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Sample records for channel molecular dynamics

  1. Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach

    SciTech Connect

    Smith, Dayle; Danyal, Karamatullah; Raugei, Simone; Seefeldt, Lance C.

    2014-03-22

    Mo-dependent nitrogenase catalyzes the biological reduction of N2 to 2NH3 at the FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized sub-microsecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel not previously reported. The viability of the proposed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, with discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

  2. Molecular modeling and dynamics of the sodium channel inactivation gate.

    PubMed Central

    Sirota, Fernanda L; Pascutti, Pedro G; Anteneodo, Celia

    2002-01-01

    The intracellular linker L(III-IV) of voltage-gated sodium channels is known to be involved in their mechanism of inactivation. Its primary sequence is well conserved in sodium channels from different tissues and species. However, the role of charged residues in this region, first thought to play an important role in inactivation, has not been well identified, whereas the IFM triad (I1488-M1490) has been characterized as the crucial element for inactivation. In this work, we constructed theoretical models and performed molecular dynamics simulations, exploring the role of L(III-IV)-charged residues in the presence of a polar/nonpolar planar interface represented by a dielectric discontinuity. From structural predictions, two alpha-helical segments are proposed. Moreover, from dynamics simulations, a time-conserved motif is detected and shown to play a relevant role in guiding the inactivation particle toward its receptor site. PMID:11867438

  3. Molecular dynamics simulations of water within models of ion channels.

    PubMed

    Breed, J; Sankararamakrishnan, R; Kerr, I D; Sansom, M S

    1996-04-01

    The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.

  4. Dynamics of the EAG1 K(+) channel selectivity filter assessed by molecular dynamics simulations.

    PubMed

    Bernsteiner, Harald; Bründl, Michael; Stary-Weinzinger, Anna

    2017-02-26

    EAG1 channels belong to the KCNH family of voltage gated potassium channels. They are expressed in several brain regions and increased expression is linked to certain cancer types. Recent cryo-EM structure determination finally revealed the structure of these channels in atomic detail, allowing computational investigations. In this study, we performed molecular dynamics simulations to investigate the ion binding sites and the dynamical behavior of the selectivity filter. Our simulations suggest that sites S2 and S4 form stable ion binding sites, while ions placed at sites S1 and S3 rapidly switched to sites S2 and S4. Further, ions tended to dissociate away from S0 within less than 20 ns, due to increased filter flexibility. This was followed by water influx from the extracellular side, leading to a widening of the filter in this region, and likely non-conductive filter configurations. Simulations with the inactivation-enhancing mutant Y464A or Na(+) ions lead to trapped water molecules behind the SF, suggesting that these simulations captured early conformational changes linked to C-type inactivation.

  5. Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Paer; Wallace, B. A.; Pohorille, Andrew

    2011-01-01

    Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

  6. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics.

    PubMed Central

    Kerr, I D; Sankararamakrishnan, R; Smart, O S; Sansom, M S

    1994-01-01

    A parallel bundle of transmembrane (TM) alpha-helices surrounding a central pore is present in several classes of ion channel, including the nicotinic acetylcholine receptor (nAChR). We have modeled bundles of hydrophobic and of amphipathic helices using simulated annealing via restrained molecular dynamics. Bundles of Ala20 helices, with N = 4, 5, or 6 helices/bundle were generated. For all three N values the helices formed left-handed coiled coils, with pitches ranging from 160 A (N = 4) to 240 A (N = 6). Pore radius profiles revealed constrictions at residues 3, 6, 10, 13, and 17. A left-handed coiled coil and a similar pattern of pore constrictions were observed for N = 5 bundles of Leu20. In contrast, N = 5 bundles of Ile20 formed right-handed coiled coils, reflecting loosened packing of helices containing beta-branched side chains. Bundles formed by each of two classes of amphipathic helices were examined: (a) M2a, M2b, and M2c derived from sequences of M2 helices of nAChR; and (b) (LSSLLSL)3, a synthetic channel-forming peptide. Both classes of amphipathic helix formed left-handed coiled coils. For (LSSLLSL)3 the pitch of the coil increased as N increased from 4 to 6. The M2c N = 5 helix bundle is discussed in the context of possible models of the pore domain of nAChR. Images FIGURE 1 FIGURE 3 PMID:7529585

  7. The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations

    PubMed Central

    Bostick, David; Berkowitz, Max L.

    2003-01-01

    Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties. PMID:12829468

  8. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations.

    PubMed

    Treptow, Werner; Marrink, Siewert-J; Tarek, Mounir

    2008-03-20

    Voltage-gated potassium (Kv) channels are ubiquitous transmembrane proteins involved in electric signaling of excitable tissues. A fundamental property of these channels is the ability to open or close in response to changes in the membrane potential. To date, their structure-based activation mechanism remains unclear, and there is a large controversy on how these gates function at the molecular level, in particular, how movements of the voltage sensor domain are coupled to channel gating. So far, all mechanisms proposed for this coupling are based on the crystal structure of the open voltage-gated Kv1.2 channel and structural models of the closed form based on electrophysiology experiments. Here, we use coarse-grain (CG) molecular dynamics simulations that allow conformational changes from the open to the closed form of the channel (embedded in its membrane environment) to be followed. Despite the low specificity of the CG force field, the obtained closed structure satisfies several experimental constraints. The overall results suggest a gating mechanism in which a lateral displacement the S4-S5 linker leads to a closing of the gate. Only a small up-down movement of the S4 helices is noticed. Additionally, the study suggests a peculiar upward motion of the intracellular tetramerization domain of the channel, hence providing a molecular view on how this domain may further regulate conduction in Kv channels.

  9. Molecular Dynamics Study for Channel Size Dependence of Shear Stress Between Droplet and Wall.

    PubMed

    Fukushima, Akinori; Mima, Toshiki; Kinefuchi, Ikuya; Tokumasu, Takashi

    2015-04-01

    In this study, the channel size dependence of the shear stress between water droplets and solid walls in nm-order channel was analyzed. We considered a several different-sized and highly hydrophobic channel whose macroscopic contact angle was about 150 degrees. We have evaluated the shear stress and the normal pressure by molecular dynamics simulation. Analyzing shear stress and normal pressure based on the macroscopic model, we have discussed the difference between the macroscopic model based on hydrodynamics and the microscopic model. As a result, in the high hydrophobic case, it became clear that the shear stress depends on the channel size due to the large Laplace pressure. Furthermore, in the case that the channel size was less than 50 A, the normal pressure by the molecular simulation didn't agree with the expected value from the Young-Laplace equation. From this study it was clear that molecular simulation is needed when the channel size is less than 40 A.

  10. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy.

    PubMed Central

    Roux, B; Prod'hom, B; Karplus, M

    1995-01-01

    The structural and thermodynamic factors responsible for the singly and doubly occupied saturation states of the gramicidin channel are investigated with molecular dynamics simulations and free energy perturbation methods. The relative free energy of binding of all of the five common cations Li+, Na+, K+, Rb+, and Cs+ is calculated in the singly and doubly occupied channel and in bulk water. The atomic system, which includes the gramicidin channel, a model membrane made of neutral Lennard-Jones particles and 190 explicit water molecules to form the bulk region, is similar to the one used in previous work to calculate the free energy profile of a Na+ ion along the axis of the channel. In all of the calculations, the ions are positioned in the main binding sites located near the entrances of the channel. The calculations reveal that the doubly occupied state is relatively more favorable for the larger ions. Thermodynamic decomposition is used to show that the origin of the trend observed in the calculations is due to the loss of favorable interactions between the ion and the single file water molecules inside the channel. Small ions are better solvated by the internal water molecules in the singly occupied state than in the doubly occupied state; bigger ions are solvated almost as well in both occupation states. Water-channel interactions play a role in the channel response. The observed trends are related to general thermodynamical properties of electrolyte solutions. Images FIGURE 2 PMID:7538804

  11. Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel.

    PubMed Central

    Capener, C E; Shrivastava, I H; Ranatunga, K M; Forrest, L R; Smith, G R; Sansom, M S

    2000-01-01

    A homology model has been generated for the pore-forming domain of Kir6.2, a component of an ATP-sensitive K channel, based on the x-ray structure of the bacterial channel KcsA. Analysis of the lipid-exposed and pore-lining surfaces of the model reveals them to be compatible with the known features of membrane proteins and Kir channels, respectively. The Kir6.2 homology model was used as the starting point for nanosecond-duration molecular dynamics simulations in a solvated phospholipid bilayer. The overall drift from the model structure was comparable to that seen for KcsA in previous similar simulations. Preliminary analysis of the interactions of the Kir6.2 channel model with K(+) ions and water molecules during these simulations suggests that concerted single-file motion of K(+) ions and water through the selectivity filter occurs. This is similar to such motion observed in simulations of KcsA. This suggests that a single-filing mechanism is conserved between different K channel structures and may be robust to changes in simulation details. Comparison of Kir6.2 and KcsA suggests some degree of flexibility in the filter, thus complicating models of ion selectivity based upon a rigid filter. PMID:10827973

  12. Gramicidin A channel as a test ground for molecular dynamics force fields.

    PubMed

    Allen, Toby W; Baştuğ, Turgut; Kuyucak, Serdar; Chung, Shin-Ho

    2003-04-01

    We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K(+) ion is calculated along the channel axis using the umbrella sampling method. Calculations are performed using two of the most common force fields in MD simulations: CHARMM and GROMACS. Both force fields lead to large central barriers for K(+) ion permeation, that are substantially higher than those deduced from the physiological data by inverse methods. In long MD simulations lasting over 60 ns, several ions are observed to enter the binding site but none of them crossed the channel despite the presence of a large driving field. The present results, taken together with many earlier studies, highlights the shortcomings of the standard force fields used in MD simulations of ion channels and calls for construction of more appropriate force fields for this purpose.

  13. Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations

    PubMed Central

    Chen, Po-chia; Kuyucak, Serdar

    2009-01-01

    Ion channel-toxin complexes are ideal systems for computational studies of protein-ligand interactions, because, in most cases, the channel axis provides a natural reaction coordinate for unbinding of a ligand and a wealth of physiological data is available to check the computational results. We use a recently determined structure of a potassium channel-charybdotoxin complex in molecular dynamics simulations to investigate the mechanism and energetics of unbinding. Pairs of residues on the channel protein and charybdotoxin that are involved in the binding are identified, and their behavior is traced during umbrella-sampling simulations as charybdotoxin is moved away from the binding site. The potential of mean force for the unbinding of charybdotoxin is constructed from the umbrella sampling simulations using the weighted histogram analysis method, and barriers observed are correlated with specific breaking of interactions and influx of water molecules into the binding site. Charybdotoxin is found to undergo conformational changes as a result of the reaction coordinate choice—a nontrivial decision for larger ligands—which we explore in detail, and for which we propose solutions. Agreement between the calculated and the experimental binding energies is obtained once the energetic consequences of these conformational changes are included in the calculations. PMID:19348743

  14. Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties.

    PubMed

    Martí, J; Nagy, G; Guàrdia, E; Gordillo, M C

    2006-11-30

    Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.

  15. Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation.

    PubMed

    Wen, Han; Qin, Feng; Zheng, Wenjun

    2016-12-01

    As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state versus the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel

  16. Dynamic Channel Allocation

    DTIC Science & Technology

    2003-09-01

    7 1 . Fixed Channel Allocation (FCA) ........................................................7 2. Dynamic Channel ...19 7. CSMA/CD-Based Multiple Network Lines .....................................20 8. Hybrid Channel Allocation in Wireless Networks...28 1 . Channel Allocation

  17. Molecular dynamics simulations on the interaction of the transmembrane NavAb channel with cholesterol and lipids in the membrane.

    PubMed

    Suwattanasophon, Chonticha; Wolschann, Peter; Faller, Roland

    2016-01-01

    Increased cholesterol levels are associated with multiple pathological conditions. In this work, molecular dynamics simulations were applied to observe the influence of membrane cholesterol levels on a voltage-gated sodium channel. Different lipid compositions are modeled around the channel to obtain information about the possible effects by which cholesterol influences NavAb channels. Cholesterol was normally not directly interacting with either the closed or inactivated conformation. Cholesterol increased lipid packing implying that it plays a crucial role in restricting lipid movement in the region around 1 nm of the channel in a 1-palmitoyl-2-oeleoyl phosphatidylcholine matrix. Our results provide the first computational indication of an indirect modulation of NavAb channels by membrane cholesterol.

  18. Applied-field molecular dynamics study of a model calcium channel selectivity filter

    NASA Astrophysics Data System (ADS)

    Yang, Yan; Henderson, Douglas; Busath, David

    2003-03-01

    The calcium channel is thought to have a short selectivity filter containing charged glutamate side chains. This filter was modeled using an atomistic cylinder of length 10 Å in which were confined eight half-charged oxygen anions representing glutamate carboxylate oxygens. Current flow through the filter was computed using applied field nonequilibrium molecular dynamics simulations at various mole fractions of Na+ and Ca2+ in 2 M chloride solutions with simple point charge/extended model water. The filter was cation selective and had conductances in the range of those extrapolated from experimental results. For this model, unlike implicit solvent models at lower voltages and concentrations, the mole fraction behavior was not anomalous and cation binding was nonselective at 2.2 V. Perturbations of filter diameter and confined charge resulted in similar behaviors. At physiological voltages, mole fraction conductance behavior could not be reliably simulated in 100 ns runs, but nonselective cation binding persisted. Nevertheless, it is of interest that ion entry into the confinement region was limited by an energy barrier and at least, in the case of Ca2+, led to an increase in the energy of the other Ca2+ ion in the confinement region and prompt exit of one of them. The filter was most commonly occupied by 2 or 3 Na+ ions in pure Na+ solutions or 1 or 2 Ca2+ ions in pure Ca2+ solutions. For CaCl2 solution, the additional ion, if present, was most commonly stalled behind the entry barrier, i.e., within the channel filter but not yet having entered the confinement region. Thus, the simulations demonstrate the concept that entry of a new mobile Ca2+ ion into the selectivity filter serves to release the prior occupant that was tightly bound.

  19. [Molecular dynamics simulations of migration of ions and molecules through the acetylcholine receptor channel].

    PubMed

    Shaĭtan, K V; Li, A; Tershkina, K B; Kirpichnikov, M P

    2007-01-01

    A dynamic model of the channel of an acetylcholine receptor in a closed state has been proposed. The channel is formed by five a-helices of subunit M2 and stabilized by the cyclic hydrocarbon (CH2)105. The migration of charged and unchanged van der Waals particles with a diameter of 7.72 A equivalent to the diameter of a hydrated sodium ion has been studied. The migration occurred by the action of external force applied to the complex along the channel axis. In the closed state, the inhibition of ions is due to two components: electrostatic interaction and steric constraints. The van der Waals channel gate is formed by residues 13'-A-Val255, B-Val261, C-Val269, D-Val255, and E-Ile264, and the negatively changed residues occurring in the upper part of the channel have a great effect on ion selectivity.

  20. Effect of sensor domain mutations on the properties of voltage-gated ion channels: molecular dynamics studies of the potassium channel Kv1.2.

    PubMed

    Delemotte, Lucie; Treptow, Werner; Klein, Michael L; Tarek, Mounir

    2010-11-03

    The effects on the structural and functional properties of the Kv1.2 voltage-gated ion channel, caused by selective mutation of voltage sensor domain residues, have been investigated using classical molecular dynamics simulations. Following experiments that have identified mutations of voltage-gated ion channels involved in state-dependent omega currents, we observe for both the open and closed conformations of the Kv1.2 that specific mutations of S4 gating-charge residues destabilize the electrostatic network between helices of the voltage sensor domain, resulting in the formation of hydrophilic pathways linking the intra- and extracellular media. When such mutant channels are subject to transmembrane potentials, they conduct cations via these so-called "omega pores." This study provides therefore further insight into the molecular mechanisms that lead to omega currents, which have been linked to certain channelopathies.

  1. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.

    PubMed

    Allen, Toby W; Andersen, Olaf S; Roux, Benoit

    2006-12-01

    Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.

  2. Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations.

    PubMed

    Amaral, Cristiano; Carnevale, Vincenzo; Klein, Michael L; Treptow, Werner

    2012-12-26

    The X-ray structure of the bacterial voltage-gated sodium channel NavAb has been reported in a conformation with a closed conduction pore. Comparison between this structure and the activated-open and resting-closed structures of the voltage-gated Kv1.2 potassium channel suggests that the voltage-sensor domains (VSDs) of the reported structure are not fully activated. Using the aforementioned structures of Kv1.2 as templates, molecular dynamics simulations are used to identify analogous functional conformations of NavAb. Specifically, starting from the NavAb crystal structure, conformations of the membrane-bound channel are sampled along likely pathways for activation of the VSD and opening of the pore domain. Gating charge computations suggest that a structural rearrangement comparable to that occurring between activated-open and resting-closed states is required to explain experimental values of the gating charge, thereby confirming that the reported VSD structure is likely an intermediate along the channel activation pathway. Our observation that the X-ray structure exhibits a low pore domain-opening propensity further supports this notion. The present molecular dynamics study also identifies conformations of NavAb that are seemingly related to the resting-closed and activated-open states. Our findings are consistent with recent structural and functional studies of the orthologous channels NavRh, NaChBac, and NavMs and offer possible structures for the functionally relevant conformations of NavAb.

  3. Nanoscale flow past a colloidal cylinder confined in a slit channel: Lubrication theory and molecular dynamics analysis

    NASA Astrophysics Data System (ADS)

    Rahmani, Amir M.; Shao, Yang; Jupiterwala, Mehlam; Colosqui, Carlos E.

    2015-08-01

    Plane Poiseuille flow past a nanoscale cylinder that is arbitrarily confined (i.e., symmetrically or asymmetrically confined) in a slit channel is studied via hydrodynamic lubrication theory and molecular dynamics simulations, considering cases where the cylinder remains static or undergoes thermal motion. Analytical expressions for the drag force and volumetric flow rate valid for high confinement and arbitrary off-center displacements are derived for the first time in this work. Lubrication theory predictions are in close agreement with molecular dynamics simulations of flows having molecularly thin lubrication gaps, despite the presence of significant structural forces induced by the crystalline structure of the modeled solid. While the maximum drag force is observed in symmetric confinement, i.e., when the cylinder is equidistant from both channel walls, the drag decays significantly as the cylinder moves away from the channel centerline and approaches a wall. Hence, significant reductions in the mean drag force on the cylinder and hydraulic resistance of the channel can be observed when thermal motion induces random off-center displacements. Analytical expressions and numerical results in this work provide useful insights into the hydrodynamics of colloidal solids and macromolecules in confinement.

  4. Modelling of ion permeation in K+ channels by nonequilibrium molecular dynamics simulations: I. Permeation energetics and structure stability.

    PubMed

    Neamţu, A; Suciu, Daniela

    2004-01-01

    Because of the great importance of physiological and pathophysiological processes in which ion channels are involved and because their operation is described by physicochemical laws, there have been many attempts to develop physical models able to describe the membrane permeability and also the structural and functional properties of the channel protein structures. In this study (in two parts) we present a series of simulations on a K+ channel model (KcsA) using Nonequilibrium Molecular Dynamics simulations (NEMD), in order to follow structure stability, permeation energetics and the possibility of obtaining quantitative information about the permeation process using the Linear Response Theory (LRT). On K+ ions were applied external forces to determine them to pass through the channel in a relatively small amount of time, accessible computationally. We ascertained a high resistance of the protein to deformation even in conditions when great forces were applied on ions (the system was far from equilibrium). The estimation of energy profiles in the course of ions passage through the channel demonstrates that these proteins create a conductivity pathway with no energetic barriers for ions movement across the channel (which could be present due to ions dehydration). The dynamic model used demonstrates (as proposed before in the literature after the examination of the static KcsA structure obtained by X-Ray crystallography) that this is due to the interaction of ions with the negatively charged carbonyl oxygens of the main polypeptide chain in the selectivity filter region.

  5. Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study.

    PubMed Central

    Jordan, P C

    1990-01-01

    This work describes a molecular dynamics study of ion-water and ion-polypeptide correlation in a model gramicidin-like channel (the polyglycine analogue) based upon interaction between polarizable, multipolar groups. The model suggests that the vicinity of the dimer junction and of the ethanolamine tail are regions of unusual flexibility. Cs+ binds weakly in the mouth of the channel: there it coordinates five water molecules and the #11CO group with which it interacts strongly and is ideally aligned. In the channel interior it is generally pentacoordinate; at the dimer junction, because of increased channel flexibility, it again becomes essentially hexacoordinate. The ion is also strongly coupled to the #13 CO but not to either #9 or #15, consistent with 13C NMR data. Water in the channel interior is strikingly different from bulk water; it has a much lower mean dipole moment. This correlates with our observation (which differs from that of previous studies) that water-water angular correlations do not persist within the channel, a result independent of ion occupancy or ionic polarity. In agreement with streaming potential measurements, there are seven single file water molecules associated with Cs+ permeation; one of these is always in direct contact with bulk water. At the mouth of an ion-free channel, there is a pattern of dipole moment alteration among the polar groups. Due to differential interaction with water, exo-carbonyls have unusually large dipole moments whereas those of the endo-carbonyls are low. The computed potential of mean force for CS+ translocation is qualitatively reasonable. However, it only exhibits a weakly articulated binding site and it does not quantitatively account for channel energetics. Correction for membrane polarization reduces, but does not eliminate, these problems. PMID:1705448

  6. Interactions of lipids and detergents with a viral ion channel protein: molecular dynamics simulation studies.

    PubMed

    Rouse, Sarah L; Sansom, Mark S P

    2015-01-22

    Structural studies of membrane proteins have highlighted the likely influence of membrane mimetic environments (i.e., lipid bilayers versus detergent micelles) on the conformation and dynamics of small α-helical membrane proteins. We have used molecular dynamics simulations to compare the conformational dynamics of BM2 (a small α-helical protein from the membrane of influenza B) in a model phospholipid bilayer environment with its behavior in protein-detergent complexes with either the zwitterionic detergent dihexanoylphosphatidylcholine (DHPC) or the nonionic detergent dodecylmaltoside (DDM). We find that DDM more closely resembles the lipid bilayer in terms of its interaction with the protein, while the short-tailed DHPC molecule forms "nonphysiological" interactions with the protein termini. We find that the intrinsic micelle properties of each detergent are conserved upon formation of the protein-detergent complex. This implies that simulations of detergent micelles may be used to help select optimal conditions for experimental studies of membrane proteins.

  7. ORF8a of SARS-CoV forms an ion channel: experiments and molecular dynamics simulations.

    PubMed

    Chen, Cheng-Chang; Krüger, Jens; Sramala, Issara; Hsu, Hao-Jen; Henklein, Peter; Chen, Yi-Ming Arthur; Fischer, Wolfgang B

    2011-02-01

    ORF8a protein is 39 residues long and contains a single transmembrane domain. The protein is synthesized using solid phase peptide synthesis and reconstituted into artificial lipid bilayers that forms cation-selective ion channels with a main conductance level of 8.9±0.8pS at elevated temperature (38.5°C). Computational modeling studies including multi nanosecond molecular dynamics simulations in a hydrated POPC lipid bilayer are done with a 22 amino acid transmembrane helix to predict a putative homooligomeric helical bundle model. A structural model of a pentameric bundle is proposed with cysteines, serines and threonines facing the pore.

