solute and the surface are strong, the solute will tend to be trapped near the surface during the simulation, thus preventing the adsorption free energy from being calculated by this method. This situation occurs even when using an advanced sampling algorithm such as replica-exchange molecular dynamics (REMD). In this paper, the authors demonstrate the fundamental basis of this problem using a model system consisting of one sodium ion (Na+) as the solute positioned over a surface functionalized with one negatively charged group (COO−) in explicit water. With this simple system, the authors show that sufficient sampling in the coordinate normal to the surface cannot be obtained by conventional REMD alone. The authors then present a method to overcome this problem through the use of an adaptive windowed-umbrella sampling technique to develop a biased-energy function that is combined with REMD. This approach provides an effective method for the calculation of adsorption free energy for solute-surface interactions. PMID:19768127

  1. Argon Interaction with Gold Surfaces: Ab Initio-Assisted Determination of Pair Ar-Au Potentials for Molecular Dynamics Simulations.

    PubMed

    Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline

    2015-07-01

    Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588

  2. Interaction potential for aluminum nitride: a molecular dynamics study of mechanical and thermal properties of crystalline and amorphous aluminum nitride

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, Jose Pedro

    2011-01-01

    An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole–dipole (van der Waals) interactions. The covalent characters of the Al–N–Al and N–Al–N bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger–Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants ( C{sub 11} , C{sub 12} , C{sub 13} , C{sub 33} , C{sub 44} , and C{sub 66} ), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.

  3. QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells

    PubMed Central

    Fisher, Ciarán P.; Plant, Nicholas J.; Moore, J. Bernadette; Kierzek, Andrzej M.

    2013-01-01

    Motivation: Dynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype–phenotype relationships. Despite advances in quantitative biology, full parameterization of whole-cell models is not yet possible. Simulation methods capable of using available qualitative data are required to develop dynamic whole-cell models through an iterative process of modelling and experimental validation. Results: We formulate quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. We present the first dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study. QSSPN simulations reproduce experimentally determined qualitative dynamic behaviours and permit mechanistic analysis of genotype–phenotype relationships. Availability and implementation: The model and simulation software implemented in C++ are available in supplementary material and at http://sysbio3.fhms.surrey.ac.uk/qsspn/. Contact: a.kierzek@surrey.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24064420

  4. Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction.

    PubMed

    Wu, Jinhong; Rong, Yuzhi; Wang, Zhengwu; Zhou, Yanfu; Wang, Shaoyun; Zhao, Bo

    2015-05-01

    This study aimed to isolate and characterise a novel sericin antifreeze peptide and investigate its ice-binding molecular mechanism. The thermal hysteresis activity of ice-binding sericin peptides (I-SP) was measured and their activity reached as high as 0.94 °C. A P4 fraction, with high hypothermia protective activity and inhibition activity of ice recrystallisation, was obtained from I-SP, and a purified sericin peptide, named SM-AFP, with the sequence of TTSPTNVSTT and a molecular weight of 1009.50 Da was then isolated from the P4 fraction. Treatment of Lactobacillus delbrueckii Subsp. bulgaricus LB340 LYO with 100 μg/ml synthetic SM-AFP led to 1.4-fold increased survival (p < 0.05). Finally, an SM-AFP/ice binding model was constructed and results of molecular dynamics simulation suggested that the binding of SM-AFP with ice and prevention of ice crystal growth could be attributed to hydrogen bond formation, hydrophobic interaction and non-bond interactions. Sericin peptides could be developed into beneficial cryoprotectants and used in frozen food processing. PMID:25529728

  5. Drug-polymer interactions at water-crystal interfaces and implications for crystallization inhibition: molecular dynamics simulations of amphiphilic block copolymer interactions with tolazamide crystals.

    PubMed

    Gao, Yi; Olsen, Kenneth W

    2015-07-01

    A diblock copolymer, poly(ethylene glycol)-block-poly(lactic acid) (PEG-b-PLA), modulates the crystal growth of tolazamide (TLZ), resulting in a crystal morphology change from needles to plates in aqueous media. To understand this crystal surface drug-polymer interaction, we conducted molecular dynamics simulations on crystal surfaces of TLZ in water containing PEG-b-PLA. A 130-ns simulation of the polymer in a large water box was run before initiating 50 ns simulations with each of the crystal surfaces. The simulations demonstrated differentiated drug-polymer interactions that are consistent with experimental studies. Interaction of PEG-b-PLA with the (001) face occurred more rapidly (≤10 ns) and strongly (total interaction energy of -121.1 kJ/mol/monomer) than that with the (010) face (∼35 ns, -85.4 kJ/mol/monomer). There was little interaction with the (100) face. Hydrophobic and van der Waals (VDW) interactions were the dominant forces, accounting for more than 90% of total interaction energies. It suggests that polymers capable of forming strong hydrophobic and VDW interactions might be more effective in inhibiting crystallization of poorly water-soluble and hydrophobic drugs in aqueous media (such as gastrointestinal fluid) than those with hydrogen-bonding capacities. Such in-depth analysis and understanding facilitate the rational selection of polymers in designing supersaturation-based enabling formulations. PMID:26045147

  6. The Molecular Mechanism of Bisphenol A (BPA) as an Endocrine Disruptor by Interacting with Nuclear Receptors: Insights from Molecular Dynamics (MD) Simulations

    PubMed Central

    Li, Lanlan; Wang, Qianqian; Zhang, Yan; Niu, Yuzhen; Yao, Xiaojun; Liu, Huanxiang

    2015-01-01

    Bisphenol A (BPA) can interact with nuclear receptors and affect the normal function of nuclear receptors in very low doses, which causes BPA to be one of the most controversial endocrine disruptors. However, the detailed molecular mechanism about how BPA interferes the normal function of nuclear receptors is still undiscovered. Herein, molecular dynamics simulations were performed to explore the detailed interaction mechanism between BPA with three typical nuclear receptors, including hERα, hERRγ and hPPARγ. The simulation results and calculated binding free energies indicate that BPA can bind to these three nuclear receptors. The binding affinities of BPA were slightly lower than that of E2 to these three receptors. The simulation results proved that the binding process was mainly driven by direct hydrogen bond and hydrophobic interactions. In addition, structural analysis suggested that BPA could interact with these nuclear receptors by mimicking the action of natural hormone and keeping the nuclear receptors in active conformations. The present work provided the structural evidence to recognize BPA as an endocrine disruptor and would be important guidance for seeking safer substitutions of BPA. PMID:25799048

  7. Interactions of the SAP Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

    NASA Technical Reports Server (NTRS)

    Hu, Shaowen; Carra, Claudio; Huff, Janice; Pluth, Janice M.; Cucinotta, Francis A.

    2007-01-01

    NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku70/80 complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The SAP domain of Ku70 (residues 556-609), contains an a helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the SAP/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the SAP domain of Ku70 and a 10 base pairs DNA duplex. Large-scale conformational changes were observed and some putative binding modes were suggested based on energetic analysis. These modes are consistent with previous experimental investigations. In addition, the results indicate that cooperation of SAP with other domains of Ku70/80 is necessary to explain the high affinity of binding as observed in experiments.

  8. Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions.

    PubMed

    Cau, Ylenia; Fiorillo, Annarita; Mori, Mattia; Ilari, Andrea; Botta, Maurizo; Lalle, Marco

    2015-12-28

    Giardiasis is a gastrointestinal diarrheal illness caused by the protozoan parasite Giardia duodenalis, which affects annually over 200 million people worldwide. The limited antigiardial drug arsenal and the emergence of clinical cases refractory to standard treatments dictate the need for new chemotherapeutics. The 14-3-3 family of regulatory proteins, extensively involved in protein-protein interactions (PPIs) with pSer/pThr clients, represents a highly promising target. Despite homology with human counterparts, the single 14-3-3 of G. duodenalis (g14-3-3) is characterized by a constitutive phosphorylation in a region critical for target binding, thus affecting the function and the conformation of g14-3-3/clients interaction. However, to approach the design of specific small molecule modulators of g14-3-3 PPIs, structural elucidations are required. Here, we present a detailed computational and crystallographic study exploring the implications of g14-3-3 phosphorylation on protein structure and target binding. Self-Guided Langevin Dynamics and classical molecular dynamics simulations show that phosphorylation affects locally and globally g14-3-3 conformation, inducing a structural rearrangement more suitable for target binding. Profitable features for g14-3-3/clients interaction were highlighted using a hydrophobicity-based descriptor to characterize g14-3-3 client peptides. Finally, the X-ray structure of g14-3-3 in complex with a mode-1 prototype phosphopeptide was solved and combined with structure-based simulations to identify molecular features relevant for clients binding to g14-3-3. The data presented herein provide a further and structural understanding of g14-3-3 features and set the basis for drug design studies. PMID:26551337

  9. Nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  10. Effects of cholesterol concentration on the interaction of cytarabine with lipid membranes: a molecular dynamics simulation study.

    PubMed

    Karami, Leila; Jalili, Seifollah

    2015-01-01

    Liposomal cytarabine, DepoCyt, is a chemotherapy agent which is used in cancer treatment. This form of cytarabine has more efficacy and fewer side effects relative to the other forms. Since DepoCyt contains the cytarabine encapsulated within phosphatidylcholine and the sterol molecules, we modeled dioleoylphosphatidylcholine (DOPC)/cholesterol bilayer membrane as a carrier for cytarabine to study drug-bilayer interactions. For this purpose, we performed a series of united-atom molecular dynamics (MD) simulations for 25 ns to investigate the interactions between cytarabine and cholesterol-containing DOPC lipid bilayers. Only the uncharged form of cytarabine molecule was investigated. In this study, different levels of the cholesterol content (0, 20, and 40%) were used. MD simulations allowed us to determine dynamical and structural properties of the bilayer membrane and to estimate the preferred location and orientation of the cytarabine molecule inside the bilayer membrane. Properties such as membrane thickness, area per lipid, diffusion coefficient, mass density, bilayer packing, order parameters, and intermolecular interactions were examined. The results show that by increasing the cholesterol concentration in the lipid bilayers, the bilayer thickness increases and area per lipid decreases. Moreover, in accordance with the experiments, our calculations show that cholesterol molecules have ordering effect on the hydrocarbon acyl chains. Furthermore, the cytarabine molecule preferentially occupies the polar region of the lipid head groups to form specific interactions (hydrogen bonds). Our results fully support the experimental data. Our finding about drug-bilayer interaction is crucial for the liposomal drug design. PMID:25068451

  11. Visualizing Protein Interactions and Dynamics: Evolving a Visual Language for Molecular Animation

    ERIC Educational Resources Information Center

    Jenkinson, Jodie; McGill, Gael

    2012-01-01

    Undergraduate biology education provides students with a number of learning challenges. Subject areas that are particularly difficult to understand include protein conformational change and stability, diffusion and random molecular motion, and molecular crowding. In this study, we examined the relative effectiveness of three-dimensional…

  12. Comprehensive molecular dynamics simulations of the stacking fault tetrahedron interacting with a mixed dislocation at elevated temperature

    NASA Astrophysics Data System (ADS)

    Fan, Haidong; Wang, Qingyuan; Ouyang, Chaojun

    2015-10-01

    The defect-free channels were frequently observed in irradiated materials, i.e. copper, as a result of the stacking fault tetrahedron (SFT) interactions with dislocations. However, the underlying mechanisms for this process are still unclear to date. To address them, a comprehensive study on the interactions between SFTs and mixed dislocations was performed using molecular dynamics simulations. In particular, eight interaction geometries were considered, in terms of the dislocation Burgers vector directions, dislocation gliding directions and intersection positions on SFT. Various interaction outcomes were revealed after dislocation detachment. (1) SFT is fully absorbed through the transformation into Lomer dislocations, and subsequently moves out of free surfaces along the dislocation. (2) SFT is partially absorbed with the absorbed SFT base moving out of free surfaces along the dislocation. (3) SFT is not absorbed but sheared with ledges left on the SFT faces. (4) SFT is unaffected by the mixed dislocation. The current simulations, especially the full SFT absorption, provide important insights into the forming mechanisms of defect-free channels in irradiated materials.

  13. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

    PubMed

    Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

    2015-12-01

    Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell. PMID:26657340

  14. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures

    PubMed Central

    Caetano, Fabiana A.; Dirk, Brennan S.; Tam, Joshua H. K.; Cavanagh, P. Craig; Goiko, Maria; Ferguson, Stephen S. G.; Pasternak, Stephen H.; Dikeakos, Jimmy D.; de Bruyn, John R.; Heit, Bryan

    2015-01-01

    Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell. PMID:26657340

  15. VMD: visual molecular dynamics.

    PubMed

    Humphrey, W; Dalke, A; Schulten, K

    1996-02-01

    VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web. PMID:8744570

  16. Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations

    PubMed Central

    Meher, Biswa Ranjan; Dixit, Anshuman; Bousfield, George R.; Lushington, Gerald H.

    2015-01-01

    The gonadotropin known as follicle-stimulating hormone (FSH) plays a key role in regulating reproductive processes. Physiologically active FSH is a glycoprotein that can accommodate glycans on up to four asparagine residues, including two sites in the FSHα subunit that are critical for biochemical function, plus two sites in the β subunit, whose differential glycosylation states appear to correspond to physiologically distinct functions. Some degree of FSHβ hypo-glycosylation seems to confer advantages toward reproductive fertility of child-bearing females. In order to identify possible mechanistic underpinnings for this physiological difference we have pursued computationally intensive molecular dynamics simulations on complexes between the high affinity site of the gonadal FSH receptor (FSHR) and several FSH glycoforms including fully-glycosylated (FSH24), hypo-glycosylated (e.g., FSH15), and completely deglycosylated FSH (dgFSH). These simulations suggest that deviations in FSH/FSHR binding profile as a function of glycosylation state are modest when FSH is adorned with only small glycans, such as single N-acetylglucosamine residues. However, substantial qualitative differences emerge between FSH15 and FSH24 when FSH is decorated with a much larger, tetra-antennary glycan. Specifically, the FSHR complex with hypo-glycosylated FSH15 is observed to undergo a significant conformational shift after 5–10 ns of simulation, indicating that FSH15 has greater conformational flexibility than FSH24 which may explain the more favorable FSH15 kinetic profile. FSH15 also exhibits a stronger binding free energy, due in large part to formation of closer and more persistent salt-bridges with FSHR. PMID:26402790

  17. Energy and structure of bonds in the interaction of organic anions with layered double hydroxide nanosheets: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Tsukanov, A. A.; Psakhie, S. G.

    2016-01-01

    The application of hybrid and hierarchical nanomaterials based on layered hydroxides and oxyhydroxides of metals is a swiftly progressing field in biomedicine. Layered double hydroxides (LDH) possess a large specific surface area, significant surface electric charge and biocompatibility. Their physical and structural properties enable them to adsorb various kinds of anionic species and to transport them into cells. However, possible side effects resulting from the interaction of LDH with anions of the intercellular and intracellular medium need to be considered, since such interaction can potentially disrupt ion transport, signaling processes, apoptosis, nutrition and proliferation of living cells. In the present paper molecular dynamics is used to determine the energies of interaction of organic anions (aspartic acid, glutamic acid and bicarbonate) with a fragment of layered double hydroxide Mg/Al-LDH. The average number of hydrogen bonds between the anions and the hydroxide surface and characteristic binding configurations are determined. Possible effects of LDH on the cell resulting from binding of protein fragments and replacement of native intracellular anions with delivered anions are considered.

  18. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    PubMed Central

    Bai, Qifeng; Yao, Xiaojun

    2016-01-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1. PMID:26887338

  19. Interaction of collagen with chlorosulphonated paraffin tanning agents: Fourier transform infrared spectroscopic analysis and molecular dynamics simulations.

    PubMed

    Monti, Susanna; Bramanti, Emilia; Della Porta, Valentina; Onor, Massimo; D'Ulivo, Alessandro; Barone, Vincenzo

    2013-09-21

    The binding of chlorosulphonated paraffins to collagen triple helices is studied by means of classical molecular dynamics simulations and experimental spectroscopic techniques in order to disclose the principal characteristics of their interaction during the leather fattening process. Indeed, collagen is the main target to develop new leather modifying agents with specific characteristics, and an accurate design of the collagen binders, supported by predictive computational strategies, could be a successful tool to obtain new effective eco-compatible compounds able to impart to the leather the required functionalities and distinctive mechanical properties. Possible effects caused by the tanning agents on the collagen matrix have been identified from both experimental and theoretical points of view. Computational data in agreement with experiment have revealed that chlorosulphonated paraffins can interact favorably with the collagen residues having amine groups in their side chains (Arg, Lys, Asn and Gln) and reduce the tendency of the solvated collagen matrix to swell. However, the interference of chlorosulphonated paraffins with the unfolding process, which is operated mainly by the action of water, can be due both to covalent cross-linking of the collagen chains and intermolecular hydrogen bonding interactions involving also the hydroxyl groups of Hyp, Ser and Thr residues. PMID:23904010

  20. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    NASA Astrophysics Data System (ADS)

    Bai, Qifeng; Yao, Xiaojun

    2016-02-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1.

  1. Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations.

    PubMed Central

    Shepherd, Craig M; Vogel, Hans J; Tieleman, D Peter

    2003-01-01

    Molecular-dynamics simulations covering 30 ns of both a natural and a synthetic antimicrobial peptide in the presence of a zwitterionic lipid bilayer were performed. In both simulations, copies of the peptides were placed in an alpha-helical conformation on either side of the bilayer about 10 A (1 A=0.1 nm) from the interface, with either the hydrophobic or the positively charged face of the helix directed toward the bilayer surface. The degree of peptide-lipid interaction was dependent on the starting configuration: surface binding and subsequent penetration of the bilayer was observed for the hydrophobically oriented peptides, while the charge-oriented peptides demonstrated at most partial surface binding. Aromatic residues near the N-termini of the peptides appear to play an important role in driving peptide-lipid interactions. A correlation between the extent of peptide-lipid interactions and helical stability was observed in the simulations. Insertion of the peptides into the bilayer caused a dramatic increase in the lateral area per lipid and decrease in the bilayer thickness, resulting in substantial disordering of the lipid chains. Results from the simulations are consistent with early stages of proposed mechanisms for the lytic activity of antimicrobial peptides. In addition to these 'free' simulations, 25 ns simulations were carried out with the peptides constrained at three different distances relative to the bilayer interface. The constraint forces are in agreement with the extent of peptide-bilayer insertion observed in the free simulations. PMID:12423203

  2. Energy and structure of bonds in the interaction of organic anions with layered double hydroxide nanosheets: A molecular dynamics study

    PubMed Central

    Tsukanov, A.A.; Psakhie, S.G.

    2016-01-01

    The application of hybrid and hierarchical nanomaterials based on layered hydroxides and oxyhydroxides of metals is a swiftly progressing field in biomedicine. Layered double hydroxides (LDH) possess a large specific surface area, significant surface electric charge and biocompatibility. Their physical and structural properties enable them to adsorb various kinds of anionic species and to transport them into cells. However, possible side effects resulting from the interaction of LDH with anions of the intercellular and intracellular medium need to be considered, since such interaction can potentially disrupt ion transport, signaling processes, apoptosis, nutrition and proliferation of living cells. In the present paper molecular dynamics is used to determine the energies of interaction of organic anions (aspartic acid, glutamic acid and bicarbonate) with a fragment of layered double hydroxide Mg/Al-LDH. The average number of hydrogen bonds between the anions and the hydroxide surface and characteristic binding configurations are determined. Possible effects of LDH on the cell resulting from binding of protein fragments and replacement of native intracellular anions with delivered anions are considered. PMID:26817816

  3. Energy and structure of bonds in the interaction of organic anions with layered double hydroxide nanosheets: A molecular dynamics study.

    PubMed

    Tsukanov, A A; Psakhie, S G

    2016-01-01

    The application of hybrid and hierarchical nanomaterials based on layered hydroxides and oxyhydroxides of metals is a swiftly progressing field in biomedicine. Layered double hydroxides (LDH) possess a large specific surface area, significant surface electric charge and biocompatibility. Their physical and structural properties enable them to adsorb various kinds of anionic species and to transport them into cells. However, possible side effects resulting from the interaction of LDH with anions of the intercellular and intracellular medium need to be considered, since such interaction can potentially disrupt ion transport, signaling processes, apoptosis, nutrition and proliferation of living cells. In the present paper molecular dynamics is used to determine the energies of interaction of organic anions (aspartic acid, glutamic acid and bicarbonate) with a fragment of layered double hydroxide Mg/Al-LDH. The average number of hydrogen bonds between the anions and the hydroxide surface and characteristic binding configurations are determined. Possible effects of LDH on the cell resulting from binding of protein fragments and replacement of native intracellular anions with delivered anions are considered. PMID:26817816

  4. Protein-Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure.

    PubMed

    Andersen, Amity; Reardon, Patrick N; Chacon, Stephany S; Qafoku, Nikolla P; Washton, Nancy M; Kleber, Markus

    2016-06-21

    Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na(+)-montmorillonite (001), Ca(2+)-montmorillonite (001), goethite (100), and Na(+)-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na(+)-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation. PMID:27243116

  5. Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study

    PubMed Central

    Jefferies, Damien; Sessions, Richard B.; Bond, Peter J.; Khalid, Syma

    2015-01-01

    Antimicrobial peptides are small, cationic proteins that can induce lysis of bacterial cells through interaction with their membranes. Different mechanisms for cell lysis have been proposed, but these models tend to neglect the role of the chemical composition of the membrane, which differs between bacterial species and can be heterogeneous even within a single cell. Moreover, the cell envelope of Gram-negative bacteria such as E. coli contains two membranes with differing compositions. To this end, we report the first molecular dynamics simulation study of the interaction of the antimicrobial peptide, polymyxin B1 with complex models of both the inner and outer membranes of E. coli. The results of >16 microseconds of simulation predict that polymyxin B1 is likely to interact with the membranes via distinct mechanisms. The lipopeptides aggregate in the lipopolysaccharide headgroup region of the outer membrane with limited tendency for insertion within the lipid A tails. In contrast, the lipopeptides readily insert into the inner membrane core, and the concomitant increased hydration may be responsible for bilayer destabilization and antimicrobial function. Given the urgent need to develop novel, potent antibiotics, the results presented here reveal key mechanistic details that may be exploited for future rational drug development. PMID:25885324

  6. Molecular Dynamics of Water Mediated Interactions of a Linear Benzimidazole-Biphenyl Diamidine with the DNA Minor Groove

    PubMed Central

    Athri, Prashanth; Wilson, W. David

    2009-01-01

    DB921 has a benzimidazole-biphenyl system with terminal amidines that gives the compound a linear conformation with a radius of curvature that does not match the DNA minor groove shape. Surprisingly, the compound binds in the groove with an unusually high equilibrium constant [Miao, Y.; Lee, M. P. H.; Parkinson, G. N.; Batista-Parra, A.; Ismail, M. A.; Neidle, S.; Boykin, D. W.; Wilson, W. D. Biochemistry 2005, 44, 14701-14708]. X-ray crystallographic analysis of DB921 bound to -AATT- in d(CGCGAATTCGCG)2 showed that the benzimidazole is in position to directly interact with bases at the floor of the groove while the phenylamidine of DB921 forms indirect contacts with the bases through an interfacial water. The DB921-water pair forms a curved, flexible module with a high Ka (or a low Kd) value of binding. To better understand the dynamics of the DB921-DNA complex and how water can be used in the design of compounds to recognize DNA, a 100 ns molecular dynamics simulation of the complex was conducted. In addition to the X-ray conformation some significantly variant, dynamic conformations, which had additional interfacial water molecules between DB921 and DNA, appeared in the MD simulation. The benzimidazole contacts remained relatively constant through the entire simulation. The biphenyl-amidine end of the bound molecule, however, undergoes much larger changes in orientation relative to the floor of the groove as well as variations in the type of water interactions. The results provide an understanding of how water couples the linear DB921 compound to the minor groove for tight binding, without a large unfavorable contribution to the entropy of binding. PMID:19445463

  7. Interaction of polar and nonpolar organic pollutants with soil organic matter: sorption experiments and molecular dynamics simulation.

    PubMed

    Ahmed, Ashour A; Thiele-Bruhn, Sören; Aziz, Saadullah G; Hilal, Rifaat H; Elroby, Shaaban A; Al-Youbi, Abdulrahman O; Leinweber, Peter; Kühn, Oliver

    2015-03-01

    The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is still lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model and carried out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), simulating the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and theoretical investigations explored four major points regarding sorption of SAA and HCB on soil, yielding the following results. 1--The interaction depends on the SOM chemical composition more than the SOM content. 2--The interaction causes a site-specific adsorption on the soil surfaces. 3--Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4--The hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA. Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution, while most of SAA-SOM complexes are accompanied by dissociation into SAA and the free SOM models. The SOM-cavity modeling had a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity>a large cavity>no cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by the presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid

  8. A microfluidic chamber to study the dynamics of muscle-contraction-specific molecular interactions.

    PubMed

    Roman, Horia Nicolae; Juncker, David; Lauzon, Anne-Marie

    2015-03-01

    In vitro motility and laser trap assays are commonly used for molecular mechanics measurements. However, chemicals cannot be added during these measurements, because they create flows that alter the molecular mechanics. Thus, we designed a microfluidic device that allows the addition of chemicals without creating bulk flows. Biocompatibility of the components of this device was tested. A microchannel chamber was created by photolithography with the patterns transferred to polydimethylsiloxane (PDMS). The PDMS chamber was bound to a polycarbonate membrane, which itself was bound to a molecular mechanics chamber. The microchannels ensured rapid distribution of the chemicals over the membrane, whereas the membrane ensured efficient delivery to the mechanics chamber while preventing bulk flow. The biocompatibility of the materials was tested by comparing the velocity (ν(max)) of propulsion by myosin of fluorescently labeled actin filaments to that of the conventional assay; no difference in ν(max) was observed. To estimate total chemical delivery time, labeled bovine serum albumin was injected in the channel chamber and TIRF was used to determine the time to reach the assay surface (2.7 ± 0.1 s). Furthermore, the standard distance of a trapped microsphere calculated during buffer diffusion using the microfluidic device (14.9 ± 3.2 nm) was not different from that calculated using the conventional assay (15.6 ± 5.3 nm, p = 0.922). Finally, ν(max) obtained by injecting adenosine triphosphate (ATP) in the microchannel chamber (2.37 ± 0.48 μm/s) was not different from that obtained when ATP was delivered directly to the mechanics chamber (2.52 ± 0.42 μm/s, p = 0.822). This microfluidic prototype validates the design for molecular mechanics measurements. PMID:25629255

  9. The Interaction Potential of an Open Nanotube and its Permeability: Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Bubenchikov, Mikhail A.; Potekaev, Alexander I.; Bubenchikov, Alexey M.; Usenko, Olesya V.; Malozemov, Alexander V.; Tarasov, Egor A.