  8. Application of Brownian motion theory to the analysis of membrane channel ionic trajectories calculated by molecular dynamics.

    PubMed Central

    Jakobsson, E; Chiu, S W

    1988-01-01

    This paper shows how Brownian motion theory can be used to analyze features of individual ion trajectories in channels as calculated by molecular dynamics, and that its use permits more precise determinations of diffusion coefficients than would otherwise be possible. We also show how a consideration of trajectories of single particles can distinguish between effects due to the magnitude of the diffusion coefficient and effects due to barriers and wells in the potential profile, effects which can not be distinguished by consideration of average fluxes. PMID:2465032

  9. Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation

    PubMed Central

    Delemotte, Lucie; Klein, Michael L.; Tarek, Mounir

    2012-01-01

    Since their discovery in the 1950s, the structure and function of voltage-gated cation channels (VGCC) has been largely understood thanks to results stemming from electrophysiology, pharmacology, spectroscopy, and structural biology. Over the past decade, computational methods such as molecular dynamics (MD) simulations have also contributed, providing molecular level information that can be tested against experimental results, thereby allowing the validation of the models and protocols. Importantly, MD can shed light on elements of VGCC function that cannot be easily accessed through “classical” experiments. Here, we review the results of recent MD simulations addressing key questions that pertain to the function and modulation of the VGCC’s voltage-sensor domain (VSD) highlighting: (1) the movement of the S4-helix basic residues during channel activation, articulating how the electrical driving force acts upon them; (2) the nature of the VSD intermediate states on transitioning between open and closed states of the VGCC; and (3) the molecular level effects on the VSD arising from mutations of specific S4 positively charged residues involved in certain genetic diseases. PMID:22654756

  10. Interactions of Lipids and Detergents with a Viral Ion Channel Protein: Molecular Dynamics Simulation Studies

    PubMed Central

    2014-01-01

    Structural studies of membrane proteins have highlighted the likely influence of membrane mimetic environments (i.e., lipid bilayers versus detergent micelles) on the conformation and dynamics of small α-helical membrane proteins. We have used molecular dynamics simulations to compare the conformational dynamics of BM2 (a small α-helical protein from the membrane of influenza B) in a model phospholipid bilayer environment with its behavior in protein–detergent complexes with either the zwitterionic detergent dihexanoylphosphatidylcholine (DHPC) or the nonionic detergent dodecylmaltoside (DDM). We find that DDM more closely resembles the lipid bilayer in terms of its interaction with the protein, while the short-tailed DHPC molecule forms “nonphysiological” interactions with the protein termini. We find that the intrinsic micelle properties of each detergent are conserved upon formation of the protein–detergent complex. This implies that simulations of detergent micelles may be used to help select optimal conditions for experimental studies of membrane proteins. PMID:25286030

  11. Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

    PubMed

    Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

    2016-09-21

    The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen

  12. IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels

    PubMed Central

    Kasahara, Kota; Kinoshita, Kengo

    2016-01-01

    Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/ PMID:27907142

  13. Kinetics of water filling the hydrophobic channels of narrow carbon nanotubes studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wu, Kefei; Zhou, Bo; Xiu, Peng; Qi, Wenpeng; Wan, Rongzheng; Fang, Haiping

    2010-11-01

    The kinetics of water filling narrow single-walled carbon nanotubes was studied using molecular dynamics simulations. The time required to fully fill a nanotube was linear with respect to the tube length. We observed that water molecules could enter into nanotubes of different lengths, either from one end or from both ends. The probability of having a nanotube filled completely from both ends increased exponentially with the tube length. For short tubes, filling usually proceeded from only one end. For long tubes, filling generally proceeded from both tube ends over three stages, i.e., filling from one end, filling from both ends, and filling from both ends with the dipole reorientation of water molecules to give a concerted ordering within the fully filled tube. The water molecules in the partially filled nanotube were hydrogen bonded similarly to those in the fully filled nanotube. Simulations for the reference Lennard-Jones fluid without hydrogen bonds were also performed and showed that the filling behavior of water molecules can be attributed to strong intermolecular hydrogen bonding.

  14. Simulation of polymer translocation through small channels: A molecular dynamics study and a new Monte Carlo approach

    NASA Astrophysics Data System (ADS)

    Gauthier, Michel G.

    With the recent completion of the Human Genome Project and the announcement of the $1000 Genome Race in 2003, the interest for developing faster and cheaper sequencing technologies is continuously growing. Nanopore sequencing offers one of the most promising new ideas. This method consists in reading DNA as it passes through a small aperture perforated through a membrane; a technique similar to decoding a magnetic tape in a tape player. The process of linearly moving a flexible chain from one side of a small channel to the other is called polymer translocation. However, the physics behind this process is still not well understood. During the last ten years, theorists proposed several scaling laws in order to describe this problem and explain experimental observations. The goal of this thesis is to shed light on some of these interesting theoretical predictions. One of the most important questions addressed in this thesis is the role of the hydrodynamic interactions in the polymer translocation process. Even though the impact of such interactions have been theoretically considered, they are neglected in most simulation models. One of our aims in this thesis is to look at the implications of increasing the pore diameter in the presence of hydrodynamic interactions. We use Molecular Dynamics simulations with explicit solvent particles to generate unbiased translocation events in order to characterize the screening of the hydrodynamic interactions by the membrane and to test the hypothesis that polymer translocation is a quasi-equilibrium process. The latter question is quite fundamental since this assumption is at the origin of most theoretical approaches. Another major goal of this thesis is to clarify the nature of the transition between the two translocation regimes dominated by the pore-polymer friction and the hydrodynamic drag of the subchains outside the channel, respectively. However, such an investigation requires the ability to simulate translocation events

  15. Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics

    PubMed Central

    Miao, Lingling; Schulten, Klaus

    2010-01-01

    Abstract The central pore of a nuclear pore complex (NPC) is filled with unstructured proteins that contain many FG-repeats separated by hydrophilic regions. An example of such protein is nsp1. By simulating an array of nsp1 segments, we identified, in an earlier study, a spontaneously formed brushlike structure that promises to explain selective transport in the NPC channel. Here we report four (350,000 atom, 200 ns) simulations probing this structure via its interaction with transport receptor NTF2 as well as with an inert protein. NTF2 dimers are observed to gradually enter the brush, but the inert protein is not. Both NTF2 and the inert protein are found to bind to FG-repeats, but binding periods lasted more briefly for the inert protein. A simulation also investigated the behavior of a brush made of mutant nsp1 that is known to be less effective in NPC-selective transport, finding that this brush does not attract NTF2. PMID:20409487

  16. Zeolites: Exploring Molecular Channels

    SciTech Connect

    Arslan, Ilke; Derewinski, Mirek

    2015-05-22

    Synthetic zeolites contain microscopic channels, sort of like a sponge. They have many uses, such as helping laundry detergent lather, absorbing liquid in kitty litter, and as catalysts to produce fuel. Of the hundreds of types of zeolites, only about 15 are used for catalysis. PNNL catalysis scientists Ilke Arslan and Mirek Derewinksi are studying these zeolites to understand what make them special. By exploring the mystery of these microscopic channels, their fundamental findings will help design better catalysts for applications such as biofuel production.

  17. Zeolites: Exploring Molecular Channels

    ScienceCinema

    Arslan, Ilke; Derewinski, Mirek

    2016-07-12

    Synthetic zeolites contain microscopic channels, sort of like a sponge. They have many uses, such as helping laundry detergent lather, absorbing liquid in kitty litter, and as catalysts to produce fuel. Of the hundreds of types of zeolites, only about 15 are used for catalysis. PNNL catalysis scientists Ilke Arslan and Mirek Derewinksi are studying these zeolites to understand what make them special. By exploring the mystery of these microscopic channels, their fundamental findings will help design better catalysts for applications such as biofuel production.

  18. Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics.

    PubMed

    Bucher, Denis; Guidoni, Leonardo; Carloni, Paolo; Rothlisberger, Ursula

    2010-05-19

    Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.

  19. Molecular modelling and molecular dynamics of CFTR.

    PubMed

    Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul

    2017-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.

  20. Molecular approaches for structural characterization of a new potassium channel blocker from Tityus stigmurus venom: cDNA cloning, homology modeling, dynamic simulations and docking.

    PubMed

    Almeida, Diego Dantas; Torres, Taffarel Melo; Barbosa, Euzébio Guimarães; Lima, João Paulo Matos Santos; de Freitas Fernandes-Pedrosa, Matheus

    2013-01-04

    Potassium channels are involved in the maintenance of resting membrane potential, control of cardiac and neuronal excitability, neurotransmitters release, muscle contractility and hormone secretion. The Tityus stigmurus scorpion is widely distributed in Northeastern Brazil and known to cause severe human envenomations, inducing pain, hypoesthesia, edema, erythema, paresthesia, headaches and vomiting. Most potassium channel blocking peptides that have been purified from scorpion venoms contain 30-40 amino acids with three or four disulfide bridges. These peptides belong to α-KTx subfamily. On the other hand, the β-KTx subfamily is poorly characterized, though it is very representative in some scorpion venoms. A transcriptomic approach of T.stigmurus scorpions developed by our group revealed the repertoire of possible molecules present in the venom, including many toxins of the β-KTx subfamily. One of the ESTs found, named TSTI0003C has a cDNA sequence of 538 bp codifying a mature protein with 47 amino acid residues, corresponding to 5299 Da. This β-KTx peptide is a new member of the BmTXKβ-related toxins, and was here named TstKMK. The three-dimensional structure of this potassium channel toxin of the T. stigmurus scorpion was obtained by computational modeling and refined by molecular dynamic simulations. Furthermore, we have made docking simulations using a Shaker kV-1.2 potassium channel from rats as receptor model and proposed which amino acid residues and interactions could be involved in its blockade.

  1. Ring-polymer molecular dynamics studies on the rate coefficient of the abstraction channel of hydrogen plus ethane, propane, and dimethyl ether

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun

    2017-01-01

    To accurately compute the rates of the abstraction channels of hydrogen plus ethane (Et), propane (Pr), and dimethyl ether (DME), ring-polymer molecular dynamics (RPMD) method is used in conjunction with the recently constructed local permutation invariant polynomial neural-networks potential energy surface of the parent H + CH4 system [Q. Meng et al., J. Chem. Phys. 144, 154312 (2016)]. For H + Et, one of the H atoms in CH4 of the parent system is replaced by a methyl group, while for the H + DME reaction, it is replaced by the methoxyl group. For the H + Pr reaction, replacing one of the H atoms in CH4 by an ethyl group, the terminal channel is built, meanwhile the middle channel is considered through replacing two H atoms in CH4 by two methyl groups. Since the potential energy barriers of the title reactions must differ from the H + CH4 barrier, the corrections have to be made by computing the ratio of free-energy barriers between H + CH4 and the title reactions at coupled cluster with a full treatment singles and doubles (where the triples contribution is calculated by perturbation theory, that is, CCSD(T)) level. Comparing the present RPMD rates with the previous theoretical and experimental results, good agreement can be found. Moreover, probable reasons for the deviation between the present RPMD rates and the previous experimental ones are discussed.

  2. Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics.

    PubMed Central

    Crozier, P S; Henderson, D; Rowley, R L; Busath, D D

    2001-01-01

    Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125-A internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and extended simple point charge water. Channel and bath currents were computed from 10 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration dependent and superlinear at high concentrations. PMID:11720976

  3. Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

    PubMed

    Araujo, Gabriela C; Silva, Ricardo H T; Scott, Luis P B; Araujo, Alexandre S; Souza, Fatima P; de Oliveira, Ronaldo Junio

    2016-12-01

    The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.

  4. 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.

  5. Single-Molecule Ion Channel Conformational Dynamics in Living Cells

    NASA Astrophysics Data System (ADS)

    Lu, H. Peter

    2014-03-01

    Stochastic and inhomogeneous conformational changes regulate the function and dynamics of ion channels that are crucial for cell functions, neuronal signaling, and brain functions. Such complexity makes it difficult, if not impossible, to characterize ion channel dynamics using conventional electrical recording alone since that the measurement does not specifically interrogate the associated conformational changes but rather the consequences of the conformational changes. Recently, new technology developments on single-molecule spectroscopy, and especially, the combined approaches of using single ion channel patch-clamp electrical recording and single-molecule fluorescence imaging have provided us the capability of probing ion channel conformational changes simultaneously with the electrical single channel recording. By combining real-time single-molecule fluorescence imaging measurements with real-time single-channel electric current measurements in artificial lipid bilayers and in living cell membranes, we were able to probe single ion-channel-protein conformational changes simultaneously, and thus providing an understanding the dynamics and mechanism of ion-channel proteins at the molecular level. The function-regulating and site-specific conformational changes of ion channels are now measurable under physiological conditions in real-time, one molecule at a time. We will focus our discussion on the new development and results of real-time imaging of the dynamics of gramicidin, colicin, and NMDA receptor ion channels in lipid bilayers and living cells. Our results shed light on new perspectives of the intrinsic interplay of lipid membrane dynamics, solvation dynamics, and the ion channel functions.

  6. 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.

  7. Computational Studies of Molecular Permeation through Connexin26 Channels.

    PubMed

    Luo, Yun; Rossi, Angelo R; Harris, Andrew L

    2016-02-02

    A signal property of connexin channels is the ability to mediate selective diffusive movement of molecules through plasma membrane(s), but the energetics and determinants of molecular movement through these channels have yet to be understood. Different connexin channels have distinct molecular selectivities that cannot be explained simply on the basis of size or charge of the permeants. To gain insight into the forces and interactions that underlie selective molecular permeation, we investigated the energetics of two uncharged derivatized sugars, one permeable and one impermeable, through a validated connexin26 (Cx26) channel structural model, using molecular dynamics and associated analytic tools. The system is a Cx26 channel equilibrated in explicit membrane/solvent, shown by Brownian dynamics to reproduce key conductance characteristics of the native channel. The results are consistent with the known difference in permeability to each molecule. The energetic barriers extend through most of the pore length, rather than being highly localized as in ion-specific channels. There is little evidence for binding within the pore. Force decomposition reveals how, for each tested molecule, interactions with water and the Cx26 protein vary over the length of the pore and reveals a significant contribution from hydrogen bonding and interaction with K(+). The flexibility of the pore width varies along its length, and the tested molecules have differential effects on pore width as they pass through. Potential sites of interaction within the pore are defined for each molecule. The results suggest that for the tested molecules, differences in hydrogen bonding and entropic factors arising from permeant flexibility substantially contribute to the energetics of permeation. This work highlights factors involved in selective molecular permeation that differ from those that define selectivity among atomic ions.

  8. Ion channels: molecular targets of neuroactive insecticides.

    PubMed

    Raymond-Delpech, Valérie; Matsuda, Kazuhiko; Sattelle, Benedict M; Rauh, James J; Sattelle, David B

    2005-11-01

    Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p'-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); gamma-aminobutyric acid (GABA) receptors (cyclodienes, gamma-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.

  9. Functional diversity and evolutionary dynamics of thermoTRP channels.

    PubMed

    Saito, Shigeru; Tominaga, Makoto

    2015-03-01

    Animals have evolved sophisticated physiological systems for sensing ambient temperature since changes in environmental temperatures affect various biological processes. Thermosensitive transient receptor potential (thermoTRP) channels serve as thermal sensors in diverse animal species. They are multimodal receptors that are activated by temperature as well as other physical and chemical stimuli. Since thermoTRP channels are calcium permeable non-selective cation channels, their activation leads to an influx of calcium and sodium ions into the cell and triggers downstream signal transduction. ThermoTRP channels have been characterized in diverse animal species over the past several years, illuminating the diversification of thermoTRP channels in the course of evolution. The gene repertoires of thermoTRP channels differ among animal species. Additionally, in some cases, the temperature and chemical sensitivities among orthologous thermoTRP channels vary among species. The evolutionary flexibility of thermoTRP channels enabled them to contribute to unique physiological systems such as infrared sensation in snakes and bats and seasonal adaptation in silk moth. On the other hand, the functional differences of thermoTRP channels among species have been utilized for understanding the molecular basis for their activation (or inhibition) mechanisms, and amino acid residues (or domains) responsible for the respective channel properties have been identified in various thermoTRP channels. Here we summarize the current understanding of the functional diversity and evolutionary dynamics of thermoTRP channels.

  10. 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.

  11. 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.

  12. Modelling Martian surface channel dynamics

    NASA Astrophysics Data System (ADS)

    Coulthard, T. J.; Skinner, C.; Kim, J.; Schumann, G.; Neal, J. C.; Bates, P. D.

    2014-12-01

    Extensive and large surface channel features found at Athabasca and Kasei have previously been attributed to the erosional power of flowing water with palaeoflood discharges being estimated from the surface channel dimensions. However, in order for these channels to be alluvial there are several basic questions to be answered. Are water flows under Martian conditions capable of eroding the amounts of sediment required to leave these channels? Are our present estimates of palaeoflood discharge of correct magnitude to carry out this erosion? And are the channels a product of one or many flood events? Here, we use a numerical model (CAESAR-Lisflood) that links a two-dimensional hydrodynamic flow scheme to a sediment transport model to simulate fluvial morphodynamics in the Athabasca and Kasei regions. CAESAR-Lisflood has been successfully applied to simulating flooding, erosion and deposition on Earth in a number of locations, and allows the development of channels, bars, braids and other fluvial features to be modelled. The numerical scheme of the model was adapted to Martian conditions by adjusting gravity, drag co-efficient, roughness and grainsize terms. Preliminary findings indicate that fluvial erosion and deposition is capable of creating mega channel features found at these sites and that existing palaeflood estimates are commensurate with channel forming discharges for these features.

  13. Robust Synchronization Schemes for Dynamic Channel Environments

    NASA Technical Reports Server (NTRS)

    Xiong, Fugin

    2003-01-01

    Professor Xiong will investigate robust synchronization schemes for dynamic channel environment. A sliding window will be investigated for symbol timing synchronizer and an open loop carrier estimator for carrier synchronization. Matlab/Simulink will be used for modeling and simulations.

  14. 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.

  15. 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

  16. 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.

  17. Construction dynamics of a lava channel

    NASA Astrophysics Data System (ADS)

    Harris, Andrew J. L.; Favalli, Massimiliano; Mazzarini, Francesco; Hamilton, Christopher W.

    2009-05-01

    We use a kinematic GPS and laser range finder survey of a 200 m-long section of the Muliwai a Pele lava channel (Mauna Ulu, Kilauea) to examine the construction processes and flow dynamics responsible for the channel-levee structure. The levees comprise three packages. The basal package comprises an 80-150 m wide 'a'a flow in which a ˜2 m deep and ˜11 m wide channel became centred. This is capped by a second package of thin (<45 cm thick) sheets of pahoehoe extending no more than 50 m from the channel. The upper-most package comprises localised 'a'a overflows. The channel itself contains two blockages located 130 m apart and composed of levee chunks veneered with overflow lava. The channel was emplaced over 50 h, spanning 30 May-2 June, 1974, with the flow front arriving at our section (4.4 km from the vent) 8 h after the eruption began. The basal 'a'a flow thickness yields effusion rates of 35 m3 s-1 for the opening phase, with the initial flow advancing across the mapped section at ˜10 m/min. Short-lived overflows of fluid pahoehoe then built the levee cap, increasing the apparent channel depth to 4.8 m. There were at least six pulses at 90-420 m3 s-1, causing overflow of limited extent lasting no more than 5 min. Brim-full flow conditions were thus extremely short-lived. During a dominant period of below-bank flow, flow depth was ˜2 m with an effusion rate of ˜35 m3 s-1, consistent with the mean output rate (obtained from the total flow bulk volume) of 23-54 m3 s-1. During pulses, levee chunks were plucked and floated down channel to form blockages. In a final low effusion rate phase, lava ponded behind the lower blockage to form a syn-channel pond that fed 'a'a overflow. After the end of the eruption the roofed-over pond continued to drain through the lower blockage, causing the roof to founder. Drainage emplaced inflated flows on the channel floor below the lower blockage for a further ˜10 h. The complex processes involved in levee-channel construction

  18. Dynamic Digital Channelizer Based on Spectrum Sensing.

    PubMed

    Hu, Junpeng; Zuo, Zhen; Huang, Zhiping; Dong, Zhi

    2015-01-01

    The ability to efficiently channelize a received signal with dynamic sub-channel bandwidths is a key requirement of software defined radio (SDR) systems. The digital channelizer, which is used to split the received signal into a number of sub-channels, plays an important role in SDR systems. In this paper, a design of dynamic digital channelizer is presented. The proposed method is novel in that it employs a cosine modulated filter bank (CMFB) to divide the received signal into multiple frequency sub-bands and a spectrum sensing technique, which is mostly used in cognitive radio, is introduced to detect the presence of signal of each sub-band. The method of spectrum sensing is carried out based on the eigenvalues of covariance matrix of received signal. The ratio of maximum-minimum eigenvalue of each sub-band is vulnerable to noise fluctuation. This paper suggests an optimized method to calculate the ratio of maximum-minimum eigenvalue. The simulation results imply that the design of digital channelizer can effectively separate the received signal with dynamically changeable sub-channel signals.

  19. In search of the mutual relationship between the structure, solid-state spectroscopy and molecular dynamics in selected calcium channel blockers.

    PubMed

    Drużbicki, Kacper; Pajzderska, Aleksandra; Kiwilsza, Anna; Jenczyk, Jacek; Chudoba, Dorota; Jarek, Marcin; Mielcarek, Jadwiga; Wąsicki, Jan

    2016-03-31

    Three isostructural 1,4-dihydropyridines (DHPs), namely, nifedipine, nitrendipine and nimodipine were selected to characterize their structure, intermolecular interactions and molecular dynamics. The studied samples were analyzed using powder X-ray diffraction (XRD), neutron (INS) and infrared spectroscopy (FT-IR) as well as solid-state nuclear magnetic resonance (NMR), where each technique was supported by the state-of-the-art theoretical calculations for solid-state. By combining multiple experimental techniques with advanced theoretical calculations we were able to shed light on the mutual relation between the structure, stabilizing intermolecular interactions and their spectral response. For the first time, unambiguous computationally-supported assignment of the most prominent spectral features in DHPs is presented to give a valuable support for polymorph screening and drug control. Molecular motions were interpreted in details, revealing that a dynamic reservoir of each compound is dominated by intra-molecular reorientations of methyl groups and large-amplitude oscillations in terminal chains. Our study successfully validates the realm of applicability of first-principles solid-state calculations in search of the mutual relation between the structure and spectroscopy in this important class of drugs. Such approach gives a first necessary step to gather combined structure-dynamics data on functionalized DHPs, which are of importance to better understand crystallization and binding tendency. The NMR relaxation experiments reveal that nitro groups significantly hinder the reorientation of methyl rotors and provide the first evidence of low-temperature methyl-group tunneling in DHPs, an intriguing quantum-effect which is to be further explored.

  20. 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.

  1. Design of a Gated Molecular Proton Channel

    SciTech Connect

    Gu, Wei; Zhou, Bo; Geyer, Tihamer; Hutter, Michael C.; Fang, Haiping; Helms, Volkhard H.

    2011-01-17

    The generation of an electrochemical pH gradient across biological membranes using energy from photosynthesis and respiration provides the universal driving force in cells for the production of adenosine triphosphate (ATP), the energy unit of life. Creating such an electrochemical potential requires the transportation of protons against a thermodynamic gradient. In biological proton pumps, chemical energy is used to induce protein conformational changes during each catalytic cycle where one or a few protons are pumped against a proton concentration gradient across the membrane. On the other hand, membrane channels also exist that mediate continuous particle exchange and may be switched between open and closed states. Being able to design nanochannels with similar functions would be of great importance for creating novel molecular devices with a wide range of applications such as molecular motors, fuel cells, rechargeable nanobatteries that provide energy to other nanomachines, and the generation of locally and temporally controlled pH jumps on microfluidic chips.

  2. Thermodynamics of competitive molecular channel transport: application to artificial nuclear pores.

    PubMed

    Bauer, Wolfgang R; Nadler, Walter

    2010-12-13

    In an analytical model channel transport is analyzed as a function of key parameters, determining efficiency and selectivity of particle transport in a competitive molecular environment. These key parameters are the concentration of particles, solvent-channel exchange dynamics, as well as particle-in-channel- and interparticle interaction. These parameters are explicitly related to translocation dynamics and channel occupation probability. Slowing down the exchange dynamics at the channel ends, or elevating the particle concentration reduces the in-channel binding strength necessary to maintain maximum transport. Optimized in-channel interaction may even shift from binding to repulsion. A simple equation gives the interrelation of access dynamics and concentration at this transition point. The model is readily transferred to competitive transport of different species, each of them having their individual in-channel affinity. Combinations of channel affinities are determined which differentially favor selectivity of certain species on the cost of others. Selectivity for a species increases if its in-channel binding enhances the species' translocation probability when compared to that of the other species. Selectivity increases particularly for a wide binding site, long channels, and fast access dynamics. Recent experiments on competitive transport of in-channel binding and inert molecules through artificial nuclear pores serve as a paradigm for our model. It explains qualitatively and quantitatively how binding molecules are favored for transport at the cost of the transport of inert molecules.

  3. Thermodynamics of Competitive Molecular Channel Transport: Application to Artificial Nuclear Pores

    PubMed Central

    Bauer, Wolfgang R.; Nadler, Walter

    2010-01-01

    In an analytical model channel transport is analyzed as a function of key parameters, determining efficiency and selectivity of particle transport in a competitive molecular environment. These key parameters are the concentration of particles, solvent-channel exchange dynamics, as well as particle-in-channel- and interparticle interaction. These parameters are explicitly related to translocation dynamics and channel occupation probability. Slowing down the exchange dynamics at the channel ends, or elevating the particle concentration reduces the in-channel binding strength necessary to maintain maximum transport. Optimized in-channel interaction may even shift from binding to repulsion. A simple equation gives the interrelation of access dynamics and concentration at this transition point. The model is readily transferred to competitive transport of different species, each of them having their individual in-channel affinity. Combinations of channel affinities are determined which differentially favor selectivity of certain species on the cost of others. Selectivity for a species increases if its in-channel binding enhances the species' translocation probablity when compared to that of the other species. Selectivity increases particularly for a wide binding site, long channels, and fast access dynamics. Recent experiments on competitive transport of in-channel binding and inert molecules through artificial nuclear pores serve as a paradigm for our model. It explains qualitatively and quantitatively how binding molecules are favored for transport at the cost of the transport of inert molecules. PMID:21179205

  4. Tidal dynamics in channels: 2. Complex channel networks

    NASA Astrophysics Data System (ADS)

    Hill, A. E.; Souza, A. J.

    2006-11-01

    Intricate networks of tidal channels such as those found in fjordic, barrier island, and branching estuarine systems are often at risk from contaminant inputs and can be important as spawning grounds or migration pathways for marine organisms. These intricate systems are rarely spatially resolved in regional-scale numerical tidal models, and setting up a specific detailed numerical model for the purpose of rapidly assessing the likely tidal behavior of such geometrically complex systems carries a high overhead. Here we describe a straightforward algorithm (implemented in MATLAB) which permits rapid assessment of the linear tidal dynamics in an arbitrarily complex network of tidal channels. The method needs only a minimum of input data, namely, (1) the forcing tidal elevation amplitude and phase at the entrances of those channels directly exposed to the open sea and (2) the length, width, and depth of each channel. The performance of the method is tested against results from the finite element regional-scale numerical model of Foreman et al. (1993) in the fjordic region of western Canada.

  5. Liquid Jet Cavitation via Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ashurst, W. T.

    1997-11-01

    A two-dimensional molecular dynamics simulation of a liquid jet is used to investigate cavitation in a diesel-like fuel injector. A channel with a length four times its width has been examined at various system sizes (widths of 20 to 160 σ, where σ is the zero energy location in the Lennard-Jones potential). The wall boundary condition is Maxwell's diffuse reflection, similar to the work by Sun & Ebner (Phys. Rev A 46, 4813, 1992). Currently, the jet exhausts into a vacuum, but a second, low density gas will be incorporated to represent the compressed air in a diesel chamber. Four different flow rates are examined. With ρ U equal to √mɛ/σ^2 (the largest flow rate) the static pressure decreases by a factor of twenty between the channel entrance and exit. The largest flow rate has a parabolic velocity profile with almost constant density across the channel. The smallest flow rate has the same velocity profile but the density exhibits a large variation, with the minimum value in the channel center. Thus, the product ρ U is nearly constant across the channel at this flow rate. The discharge coefficient CD has a small variation with flow rate, but the velocity coefficient CV varies with the amount of two-phase fluid within the channel. The ratio of CV to CD varies from 1.3 (largest flow rate) to 2.0 (the smallest flow rate, which is one-eighth of the largest).

  6. 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.

  7. Molecular dynamics of silicon indentation

    NASA Astrophysics Data System (ADS)

    Kallman, J. S.; Hoover, W. G.; Hoover, C. G.; de Groot, A. J.; Lee, S. M.; Wooten, F.

    1993-04-01

    We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.

  8. Water Channel Facility for Fluid Dynamics Experiments

    NASA Astrophysics Data System (ADS)

    Eslam-Panah, Azar; Sabatino, Daniel

    2016-11-01

    This study presents the design, assembly, and verification process of the circulating water channel constructed by undergraduate students at the Penn State University at Berks. This work was significantly inspired from the closed-loop free-surface water channel at Lafayette College (Sabatino and Maharjan, 2015) and employed for experiments in fluid dynamics. The channel has a 11 ft length, 2.5 ft width, and 2 ft height glass test section with a maximum velocity of 3.3 ft/s. First, the investigation justifies the needs of a water channel in an undergraduate institute and its potential applications in the whole field of engineering. Then, the design procedures applied to find the geometry and material of some elements of the channel, especially the contraction, the test section, the inlet and end tanks, and the pump system are described. The optimization of the contraction design, including the maintenance of uniform exit flow and avoidance of flow separation, is also included. Finally, the discussion concludes by identifying the problems with the undergraduate education through this capstone project and suggesting some new investigations to improve flow quality.

  9. Dynamic Modeling of Meandering Alluvial Channels

    NASA Astrophysics Data System (ADS)

    Lan, Yongqiang

    1990-01-01

    The migration of meandering alluvial channels is investigated theoretically, numerically, and experimentally. An equation for the rate of bank erosion is derived from a two-dimensional continuity equation for sediment transport linked with the depth-averaged dynamic flow equations. A simple one-dimensional theoretical analysis of meander migration leads to a relationship between the migration rate and the relative channel curvature and sediment properties. The simple model appropriately simulates the pattern and rate of meander expansion and migrations of the White River, Indiana and the East Nishnabotna River, Iowa. Application of the one-dimensional model to sine -generated alluvial channels indicates that meander migration reaches its maximum when the relative radius of curvature reaches about 4.8, or when the sinuosity of meander approaches 1.3. A two-dimensional numerical model, DYNAMIC, which predicts both lateral and longitudinal migration of alluvial channels is then developed, based on a system of quasi -steady depth-averaged flow dynamic equations, a sediment continuity equation, and a bank erosion equation. A linear analysis of the two-dimensional model leads to a convolutional relation between the rate of meander migration and flow and sediment properties. In the two-dimensional numerical analysis, a numerical algorithm called FLOWSOL is developed to solve the flow dynamic equations. The flow algorithm is then linked to the sediment continuity equation and bank erosion equation to simulate bed deformation and bank erosion. The developed two-dimensional model is applied to calculate the velocity profiles in Rozovskii's experiments and the bed deformation and shear stress in Hooke's experiments. Good agreement is obtained between the calculated and measured velocities, shear stresses and bed profiles in all experiments. Small scaled meandering rivers are developed successfully on a floodplain with or without cohesive materials (about 3%) in a wide

  10. Molecular dynamics simulation of pyridine

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

    Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.

  11. GAS PHASE MOLECULAR DYNAMICS

    SciTech Connect

    SEARS,T.J.; HALL,G.E.; PRESES,J.M.; WESTON,R.E.,JR.

    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 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 free 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. The work of group members Fockenberg and Muckerman is described in separate abstracts of this volume.

  12. Intra-membrane molecular interactions of K+ channel proteins :

    SciTech Connect

    Moczydlowski, Edward G.

    2013-07-01

    Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability was investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.

  13. Molecular biology of insect sodium channels and pyrethroid resistance.

    PubMed

    Dong, Ke; Du, Yuzhe; Rinkevich, Frank; Nomura, Yoshiko; Xu, Peng; Wang, Lingxin; Silver, Kristopher; Zhorov, Boris S

    2014-07-01

    Voltage-gated sodium channels are essential for the initiation and propagation of the action potential in neurons and other excitable cells. Because of their critical roles in electrical signaling, sodium channels are targets of a variety of naturally occurring and synthetic neurotoxins, including several classes of insecticides. This review is intended to provide an update on the molecular biology of insect sodium channels and the molecular mechanism of pyrethroid resistance. Although mammalian and insect sodium channels share fundamental topological and functional properties, most insect species carry only one sodium channel gene, compared to multiple sodium channel genes found in each mammalian species. Recent studies showed that two posttranscriptional mechanisms, alternative splicing and RNA editing, are involved in generating functional diversity of sodium channels in insects. More than 50 sodium channel mutations have been identified to be responsible for or associated with knockdown resistance (kdr) to pyrethroids in various arthropod pests and disease vectors. Elucidation of molecular mechanism of kdr led to the identification of dual receptor sites of pyrethroids on insect sodium channels. Many of the kdr mutations appear to be located within or close to the two receptor sites. The accumulating knowledge of insect sodium channels and their interactions with insecticides provides a foundation for understanding the neurophysiology of sodium channels in vivo and the development of new and safer insecticides for effective control of arthropod pests and human disease vectors.

  14. Molecular Biology of Insect Sodium Channels and Pyrethroid Resistance

    PubMed Central

    Dong, Ke; Du, Yuzhe; Rinkevich, Frank; Nomura, Yoshiko; Xu, Peng; Wang, Lingxin; Silver, Kristopher; Zhorov, Boris S.

    2015-01-01

    Voltage-gated sodium channels are essential for the initiation and propagation of the action potential in neurons and other excitable cells. Because of their critical roles in electrical signaling, sodium channels are targets of a variety of naturally occurring and synthetic neurotoxins, including several classes of insecticides. This review is intended to provide an update on the molecular biology of insect sodium channels and the molecular mechanism of pyrethroid resistance. Although mammalian and insect sodium channels share fundamental topological and functional properties, most insect species carry only one sodium channel gene, compared to multiple sodium channel genes found in each mammalian species. Recent studies showed that two posttranscriptional mechanisms, alternative splicing and RNA editing, are involved in generating functional diversity of sodium channels in insects. More than 50 sodium channel mutations have been identified to be responsible for or associated with knockdown resistance (kdr) to pyrethroids in various arthropod pests and disease vectors. Elucidation of molecular mechanism of kdr led to the identification of dual receptor sites of pyrethroids on insect sodium channels. Most of the kdr mutations appear to be located within or close to the two receptor sites. The accumulating knowledge of insect sodium channels and their interactions with insecticides provides a foundation for understanding the neurophysiology of sodium channels in vivo and the development of new and safer insecticides for effective control of arthropod pests and human disease vectors. PMID:24704279

  15. Dynamic molecular graphs: "hopping" structures.

    PubMed

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.

  16. 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.

  17. Two classes of alamethicin transmembrane channels: molecular models from single-channel properties.

    PubMed

    Mak, D O; Webb, W W

    1995-12-01

    Molecular structures of transmembrane channels formed by alamethicin polypeptide aggregates were analyzed by measuring open-channel conductances and state-transition kinetics using voltage-clamp technique with artificial phospholipid bilayers isolated onto micropipettes by a novel solvent-free tip-dip method. Two distinct classes of alamethicin channels, each with a unique set of conductance states and kinetic properties, were identified. Alamethicin Rf50 at low temperatures forms mostly nonpersistent channels with lifetimes of < 1 min. Long-lasting persistent channels are formed by alamethicin Rf30 at all temperatures and by alamethicin Rf50 at room temperature. In the "modified barrel-stave" model for persistent channels based on the crystalline alamethicin secondary structure, the aqueous pore of the channel surrounded by parallel alamethicin monomers has a constriction generated by amino acid side chains protruding from the alamethicin helices into the pore. The model explains quantitatively the nonohmic channel conductance at high applied voltages and the conductance values and ion selectivities of various persistent channel states. The kinetic properties of nonpersistent channels are explained qualitatively by the "reversed-molecule" model in which nonpersistent channels differ from persistent channels by having one of the channel-forming alamethicin monomers oriented antiparallel to the others.

  18. Two classes of alamethicin transmembrane channels: molecular models from single-channel properties.

    PubMed Central

    Mak, D O; Webb, W W

    1995-01-01

    Molecular structures of transmembrane channels formed by alamethicin polypeptide aggregates were analyzed by measuring open-channel conductances and state-transition kinetics using voltage-clamp technique with artificial phospholipid bilayers isolated onto micropipettes by a novel solvent-free tip-dip method. Two distinct classes of alamethicin channels, each with a unique set of conductance states and kinetic properties, were identified. Alamethicin Rf50 at low temperatures forms mostly nonpersistent channels with lifetimes of < 1 min. Long-lasting persistent channels are formed by alamethicin Rf30 at all temperatures and by alamethicin Rf50 at room temperature. In the "modified barrel-stave" model for persistent channels based on the crystalline alamethicin secondary structure, the aqueous pore of the channel surrounded by parallel alamethicin monomers has a constriction generated by amino acid side chains protruding from the alamethicin helices into the pore. The model explains quantitatively the nonohmic channel conductance at high applied voltages and the conductance values and ion selectivities of various persistent channel states. The kinetic properties of nonpersistent channels are explained qualitatively by the "reversed-molecule" model in which nonpersistent channels differ from persistent channels by having one of the channel-forming alamethicin monomers oriented antiparallel to the others. PMID:8599639

  19. Ultraviolet Channeling Dynamics in Gaseous Media for X -- Ray Production

    NASA Astrophysics Data System (ADS)

    McCorkindale, John Charters

    The development of a coherent high brightness / short duration X -- ray source has been of considerable interest to the scientific community as well as various industries since the invention of the technology. Possible applications include X -- ray lithography, biological micro-imaging and the probing of molecular and atomic dynamics. One such source under investigation involves the interaction of a high pulsed power KrF UV laser with a noble gas target (krypton or xenon), producing a photon energy from 1 -- 5 keV. Amplification in this regime requires materials with very special properties found in spatially organized hollow atom clusters. One of the driving forces behind X -- ray production is the UV laser. Theoretical analysis shows that above a critical laser power, the formation of a stable plasma channel in the gaseous medium will occur which can act as a guide for the X-ray pulse and co-propagating UV beam. These plasma channels are visualized with a triple pinhole camera, axial and transverse von Hamos spectrometers and a Thomson scattering setup. In order to understand observed channel morphologies, full characterization of the drive laser was achieved using a Transient Grating -- Frequency Resolved Optical Gating (TG-FROG) technique which gives a full temporal representation of the electric field and associated phase of the ultrashort pulse. Insights gleaned from the TG -- FROG data as well as analysis of photodiode diagnostics placed along the UV laser amplification chain provide explanations for the plasma channel morphology and X -- ray output.

  20. 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

  1. Novel methods for molecular dynamics simulations.

    PubMed

    Elber, R

    1996-04-01

    In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.

  2. Molecular analysis of a thylakoid K+ channel

    SciTech Connect

    2000-05-01

    The work undertaken during the prior granting period sought to use a novel probe to identify and clone plant ion (K) channels. It was also proposed that in vitro biochemical studies of cation transport across purified preparations of thylakoid membrane be employed to characterize a putative K channel in this membrane system. Over the last several years (including those of the previous grant period), an enormous data base of partially-sequenced mRNAs and numerous genomes (including those of plants) has evolved and provides a powerful alternative to this brute-force approach to identify and clone cDNAs ending physiologically important membrane proteins such as channels. The utility of searching genetic databases for relevant sequences, in addition to the difficulty of working with membrane proteins, led to changes in research focus during the prior granting period, and has resulted in the identification of a new class of plant ion channels, which will be the focus of research during the proposed new granting period.

  3. 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

  4. 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.

  5. Wavelet Analysis for Molecular Dynamics

    DTIC Science & Technology

    2015-06-01

    simulation (and the computational work performed in the process). Slower processes, such as torsions and translations, are usually the more relevant ones. The...is no longer as simple as for H2O, nor are the eigenvalues except 0 simple; for the generalized Amber force field (GAFF), they are 14.7 and...short-range molecular dynamics. J Comput Phys. 1995;117(1):1–19. 9. Sun H, Mumby SJ, Maple JR, Hagler AT. An ab initio CFF93 all-atom force field for

  6. Non-Equilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ciccotti, Giovanni; Kapral, Raymond; Sergi, Alessandro

    Statistical mechanics provides a well-established link between microscopic equilibrium states and thermodynamics. If one considers systems out of equilibrium, the link between microscopic dynamical properties and non-equilibrium macroscopic states is more difficult to establish [1,2]. For systems lying near equilibrium, linear response theory provides a route to derive linear macroscopic laws and the microscopic expressions for the transport properties that enter the constitutive relations. If the system is displaced far from equilibrium, no fully general theory exists to treat such systems. By restricting consideration to a class of non-equilibrium states which arise from perturbations (linear or non-linear) of an equilibrium state, methods can be developed to treat non-equilibrium states. Furthermore, non-equilibrium molecular dynamics (NEMD) simulation methods can be devised to provide estimates for the transport properties of these systems.

  7. Molecular dynamics of interface rupture

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

    Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

  8. Channel Pattern and the Dynamics of River-floodplain Ecosystems

    NASA Astrophysics Data System (ADS)

    Beechie, T.; Pollock, M.; Baker, S.; Morley, S.; Pess, G.

    2006-05-01

    Channel pattern is both a reflection of fluvial geomorphic processes and a predictor of ecological diversity in river-floodplain ecosystems. Channel slope, discharge, sediment supply, and sediment size are dominant drivers of channel pattern (straight, meandering, island-braided, or braided), and the spatial distribution of channel patterns in Pacific Northwest River networks typically reflects downstream declines in channel slope and ratio of bed load to suspended load. Straight channels are least dynamic, with relatively slow floodplain turnover and floodplains dominated by old surfaces. Braided channels are most dynamic, with floodplain turnover as low as 25 years and predominantly young floodplain surfaces. Island-braided and meandering channels have intermediate dynamics and a mix of young and old patches. Floodplain erosion return intervals increase in the order of braided, island-braided, meandering, and straight (8, 33, 60, and 89 years, respectively). These dynamics drive two important aspects of environmental complexity, which in turn drive biological diversity in river floodplain ecosystems: diversity of patch ages, and diversity of patch types. High diversity of patch ages in island-braided channels predicts high forest diversity, following the intermediate disturbance hypothesis (IDH). Diversity of aquatic invertebrates should also be highest in island-braided channels, in part due to shifting composition of detrital resources entering floodplain channels of varying ages. Diversity of habitat types is also highest in island-braided channels, where side channel lengths can be as much as five times greater than main channel length. We expect highest fish diversity where varied size and connectivity of side channels is greatest.

  9. NMR and restrained molecular dynamics study of the three-dimensional solution structure of toxin FS2, a specific blocker of the L-type calcium channel, isolated from black mamba venom.

    PubMed

    Albrand, J P; Blackledge, M J; Pascaud, F; Hollecker, M; Marion, D

    1995-05-02

    The three-dimensional solution structure of toxin FS2, a 60-residue polypeptide isolated from the venom of black mamba snake (Dendroaspis polylepis polylepis), has been determined by nuclear magnetic resonance spectroscopy. Using 600 NOE constraints and 55 dihedral angle constraints, a set of 20 structures obtained from distance-geometry calculations was further refined by molecular dynamics calculations using a combined simulated annealing-restrained MD protocol. The resulting 20 conformers, taken to represent the solution structure, give an average rmsd of 1.2 A for their backbone atoms, relative to the average structure. The overall resulting three-fingered structure is similar to those already observed in several postsynaptic neurotoxins, cardiotoxins, and fasciculins, which all share with toxin FS2 the same network of four disulfide bridges. The overall concavity of the molecule, considered as a flat bottomed dish, is oriented toward the C-terminal loop of the molecule. This orientation is similar to that of fasciculins and cardiotoxins but opposite to that of neurotoxins. On the basis of the local rms displacements between the 20 conformers, the structure of the first loop appears to be less well defined in FS2 than in the previously reported neurotoxin structures, but fasciculin 1 shows a similar trend with particularly high temperature factors for this part of the X-ray structure. The concave side which presents most of the positively charged residues is quite similar in FS2 and fasciculin 1. The main difference is shown by the convex side of the third loop, mostly hydrophobic in FS2, in contrast to the pair of negatively charged aspartates in fasciculin 1. This difference could be one of the factors leading to the distinct pharmacological properties-L-type calcium channel blocker for FS2 and cholinesterase inhibitor for fasciculin--observed for these two subgroups of the "angusticeps-type" toxins.