    2016-02-01

    The integration of the modified LJ-potential allowed revealing the universal effect of the open carbon tube on the molecular objects moving within or proximate to the tube. There has been established that there are modes of the molecule motion without the energy exchange with the atoms of the carbon framing, under which the moving molecules are subjected to the considerable activation in the tube. The potential holes being the sorption zones in fact are localized.

  10. Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer.

    PubMed

    Malajczuk, Chris J; Hughes, Zak E; Mancera, Ricardo L

    2013-09-01

    Molecular dynamics (MD) simulations have been used to investigate the interactions of a variety of hydroxylated cryosolvents (glycerol, propylene glycol and ethylene glycol), methanol and dimethyl sulfoxide (DMSO) in aqueous solution with a 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) bilayer in its fluid phase at 323K. Each cryosolvent induced lateral expansion of the membrane leading to thinning of the bilayer and resulting in disordering of the lipid hydrocarbon chains. Propylene glycol and DMSO were observed to exhibit a greater disordering effect on the structure of the membrane than the other three alcohols. Closer examination exposed a number of effects on the lipid bilayer as a function of the molecular size and hydrogen bonding capacity of the cryosolvents. Analyses of hydrogen bonds revealed that increased concentrations of the polyhydroxylated cryosolvents induced the formation of a cross-linked cryosolvent layer across the surface of the membrane bilayer. This effect was most pronounced for glycerol at sufficiently high concentrations, which displayed a comparatively enhanced capacity to induce cross-linking of lipid headgroups resulting in the formation of extensive hydrogen bonding bridges and the promotion of a dense cryosolvent layer across the phospholipid bilayer. PMID:23707690

  11. Substructured multibody molecular dynamics.

    SciTech Connect

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  12. Superposition State Molecular Dynamics.

    PubMed

    Venkatnathan, Arun; Voth, Gregory A

    2005-01-01

    The ergodic sampling of rough energy landscapes is crucial for understanding phenomena like protein folding, peptide aggregation, polymer dynamics, and the glass transition. These rough energy landscapes are characterized by the presence of many local minima separated by high energy barriers, where Molecular Dynamics (MD) fails to satisfy ergodicity. To enhance ergodic behavior, we have developed the Superposition State Molecular Dynamics (SSMD) method, which uses a superposition of energy states to obtain an effective potential for the MD simulation. In turn, the dynamics on this effective potential can be used to sample the configurational free energy of the real potential. The effectiveness of the SSMD method for a one-dimensional rough potential energy landscape is presented as a test case. PMID:26641113

  13. Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations.

    PubMed

    Yi, Changhong; Wambo, Thierry O

    2015-09-21

    Beta-lactoglobulin (BLG), a bovine dairy protein, is a promiscuously interacting protein that can bind multiple hydrophobic ligands. Fatty acids (FAs), common hydrophobic molecules bound to BLG, are important sources of fuel for life because they yield large quantities of ATP when metabolized. The binding affinity increases with the length of the ligands, indicating the importance of the van der Waals (vdW) interactions between the hydrocarbon tail and the hydrophobic calyx of BLG. An exception to this rule is caprylic acid (OCA) which is two-carbon shorter but has a stronger binding affinity than capric acid. Theoretical calculations in the current literature are not accurate enough to shed light on the underlying physics of this exception. The computed affinity values are greater for longer fatty acids without respect for the caprylic exception and those values are generally several orders of magnitude away from the experimental data. In this work, we used hybrid steered molecular dynamics to accurately compute the binding free energies between BLG and the five saturated FAs of 8 to 16 carbon atoms. The computed binding free energies agree well with experimental data not only in rank but also in absolute values. We gained insights into the exceptional behavior of caprylic acid in the computed values of entropy and electrostatic interactions. We found that the electrostatic interaction between the carboxyl group of caprylic acid and the two amino groups of K60/69 in BLG is much stronger than the vdW force between the OCA's hydrophobic tail and the BLG calyx. This pulls OCA to the top of the beta barrel where it is easier to fluctuate, giving rise to greater entropy of OCA at the binding site. PMID:26272099

  14. Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

    2013-08-01

    In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.

  15. A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods.

    PubMed

    VandeVondele, Joost; Sprik, Michiel

    2005-04-01

    We have performed density functional theory based molecular dynamics (MD) simulations of the *OH radical in solution using self-interaction corrected (SIC) methods. We use a scheme recently proposed by M. d'Avezac, M. Calandra and F. Mauri [arXiv:cond-mat/0407750] in which a correction is only applied to the spin density within a restricted open shell formulation. In addition to two correction formulas employed within this scheme by M. d'Avezac, M. Calandra and F. Mauri, we propose and test an new empirical form which only introduces a scaled Coulomb term. This new functional leads to good agreement with reference calculations on radical cation dimers and on the hydroxyl water dimer in the gas phase. Applied in ab initio MD simulations, these three SIC methods provide a picture of the *OH solvation that differs qualitatively from the one obtained using the standard generalised gradient approximation (GGA). Hemibonded water, observed in GGA simulations and believed to be an artefact due to self-interaction error, is not present. We find that the *OH acts as a good hydrogen bond donor, but accepts less than two hydrogen bonds on average. These hydrogen bonds are part of a mobile, otherwise quasi-hydrophobic solvation cage. Our results show the potential of this computationally expedient scheme, which might extend the range of problems that can be modelled adequately with density functional theory. PMID:19787955

  16. Molecular dynamics study on the interactions between helium projectiles and helium bubbles pre-existing in tungsten surfaces

    NASA Astrophysics Data System (ADS)

    Ding, Yuan; Ma, Chaoqiong; Li, Min; Hou, Qing

    2016-02-01

    Molecular dynamics simulations were performed to study the interactions between low-energy (⩽100 eV) helium (He) projectiles and helium bubbles pre-existing near tungsten (W) surfaces. It is observed that with increasing bubble size, the reflection coefficient of the He projectiles was reduced, and the channelling effect that could be observed with no pre-existing He bubble was depressed. The He projectiles can be captured by pre-existing He bubbles and also knock He atoms out of the bubbles. The spatial distribution of the single He atoms, including both the slowed-down projectiles and the knocked-out He atoms, was extracted. The single He atoms were found distributed around the bubbles in a region with the width of 3-5.5 in lattice lengths of W. Although the results were obtained for the interaction of He projectiles with isolated He bubbles pre-existing in W, they suggest that the reflection and retention status of He projectiles would change during the irradiation of high flux/fluence He on W surfaces due to the change of He bubbles coverage near W surfaces. The results can be coupled with Monte Carlo modelling in conditions closer to that in experiments of high flux/fluence He bombardments on W surfaces.

  17. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase

    PubMed Central

    Sharma, Reetu; Sastry, G. Narahari

    2015-01-01

    Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant’s functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies. PMID:26657745

  18. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

    PubMed

    Sharma, Reetu; Sastry, G Narahari

    2015-01-01

    Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies. PMID:26657745

  19. Environmental Changes in MoTe2 Excitonic Dynamics by Defects-Activated Molecular Interaction.

    PubMed

    Chen, Bin; Sahin, Hasan; Suslu, Aslihan; Ding, Laura; Bertoni, Mariana I; Peeters, F M; Tongay, Sefaattin

    2015-05-26

    Monolayers of group VI transition metal dichalcogenides possess direct gaps in the visible spectrum with the exception of MoTe2, where its gap is suitably located in the infrared region but its stability is of particular interest, as tellurium compounds are acutely sensitive to oxygen exposure. Here, our environmental (time-dependent) measurements reveal two distinct effects on MoTe2 monolayers: For weakly luminescent monolayers, photoluminescence signal and optical contrast disappear, as if they are decomposed, but yet remain intact as evidenced by AFM and Raman measurements. In contrast, strongly luminescent monolayers retain their optical contrast for a prolonged amount of time, while their PL peak blue-shifts and PL intensity saturates to slightly lower values. Our X-ray photoelectron spectroscopy measurements and DFT calculations suggest that the presence of defects and functionalization of these defect sites with O2 molecules strongly dictate their material properties and aging response by changing the excitonic dynamics due to deep or shallow states that are created within the optical band gap. Presented results not only shed light on environmental effects on fundamental material properties and excitonic dynamics of MoTe2 monolayers but also highlight striking material transformation for metastable 2D systems such as WTe2, silicone, and phosphorene. PMID:25868985

  20. Structures of [Li(glyme)](+) complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: analysis by molecular dynamics simulations.

    PubMed

    Tsuzuki, Seiji; Shinoda, Wataru; Matsugami, Masaru; Umebayashi, Yasuhiro; Ueno, Kazuhide; Mandai, Toshihiko; Seki, Shiro; Dokko, Kaoru; Watanabe, Masayoshi

    2015-01-01

    Molecular dynamics simulations of equimolar mixtures of glymes (triglyme and tetraglyme) and Li[TFSA] (lithium bis(trifluoromethylsulfonyl)amide) show that the glyme chain length affects the coordination geometries of Li(+), which induces the changes in interactions between the [Li(glyme)](+) complex and [TFSA](-) anions and diffusion of ions in the equimolar mixtures. PMID:25407234

  1. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    PubMed

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions. PMID:17518448

  2. The distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of two distal histidine tautomers.

    PubMed Central

    Jewsbury, P; Kitagawa, T

    1994-01-01

    Four independent 90 ps molecular dynamics simulations of sperm-whale wild-type carbonmonoxy myoglobin (MbCO) have been calculated using a new AMBER force field for the haem prosthetic group. Two trajectories have the distal 64N delta nitrogen protonated, and two have the 64N epsilon nitrogen protonated; all water molecules within 16 A of the carbonyl O are included. In three trajectories, the distal residue remains part of the haem pocket, with the protonated distal nitrogen pointing into the active site. This is in contrast with the neutron diffraction crystal structure, but is consistent with the solution phase CO stretching frequencies (upsilon CO) of MbCO and various of its mutants. There are significant differences in the "closed" pocket structures found for each tautomer: the 64N epsilon H trajectories both show stable distal-CO interactions, whereas the 64N delta H tautomer) has a weaker interaction resulting in a more mobile distal side chain. One trajectory (a 64N delta H tautomer) has the distal histidine moving out into the "solvent", leaving the pocket in an "open" structure, with a large unhindered entrance to the active site. These trajectories suggest that the three upsilon CO frequencies observed for wild-type MbCO in solution, rather than representing significantly different Fe-C-O geometries as such, arise from three different haem pocket structures, each with different electric fields at the ligand. Each pocket structure corresponds to a different distal histidine conformer: the A3 band to the 64N epsilon H tautomer, the A1,2 band to the 64N delta H tautomer, and the A0 band to the absence of any significant interaction with the distal side chain. PMID:7696465

  3. On the interactions between nucleotide binding domains and membrane spanning domains in cystic fibrosis transmembrane regulator: A molecular dynamic study.

    PubMed

    Belmonte, Luca; Moran, Oscar

    2015-04-01

    The Cystic Fibrosis Transmembrane Regulator (CFTR) is a membrane protein whose mutations cause cystic fibrosis, a lethal genetic disease. We performed a molecular dynamic (MD) study of the properties of the nucleotide binding domains (NBD) whose conformational changes, upon ATP binding, are the direct responsible of the gating mechanisms of CFTR. This study was done for the wild type (WT) CFTR and for the two most common mutations, ΔF508, that produces a traffic defect of the protein, and the mutation G551D, that causes a gating defect on CFTR. Using an homology model of the open channel conformation of the CFTR we thus introduced the mutations to the structure. Although the overall structures of the G551D and ΔF508 are quite well conserved, the NBD1-NBD2 interactions are severely modified in both mutants. NBD1 and NBD2 are indeed destabilized with a higher internal energy (Ei) in the ΔF508-CFTR. Differently, Ei does not change in the NBDs of G551D but, while the number of close contacts between NBD1 and NBD2 in ΔF508 is increased, a significant reduction of close contacts is found in the G551D mutated form. Hydrogen bonds formation between NBDs of the two mutated forms is also altered and it is slightly increased for the ΔF508, while are severely reduced in G551D. A consequent modification of the NBDs-ICLs interactions between residues involved in the transduction of the ATP binding and the channel gating is also registered. Indeed, while a major interaction is noticed between NBDs interface and ICL2 and ICL4 in the WT, this interaction is somehow altered in both mutated forms plausibly with effect on channel gating. Thus, single point mutations of the CFTR protein can reasonably results in channel gating defects due to alteration of the interaction mechanisms between the NBDs and NBDs-ICLs interfaces upon ATP-binding process. PMID:25640670

  4. Exploring the Interaction of SV2A with Racetams Using Homology Modelling, Molecular Dynamics and Site-Directed Mutagenesis

    PubMed Central

    Lee, Joanna; Daniels, Veronique; Sands, Zara A.; Lebon, Florence; Shi, Jiye; Biggin, Philip C.

    2015-01-01

    The putative Major Facilitator Superfamily (MFS) transporter, SV2A, is the target for levetiracetam (LEV), which is a successful anti-epileptic drug. Furthermore, SV2A knock out mice display a severe seizure phenotype and die after a few weeks. Despite this, the mode of action of LEV is not known at the molecular level. It would be extremely desirable to understand this more fully in order to aid the design of improved anti-epileptic compounds. Since there is no structure for SV2A, homology modelling can provide insight into the ligand-binding site. However, it is not a trivial process to build such models, since SV2A has low sequence identity to those MFS transporters whose structures are known. A further level of complexity is added by the fact that it is not known which conformational state of the receptor LEV binds to, as multiple conformational states have been inferred by tomography and ligand binding assays or indeed, if binding is exclusive to a single state. Here, we explore models of both the inward and outward facing conformational states of SV2A (according to the alternating access mechanism for MFS transporters). We use a sequence conservation analysis to help guide the homology modelling process and generate the models, which we assess further with Molecular Dynamics (MD). By comparing the MD results in conjunction with docking and simulation of a LEV-analogue used in radioligand binding assays, we were able to suggest further residues that line the binding pocket. These were confirmed experimentally. In particular, mutation of D670 leads to a complete loss of binding. The results shed light on the way LEV analogues may interact with SV2A and may help with the on-going design of improved anti-epileptic compounds. PMID:25692762

  5. Open boundary molecular dynamics

    NASA Astrophysics Data System (ADS)

    Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.

    2015-09-01

    This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.

  6. Interaction of run-in edge dislocations with twist grain boundaries in Al-a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Chandra, S.; Naveen Kumar, N.; Samal, M. K.; Chavan, V. M.; Patel, R. J.

    2016-06-01

    Grain boundaries play an important role in outlining the mechanical properties of crystalline materials. They act as sites for absorption/nucleation of dislocations, which are the main carriers of plastic deformation. In view of this, the interactions between edge dislocations and twist grain boundaries-dislocation pileup, dislocation absorption and dislocation emission were explored by performing molecular dynamics simulations in face-centered cubic Al using embedded atom method. The ?1 1 0? twist grain boundaries with various misorientation angles were selected for this purpose. It was found that the misorientation angle of boundary and stress anomalies arising from repeated dislocation absorption at the grain boundaries are the important parameters in determining the ability of the boundary to emit dislocations. Complex network of dislocations results in later stages of deformation, which may have a significant effect on the mechanical properties of the material. The peculiarities of dislocation nucleation, their emission from twist grain boundaries and the ramifications of this study towards development of higher length scale material models are discussed.

  7. dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.

    PubMed

    Drusin, Salvador I; Suarez, Irina P; Gauto, Diego F; Rasia, Rodolfo M; Moreno, Diego M

    2016-04-15

    Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex. PMID:26987516

  8. Detection of non-native hydrophobic interactions in the denatured state of lysozyme by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Paci, Emanuele; Vendruscolo, Michele

    2005-05-01

    The presence of native and non-native hydrophobic clusters of amino acids has been detected experimentally for the protein hen egg white lysozyme even under strongly denaturing conditions. We characterize the structure of these hydrophobic clusters by two series of molecular dynamics simulations. The first series shows that in the wild type protein a non-native cluster formed by four tryptophan residues (W62, W63, W108 and W111) is formed with significant probability under denaturing conditions. In contrast, as observed experimentally and indicated by the second series of simulations presented here, the same cluster is formed much more rarely in the W62G mutant, which reduces the hydrophobicity of the polypeptide chain in the interface region between the two structural domains in the native state of the protein. These results support the observation that non-native interactions may play an important role in the folding process of complex proteins by stabilizing intermediate states in which hydrophobic groups are sequestered from the solvent and thus prevented from initiating aggregation.

  9. Structural insights into the interactions of xpt riboswitch with novel guanine analogues: a molecular dynamics simulation study.

    PubMed

    Jain, Swapan S; Sonavane, Uddhavesh B; Uppuladinne, Mallikarjunachari V N; McLaughlin, Emily C; Wang, Weiqing; Black, Sheneil; Joshi, Rajendra R

    2015-01-01

    Ligand recognition in purine riboswitches is a complex process requiring different levels of conformational changes. Recent efforts in the area of purine riboswitch research have focused on ligand analogue binding studies. In the case of the guanine xanthine phosphoribosyl transferase (xpt) riboswitch, synthetic analogues that resemble guanine have the potential to tightly bind and subsequently influence the genetic expression of xpt mRNA in prokaryotes. We have carried out 25 ns Molecular Dynamics (MD) simulation studies of the aptamer domain of the xpt G-riboswitch in four different states: guanine riboswitch in free form, riboswitch bound with its cognate ligand guanine, and with two guanine analogues SJ1 and SJ2. Our work reveals novel interactions of SJ1 and SJ2 ligands with the binding core residues of the riboswitch. The ligands proposed in this work bind to the riboswitch with greater overall stability and lower root mean square deviations and fluctuations compared to guanine ligand. Reporter gene assay data demonstrate that the ligand analogues, upon binding to the RNA, lower the genetic expression of the guanine riboswitch. Our work has important implications for future ligand design and binding studies in the exciting field of riboswitches. PMID:24404773

  10. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    SciTech Connect

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-07

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  11. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-01

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  12. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations.

    PubMed

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-01

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper--the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO--it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile. PMID:24606380

  13. Interactions of hydrogen with the iron and iron carbide interfaces: a ReaxFF molecular dynamics study.

    PubMed

    Islam, Md Mahbubul; Zou, Chenyu; van Duin, Adri C T; Raman, Sumathy

    2016-01-14

    Hydrogen embrittlement (HE) is a well-known material phenomenon that causes significant loss in the mechanical strength of structural iron and often leads to catastrophic failures. In order to provide a detailed atomistic description of HE we have used a reactive bond order potential to adequately describe the diffusion of hydrogen as well as its chemical interaction with other hydrogen atoms, defects, and the host metal. The currently published ReaxFF force field for Fe/C/H systems was originally developed to describe Fischer-Tropsch (FT) catalysis [C. Zou, A. C. T. van Duin and D. C. Sorescu, Top. Catal., 2012, 55, 391-401], and especially had been trained for surface formation energies, binding energies of small hydrocarbon radicals on different surfaces of iron and the barrier heights of surface reactions. We merged this force field with the latest ReaxFF carbon parameters [S. Goverapet Srinivasan, A. C. T. van Duin and P. Ganesh, J. Phys. Chem. A, 2015, 119, 1089-5639] and used the same training data set to refit the Fe/C interaction parameters. The present work is focused on evaluating the applicability of this reactive force field to describe material characteristics and study the role of defects and impurities in the bulk and at the precipitator interfaces. We study the interactions of hydrogen with pure and defective α-iron (ferrite), Fe3C (cementite), and ferrite-cementite interfaces with a vacancy cluster. We also investigate the growth of nanovoids in α-iron using a grand canonical Monte Carlo (GCMC) scheme. The calculated hydrogen diffusion coefficients for both ferrite and cementite phases predict a decrease in the work of separation with increasing hydrogen concentration at the ferrite-cementite interface, suggesting a hydrogen-induced decohesion behavior. Hydrogen accumulation at the interface was observed during molecular dynamics (MD) simulations, which is consistent with experimental findings. These results demonstrate the ability of the Reax

  14. Molecular Dynamics of Acetylcholinesterase

    SciTech Connect

    Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy

    2002-06-01

    Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.

  15. Defect-Enhanced Charge Transfer by Ion-Solid Interactions in SiC using Large-Scale Ab Initio Molecular Dynamics Simulations

    SciTech Connect

    Gao, Fei; Xiao, H. Y.; Zu, Xiaotao T.; Posselt, Matthias; Weber, William J.

    2009-07-10

    Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge-transfer occurs between atoms and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge transfer effects on recoil atoms.

  16. Defect-Enhanced Charge Transfer by Ion-Solid Interactions in SiC using Large-Scale Ab Initio Molecular Dynamics Simulations

    SciTech Connect

    Gao Fei; Weber, William J.; Xiao Haiyan; Zu Xiaotao; Posselt, Matthias

    2009-07-10

    Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge transfer occurs between atoms, and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge-transfer effects on recoil atoms.

  17. Parallel Molecular Dynamics Program for Molecules

    Energy Science and Technology Software Center (ESTSC)

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  18. Cholesterol-Ceramide Interactions in Phospholipid and Sphingolipid Bilayers As Observed by Positron Annihilation Lifetime Spectroscopy and Molecular Dynamics Simulations.

    PubMed

    García-Arribas, Aritz B; Axpe, Eneko; Mujika, Jon Iñaki; Mérida, David; Busto, Jon V; Sot, Jesús; Alonso, Alicia; Lopez, Xabier; García, Jose Ángel; Ugalde, Jesus M; Plazaola, Fernando; Goñi, Félix M

    2016-05-31

    Free volume voids in lipid bilayers can be measured by positron annihilation lifetime spectroscopy (PALS). This technique has been applied, together with differential scanning calorimetry and molecular dynamics (MD) simulations, to study the effects of cholesterol (Chol) and ceramide (Cer) on free volume voids in sphingomyelin (SM) or dipalmitoylphosphatidylcholine (DPPC) bilayers. Binary lipid samples with Chol were studied (DPPC:Chol 60:40, SM:Chol 60:40 mol ratio), and no phase transition was detected in the 20-60 °C range, in agreement with calorimetric data. Chol-driven liquid-ordered phase showed an intermediate free volume void size as compared to gel and fluid phases. For SM and SM:Cer (85:15 mol:mol) model membranes measured in the 20-60 °C range the gel-to-fluid phase transition could be observed with a related increase in free volume, which was more pronounced for the SM:Cer sample. MD simulations suggest a hitherto unsuspected lipid tilting in SM:Cer bilayers but not in pure SM. Ternary samples of DPPC:Cer:Chol (54:23:23) and SM:Cer:Chol (54:23:23) were measured, and a clear pattern of free volume increase was observed in the 20-60 °C because of the gel-to-fluid transition. Interestingly, MD simulations showed a tendency of Cer to change its distribution along the membrane to make room for Chol in ternary mixtures. The results suggest that the gel phase formed in these ternary mixtures is stabilized by Chol-Cer interactions. PMID:27158737

  19. Interactions of the C-terminal Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

    NASA Technical Reports Server (NTRS)

    Hu, Shaowen; Huff, Janice; Pluth, Janice M.; Cucinotta, Francis A.

    2007-01-01

    NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku(sub 70/80) complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The C-terminal domain of Ku70 (Ku70c, residues 559-609), contains an helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the Ku70c/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the subunit Ku70c and a 14 base pairs DNA duplex, whose starting structures are designed to be variable so as to mimic their different binding modes. By analyzing conformational changes and energetic properties of the complex during MD simulations, we found that interactions are preferred at DNA ends, and within the major groove, which is consistent with previous experimental investigations. In addition, the results indicate that cooperation of Ku70c with other subunits of Ku(sub 70/80) is necessary to explain the high affinity of binding as observed in experiments.

  20. Interactive Modelling of Molecular Structures

    NASA Astrophysics Data System (ADS)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  1. Molecular ions, Rydberg spectroscopy and dynamics

    SciTech Connect

    Jungen, Ch.

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  2. Influence of the R823W mutation on the interaction of the ANKS6-ANKS3: insights from molecular dynamics simulation and free energy analysis.