  10. 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

  11. Recent molecular insights from mutated IKS channels in cardiac arrhythmia.

    PubMed

    Dvir, Meidan; Peretz, Asher; Haitin, Yoni; Attali, Bernard

    2014-04-01

    Co-assembly of KCNQ1 with KCNE1 generates the IKS potassium current that is vital for the proper repolarization of the cardiac action potential. Mutations in either KCNQ1 or KCNE1 genes lead to life-threatening cardiac arrhythmias causing long QT syndrome, short QT syndrome, sinus bradycardia and atrial fibrillation. Findings emerging from recent studies are beginning to provide a picture of how gain-of-function and loss-of-function mutations are associated with pleiotropic cardiac phenotypes in the clinics. In this review, we discuss recent molecular insights obtained from mutations altering different structural modules of the channel complex that are essential for proper IKS function. We present the possible molecular mechanisms underlying mutations impairing the voltage sensing functions, as well as those altering the channel regulation by phosphatidylinositol-4,5-bisphosphate, calmodulin and protein kinase A. We also discuss the significance of diseased IKS channels for adequate pharmacological targeting of cardiac arrhythmias.

  12. Uncertainty quantification in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rizzi, Francesco

    This dissertation focuses on uncertainty quantification (UQ) in molecular dynamics (MD) simulations. The application of UQ to molecular dynamics is motivated by the broad uncertainty characterizing MD potential functions and by the complexity of the MD setting, where even small uncertainties can be amplified to yield large uncertainties in the model predictions. Two fundamental, distinct sources of uncertainty are investigated in this work, namely parametric uncertainty and intrinsic noise. Intrinsic noise is inherently present in the MD setting, due to fluctuations originating from thermal effects. Averaging methods can be exploited to reduce the fluctuations, but due to finite sampling, this effect cannot be completely filtered, thus yielding a residual uncertainty in the MD predictions. Parametric uncertainty, on the contrary, is introduced in the form of uncertain potential parameters, geometry, and/or boundary conditions. We address the UQ problem in both its main components, namely the forward propagation, which aims at characterizing how uncertainty in model parameters affects selected observables, and the inverse problem, which involves the estimation of target model parameters based on a set of observations. The dissertation highlights the challenges arising when parametric uncertainty and intrinsic noise combine to yield non-deterministic, noisy MD predictions of target macroscale observables. Two key probabilistic UQ methods, namely Polynomial Chaos (PC) expansions and Bayesian inference, are exploited to develop a framework that enables one to isolate the impact of parametric uncertainty on the MD predictions and, at the same time, properly quantify the effect of the intrinsic noise. Systematic applications to a suite of problems of increasing complexity lead to the observation that an uncertain PC representation built via Bayesian regression is the most suitable model for the representation of uncertain MD predictions of target observables in the

  13. 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.

  14. Molecular Determinants of BK Channel Functional Diversity and Functioning.

    PubMed

    Latorre, Ramon; Castillo, Karen; Carrasquel-Ursulaez, Willy; Sepulveda, Romina V; Gonzalez-Nilo, Fernando; Gonzalez, Carlos; Alvarez, Osvaldo

    2017-01-01

    Large-conductance Ca(2+)- and voltage-activated K(+) (BK) channels play many physiological roles ranging from the maintenance of smooth muscle tone to hearing and neurosecretion. BK channels are tetramers in which the pore-forming α subunit is coded by a single gene (Slowpoke, KCNMA1). In this review, we first highlight the physiological importance of this ubiquitous channel, emphasizing the role that BK channels play in different channelopathies. We next discuss the modular nature of BK channel-forming protein, in which the different modules (the voltage sensor and the Ca(2+) binding sites) communicate with the pore gates allosterically. In this regard, we review in detail the allosteric models proposed to explain channel activation and how the models are related to channel structure. Considering their extremely large conductance and unique selectivity to K(+), we also offer an account of how these two apparently paradoxical characteristics can be understood consistently in unison, and what we have learned about the conduction system and the activation gates using ions, blockers, and toxins. Attention is paid here to the molecular nature of the voltage sensor and the Ca(2+) binding sites that are located in a gating ring of known crystal structure and constituted by four COOH termini. Despite the fact that BK channels are coded by a single gene, diversity is obtained by means of alternative splicing and modulatory β and γ subunits. We finish this review by describing how the association of the α subunit with β or with γ subunits can change the BK channel phenotype and pharmacology.

  15. Molecular dynamics simulations of cluster nucleation during inert gas condensation.

    PubMed

    Krasnochtchekov, Pavel; Averback, R S

    2005-01-22

    Molecular dynamics simulations of vapor-phase nucleation of germanium in an argon atmosphere were performed and a unexpected channel of nucleation was observed. This channel, vapor-induced cluster splitting, is important for more refractory materials since the critical nucleus size can fall below the size of a dimer. As opposed to conventional direct vapor nucleation of the dimer, which occurs by three-body collisions, cluster-splitting nucleation is a second-order reaction. The most important cluster-splitting reaction is the collision of a vapor atom and a trimer that leads to the formation of two dimers. The importance of the cluster-splitting nucleation channel relative to the direct vapor nucleation channel is observed to increase with decreasing vapor density and increasing ratio of vapor to carrier gas atoms.

  16. Efficient mapping of ligand migration channel networks in dynamic proteins.

    PubMed

    Lin, Tu-Liang; Song, Guang

    2011-08-01

    For many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. Ligand migration in a dynamic protein resembles closely a well-studied problem in robotics, namely, the navigation of a mobile robot in a dynamic environment. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their inter-connectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory-based approaches, are in agreement with previous simulation results. Additionally, the method clearly illustrates how and what conformational changes open or close a channel.

  17. Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

    DTIC Science & Technology

    2015-01-01

    Maximum 200 Words) The minimum energy configuration for Molecular Dynamics (MD) simulations is found for a carbon nanotube (CNT)/polymer...Carbon Nanotubes (CNTs), Molecular Dynamics Simulations 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT...fiber composites have shown success in improving mechanical properties. Carbon nanotube (CNT)-based nanocomposites have been studied for

  18. 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.

  19. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    NASA Astrophysics Data System (ADS)

    Uppulury, Karthik; Kolomeisky, Anatoly B.

    2016-12-01

    Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  20. Molecular basis of potassium channels in pancreatic duct epithelial cells.

    PubMed

    Hayashi, Mikio; Novak, Ivana

    2013-01-01

    Potassium channels regulate excitability, epithelial ion transport, proliferation, and apoptosis. In pancreatic ducts, K(+) channels hyperpolarize the membrane potential and provide the driving force for anion secretion. This review focuses on the molecular candidates of functional K(+) channels in pancreatic duct cells, including KCNN4 (KCa 3.1), KCNMA1 (KCa 1.1), KCNQ1 (Kv 7.1), KCNH2 (Kv 11.1), KCNH5 (Kv 10.2), KCNT1 (KCa 4.1), KCNT2 (KCa 4.2), and KCNK5 (K 2P 5.1). We will give an overview of K(+) channels with respect to their electrophysiological and pharmacological characteristics and regulation, which we know from other cell types, preferably in epithelia, and, where known, their identification and functions in pancreatic ducts and in adenocarcinoma cells. We conclude by pointing out some outstanding questions and future directions in pancreatic K(+) channel research with respect to the physiology of secretion and pancreatic pathologies, including pancreatitis, cystic fibrosis, and cancer, in which the dysregulation or altered expression of K(+) channels may be of importance.

  1. Molecular basis of potassium channels in pancreatic duct epithelial cells

    PubMed Central

    Hayashi, Mikio; Novak, Ivana

    2013-01-01

    Potassium channels regulate excitability, epithelial ion transport, proliferation, and apoptosis. In pancreatic ducts, K+ channels hyperpolarize the membrane potential and provide the driving force for anion secretion. This review focuses on the molecular candidates of functional K+ channels in pancreatic duct cells, including KCNN4 (KCa3.1), KCNMA1 (KCa1.1), KCNQ1 (Kv7.1), KCNH2 (Kv11.1), KCNH5 (Kv10.2), KCNT1 (KCa4.1), KCNT2 (KCa4.2), and KCNK5 (K2P5.1). We will give an overview of K+ channels with respect to their electrophysiological and pharmacological characteristics and regulation, which we know from other cell types, preferably in epithelia, and, where known, their identification and functions in pancreatic ducts and in adenocarcinoma cells. We conclude by pointing out some outstanding questions and future directions in pancreatic K+ channel research with respect to the physiology of secretion and pancreatic pathologies, including pancreatitis, cystic fibrosis, and cancer, in which the dysregulation or altered expression of K+ channels may be of importance. PMID:23962792

  2. 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

  3. Molecular Dynamics Simulation of Supercritical Spray Phenomena

    DTIC Science & Technology

    2008-09-26

    Dynamics of the Rheological and Structural Properties of Linear and Branched Molecules. Simple Shear and Poiseuille Flows ; Instabilities and Slip...Michael Barrucco Publications: "Comparison of Wall Models for the Molecular Dynamics Simulation of Micro flows ," R. D. Branam and M. M...Performance 3. DATES COVERED (From - To) 1 Dec. 2003 - 31 May 2008 4. TITLE AND SUBTITLE Molecular Dynamics Simulation of Supercritical

  4. Molecular mapping of general anesthetic sites in a voltage-gated ion channel.

    PubMed

    Barber, Annika F; Liang, Qiansheng; Amaral, Cristiano; Treptow, Werner; Covarrubias, Manuel

    2011-10-05

    Several voltage-gated ion channels are modulated by clinically relevant doses of general anesthetics. However, the structural basis of this modulation is not well understood. Previous work suggested that n-alcohols and inhaled anesthetics stabilize the closed state of the Shaw2 voltage-gated (Kv) channel (K-Shaw2) by directly interacting with a discrete channel site. We hypothesize that the inhibition of K-Shaw2 channels by general anesthetics is governed by interactions between binding and effector sites involving components of the channel's activation gate. To investigate this hypothesis, we applied Ala/Val scanning mutagenesis to the S4-S5 linker and the post-PVP S6 segment, and conducted electrophysiological analysis to evaluate the energetic impact of the mutations on the inhibition of the K-Shaw2 channel by 1-butanol and halothane. These analyses identified residues that determine an apparent binding cooperativity and residue pairs that act in concert to modulate gating upon anesthetic binding. In some instances, due to their critical location, key residues also influence channel gating. Complementing these results, molecular dynamics simulations and in silico docking experiments helped us visualize possible anesthetic sites and interactions. We conclude that the inhibition of K-Shaw2 by general anesthetics results from allosteric interactions between distinct but contiguous binding and effector sites involving inter- and intrasubunit interfaces.

  5. 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.

  6. Molecular rheology of perfluoropolyether lubricant via nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Guo, Qian; Chung, Pil Seung; Chen, Haigang; Jhon, Myung S.

    2006-04-01

    Molecular rheology of perfluoropolyether (PFPE) systems is particularly important in designing effective lubricants that control the friction and wear in tribological applications. Using the coarse-grained, bead-spring model, equilibrium molecular dynamics based on the Langevin equation in a quiescent flow was first employed to examine the nanostructure of PFPE. Further, by integrating the modified Langevin equation and imposing the Lees-Edwards boundary condition, nonequilibrium molecular dynamics of steady shear was investigated. We observe that the shear viscosity of PFPE system depends strongly on molecular architecture (e.g., molecular weight and endgroup functionality) and external conditions (e.g., temperature and shear rate). Our study of the flow activation energy/entropy and their correlations with nanostructure visualization showed that the PFPE structure was substantially modified.

  7. The dynamic TRPA1 channel: a suitable pharmacological pain target?

    PubMed

    Garrison, Sheldon R; Stucky, Cheryl L

    2011-10-01

    Acute pain detection is vital to navigate and survive in one's environment. Protection and preservation occur because primary afferent nociceptors transduce adverse environmental stimuli into electrical impulses that are transmitted to and interpreted within high levels of the central nervous system. Therefore, it is critical that the molecular mechanisms that convert noxious information into neural signals be identified, and their specific functional roles delineated in both acute and chronic pain settings. The Transient Receptor Potential (TRP) channel family member TRP ankyrin 1 (TRPA1) is an excellent candidate molecule to explore and intricately understand how single channel properties can tailor behavioral nociceptive responses. TRPA1 appears to dynamically respond to an amazingly wide range of diverse stimuli that include apparently unrelated modalities such as mechanical, chemical and thermal stimuli that activate somatosensory neurons. How such dissimilar stimuli activate TRPA1, yet result in modality-specific signals to the CNS is unclear. Furthermore, TRPA1 is also involved in persistent to chronic painful states such as inflammation, neuropathic pain, diabetes, fibromyalgia, bronchitis and emphysema. Yet how TRPA1's role changes from an acute sensor of physical stimuli to its contribution to these diseases that are concomitant with implacable, chronic pain is unknown. TRPA1's involvement in the nociceptive machinery that relays the adverse stimuli during painful disease states is of considerable interest for drug delivery and design by many pharmaceutical entities. In this review, we will assess the current knowledge base of TRPA1 in acute nociception and persistent inflammatory pain states, and explore its potential as a therapeutic pharmacological target in chronic pervasive conditions such neuropathic pain, persistent inflammation and diabetes.

  8. The Dynamic TRPA1 Channel: A Suitable Pharmacological Pain Target?

    PubMed Central

    Garrison, Sheldon R.; Stucky, Cheryl L.

    2014-01-01

    Acute pain detection is vital to navigate and survive in one’s environment. Protection and preservation occur because primary afferent nociceptors transduce adverse environmental stimuli into electrical impulses that are transmitted to and interpreted within high levels of the central nervous system. Therefore, it is critical that the molecular mechanisms that convert noxious information into neural signals be identified and their specific functional roles delineated in both acute and chronic pain settings. The Transient Receptor Potential (TRP) channel family member TRP ankyrin 1 (TRPA1) is an excellent candidate molecule to explore and intricately understand how single channel properties can tailor behavioral nociceptive responses. TRPA1 appears to dynamically respond to an amazingly wide range of diverse stimuli that include apparently unrelated modalities such as mechanical, chemical and thermal stimuli that activate somatosensory neurons. How such dissimilar stimuli activate TRPA1, yet result in modality-specific signals to the CNS is unclear. Furthermore, TRPA1 is also involved in persistent to chronic painful states such as inflammation, neuropathic pain, diabetes, fibromyalgia, bronchitis and emphysema. Yet how TRPA1’s role changes from an acute sensor of physical stimuli to its contribution to these diseases that are concomitant with implacable, chronic pain is unknown. TRPA1’s involvement in the nociceptive machinery that relays the adverse stimuli during painful disease states is of considerable interest for drug delivery and design by many pharmaceutical entities. In this review, we will assess the current knowledge base of TRPA1 in acute nociception and persistent inflammatory pain states, and explore its potential as a therapeutic pharmacological target in chronic pervasive conditions such neuropathic pain, persistent inflammation and diabetes. PMID:21466445

  9. Molecular dynamics on hypercube parallel computers

    NASA Astrophysics Data System (ADS)

    Smith, W.

    1991-03-01

    The implementation of molecular dynamics on parallel computers is described, with particular reference to hypercube computers. Three particular algorithms are described: replicated data (RD); systolic loop (SLS-G), and parallelised link-cells (PLC), all of which have good load balancing. The performance characteristics of each algorithm and the factors affecting their scaling properties are discussed. The article is pedagogic in intent, to introduce a novice to the main aspects of parallel computing in molecular dynamics.

  10. The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel

    PubMed Central

    Yazdi, Samira; Stein, Matthias; Elinder, Fredrik; Andersson, Magnus; Lindahl, Erik

    2016-01-01

    Voltage-gated potassium (KV) channels are membrane proteins that respond to changes in membrane potential by enabling K+ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs) induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD), the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker KV channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA) and the Shaker KV channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins. PMID:26751683

  11. Surface dynamics of voltage-gated ion channels

    PubMed Central

    Heine, Martin; Ciuraszkiewicz, Anna; Voigt, Andreas; Heck, Jennifer; Bikbaev, Arthur

    2016-01-01

    ABSTRACT Neurons encode information in fast changes of the membrane potential, and thus electrical membrane properties are critically important for the integration and processing of synaptic inputs by a neuron. These electrical properties are largely determined by ion channels embedded in the membrane. The distribution of most ion channels in the membrane is not spatially uniform: they undergo activity-driven changes in the range of minutes to days. Even in the range of milliseconds, the composition and topology of ion channels are not static but engage in highly dynamic processes including stochastic or activity-dependent transient association of the pore-forming and auxiliary subunits, lateral diffusion, as well as clustering of different channels. In this review we briefly discuss the potential impact of mobile sodium, calcium and potassium ion channels and the functional significance of this for individual neurons and neuronal networks. PMID:26891382

  12. Molecular Diversity and Functional Evolution of Scorpion Potassium Channel Toxins*

    PubMed Central

    Zhu, Shunyi; Peigneur, Steve; Gao, Bin; Luo, Lan; Jin, Di; Zhao, Yong; Tytgat, Jan

    2011-01-01

    Scorpion toxins affecting K+ channels (KTxs) represent important pharmacological tools and potential drug candidates. Here, we report molecular characterization of seven new KTxs in the scorpion Mesobuthus eupeus by cDNA cloning combined with biochemical approaches. Comparative modeling supports that all these KTxs share a conserved cysteine-stabilized α-helix/β-sheet structural motif despite the differences in protein sequence and size. We investigated functional diversification of two orthologous α-KTxs (MeuTXKα1 from M. eupeus and BmP01 from Mesobuthus martensii) by comparing their K+ channel-blocking activities. Pharmacologically, MeuTXKα1 selectively blocked Kv1.3 channel with nanomolar affinity (IC50, 2.36 ± 0.9 nm), whereas only 35% of Kv1.1 currents were inhibited at 3 μm concentration, showing more than 1271-fold selectivity for Kv1.3 over Kv1.1. This peptide displayed a weak effect on Drosophila Shaker channel and no activity on Kv1.2, Kv1.4, Kv1.5, Kv1.6, and human ether-a-go-go-related gene (hERG) K+ channels. Although BmB01 and MeuTXKα1 have a similar channel spectrum, their affinity and selectivity for these channels largely varies. In comparison with MeuTXKα1, BmP01 only exhibits a submicromolar affinity (IC50, 133.72 ± 10.98 nm) for Kv1.3, showing 57-fold less activity than MeuTXKα1. Moreover, it lacks the ability to distinguish between Kv1.1 and Kv1.3. We also found that MeuTXKα1 inhibited the proliferation of activated T cells induced by phorbol myristate acetate and ionomycin at micromolar concentrations. Our results demonstrate that accelerated evolution drives affinity variations of orthologous α-KTxs on Kv channels and indicate that MeuTXKα1 is a promising candidate to develop an immune modulation agent for human autoimmune diseases. PMID:20889474

  13. 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.

  14. 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.

  15. Protein dynamics: Moore's law in molecular biology.

    PubMed

    Vendruscolo, Michele; Dobson, Christopher M

    2011-01-25

    The millisecond barrier has been broken in molecular dynamics simulations of proteins. Such simulations are increasingly revealing the inner workings of biological systems by generating atomic-level descriptions of their behaviour that make testable predictions about key molecular processes.

  16. 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.

  17. Silicon photonic dynamic optical channel leveler with external feedback loop.

    PubMed

    Doylend, J K; Jessop, P E; Knights, A P

    2010-06-21

    We demonstrate a dynamic optical channel leveler composed of a variable optical attenuator (VOA) integrated monolithically with a defect-mediated photodiode in a silicon photonic waveguide device. An external feedback loop mimics an analog circuit such that the photodiode directly controls the VOA to provide blind channel leveling within +/-1 dB across a 7-10 dB dynamic range for wavelengths from 1530 nm to 1570 nm. The device consumes approximately 50 mW electrical power and occupies a 6 mm x 0.1 mm footprint per channel. Dynamic leveling is accomplished without tapping optical power from the output path to the photodiode and thus the loss penalty is minimized.

  18. Modeling ion channel dynamics through reflected stochastic differential equations

    NASA Astrophysics Data System (ADS)

    Dangerfield, Ciara E.; Kay, David; Burrage, Kevin

    2012-05-01

    Ion channels are membrane proteins that open and close at random and play a vital role in the electrical dynamics of excitable cells. The stochastic nature of the conformational changes these proteins undergo can be significant, however current stochastic modeling methodologies limit the ability to study such systems. Discrete-state Markov chain models are seen as the “gold standard,” but are computationally intensive, restricting investigation of stochastic effects to the single-cell level. Continuous stochastic methods that use stochastic differential equations (SDEs) to model the system are more efficient but can lead to simulations that have no biological meaning. In this paper we show that modeling the behavior of ion channel dynamics by a reflected SDE ensures biologically realistic simulations, and we argue that this model follows from the continuous approximation of the discrete-state Markov chain model. Open channel and action potential statistics from simulations of ion channel dynamics using the reflected SDE are compared with those of a discrete-state Markov chain method. Results show that the reflected SDE simulations are in good agreement with the discrete-state approach. The reflected SDE model therefore provides a computationally efficient method to simulate ion channel dynamics while preserving the distributional properties of the discrete-state Markov chain model and also ensuring biologically realistic solutions. This framework could easily be extended to other biochemical reaction networks.

  19. Molecular dynamics simulations of nanostructures

    NASA Astrophysics Data System (ADS)

    Yuan, Zaoshi

    This dissertation is focused on multimillion-atom molecular dynamics (MD) simulations of nanoscale materials. In the past decade, nanoscale materials have made significant commercial impacts, which will potentially lead to the next industrial revolution. The interest lies in the novel and promising features nanoscale materials exhibit due to their confined sizes. However, not all novel behaviors are understood or controllable. Many uncontrollable parameters, e.g. defects and dangling bonds, are known to hinder the performance of nanodevices. Solutions to these problems rely on our understanding of fundamental elements in nanoscience: isolated individual nanostructures and their assemblies. In this dissertation, we will address atomistic foundations of several problems of technological importance in nanoscience. Specifically, three basic problems are discussed: (1) embrittlement of nanocrystalline metal; (2) novel thermo-mechanical behaviors of nanowires (NWs); and (3) planar defect generation in NWs. With a scalable algorithm implemented on massively parallel computing platforms and various data mining methods, MD simulations can provide valuable insights into these problems. An essential role of sulfur segregation-induced amorphization of crystalline nickel was recently discovered experimentally, but the atomistic mechanism of the amorphization remains unexplained. Our MD simulations reveal that the large steric size of sulfur impurity causes strong sulfur-sulfur interaction mediated by lattice distortion, which leads to amorphization near the percolation threshold at the sulfur-sulfur network in nickel crystal. The generality of the mechanism due to the percolation of an impurity network is further confirmed by a model binary system. In our study of novel behaviors of semiconductor NWs, MD simulations construct a rich size-temperature `phase diagram' for the mechanical response of a zinc-oxide NW under tension. For smaller diameters and higher temperatures, novel

  20. Adsorption dynamics of molecular nitrogen at an Fe(111) surface.

    PubMed

    Nosir, M A; Martin-Gondre, L; Bocan, G A; Díez Muiño, R

    2017-03-08

    We present an extensive theoretical study of N2 adsorption mechanisms on an Fe(111) surface. We combine the static analysis of a six-dimensional potential energy surface (6D-PES), based on ab initio density functional theory (DFT) calculations for the system, with quasi-classical trajectory (QCT) calculations to simulate the adsorption dynamics. There are four molecular adsorption states, usually called γ, δ, α, and ε, arising from our DFT calculations. We find that N2 adsorption in the γ-state is non-activated, while the threshold energy is associated with the entrance channel for the other three adsorption states. Our QCT calculations confirm that there are activated and nonactivated paths for the adsorption of N2 on the Fe(111) surface, which is in agreement with previous experimental investigations. Molecular dynamics at a surface temperature Ts = 300 K and impact energies Ei in the 0-5 eV range show the relative occupancy of the γ, δ, α, and ε states. The δ-state, however, is only marginally populated despite its adsorption energy being very similar to that of the γ-state. Our QCT calculations trace the dependence of molecular trapping on the surface temperature Ts and initial impact energy Ei and quantify the rates of the different competitive channels that eventually lead to molecular adsorption.