    PubMed

    Kan, Wei; Fang, Fengqin; Chen, Lin; Wang, Ruige; Deng, Qigang

    2016-05-01

    The sterile alpha motif (SAM) domain of the protein ANKS6, a protein-protein interaction domain, is responsible for autosomal dominant polycystic kidney disease. Although the disease is the result of the R823W point mutation in the SAM domain of the protein ANKS6, the molecular details are still unclear. We applied molecular dynamics simulations, the principal component analysis, and the molecular mechanics Poisson-Boltzmann surface area binding free energy calculation to explore the structural and dynamic effects of the R823W point mutation on the complex ANKS6-ANKS3 (PDB ID: 4NL9) in comparison to the wild proteins. The energetic analysis presents that the wild type has a more stable structure than the mutant. The R823W point mutation not only disrupts the structure of the ANKS6 SAM domain but also negatively affects the interaction of the ANKS6-ANKS3. These results further clarify the previous experiments to understand the ANKS6-ANKS3 interaction comprehensively. In summary, this study would provide useful suggestions to understand the interaction of these proteins and their fatal action on mediating kidney function. PMID:26295479

  3. Introduction to Accelerated Molecular Dynamics

    SciTech Connect

    Perez, Danny

    2012-07-10

    Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.

  4. Molecular Dynamics Calculations

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two

  5. Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems

    SciTech Connect

    Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi

    2015-01-22

    In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.

  6. Specific ion interactions with aromatic rings in aqueous solutions: Comparison of molecular dynamics simulations with a thermodynamic solute partitioning model and Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Vincent, Jordan C.; Matt, Sarah M.; Rankin, Blake M.; D'Auria, Raffaella; Freites, J. Alfredo; Ben-Amotz, Dor; Tobias, Douglas J.

    2015-10-01

    Specific ion interactions of KF, and the Na+ salts of SO42-, F-, Cl-, NO3-, I-, and ClO4- with benzene in aqueous solutions were investigated using molecular dynamics simulations and compared with experimental Raman multivariate curve resolution (Raman-MCR) and thermodynamic results. Good agreement is found with the hydration-shell partition coefficients of salts obtained from the thermodynamic analysis and of halogen anions obtained from the Raman-MCR spectra of benzene and pyridine. Larger discrepancies between the simulation and thermodynamic cation partitioning results point to the influence of counter-ion interaction on cation partitioning.

  7. Molecular dynamics simulations

    SciTech Connect

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.

  8. Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

    NASA Astrophysics Data System (ADS)

    Makarov, G. N.; Petin, A. N.

    2016-03-01

    We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF6 and CF3I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF6 molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation.

  9. A molecular dynamics study of model SI clathrate hydrates: the effect of guest size and guest-water interaction on decomposition kinetics.

    PubMed

    Das, Subhadip; Baghel, Vikesh Singh; Roy, Sudip; Kumar, Rajnish

    2015-04-14

    One of the options suggested for methane recovery from natural gas hydrates is molecular replacement of methane by suitable guests like CO2 and N2. This approach has been found to be feasible through many experimental and molecular dynamics simulation studies. However, the long term stability of the resultant hydrate needs to be evaluated; the decomposition rate of these hydrates is expected to depend on the interaction between these guest and water molecules. In this work, molecular dynamics simulation has been performed to illustrate the effect of guest molecules with different sizes and interaction strengths with water on structure I (SI) hydrate decomposition and hence the stability. The van der Waals interaction between water of hydrate cages and guest molecules is defined by Lennard Jones potential parameters. A wide range of parameter spaces has been scanned by changing the guest molecules in the SI hydrate, which acts as a model gas for occupying the small and large cages of the SI hydrate. All atomistic simulation results show that the stability of the hydrate is sensitive to the size and interaction of the guest molecules with hydrate water. The increase in the interaction of guest molecules with water stabilizes the hydrate, which in turn shows a slower rate of hydrate decomposition. Similarly guest molecules with a reasonably small (similar to Helium) or large size increase the decomposition rate. The results were also analyzed by calculating the structural order parameter to understand the dynamics of crystal structure and correlated with the release rate of guest molecules from the solid hydrate phase. The results have been explained based on the calculation of potential energies felt by guest molecules in amorphous water, hydrate bulk and hydrate-water interface regions. PMID:25767053

  10. Molecular dynamics simulation of benzene

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

    Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.

  11. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

    PubMed Central

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue–residue couplings associated with cooperative folding emerges. Such thermodynamic residue–residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins. PMID:25924808

  12. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations.

    PubMed

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano; Lindorff-Larsen, Kresten; Cerminara, Michele; Santiveri, Clara M; Shaw, David E; de Alba, Eva; Muñoz, Victor

    2015-05-27

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue-residue couplings associated with cooperative folding emerges. Such thermodynamic residue-residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins. PMID:25924808

  13. Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics.

    PubMed

    Yamamoto, Eiji; Kalli, Antreas C; Yasuoka, Kenji; Sansom, Mark S P

    2016-08-01

    A molecular simulation pipeline for determining the mode of interaction of pleckstrin homology (PH) domains with phosphatidylinositol phosphate (PIP)-containing lipid bilayers is presented. We evaluate our methodology for the GRP1 PH domain via comparison with structural and biophysical data. Coarse-grained simulations yield a 2D density landscape for PH/membrane interactions alongside residue contact profiles. Predictions of the membrane localization and interactions of 13 PH domains reveal canonical, non-canonical, and dual PIP-binding sites on the proteins. Thus, the PH domains associate with the PIP molecules in the membrane via a highly positively charged loop. Some PH domains exhibit modes of interaction with PIP-containing membranes additional to this canonical binding mode. All 13 PH domains cause a degree of local clustering of PIP molecules upon binding to the membrane. This provides a global picture of PH domain interactions with membranes. The high-throughput approach could be extended to other families of peripheral membrane proteins. PMID:27427480

  14. Dynamics of Galaxy Interactions

    NASA Astrophysics Data System (ADS)

    Barnes, Joshua E.

    Preface Theory of Interacting Galaxies The Role of Gravity Holmberg's Work on Tidal Interactions "Galactic Bridges and Tails" Dark Matter Numerical Stellar Dynamics Collisionless Stellar Systems Simulating the Stars Force Calculation Time Integration Errors and Relaxation Effects Initial Conditions Numerical Gas Dynamics A Sketch of the Interstellar Medium Simulating the ISM Gas in B/D/H Models Tidal Interactions Test-Particle Studies: Bridges and Tails Self-Consistent Studies Bars and Spirals Tidal Dwarf Galaxies Self-Consistent "Lookalikes" Getting the Feel of the Antennae Sneaking Up on the Mice What Happened to the Whirlpool? Unresolved Issues Mechanics of Merging Tidal Drag Orbit Decay Violent Relaxation Final Encounters Remnant Structure Phase Mixing Characteristics Scales Radial Profiles Shapes and Kinematics Orbit Structure Gas Dynamics in Mergers Inflows in Perturbed Disks Merging Encounters Remnant Structure Dissipation and Stellar Backlash Galaxy transformation and the Arrow of Time

  15. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

    We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690

  16. Radiation in molecular dynamic simulations

    SciTech Connect

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M

    2008-10-13

    Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

  17. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    SciTech Connect

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.

  18. Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields.

    PubMed

    Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-12

    Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields, which have been developed and validated using relatively short simulations of small molecules, become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge-charge interactions. Here, we report a systematic atom pair-specific refinement of Lennard-Jones parameters (NBFIX) describing amine-carboxylate and amine-phosphate interactions, which bring MD simulations of basic peptide-mediated nucleic acid assemblies and lipid bilayer membranes into better agreement with experimental data. As our refinement does not affect the existing parametrization of bonded interactions or alter the solvation free energies, it improves the realism of an MD simulation without introducing additional artifacts. PMID:26632962

  19. Effects of hesperidin, a flavanone glycoside interaction on the conformation, stability, and aggregation of lysozyme: multispectroscopic and molecular dynamic simulation studies?

    PubMed

    Ratnaparkhi, Aditi; Muthu, Shivani A; Shiriskar, Sonali M; Pissurlenkar, Raghuvir R S; Choudhary, Sinjan; Ahmad, Basir

    2015-09-01

    Hesperidin (HESP), a flavanone glycoside, shows high antioxidant properties and possess ability to go through the blood-brain barrier. Therefore, it could be a potential drug molecule against aggregation based diseases such as Alzheimer's, Parkinson's, and systemic amyloidoses. In this work, we investigated the potential of HESP to interact with hen egg-white lysozyme (HEWL) monomer and prevent its aggregation. The HESP-HEWL binding studies were performed using a fluorescence quenching technique, molecular docking and molecular dynamics simulations. We found a strong interaction of HESP with the lysozyme monomer (Ka, ~ 5 × 10(4) M(-1)) mainly through hydrogen bonding, water bridges, and hydrophobic interactions. We showed that HESP molecule spanned the highly aggregation prone region (amino acid residues 48-101) of HEWL and prevented its fibrillar aggregation. Further, we found that HESP binding completely inhibited amorphous aggregation of the protein induced by disulfide-reducing agent tries-(2-carboxyethyl) phosphine. Conformational and stability studies as followed by various tertiary and secondary structure probes revealed that HESP binding only marginally affected the lysozyme monomer conformation and increased both stability and reversibility of the protein against thermal denaturation. Future studies should investigate detail effects of HESP on solvent dynamics, structure, and toxicity of various aggregates. The answers to these questions will not only target the basic sciences, but also have application in biomedical and biotechnological sciences. PMID:25301518

  20. Theoretical studies of molecular interactions

    SciTech Connect

    Lester, W.A. Jr.

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  1. Molecular Dynamics Simulation and Experimental Verification of the Interaction between Cyclin T1 and HIV-1 Tat Proteins

    PubMed Central

    Asamitsu, Kaori; Hibi, Yurina

    2015-01-01

    The viral encoded Tat protein is essential for the transcriptional activation of HIV proviral DNA. Interaction of Tat with a cellular transcription elongation factor P-TEFb containing CycT1 is critically required for its action. In this study, we performed MD simulation using the 3D data for wild-type and 4CycT1mutants3D data. We found that the dynamic structural change of CycT1 H2’ helix is indispensable for its activity for the Tat action. Moreover, we detected flexible structural changes of the Tat-recognition cavity in the WT CycT1 comprising of ten AAs that are in contact with Tat. These structural fluctuations in WT were lost in the CycT1 mutants. We also found the critical importance of the hydrogen bond network involving H1, H1’ and H2 helices of CycT1. Since similar AA substitutions of the Tat-CycT1 chimera retained the Tat-supporting activity, these interactions are considered primarily involved in interaction with Tat. These findings described in this paper should provide vital information for the development of effective anti-Tat compound. PMID:25781978

  2. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    NASA Astrophysics Data System (ADS)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  3. Molecular dynamics simulation and experimental verification of the interaction between cyclin T1 and HIV-1 Tat proteins.

    PubMed

    Asamitsu, Kaori; Hirokawa, Takatsugu; Hibi, Yurina; Okamoto, Takashi

    2015-01-01

    The viral encoded Tat protein is essential for the transcriptional activation of HIV proviral DNA. Interaction of Tat with a cellular transcription elongation factor P-TEFb containing CycT1 is critically required for its action. In this study, we performed MD simulation using the 3D data for wild-type and 4CycT1mutants3D data. We found that the dynamic structural change of CycT1 H2' helix is indispensable for its activity for the Tat action. Moreover, we detected flexible structural changes of the Tat-recognition cavity in the WT CycT1 comprising of ten AAs that are in contact with Tat. These structural fluctuations in WT were lost in the CycT1 mutants. We also found the critical importance of the hydrogen bond network involving H1, H1' and H2 helices of CycT1. Since similar AA substitutions of the Tat-CycT1 chimera retained the Tat-supporting activity, these interactions are considered primarily involved in interaction with Tat. These findings described in this paper should provide vital information for the development of effective anti-Tat compound. PMID:25781978

  4. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

    PubMed

    Lipska, Agnieszka G; Seidman, Steven R; Sieradzan, Adam K; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A

    2016-05-14

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models. PMID:27179474

  5. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.

    PubMed

    Stetz, Gabrielle; Verkhivker, Gennady M

    2016-08-22

    Although molecular mechanisms of allosteric regulation in the Hsp70 chaperones have been extensively studied at both structural and functional levels, the current understanding of allosteric inhibition of chaperone activities by small molecules is still lacking. In the current study, using a battery of computational approaches, we probed allosteric inhibition mechanisms of E. coli Hsp70 (DnaK) and human Hsp70 proteins by small molecule inhibitors PET-16 and novolactone. Molecular dynamics simulations and binding free energy analysis were combined with network-based modeling of residue interactions and allosteric communications to systematically characterize and compare molecular signatures of the apo form, substrate-bound, and inhibitor-bound chaperone complexes. The results suggested a mechanism by which the allosteric inhibitors may leverage binding energy hotspots in the interaction networks to stabilize a specific conformational state and impair the interdomain allosteric control. Using the network-based centrality analysis and community detection, we demonstrated that substrate binding may strengthen the connectivity of local interaction communities, leading to a dense interaction network that can promote an efficient allosteric communication. In contrast, binding of PET-16 to DnaK may induce significant dynamic changes and lead to a fractured interaction network and impaired allosteric communications in the DnaK complex. By using a mechanistic-based analysis of distance fluctuation maps and allosteric propensities of protein residues, we determined that the allosteric network in the PET-16 complex may be small and localized due to the reduced communication and low cooperativity of the substrate binding loops, which may promote the higher rates of substrate dissociation and the decreased substrate affinity. In comparison with the significant effect of PET-16, binding of novolactone to HSPA1A may cause only moderate network changes and preserve allosteric

  6. Detection of molecular interactions

    DOEpatents

    Groves, John T.; Baksh, Michael M.; Jaros, Michal

    2012-02-14

    A method and assay are described for measuring the interaction between a ligand and an analyte. The assay can include a suspension of colloidal particles that are associated with a ligand of interest. The colloidal particles are maintained in the suspension at or near a phase transition state from a condensed phase to a dispersed phase. An analyte to be tested is then added to the suspension. If the analyte binds to the ligand, a phase change occurs to indicate that the binding was successful.

  7. Dynamic molecular crystals with switchable physical properties.

    PubMed

    Sato, Osamu

    2016-06-21

    The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials. PMID:27325090

  8. Molecular dynamics investigation of the interaction of an edge dislocation with Frank loops in Fe-Ni10-Cr20 alloy

    NASA Astrophysics Data System (ADS)

    Baudouin, Jean-Baptiste; Nomoto, Akiyoshi; Perez, Michel; Monnet, Ghiath; Domain, Christophe

    2015-10-01

    The inhibition of dislocations motion by irradiation-induced defects, such as dislocation loops, is one of the main mechanisms of irradiation hardening of austenitic stainless steels. In this work, Molecular Dynamics (MD) simulations of interaction between an edge dislocation and Frank loops in Fe-Ni10-Cr20 ternary alloy mimicking austenitic stainless steels are carried out to investigate and model dislocation behavior. An empirical interatomic potential developed recently for a ternary FeNiCr system is used for the MD calculations. The interactions are calculated at different temperatures, loop orientations, loop size and solute atom configurations. The results show that the loop strength and the interaction processes depend on the solute atom configuration, the geometrical configurations between the dislocation and the loop and temperature. It is also demonstrated that a small Frank loop is not so weak an obstacle in the alloy. The interaction leads microstructural change such as loop shearing, loop unfaulting and loop absorption in the dislocation. In the former two cases, the loop remains after the interaction, however in some cases an absorption of the remaining loop by subsequent interactions with successive dislocations is observed.

  9. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

    NASA Astrophysics Data System (ADS)

    Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

    2009-10-01

    In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

  10. Topology of molecular interaction networks.

    PubMed

    Winterbach, Wynand; Van Mieghem, Piet; Reinders, Marcel; Wang, Huijuan; de Ridder, Dick

    2013-01-01

    Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further. PMID:24041013

  11. Topology of molecular interaction networks

    PubMed Central

    2013-01-01

    Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks. Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs. Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes. Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further. PMID:24041013

  12. Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation

    PubMed Central

    Fukunishi, Yoshifumi; Nakamura, Haruki

    2012-01-01

    We have developed a method for estimating protein-ligand binding free energy (ΔG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the ΔG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the ΔG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated ΔG values was 0.81, and the average error of ΔG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation. PMID:24281257

  13. Structural insights into the interaction between molluscan hemocyanins and phenolic substrates: An in silico study using docking and molecular dynamics.

    PubMed

    Naresh, K N; Sreekumar, Arun; Rajan, S S

    2015-09-01

    Hemocyanin is a multimeric type-3 copper containing oxygen carrier protein that exhibits phenoloxidase-like activity and is found in selected species of arthropoda and mollusca. The phenoloxidase activity in the molluscan hemocyanins can be triggered by the proteolytic removal of the C-terminal β-rich sandwich domain of the protein or by the treatment with chemical agents like SDS, both of which enable active site access to the phenolic substrates. The mechanism by which SDS treatment enhances active site access to the substrates is however not well understood in molluscan hemocyanins. Here, using a combination of in silico molecular dynamics (MD) and docking studies on the crystal structure of Octopus dofleini hemocyanin (PDB code:1JS8), we demonstrate that the C-terminal β-domain of the protein plays a crucial role in regulating active site access to bulky phenolic substrates. Furthermore, MD simulation of hemocyanin in SDS revealed displacement of β-domain, enhanced active site access and a resulting increase in binding affinity for substrates. These observations were further validated by enzyme kinetics experiments. PMID:26300244

  14. Molecular photoionization dynamics

    SciTech Connect

    Dehmer, Joseph L.

    1982-05-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)

  15. Methyl Radical in Clathrate Silica Voids. The Peculiar Physisorption Features of the Guest-Host Molecular Dynamics Interaction.

    PubMed

    Dmitriev, Yurij A; Buscarino, Gianpiero; Benetis, Nikolas P

    2016-08-11

    EPR line shape simulations of CH3/SiO2 clathrates and comparison to CH3/N2O and CH3/SiO2 experiments reveal the motional conditions of the CH3 radical up to the unusual regime of its stability, the high-temperature diffusional regime, at 300 K. In the low-temperature region, the CH3 in clathrates is found to rotate around the in-plane axes even at as low temperatures as 3.8 K. However, nonrotating methyls performing only libration about the C2-axes as well as around the C3-axis are also found, proving the existence of special sites in the clathrate voids that begin to accumulate a significant fraction of methyl radicals at temperatures below approximately 7 K. A distinctive feature in the spectrum anisotropy and line width temperature profiles is found nearby 25 K, which is interpreted as the radical physisorption inside the voids that occurs with the sample temperature lowering. The unusual increase of the CH3/SiO2 clathrate EPR spectral width with temperature over approximately 120 K has its origin in repeated angular momentum vector alterations due to frequent collisions with the clathrate void walls between periodical free rotation periods. This relaxation mechanism resembles to spin-rotation interaction known only for small molecular species in nonviscous fluids but unknown earlier for methyl hosted in solids. PMID:27405003

  16. Molecular dynamics of membrane proteins.

    SciTech Connect

    Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  17. 2010 Atomic & Molecular Interactions Gordon Research Conference

    SciTech Connect

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

  18. Dynamic-domain-decomposition parallel molecular dynamics

    NASA Astrophysics Data System (ADS)

    Srinivasan, S. G.; Ashok, I.; Jônsson, Hannes; Kalonji, Gretchen; Zahorjan, John

    1997-05-01

    Parallel molecular dynamics with short-range forces can suffer from load-imbalance problems and attendant performance degradation due to density variations in the simulated system. In this paper, we describe an approach to dynamical load balancing, enabled by the Ādhāra runtime system. The domain assigned to each processor is automatically and dynamically resized so as to evenly distribute the molecular dynamics computations across all the processors. The algorithm was tested on an Intel Paragon parallel computer for two and three-dimensional Lennard-Jones systems containing 99 458 and 256000 atoms, respectively, and using up to 256 processors. In these benchmarks, the overhead for carrying out the load-balancing operations was found to be small and the total computation time was reduced by as much as 50%.

  19. An investigation on the interaction modes of a single-strand DNA aptamer and RBP4 protein: a molecular dynamic simulations approach.

    PubMed

    Torabi, Raheleh; Bagherzadeh, Kowsar; Ghourchian, Hedayatollah; Amanlou, Massoud

    2016-09-14

    Type two diabetes is one of the primary health issues threatening public well-being worldwide. One of the pre-diagnosis biomarkers of this disease, retinol binding protein 4 (RBP4), has been demonstrated to be detected with a 76-mer ssDNA aptamer instead of conventional antibodies. However, there is no structural information on the RBP4 binding aptamer (RBA) and the mechanism of its binding to RBP4 still remains unexplored. The objective of the present study is to achieve a better understanding of specific binding interactions of the target protein (RBP4) and RBA, employing Molecular Dynamics simulations (MDs) to provide detailed information on fluctuations, conformational changes, critical bases and effective forces to develop regulated aptamers to be employed in designing new aptamers for many useful recognition applications. RBA was designed according to its reported base pair sequence and secondary structure. The HADDOCK on line docking program was used to predict a suitable RBP4-RBA mode of interaction to start MDs with. MDs methodology was used to analyze the final complex stability and detect interacting residues. Eventually, we conclude that single strand located bases are the key components that conduct the intercalation phenomenon with big targets rather than those involving loops and folded motifs, to encompass targets and probably inhibit their activity. Also, UV-visible, circular dichroism and fluorescence spectroscopy measurements confirmed the interactions between RBA and RBP4 and RBP4-RBA complex formation. PMID:27511589

  20. Antimicrobial peptide dendrimer interacts with phosphocholine membranes in a fluidity dependent manner: A neutron reflection study combined with molecular dynamics simulations.

    PubMed

    Lind, T K; Darré, L; Domene, C; Urbanczyk-Lipkowska, Z; Cárdenas, M; Wacklin, H P

    2015-10-01

    The interaction mechanism of a novel amphiphilic antimicrobial peptide dendrimer, BALY, with model lipid bilayers was explored through a combination of neutron reflection and molecular dynamics simulations. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phos-phocholine (DPPC) lipid bilayers were examined at room temperature to extract information on the interaction of BALY with fluid and gel phases, respectively. Furthermore, a 1:4 mixture of POPC and DPPC was used as a model of a phase-separated membrane. Upon interaction with fluid membranes, BALY inserted in the distal leaflet and caused thinning and disordering of the headgroups. Membrane thinning and expansion of the lipid cross-sectional area were observed for gel phase membranes, also with limited insertion to the distal leaflet. However, dendrimer insertion through the entire lipid tail region was observed upon crossing the lipid phase transition temperature of DPPC and in phase separated membranes. The results show clear differences in the interaction mechanism of the dendrimer depending on the lipid membrane fluidity, and suggest a role for lipid phase separation in promoting its antimicrobial activity. PMID:26025586

  1. Intermolecular interactions of liquid dichloromethane and equilibrium properties of liquid{endash}vapor and liquid{endash}liquid interfaces: A molecular dynamics study

    SciTech Connect

    Dang, L.X.

    1999-05-01

    Extensive molecular dynamics simulations are carried out to study the molecular interactions, liquid states, and liquid/vapor properties of dichloromethane. The study is also extended to the equilibrium properties of the liquid/liquid interface of water-dichloromethane. The intermolecular interactions among water, dichloromethane, and water-dichloromethane are described using our polarizable potential models. The equilibrium properties of liquid dichloromethane, including the radial distribution functions, the intermolecular structural factor, the self-diffusion coefficient, and the dielectric constant, are evaluated. The dielectric constant is computed using Ewald summation techniques and the computed result compared reasonably well with the available experimental data. Properties such as surface tensions and density profiles of liquid/vapor dichloromethane are evaluated. We found that the computed surface tensions for several temperatures are in excellent agreement with experimental data. The computed density profile of the liquid/liquid interface of water-dichloromethane is averaged over 1 ns and we found the computed profile to be quite smooth and stable. The effect of polarization on the liquid/liquid interfacial equilibrium properties is evaluated by computing the dipole moments of water and dichloromethane molecules as a function of the distance normal to the interface. We found that these values deviated significantly from the simulations that are based on nonpolarizable potential models. We attribute these observations to the changes in the electric fields around the water and dichloromethane molecules near the interface. {copyright} {ital 1999 American Institute of Physics.}

  2. Multielectron effects in high harmonic generation in N2 and benzene: Simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions

    NASA Astrophysics Data System (ADS)

    Dundas, Daniel

    2012-05-01

    A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N2 and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N2 an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital.

  3. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: analysis by molecular dynamics simulations.

    PubMed

    Nimmanpipug, Piyarat; Khampa, Chalermpon; Lee, Vannajan Sanghiran; Nangola, Sawitree; Tayapiwatana, Chatchai

    2011-11-01

    We applied molecular dynamics simulations to investigate the binding properties of a designed ankyrin repeat protein, the DARPin-CD4 complex. DARPin 23.2 has been reported to disturb the human immunodeficiency virus (HIV) viral entry process by Schweizer et al. The protein docking simulation was analysed by comparing the specific ankyrin binder (DARPin 23.2) to an irrelevant control (2JAB) in forming a composite with CD4. To determine the binding free energy of both ankyrins, the MM/PBSA and MM/GBSA protocols were used. The free energy decomposition of both complexes were analysed to explore the role of certain amino acid residues in complex configuration. Interestingly, the molecular docking analysis of DARPin 23.2 revealed a similar CD4 interaction regarding the gp120 theoretical anchoring motif. In contrast, the binding of control ankyrin to CD4 occurred at a different location. This observation suggests that there is an advantage to the molecular modification of DARPin 23.2, an enhanced affinity for CD4. PMID:21962990

  4. Correlation between inter-spin interaction and molecular dynamics of organic radicals in organic 1D nanochannels

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hirokazu

    2015-12-01

    One-dimensional (1D) molecular chains of 4-substituted-2,2,6,6-tetramethyl-1-piperidinyloxyl (4-X-TEMPO) radicals were constructed in the crystalline 1D nanochannels of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) used as a template. The ESR spectra of CLPOT inclusion compounds (ICs) using 4-X-TEMPO were examined on the basis of spectral simulation using EasySpin program package for simulating and fitting ESR spectra. The ESR spectra of [(CLPOT)2-(TEMPO)1.0] IC were isotropic in the total range of temperatures. The peak-to-peak line width (ΔBpp) became monotonically narrower from 2.8 to 1.3 mT with increase in temperature in the range of 4.2-298 K. The effect of the rotational diffusion motion of TEMPO radicals in the CLPOT nanochannels for the inter-spin interaction of the [(CLPOT)2-(TEMPO)1.0] IC was found to be smaller than the case of [(TPP)2-(TEMPO)1.0] IC (TPP = tris(o-phenylenedioxy)cyclotriphosphazene) reported in our previous study. The ΔBpp of the [(CLPOT)2-(TEMPO)1.0] IC in the whole range of temperatures was much narrower than the estimation to be based on the Van Vleck's formula for the second moment of the rigid lattice model where the electron spin can be considered as fixed; 11 mT of Gaussian line-width component. This suggests the possibility of exchange narrowing in the 1D organic-radical chains of the [(CLPOT)2-(TEMPO)1.0] IC. On the other hand, the ESR spectra of [(CLPOT)2-(MeO-TEMPO)0.41] IC (MeO-TEMPO = 4-methoxy-TEMPO) were reproduced by a superposition of major broad isotropic adsorption line and minor temperature-dependent modulated triplet component. This suggests that the IC has the part of 1D organic-radical chains and MeO-TEMPO molecules isolated in the CLPOT nanochannels.

  5. Correlation between inter-spin interaction and molecular dynamics of organic radicals in organic 1D nanochannels

    SciTech Connect

    Kobayashi, Hirokazu

    2015-12-31

    One-dimensional (1D) molecular chains of 4-substituted-2,2,6,6-tetramethyl-1-piperidinyloxyl (4-X-TEMPO) radicals were constructed in the crystalline 1D nanochannels of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) used as a template. The ESR spectra of CLPOT inclusion compounds (ICs) using 4-X-TEMPO were examined on the basis of spectral simulation using EasySpin program package for simulating and fitting ESR spectra. The ESR spectra of [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC were isotropic in the total range of temperatures. The peak-to-peak line width (ΔB{sub pp}) became monotonically narrower from 2.8 to 1.3 mT with increase in temperature in the range of 4.2–298 K. The effect of the rotational diffusion motion of TEMPO radicals in the CLPOT nanochannels for the inter-spin interaction of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC was found to be smaller than the case of [(TPP){sub 2}−(TEMPO){sub 1.0}] IC (TPP = tris(o-phenylenedioxy)cyclotriphosphazene) reported in our previous study. The ΔB{sub pp} of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC in the whole range of temperatures was much narrower than the estimation to be based on the Van Vleck’s formula for the second moment of the rigid lattice model where the electron spin can be considered as fixed; 11 mT of Gaussian line-width component. This suggests the possibility of exchange narrowing in the 1D organic-radical chains of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC. On the other hand, the ESR spectra of [(CLPOT){sub 2}-(MeO-TEMPO){sub 0.41}] IC (MeO-TEMPO = 4-methoxy-TEMPO) were reproduced by a superposition of major broad isotropic adsorption line and minor temperature-dependent modulated triplet component. This suggests that the IC has the part of 1D organic-radical chains and MeO-TEMPO molecules isolated in the CLPOT nanochannels.

  6. Molecular dynamics and protein function

    PubMed Central

    Karplus, M.; Kuriyan, J.

    2005-01-01

    A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F1 ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems. PMID:15870208

  7. A sampling of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sindhikara, Daniel Jon

    The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel

  8. Gas Phase Molecular Dynamics

    SciTech Connect

    Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

    1999-05-21

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.

  9. Integration methods for molecular dynamics

    SciTech Connect

    Leimkuhler, B.J.; Reich, S.; Skeel, R.D.

    1996-12-31

    Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches. 48 refs., 2 figs.

  10. Transcript dynamics at early stages of molecular interactions of MYMIV with resistant and susceptible genotypes of the leguminous host, Vigna mungo.

    PubMed

    Kundu, Anirban; Patel, Anju; Paul, Sujay; Pal, Amita

    2015-01-01

    Initial phases of the MYMIV-Vigna mungo interaction is crucial in determining the infection phenotype upon challenging with the virus. During incompatible interaction, the plant deploys multiple stratagems that include extensive transcriptional alterations defying the virulence factors of the pathogen. Such molecular events are not frequently addressed by genomic tools. In order to obtain a critical insight to unravel how V. mungo respond to Mungbean yellow mosaic India virus (MYMIV), we have employed the PCR based suppression subtractive hybridization technique to identify genes that exhibit altered expressions. Dynamics of 345 candidate genes are illustrated that differentially expressed either in compatible or incompatible reactions and their possible biological and cellular functions are predicted. The MYMIV-induced physiological aspects of the resistant host include reactive oxygen species generation, induction of Ca2+ mediated signaling, enhanced expression of transcripts involved in phenylpropanoid and ubiquitin-proteasomal pathways; all these together confer resistance against the invader. Elicitation of genes implicated in salicylic acid (SA) pathway suggests that immune response is under the regulation of SA signaling. A significant fraction of modulated transcripts are of unknown function indicating participation of novel candidate genes in restricting this viral pathogen. Susceptibility on the other hand, as exhibited by V. mungo Cv. T9 is perhaps due to the poor execution of these transcript modulation exhibiting remarkable repression of photosynthesis related genes resulting in chlorosis of leaves followed by penalty in crop yield. Thus, the present findings revealed an insight on the molecular warfare during host-virus interaction suggesting plausible signaling mechanisms and key biochemical pathways overriding MYMIV invasion in resistant genotype of V. mungo. In addition to inflate the existing knowledge base, the genomic resources identified in

  11. Transcript Dynamics at Early Stages of Molecular Interactions of MYMIV with Resistant and Susceptible Genotypes of the Leguminous Host, Vigna mungo

    PubMed Central

    Kundu, Anirban; Patel, Anju; Paul, Sujay; Pal, Amita

    2015-01-01

    Initial phases of the MYMIV- Vigna mungo interaction is crucial in determining the infection phenotype upon challenging with the virus. During incompatible interaction, the plant deploys multiple stratagems that include extensive transcriptional alterations defying the virulence factors of the pathogen. Such molecular events are not frequently addressed by genomic tools. In order to obtain a critical insight to unravel how V. mungo respond to Mungbean yellow mosaic India virus (MYMIV), we have employed the PCR based suppression subtractive hybridization technique to identify genes that exhibit altered expressions. Dynamics of 345 candidate genes are illustrated that differentially expressed either in compatible or incompatible reactions and their possible biological and cellular functions are predicted. The MYMIV-induced physiological aspects of the resistant host include reactive oxygen species generation, induction of Ca2+ mediated signaling, enhanced expression of transcripts involved in phenylpropanoid and ubiquitin-proteasomal pathways; all these together confer resistance against the invader. Elicitation of genes implicated in salicylic acid (SA) pathway suggests that immune response is under the regulation of SA signaling. A significant fraction of modulated transcripts are of unknown function indicating participation of novel candidate genes in restricting this viral pathogen. Susceptibility on the other hand, as exhibited by V. mungo Cv. T9 is perhaps due to the poor execution of these transcript modulation exhibiting remarkable repression of photosynthesis related genes resulting in chlorosis of leaves followed by penalty in crop yield. Thus, the present findings revealed an insight on the molecular warfare during host-virus interaction suggesting plausible signaling mechanisms and key biochemical pathways overriding MYMIV invasion in resistant genotype of V. mungo. In addition to inflate the existing knowledge base, the genomic resources identified in

  12. Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method.

    PubMed

    Amisaki, Takashi; Toyoda, Shinjiro; Miyagawa, Hiroh; Kitamura, Kunihiro

    2003-04-15

    Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby

  13. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    PubMed

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  14. Molecular Dynamics Simulations of Graphene Oxide Frameworks

    SciTech Connect

    Zhu, Pan; Sumpter, Bobby G; Meunier, V.; Nicolai, Adrien

    2013-01-01

    We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.

  15. Dynamical interactions of galaxy pairs

    NASA Technical Reports Server (NTRS)

    Athanassoula, E.

    1990-01-01

    Here the author briefly reviews the dynamics of sinking satellites and the effect of companions on elliptical galaxies. The author then discusses recent work on interacting disk systems, and finally focuses on a favorite interacting pair, NGC 5194/5195.

  16. Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer.

    PubMed

    Berhanu, Workalemahu M; Masunov, Artëm E

    2015-01-01

    Amyloid fibrils are highly ordered protein aggregates associated with many diseases affecting millions of people worldwide. Polyphenols such as Curcumin, Exifone, and Myricetin exhibit modest inhibition toward fibril formation of tau peptide which is associated with Alzheimer's disease. However, the molecular mechanisms of this inhibition remain elusive. We investigated the binding of three polyphenol molecules to the protofibrils of an amyloidogenic fragment VQIVYK of tau peptide by molecular dynamics simulations in explicit solvent. We find that polyphenols induce conformational changes in the oligomer aggregate. These changes disrupt the amyloid H bonding, perturbing the aggregate. While the structural evolution of the control oligomer with no ligand is limited to the twisting of the β-sheets without their disassembly, the presence of polyphenol molecule pushes the β-sheets apart, and leads to a loosely packed structure where two of four β-sheets dissociate in each of the three cases considered here. The H-bonding capacity of polyphenols is responsible for the observed behavior. The calculated binding free energies and its individual components enabled better understanding of the binding. Results indicated that the contribution from Van der Waals interactions is more significant than electrostatic contribution to the binding. The findings from this study are expected to assist in the development of aggregation inhibitors. Significant binding between polyphenols and aggregate oligomer identified in our simulations confirms the previous experimental observations in which polyphenols refold the tau peptide without forming covalent bonds. PMID:25093402

  17. Molecular dynamics investigation of nanoscale cavitation dynamics

    NASA Astrophysics Data System (ADS)

    Sasikumar, Kiran; Keblinski, Pawel

    2014-12-01

    We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ˜90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ˜20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse.

  18. Ab initio molecular dynamics simulations of ion–solid interactions in Gd2Zr2O7 and Gd2Ti2O7

    SciTech Connect

    Wang, X. J.; Xiao, Haiyan Y.; Zu, Xiaotao; Zhang, Yanwen; Weber, William J.

    2012-12-21

    The development of the ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion–solid interactions in materials, with the determination of threshold displacement energies with ab initio accuracy, and prediction of a new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order–disorder is more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be [similar]0.15, [similar]0.11 to 0.27 and [similar]0.1 to 0.13 |e| for Gd, Zr (or Ti), and O, respectively. Neglecting the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.

  19. Ab initio molecular dynamics simulations of ion-solid interactions in Gd2Zr2O7 and Gd2Ti2O7

    SciTech Connect

    Wang, X J; Xiao, Haiyan; Zu, X T; Zhang, Yanwen; Weber, William J

    2013-01-01

    The development of ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion-solid interactions in materials, with identification determination of threshold displacement energies with ab initio accuracy, and prediction of new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order-disorder are more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be ~0.15, ~0.11-0.27 and ~0.1-0.13 |e| for Gd, Zr (or Ti), and O, respectively. Negligence of the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.

  20. Structure, Dynamics, and Interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 Examined by Molecular Modeling, Simulation, and Electrostatic Studies

    PubMed Central

    Bhutani, Isha; Loharch, Saurabh; Gupta, Pawan; Madathil, Rethi; Parkesh, Raman

    2015-01-01

    The enzymes decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-β-D-ribose-2-epimerase (DprE2) catalyze epimerization of decaprenylphosporyl ribose (DPR) todecaprenylphosporyl arabinose (DPA) and are critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Analysis (PCA) demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269–330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal structures. In DprE2, large fluctuations were detected in residues 95–113, 146–157, and 197–226. The study combined docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB) drug discovery and will facilitate drug development efforts against TB

  1. Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies.

    PubMed

    Bhutani, Isha; Loharch, Saurabh; Gupta, Pawan; Madathil, Rethi; Parkesh, Raman

    2015-01-01

    The enzymes decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-β-D-ribose-2-epimerase (DprE2) catalyze epimerization of decaprenylphosporyl ribose (DPR) todecaprenylphosporyl arabinose (DPA) and are critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Analysis (PCA) demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269-330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal structures. In DprE2, large fluctuations were detected in residues 95-113, 146-157, and 197-226. The study combined docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB) drug discovery and will facilitate drug development efforts against TB. PMID

  2. Solubilization Behavior of Polyene Antibiotics in Nanomicellar System: Insights from Molecular Dynamics Simulation of the Amphotericin B and Nystatin Interactions with Polysorbate 80.

    PubMed

    Mobasheri, Meysam; Attar, Hossein; Rezayat Sorkhabadi, Seyed Mehdi; Khamesipour, Ali; Jaafari, Mahmoud Reza

    2015-01-01

    Amphotericin B (AmB) and Nystatin (Nys) are the drugs of choice for treatment of systemic and superficial mycotic infections, respectively, with their full clinical potential unrealized due to the lack of high therapeutic index formulations for their solubilized delivery. In the present study, using a coarse-grained (CG) molecular dynamics (MD) simulation approach, we investigated the interaction of AmB and Nys with Polysorbate 80 (P80) to gain insight into the behavior of these polyene antibiotics (PAs) in nanomicellar solution and derive potential implications for their formulation development. While the encapsulation process was predominantly governed by hydrophobic forces, the dynamics, hydration, localization, orientation, and solvation of PAs in the micelle were largely controlled by hydrophilic interactions. Simulation results rationalized the experimentally observed capability of P80 in solubilizing PAs by indicating (i) the dominant kinetics of drugs encapsulation over self-association; (ii) significantly lower hydration of the drugs at encapsulated state compared with aggregated state; (iii) monomeric solubilization of the drugs; (iv) contribution of drug-micelle interactions to the solubilization; (v) suppressed diffusivity of the encapsulated drugs; (vi) high loading capacity of the micelle; and (vii) the structural robustness of the micelle against drug loading. Supported from the experimental data, our simulations determined the preferred location of PAs to be the core-shell interface at the relatively shallow depth of 75% of micelle radius. Deeper penetration of PAs was impeded by the synergistic effects of (i) limited diffusion of water; and (ii) perpendicular orientation of these drug molecules with respect to the micelle radius. PAs were solvated almost exclusively in the aqueous poly-oxyethylene (POE) medium due to the distance-related lack of interaction with the core, explaining the documented insensitivity of Nys solubilization to drug

  3. Rich spectroscopic and molecular dynamic studies on the interaction of cytotoxic Pt(II) and Pd(II) complexes of glycine derivatives with calf thymus DNA.

    PubMed

    Eslami Moghadam, Mahboube; Saidifar, Maryam; Divsalar, Adeleh; Mansouri-Torshizi, Hassan; Saboury, Ali Akbar; Farhangian, Hossein; Ghadamgahi, Maryam

    2016-01-01

    Some amino acid derivatives, such as R-glycine, have been synthesized together with their full spectroscopic characterization. The sodium salts of these bidentate amino acid ligands have been interacted with [M(bpy)(H2O)2](NO3)2 giving the corresponding some new complexes with formula [M(bpy)(R-gly)]NO3 (where M is Pt(II) or Pd(II), bpy is 2,2'-bipyridine and R-gly is butyl-, hexyl- and octyl-glycine). Due to less solubility of octyl derivatives, the biological activities of butyl and hexyl derivatives have been tested against chronic myelogenous leukemia cell line, K562. The interaction of these complexes with highly polymerized calf thymus DNA has been extensively studied by means of electronic absorption, fluorescence and other measurements. The experimental results suggest that these complexes positive cooperatively bind to DNA presumably via groove binding. Molecular dynamic results show that the DNA structure is largely maintained its native structure in hexylglycine derivative-water mixtures and at lower temperatures. The simulation data indicates that the more destabilizing effect of butylglycine is induced by preferential accumulation of these molecules around the DNA and due to their more negative free energy of binding via groove binding. PMID:25734364

  4. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

    NASA Astrophysics Data System (ADS)

    Gsponer, Jörg; Haberthür, Urs; Caflisch, Amedeo

    2003-04-01

    Understanding the early steps of aggregation at atomic detail might be crucial for the rational design of therapeutics preventing diseases associated with amyloid deposits. In this paper, aggregation of the heptapeptide GNNQQNY, from the N-terminal prion-determining domain of the yeast protein Sup35, was studied by 20 molecular dynamics runs for a total simulation time of 20 μs. The simulations generate in-register parallel packing of GNNQQNY -strands that is consistent with x-ray diffraction and Fourier transform infrared data. The statistically preferred aggregation pathway does not correspond to a purely downhill profile of the energy surface because of the presence of enthalpic barriers that originate from out-of-register interactions. The parallel -sheet arrangement is favored over the antiparallel because of side-chain contacts; in particular, stacking interactions of the tyrosine rings and hydrogen bonds between amide groups. No ordered aggregation was found in control simulations with the mutant sequence SQNGNQQRG in accord with experimental data and the strong sequence dependence of aggregation.

  5. The dopamine D2 receptor dimer and its interaction with homobivalent antagonists: homology modeling, docking and molecular dynamics.

    PubMed

    Kaczor, Agnieszka A; Jörg, Manuela; Capuano, Ben

    2016-09-01

    In order to apply structure-based drug design techniques to G protein-coupled receptor complexes, it is essential to model their 3D structure and to identify regions that are suitable for selective drug binding. For this purpose, we have developed and tested a multi-component protocol to model the inactive conformation of the dopamine D2 receptor dimer, suitable for interaction with homobivalent antagonists. Our approach was based on protein-protein docking, applying the Rosetta software to obtain populations of dimers as present in membranes with all the main possible interfaces. Consensus scoring based on the values and frequencies of best interfaces regarding four scoring parameters, Rosetta interface score, interface area, free energy of binding and energy of hydrogen bond interactions indicated that the best scored dimer model possesses a TM4-TM5-TM7-TM1 interface, which is in agreement with experimental data. This model was used to study interactions of the previously published dopamine D2 receptor homobivalent antagonists based on clozapine,1,4-disubstituted aromatic piperidines/piperazines and arylamidoalkyl substituted phenylpiperazine pharmacophores. It was found that the homobivalent antagonists stabilize the receptor-inactive conformation by maintaining the ionic lock interaction, and change the dimer interface by disrupting a set of hydrogen bonds and maintaining water- and ligand-mediated hydrogen bonds in the extracellular and intracellular part of the interface. Graphical Abstract Structure of the final model of the dopamine D2 receptor homodimer, indicating the distancebetween Tyr37 and Tyr 5.42 in the apo form (left) and in the complex with the ligand (right). PMID:27491852

  6. Stochastic Event-Driven Molecular Dynamics

    SciTech Connect

    Donev, Aleksandar Garcia, Alejandro L.; Alder, Berni J.

    2008-02-01

    A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in EDMD, rather, the momentum and energy exchange in the solvent is determined stochastically using DSMC. The coupling between the solvent and the solute is consistently represented at the particle level retaining hydrodynamic interactions and thermodynamic fluctuations. However, unlike full MD simulations of both the solvent and the solute, in SEDMD the spatial structure of the solvent is ignored. The SEDMD algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard-wall subjected to uniform shear. SEDMD closely reproduces results obtained using traditional EDMD simulations with two orders of magnitude greater efficiency. Results question the existence of periodic (cycling) motion of the polymer chain.

  7. Dynamic fracture toughness determined using molecular dynamics

    SciTech Connect

    Swadener, J. G.; Baskes, M. I.; Nastasi, Michael Anthony,

    2004-01-01

    Molecular dynamics (MD) simulations of fracture in crystalline silicon are conducted in order to determine the dynamic fracture toughness. The MD simulations show how the potential energy released during fracture is partitioned into surface energy, energy stored in defects and kinetic energy. First, the MD fracture simulations are shown to produce brittle fracture and be in reasonable agreement with experimental results. Then dynamic hcture toughness is calculated as the sum of the surface energy and the energy stored as defects directly from the MD models. Models oriented to produce fracture on either (111) or (101) planes are used. For the (101) fracture orientation, equilibrium crack speeds of greater than 80% of the Rayleigh wave speed are obtained. Crack speeds initially show a steep increase with increasing energy release rate followed by a much more gradual increase. No plateau in crack speed is observed for static energy release rates up to 20 J/m{sup 2}. At the point where the change in crack speed behavior occur, the dynamic fracture toughness (J{sub d}) is still within 10% of two times the surface energy (2{gamma}{sub 0}) and changing very slowly. From these MD simulations, it appears that the change in crack speed behavior is due to a change in the kinetic energy generation during dynamic fracture. In addition, MD simulations of facture in silicon with defects were conducted. The addition of defects increases the inelastic dissipation and the energy stored in defects.

  8. Fiftieth anniversary of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Melker, Alexander I.

    2007-04-01

    The history of computer application in physics for solving nonlinear problems is considered. Examples from different branches of condensed matter physics (nonlinear vibrations of anharmonic chains of atoms, dynamics of radiation damage of crystals, deformation and fracture of crystals) are given. A new line of investigation and the results obtained in the field of computer simulation of physical processes realized in the department of metal physics and computer technologies in materials science are considered. This line incorporates both a study of self-organization and properties of new materials (fullerenes, carbon nanotubes) and biological objects by molecular dynamics technique as well as the development of new computer simulation methods.

  9. Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts.

    PubMed

    Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W

    2003-10-01

    Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101

  10. Available Instruments for Analyzing Molecular Dynamics Trajectories

    PubMed Central

    Likhachev, I. V.; Balabaev, N. K.; Galzitskaya, O. V.

    2016-01-01

    Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. PMID:27053964

  11. Molecular dynamics on vector computers

    NASA Astrophysics Data System (ADS)

    Sullivan, F.; Mountain, R. D.; Oconnell, J.

    1985-10-01

    An algorithm called the method of lights (MOL) has been developed for the computerized simulation of molecular dynamics. The MOL, implemented on the CYBER 205 computer, is based on sorting and reformulating the manner in which neighbor lists are compiled, and it uses data structures compatible with specialized vector statements that perform parallel computations. The MOL is found to reduce running time over standard methods in scalar form, and vectorization is shown to produce an order-of-magnitude reduction in execution time.

  12. a Mechanistic View of the Ion/solid Interaction Using Laser Postionization, Time-Of Mass Spectrometry, and Molecular Dynamics Computer Simulations

    NASA Astrophysics Data System (ADS)

    Rosencrance, Scott William

    1995-01-01

    Simultaneous collection of energy and angle resolved neutral (EARN) distributions resulting from keV ion bombardment of various materials is performed using a novel position sensitive detection scheme in tandem with multiphoton laser ionization of desorbed neutral species. This enables experimental investigation of desorption processes at the atomic level. Insight into long-standing mechanistic uncertainties surrounding ion/solid interactions is set forth. When these results are viewed collectively a coherent picture of the desorption event emerges. In the first study, experimentally obtained EARN distributions for ground state Ni and Rh atoms desorbed from the { 001} crystal face by 5 keV Ar^+ bombardment are compared with molecular dynamics (MD) simulations. These calculations utilize the molecular dynamics/Monte Carlo -corrected effective medium (MD/MC-CEM) interaction potential. The similarity of the mechanistically resolved quantities reinforces the view that inherent registry in the crystal lattice dictates microscopic events leading to the observed angular distributions of particles ejected subsequent to keV ion bombardment of solid surfaces. Additional evaluation of quantum state resolved energy distributions and populations of atoms desorbed from rm Ni{ 001} reveals that particles ejecting in the rm a^3F_{4,3,2} states have kinetic energy distributions which peak at 3 eV while particles ejecting in the rm a^3D_{3,2 } or rm a^1D_2 states have distributions which peak at 4.3 eV. Furthermore, the population in the ^3D_ {3,2} states is larger than the ground F state. These are the first results demonstrating that the band structure of the solid dictates desorption energetics and populations. Further investigation into desorption processes utilizes MD simulations that incorporate sample temperature. These calculations reproduce experimentally observed temperature dependence in ejection and suggests that the effect predominately results from surface quenching

  13. Molecular dynamics for dense matter

    NASA Astrophysics Data System (ADS)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

  14. Symmetry Reduced Dynamics of Charged Molecular Strands

    NASA Astrophysics Data System (ADS)

    Ellis, David C. P.; Gay-Balmaz, François; Holm, Darryl D.; Putkaradze, Vakhtang; Ratiu, Tudor S.