  1. Permeation of ions across the potassium channel: Brownian dynamics studies.

    PubMed

    Chung, S H; Allen, T W; Hoyles, M; Kuyucak, S

    1999-11-01

    The physical mechanisms underlying the transport of ions across a model potassium channel are described. The shape of the model channel corresponds closely to that deduced from crystallography. From electrostatic calculations, we show that an ion permeating the channel, in the absence of any residual charges, encounters an insurmountable energy barrier arising from induced surface charges. Carbonyl groups along the selectivity filter, helix dipoles near the oval chamber, and mouth dipoles near the channel entrances together transform the energy barrier into a deep energy well. Two ions are attracted to this well, and their presence in the channel permits ions to diffuse across it under the influence of an electric field. Using Brownian dynamics simulations, we determine the magnitude of currents flowing across the channel under various conditions. The conductance increases with increasing dipole strength and reaches its maximum rapidly; a further increase in dipole strength causes a steady decrease in the channel conductance. The current also decreases systematically when the effective dielectric constant of the channel is lowered. The conductance with the optimal choice of dipoles reproduces the experimental value when the dielectric constant of the channel is assumed to be 60. The current-voltage relationship obtained with symmetrical solutions is linear when the applied potential is less than approximately 100 mV but deviates from Ohm's law at a higher applied potential. The reversal potentials obtained with asymmetrical solutions are in agreement with those predicted by the Nernst equation. The conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings for the transport of ions across the potassium channels and membrane channels in general.

  2. Modeling hybrid perovskites by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  3. Modeling hybrid perovskites by molecular dynamics.

    PubMed

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  4. Stochastic Evaluation of Riparian Vegetation Dynamics in River Channels

    NASA Astrophysics Data System (ADS)

    Miyamoto, H.; Kimura, R.; Toshimori, N.

    2013-12-01

    Vegetation overgrowth in sand bars and floodplains has been a serious problem for river management in Japan. From the viewpoints of flood control and ecological conservation, it would be necessary to accurately predict the vegetation dynamics for a long period of time. In this study, we have developed a stochastic model for predicting the dynamics of trees in floodplains with emphasis on the interaction with flood impacts. The model consists of the following four processes in coupling ecohydrology with biogeomorphology: (i) stochastic behavior of flow discharge, (ii) hydrodynamics in a channel with vegetation, (iii) variation of riverbed topography and (iv) vegetation dynamics on the floodplain. In the model, the flood discharge is stochastically simulated using a Poisson process, one of the conventional approaches in hydrological time-series generation. The model for vegetation dynamics includes the effects of tree growth, mortality by flood impacts, and infant tree invasion. To determine the model parameters, vegetation conditions have been observed mainly before and after flood impacts since 2008 at a field site located between 23.2-24.0 km from the river mouth in Kako River, Japan. This site is one of the vegetation overgrowth locations in Kako River floodplains, where the predominant tree species are willows and bamboos. In this presentation, sensitivity of the vegetation overgrowth tendency is investigated in Kako River channels. Through the Monte Carlo simulation for several cross sections in Kako River, responses of the vegetated channels are stochastically evaluated in terms of the changes of discharge magnitude and channel geomorphology. The expectation and standard deviation of vegetation areal ratio are compared in the different channel cross sections for different river discharges and relative floodplain heights. The result shows that the vegetation status changes sensitively in the channels with larger discharge and insensitive in the lower floodplain

  5. 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. PMID:26604800

  6. Selective excitation, relaxation, and energy channeling in molecular systems

    SciTech Connect

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems.

  7. Transport Phenomena of Water in Molecular Fluidic Channels

    PubMed Central

    Vo, Truong Quoc; Kim, BoHung

    2016-01-01

    In molecular-level fluidic transport, where the discrete characteristics of a molecular system are not negligible (in contrast to a continuum description), the response of the molecular water system might still be similar to the continuum description if the time and ensemble averages satisfy the ergodic hypothesis and the scale of the average is enough to recover the classical thermodynamic properties. However, even in such cases, the continuum description breaks down on the material interfaces. In short, molecular-level liquid flows exhibit substantially different physics from classical fluid transport theories because of (i) the interface/surface force field, (ii) thermal/velocity slip, (iii) the discreteness of fluid molecules at the interface and (iv) local viscosity. Therefore, in this study, we present the result of our investigations using molecular dynamics (MD) simulations with continuum-based energy equations and check the validity and limitations of the continuum hypothesis. Our study shows that when the continuum description is subjected to the proper treatment of the interface effects via modified boundary conditions, the so-called continuum-based modified-analytical solutions, they can adequately predict nanoscale fluid transport phenomena. The findings in this work have broad effects in overcoming current limitations in modeling/predicting the fluid behaviors of molecular fluidic devices. PMID:27650138

  8. Random Matrix Theory in molecular dynamics analysis.

    PubMed

    Palese, Luigi Leonardo

    2015-01-01

    It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.

  9. Improving flow distribution in influent channels using computational fluid dynamics.

    PubMed

    Park, No-Suk; Yoon, Sukmin; Jeong, Woochang; Lee, Seungjae

    2016-10-01

    Although the flow distribution in an influent channel where the inflow is split into each treatment process in a wastewater treatment plant greatly affects the efficiency of the process, and a weir is the typical structure for the flow distribution, to the authors' knowledge, there is a paucity of research on the flow distribution in an open channel with a weir. In this study, the influent channel of a real-scale wastewater treatment plant was used, installing a suppressed rectangular weir that has a horizontal crest to cross the full channel width. The flow distribution in the influent channel was analyzed using a validated computational fluid dynamics model to investigate (1) the comparison of single-phase and two-phase simulation, (2) the improved procedure of the prototype channel, and (3) the effect of the inflow rate on flow distribution. The results show that two-phase simulation is more reliable due to the description of the free-surface fluctuations. It should first be considered for improving flow distribution to prevent a short-circuit flow, and the difference in the kinetic energy with the inflow rate makes flow distribution trends different. The authors believe that this case study is helpful for improving flow distribution in an influent channel.

  10. Fluctuation driven active molecular transport in passive channel proteins

    NASA Astrophysics Data System (ADS)

    Kosztin, Ioan

    2006-03-01

    Living cells interact with their extracellular environment through the cell membrane, which acts as a protective permeability barrier for preserving the internal integrity of the cell. However, cell metabolism requires controlled molecular transport across the cell membrane, a function that is fulfilled by a wide variety of transmembrane proteins, acting as either passive or active transporters. In this talk it is argued that, contrary to the general belief, in active cell membranes passive and spatially asymmetric channel proteins can act as active transporters by consuming energy from nonequilibrium fluctuations fueled by cell metabolism. This assertion is demonstrated in the case of the E. coli aquaglyceroporin GlpF channel protein, whose high resolution crystal structure is manifestly asymmetric. By calculating the glycerol flux through GlpF within the framework of a stochastic model, it is found that, as a result of channel asymmetry, glycerol uptake driven by a concentration gradient is enhanced significantly in the presence of non-equilibrium fluctuations. Furthermore, the enhancement caused by a ratchet-like mechanism is larger for the outward, i.e., from the cytoplasm to the periplasm, flux than for the inward one, suggesting that the same non-equilibrium fluctuations also play an important role in protecting the interior of the cell against poisoning by excess uptake of glycerol. Preliminary data on water and sugar transport through aquaporin and maltoporin channels, respectively, are indicative of the universality of the proposed nonequilibrium-fluctuation-driven active transport mechanism. This work was supported by grants from the Univ. of Missouri Research Board, the Institute for Theoretical Sciences and the Department of Energy (DOE Contract W-7405-ENG-36), and the National Science Foundation (FIBR-0526854).

  11. Liouville-von Neumann molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jakowski, Jacek; Morokuma, Keiji

    2009-06-01

    We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.

  12. Molecular dynamics simulations of substitutional diffusion

    SciTech Connect

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

    2016-12-18

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

  13. Molecular dynamics simulations of substitutional diffusion

    DOE PAGES

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

    2016-12-18

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

  14. Non-Equilibrium Dynamics Contribute to Ion Selectivity in the KcsA Channel

    PubMed Central

    Haas, Stephan; Farley, Robert A.

    2014-01-01

    The ability of biological ion channels to conduct selected ions across cell membranes is critical for the survival of both animal and bacterial cells. Numerous investigations of ion selectivity have been conducted over more than 50 years, yet the mechanisms whereby the channels select certain ions and reject others are not well understood. Here we report a new application of Jarzynski’s Equality to investigate the mechanism of ion selectivity using non-equilibrium molecular dynamics simulations of Na+ and K+ ions moving through the KcsA channel. The simulations show that the selectivity filter of KcsA adapts and responds to the presence of the ions with structural rearrangements that are different for Na+ and K+. These structural rearrangements facilitate entry of K+ ions into the selectivity filter and permeation through the channel, and rejection of Na+ ions. A mechanistic model of ion selectivity by this channel based on the results of the simulations relates the structural rearrangement of the selectivity filter to the differential dehydration of ions and multiple-ion occupancy and describes a mechanism to efficiently select and conduct K+. Estimates of the K+/Na+ selectivity ratio and steady state ion conductance for KcsA from the simulations are in good quantitative agreement with experimental measurements. This model also accurately describes experimental observations of channel block by cytoplasmic Na+ ions, the “punch through” relief of channel block by cytoplasmic positive voltages, and is consistent with the knock-on mechanism of ion permeation. PMID:24465882

  15. Molecular origins of conduction channels observed in shot-noise measurements.

    PubMed

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

    2006-11-01

    Measurements of shot noise from single molecules have indicated the presence of various conduction channels. We present three descriptions of these channels in molecular terms showing that the number of conduction channels is limited by bottlenecks in the molecule and that the channels can be linked to transmission through different junction states. We introduce molecular-conductance orbitals, which allow the transmission to be separated into contributions from individual orbitals and contributions from interference between pairs of orbitals.

  16. 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.

  17. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.

    PubMed

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-02-21

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular

  18. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

    PubMed Central

    2017-01-01

    Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition

  19. Understanding Modularity in Molecular Networks Requires Dynamics

    PubMed Central

    Alexander, Roger P.; Kim, Philip M.; Emonet, Thierry; Gerstein, Mark B.

    2014-01-01

    The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as non-genetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics – and therefore to behavior – remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular – that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function. PMID:19638611

  20. 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.

  1. 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.

  2. 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.

  3. Dynamic Quantum Tomography Model for Phase-Damping Channels

    NASA Astrophysics Data System (ADS)

    Czerwiński, Artur; Jamiołkowski, Andrzej

    In this paper we propose a dynamic quantum tomography model for open quantum systems with evolution given by phase-damping channels. Mathematically, these channels correspond to completely positive trace-preserving maps defined by the Hadamard product of the initial density matrix with a time-dependent matrix which carries the knowledge about the evolution. Physically, there is a strong motivation for considering this kind of evolution because such channels appear naturally in the theory of open quantum systems. The main idea behind a dynamic approach to quantum tomography claims that by performing the same kind of measurement at some time instants one can obtain new data for state reconstruction. Thus, this approach leads to a decrease in the number of distinct observables which are required for quantum tomography; however, the exact benefit for employing the dynamic approach depends strictly on how the quantum system evolves in time. Algebraic analysis of phase-damping channels allows one to determine criteria for quantum tomography of systems in question. General theorems and observations presented in the paper are accompanied by a specific example, which shows step by step how the theory works. The results introduced in this paper can potentially be applied in experiments where there is a tendency to look at quantum tomography from the point of view of economy of measurements, because each distinct kind of measurement requires, in general, preparing a separate setup.

  4. Molecular dynamics study of the archaeal aquaporin AqpM

    PubMed Central

    2011-01-01

    Background Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO2 or urea. Recently, the identification and characterization of a number of archaeal and bacterial aquaporins suggested the existence of a third sub-family; one that is neither a strict aquaporin nor an aquaglyceroporin. The function and phylogeny of this third family is still a matter of debate. Results Twenty nanosecond molecular dynamics (MD) simulation of a fully hydrated tetramer of AqpM embedded in a lipid bilayer permitted predictions to be made of key biophysical parameters including: single channel osmotic permeability constant (pf), single channel diffusive permeability constant (pd), channel radius, potential water occupancy of the channel and water orientation inside the pore. These properties were compared with those of well characterized representatives of the two main aquaporin sub-families. Results show that changes in the amino acid composition of the aromatic/arginine region affect the size and polarity of the selectivity filter (SF) and could help explain the difference in water permeability between aquaporins. In addition, MD simulation results suggest that AqpM combines characteristics of strict aquaporins, such as the narrow SF and channel radius, with those of aquaglyceroporins, such as a more hydrophobic and less polar SF. Conclusions MD simulations of AqpM extend previous evidence that this archaeal aquaporin exhibits hybrid features intermediate between the two known aquaporin sub-families, supporting the idea that it may constitute a

  5. 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.

  6. 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.

  7. Modeling diverse range of potassium channels with Brownian dynamics.

    PubMed Central

    Chung, Shin-Ho; Allen, Toby W; Kuyucak, Serdar

    2002-01-01

    Using the experimentally determined KcsA structure as a template, we propose a plausible explanation for the diversity of potassium channels seen in nature. A simplified model of KcsA is constructed from its atomic resolution structure by smoothing out the protein-water boundary and representing the atoms forming the channel protein as a homogeneous, low dielectric medium. The properties of the simplified and atomic-detail models, deduced from electrostatic calculations and Brownian dynamics simulations, are shown to be qualitatively similar. We then study how the current flowing across the simplified model channel changes as the shape of the intrapore region is modified. This is achieved by increasing the radius of the intracellular pore systematically from 1.5 to 5 A while leaving the dimensions of the selectivity filter and inner chamber unaltered. The strengths of the dipoles located near the entrances of the channel, the carbonyl groups lining the selectivity filter, and the helix macrodipoles are kept constant. The channel conductance increases steadily as the radius of the intracellular pore is increased. The rate-limiting step for both the outward and inward current is the time it takes for an ion to cross the residual energy barrier located in the intrapore region. The current-voltage relationship obtained with symmetrical solutions is linear when the applied potential is less than approximately 100 mV but deviates slightly from Ohm's law at higher applied potentials. The nonlinearity in the current-voltage curve becomes less pronounced as the radius of the intracellular pore is increased. When the strengths of the dipoles near the intracellular entrance are reduced, the channel shows a pronounced inward rectification. Finally, the conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings on the transport of ions across the potassium channels and membrane channels in general. PMID:12080118

  8. Photodissociation of vinyl cyanide at 193 nm: Nascent product distributions of the molecular elimination channels

    SciTech Connect

    Wilhelm, Michael J.; Nikow, Matthew; Letendre, Laura; Dai Hailung

    2009-01-28

    The photodissociation dynamics of vinyl cyanide (H{sub 2}CCHCN, acrylonitrile) and deuterated vinyl cyanide (D{sub 2}CCDCN) at 193 nm are examined using time-resolved Fourier transform infrared emission spectroscopy. Prior photofragment translational spectroscopy studies [D. A. Blank et al., J. Chem. Phys. 108, 5784 (1998)] of the dissociation have observed the presence of four main dissociation channels; two molecular and two radical in nature. However, with the exception of a<0.01 quantum yield determined for the CN radical loss channel, the branching ratios of the remaining three elimination channels were not measured. The time-resolved emission spectra, including those from the deuterated samples, revealed the presence of acetylene, hydrogen cyanide (HCN), as well as the energetically less stable isomer hydrogen isocyanide (HNC). Acetylene is found in two distinct energetic distributions, suggesting that both three- and four-centered elimination reactions are occurring significantly in the dissociation. In contrast to prior ab initio studies that have suggested the dominant nature of the three-center elimination of molecular hydrogen (H{sub 2}) and cyanovinylidene (:C=CHCN), we find this reaction channel to be of little importance as there is no evidence to support any significant presence of rovibrationally excited cyanoacetylene. Spectral modeling of the product distributions allows for the first experimental determination of the relative occurrence of the three-centered (resulting in HCN+vinylidene) versus four-centered (HNC+acetylene) elimination channels as 3.34 to 1.00, in contrast to the previously calculated value of 126:1. Rice-Ramsperger-Kassel-Marcus analysis depicts that the transition state energy of the four-centered reaction should be about 10 kcal mole{sup -1} lower than the three-centered reaction.

  9. Analysis of molecular oxygen exit pathways in cyanobacterial photosystem II: Molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Gabdulkhakov, A. G.; Kljashtorny, V. G.; Dontsova, M. V.

    2015-11-01

    In thylakoids of cyanobacteria and other photosynthetic organisms, the light-induced production of molecular oxygen is catalyzed by the giant lipid-pigment-protein complex called photosystem II (PSII). The oxygen-evolving complex is buried deep in the lumenal part of PSII, and dioxygen molecules need to pass through the protein environment in order to leave the active site of the enzyme free. Previous studies aimed at finding oxygen channels in PSII were based on either an analysis of the cavities within is static structure or experiments on the insertion of noble gas molecules into PSII crystals under elevated pressure. In these studies, some possible exit pathways for the molecules were found and the static positions of molecular oxygen were determined. In the present work, the oxygen movement in the transport system of PSII is simulated by molecular dynamics.

  10. Event scale variability of mixed alluvial-bedrock channel dynamics

    NASA Astrophysics Data System (ADS)

    Cook, Kristen; Turowski, Jens; Hovius, Niels

    2015-04-01

    between sediment supply, channel width, and flood characteristics on aggradation and erosion of the channel bed. Heimann, F. U. M., Rickenmann, D., Turowski, J. M., and Kirchner, J. W.: sedFlow - an efficient tool for simulating bedload transport, bed roughness, and longitudinal profile evolution in mountain streams, Earth Surf. Dynam. Discuss., 2, 733-772, doi:10.5194/esurfd-2-733-2014, 2014.

  11. 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.

  12. Rigid body Brownian dynamics as a tool for studying ion channel blockers.

    PubMed

    Gordon, Dan; Chen, Rong; Ho, Junming; Coote, Michelle L; Chung, Shin-Ho

    2012-02-16

    Using a novel rigid body Brownian dynamics algorithm, we investigate how a spherically asymmetrical polyamine molecule, a branched analogue of spermine, interacts with the external vestibule of the voltage-gated potassium channel, Kv1.2. Simulations reveal that the blocker, with a charge of +4e, inserts one of its charged amine groups into the selectivity filter, while another forms a salt bridge with an aspartate residue located just outside the entrance of the pore. This binding mode mimics features of the binding of polypeptides such as the scorpion venom charybdotoxin to the channel. The potential of mean force constructed with Brownian dynamics is a reasonable match to that obtained from molecular dynamics simulations, with dissociation constants of 4.7 and 22 μM, respectively. The current-voltage relationships obtained with and without a blocker in the external reservoir show that the inward current is severely attenuated by the presence of the blocker, whereas the outward current is only moderately reduced. The computational molecular modeling technique we introduce here can provide detailed insights into ligand-channel interactions and can be used for rapidly screening potential blocker molecules.

  13. Mechanisms of molecular transport through the urea channel of Helicobacter pylori

    NASA Astrophysics Data System (ADS)

    McNulty, Reginald; Ulmschneider, Jakob P.; Luecke, Hartmut; Ulmschneider, Martin B.

    2013-12-01

    Helicobacter pylori survival in acidic environments relies on cytoplasmic hydrolysis of gastric urea into ammonia and carbon dioxide, which buffer the pathogen’s periplasm. Urea uptake is greatly enhanced and regulated by HpUreI, a proton-gated inner membrane channel protein essential for gastric survival of H. pylori. The crystal structure of HpUreI describes a static snapshot of the channel with two constriction sites near the center of the bilayer that are too narrow to allow passage of urea or even water. Here we describe the urea transport mechanism at atomic resolution, revealed by unrestrained microsecond equilibrium molecular dynamics simulations of the hexameric channel assembly. Two consecutive constrictions open to allow conduction of urea, which is guided through the channel by interplay between conserved residues that determine proton rejection and solute selectivity. Remarkably, HpUreI conducts water at rates equivalent to aquaporins, which might be essential for efficient transport of urea at small concentration gradients.

  14. Excited State Quantum-Classical Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Krstic, Predrag

    2005-05-01

    The development of a new theoretical, algorithmic, and computational framework is reported describing the corresponding excited state many-body dynamics by applying multiphysics described by classical equations of motion for nuclei and Hartree-Fock/Multi-Configuration Hartree-Fock and multiresolution techniques for solving the quantum part of the problem (i.e. the motion of the electrons). We primarily have in mind reactive and electron-transition dynamics which involves molecular clusters, containing hundreds of atoms, perturbed by a slow ionic/atomic/molecular projectile, with possible applications in plasma-surface interactions, cluster physics, chemistry and biotechnology. The validation of the developed technique is performed at three-body systems. Application to the transition dynamics in small carbon clusters and hydrocarbons perturbed by slow carbon ions resolves some long-standing issues in the ion-surface interactions in fusion tokamaks.

  15. Cooperative Nature of Gating Transitions in K+ Channels as seen from Dynamic Importance Sampling Calculations

    PubMed Central

    Denning, Elizabeth J.; Woolf, Thomas B.

    2009-01-01

    The growing dataset of K+ channel x-ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply Dynamic Importance Sampling (DIMS) to a set of homology models for the molecular conformations of K+ channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the PVP region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the cooperative behavior of all four subunits of the K+ channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter- S5-S6 subunit motions, and lastly the large-scale domain rearrangements. PMID:19950367

  16. Evaluation of Dynamic Channel and Power Assignment for Cognitive Networks

    SciTech Connect

    Syed A. Ahmad; Umesh Shukla; Ryan E. Irwin; Luiz A. DaSilva; Allen B. MacKenzie

    2011-03-01

    In this paper, we develop a unifying optimization formulation to describe the Dynamic Channel and Power Assignment (DCPA) problem and evaluation method for comparing DCPA algorithms. DCPA refers to the allocation of transmit power and frequency channels to links in a cognitive network so as to maximize the total number of feasible links while minimizing the aggregate transmit power. We apply our evaluation method to five algorithms representative of DCPA used in literature. This comparison illustrates the tradeoffs between control modes (centralized versus distributed) and channel/power assignment techniques. We estimate the complexity of each algorithm. Through simulations, we evaluate the effectiveness of the algorithms in achieving feasible link allocations in the network, as well as their power efficiency. Our results indicate that, when few channels are available, the effectiveness of all algorithms is comparable and thus the one with smallest complexity should be selected. The Least Interfering Channel and Iterative Power Assignment (LICIPA) algorithm does not require cross-link gain information, has the overall lowest run time, and highest feasibility ratio of all the distributed algorithms; however, this comes at a cost of higher average power per link.