    2010-09-01

    The equations of motion are derived for the dynamical folding of charged molecular strands (such as DNA) modeled as flexible continuous filamentary distributions of interacting rigid charge conformations. The new feature is that these equations are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges, are included. The nonlocal dynamics is derived in the convective representation of continuum motion by using modified Euler-Poincaré and Hamilton-Pontryagin variational formulations that illuminate the various approaches within the framework of symmetry reduction of Hamilton’s principle for exact geometric rods. In the absence of nonlocal interactions, the equations recover the classical Kirchhoff theory of elastic rods. The motion equations in the convective representation are shown to arise by a classical Lagrangian reduction associated to the symmetry group of the system. This approach uses the process of affine Euler-Poincaré reduction initially developed for complex fluids. On the Hamiltonian side, the Poisson bracket of the molecular strand is obtained by reduction of the canonical symplectic structure on phase space. A change of variables allows a direct passage from this classical point of view to the covariant formulation in terms of Lagrange-Poincaré equations of field theory. In another revealing perspective, the convective representation of the nonlocal equations of molecular strand motion is transformed into quaternionic form.

  15. Molecular dynamics studies of polyurethane nanocomposite hydrogels

    NASA Astrophysics Data System (ADS)

    Strankowska, J.; Piszczyk, Ł.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.

    2013-10-01

    Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.

  16. Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations.

    PubMed

    Ostermeir, Katja; Springer, Sebastian; Zacharias, Martin

    2015-02-01

    MHC class I molecules present antigenic peptides to cytotoxic T-cells at the cell surface. Peptide loading of class I molecules in the endoplasmatic reticulum can involve interaction with the tapasin chaperone protein. The human class I allotype HLA-B*44:02 with an Asp at position 116 at the floor of the F pocket (which binds the peptide C-terminal residues) depends on tapasin for efficient peptide loading. However, HLA-B*44:05 (identical to B*44:02 except for tyrosine 116) can efficiently load peptides in the absence of tapasin. Both allotypes adopt very similar structures in the presence of the same peptide. Molecular dynamics simulations indicate a significantly higher conformational flexibility of the F pocket in the absence of a peptide for B*44:02 compared to B*44:05. Free energy simulations to open the F pocket indicate a molecular side chain switch mechanism that underlies the global opening motion. This side chain switch involves the rearrangement of salt bridges and hydrogen bonding of the basic arginine 97 with three acidic aspartate residues 114, 116 and 156 near the F pocket. A replica exchange simulation to specifically accelerate side chain motions demonstrates that the same side chain rearrangements induce global opening motions of the F pocket. In case of B*44:05 the free energy barrier for F pocket opening was significantly higher compared to B*44:02 and no associated side chain rearrangement was observed. Such coupling of local side chain rearrangements with global conformational changes might be the basis for allosteric changes in other class I allotypes as well as for allosteric changes in other proteins. PMID:25146482

  17. Interactions of water with the nonionic surfactant polyoxyethylene glycol alkyl ethers studied by phase-sensitive sum frequency generation and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Mafi, Amirhossein; Hu, Dan; Chou, Keng C.

    2016-06-01

    Phase-sensitive sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation were used to study the interactions between water molecules and the surfactant polyoxyethylene glycol alkyl ether (C12E4) at its critical micelle concentration. The surfactant enhanced the positive peak of water's SFG spectrum suggesting that C12E4 was more anionic-like, even though the surfactant was overall neutral. MD simulations showed that the surfactant increased the depth of the surface anisotropic layer from 0.31 to 1.82 nm and the average number of hydrogen bonds per water molecule from 2.7 to 3.1. For water molecules near the surfactant, their H and O atoms are confined in well-separated shells. Both the O and C atoms in the head group of the surfactant are surrounded by the H atoms, instead of the O atoms, of water indicating that the negatively charged O atoms of the surfactant play a more important role than the C atoms in determining the orientation of water. The simulation also showed that the orientation of surface water molecules was flipped in the presence of the surfactant, which was consistent with the observed SFG spectra.

  18. Structural insights into the interactions of phorbol ester and bryostatin complexed with protein kinase C: a comparative molecular dynamics simulation study.

    PubMed

    Thangsunan, Patcharapong; Tateing, Suriya; Hannongbua, Supa; Suree, Nuttee

    2016-07-01

    Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the drug development. However, structural details on the binding between PKC and its modulators, especially bryostatin - the highly potent and non-tumor promoting activator for PKCs, are still lacking. Here, we report the first comparative molecular dynamics study aimed at gaining structural insight into the mechanisms by which the PKC delta cys2 activator domain is used in its binding to phorbol ester and bryostatin-1. As anticipated in the phorbol ester binding, hydrogen bonds are formed through the backbone atoms of Thr242, Leu251, and Gly253 of PKC. However, the opposition of H-bond formation between Thr242 and Gly253 may cause the phorbol ester complex to become less stable when compared with the bryostatin binding. For the PKC delta-bryostatin complex, hydrogen bonds are formed between the Gly253 backbone carbonyl and the C30 carbomethoxy substituent of the ligand. Additionally, the indole Nε1 of the highly homologous Trp252 also forms an H-bond to the C20 ester group on bryostatin. Backbone fluctuations also suggest that this latter H-bond formation may abrogate the transient interaction between Trp252 and His269, thus dampening the fluctuations observed on the nearby Zn(2+)-coordinating residues. This new dynamic fluctuation dampening model can potentially benefit future design of new PKC modulators. PMID:26292580

  19. Molecular crowding and protein enzymatic dynamics.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2012-05-21

    The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding. PMID:22476233

  20. Scalable Molecular Dynamics with NAMD

    PubMed Central

    Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus

    2008-01-01

    NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654

  1. Multisurface Adiabatic Reactive Molecular Dynamics.

    PubMed

    Nagy, Tibor; Yosa Reyes, Juvenal; Meuwly, Markus

    2014-04-01

    Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations. PMID:26580356

  2. Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

    PubMed

    Croll, Tristan Ian; Andersen, Gregers Rom

    2016-09-01

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement. PMID

  3. Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter

    NASA Astrophysics Data System (ADS)

    Miyata, Tatsuhiko; Ikuta, Yasuhiro; Hirata, Fumio

    2010-07-01

    This article proposes a free energy calculation method based on the molecular dynamics simulation combined with the three dimensional reference interaction site model theory. This study employs the free energy perturbation (FEP) and the thermodynamic integration (TDI) along the coupling parameters to control the interaction potential. To illustrate the method, we applied it to a complex formation process in aqueous solutions between a crown ether molecule 18-Crown-6 (18C6) and a potassium ion as one of the simplest model systems. Two coupling parameters were introduced to switch the Lennard-Jones potential and the Coulomb potential separately. We tested two coupling procedures: one is a "sequential-coupling" to couple the Lennard-Jones interaction followed by the Coulomb coupling, and the other is a "mixed-coupling" to couple both the Lennard-Jones and the Coulomb interactions together as much as possible. The sequential-coupling both for FEP and TDI turned out to be accurate and easily handled since it was numerically well-behaved. Furthermore, it was found that the sequential-coupling had relatively small statistical errors. TDI along the mixed-coupling integral path was to be carried out carefully, paying attention to a numerical behavior of the integrand. The present model system exhibited a nonmonotonic behavior in the integrands for TDI along the mixed-coupling integral path and also showed a relatively large statistical error. A coincidence within a statistical error was obtained among the results of the free energy differences evaluated by FEP, TDI with the sequential-coupling, and TDI with the mixed-coupling. The last one is most attractive in terms of the computer power and is accurate enough if one uses a proper set of windows, taking the numerical behavior of the integrands into account. TDI along the sequential-coupling integral path would be the most convenient among the methods we tested, since it seemed to be well-balanced between the computational

  4. Dynamic interactions in neural networks

    SciTech Connect

    Arbib, M.A. ); Amari, S. )

    1989-01-01

    The study of neural networks is enjoying a great renaissance, both in computational neuroscience, the development of information processing models of living brains, and in neural computing, the use of neurally inspired concepts in the construction of intelligent machines. This volume presents models and data on the dynamic interactions occurring in the brain, and exhibits the dynamic interactions between research in computational neuroscience and in neural computing. The authors present current research, future trends and open problems.

  5. Better, Cheaper, Faster Molecular Dynamics

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

  6. Molecular Dynamics Simulations of Polymers

    NASA Astrophysics Data System (ADS)

    Han, Jie

    1995-01-01

    Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from

  7. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  8. Application of optimal prediction to molecular dynamics

    SciTech Connect

    Barber IV, John Letherman

    2004-12-01

    Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.

  9. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

    Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)

  10. A concurrent multiscale micromorphic molecular dynamics

    SciTech Connect

    Li, Shaofan 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 first 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.

  11. Nonadiabatic Molecular Dynamics with Trajectories

    NASA Astrophysics Data System (ADS)

    Tavernelli, Ivano

    2012-02-01

    In the mixed quantum-classical description of molecular systems, only the quantum character of the electronic degrees of freedom is considered while the nuclear motion is treated at a classical level. In the adiabatic case, this picture corresponds to the Born-Oppenheimer limit where the nuclei move as point charges on the potential energy surface (PES) associated with a given electronic state. Despite the success of this approximation, many physical and chemical processes do not fall in the regime where nuclei and electrons can be considered decoupled. In particular, most photoreactions pass through regions of the PES in which electron-nuclear quantum interference effects are sizeable and often crucial for a correct description of the phenomena. Recently, we have developed a trajectory-based nonadiabatic molecular dynamics scheme that describes the nuclear wavepacket as an ensemble of particles following classical trajectories on PESs derived from time-dependent density functional theory (TDDFT) [1]. The method is based on Tully's fewest switches trajectories surface hopping (TSH) where the nonadiabatic coupling elements between the different potential energy surfaces are computed on-the-fly as functionals of the ground state electron density or, equivalently, of the corresponding Kohn-Sham orbitals [2]. Here, we present the theoretical fundamentals of our approach together with an extension that allows for the direct coupling of the dynamics to an external electromagnetic field [3] as well as to the external potential generated by the environment (solvent effects) [4]. The method is applied to the study of the photodissociation dynamics of simple molecules in gas phase and to the description of the fast excited state dynamics of molecules in solution (in particular Ruthenium (II) tris(bipyridine) in water). [4pt] [1] E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett., 98, (2007) 023001. [0pt] [2] Tavernelli I.; Tapavicza E.; Rothlisberger U., J. Chem

  12. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V

    2015-03-01

    Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672

  13. Fiber lubrication: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Liu, Hongyi

    Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence

  14. Differential Interactions of Cytochrome P450 3A5 and 3A4 with Chemotherapeutic Agent-Vincristine: A Comparative Molecular Dynamics Study.

    PubMed

    Saba, Nikhat; Bhuyan, Rajabrata; Nandy, Suman Kumar; Seal, Alpana

    2015-01-01

    The chemotherapeutic agent vincristine, used for treatment of acute lymphoblastic leukemia is metabolized preferentially by polymorphic cytochrome P450 3A5 (CYP3A5) with higher clearance rate than cytochrome P450 3A4 (CYP3A4). As a result, CYP3A5 expressers have a reduced amount of vincristine-induced peripheral neuropathy than non-expressers. We modeled the structure of CYP3A5 and its interaction with vincristine, compared with CYP3A4-vincristine complex using molecular docking and simulation studies. This relative study helped us to understand the molecular mechanisms behind the interaction at the atomic level through interaction energy, binding free energy, hydrogen bond and solvent accessible surface area analysis - giving an insight into the binding mode and the main residues involved in this particular interaction. Our results show that the interacting groups get closer in CYP3A5-vincristine complex due to different orientation of vincristine. This leads to higher binding affinity of vincristine towards CYP3A5 compared to CYP3A4 and explains the preferential metabolism of vincristine by CYP3A5. We believe that, the results of the current study will be helpful for future studies on structure-based drug design in this area. PMID:25634447

  15. Molecular dynamics studies of aromatic hydrocarbon liquids

    SciTech Connect

    McLaughlin, E.; Gupta, S.

    1990-01-01

    This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.

  16. Molecular dynamics in high electric fields

    NASA Astrophysics Data System (ADS)

    Apostol, M.; Cune, L. C.

    2016-06-01

    Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called "dipolons"); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

  17. Study of molecular interactions with 13C DNP-NMR

    NASA Astrophysics Data System (ADS)

    Lerche, Mathilde H.; Meier, Sebastian; Jensen, Pernille R.; Baumann, Herbert; Petersen, Bent O.; Karlsson, Magnus; Duus, Jens Ø.; Ardenkjær-Larsen, Jan H.

    2010-03-01

    NMR spectroscopy is an established, versatile technique for the detection of molecular interactions, even when these interactions are weak. Signal enhancement by several orders of magnitude through dynamic nuclear polarization alleviates several practical limitations of NMR-based interaction studies. This enhanced non-equilibrium polarization contributes sensitivity for the detection of molecular interactions in a single NMR transient. We show that direct 13C NMR ligand binding studies at natural isotopic abundance of 13C gets feasible in this way. Resultant screens are easy to interpret and can be performed at 13C concentrations below μM. In addition to such ligand-detected studies of molecular interaction, ligand binding can be assessed and quantified with enzymatic assays that employ hyperpolarized substrates at varying enzyme inhibitor concentrations. The physical labeling of nuclear spins by hyperpolarization thus provides the opportunity to devise fast novel in vitro experiments with low material requirement and without the need for synthetic modifications of target or ligands.

  18. Molecular Handshake: Recognition through Weak Noncovalent Interactions

    ERIC Educational Resources Information Center

    Murthy, Parvathi S.

    2006-01-01

    The weak noncovalent interactions between substances, the handshake in the form of electrostatic interactions, van der Waals' interactions or hydrogen bonding is universal to all living and nonliving matter. They significantly influence the molecular and bulk properties and behavior of matter. Their transient nature affects chemical reactions and…

  19. Gas-surface interactions using accommodation coefficients for a dilute and a dense gas in a micro- or nanochannel: heat flux predictions using combined molecular dynamics and Monte Carlo techniques.

    PubMed

    Nedea, S V; van Steenhoven, A A; Markvoort, A J; Spijker, P; Giordano, D

    2014-05-01

    The influence of gas-surface interactions of a dilute gas confined between two parallel walls on the heat flux predictions is investigated using a combined Monte Carlo (MC) and molecular dynamics (MD) approach. The accommodation coefficients are computed from the temperature of incident and reflected molecules in molecular dynamics and used as effective coefficients in Maxwell-like boundary conditions in Monte Carlo simulations. Hydrophobic and hydrophilic wall interactions are studied, and the effect of the gas-surface interaction potential on the heat flux and other characteristic parameters like density and temperature is shown. The heat flux dependence on the accommodation coefficient is shown for different fluid-wall mass ratios. We find that the accommodation coefficient is increasing considerably when the mass ratio is decreased. An effective map of the heat flux depending on the accommodation coefficient is given and we show that MC heat flux predictions using Maxwell boundary conditions based on the accommodation coefficient give good results when compared to pure molecular dynamics heat predictions. The accommodation coefficients computed for a dilute gas for different gas-wall interaction parameters and mass ratios are transferred to compute the heat flux predictions for a dense gas. Comparison of the heat fluxes derived using explicit MD, MC with Maxwell-like boundary conditions based on the accommodation coefficients, and pure Maxwell boundary conditions are discussed. A map of the heat flux dependence on the accommodation coefficients for a dense gas, and the effective accommodation coefficients for different gas-wall interactions are given. In the end, this approach is applied to study the gas-surface interactions of argon and xenon molecules on a platinum surface. The derived accommodation coefficients are compared with values of experimental results. PMID:25353885

  20. Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein

    2015-12-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  1. Complex molecular assemblies at hand via interactive simulations.

    PubMed

    Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

    2009-11-30

    Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. PMID:19353597

  2. Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT2C G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

    NASA Astrophysics Data System (ADS)

    Córdova-Sintjago, Tania C.; Liu, Yue; Booth, Raymond G.

    2015-02-01

    To understand molecular determinants for ligand activation of the serotonin 5-HT2C G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT2C homology model was built according to an adrenergic β2 GPCR (β2AR) structure and validated using a 5-HT2B GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2S, 4R)-(-)-trans-4-(3'-bromo- and trifluoro-phenyl)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3'-Br-PAT and 3'-CF3-PAT), a 5-HT2C agonist and inverse agonist, respectively. Distinct interactions of 3'-Br-PAT and 3'-CF3-PAT at the wild-type (WT) 5-HT2C receptor model were observed and experimental 5-HT2C receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3'-CF3-PAT docked deeper in the WT 5-HT2C binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3'-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT2C residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT2C residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT2C receptor modelling studies was similar to movements reported for the activation and deactivation of the β2AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.

  3. Langevin stabilization of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Izaguirre, Jesús A.; Catarello, Daniel P.; Wozniak, Justin M.; Skeel, Robert D.

    2001-02-01

    In this paper we show the possibility of using very mild stochastic damping to stabilize long time step integrators for Newtonian molecular dynamics. More specifically, stable and accurate integrations are obtained for damping coefficients that are only a few percent of the natural decay rate of processes of interest, such as the velocity autocorrelation function. Two new multiple time stepping integrators, Langevin Molly (LM) and Brünger-Brooks-Karplus-Molly (BBK-M), are introduced in this paper. Both use the mollified impulse method for the Newtonian term. LM uses a discretization of the Langevin equation that is exact for the constant force, and BBK-M uses the popular Brünger-Brooks-Karplus integrator (BBK). These integrators, along with an extrapolative method called LN, are evaluated across a wide range of damping coefficient values. When large damping coefficients are used, as one would for the implicit modeling of solvent molecules, the method LN is superior, with LM closely following. However, with mild damping of 0.2 ps-1, LM produces the best results, allowing long time steps of 14 fs in simulations containing explicitly modeled flexible water. With BBK-M and the same damping coefficient, time steps of 12 fs are possible for the same system. Similar results are obtained for a solvated protein-DNA simulation of estrogen receptor ER with estrogen response element ERE. A parallel version of BBK-M runs nearly three times faster than the Verlet-I/r-RESPA (reversible reference system propagator algorithm) when using the largest stable time step on each one, and it also parallelizes well. The computation of diffusion coefficients for flexible water and ER/ERE shows that when mild damping of up to 0.2 ps-1 is used the dynamics are not significantly distorted.

  4. Molecular dynamics simulation of liquid sulfur dioxide.

    PubMed

    Ribeiro, Mauro C C

    2006-05-01

    A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437

  5. Dynamics of molecular superrotors in an external magnetic field

    NASA Astrophysics Data System (ADS)

    Korobenko, Aleksey; Milner, Valery

    2015-08-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  6. Dynamics of dewetting at the nanoscale using molecular dynamics.

    PubMed

    Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J

    2007-03-27

    Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565

  7. Dynamical Localization in Molecular Systems.

    NASA Astrophysics Data System (ADS)

    Wang, Xidi

    In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems

  8. DockingShop: A Tool for Interactive Molecular Docking

    SciTech Connect

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  9. Molecular dynamics on APE100

    NASA Astrophysics Data System (ADS)

    Barone, Luciano Maria; Simonazzi, Riccardo; Tenenbaum, Alexander

    1995-09-01

    We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long range potentials, APE turns out to be faster than a conventional computer; large systems can be conveniently simulated using either the cloning approach (up to ˜ 10 5 particles) or a domain decomposition with the systolic method. In the case of short range potentials and systems with diffusion (like a liquid), APE is convenient only when using a large number of processors. In a special case (a crystal without diffusion), a specific domain decomposition technique with frames makes APE advantageous for intermediate and large systems. Using the latter technique we have studied in detail the effect of different numerical error sources, and compared the accuracy of APE with that of a conventional computer.

  10. Dynamics of riboswitches: Molecular simulations.

    PubMed

    Sanbonmatsu, Karissa Y

    2014-10-01

    Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating the key principles of riboswitch operation, computation may aid in the effort to design more specific antibiotics with affinities greater than those of the native ligand. Such a detailed understanding may be required to improve efficacy and reduce side effects. These studies are laying the groundwork for understanding the action mechanism of new compounds that inhibit riboswitch activity. Future directions such as magnesium effects, large-scale conformational changes, expression platforms and co-transcriptional folding are also discussed. This article is part of a Special Issue entitled: Riboswitches. PMID:24953187

  11. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  12. 2004 Atomic and Molecular Interactions Gordon Research Conference

    SciTech Connect

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  13. Dynamical Interactions Among Extrasolar Planets

    NASA Astrophysics Data System (ADS)

    Laughlin, G.

    For certain multiple planet systems such as GJ 876 and 55 Cancri, which have (1) been observed for a large number of orbital periods, and which (2) have strong planet-planet gravitational interactions, the approximation that the planets are orbiting on independent Keplerian ellipses is inadequate. We discuss the production of self-consistent dynamical fits to these interacting systems, in which a minimization scheme (such as the Levenberg-Marquardt technique, or a Genetic Algorithm) is used to repeatedly drive an N-body integrator and improve the agreement between the integrated reflex motion of the central star and the observed radial velocities.

  14. Dynamics of convective scale interaction

    NASA Technical Reports Server (NTRS)

    Purdom, James F. W.; Sinclair, Peter C.

    1988-01-01

    Several of the mesoscale dynamic and thermodynamic aspects of convective scale interaction are examined. An explanation of how sounding data can be coupled with satellite observed cumulus development in the warm sector and the arc cloud line's time evolution to develop a short range forecast of expected convective intensity along an arc cloud line. The formative, mature and dissipating stages of the arc cloud line life cycle are discussed. Specific properties of convective scale interaction are presented and the relationship between arc cloud lines and tornado producing thunderstorms is considered.

  15. Thermal transpiration: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    T, Joe Francis; Sathian, Sarith P.

    2014-12-01

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  16. Thermal transpiration: A molecular dynamics study

    SciTech Connect

    T, Joe Francis; Sathian, Sarith P.

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  17. Cell list algorithms for nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew; Fox, Ian; Saracino, Alexandra

    2016-06-01

    We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.

  18. Combined molecular dynamics-spin dynamics simulations of bcc iron

    SciTech Connect

    Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg

    2014-01-01

    Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.

  19. Effect of guanidine hydrochloride and urea on the interaction of 6-thioguanine with human serum albumin: a spectroscopic and molecular dynamics based study.

    PubMed

    Ishtikhar, Mohd; Khan, Anam; Chang, Chih-Kai; Lin, Lilian Tsai-Wei; Wang, Steven S-S; Khan, Rizwan Hasan

    2016-07-01

    6-thioguanine (6-TG) is an antineoplastic, nucleobase guanine, purine analog drug belongs to thiopurine drug-family of antimetabolites. In the present study, we report an experimental approach towards interaction mechanism of 6-TG with human serum albumin (HSA) and examine the chemical stability of HSA in the presence of denaturants such as guanidine hydrochloride (GdnHCl) and urea. Interaction of 6-TG with HSA has been studied by various spectroscopic and spectropolarimeteric methods to investigate what short of binding occurs at physiological conditions. 6-TG binds in the hydrophobic cavity of subdomain IIA of HSA by static quenching mechanism which induces conformation alteration in the protein structure. That helpful for further study of denaturation process where change in secondary structures causes unfolding of protein that also responsible for severance of domain III from rest of the protein part. We have also performed molecular simulation and molecular docking study in the presence of denaturating agents to determine the binding property of 6-TG and the effect of denaturating agents on the structural activity of HSA. We had found that GdnHCl is more effective denaturating agent when compared to urea. Hence, this study provides straight evidence of the binding mechanism of 6-TG with HSA and the formation of intermediate or unfolding transition that causes unfolding of HSA. PMID:26208966

  20. Dynamic regulation of lipid-protein interactions.

    PubMed

    Martfeld, Ashley N; Rajagopalan, Venkatesan; Greathouse, Denise V; Koeppe, Roger E

    2015-09-01

    We review the importance of helix motions for the function of several important categories of membrane proteins and for the properties of several model molecular systems. For voltage-gated potassium or sodium channels, sliding, tilting and/or rotational movements of the S4 helix accompanied by a swapping of cognate side-chain ion-pair interactions regulate the channel gating. In the seven-helix G protein-coupled receptors, exemplified by the rhodopsins, collective helix motions serve to activate the functional signaling. Peptides which initially associate with lipid-bilayer membrane surfaces may undergo dynamic transitions from surface-bound to tilted-transmembrane orientations, sometimes accompanied by changes in the molecularity, formation of a pore or, more generally, the activation of biological function. For single-span membrane proteins, such as the tyrosine kinases, an interplay between juxtamembrane and transmembrane domains is likely to be crucial for the regulation of dimer assembly that in turn is associated with the functional responses to external signals. Additionally, we note that experiments with designed single-span transmembrane helices offer fundamental insights into the molecular features that govern protein-lipid interactions. This article is part of a Special Issue entitled: Lipid-protein interactions. PMID:25666872

  1. Time-Dependent Molecular Reaction Dynamics

    SciTech Connect

    Oehrn, Yngve

    2007-11-29

    This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.

  2. The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.

    PubMed

    Fukuda, Ikuo; Kamiya, Narutoshi; Nakamura, Haruki

    2014-05-21

    In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother

  3. The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: Analysis of the accuracy and application to liquid systems

    SciTech Connect

    Fukuda, Ikuo; Kamiya, Narutoshi; Nakamura, Haruki

    2014-05-21

    In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother

  4. A computational perspective of molecular interactions through virtual screening, pharmacokinetic and dynamic prediction on ribosome toxin A chain and inhibitors of Ricinus communis

    PubMed Central

    Kumar, R. Barani; Suresh, M. Xavier

    2012-01-01

    Background: Ricin is considered to be one of the most deadly toxins and gained its favor as a bioweapon that has a serious social and biological impact, due to its widespread nature and abundant availability. The hazardous effects of this toxin in human being are seen in almost all parts of the organ system. The severe consequences of the toxin necessitate the need for developing potential inhibitors that can effectively block its interaction with the host system. Materials and Methods: In order to identify potential inhibitors that can effectively block ricin, we employed various computational approaches. In this work, we computationally screened and analyzed 66 analogs and further tested their ADME/T profiles. From the kinetic and toxicity studies we selected six analogs that possessed appropriate pharmacokinetic and dynamic property. We have also performed a computational docking of these analogs with the target. Results: On the basis of the dock scores and hydrogen bond interactions we have identified analog 64 to be the best interacting molecule. Molecule 64 seems to have stable interaction with the residues Tyr80, Arg180, and Val81. The pharmacophore feature that describes the key functional features of a molecule was also studied and presented. Conclusion: The pharmacophore features of the drugs provided suggests the key functional groups that can aid in the design and synthesis of more potential inhibitors. PMID:22224054

  5. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    SciTech Connect

    Lau, E Y; Krishnan, V V

    2007-07-18

    The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

  6. Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics

    SciTech Connect

    Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.

    2015-05-21

    We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.

  7. First-principles molecular dynamics simulations of uranyl ion interaction at the water/rutile TiO2(110) interface

    NASA Astrophysics Data System (ADS)

    Sebbari, K.; Roques, J.; Simoni, E.; Domain, C.; Perron, H.; Catalette, H.

    2012-08-01

    The effects of temperature and solvation on uranyl ion adsorption at the water/rutile TiO2(110) interface are investigated by Density Functional Theory (DFT) in both static and Born-Oppenheimer molecular dynamics approaches. According to experimental observations, uranyl ion can form two surface complexes in a pH range from 1.5 to 4.5. Based on these observations, the structures of the complexes at 293 K are first calculated in agreement with vacuum static calculations. Then, an increase in temperature (293 to 425 K) induces the reinforcement of uranyl ion adsorption due to the release of water molecules from the solvation shell of uranyl ion. Finally, temperature can modify the nature of the surface species.

  8. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    NASA Astrophysics Data System (ADS)

    Sebbari, Karim; Roques, Jérôme; Domain, Christophe; Simoni, Eric

    2012-10-01

    The behavior of the UO22+ uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT + U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 Å above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d_{U{-O}_{adsorption}}= 2.39 Å. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  9. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    SciTech Connect

    Sebbari, Karim; Roques, Jerome; Simoni, Eric; Domain, Christophe

    2012-10-28

    The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  10. Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

    NASA Technical Reports Server (NTRS)

    Menon, Madhu

    1998-01-01

    In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

  11. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect

    Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

    1998-02-01

    Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

  12. Modeling the Hydrogen Bond within Molecular Dynamics

    ERIC Educational Resources Information Center

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  13. Molecular Dynamics Simulations of Simple Liquids

    ERIC Educational Resources Information Center

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  14. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    SciTech Connect

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-09-29

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.

  15. Tensor-optimized antisymmetrized molecular dynamics in nuclear physics

    NASA Astrophysics Data System (ADS)

    Myo, Takayuki; Toki, Hiroshi; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro

    2015-07-01

    We develop a new formalism to treat nuclear many-body systems using the bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays an important role in nuclear many-body systems due to the role of the pion in strongly interacting systems. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model. We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".

  16. How to Predict Molecular Interactions between Species?

    PubMed Central

    Schulze, Sylvie; Schleicher, Jana; Guthke, Reinhard; Linde, Jörg

    2016-01-01

    Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We

  17. Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics

    NASA Astrophysics Data System (ADS)

    Hasnaoui, K. H. O.; Chomaz, Ph; Gulminelli, F.

    A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented.

  18. Molecular dynamics: A stitch in time

    NASA Astrophysics Data System (ADS)

    Deupi, Xavier

    2014-01-01

    Lengthy molecular dynamics simulations of complex systems at the atomic scale usually require supercomputers. Now, by stitching together many shorter independent simulations run 'in the cloud', this requirement has been circumvented, allowing two milliseconds of the dynamics of a G-protein-coupled receptor to be simulated.

  19. Molecular chaperone-mediated nuclear protein dynamics.

    PubMed

    Echtenkamp, Frank J; Freeman, Brian C

    2014-05-01

    Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369

  20. Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics

    NASA Astrophysics Data System (ADS)

    Rakesh, L.

    2009-09-01

    Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the

  1. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.

  2. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

    Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-01-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  3. Dynamic neurotransmitter interactions measured with PET

    SciTech Connect

    Schiffer, W.K.; Dewey, S.L.

    2001-04-02

    Positron emission tomography (PET) has become a valuable interdisciplinary tool for understanding physiological, biochemical and pharmacological functions at a molecular level in living humans, whether in a healthy or diseased state. The utility of tracing chemical activity through the body transcends the fields of cardiology, oncology, neurology and psychiatry. In this, PET techniques span radiochemistry and radiopharmaceutical development to instrumentation, image analysis, anatomy and modeling. PET has made substantial contributions in each of these fields by providing a,venue for mapping dynamic functions of healthy and unhealthy human anatomy. As diverse as the disciplines it bridges, PET has provided insight into an equally significant variety of psychiatric disorders. Using the unique quantitative ability of PET, researchers are now better able to non-invasively characterize normally occurring neurotransmitter interactions in the brain. With the knowledge that these interactions provide the fundamental basis for brain response, many investigators have recently focused their efforts on an examination of the communication between these chemicals in both healthy volunteers and individuals suffering from diseases classically defined as neurotransmitter specific in nature. In addition, PET can measure the biochemical dynamics of acute and sustained drug abuse. Thus, PET studies of neurotransmitter interactions enable investigators to describe a multitude of specific functional interactions in the human brain. This information can then be applied to understanding side effects that occur in response to acute and chronic drug therapy, and to designing new drugs that target multiple systems as opposed to single receptor types. Knowledge derived from PET studies can be applied to drug discovery, research and development (for review, see (Fowler et al., 1999) and (Burns et al., 1999)). Here, we will cover the most substantial contributions of PET to understanding

  4. Molecular dynamics studies on nanoscale gas transport

    NASA Astrophysics Data System (ADS)

    Barisik, Murat

    Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the

  5. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    SciTech Connect

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  6. Spin vibronics in interacting nonmagnetic molecular nanojunctions

    NASA Astrophysics Data System (ADS)

    Weiss, S.; Brüggemann, J.; Thorwart, M.

    2015-07-01

    We show that in the presence of ferromagnetic electronic reservoirs and spin-dependent tunnel couplings, molecular vibrations in nonmagnetic single molecular transistors induce an effective intramolecular exchange magnetic field. It generates a finite spin accumulation and precession for the electrons confined on the molecular bridge and occurs under (non)equilibrium conditions. The effective exchange magnetic field is calculated here to lowest order in the tunnel coupling for a nonequilibrium transport setup. Coulomb interaction between electrons is taken into account as well as a finite electron-phonon coupling. We show that for realistic physical parameters, an effective spin-phonon coupling emerges. It is induced by quantum many-body interactions, which are either of electron-phonon or Coulomb type. We investigate the precession and accumulation of the confined spins as function of bias and gate voltages as well as their dependence on the angle enclosed by the magnetizations between the left and right reservoir.

  7. How Dynamic Visualization Technology can Support Molecular Reasoning

    NASA Astrophysics Data System (ADS)

    Levy, Dalit

    2012-11-01

    This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and gas. They interact with the visualizations and carry out inquiry activities to make and refine connections between observable phenomena and atomic level processes related to phase change. The explanations proposed by 300 pairs of students in response to pre/post-assessment items have been analyzed using a scale for measuring the level of molecular reasoning. Results indicate that from pretest to posttest, students make progress in their level of molecular reasoning and are better able to connect intermolecular forces and phase change in their explanations. The paper presents the results through the lens of improvement patterns and the metaphor of the "ladder of molecular reasoning," and discusses how this adds to our understanding of the benefits of interacting with dynamic molecular visualizations.

  8. Concise NMR approach for molecular dynamics characterizations in organic solids.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2013-08-22

    Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics. PMID:23879450

  9. Multiple interactions between molecular and supramolecular ordering

    NASA Astrophysics Data System (ADS)

    Manno, M.; Emanuele, A.; Martorana, V.; Bulone, D.; San Biagio, P. L.; Palma-Vittorelli, M. B.; Palma, M. U.

    1999-02-01

    We report studies of the interplay among processes of molecular conformational changes, spinodal demixing of the solution, and molecular crosslinking involved in the physical gelation of a biopolysaccharide-water system. Multiple interactions and kinetic competition among these processes were studied under largely different absolute and relative values of their individual rates by appropriate choices of the quenching temperature at constant polymer concentration. Quenching temperature strongly affects the rate of growth but not the final value of the fractal dimension of the gel. Kinetic competition plays a central role in determining the final conformation of individual molecules and the structure and properties of the final gel. This behavior highlights the frustrated nature of the system, and the need of bringing kinetics sharply into focus in gelation theories. General aspects of the present findings and, specifically, the interplay of molecular conformation changes, solution demixing, and molecular crosslinking extend the relevance of these studies to the fast growing field of amyloid condensation and Prion diseases.

  10. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    NASA Astrophysics Data System (ADS)

    Lühmann, Dirk-Sören; Weitenberg, Christof; Sengstock, Klaus

    2015-07-01

    In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  11. Molecular dynamics simulation of amorphous indomethacin.

    PubMed

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-01-01

    Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal

  12. Michigan molecular interactions r2: from interacting proteins to pathways.

    PubMed

    Tarcea, V Glenn; Weymouth, Terry; Ade, Alex; Bookvich, Aaron; Gao, Jing; Mahavisno, Vasudeva; Wright, Zach; Chapman, Adriane; Jayapandian, Magesh; Ozgür, Arzucan; Tian, Yuanyuan; Cavalcoli, Jim; Mirel, Barbara; Patel, Jignesh; Radev, Dragomir; Athey, Brian; States, David; Jagadish, H V

    2009-01-01

    Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIH's; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org. PMID:18978014

  13. Molecular Dynamics Simulations of Coulomb Explosion

    SciTech Connect

    Bringa, E M

    2002-05-17

    A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.

  14. A molecular dynamics study of dielectric friction

    SciTech Connect

    Kurnikova, M.G.; Waldeck, D.H.; Coalson, R.D.

    1996-07-01

    A molecular dynamics study of the friction experienced by the dye molecule resorufamine rotating in a polar solvent is performed. The validity of simple continuum theories of dielectric friction is tested. It is found that the Alavi{endash}Waldeck theory gives reasonable results for the zero frequency dielectric friction coefficient while the Nee{endash}Zwanzig theory requires an unphysically small cavity radius. A procedure for evaluating the time dependent friction kernel from torques and angular velocities, which enables the contributions to the friction from the van der Waals and Coulomb forces to be evaluated separately, is suggested. This study of a realistic system shows that electrostatic interactions can enhance friction by at least two physical mechanisms. First is a contribution to the friction which arises solely from retardation of the solvent reaction field. Second is a contribution arising from local structural changes of the solvent which are driven by the electrostatic field, i.e., a change in the local viscosity. {copyright} {ital 1996 American Institute of Physics.}

  15. Quantum molecular dynamics simulations of dense matter

    SciTech Connect

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  16. Molecular dynamic simulations of ocular tablet dissolution.

    PubMed

    Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire

    2013-11-25

    Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies. PMID:24073784

  17. Molecular Scale Dynamics of Large Ring Polymers

    NASA Astrophysics Data System (ADS)

    Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.

    2014-10-01

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.

  18. Dynamic signature of molecular association in methanol

    NASA Astrophysics Data System (ADS)

    Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.

    2016-07-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

  19. Dynamic signature of molecular association in methanol.

    PubMed

    Bertrand, C E; Self, J L; Copley, J R D; Faraone, A

    2016-07-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids. PMID:27394112

  20. Molecular scale dynamics of large ring polymers.

    PubMed

    Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D

    2014-10-17

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture. PMID:25361284

  1. Numerical methods for molecular dynamics

    SciTech Connect

    Skeel, R.D.

    1991-01-01

    This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.

  2. Homology modeling, docking, and molecular dynamics simulation of the receptor GALR2 and its interactions with galanin and a positive allosteric modulator.

    PubMed

    Hui, Wen-Qi; Cheng, Qi; Liu, Tian-Yu; Ouyang, Qin

    2016-04-01

    Galanin receptor type 2 (GALR2) is a class A G-protein-coupled receptor (GPCR), and it has been reported that orthosteric ligands and positive allosteric modulators (PAMs) of GALR2 could potentially be used to treat epilepsy. So far, the X-ray structure of this receptor has not been resolved, and knowledge of the 3D structure of GALR2 may prove informative in attempts to design novel ligands and to explore the mechanism for the allosteric modulation of this receptor. In this study, homology modeling was used to obtain several GALR2 models using known templates. ProSA-web Z-scores and Ramachandran plots as well as pre-screening against a test dataset of known compounds were all utilized to select the best model of GALR2. Molecular dockings of galanin (a peptide) and a nonpeptide ligand were carried out to choose the (GALR2 model)-galanin complex that showed the closest agreement with the corresponding experimental data. Finally, a 50-ns MD simulation was performed to study the interactions between the GALR2 model and the synthetic and endogenous ligands. The results from docking and MD simulation showed that, besides the reported residues, Tyr160(4.60), Ile105(3.32), Ala274(7.35), and Tyr163(ECL2) also appear to play important roles in the binding of galanin. The potential allosteric binding pockets in the GALR2 model were then investigated via MD simulation. The results indicated that the mechanism for the allosteric modulation caused by PAMs is the binding of the PAM at pocket III, which is formed by galanin, ECL2, TM2, TM3, and ECL1; this results in the disruption of the Na(+)-binding site and/or the Na(+) ion pathway, leading to GALR2 agonism. PMID:27021209

  3. Dynamic and interacting complex networks

    NASA Astrophysics Data System (ADS)

    Dickison, Mark E.

    This thesis employs methods of statistical mechanics and numerical simulations to study some aspects of dynamic and interacting complex networks. The mapping of various social and physical phenomena to complex networks has been a rich field in the past few decades. Subjects as broad as petroleum engineering, scientific collaborations, and the structure of the internet have all been analyzed in a network physics context, with useful and universal results. In the first chapter we introduce basic concepts in networks, including the two types of network configurations that are studied and the statistical physics and epidemiological models that form the framework of the network research, as well as covering various previously-derived results in network theory that are used in the work in the following chapters. In the second chapter we introduce a model for dynamic networks, where the links or the strengths of the links change over time. We solve the model by mapping dynamic networks to the problem of directed percolation, where the direction corresponds to the time evolution of the network. We show that the dynamic network undergoes a percolation phase transition at a critical concentration pc, that decreases with the rate r at which the network links are changed. The behavior near criticality is universal and independent of r. We find that for dynamic random networks fundamental laws are changed: i) The size of the giant component at criticality scales with the network size N for all values of r, rather than as N2/3 in static network, ii) In the presence of a broad distribution of disorder, the optimal path length between two nodes in a dynamic network scales as N1/2, compared to N1/3 in a static network. The third chapter consists of a study of the effect of quarantine on the propagation of epidemics on an adaptive network of social contacts. For this purpose, we analyze the susceptible-infected-recovered model in the presence of quarantine, where susceptible

  4. Semiclassical guided optimal control of molecular dynamics

    SciTech Connect

    Kondorskiy, A.; Mil'nikov, G.; Nakamura, H.

    2005-10-15

    An efficient semiclassical optimal control theory applicable to multidimensional systems is formulated for controlling wave packet dynamics on a single adiabatic potential energy surface. The approach combines advantages of different formulations of optimal control theory: quantum and classical on one hand and global and local on the other. Numerical applications to the control of HCN-CNH isomerization demonstrate that this theory can provide an efficient tool to manipulate molecular dynamics of many degrees of freedom by laser pulses.

  5. The classical and quantum dynamics of molecular spins on graphene.

    PubMed

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2016-02-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices. PMID:26641019

  6. The classical and quantum dynamics of molecular spins on graphene

    NASA Astrophysics Data System (ADS)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2016-02-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

  7. Molecular Mediators Governing Iron-Copper Interactions

    PubMed Central

    Gulec, Sukru; Collins, James F.

    2015-01-01

    Given their similar physiochemical properties, it is a logical postulate that iron and copper metabolism are intertwined. Indeed, iron-copper interactions were first documented over a century ago, but the homeostatic effects of one on the other has not been elucidated at a molecular level to date. Recent experimental work has, however, begun to provide mechanistic insight into how copper influences iron metabolism. During iron deficiency, elevated copper levels are observed in the intestinal mucosa, liver, and blood. Copper accumulation and/or redistribution within enterocytes may influence iron transport, and high hepatic copper may enhance biosynthesis of a circulating ferroxidase, which potentiates iron release from stores. Moreover, emerging evidence has documented direct effects of copper on the expression and activity of the iron-regulatory hormone hepcidin. This review summarizes current experimental work in this field, with a focus on molecular aspects of iron-copper interplay and how these interactions relate to various disease states. PMID:24995690

  8. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

    This dissertation consists of topics in two related areas of research that together provide quantum mechanical descriptions of atomic and molecular interactions and reactions. The first is the ab initio electronic structure calculation that provides the atomic and molecular interaction potential, including the long-range potential. The second is the quantum theory of interactions that uses such potentials to understand scattering, long-range molecules, and reactions. In ab initio electronic structure calculations, we present results of dynamic polarizabilities for a variety of atoms and molecules, and the long-range dispersion coefficients for a number of atom-atom and atom-molecule cases. We also present results of a potential energy surface for the triatomic lithium-ytterbium-lithium system, aimed at understanding the related chemical reactions. In the quantum theory of interactions, we present a multichannel quantum-defect theory (MQDT) for atomic interactions in a magnetic field. This subject, which is complex especially for atoms with hyperfine structure, is essential for the understanding and the realization of control and tuning of atomic interactions by a magnetic field: a key feature that has popularized cold atom physics in its investigations of few-body and many-body quantum systems. Through the example of LiK, we show how MQDT provides a systematic and an efficient understanding of atomic interaction in a magnetic field, especially magnetic Feshbach resonances in nonzero partial waves.

  9. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  10. Optimizing replica exchange moves for molecular dynamics.

    PubMed

    Nadler, Walter; Hansmann, Ulrich H E

    2007-11-01

    We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method. PMID:18233794

  11. Molecular dynamics calculations of nuclear stimulated desorption

    SciTech Connect

    Glikman, E.; Kelson, I. ); Doan, N.V. )

    1991-09-01

    Molecular dynamics calculations of nuclear stimulated desorption are carried out for a palladium crystal containing radioactive palladium atoms. The total desorption probability from various sites are computed, as well as the angular distribution of the desorbing atoms. The implications of the results to different experimental scenarios are discussed.

  12. Reaction dynamics in polyatomic molecular systems

    SciTech Connect

    Miller, W.H.

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  13. Molecular dynamics simulations of weak detonations.

    PubMed

    Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie

    2011-12-01

    Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055

  14. Molecular dynamics of PLK1 during mitosis

    PubMed Central

    Schmucker, Stephane; Sumara, Izabela

    2014-01-01

    Polo-like kinase 1 (PLK1) is a key regulator of eukaryotic cell division. During mitosis, dynamic regulation of PLK1 is crucial for its roles in centrosome maturation, spindle assembly, microtubule–kinetochore attachment, and cytokinesis. Similar to other members of the PLK family, the molecular architecture of PLK1 protein is characterized by 2 domains—the kinase domain and the regulatory substrate-binding domain (polo-box domain)—that cooperate and control PLK1 function during mitosis. Mitotic cells employ many layers of regulation to activate and target PLK1 to different cellular structures in a timely manner. During the last decade, numerous studies have shed light on the precise molecular mechanisms orchestrating the mitotic activity of PLK1 in time and space. This review aims to discuss available data and concepts related to regulation of the molecular dynamics of human PLK1 during mitotic progression. PMID:27308323

  15. An implicit divalent counterion force field for RNA molecular dynamics

    NASA Astrophysics Data System (ADS)

    Henke, Paul S.; Mak, Chi H.

    2016-03-01

    How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

  16. Rational Prediction with Molecular Dynamics for Hit Identification

    PubMed Central

    Nichols, Sara E; Swift, Robert V; Amaro, Rommie E

    2012-01-01

    Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline. PMID:23110535

  17. Probing Molecular Dynamics at Attosecond Resolution with Femtosecond Laser Pulses

    NASA Astrophysics Data System (ADS)

    Tong, X. M.; Zhao, Z. X.; Lin, C. D.

    2003-12-01

    The kinetic energy distribution of D+ ions resulting from the interaction of a femtosecond laser pulse with D2 molecules is calculated based on the rescattering model. From analyzing the molecular dynamics, it is shown that the recollision time between the ionized electron and the D+2 ion can be read from the D+ kinetic energy peaks to attosecond accuracy. We further suggest that a more precise reading of the clock can be achieved by using shorter fs laser pulses (about 15fs).

  18. Dispersion Interactions in High-Density Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Csernica, Peter; Maitra, Rahul; Distasio, Robert

    Dispersion interactions are ubiquitous quantum mechanical phenomena arising from correlated electron density fluctuations in molecules and materials. As a key component of non-bonded interactions, dispersion forces play a critical role in determining the structure and stability of molecular crystals. Due to the relative intermolecular separation in high-density molecular crystals, an accurate description of these non-bonded interactions requires the inclusion of terms beyond the asymptotic induced-dipole-induced-dipole (C6 /R6) contribution. In this work, we have developed a first principles based approach within the framework of Density Functional Theory (i.e., that only depends on the charge density n (r)) for capturing the higher-order induced multipolar contributions to the correlation energy. As a first application of this method, we have investigated the structure and stability of the high-density ice molecular crystal polymorphs at the ice VI--ice VII--ice VIII triple point (278K, 2.1GPa) using ab-initio molecular dynamics in the isobaric-isothermal (NpT) ensemble.

  19. A Dynamic Interactive Theory of Person Construal

    ERIC Educational Resources Information Center

    Freeman, Jonathan B.; Ambady, Nalini

    2011-01-01

    A dynamic interactive theory of person construal is proposed. It assumes that the perception of other people is accomplished by a dynamical system involving continuous interaction between social categories, stereotypes, high-level cognitive states, and the low-level processing of facial, vocal, and bodily cues. This system permits lower-level…

  20. Screened Electrostatic Interactions in Molecular Mechanics.

    PubMed

    Wang, Bo; Truhlar, Donald G

    2014-10-14

    In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal

  1. Quench dynamics in long-range interacting quantum systems

    NASA Astrophysics Data System (ADS)

    Gong, Zhexuan

    2016-05-01

    A distinctive feature of atomic, molecular, and optical systems is that interactions between particles are often long-ranged. Control techniques from quantum optics often allow one to tune the pattern of these long-range interactions, creating an entirely new degree of freedom, absent in typical condensed matter systems. These tunable long-range interactions can result in very different far-from-equilibrium dynamics compared to systems with only short-range interactions. In the first half of the talk, I will describe how very general types of long-range interactions can qualitatively change the entanglement and correlation growth shortly after a quantum quench. In the second half of the talk I will show that, at longer times, long-range interactions can lead to exotic quasi-stationary states and dynamical phase transitions. These theoretical ideas have been explored in recent trapped-ion experiments, and connections to these experiments will be emphasized in both parts of the talk.

  2. Laser-enhanced dynamics in molecular rate processes

    NASA Technical Reports Server (NTRS)

    George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.

    1978-01-01

    The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

  3. Molecular mechanisms of membrane interaction at implantation.

    PubMed

    Davidson, Lien M; Coward, Kevin

    2016-03-01

    Successful pregnancy is dependent upon the implantation of a competent embryo into a receptive endometrium. Despite major advancement in our understanding of reproductive medicine over the last few decades, implantation failure still occurs in both normal pregnancies and those created artificially by assisted reproductive technology (ART). Consequently, there is significant interest in elucidating the etiology of implantation failure. The complex multistep process of implantation begins when the developing embryo first makes contact with the plasma membrane of epithelial cells within the uterine environment. However, although this biological interaction marks the beginning of a fundamental developmental process, our knowledge of the intricate physiological and molecular processes involved remains sparse. In this synopsis, we aim to provide an overview of our current understanding of the morphological changes which occur to the plasma membrane of the uterine endothelium, and the molecular mechanisms that control communication between the early embryo and the endometrium during implantation. A multitude of molecular factors have been implicated in this complex process, including endometrial integrins, extracellular matrix molecules, adhesion molecules, growth factors, and ion channels. We also explore the development of in vitro models for embryo implantation to help researchers investigate mechanisms which may underlie implantation failure. Understanding the precise molecular pathways associated with implantation failure could help us to generate new prognostic/diagnostic biomarkers, and may identify novel therapeutic targets. PMID:26969610

  4. Molecular dynamics simulation of interfacial adhesion

    SciTech Connect

    Yarovsky, I.; Chaffee, A.L.

    1996-12-31

    Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.

  5. Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays.