  17. Multi-channel electronic and vibrational dynamics in polyatomic resonant high-order harmonic generation

    PubMed Central

    Ferré, A.; Boguslavskiy, A. E.; Dagan, M.; Blanchet, V.; Bruner, B. D.; Burgy, F.; Camper, A.; Descamps, D.; Fabre, B.; Fedorov, N.; Gaudin, J.; Geoffroy, G.; Mikosch, J.; Patchkovskii, S.; Petit, S.; Ruchon, T.; Soifer, H.; Staedter, D.; Wilkinson, I.; Stolow, A.; Dudovich, N.; Mairesse, Y.

    2015-01-01

    High-order harmonic generation in polyatomic molecules generally involves multiple channels of ionization. Their relative contribution can be strongly influenced by the presence of resonances, whose assignment remains a major challenge for high-harmonic spectroscopy. Here we present a multi-modal approach for the investigation of unaligned polyatomic molecules, using SF6 as an example. We combine methods from extreme-ultraviolet spectroscopy, above-threshold ionization and attosecond metrology. Fragment-resolved above-threshold ionization measurements reveal that strong-field ionization opens at least three channels. A shape resonance in one of them is found to dominate the signal in the 20–26 eV range. This resonance induces a phase jump in the harmonic emission, a switch in the polarization state and different dynamical responses to molecular vibrations. This study demonstrates a method for extending high-harmonic spectroscopy to polyatomic molecules, where complex attosecond dynamics are expected. PMID:25608712

  18. Multi-channel electronic and vibrational dynamics in polyatomic resonant high-order harmonic generation

    NASA Astrophysics Data System (ADS)

    Ferré, A.; Boguslavskiy, A. E.; Dagan, M.; Blanchet, V.; Bruner, B. D.; Burgy, F.; Camper, A.; Descamps, D.; Fabre, B.; Fedorov, N.; Gaudin, J.; Geoffroy, G.; Mikosch, J.; Patchkovskii, S.; Petit, S.; Ruchon, T.; Soifer, H.; Staedter, D.; Wilkinson, I.; Stolow, A.; Dudovich, N.; Mairesse, Y.

    2015-01-01

    High-order harmonic generation in polyatomic molecules generally involves multiple channels of ionization. Their relative contribution can be strongly influenced by the presence of resonances, whose assignment remains a major challenge for high-harmonic spectroscopy. Here we present a multi-modal approach for the investigation of unaligned polyatomic molecules, using SF6 as an example. We combine methods from extreme-ultraviolet spectroscopy, above-threshold ionization and attosecond metrology. Fragment-resolved above-threshold ionization measurements reveal that strong-field ionization opens at least three channels. A shape resonance in one of them is found to dominate the signal in the 20-26 eV range. This resonance induces a phase jump in the harmonic emission, a switch in the polarization state and different dynamical responses to molecular vibrations. This study demonstrates a method for extending high-harmonic spectroscopy to polyatomic molecules, where complex attosecond dynamics are expected.

  19. On the putative binding site of RFamide-family neuropeptides from the western Atlantic clam Sunray Venus and cephalopods on acid-sensing ion channels. An automated docking and molecular-dynamics study with hASIC1a homology model.

    PubMed

    Pietra, Francesco

    2011-05-01

    Investigated here are interactions of C-terminal amidated peptides with the hASIC1a acid-sensing ion channel. The peptides comprise endogenous FMRFa, present in the western Atlantic clam Sunray Venus, and FIRFa, present in cephalopods, as well as non-endogenous ones for comparison. The interaction is investigated by automated docking. The resulting key hASIC1a-FMRFa complex, set in a lipidic POPC (=1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane surrounded by H(2) O and Na(+) -neutralized, was also investigated by molecular dynamics. It was observed that all investigated peptides become encapsulated into the ion channel, on one side by the thumb and finger of a subunit, and, on the opposite side, by the knuckle and β-ball of a second subunit. The third subunit is not involved. This is much the same binding site that was disclosed previously by both a similar computational approach, and electrophysiological and binding experiments for the hASIC1a ion channel-blocker tarantula toxin PCTX1. This paves the way to a better understanding of the role of these peptides in invertebrates.

  20. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

    PubMed Central

    Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

    2012-01-01

    It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

  1. Origin of the Shape of Current-Voltage Curve through Nanopores: A Molecular Dynamics Study

    PubMed Central

    Sumikama, Takashi

    2016-01-01

    Ion transports through ion channels, biological nanopores, are essential for life: Living cells generate electrical signals by utilizing ion permeation through channels. The measured current-voltage (i-V) relations through most ion channels are sublinear, however, its physical meaning is still elusive. Here we calculated the i-V curves through anion-doped carbon nanotubes, a model of an ion channel, using molecular dynamics simulation. It was found the i-V curve reflects the physical origin of the rate-determining step: the i-V curve is sublinear when the permeation is entropy bottlenecked, while it is superlinear in the case of the energy bottlenecked permeation. Based on this finding, we discuss the relation between the molecular mechanism of ion permeation through the biological K+ channels and the shape of the i-V curves through them. This work also provides a clue for a novel design of nanopores that show current rectification. PMID:27167118

  2. Origin of the Shape of Current-Voltage Curve through Nanopores: A Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Sumikama, Takashi

    2016-05-01

    Ion transports through ion channels, biological nanopores, are essential for life: Living cells generate electrical signals by utilizing ion permeation through channels. The measured current-voltage (i-V) relations through most ion channels are sublinear, however, its physical meaning is still elusive. Here we calculated the i-V curves through anion-doped carbon nanotubes, a model of an ion channel, using molecular dynamics simulation. It was found the i-V curve reflects the physical origin of the rate-determining step: the i-V curve is sublinear when the permeation is entropy bottlenecked, while it is superlinear in the case of the energy bottlenecked permeation. Based on this finding, we discuss the relation between the molecular mechanism of ion permeation through the biological K+ channels and the shape of the i-V curves through them. This work also provides a clue for a novel design of nanopores that show current rectification.

  3. 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

  4. Choice of timestep in molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Fincham, David

    1986-06-01

    In molecular dynamics computer simulation of liquids it is important to use as large a timestep as possible in order to sample phase space rapidly and save on computer expense. The effect of the resulting algorithm errors in the trajectories of the molecules is not well understood. An empirical investigation into this question is reported. Several simulations differing only in the timestep used are compared. It is found that much larger timesteps than usual can be employed without producing significant errors in observed thermodynamic, structural or dynamic properties.

  5. Water Transport in Aquaporins: Osmotic Permeability Matrix Analysis of Molecular Dynamics Simulations

    PubMed Central

    Hashido, Masanori; Kidera, Akinori; Ikeguchi, Mitsunori

    2007-01-01

    Single-channel osmotic water permeability (pf) is a key quantity for investigating the transport capability of the water channel protein, aquaporin. However, the direct connection between the single scalar quantity pf and the channel structure remains unclear. In this study, based on molecular dynamics simulations, we propose a pf-matrix method, in which pf is decomposed into contributions from each local region of the channel. Diagonal elements of the pf matrix are equivalent to the local permeability at each region of the channel, and off-diagonal elements represent correlated motions of water molecules in different regions. Averaging both diagonal and off-diagonal elements of the pf matrix recovers pf for the entire channel; this implies that correlated motions between distantly-separated water molecules, as well as adjacent water molecules, influence the osmotic permeability. The pf matrices from molecular dynamics simulations of five aquaporins (AQP0, AQP1, AQP4, AqpZ, and GlpF) indicated that the reduction in the water correlation across the Asn-Pro-Ala region, and the small local permeability around the ar/R region, characterize the transport efficiency of water. These structural determinants in water permeation were confirmed in molecular dynamics simulations of three mutants of AqpZ, which mimic AQP1. PMID:17449664

  6. 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.

  7. 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.

  8. Accurate Langevin approaches to simulate Markovian channel dynamics

    NASA Astrophysics Data System (ADS)

    Huang, Yandong; Rüdiger, Sten; Shuai, Jianwei

    2015-12-01

    The stochasticity of ion-channels dynamic is significant for physiological processes on neuronal cell membranes. Microscopic simulations of the ion-channel gating with Markov chains can be considered to be an accurate standard. However, such Markovian simulations are computationally demanding for membrane areas of physiologically relevant sizes, which makes the noise-approximating or Langevin equation methods advantageous in many cases. In this review, we discuss the Langevin-like approaches, including the channel-based and simplified subunit-based stochastic differential equations proposed by Fox and Lu, and the effective Langevin approaches in which colored noise is added to deterministic differential equations. In the framework of Fox and Lu’s classical models, several variants of numerical algorithms, which have been recently developed to improve accuracy as well as efficiency, are also discussed. Through the comparison of different simulation algorithms of ion-channel noise with the standard Markovian simulation, we aim to reveal the extent to which the existing Langevin-like methods approximate results using Markovian methods. Open questions for future studies are also discussed.

  9. Dynamic propagation channel characterization and modeling for human body communication.

    PubMed

    Nie, Zedong; Ma, Jingjing; Li, Zhicheng; Chen, Hong; Wang, Lei

    2012-12-18

    This paper presents the first characterization and modeling of dynamic propagation channels for human body communication (HBC). In-situ experiments were performed using customized transceivers in an anechoic chamber. Three HBC propagation channels, i.e., from right leg to left leg, from right hand to left hand and from right hand to left leg, were investigated under thirty-three motion scenarios. Snapshots of data (2,800,000) were acquired from five volunteers. Various path gains caused by different locations and movements were quantified and the statistical distributions were estimated. In general, for a given reference threshold è = -10 dB, the maximum average level crossing rate of the HBC was approximately 1.99 Hz, the maximum average fade time was 59.4 ms, and the percentage of bad channel duration time was less than 4.16%. The HBC exhibited a fade depth of -4 dB at 90% complementary cumulative probability. The statistical parameters were observed to be centered for each propagation channel. Subsequently a Fritchman model was implemented to estimate the burst characteristics of the on-body fading. It was concluded that the HBC is motion-insensitive, which is sufficient for reliable communication link during motions, and therefore it has great potential for body sensor/area networks.

  10. Chaotic dynamics in cardiac aggregates induced by potassium channel block

    NASA Astrophysics Data System (ADS)

    Quail, Thomas; McVicar, Nevin; Aguilar, Martin; Kim, Min-Young; Hodge, Alex; Glass, Leon; Shrier, Alvin

    2012-09-01

    Chaotic rhythms in deterministic models can arise as a consequence of changes in model parameters. We carried out experimental studies in which we induced a variety of complex rhythms in aggregates of embryonic chick cardiac cells using E-4031 (1.0-2.5 μM), a drug that blocks the hERG potassium channel. Following the addition of the drug, the regular rhythm evolved to display a spectrum of complex dynamics: irregular rhythms, bursting oscillations, doublets, and accelerated rhythms. The interbeat intervals of the irregular rhythms can be described by one-dimensional return maps consistent with chaotic dynamics. A Hodgkin-Huxley-style cardiac ionic model captured the different types of complex dynamics following blockage of the hERG mediated potassium current.

  11. 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.

  12. 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.

  13. Three-dimensional flow dynamics of an active submarine channel

    NASA Astrophysics Data System (ADS)

    Sumner, E. J.; Dorrell, R. M.; Peakall, J.; Darby, S. E.; Parsons, D. R.; Wynn, R.

    2012-12-01

    Field scale submarine channel gravity currents are notoriously difficult to measure and thus directly investigate due to their inaccessible location and infrequent nature, which is compounded by present sea-level high-stand. An exception to this is the almost continuous density-driven current that results from the inflow of saline Mediterranean water, via the Bosporus strait, into the Black Sea. This flow has carved a sinuous channel system in water depths of 70 to 120 m. The relatively shallow depths of the channel and the continuous nature of this current provide a rare opportunity to study three-dimensional flow dynamics and the interaction of the flow with a seafloor channel network. Thus, it provides a rare analogue for channelized dilute sediment-laden turbidity currents. Sediment erosion, transport and deposition within submarine channel bends is primarily controlled by the magnitude and direction of near bed flow. Flow around channel bends is characterized by a helical or spiralling structure. In rivers this helical flow is characterized by near-surface fluid moving toward the outer bank and near-bed fluid moving toward the inner bank. Following fierce debate over the last decade, it is now accepted that helical flow in submarine channel bends can display a variety of complex structures. Most importantly for understanding sediment transport, near bed flow can be directed towards the outer bank, which is in the opposite sense to in a river. The next challenge is to understand what the exact controls on the orientation of helical flow cells within submarine flows are, and their spatial evolution around bends. We present data from the Black Sea showing how the three-dimensional velocity and density of a submarine gravity current evolves at multiple cross sections as the flow travels around a bend. We use this data to calculate the magnitude, relative importance and interaction of centrifugal, coriolis and pressure gradients in controlling the structure of

  14. Equipartition Principle for Internal Coordinate Molecular Dynamics.

    PubMed

    Jain, Abhinandan; Park, In-Hee; Vaidehi, Nagarajan

    2012-08-14

    The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ½kT of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper we introduce non-canonical modal coordinates to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations thus replacing the ad hoc methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates.

  15. 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

  16. Bead-Fourier path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto

    2003-06-01

    Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.

  17. Learning generative models of molecular dynamics

    PubMed Central

    2012-01-01

    We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 reg-ularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories. PMID:22369071

  18. Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems.

    PubMed

    Nebgen, Ben; Prezhdo, Oleg V

    2016-09-15

    A method for efficiently simulating nonadiabatic molecular dynamics (NAMD) of nanoscale and condensed phase systems is developed and tested. The electronic structure, including force and nonadiabatic coupling, are obtained with the fragment molecular orbital (FMO) approximation, which provides significant computational savings by splitting the system into fragments and computing electronic properties of each fragment subject to the external field due to other all other fragments. The efficiency of the developed technique is demonstrated by studying the effect of explicit solvent molecules on excited state relaxation in the Fe(CO)4 complex. The relaxation in the gas phase occurs on a 50 fs time scale, which is in excellent agreement with previously recorded femtosecond pump-probe spectroscopy. Adding a solvation shell of ethanol molecules to the simulation results in an increase in the excited state lifetime to 100 fs, in agreement with recent femtosecond X-ray spectroscopy measurements.

  19. 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

  20. Dynamics of premixed hydrogen/air flames in mesoscale channels

    SciTech Connect

    Pizza, Gianmarco; Frouzakis, Christos E.; Boulouchos, Konstantinos; Mantzaras, John; Tomboulides, Ananias G.

    2008-10-15

    Direct numerical simulation with detailed chemistry and transport is used to study the stabilization and dynamics of lean ({phi}=0.5) premixed hydrogen/air atmospheric pressure flames in mesoscale planar channels. Channel heights of h=2, 4, and 7 mm, and inflow velocities in the range 0.3{<=}U{sub IN}{<=}1100cm/ s are investigated. Six different burning modes are identified: mild combustion, ignition/extinction, closed steady symmetric flames, open steady symmetric flames, oscillating and, finally, asymmetric flames. Chaotic behavior of cellular flame structures is observed for certain values of U{sub IN}. Stability maps delineating the regions of the different flame types are finally constructed. (author)

  1. Viscoelastic droplet dynamics in a Y-shaped capillary channel

    NASA Astrophysics Data System (ADS)

    Wang, Yuli; Do-Quang, Minh; Amberg, Gustav

    2016-03-01

    Non-Newtonian droplet dynamics commonly exist in microfluidic systems. We report simulations of viscoelastic (VE) droplets traveling in a two dimensional capillary bifurcation channel. A numerical system combining phase field method, VE rheology, and Stokes flow equations is built. As a generic microfluidic two-phase problem, we study how a non-Newtonian droplet that approaches a channel bifurcation will behave. We identify conditions for when a droplet will either split into two or be directed into one of the branches. In particular, we study the importance of the non-Newtonian properties. Our results reveal two different non-Newtonian mechanisms that can enhance splitting and non-splitting of droplets with respect to Newtonian droplets, depending on the size of droplet and capillary number.

  2. Molecular dynamics simulations of magnetized dusty plasmas

    NASA Astrophysics Data System (ADS)

    Piel, Alexander; Reichstein, Torben; Wilms, Jochen

    2012-10-01

    The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)

  3. Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.

    2017-03-01

    We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

  4. 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 δ-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.

  5. 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

  6. Polymer Fluid Dynamics: Continuum and Molecular Approaches.

    PubMed

    Bird, R B; Giacomin, A J

    2016-06-07

    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.

  7. The dynamic behaviors of complementary correlations under decoherence channels

    PubMed Central

    Du, Ming-Ming; Wang, Dong; Ye, Liu

    2017-01-01

    Complementary correlations can reveal the genuine quantum correlations present in a composite quantum system. Here, we explore an effective method to identify the entangled Bell diagonal states by means of Pearson correlation, one of the complementary correlations. Then, we extend this method to expose the dynamic behavior of complementary correlations under various kinds of decoherence channels. The sudden death and revival of entanglement can be explained by the idea of Pearson correlation. The threshold that is used to identify entanglement is proposed. Furthermore, we put forward a new method to expound the underlying physical mechanisms for which classical and quantum correlations suffer a sudden change in the decoherence process. PMID:28134291

  8. The dynamic behaviors of complementary correlations under decoherence channels

    NASA Astrophysics Data System (ADS)

    Du, Ming-Ming; Wang, Dong; Ye, Liu

    2017-01-01

    Complementary correlations can reveal the genuine quantum correlations present in a composite quantum system. Here, we explore an effective method to identify the entangled Bell diagonal states by means of Pearson correlation, one of the complementary correlations. Then, we extend this method to expose the dynamic behavior of complementary correlations under various kinds of decoherence channels. The sudden death and revival of entanglement can be explained by the idea of Pearson correlation. The threshold that is used to identify entanglement is proposed. Furthermore, we put forward a new method to expound the underlying physical mechanisms for which classical and quantum correlations suffer a sudden change in the decoherence process.

  9. Influence of solid-liquid interactions on dynamic wetting: a molecular dynamics study.

    PubMed

    Bertrand, Emilie; Blake, Terence D; Coninck, Joël De

    2009-11-18

    Large-scale molecular dynamics (MD) simulations of liquid drops spreading on a solid substrate have been carried out for a very wide range of solid-liquid interactions and equilibrium contact angles. The results for these systems are shown to be consistent with the molecular-kinetic theory (MKT) of dynamic wetting, which emphasizes the role of contact-line friction as the principal channel of energy dissipation. Several predictions have been confirmed. These include a quantitative link between the dynamics of wetting and the work of adhesion and the existence of an optimum equilibrium contact angle that maximizes the speed of wetting. A feature of the new work is that key parameters (κ(0) and λ), normally accessible only by fitting the MKT to dynamic contact angle data, are also obtained directly from the simulations, with good agreement between the two sources. This validates the MKT at some fundamental level. Further verification is provided by contact angle relaxation studies, which also lend support to the interfacial tension relaxation process invoked in Shikhmurzaev's hydrodynamic model of dynamic wetting.

  10. Influence of solid-liquid interactions on dynamic wetting: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Bertrand, Emilie; Blake, Terence D.; De Coninck, Joël

    2009-11-01

    Large-scale molecular dynamics (MD) simulations of liquid drops spreading on a solid substrate have been carried out for a very wide range of solid-liquid interactions and equilibrium contact angles. The results for these systems are shown to be consistent with the molecular-kinetic theory (MKT) of dynamic wetting, which emphasizes the role of contact-line friction as the principal channel of energy dissipation. Several predictions have been confirmed. These include a quantitative link between the dynamics of wetting and the work of adhesion and the existence of an optimum equilibrium contact angle that maximizes the speed of wetting. A feature of the new work is that key parameters (κ0 and λ), normally accessible only by fitting the MKT to dynamic contact angle data, are also obtained directly from the simulations, with good agreement between the two sources. This validates the MKT at some fundamental level. Further verification is provided by contact angle relaxation studies, which also lend support to the interfacial tension relaxation process invoked in Shikhmurzaev's hydrodynamic model of dynamic wetting.

  11. Virtual-Wall Model for Molecular Dynamics Simulation.

    PubMed

    Qian, Lijuan; Tu, Chengxu; Bao, Fubing; Zhang, Yonghao

    2016-12-09

    A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed.

  12. The molecular choreography of a store-operated calcium channel.

    PubMed

    Lewis, Richard S

    2007-03-15

    Store-operated calcium channels (SOCs) serve essential functions from secretion and motility to gene expression and cell growth. A fundamental mystery is how the depletion of Ca2+ from the endoplasmic reticulum (ER) activates Ca2+ entry through SOCs in the plasma membrane. Recent studies using genetic approaches have identified genes encoding the ER Ca2+ sensor and a prototypic SOC, the Ca2+-release-activated Ca2+ (CRAC) channel. New findings reveal a unique mechanism for channel activation, in which the CRAC channel and its sensor migrate independently to closely apposed sites of interaction in the ER and the plasma membrane.

  13. Dynamic wall shear stress measurements in a turbulent channel flow

    NASA Astrophysics Data System (ADS)

    Amili, Omid; Soria, Julio

    2010-11-01

    To quantify and understand the dynamics of near wall momentum transfer, high spatial resolution, time-resolved measurements of wall shear stress distribution are essential. In this study, a film-based shear stress sensor has been used to measure the time-resolved local wall shear stress distribution in a turbulent channel flow. Measurements have been undertaken in a turbulent channel flow at Reynolds numbers up to 130,000 based on the bulk velocity and channel height. The measured fluctuating wall shear stress distribution provides spatio-temporal information of the characteristics of near wall structures by detecting their footprints. The span-wise extent of the positive two-point correlation of the stream-wise shear stress fluctuations provides the average width in the order of 100 wall units for the near-wall coherent structures. An investigation of the topological features of the velocity gradient and rate of strain tensors enables us to show an intrinsic characteristic of the near wall flow, which follows a two-dimensional flow pattern.

  14. Dynamical coupled channels calculation of pion and omega meson production

    SciTech Connect

    Paris, Mark W.