    PubMed

    Liu, Ji-Yuan; Chen, Xi-En; Zhang, Ya-Lin

    2015-01-01

    Serine/threonine protein phosphatase 5 (PP5) is a promising novel target for anticancer therapies. This work aims to uncover the key interactions at the atomic level between PP5 and three inhibitors (cantharidin, norcantharidin and endothall). We found that, unlike previous report, Arg 100 contributes less to PP5-inhibitor binding, and the residues His 69, Asn 128, His 129, Arg 225, His 252 and Arg 250 are of importance to PP5-inhibitor binding. The hydrophobic interactions established between the residues Val 254, Phe 271 and Tyr 276, especially Glu 253, are very important to enhance the inhibitive interaction. We suggested that, to increase the inhibitory activity, the interactions of inhibitor with three negatively charged unfavorable interaction residues, Asp 99, Glu 130 and Asp 213, should be avoided. However, the interactions of inhibitor with favorable interaction residue Arg 250 could enhance the inhibitory activity. The Manganese ion 2 (MN2) unfavorably contribute to the total interaction free energies. The coordination between MN2 and chemical group of inhibitor should be eliminated. This work provides insight into how cantharidin and its analogs bind to PP5c at the atomic level and will facilitate modification of cantharidin-like chemicals to rationally develop more specific and less cytotoxic anti-cancer drugs. PMID:26190207

  6. Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays

    PubMed Central

    Liu, Ji-Yuan; Chen, Xi-En; Zhang, Ya-Lin

    2015-01-01

    Serine/threonine protein phosphatase 5 (PP5) is a promising novel target for anticancer therapies. This work aims to uncover the key interactions at the atomic level between PP5 and three inhibitors (cantharidin, norcantharidin and endothall). We found that, unlike previous report, Arg 100 contributes less to PP5-inhibitor binding, and the residues His 69, Asn 128, His 129, Arg 225, His 252 and Arg 250 are of importance to PP5-inhibitor binding. The hydrophobic interactions established between the residues Val 254, Phe 271 and Tyr 276, especially Glu 253, are very important to enhance the inhibitive interaction. We suggested that, to increase the inhibitory activity, the interactions of inhibitor with three negatively charged unfavorable interaction residues, Asp 99, Glu 130 and Asp 213, should be avoided. However, the interactions of inhibitor with favorable interaction residue Arg 250 could enhance the inhibitory activity. The Manganese ion 2 (MN2) unfavorably contribute to the total interaction free energies. The coordination between MN2 and chemical group of inhibitor should be eliminated. This work provides insight into how cantharidin and its analogs bind to PP5c at the atomic level and will facilitate modification of cantharidin-like chemicals to rationally develop more specific and less cytotoxic anti-cancer drugs. PMID:26190207

  7. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    PubMed Central

    De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.

    2015-01-01

    Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

  8. Clustering molecular dynamics trajectories for optimizing docking experiments.

    PubMed

    De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

    2015-01-01

    Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

  9. Open boundary molecular dynamics of sheared star-polymer melts.

    PubMed

    Sablić, Jurij; Praprotnik, Matej; Delgado-Buscalioni, Rafael

    2016-02-28

    Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. PMID:26820315

  10. Exciton dynamics in perturbed vibronic molecular aggregates

    PubMed Central

    Brüning, C.; Wehner, J.; Hausner, J.; Wenzel, M.; Engel, V.

    2015-01-01

    A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840

  11. Exciton dynamics in perturbed vibronic molecular aggregates.

    PubMed

    Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V

    2016-07-01

    A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840

  12. A molecular dynamics study of the ionic liquid, choline acetate.

    PubMed

    Willcox, Jon A L; Kim, Hyunjin; Kim, Hyung J

    2016-06-01

    Structural and dynamic properties of the ionic liquid (IL) choline acetate are studied using molecular dynamics (MD) simulations. The hydroxyl group of choline shows significant hydrogen-bonding interactions with the oxygen atoms of acetate. Nearly all choline cations are found to form a hydrogen bond with acetate anions at 400 K, while about 67% of cations participate in hydrogen-bonding interactions at 600 K. At 400 K, subdiffusive and prominent non-Gaussian behavior persist for t > 10 ns. At 600 K, the usual diffusion regime is obtained after a few hundred ps of subdiffusive behavior. Analysis of reorientational motions of acetate ions, particularly those of their short axes, indicates a high degree of dynamic heterogeneity, in agreement with previous work on different IL systems. PMID:27188287

  13. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

    Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.

    2014-05-14

    The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.

  14. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    SciTech Connect

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  15. Molecular dynamics at constant Cauchy stress

    NASA Astrophysics Data System (ADS)

    Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio

    2016-05-01

    The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.

  16. Molecular dynamics at constant Cauchy stress.

    PubMed

    Miller, Ronald E; Tadmor, Ellad B; Gibson, Joshua S; Bernstein, Noam; Pavia, Fabio

    2016-05-14

    The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress. PMID:27179471

  17. Molecular dynamics study of cyclohexane interconversion

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Chandler, David

    1990-12-01

    Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.

  18. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  19. Combined Molecular Dynamics-Spin Dynamics Simulation of α-Iron in an External Magnetic Field

    NASA Astrophysics Data System (ADS)

    Mudrick, Mark; Perera, Dilina; Landau, David P.

    Using an atomistic model that treats both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to study dynamic properties of α-iron. Atomic interactions are described by an empirical many-body potential while spin-spin interactions are handled with a Heisenberg-like Hamiltonian with a coordinate dependent exchange interaction. Each of these interactions are parameterized by first-principles calculations. These simulations numerically solve equations of motion using an algorithm based on the second-order Suzuki-Trotter decomposition for the time evolution operator. Through calculation of the Fourier transform of space-displaced time-displaced correlation functions, vibrational and magnetic excitations have been studied. The application of an external magnetic field up to 10-T has now been included and has been shown to increase the characteristic frequencies of the single-spin-wave excitations. Two-spin-wave interactions have also been investigated.

  20. Introduction to the quantum trajectory method and to Fermi molecular dynamics

    NASA Astrophysics Data System (ADS)

    La Gattuta, K. J.

    2003-06-01

    The quantum trajectory method (QTM) will be introduced, and an approximation to the QTM known as Fermi molecular dynamics (FMD) will be described. Results of simulations based on FMD will be mentioned for specific nonequilibrium systems dominated by Coulomb interactions.

  1. New faster CHARMM molecular dynamics engine

    PubMed Central

    Hynninen, Antti-Pekka; Crowley, Michael F

    2014-01-01

    We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199

  2. Nanoindentation of Zr by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.

    2015-12-01

    Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.

  3. Molecular dynamics modelling of solidification in metals

    SciTech Connect

    Boercker, D.B.; Belak, J.; Glosli, J.

    1997-12-31

    Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.

  4. Aromatic interactions impact ligand binding and function at serotonin 5-HT2C G protein-coupled receptors: receptor homology modelling, ligand docking, and molecular dynamics results validated by experimental studies

    NASA Astrophysics Data System (ADS)

    Córdova-Sintjago, Tania; Villa, Nancy; Fang, Lijuan; Booth, Raymond G.

    2014-02-01

    The serotonin (5-hydroxytryptamine, 5-HT) 5-HT2 G protein-coupled receptor (GPCR) family consists of types 2A, 2B, and 2C that share ∼75% transmembrane (TM) sequence identity. Agonists for 5-HT2C receptors are under development for psychoses; whereas, at 5-HT2A receptors, antipsychotic effects are associated with antagonists - in fact, 5-HT2A agonists can cause hallucinations and 5-HT2B agonists cause cardiotoxicity. It is known that 5-HT2A TM6 residues W6.48, F6.51, and F6.52 impact ligand binding and function; however, ligand interactions with these residues at the 5-HT2C receptor have not been reported. To predict and validate molecular determinants for 5-HT2C-specific activation, results from receptor homology modelling, ligand docking, and molecular dynamics simulation studies were compared with experimental results for ligand binding and function at wild type and W6.48A, F6.51A, and F6.52A point-mutated 5-HT2C receptors.

  5. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  6. Optimally designed fields for controlling molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rabitz, Herschel

    1991-10-01

    This research concerns the development of molecular control theory techniques for designing optical fields capable of manipulating molecular dynamic phenomena. Although is has been long recognized that lasers should be capable of manipulating dynamic events, many frustrating years of intuitively driven laboratory studies only serve to illustrate the point that the task is complex and defies intuition. The principal new component in the present research is the recognition that this problem falls into the category of control theory and its inherent complexities require the use of modern control theory tools largely developed in the engineering disciplines. Thus, the research has initiated a transfer of the control theory concepts to the molecular scale. Although much contained effort will be needed to fully develop these concepts, the research in this grant set forth the basic components of the theory and carried out illustrative studies involving the design of optical fields capable of controlling rotational, vibrational and electronic degrees of freedom. Optimal control within the quantum mechanical molecular realm represents a frontier area with many possible ultimate applications. At this stage, the theoretical tools need to be joined with merging laboratory optical pulse shaping capabilities to illustrate the power of the concepts.

  7. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  8. Dynamic Maintenance and Visualization of Molecular Surfaces

    SciTech Connect

    Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N

    2004-12-16

    Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.

  9. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  10. Polymer Fluid Dynamics: Continuum and Molecular Approaches.

    PubMed

    Bird, R B; Giacomin, A J

    2016-06-01

    To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems. PMID:27276553

  11. Spectroscopy and molecular dynamics in nonpolar fluids

    NASA Astrophysics Data System (ADS)

    Everitt, Karl Frederick

    This thesis considers the mechanisms by which molecular dynamics in nonpolar liquids influences solvation dynamics and vibrational energy relaxation. We use semiclassical molecular dynamics simulations to calculate photon echo signals for two simple fluids. We demonstrate that two new observables are directly related to the relevant molecular quantity, the frequency- frequency time correlation function (TCF), in contrast to the commonly measured 3PEPS, which cannot be simply related to this TCF at short times. We also present a semianalytic photon echo theory, based on an ansatz which determines the full time dependence from the short time expansion coefficients of the TCF. We demonstrate that this theory accurately predicts most photon echo observables, even when the theory's gaussian approximation is not accurate. We also consider vibrational energy relaxation (VER) in liquid oxygen. Using semiclassical molecular dynamics simulations and an intermolecular potential from the literature, we evaluate the required quantity (the spectral density of a certain force-force TCF) using the same ansatz described above. We demonstrate numerically that this procedure is accurate. Approximately relating this semiclassical rate to the fully quantum mechanical VER rate, using one of the more accurate ``quantum corrections'' available in the literature, yields a result which is in order-of-magnitude agreement with the experimental VER rate. We also calculate the VER rate for liquid oxygen/argon mixtures. The rotations of the solvent near a vibrationally excited molecule, and of that molecule itself, have important consequences for the short-time dynamics of the force-force TCF. We propose a simple statistical model which quantitatively explains the mole- fraction dependence of the observed VER rate. Next, we demonstrate that a newly-developed model for oxygen very accurately describes the liquid, by comparing to experimental measures of microscopic structure and dynamics. We also

  12. Human Lactate Dehydrogenase A Inhibitors: A Molecular Dynamics Investigation

    PubMed Central

    Shi, Yun; Pinto, B. Mario

    2014-01-01

    Lactate dehydrogenase A (LDHA) is an important enzyme in fermentative glycolysis, generating most energy for cancer cells that rely on anaerobic respiration even under normal oxygen concentrations. This renders LDHA a promising molecular target for the treatment of various cancers. Several efforts have been made recently to develop LDHA inhibitors with nanomolar inhibition and cellular activity, some of which have been studied in complex with the enzyme by X-ray crystallography. In this work, we present a molecular dynamics (MD) study of the binding interactions of selected ligands with human LDHA. Conventional MD simulations demonstrate different binding dynamics of inhibitors with similar binding affinities, whereas steered MD simulations yield discrimination of selected LDHA inhibitors with qualitative correlation between the in silico unbinding difficulty and the experimental binding strength. Further, our results have been used to clarify ambiguities in the binding modes of two well-known LDHA inhibitors. PMID:24466056

  13. 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

  14. Molecular Determinants in Phagocyte-Bacteria Interactions.

    PubMed

    Kaufmann, Stefan H E; Dorhoi, Anca

    2016-03-15

    Phagocytes are crucial for host defense against bacterial pathogens. As first demonstrated by Metchnikoff, neutrophils and mononuclear phagocytes share the capacity to engulf, kill, and digest microbial invaders. Generally, neutrophils focus on extracellular, and mononuclear phagocytes on intracellular, pathogens. Reciprocally, extracellular pathogens often capitalize on hindering phagocytosis and killing of phagocytes, whereas intracellular bacteria frequently allow their engulfment and then block intracellular killing. As foreseen by Metchnikoff, phagocytes become highly versatile by acquiring diverse phenotypes, but still retaining some plasticity. Further, phagocytes engage in active crosstalk with parenchymal and immune cells to promote adjunctive reactions, including inflammation, tissue healing, and remodeling. This dynamic network allows the host to cope with different types of microbial invaders. Here we present an update of molecular and cellular mechanisms underlying phagocyte functions in antibacterial defense. We focus on four exemplary bacteria ranging from an opportunistic extracellular to a persistent intracellular pathogen. PMID:26982355

  15. Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations.

    PubMed

    Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan

    2013-05-01

    Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly. PMID:23586433

  16. VUV studies of molecular photofragmentation dynamics

    SciTech Connect

    White, M.G.

    1993-12-01

    State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

  17. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  18. Electronic continuum model for molecular dynamics simulations.

    PubMed

    Leontyev, I V; Stuchebrukhov, A A

    2009-02-28

    A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627

  19. Clustering effects in ionic polymers: Molecular dynamics simulations

    DOE PAGESBeta

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less

  20. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

  1. Molecular dynamics simulation and NMR investigation of the association of the β-blockers atenolol and propranolol with a chiral molecular micelle

    NASA Astrophysics Data System (ADS)

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2015-08-01

    Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies.

  2. Interactions between halide anions and a molecular hydrophobic interface.

    PubMed

    Rankin, Blake M; Hands, Michael D; Wilcox, David S; Fega, K Rebecca; Slipchenko, Lyudmila V; Ben-Amotz, Dor

    2013-01-01

    Interactions between halide ions (fluoride and iodide) and t-butyl alcohol (TBA) dissolved in water are probed using a recently developed hydration-shell spectroscopic technique and theoretical cluster and liquid calculations. High ignal-to-noise Raman spectroscopic measurements are combined with multivariate curve resolution (Raman-MCR) to reveal that while there is little interaction between aqueous fluoride ions and TBA, iodide ions break down the tetrahedral hydration-shell structure of TBA and produce a red-shift in its CH stretch frequency, in good agreement with the theoretical effective fragment potential (EFP) molecular dynamics simulations and hybrid quantum/EFP frequency calculations. The results imply that there is a significantly larger probability of finding iodide than fluoride in the first hydration shell of TBA, although the local iodide concentration is apparently not as high as in the surrounding bulk aqueous NaI solution. PMID:23795504

  3. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

    PubMed Central

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy. PMID:26863418

  4. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.

    PubMed

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy. PMID:26863418

  5. Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

    NASA Astrophysics Data System (ADS)

    Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

    2015-05-01

    Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

  6. Comprehensive Characterization of Molecular Interactions Based on Nanomechanics

    PubMed Central

    Lang, Hans-Peter; Gerber, Christoph; Hegner, Martin

    2008-01-01

    Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (∼748*106 Da) adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da) to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions. PMID:18978938

  7. Visual verification and analysis of cluster detection for molecular dynamics.

    PubMed

    Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas

    2007-01-01

    A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented. PMID:17968118

  8. Molecular dynamics studies of interfacial water at the alumina surface.

    SciTech Connect

    Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David

    2011-01-01

    Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.

  9. Influenza virus binds its host cell using multiple dynamic interactions

    PubMed Central

    Sieben, Christian; Kappel, Christian; Zhu, Rong; Wozniak, Anna; Rankl, Christian; Hinterdorfer, Peter; Grubmüller, Helmut; Herrmann, Andreas

    2012-01-01

    Influenza virus belongs to a wide range of enveloped viruses. The major spike protein hemagglutinin binds sialic acid residues of glycoproteins and glycolipids with dissociation constants in the millimolar range [Sauter NK, et al. (1992) Biochemistry 31:9609–9621], indicating a multivalent binding mode. Here, we characterized the attachment of influenza virus to host cell receptors using three independent approaches. Optical tweezers and atomic force microscopy-based single-molecule force spectroscopy revealed very low interaction forces. Further, the observation of sequential unbinding events strongly suggests a multivalent binding mode between virus and cell membrane. Molecular dynamics simulations reveal a variety of unbinding pathways that indicate a highly dynamic interaction between HA and its receptor, allowing rationalization of influenza virus–cell binding quantitatively at the molecular level. PMID:22869709

  10. Thermostability of Enzymes from Molecular Dynamics Simulations.

    PubMed

    Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G

    2016-06-14

    Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810

  11. 8B structure in Fermionic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Henninger, K. R.; Neff, T.; Feldmeier, H.

    2015-04-01

    The structure of the light exotic nucleus 8B is investigated in the Fermionic Molecular Dynamics (FMD) model. The decay of 8B is responsible for almost the entire high- energy solar-neutrino flux, making structure calculations of 8B important for determining the solar core temperature. 8B is a proton halo candidate thought to exhibit clustering. FMD uses a wave-packet basis and is well-suited for modelling clustering and halos. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo.

  12. Molecular dynamics simulations of dense plasmas

    SciTech Connect

    Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.

    1993-12-31

    We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

  13. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Y.T.

    1987-03-01

    Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.

  14. Molecular dynamics simulation of ice XII

    NASA Astrophysics Data System (ADS)

    Borzsák, István; Cummings, Peter T.

    1999-02-01

    Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.

  15. Crystallization of nickel nanoclusters by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Chamati, H.; Gaminchev, K.

    2012-12-01

    We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.

  16. Dynamic Heterogeneity in Interacting Miscible Polymer Blends

    NASA Astrophysics Data System (ADS)

    Gaikwad, Ashish; Lodge, Timothy

    2008-03-01

    Dynamic heterogeneity leading to time-temperature superposition (tTS) failure has been widely reported in non-interacting/weakly interacting miscible polymer blends. However, coupling of the component dynamic response in blends, even with a huge dynamic asymmetry in the pure components, is possible with H-bonding interactions. This study is focused on finding the minimum level of interaction necessary for thermo-rheological simplicity in blends. Blends of styrene-co-vinylphenol (PSVPh) and poly(vinyl methyl ether) (PVME) were chosen. Incorporation of styrene provides an effective way to modulate H-bonding interactions in the system. Linear viscoelastic data indicate that tTS fails for PS/PVME blends, whereas data obtained for different PVPh/PVME blends showed that tTS was obeyed a over wide temperature range. For PSVPh/PVME blends with low PSVPh content, tTS was successful. This suggests that the presence of alternating styrene and vinyl phenol units was insufficient for dynamic response decoupling. Further studies are in progress, with varying vinyl phenol content in PSVPh, to explore the influence of H-bonding on dynamic heterogeneity and blend dynamics.

  17. Molecular dynamics at constant temperature and pressure

    NASA Astrophysics Data System (ADS)

    Toxvaerd, S.

    1993-01-01

    Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.

  18. Charge transport network dynamics in molecular aggregates.

    PubMed

    Jackson, Nicholas E; Chen, Lin X; Ratner, Mark A

    2016-08-01

    Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, [Formula: see text] Simulations reveal the relevant timescale for local transfer integral decorrelation to be [Formula: see text]100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed. PMID:27439871

  19. Dynamical Simulations of Molecular Clouds in the Galactic Center

    NASA Astrophysics Data System (ADS)

    Salas, Jesus; Morris, Mark

    2016-06-01

    The formation of the central massive cluster of young stars orbiting the Galactic black hole, Sgr A*, has been modeled by several groups by invoking an almost radially infalling molecular cloud that interacts with the black hole and creates a dense, gaseous disk in which stars can then form. However, the dynamical origin of such a cloud remains an open question. We present simulations of the central 30-100 pc of the Milky Way, starting from a population of molecular clouds located in a disk with scale height of ~30 pc, using the N-body/smoothed-particle hydrodynamics code, Gadget2. We followed the dynamical evolution of clouds in a galactic potential that includes a bar to explore whether cloud collisions or a succession of cloud scatterings can remove sufficient angular momentum from a massive cloud to endow it with a predominantly radial orbit. Initial results illustrate the importance of tidal shear; while dense cloud cores remain identifiable for extended periods of time, much of the molecular mass ends up in tidal streams, so cannot be deflected onto low angular momentum orbits by their mutual interactions. At the completion of our ongoing computations, we will report on whether the cloud cores can undergo sufficient scattering to achieve low-angular-momentum orbits.

  20. Molecular dynamics of interactions between rigid and flexible antifolates and dihydrofolate reductase from pyrimethamine-sensitive and pyrimethamine-resistant Plasmodium falciparum.

    PubMed

    Mokmak, Wanwimon; Chunsrivirot, Surasak; Hannongbua, Supa; Yuthavong, Yongyuth; Tongsima, Sissades; Kamchonwongpaisan, Sumalee

    2014-10-01

    Currently, the usefulness of antimalarials such as pyrimethamine (PYR) is drastically reduced due to the emergence of resistant Plasmodium falciparum (Pf) caused by its dihydrofolate reductase (PfDHFR) mutations, especially the quadruple N51I/C59R/S108N/I164L mutations. The resistance was due to the steric conflict of PYR with S108N. WR99210 (WR), a dihydrotriazine antifolate with a flexible side chain that can avoid such conflict, can overcome this resistance through tight binding with the mutant. To understand factors contributing to different binding affinities of PYR/WR to the wild type (WT) and quadruple mutant (QM), we performed simulations on WR-WT, WR-QM, PYR-WT, and PYR-QM complexes and found that Ile14 and Asp54 were crucial for PYR/WR binding to PfDHFR due to strong hydrogen bonds. The quadruple mutations cause PYR to form, on average, fewer hydrogen bonds with Ile14 and Leu164, and to be displaced from its optimal orientation for Asp54 interaction. The predicted binding affinity ranking (WR-QM ≈ WR-WT ≈ PYR-WT > PYR-QM) reasonably agrees with the inhibition constant (K(i)) ranking. Our results reveal important residues for tight binding of PYR/WR to WT/QM, which may be used to evaluate the inhibition effectiveness of antimalarials and to provide fundamental information for designing new drugs effective against drug-resistant P. falciparum. PMID:24716467

  1. Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

    PubMed

    Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

    2014-11-01

    Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC. PMID:25244002

  2. Virtual reality visualization of parallel molecular dynamics simulation

    SciTech Connect

    Disz, T.; Papka, M.; Stevens, R.; Pellegrino, M.; Taylor, V.

    1995-12-31

    When performing communications mapping experiments for massively parallel processors, it is important to be able to visualize the mappings and resulting communications. In a molecular dynamics model, visualization of the atom to atom interaction and the processor mappings provides insight into the effectiveness of the communications algorithms. The basic quantities available for visualization in a model of this type are the number of molecules per unit volume, the mass, and velocity of each molecule. The computational information available for visualization is the atom to atom interaction within each time step, the atom to processor mapping, and the energy resealing events. We use the CAVE (CAVE Automatic Virtual Environment) to provide interactive, immersive visualization experiences.

  3. Molecular-level dynamics of refractory dissolved organic matter

    NASA Astrophysics Data System (ADS)

    Niggemann, J.; Gerdts, G.; Dittmar, T.

    2012-04-01

    Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.

  4. Molecular interactions with ice: Molecular embedding, adsorption, detection, and release

    SciTech Connect

    Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J.; Killelea, Daniel R.

    2014-11-14

    The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF{sub 4} molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF{sub 4} embedding probability is much less than for Xe. In addition, a larger molecule, SF{sub 6}, did not embed at the same translational energies that both CF{sub 4} and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF{sub 4} > SF{sub 6}. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF{sub 4}. Tentatively, this order suggests that for Xe and CF{sub 4}, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF{sub 6} molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas

  5. Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

    2010-06-01

    Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

  6. Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations.

    PubMed

    Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

    2010-06-14

    Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 A), and polyol molecules cluster around the protein at a distance of about 4 A. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions. PMID:20550422

  7. Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Byutner, Oleksiy; Smith, Grant

    2001-03-01

    In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.

  8. Exact dynamic properties of molecular motors

    NASA Astrophysics Data System (ADS)

    Boon, N. J.; Hoyle, R. B.

    2012-08-01

    Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

  9. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  10. Exact dynamic properties of molecular motors.

    PubMed

    Boon, N J; Hoyle, R B

    2012-08-28

    Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)] on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods. PMID:22938213

  11. Network Physiology: How Organ Systems Dynamically Interact

    PubMed Central

    Bartsch, Ronny P.; Liu, Kang K. L.; Bashan, Amir; Ivanov, Plamen Ch.

    2015-01-01

    We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems. PMID:26555073

  12. Network Physiology: How Organ Systems Dynamically Interact.

    PubMed

    Bartsch, Ronny P; Liu, Kang K L; Bashan, Amir; Ivanov, Plamen Ch

    2015-01-01

    We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems. PMID:26555073

  13. A molecular dynamics study of freezing in a confined geometry

    NASA Technical Reports Server (NTRS)

    Ma, Wen-Jong; Banavar, Jayanth R.; Koplik, Joel

    1992-01-01

    The dynamics of freezing of a Lennard-Jones liquid in narrow channels bounded by molecular walls is studied by computer simulation. The time development of ordering is quantified and a novel freezing mechanism is observed. The liquid forms layers and subsequent in-plane ordering within a layer is accompanied by a sharpening of the layer in the transverse direction. The effects of channel size, the methods of quench, the liquid-wall interaction and the roughness of walls on the freezing mechanism are elucidated. Comparison with recent experiments on freezing in confined geometries is presented.

  14. Molecular dynamics modeling and characterization of graphene/polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Rahman, Rezwanur

    The current work focuses on the characterization of graphene based nanocomposites using molecular dynamic simulation and multiscale modeling approaches. Both graphene-epoxy and graphene-cellulose nanocomposites were considered in this study. A hierarchical multiscale modeling approach has been proposed using peridynamics and molecular dynamics simulation. Firstly, the mechanical properties of crosslinked graphene/epoxy (G-Ep) nanocomposites were investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. The influence of graphene's weight concentration, aspect ratio and dispersion on stress-strain response and elastic properties were studied. The results show significant improvement in Young's modulus and shear modulus for the G-Ep system in comparison to the neat epoxy resin. It appears that the RDF, molecular energy and aspect ratios are influenced by both graphene concentrations and aspect ratios. The graphene concentrations in the range of 1-3% are seen to improve Young's modulus and shorter graphenes are observed to be more effective than larger ones. In addition, the dispersed graphene system is more promising in enhancing in-plane elastic modulus than the agglomerated graphene system. The cohesive and pullout forces versus displacements data were plotted under normal and shear modes in order to characterize interfacial properties. The cohesive force is significantly improved by attaching the graphene with a chemical bond at the graphene-epoxy interface. In the second part of the work, cellulose was considered to study the mechanical properties of graphene-cellulose bionanocomposite. Similar to graphene-epoxy systems, the effect of graphene dispersion and agglomeration were studied in the stress-strain plots of graphene-cellulose system. A pcff forcefield was used to define intermolecular and intramolecular interactions. The effect of graphene's aspect ratio and weight concentration on the structural property of each unitcell was

  15. Interactive Beam-Dynamics Program

    Energy Science and Technology Software Center (ESTSC)

    2001-01-08

    TRACE3D is an interactive program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined system. The transport system may consist of the following elements: drift, thin lens, quadrupole, permanent magnet quadrupole, solenoid, doublet, triplet, bending magnet, edge angle (for bend), RF gap, radio-frequency-quadrupole cell, RF cavity, coupled-cavity tank, user-desired element, coordinate rotation, and identical element. The beam is represented by a 6X6 matrix defining a hyper-ellipsoid in six-dimensional phasemore » space. The projection of this hyperellipsoid on any two-dimensional plane is an ellipse that defines the boundary of the beam in that plane.« less

  16. Dynamic transitions in molecular dynamics simulations of supercooled silicon

    NASA Astrophysics Data System (ADS)

    Mei, Xiaojun; Eapen, Jacob

    2013-04-01

    Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.

  17. Molecular Recognition and Specific Interactions for Biosensing Applications

    PubMed Central

    Kim, Dong Chung; Kang, Dae Joon

    2008-01-01

    Molecular recognition and specific interactions are reliable and versatile routes for site-specific and well-oriented immobilization of functional biomolecules on surfaces. The control of surface properties via the molecular recognition and specific interactions at the nanoscale is a key element for the nanofabrication of biosensors with high sensitivity and specificity. This review intends to provide a comprehensive understanding of the molecular recognition- and specific interaction-mediated biosensor fabrication routes that leads to biosensors with well-ordered and controlled structures on both nanopatterned surfaces and nanomaterials. Herein self-assembly of the biomolecules via the molecular recognition and specific interactions on nanoscaled surfaces as well as nanofabrication techniques of the biomolecules for biosensor architecture are discussed. We also describe the detection of molecular recognition- and specific interaction-mediated molecular binding as well as advantages of nanoscale detection.

  18. Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

    PubMed

    Graziani, F R; Bauer, J D; Murillo, M S

    2014-09-01

    Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD

  19. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    PubMed

    Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A

    2016-01-01

    Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. PMID:26013419

  20. Interactive Data Mining for Molecular Graphs

    PubMed Central

    Yılmaz, Burcu; Göktürk, Mehmet

    2009-01-01

    Designing new medical drugs for a specific disease requires extensive analysis of many molecules that have an activity for the disease. The main goal of these extensive analyses is to discover substructures (fragments) that account for the activity of these molecules. Once they are discovered, these fragments are used to understand the structure of new drugs and design new medicines for the disease. In this paper, we propose an interactive approach for visual molecule mining to discover fragments of molecules that are responsible for the desired activity with respect to a specific disease. Our approach visualizes molecular data in a form that can be interpreted by a human expert. Using a pipelining structure, it enables experts to contribute to the solution with their expertise at different levels. In order to derive desired fragments, it combines histogram-based filtering and clustering methods in a novel way. This combination enables a flexible determination of frequent fragments that repeat in molecules exactly or with some variations. PMID:20052387

  1. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  2. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  3. Spiking dynamics of interacting oscillatory neurons

    NASA Astrophysics Data System (ADS)

    Kazantsev, V. B.; Nekorkin, V. I.; Binczak, S.; Jacquir, S.; Bilbault, J. M.

    2005-06-01

    Spiking sequences emerging from dynamical interaction in a pair of oscillatory neurons are investigated theoretically and experimentally. The model comprises two unidirectionally coupled FitzHugh-Nagumo units with modified excitability (MFHN). The first (master) unit exhibits a periodic spike sequence with a certain frequency. The second (slave) unit is in its excitable mode and responds on the input signal with a complex (chaotic) spike trains. We analyze the dynamic mechanisms underlying different response behavior depending on interaction strength. Spiking phase maps describing the response dynamics are obtained. Complex phase locking and chaotic sequences are investigated. We show how the response spike trains can be effectively controlled by the interaction parameter and discuss the problem of neuronal information encoding.

  4. How Interactions Affect Multiple Kinesin Dynamics

    NASA Astrophysics Data System (ADS)

    Kolomeisky, Anatoly

    2013-03-01

    Intracellullar transport is supported by several classes of enzymatic molecules known as motor proteins. Cellular cargos are frequently transported by teams of motor proteins, and recent experimental and theoretical studies uncovered many features of such complex dynamics. Here we investigate theoretically the role of nonmechanical interactions between kinesin motor proteins and microtubules in the collective motion of motor proteins. Our analysis is based on stochastic model that explicitly takes into account all chemical and mechanical transitions. Nonmechanical interactions are assumed to affect kinesin mechanochemistry only when the motors are separated by less than 3 microtubule lattice sites, and it is shown that relatively weak interaction energies can have a significant effect on collective motor dynamics. In agreement with optical trapping experiments on structurally defined kinesin complexes, the model predicts that these effects primarily occur when cargos are transported against loads exceeding single-kinesin stalling forces. These results highlights the complex dynamics of multiple motor proteins in cellular transport phenomena.

  5. Single Molecular Film for Recognizing Biological Molecular Interaction: DNA-Protein Interaction and Enzyme Reaction

    NASA Astrophysics Data System (ADS)

    Kurihara, Kazue

    Protein-protein and protein-substrate interactions play essential roles in biological functions. Surface forces measurement and atomic force microscopy, which directly measure the interaction forces as a function of the surface separation, enable us to quantitatively evaluate these interactions [1-3]. We have employed the surface forces measurement [4] and colloidal probe atomic force microscopy [5] to study interactions involved in specific molecular recognition of DNA-protein and enzyme-substrate reaction. Studied are interactions between nucleic acid bases (adenine and thymine) [6], Spo0A-DB (the DNA-binding site of a transcription factor Spo0A), and DNA [7,8], those between subunits I and II of heptaprenyl diphosphate (HepPP) synthase in the presence of a substrate ((E,E)-farnesyl diphosphate, FPP) and a cofactor (Mg2+) [9-11], and the selectivity of the substrates in this enzymatic reaction [12]. Keys of our approach are the preparation of well-defined samples and the appropriate analysis. We have modified he substrate surfaces with these proteins using the Langmuir-Blodgett (LB) method. This chapter reviews the LB modification method and subsequent demonstrations of biological specific interactions employing this approach.

  6. The classical and quantum dynamics of molecular spins on graphene

    PubMed Central

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2015-01-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019

  7. DASMI: exchanging, annotating and assessing molecular interaction data

    PubMed Central

    Blankenburg, Hagen; Finn, Robert D.; Prlić, Andreas; Jenkinson, Andrew M.; Ramírez, Fidel; Emig, Dorothea; Schelhorn, Sven-Eric; Büch, Joachim; Lengauer, Thomas; Albrecht, Mario

    2009-01-01

    Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet. Results: We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions. Availability: The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/. Contact: mario.albrecht@mpi-inf.mpg.de Supplementary information: Supplementary data and all figures in color are available at Bioinformatics online. PMID:19420069

  8. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  9. Molecular-dynamics simulations of void collapse in shocked model-molecular solids

    NASA Astrophysics Data System (ADS)

    Mintmire, J. W.; Robertson, D. H.; White, C. T.

    1994-06-01

    We have carried out a series of molecular-dynamics simulations on a model three-dimensional molecular solid to study the dynamics of shock-induced collapse of void defects. Molecular-dynamics methods were used for a model system of identical particles arranged as diatomic molecules aligned with the center of mass of each molecule at fcc lattice sites, using a \\{111\\} layering for the two-dimensional boundary conditions. The diatoms were internally coupled via a harmonic potential; all other interactions were modeled with Morse potentials between all particles other than the immediate diatomic partner. Using this model, we have investigated the effect of a cylindrical void at right angles to the direction of layering (and impact). Depending on the strength of the incident shock wave, the void is found to collapse either smoothly and symmetrically (like a balloon gradually losing air), or asymmetrically and turbulently. In the latter case, we note the transient formation (for periods of several hundreds of femtoseconds) of ``hot spots'' at the void location both in terms of the local effective temperature and the vibrational energies of the diatoms.

  10. Tuning the spin dynamics of single molecule magnets via dipolar interactions

    NASA Astrophysics Data System (ADS)

    Hofmann, A.; Salman, Z.

    2014-12-01

    We present calculations of the dipolar field distribution acting on a single molecule magnet due to its neighbours in thin films. The calculations are presented for different packing/configuration scenarios, with different easy axis orientations. The potential for controlling the molecular spin dynamics by tuning the molecule-substrate interaction and its competition with intra-molecular interactions is discussed. We argue that by altering the configuration of the molecular moments, and thus their dipolar interactions, one can enhance or slow down their spin dynamics.

  11. Development of semiclassical molecular dynamics simulation method.

    PubMed

    Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi

    2016-04-28

    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383

  12. Molecular Dynamics Simulation of Shock Induced Detonation

    NASA Astrophysics Data System (ADS)

    Tomar, Vikas; Zhou, Min

    2004-07-01

    This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.

  13. Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.

    PubMed

    Schwabe, Tobias

    2015-08-20

    For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273

  14. Nonequilibrium molecular dynamics: The first 25 years

    SciTech Connect

    Hoover, W.G. |

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.

  15. Molecular Dynamics Simulations of Water Evaporation

    NASA Astrophysics Data System (ADS)

    Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng

    2015-03-01

    The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

  16. Cluster production within antisymmetrized molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ono, Akira

    2016-06-01

    Clusters are quite important at various situations in heavy-ion collisions. Antisymmetrized molecular dynamics was improved to take into account the correlations to form light clusters, such as deuterons and α particles, and light nuclei composed of several clusters. The momentum fluctuations of emitted particles are also taken into account by a simple method. Formation of fragments and light clusters in a wide range of heavy-ion collisions was well described with a single set of model parameters. Fragmentation in a proton induced reaction was also well reproduced by introducing cluster correlations. Calculated results demonstrate strong impacts of clusters in various observables including those usually regarded as probes of the density dependence of symmetry energy.

  17. Molecular-dynamics simulations of lead clusters

    NASA Astrophysics Data System (ADS)

    Hendy, S. C.; Hall, B. D.

    2001-08-01

    Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.

  18. Dielectrophoresis of nanocolloids: a molecular dynamics study.

    PubMed

    Salonen, E; Terama, E; Vattulainen, I; Karttunen, M

    2005-10-01

    Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature. PMID:16195818

  19. Molecular Dynamics Simulation on Stability of Insulin on Graphene

    NASA Astrophysics Data System (ADS)

    Liang, Li-jun; Wang, Qi; Wu, Tao; Shen, Jia-wei; Kang, Yu

    2009-12-01

    The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.

  20. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect

    Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  1. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv

    2005-02-24

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.

  2. Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol

    PubMed Central

    Hofsäß, Christofer; Lindahl, Erik; Edholm, Olle

    2003-01-01

    To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0–40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations—corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols. PMID:12668428

  3. GPU-enabled molecular dynamics simulations of ankyrin kinase complex

    NASA Astrophysics Data System (ADS)

    Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran

    2014-10-01

    The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

  4. Dynamics simulations for engineering macromolecular interactions

    NASA Astrophysics Data System (ADS)

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-06-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  5. Dynamics simulations for engineering macromolecular interactions

    PubMed Central

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-01-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  6. Molecular dynamics simulations of supramolecular polymer rheology

    NASA Astrophysics Data System (ADS)

    Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.

    2010-11-01

    Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.

  7. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  8. Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration.

    PubMed

    Tosso, Rodrigo D; Andujar, Sebastian A; Gutierrez, Lucas; Angelina, Emilio; Rodríguez, Ricaurte; Nogueras, Manuel; Baldoni, Héctor; Suvire, Fernando D; Cobo, Justo; Enriz, Ricardo D

    2013-08-26

    A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC₅₀ values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper. PMID:23834278

  9. Thermodynamic evaluation of aromatic CH/π interactions and rotational entropy in a molecular rotor.

    PubMed

    Pérez-Estrada, Salvador; Rodríguez-Molina, Braulio; Xiao, Leilei; Santillan, Rosa; Jiménez-Osés, Gonzalo; Houk, K N; Garcia-Garibay, Miguel A

    2015-02-18

    A molecular rotor built with a stator formed by two rigid 9β-mestranol units having a 90° bent angle linked to a central phenylene rotator has an ideal structure to examine aromatic CH/π interactions. Energies and populations of the multiple solution conformations from quantum-mechanical calculations and molecular dynamics simulations were combined with variable-temperature (VT) (1)H NMR data to establish the enthalpy of this interaction and the entropy associated with rotation about a single bond. Rotational dynamics in the solid state were determined via VT cross-polarization magic-angle spinning (13)C NMR spectroscopy. PMID:25635355

  10. The MIntAct Project and Molecular Interaction Databases.

    PubMed

    Licata, Luana; Orchard, Sandra

    2016-01-01

    Molecular interaction databases collect, organize, and enable the analysis of the increasing amounts of molecular interaction data being produced and published as we move towards a more complete understanding of the interactomes of key model organisms. The organization of these data in a structured format supports analyses such as the modeling of pairwise relationships between interactors into interaction networks and is a powerful tool for understanding the complex molecular machinery of the cell. This chapter gives an overview of the principal molecular interaction databases, in particular the IMEx databases, and their curation policies, use of standardized data formats and quality control rules. Special attention is given to the MIntAct project, in which IntAct and MINT joined forces to create a single resource to improve curation and software development efforts. This is exemplified as a model for the future of molecular interaction data collation and dissemination. PMID:27115627

  11. Unraveling the molecular effects of mutation L270P on Wiskkot-Aldrich syndrome protein: insights from molecular dynamics approach.

    PubMed

    Palaniappan, Chandrasekaran; Rao, Sethumadhavan; Ramalingam, Rajasekaran

    2016-09-01

    Missense mutation L270P disrupts the auto-inhibited state of "Wiskkot-Aldrich syndrome protein" (WASP), thereby constitutively activating the mutant structure, a key event for pathogenesis of X-linked neutropenia (XLN). In this study, we comprehensively deciphered the molecular feature of activated mutant structure by all atom molecular dynamics (MD) approach. MD analysis revealed that mutant structure exposed a wide variation in the spatial environment of atoms, resulting in enhanced residue flexibility. The increased flexibility of residues favored to decrease the number of intra-molecular hydrogen bonding interactions in mutant structure. The reduction of hydrogen bonds in the mutant structure resulted to disrupt the local folding of secondary structural elements that eventually affect the proper folding of mutants. The unfolded state of mutant structure established more number of inter-molecular hydrogen bonding interaction at interface level due to the conformational variability, thus mediated high binding affinity with its interacting partner, Cdc42. PMID:26457828

  12. Interactions Dominate the Dynamics of Visual Cognition

    ERIC Educational Resources Information Center

    Stephen, Damian G.; Mirman, Daniel

    2010-01-01

    Many cognitive theories have described behavior as the summation of independent contributions from separate components. Contrasting views have emphasized the importance of multiplicative interactions and emergent structure. We describe a statistical approach to distinguishing additive and multiplicative processes and apply it to the dynamics of…

  13. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Y.T.

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  14. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  15. Molecular dynamics simulation studies of liquid crystalline materials

    NASA Astrophysics Data System (ADS)

    Tian, Pu

    Molecular dynamics (MD) simulation studies of the phase behavior, the response to an applied field of nematic liquid crystalline (LC) materials and interactions of nanoparticles in isotropic mesogenic materials are presented in this work. Molecular models used include the rigid bead-necklace model and soft spherocylinders. Free energy calculations applying thermodynamic integration and the Gibbs-Duhem integration method were used to establish the (T, P) phase diagram of the repulsive bead-necklace model, subsequently the Gibbs-Duhem integration method was further utilized to investigate the influence of attractive interactions on the phase behavior of the bead-necklace model. Analysis of order and thermodynamics of LC phase transitions (Isotropic-Nematic transition and Nematic-Smectic A transition) demonstrate that this simple model can capture the basic physics of liquid crystalline phases, and good agreement with experimental results is obtained. Further addition of chemical details to this multiple interaction sites model is much easier than to the idealized models (Gay-Berne, Spherocylinders) while the computation cost increase with respect to these idealized models is minimal. With a mean field representation of field-molecules interaction, MD simulation studies of the switching behavior of nematic LC, which is the basis of many LC devices, were performed. The switching mechanisms were explained in terms of the compromise between the elastic energy and field-molecules interactions. Qualitative agreement with experiments confirmed the validity of the mean field approximation. Finally, using the standard umbrella sampling technique and MD simulations, the potential of mean force between two nanoparticles in solvent of spherocylinders is calculated. It is found that while dispersed nanoparticles will delay the Isotropic-Nematics transition to higher density (lower temperature), they can induce local ordering fluctuations (within a few molecular lengths of the

  16. Differential molecular interactions between the crystalline and the amorphous phases of celecoxib.

    PubMed

    Gupta, Piyush; Thilagavathi, R; Chakraborti, Asit K; Bansal, Arvind K

    2005-10-01

    We have investigated the differences in molecular interactions between the crystalline (ordered) and amorphous (disordered) phase of a poorly soluble drug, celecoxib. Molecular interactions in the crystalline phase were investigated with the help of Mercury software, using single crystal X-ray diffractometric data for celecoxib. A simulated annealing molecular dynamics approach was used for the assessment of altered molecular interactions in the amorphous phase. Crystalline celecoxib was found to contain an ordered network of H-bonding between all its electron donors (-S=O group, 2-N of pyrazole ring and -C-F) and the acceptor (-N-H). Amorphous celecoxib retained all these interactions in its disordered molecular arrangement, with a relatively stronger H-bonding between the interacting groups, as compared with crystalline celecoxib. However, these inter-molecular interactions differed in strength in the two solid-state forms. The altered configurations of the molecular arrangement in the two phases were supported by the shifts observed in the Fourier-transform infra-red vibrational spectra of respective states. These interactions could have strong implications on devitrification kinetics of amorphous celecoxib, and could further guide the choice of stabilizers for the amorphous form. PMID:16259755

  17. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity.

    PubMed

    Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-07-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806

  18. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    PubMed Central

    Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806

  19. Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

    PubMed

    Fang, Jiansong; Wu, Ping; Yang, Ranyao; Gao, Li; Li, Chao; Wang, Dongmei; Wu, Song; Liu, Ai-Lin; Du, Guan-Hua

    2014-12-01

    In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds. PMID:26579414

  20. Nanochannel flow past permeable walls via molecular dynamics

    NASA Astrophysics Data System (ADS)

    Xie, Jian-Fei; Cao, Bing-Yang

    2016-07-01

    The nanochannel flow past permeable walls with nanopores is investigated by molecular dynamics (MD) simulations, including the density distribution, velocity field, molecular penetration mechanism and surface friction coefficient. A low density distribution has been found at the gas-wall interface demonstrating the low pressure region. In addition, there exists a jump of the gas density on the permeable surface, which indicates the discontinuity of the density distribution across the permeable surface. On the other hand, the nanoscale vortices are observed in nanopores of the permeable wall, and the reduced mass flux of the flow in nanopores results in a shifted hydrodynamic boundary above the permeable surface. Particularly the slip length of the gas flow on the permeable surface is pronounced a non-linear function of the molecular mean free path, which produces a large value of the tangential momentum accommodation coefficient (TMAC) and a big portion of the diffusive refection. Moreover, the gas-gas interaction and multi-collision among gas molecules may take place in nanopores, which contribute to large values of TMAC. Consequently the boundary friction coefficient on the permeable surface is increased because of the energy dissipation consumed by the nanoscale vortices in nanopores. The molecular boundary condition provides us with a new picture of the nanochannel flow past the permeable wall with nanopores.

  1. Interactions Dominate the Dynamics of Visual Cognition

    PubMed Central

    Stephen, Damian G.; Mirman, Daniel

    2010-01-01

    Many cognitive theories have described behavior as the summation of independent contributions from separate components. Contrasting views have emphasized the importance of multiplicative interactions and emergent structure. We describe a statistical approach to distinguishing additive and multiplicative processes and apply it to the dynamics of eye movements during classic visual cognitive tasks. The results reveal interaction-dominant dynamics in eye movements in each of the three tasks, and that fine-grained eye movements are modulated by task constraints. These findings reveal the interactive nature of cognitive processing and are consistent with theories that view cognition as an emergent property of processes that are broadly distributed over many scales of space and time rather than a componential assembly line. PMID:20070957

  2. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  3. GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES

    SciTech Connect

    MUCKERMAN,J.T.

    1999-06-09

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

  4. Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules

    SciTech Connect

    Muckerman, J.T.

    1999-05-21

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometic sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

  5. Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics

    PubMed Central

    2015-01-01

    Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406

  6. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

    PubMed Central

    Pasi, Marco; Lavery, Richard

    2016-01-01

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  7. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.

    PubMed

    Pasi, Marco; Lavery, Richard

    2016-06-20

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA-core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA-core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  8. Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Cavazzoni, Carlo; Cardini, Gianni; Erbacci, Giovanni; Parrinello, Michele; Schettino, Vincenzo

    2008-06-01

    The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.

  9. A Method for Molecular Dynamics on Curved Surfaces.

    PubMed

    Paquay, Stefan; Kusters, Remy

    2016-03-29

    Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focused on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to take such interactions into account by combining standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates, allowing for the reuse of many other standard tools without modifications, including parallelization through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, we obtain confined Brownian motion, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: 1) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes; and 2) the self-assembly of a coarse-grained virus capsid protein model. PMID:27028633

  10. EDITORIAL: 18th European Conference on Dynamics of Molecular Systems 18th European Conference on Dynamics of Molecular Systems

    NASA Astrophysics Data System (ADS)

    Varandas, A. J. C.

    2011-08-01

    This special section of Comments on Atomic, Molecular and Optical Physics (CAMOP) in Physica Scripta collects some of the papers that have been presented at the 18th European Conference on Dynamics of Molecular Systems MOLEC 2010 held in September 2010 in Curia, Portugal, as part of a series of biennial MOLEC conferences. This started in 1976 in Trento, Italy, and has continued, visiting 17 cities in 11 countries, namely Denmark, The Netherlands, Israel, France, Italy, Germany, Czech Republic, Spain, United Kingdom, Turkey and Russia. Following the MOLEC tradition, the scientific programme of the Curia meeting focused on experimental and theoretical studies of molecular interactions, collision dynamics, spectroscopy, and related fields. It included invited speakers from 22 countries, who were asked to summarize the problems reported in their presentations with the objective of revealing the current thinking of leading researchers in atomic, molecular and optical physics. It is hoped that their authoritative contributions presented in this CAMOP special section will also appeal to non-specialists through their clear and broad introductions to the field as well as references to the accessible literature. This CAMOP special section comprises ten contributions, which cover theoretical studies on the electronic structure of molecules and clusters as well as dynamics of elastic, inelastic and reactive encounters between atoms, molecules, ions, clusters and surfaces. Specifically, it includes electronic structure calculations using the traditional coupled-cluster method (Barreto et al 028111), the electron-attached equation-of-motion coupled cluster method (Hansen et al 028110), the diffusion Monte Carlo method (López-Durán et al 028107) and the path-integral Monte Carlo method (Barragán et al 028109). The contributions on molecular dynamics include on-the-fly quasi-classical trajectories on a five-atom molecule (Yu 028104), quantum reaction dynamics on triatomics

  11. Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

    PubMed Central

    Paquet, Eric; Viktor, Herna L.

    2015-01-01

    Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

  12. Effect of temperature on structural and dynamic properties of liquid silver - A study in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Banuelos, E. U.; Amarillas, A. P.

    2004-02-01

    In this work we studied the temperature-induced changes in the structural and dynamical properties of liquid Ag using molecular dynamics (DM) computer simulation. The atomic interactions are modeled through a semiempirical potential function which incorporates n-body effects and is based on the second moments approximation of the density of states of a tight-binding Hamiltonian. The caloric curve was used to calculate the latent heat of fusion and the pair distribution function, g(r), was calculated from a set of atomic configurations collected at several time-steps. The dynamical properties are studied through the velocity autocorrelation function and the mean-square displacement. The self-diffusion coefficient and its behavior with the temperature, obtained from our simulations, shows the typical behavior of the simple liquids. Our results are compared to available experimental data.

  13. Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.

    PubMed

    Paquet, Eric; Viktor, Herna L

    2015-01-01

    Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

  14. Computational Studies on the Anharmonic Dynamics of Molecular Clusters

    NASA Astrophysics Data System (ADS)

    Mancini, John S.

    Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as cl