    2009-02-15

    The dynamical coupled-channels approach developed at the Excited Baryon Analysis Center is extended to include the {omega}N channel to study {pi}- and {omega}-meson production induced by scattering pions and photons from the proton. Six intermediate channels, including {pi}N, {eta}N, {pi}{delta}, {sigma}N, {rho}N, and {omega}N, are employed to describe unpolarized and polarized data. Bare parameters in an effective hadronic Lagrangian are determined in a fit to the data for {pi}N{yields}{pi}N, {gamma}N{yields}{pi}N, {pi}{sup -}p{yields}{omega}n, and {gamma}p{yields}{omega}p reactions at center-of-mass energies from threshold to W<2.0 GeV. The T matrix determined in these fits is used to calculate the photon beam asymmetry for {omega}-meson production and the {omega}N{yields}{omega}N total cross section and {omega}N-scattering lengths. The calculated beam asymmetry is in good agreement with the observed in the range of energies near threshold to W < or approx. 2.0 GeV.

  15. Dynamic regulation of aquaporin-4 water channels in neurological disorders

    PubMed Central

    Hsu, Ying; Tran, Minh; Linninger, Andreas A.

    2015-01-01

    Aquaporin-4 water channels play a central role in brain water regulation in neurological disorders. Aquaporin-4 is abundantly expressed at the astroglial endfeet facing the cerebral vasculature and the pial membrane, and both its expression level and subcellular localization significantly influence brain water transport. However, measurements of aquaporin-4 levels in animal models of brain injury often report opposite trends of change at the injury core and the penumbra. Furthermore, aquaporin-4 channels play a beneficial role in brain water clearance in vasogenic edema, but a detrimental role in cytotoxic edema and exacerbate cell swelling. In light of current evidence, we still do not have a complete understanding of the role of aquaporin-4 in brain water transport. In this review, we propose that the regulatory mechanisms of aquaporin-4 at the transcriptional, translational, and post-translational levels jointly regulate water permeability in the short and long time scale after injury. Furthermore, in order to understand why aquaporin-4 channels play opposing roles in cytotoxic and vasogenic edema, we discuss experimental evidence on the dynamically changing osmotic gradients between blood, extracellular space, and the cytosol during the formation of cytotoxic and vasogenic edema. We conclude with an emerging picture of the distinct osmotic environments in cytotoxic and vasogenic edema, and propose that the directions of aquaporin-4-mediated water clearance in these two types of edema are distinct. The difference in water clearance pathways may provide an explanation for the conflicting observations of the roles of aquaporin-4 in edema resolution. PMID:26526878

  16. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    NASA Astrophysics Data System (ADS)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  17. Thermostats and thermostat strategies for molecular dynamics simulations of nanofluidics.

    PubMed

    Yong, Xin; Zhang, Lucy T

    2013-02-28

    The thermostats in molecular dynamics (MD) simulations of highly confined channel flow may have significant influences on the fidelity of transport phenomena. In this study, we exploit non-equilibrium MD simulations to generate Couette flows with different combinations of thermostat algorithms and strategies. We provide a comprehensive analysis on the effectiveness of three thermostat algorithms Nosé-Hoover chain (NHC), Langevin (LGV) and dissipative particle dynamics (DPD) when applied in three thermostat strategies, thermostating either walls (TW) or fluid (TF), and thermostating both the wall and fluid (TWTF). Our results of thermal and mechanical properties show that the TW strategy more closely resembles experimental conditions. The TF and TWTF systems also produce considerably similar behaviors in weakly sheared systems, but deviate the dynamics in strongly sheared systems due to the isothermal condition. The LGV and DPD thermostats used in the TF and TWTF systems provide vital ways to yield correct dynamics in coarse-grained systems by tuning the fluid transport coefficients. Using conventional NHC thermostat to thermostat fluid only produces correct thermal behaviors in weakly sheared systems, and breaks down due to significant thermal inhomogeneity in strongly sheared systems.

  18. Low dimensional molecular dynamics of water inside a carbon nanotube

    NASA Astrophysics Data System (ADS)

    Shiomi, Junichiro; Lin, Yuan; Amberg, Gustav; Maruyama, Shigeo

    2008-11-01

    While carbon nanotubes (CNTs) have attracted a number of researches as the key building blocks for nanotechnology, they have also caught attentions as ideal materials that realize quasi-one-dimensional channel environment, a key system in bioscience. Such materials stimulate studies in fluid dynamics under low dimensional confinement, which is restricted and departs significantly from that in three-dimension. The current study serves to explore such atomic scale dynamics by performing a series of molecular dynamics (MD) simulations on water confined in a CNT with a diameter of the order of 1 nm. The MD simulations have successfully probed the phase transition of a water cluster confined in a CNT to an ice-nanotube with anomalous diameter dependence. It has also been applied to investigate the possibility of transporting water through a CNT by a temperature gradient. In this study, we particularly highlight the dielectric properties of water confined inside a CNT. The confinement gives rise to strongly anisotropic dielectric relaxation, where the relaxation becomes faster and slower in the cross sectional and axial directions, respectively. The diameter dependences of the dielectric properties are discussed in connection with water dynamics and structures in quasi-one-dimension.

  19. A molecular dynamics simulation of the turbulent Couette minimal flow unit

    NASA Astrophysics Data System (ADS)

    Smith, E. R.

    2015-11-01

    A molecular dynamics simulation of planar Couette flow is presented for the minimal channel in which turbulence structures can be sustained. Evolution over a single breakdown and regeneration cycle is compared to computational fluid dynamics simulations. Qualitative similar structures are observed and turbulent statistics show excellent quantitative agreement. The molecular scale law of the wall is presented in which stick-slip molecular wall-fluid interactions replace the no-slip conditions. The impact of grid resolution is explored and the observed structures are seen to be dependent on averaging time and length scales. The kinetic energy spectra show that a range of scales are present in the molecular system and that spectral content is dependent on the grid resolution employed. The subgrid velocity of the molecules is studied using joint probability density functions, molecular trajectories, diffusion, and Lagrangian statistics. The importance of sub-grid scales, relevance of the Kolmogorov lengthscale, and implications of molecular turbulence are discussed.

  20. Planform dynamics of meandering channels based on Wavelet analysis

    NASA Astrophysics Data System (ADS)

    Abad, J. D.

    2009-12-01

    Meandering rivers migrate along the floodplain describing upstream-, laterally, and downstream-valley bend orientations. The prediction of these features is still unresolved, therefore not allowing their direct integration into the river restoration framework. Abad and Garcia (2008a, b) investigated experimentally the implications of bend orientation (upstream- and downstream-valley) on hydrodynamics and bed morphodynamics of periodic asymmetric meandering channels. Downstream-valley bends produce a more coherent secondary flow and higher erosional power near the outer bank. Therefore, downstream oriented bends might migrate much faster than upstream oriented bends. Based on digital information of meandering planform dynamics, spectral analysis (Fast Fourier Transform, FFT) and wavelet analysis are carried out to describe the planform dynamics of meandering channels. Additional relevant parameters and observations based on these metrics (dominant modes along the planform configuration, location of oriented bends along the valley centerline, change of migration rate along the valley, among others) are also discussed in the present work. This work is relevant for river restoration such as the development of design criteria of in-stream structures taking into consideration not only hydraulic and morphologic parameters but also the impact of such structures on stream ecosystem.

  1. Flame dynamics in a micro-channeled combustor

    SciTech Connect

    Hussain, Taaha; Balachandran, Ramanarayanan; Markides, Christos N.

    2015-01-22

    The increasing use of Micro-Electro-Mechanical Systems (MEMS) has generated a significant interest in combustion-based power generation technologies, as a replacement of traditional electrochemical batteries which are plagued by low energy densities, short operational lives and low power-to-size and power-to-weight ratios. Moreover, the versatility of integrated combustion-based systems provides added scope for combined heat and power generation. This paper describes a study into the dynamics of premixed flames in a micro-channeled combustor. The details of the design and the geometry of the combustor are presented in the work by Kariuki and Balachandran [1]. This work showed that there were different modes of operation (periodic, a-periodic and stable), and that in the periodic mode the flame accelerated towards the injection manifold after entering the channels. The current study investigates these flames further. We will show that the flame enters the channel and propagates towards the injection manifold as a planar flame for a short distance, after which the flame shape and propagation is found to be chaotic in the middle section of the channel. Finally, the flame quenches when it reaches the injector slots. The glow plug position in the exhaust side ignites another flame, and the process repeats. It is found that an increase in air flow rate results in a considerable increase in the length (and associated time) over which the planar flame travels once it has entered a micro-channel, and a significant decrease in the time between its conversion into a chaotic flame and its extinction. It is well known from the literature that inside small channels the flame propagation is strongly influenced by the flow conditions and thermal management. An increase of the combustor block temperature at high flow rates has little effect on the flame lengths and times, whereas at low flow rates the time over which the planar flame front can be observed decreases and the time of

  2. Flame dynamics in a micro-channeled combustor

    NASA Astrophysics Data System (ADS)

    Hussain, Taaha; Markides, Christos N.; Balachandran, Ramanarayanan

    2015-01-01

    The increasing use of Micro-Electro-Mechanical Systems (MEMS) has generated a significant interest in combustion-based power generation technologies, as a replacement of traditional electrochemical batteries which are plagued by low energy densities, short operational lives and low power-to-size and power-to-weight ratios. Moreover, the versatility of integrated combustion-based systems provides added scope for combined heat and power generation. This paper describes a study into the dynamics of premixed flames in a micro-channeled combustor. The details of the design and the geometry of the combustor are presented in the work by Kariuki and Balachandran [1]. This work showed that there were different modes of operation (periodic, a-periodic and stable), and that in the periodic mode the flame accelerated towards the injection manifold after entering the channels. The current study investigates these flames further. We will show that the flame enters the channel and propagates towards the injection manifold as a planar flame for a short distance, after which the flame shape and propagation is found to be chaotic in the middle section of the channel. Finally, the flame quenches when it reaches the injector slots. The glow plug position in the exhaust side ignites another flame, and the process repeats. It is found that an increase in air flow rate results in a considerable increase in the length (and associated time) over which the planar flame travels once it has entered a micro-channel, and a significant decrease in the time between its conversion into a chaotic flame and its extinction. It is well known from the literature that inside small channels the flame propagation is strongly influenced by the flow conditions and thermal management. An increase of the combustor block temperature at high flow rates has little effect on the flame lengths and times, whereas at low flow rates the time over which the planar flame front can be observed decreases and the time of

  3. Molecular mechanism of pharmacological activation of BK channels

    PubMed Central

    Gessner, Guido; Cui, Yong-Mei; Otani, Yuko; Ohwada, Tomohiko; Soom, Malle; Hoshi, Toshinori; Heinemann, Stefan H.

    2012-01-01

    Large-conductance voltage- and Ca2+-activated K+ (Slo1 BK) channels serve numerous cellular functions, and their dysregulation is implicated in various diseases. Drugs activating BK channels therefore bear substantial therapeutic potential, but their deployment has been hindered in part because the mode of action remains obscure. Here we provide mechanistic insight into how the dehydroabietic acid derivative Cym04 activates BK channels. As a representative of NS1619-like BK openers, Cym04 reversibly left-shifts the half-activation voltage of Slo1 BK channels. Using an established allosteric BK gating model, the Cym04 effect can be simulated by a shift of the voltage sensor and the ion conduction gate equilibria toward the activated and open state, respectively. BK activation by Cym04 occurs in a splice variant-specific manner; it does not occur in such Slo1 BK channels using an alternative neuronal exon 9, which codes for the linker connecting the transmembrane segment S6 and the cytosolic RCK1 domain—the S6/RCK linker. In addition, Cym04 does not affect Slo1 BK channels with a two-residue deletion within this linker. Mutagenesis and model-based gating analysis revealed that BK openers, such as Cym04 and NS1619 but not mallotoxin, activate BK channels by functionally interacting with the S6/RCK linker, mimicking site-specific shortening of this purported passive spring, which transmits force from the cytosolic gating ring structure to open the channel's gate. PMID:22331907

  4. Molecular Dynamics: New Frontier in Personalized Medicine.

    PubMed

    Sneha, P; Doss, C George Priya

    2016-01-01

    The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.

  5. Molecular Dynamics Simulations of Interface Failure

    NASA Astrophysics Data System (ADS)

    Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.

    2007-03-01

    The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.

  6. 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.

  7. Exchange frequency in replica exchange molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.

    2008-01-01

    The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.

  8. Exploring Hamiltonian dielectric solvent molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

    2014-09-01

    Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

  9. 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.

  10. Charge transport network dynamics in molecular aggregates

    SciTech Connect

    Jackson, Nicholas E.; Chen, Lin X.; Ratner, Mark A.

    2016-07-20

    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, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ~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.

  11. Charge transport network dynamics in molecular aggregates

    PubMed Central

    Jackson, Nicholas E.; Chen, Lin X.; Ratner, Mark A.

    2016-01-01

    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, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ∼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

  12. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.

    2016-10-01

    SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.

  13. Coarse-grained protein molecular dynamics simulations.

    PubMed

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-14

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  14. Coarse-grained protein molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-01

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  15. MDLab: a molecular dynamics simulation prototyping environment.

    PubMed

    Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A

    2010-05-01

    Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.

  16. 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.

  17. 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.

  18. Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation

    NASA Astrophysics Data System (ADS)

    Hung, Shih-Wei; Shiomi, Junichiro

    2015-11-01

    Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.

  19. 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

  20. Dynamics of energy distribution in three channel alpha helix protein based on Davydov’s ansatz

    SciTech Connect

    Ahmad, Faozan; Alatas, Husin

    2015-04-16

    An important aspect of many biological processes at molecular level is the transfer and storage mechanism of bioenergy released in the reaction of the hydrolysis of Adenosinetriphosphate (ATP) by biomacromolecule especially protein. Model of Soliton Davydov is a new break-through that could describe that mechanism. Here we have reformulated quantum mechanical the Davydov theory, using least action principle. Dynamical aspect of the model is analyzed by numerical calculation. We found two dynamical cases: the traveling and pinning soliton that we suggest they are related to the energy transfer and storage mechanism in the protein. Traveling and pinning soliton can be controlled by strength of coupling. In 3- channel approach, we found the breather phenomena in which its frequency is determined by interchannel coupling parameter.

  1. 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

  2. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  3. Connecting exact coherent states to turbulent dynamics in channel flow

    NASA Astrophysics Data System (ADS)

    Park, Jae Sung; Graham, Michael D.

    2015-11-01

    The discovery of nonlinear traveling wave solutions to the Navier-Stokes equations or exact coherent states has greatly advanced the understanding of the nature of turbulent shear flows. These solutions are unstable saddle points in state space, while the time evolution of a turbulent flow is a dynamical trajectory wandering around them. In this regard, it is of interest to investigate how closely the turbulent trajectories approach these invariant states. Here, we present connections between turbulent trajectories and one intriguing solution family in channel flow. A state space visualization of turbulent trajectories is presented in a three-dimensional space. The lifetime of the trajectories is well represented by closeness to two distinct solutions resembling in many ways the active and hibernating phases of minimal channel turbulence (Xi & Graham PRL 2010). The connections are then examined by comparing mean profiles and flow structures. More importantly, the connections are confirmed by calculating the L2 distance between the trajectories and the traveling waves. Lastly, paths of an intermittent bursting phenomenon are identified in state space and the relationship between bursting paths and the traveling waves or hibernating turbulence is further discussed. This work was supported by the Air Force Office of Scientific Research through grant FA9550-15-1-0062 (Flow Interactions and Control Program).

  4. A channel dynamics model for real-time flood forecasting

    USGS Publications Warehouse

    Hoos, A.B.; Koussis, A.D.; Beale, G.O.

    1989-01-01

    A new channel dynamics scheme ASPIRE (alternative system predictor in real time), designed specifically for real-time river flow forecasting, is introduced to reduce uncertainty in the forecast. ASPIRE is a storage routing model that limits the influence of catchment model forecast errors to the downstream station closest to the catchment. Comparisons with the Muskingum routing scheme in field tests suggest that the ASPIRE scheme can provide more accurate forecasts, probably because discharge observations are used to a maximum advantage and routing reaches (and model errors in each reach) are uncoupled. Using ASPIRE in conjunction with the Kalman filter did not improve forecast accuracy relative to a deterministic updating procedure. Theoretical analysis suggests that this is due to a large process noise to measurement noise ratio. -Authors

  5. Molecular analysis of a thylakoid K+channel

    SciTech Connect

    1999-09-10

    The work undertaken sought to use a novel probe to identify and clone plant ion (K) channels. It was also proposed that in vitro biochemical studies of cation transport across purified preparations of thylakoid membrane be employed to characterize a putative K channel in this membrane system. Over the last several years, an enormous data base of partially-sequenced mRNAs and numerous genomes (including those of plants) has evolved and provides a powerful alternative to this brute-force approach to identify and clone cDNAs encoding physiologically important membrane proteins such as channels. The utility of searching genetic databases for relevant sequences, in addition to the difficulty of working with membrane proteins, led to changes in research focus during the granting period. During the course of the funding period, work was finished up which documented the presence of a K channel in the thylakoid membrane and demonstrated that K fluxes through this channel were required for optimal photosynthetic activity, likely due to the requirement for charge balancing of proton flux.

  6. The molecular interactions of pyrethroid insecticides with insect and mammalian sodium channels.

    PubMed

    Vais, H; Williamson, M S; Devonshire, A L; Usherwood, P N

    2001-10-01

    Recent progress in the cloning of alpha (para) and beta (TipE) Na channel sub-units from Drosophila melanogaster (fruit fly) and Musca domestica (housefly) have facilitated functional expression studies of insect Na channels in Xenopus laevis oocytes, assayed by voltage clamp techniques. The effects of Type I and Type III pyrethroids on the biophysical properties of these channels are critically reviewed. Pyrethroid resistance mutations (termed kdr and super-kdr) that reduce the sensitivity of the insect Na channel to pyrethroids have been identified in a range of insect species. Some of these mutations (e.g. L1014F, M918T and T929I) have been incorporated into the para Na channel of Drosophila, either individually or in combination, to investigate their effects on the sensitivity of this channel to pyrethroids. The kdr mutation (L1014F) shifts the voltage dependence of both activation and steady-state inactivation by approximately 5 mV towards more positive potentials and facilitates Na channel inactivation. Incorporation of the super-kdr mutation (M918T) into the Drosophila Na channel also increases channel inactivation and causes a > 100-fold reduction in deltamethrin sensitivity. These effects are shared by T929I, an alternative mutation that confers super-kdr-like resistance. Parallel studies have been undertaken using the rat IIA Na channel to investigate the molecular basis for the low sensitivity of mammalian brain Na channels to pyrethroids. Rat IIA channels containing the mutation L1014F exhibit a shift in their mid-point potential for Na activation, but their overall sensitivity to permethrin remains similar to that of the wild-type rat channel (i.e. both are 1000-fold less sensitive than the wild-type insect channel). Mammalian neuronal Na channels have an isoleucine rather than a methionine at the position (874) corresponding to the super-kdr (M918) residue of the insect channel. Replacement of the isoleucine of the wild-type rat IIA Na channel with a

  7. Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A

    SciTech Connect

    Tara, Sylvia; Helms, Volkhard H.; Straatsma, TP; Mccammon, J Andrew A.

    1999-03-16

    Two molecular dynamics simulations were performed for a modeled complex of mouse acetylcholinesterase liganded with huperzine A (HupA). Analysis of these simulations shows that HupA shifts in the active site toward Tyr 337 and Phe 338, and that several residues in the active site area reach out to make hydrogen bonds with the inhibitor. Rapid fluctuations of the gorge width are observed, ranging from widths that allow substrate access to the active site, to pinched structures that do not allow access of molecules as small as water. Additional openings or channels to the active site are found. One opening is formed in the side wall of the active site gorge by residues Val 73, Asp 74, Thr 83, Glu 84, and Asn 87. Another opening is formed at the base of the gorge by residues Trp 86, Val 132, Glu 202, Gly 448, and Ile 451. Both of these openings have been observed separately in the Torpedo californica form of the enzyme. These channels could allow transport of waters and ions to and from the bulk solution.

  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. Channel Protein Engineering: A Novel Approach Towards the Molecular Dissection Determinants in Ligand-Regulated Channels

    DTIC Science & Technology

    1991-01-23

    also carried out on a tetrameric potassium channel (of the delayed rectifier type) and on a tetrameric calcium channel (of the dihydropyridine ...structurally related dihydropyridine enantiomers of BayK 8644 [ (+) - antagonist and (-) - agonist] may cause opposite actions. Binding sites for drugs are...interactions, simultaneously. We identified a potential binding site for the 1, 4- dihydropyridine located in the middle of the bundle and formed by a serine

  10. Molecular action of sulphonylureas on KATP channels: a real partnership between drugs and nucleotides

    PubMed Central

    de Wet, Heidi; Proks, Peter

    2015-01-01

    Sulphonylureas stimulate insulin secretion from pancreatic β-cells primarily by closing ATP-sensitive K+ channels in the β-cell plasma membrane. The mechanism of channel inhibition by these drugs is unusually complex. As direct inhibitors of channel activity, sulphonylureas act only as partial antagonists at therapeutic concentrations. However, they also exert an additional indirect inhibitory effect via modulation of nucleotide-dependent channel gating. In this review, we summarize current knowledge and recent advances in our understanding of the molecular mechanism of action of these drugs. PMID:26517901

  11. 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.

  12. Molecular Dynamics Simulations of Hypervelocity Impacts

    NASA Astrophysics Data System (ADS)

    Owens, Eli T.; Bachlechner, Martina E.

    2007-03-01

    Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.

  13. 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.

  14. 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.

  15. On the parallelization of molecular dynamics codes

    NASA Astrophysics Data System (ADS)

    Trabado, G. P.; Plata, O.; Zapata, E. L.

    2002-08-01

    Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code with message passing routines or using specific libraries intended for writing new MD programs. In this paper we propose a new library-based approach (DDLY) which supports parallelization of existing short-range MD sequential codes. The novelty of this approach is that it can directly handle the distribution of common data structures used in MD codes to represent data (arrays, Verlet lists, link cells), using domain decomposition. Thus, the insertion of run-time support for distribution and communication in a MD program does not imply significant changes to its structure. The method is simple, efficient and portable. It may be also used to extend existing parallel programming languages, such as HPF.

  16. Nanodrop contact angles from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim

    2016-11-01

    The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.

  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. Ion mobility analysis of molecular dynamics.

    PubMed

    Wyttenbach, Thomas; Pierson, Nicholas A; Clemmer, David E; Bowers, Michael T

    2014-01-01

    The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.

  19. Classical Molecular Dynamics Simulation of Nuclear Fuel

    SciTech Connect

    Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

    2015-10-10

    Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.

  20. 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

  1. Molecular Dynamics Simulation of a RNA Aptasensor.

    PubMed

    Ruan, Min; Seydou, Mahamadou; Noel, Vincent; Piro, Benoit; Maurel, François; Barbault, Florent

    2017-04-14

    Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.

  2. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

    PubMed Central

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-01-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6. PMID:27291418

  3. Molecular tectonics: tubular crystals with controllable channel size and orientation.

    PubMed

    Lin, Mei-Jin; Jouaiti, Abdelaziz; Pocic, David; Kyritsakas, Nathalie; Planeix, Jean-Marc; Hosseini, Mir Wais

    2010-01-07

    The combination of flexible neutral organic tectons based on two pyridines interconnected by a thioether or thioester type spacer with an inorganic ZnSiF(6) pillar leads to the formation of 2-D coordination networks and the packing of the latter generates crystals offering controllable tubular channels with imposed orientation along the pillar axis.

  4. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

    NASA Astrophysics Data System (ADS)

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-06-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6.

  5. Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations?

    PubMed

    Hub, Jochen S; Grubmüller, Helmut; de Groot, Bert L

    2009-01-01

    Aquaporins (AQPs) are a family of integral membrane proteins, which facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Molecular dynamics (MD) simulations contributed substantially to the understanding of the molecular mechanisms that underlie this remarkable efficiency and selectivity of aquaporin channels. This chapter reviews the current state of MD simulations of aquaporins and related aquaglyceroporins as well as the insights these simulations have provided. The mechanism of water permeation through AQPs and methods to determine channel permeabilities from simulations are described. Protons are strictly excluded from AQPs by a large electrostatic barrier and not by an interruption of the Grotthuss mechanism inside the pore. Both the protein's electric field and desolvation effects contribute to this barrier. Permeation of apolar gas molecules such as CO(2) through AQPs is accompanied by a large energetic barrier and thus can only be expected in membranes with a low intrinsic gas permeability. Additionally, the insights from simulations into the mechanism of glycerol permeation through the glycerol facilitator GlpF from E. coli are summarized. Finally, MD simulations are discussed that revealed that the aro-matic/arginine constriction region is generally the filter for uncharged solutes, and that AQP selectivity is controlled by a hydrophobic effect and steric restraints.

  6. Molecular dynamics modelling of radiation damage in zircon

    NASA Astrophysics Data System (ADS)

    Grechanovsky, A. E.

    2009-04-01

    Zircon (ZrSiO4) is among actinide-bearing phases which has been proposed as a crystalline confinement matrix for nuclear waste management, especially for weapon-grade plutonium and UO2 spent fuel in the USA. Zircon is also widely used in geochronology. But, with accumulating α-decay damage, zircon undergoes a radiation induced transition to an amorphous (or metamict) state. So, in the present work molecular dynamics simulations (MD simulations) of zircon structure have been performed to study radiation damage in zircon. In this technique, one simulates the propagation of an energetic particle in a system of atoms interacting via model potentials, by integrating the Newton equations of motion. Author has used version 3.09 of the DL_POLY molecular simulation package. Zircon structure containing 181944 atoms (19x19x21 unit cells) was equilibrated at 300 K for 10 ps, and one Zr atom (usually called the primary knock-on atom, PKA) was given a velocity corresponding to an implantation energy of about 20 keV. MD simulations were performed in the microcanonical ensemble that is under conditions of constant particle number, volume and energy. Results of the MD simulations show that the number of interstitials is equal to 840 atoms. This is very close (4000-5000 atoms for 70 keV recoil atom 234Th) to what is measured in the diffuse x-ray scattering and NMR experiments on amorphous metamict samples (damaged by natural irradiation) of geological age. It has been shown that the damaged structure contains several depleted regions with characteristic sized up to 2,5 nm after single event and up to 4,5 nm after three overlapping events. Furthermore, these events produce channels of depleted matter between the overlapping damaged regions. These channels provide a high-diffusivity path for radiogenic Pb (percolation effect). Loss of radiogenic Pb may result in to incorrect dating of rocks.

  7. 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.

  8. Molecular dynamics simulation in virus research

    PubMed Central

    Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori

    2012-01-01

    Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. PMID:22833741

  9. Molecular-dynamic study of liquid ethylenediamine

    NASA Astrophysics Data System (ADS)

    Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.

    2016-10-01

    Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.

  10. 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.

  11. 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.

  12. Internal coordinate molecular dynamics: a foundation for multiscale dynamics.

    PubMed

    Vaidehi, Nagarajan; Jain, Abhinandan

    2015-01-29

    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.

  13. 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

  14. Molecular determinants on the insect sodium channel for the specific action of type II pyrethroid insecticides

    SciTech Connect

    Du Yuzhe; Nomura, Yoshiko; Luo Ningguang; Liu Zhiqi; Lee, Jung-Eun; Khambay, Bhupinder; Dong Ke

    2009-01-15

    Pyrethroid insecticides are classified as type I or type II based on their distinct symptomology and effects on sodium channel gating. Structurally, type II pyrethroids possess an {alpha}-cyano group at the phenylbenzyl alcohol position, which is lacking in type I pyrethroids. Both type I and type II pyrethroids inhibit deactivation consequently prolonging the opening of sodium channels. However, type II pyrethroids inhibit the deactivation of sodium channels to a greater extent than type I pyrethroids inducing much slower decaying of tail currents upon repolarization. The molecular basis of a type II-specific action, however, is not known. Here we report the identification of a residue G{sup 1111} and two positively charged lysines immediately downstream of G{sup 1111} in the intracellular linker connecting domains II and III of the cockroach sodium channel that are specifically involved in the action of type II pyrethroids, but not in the action of type I pyrethroids. Deletion of G{sup 1111}, a consequence of alternative splicing, reduced the sodium channel sensitivity to type II pyrethroids, but had no effect on channel sensitivity to type I pyrethroids. Interestingly, charge neutralization or charge reversal of two positively charged lysines (Ks) downstream of G{sup 1111} had a similar effect. These results provide the molecular insight into the type II-specific interaction of pyrethroids with the sodium channel at the molecular level.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  16. Time-dependent molecular memory in single voltage-gated sodium channel.

    PubMed

    Nayak, Tapan K; Sikdar, S K

    2007-10-01

    Excitability in neurons is associated with firing of action potentials and requires the opening of voltage-gated sodium channels with membrane depolarization. Sustained membrane depolarization, as seen in pathophysiological conditions like epilepsy, can have profound implications on the biophysical properties of voltage-gated ion channels. Therefore, we sought to characterize the effect of sustained membrane depolarization on single voltage-gated Na+ channels. Single-channel activity was recorded in the cell-attached patch-clamp mode from the rNa(v)1.2 alpha channels expressed in CHO cells. Classical statistical analysis revealed complex nonlinear changes in channel dwell times and unitary conductance of single Na+ channels as a function of conditioning membrane depolarization. Signal processing tools like weighted wavelet Z (WWZ) and discrete Fourier transform analyses attributed a "pseudo-oscillatory" nature to the observed nonlinear variation in the kinetic parameters. Modeling studies using the hidden Markov model (HMM) illustrated significant changes in kinetic states and underlying state transition rate constants upon conditioning depolarization. Our results suggest that sustained membrane depolarization induces novel nonlinear properties in voltage-gated Na+ channels. Prolonged membrane depolarization also induced a "molecular memory" phenomenon, characterized by clusters of dwell time events and strong autocorrelation in the dwell time series similar to that reported recently for single enzyme molecules. The persistence of such molecular memory was found to be dependent on the duration of depolarization. Voltage-gated Na+ channel with the observed time-dependent nonlinear properties and the molecular memory phenomenon may determine the functional state of the channel and, in turn, the excitability of a neuron.

  17. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

    This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the

  18. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    DTIC Science & Technology

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  19. High-resolution polypeptide structure and dynamics in anisotropic environments: The gramicidin channel

    SciTech Connect

    Cross, T.A.; Lee, K.C.; Ketchem, R.R.; Hu, W.; Lazo, N.D.; Huo, S.

    1994-12-01

    To understand the details of macromolecular function, high-resolution structural and dynamic detail is essential. The polypeptide fold of the gramicidin channel has been effectively modeled for the past 20 years, yet the functional changes in conductance and channel lifetime associated with amino acid substitutions cannot be predicted. To accomplish this goal, high-resolution electrostatic modeling and the precise orientation of all dipoles are required. Furthermore, an enhanced knowledge of the complex molecular environment of this membrane-bound peptide is needed. An aqueous environment is relatively uniform and achiral. The membrane environment is very heterogenous and chiral. A knowledge of the interactions, specific and nonspecific, between peptide and lipid will aid in developing a better understanding of this environment. To accomplish this goal, it is necessary to study the peptide in an extended lipid bilayer, rather than in a vesicular or micellar form. These latter environments are likely to possess increased dynamics, increased water penetration, and distorted interactions between the polypeptide and membrane surface. To perform NMR studies on bilayer bound peptides, solid state NMR methods are required, and for specific site information, isotopic labels are incorporated using solid phase peptide synthesis.

  20. Brownian dynamics study of a multiply-occupied cation channel: application to understanding permeation in potassium channels.

    PubMed Central

    Bek, S; Jakobsson, E

    1994-01-01

    The behavior of a multiply-occupied cation-selective channel has been computed by Brownian dynamics. The length, cross-section, ion-ion repulsion force, and ionic mobility within the channel are all estimated from data and physical reasoning. The only free parameter is a partition energy at the mouth of the channel, defining the free energy of an ion in the channel compared to the bath. It is presumed that this partition energy is associated with the energetics of exchanging a bulk hydration environment for a channel hydration environment. Varying the partition energy alone, keeping all other parameters fixed, gives approximately the full range of magnitudes of single channel conductances seen experimentally for K channels. Setting the partition energy at -11 kT makes the computed channel look similar to a squid axon K channel with respect to magnitude of conductance, shape of the I-V curve, non-unity of Ussing flux ratio exponents, decrease of current and increase of conductance with extracellular ion accumulation, and saturation at high ion concentration in the bathing solution. The model includes no preferred binding sites (local free energy minima) for ions in the channel. Therefore it follows that none of the above-mentioned properties of K channels are strong evidence for the existence of such sites. The model does not show supersaturation of current at very high bathing concentrations nor any pronounced voltage-dependence of the Ussing flux ratio exponent, suggesting that these features would require additional details not included in the model presented herein. PMID:7518703

  1. Molecular dynamics and spectra. II. Diatomic Raman

    NASA Astrophysics Data System (ADS)

    Berens, Peter H.; White, Steven R.; Wilson, Kent R.

    1981-07-01

    This paper and paper I in this series [P.H. Berens and K.R. Wilison, J. Chem. Phys. 74, 4872 (1981)] indicate that infrared and Raman rotational and fundamental vibrational-rotational spectra of dense systems (high pressure gases, liquids, and solids) are essentially classical, in that they can be computed and understood from a basically classical mechanical viewpoint, with some caveats for features in which anharmonicity is important, such as the detailed shape of Q branches. It is demonstrated here, using the diatomic case as an example, that ordinary, i.e., nonresonant, Raman band contours can be computed from classical mechanics plus simple quantum corrections. Classical versions of molecular dynamics, linear response theory, and ensemble averaging, followed by straightforward quantum corrections, are used to compute the pure rotational and fundamental vibration-rotational Raman band contours of N2 for the gas phase and for solutions of N2 in different densities of gas phase Ar and in liquid Ar. The evolution is seen from multiple peaked line shapes characteristic of free rotation in the gas phase to single peaks characteristic of hindered rotation in the liquid phase. Comparison is made with quantum and correspondence principle classical gas phase spectral calculations and with experimental measurements for pure N2 and N2 in liquid Ar. Three advantages are pointed out for a classical approach to infrared and Raman spectra. First, a classical approach can be used to compute the spectra of complex molecular systems, e.g., of large molecules, clusters, liquids, solutions, and solids. Second, this classical approach can be extended to compute the spectra of nonequilibrium and time-dependent systems, e.g., infrared and Raman spectra during the course of chemical reactions. Third, a classical viewpoint allows experimental infrared and Raman spectra to be understood and interpreted in terms of atomic motions with the considerable aid of classical models and of our

  2. How Dynamic Visualization Technology Can Support Molecular Reasoning

    ERIC Educational Resources Information Center

    Levy, Dalit

    2013-01-01

    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…

  3. Nonlinear Resonance Artifacts in Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Schlick, Tamar; Mandziuk, Margaret; Skeel, Robert D.; Srinivas, K.

    1998-02-01

    The intriguing phenomenon of resonance, a pronounced integrator-induced corruption of a system's dynamics, is examined for simple molecular systems subject to the classical equations of motion. This source of timestep limitation is not well appreciated in general, and certainly analyses of resonance patterns have been few in connection to biomolecular dynamics. Yet resonances are present in the commonly used Verlet integrator, in symplectic implicit schemes, and also limit the scope of current multiple-timestep methods that are formulated as symplectic and reversible. The only general remedy to date has been to reduce the timestep. For this purpose, we derive method-dependent timestep thresholds (e.g., Tables 1 and 2) that serve as useful guidelines in practice for biomolecular simulations. We also devise closely related symplectic implicit schemes for which the limitation on the discretization stepsize is much less severe. Specifically, we design methods to remove third-order, or both the third- and fourth-order, resonances. These severe low-order resonances can lead to instability or very large energies. Our tests on two simple molecular problems (Morse and Lennard-Jones potentials), as well as a 22-atom molecule, N-acetylalanyl-N '-methylamide, confirm this prediction; our methods can delay resonances so that they occur only at larger timesteps (EW method) or are essentially removed (LIM2 method). Although stable for large timesteps by this approach, trajectories show large energy fluctuations, perhaps due to the coupling with other factors that induce instability in complex nonlinear systems. Thus, the methods developed here may be more useful for conformational sampling of biomolecular structures. The analysis presented here for the blocked alanine model emphasizes that one-dimensional analysis of resonances can be applied to a more complex, multimode system to analyze resonance behavior, but that resonance due to frequency coupling is more complex to pinpoint

  4. Nanoscale deicing by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

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

  5. Molecular dynamics simulations of ballistic He penetration into W fuzz

    NASA Astrophysics Data System (ADS)

    Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

    2016-12-01

    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers than He diffusion through fuzz nanorods. Instead of trying to grow a fuzz layer starting from a flat piece of bulk W, a new approach of creating a fully formed fuzz structure 0.43 µm thick out of ellipsoidal pieces of W is employed. Lack of detailed experimental knowledge of the 3D structure of fuzz is dealt with by simulating He bombardment on five different structures of 15 vol% W and determining the variation in He penetration for each case. The results show that by far the most important factor determining He penetration is the amount of open channels through which He ions can travel unimpeded. For a more or less even W density distribution He penetration into fuzz falls off exponentially with distance and can thus be described by a ‘half depth’. In a 15 vol% fuzz structure, the half depth can reach 0.18 µm. In the far sparser fuzz structures that were recently reported, the half depth might be 1 µm or more. This means that ballistic He penetration offers a more likely scenario than He diffusion through nanorods for how He moves through fuzz and may provide an adequate explanation for how He penetrates through the thickest fuzz layers reported so far. Furthermore, the exponential decrease in penetration with depth would follow a logarithmic dependence on fluence which is compatible with experiments. A comparison of these results and molecular dynamics calculations carried out in the recoil interaction approximation shows that results for W fuzz are qualitatively very different from conventional stopping power calculations on W with a similarly low but homogeneous density distribution.

  6. Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations.

    PubMed

    Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

    2012-02-27

    Molecular channel exploration perseveres to be the prominent solution for eliciting structure and accessibility of active site and other internal spaces of macromolecules. The volume and silhouette characterization of these channels provides answers for the issues of substrate access and ligand swapping between the obscured active site and the exterior of the protein. Histone deacetylases (HDACs) are metal-dependent enzymes that are involved in the cell growth, cell cycle regulation, and progression, and their deregulations have been linked with different types of cancers. Hence HDACs, especially the class I family, are widely recognized as the important cancer targets, and the characterizations of their structures and functions have been of special interest in cancer drug discovery. The class I HDACs are known to possess two different protein channels, an 11 Å and a 14 Å (named channels A and B1, respectively), of which the former is a ligand or substrate occupying tunnel that leads to the buried active site zinc ion and the latter is speculated to be involved in product release. In this work, we have carried out random acceleration molecular dynamics (RAMD) simulations coupled with the classical molecular dynamics to explore the release of the ligand, N-(2-aminophenyl) benzamide (LLX) from the active sites of the recently solved X-ray crystal structure of HDAC2 and the computationally modeled HDAC1 proteins. The RAMD simulations identified significant structural and dynamic features of the HDAC channels, especially the key 'gate-keeping' amino acid residues that control these channels and the ligand release events. Further, this study identified a novel and unique channel B2, a subchannel from channel B1, in the HDAC1 protein structure. The roles of water molecules in the LLX release from the HDAC1 and HDAC2 enzymes are also discussed. Such structural and dynamic properties of the HDAC protein channels that govern the ligand escape reactions will provide

  7. Superelevation and overspill control secondary flow dynamics in submarine channels

    NASA Astrophysics Data System (ADS)

    Dorrell, R. M.; Darby, S. E.; Peakall, J.; Sumner, E. J.; Parsons, D. R.; Wynn, R. B.

    2013-08-01

    In subaerial and submarine meander bends, fluid flow travels downstream in a helical spiral, the structure of which is determined by centrifugal, hydrostatic, baroclinic, and Coriolis forces that together balance frictional stresses generated by the flow. The sense of rotation of this helical flow, and in particular, whether the near bed flow is directed toward the inner bank, e.g., "river-normal," or outer bank, e.g., "river-reversed," is crucial to the morphodynamic evolution of the channel. However, in recent years, there has been a debate over the river-normal or river-reversed nature of submarine flows. Herein, we develop a novel three-dimensional closure of secondary flow dynamics, incorporating downstream convective material transport, to cast new light on this debate. Specifically, we show that the presence of net radial material transport, arising from flow superelevation and overspill, exerts a key control on the near bed orientation of secondary flow in submarine meanders. Our analysis implies that river-reversed flows are likely to be much more prevalent throughout submarine-canyon fan systems than prior studies have indicated.

  8. Dynamics of capillary transport in semi-solid channels.

    PubMed

    Andersson, Johanna; Ström, Anna; Gebäck, Tobias; Larsson, Anette

    2017-02-08

    Capillary action has been described by Lucas and Washburn and extensively studied experimentally in hard materials, but few studies have examined capillary action in soft materials such as hydrogels. In tissue engineering, cells or dispersions must be often distributed within a hydrogel via microporous paths. Capillary action is one way to disperse such substances. Here, we examine the dynamics of capillary action in a model system of straight capillaries in two hydrogels. The channels had a circular cross-section in the micrometer size range (180-630 μm). The distance travelled over time was recorded and compared with the predictions of Lucas and Washburn. Besides water, we used a sucrose solution and a hydroxyethyl cellulose solution, both with viscosities slightly higher than that of water. The results showed that the distance travelled is proportional to the square root of time, , and that larger capillaries and lower viscosities result, as expected, in faster speeds. However, the absolute experimental values display large discrepancies from the predictions. We demonstrate that several possible reasons for these discrepancies can be ruled out and we describe a novel hypothesis for the cause of the retarded meniscus movement.

  9. Statistical coarse-graining of molecular dynamics into peridynamics.

    SciTech Connect

    Silling, Stewart Andrew; Lehoucq, Richard B.

    2007-10-01

    This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.

  10. Multimillion atom molecular dynamics simulations of glasses and ceramic materials

    NASA Astrophysics Data System (ADS)

    Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro

    1999-11-01

    Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed.

  11. Molecular Information of charybdotoxin blockade in the large conductance calcium-activated potassium channel.

    PubMed

    Qiu, Su; Yi, Hong; Liu, Hui; Cao, Zhijian; Wu, Yingliang; Li, Wenxin

    2009-07-01

    The scorpion toxin, charybdotoxin (ChTX), is the first identified peptide inhibitor for the large-conductance Ca2+ and voltage-dependent K+ (BK) channel, and the chemical information of the interaction between ChTX and BK channel remains unclear today. Using combined computational methods, we obtained a ChTX-BK complex structure model, which correlated well with the mutagenesis data. In this complex, ChTX mainly used its beta-sheet domains to associate the BK channel with a conserved pore-blocking Lys27. Another crucial Tyr36 residue of ChTX lied over the loop connecting selectivity filter and S6 helix of BK channel, forming a hydrogen bond with Gly291 of BK channel. Besides, the unique turret region of BK channel was found to be far away from bound ChTX, which could explain the fact that many BK channel blockers show less selectivity over Kv channels. Together, all these information is helpful to reveal the diverse interactions between scorpion toxins and potassium channels and can accelerate the molecular engineering of specific inhibitor design.

  12. Ion channels or aquaporins as novel molecular targets in gastric cancer.

    PubMed

    Xia, Jianling; Wang, Hongqiang; Li, Shi; Wu, Qinghui; Sun, Li; Huang, Hongxiang; Zeng, Ming

    2017-03-06

    Gastric cancer (GC) is a common disease with few effective treatment choices and poor prognosis, and has the second-highest mortality rates among all cancers worldwide. Dysregulation and/or malfunction of ion channels or aquaporins (AQPs) are common in various human cancers. Furthermore, ion channels are involved in numerous important aspects of the tumor aggressive phonotype, such as proliferation, cell cycle, apoptosis, motility, migration, and invasion. Indeed, by localizing in the plasma membrane, ion channels or AQPs can sense and respond to extracellular environment changes; thus, they play a crucial role in cell signaling and cancer progression. These findings have expanded a new area of pharmaceutical exploration for various types of cancer, including GC. The involvement of multiple ion channels, such as voltage-gated potassium and sodium channels, intracellular chloride channels, 'transient receptor potential' channels, and AQPs, which have been shown to facilitate the pathogenesis of other tumors, also plays a role in GC. In this review, an overview of ion channel and aquaporin expression and function in carcinogenesis of GC is presented. Studies of ion channels or AQPs will advance our understanding of the molecular genesis of GC and may identify novel and effective targets for the clinical application of GC.

  13. Dynamical Systems and Control Theory Inspired by Molecular Biology

    DTIC Science & Technology

    2014-10-02

    AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247...is to develop new concepts, theory, and algorithms for control and signal processing using ideas inspired by molecular systems biology. Cell biology

  14. Molecular Simulations of Shear-Induced Dynamics in Nitromethane

    DTIC Science & Technology

    2016-09-01

    the shear response of single-crystal and bicrystal nitromethane (NM) are simulated using molecular dynamics simulations. The atomic interactions are...compressed to 28 GPa and then sheared, Raman studies show that the decomposition is sudden and explosive.5 In addition, structural modifications are...Molecular dynamics simulations are performed using the LAMMPS (Large-scale Atomic /Molecular Massively Parallel Simulator) simulation package.9 The

  15. Molecular mechanism of voltage sensor movements in a potassium channel.

    PubMed

    Elliott, David J S; Neale, Edward J; Aziz, Qadeer; Dunham, James P; Munsey, Tim S; Hunter, Malcolm; Sivaprasadarao, Asipu

    2004-12-08

    Voltage-gated potassium channels are six-transmembrane (S1-S6) proteins that form a central pore domain (4 x S5-S6) surrounded by four voltage sensor domains (S1-S4), which detect changes in membrane voltage and control pore opening. Upon depolarization, the S4 segments move outward carrying charged residues across the membrane field, thereby leading to the opening of the pore. The mechanism of S4 motion is controversial. We have investigated how S4 moves relative to the pore domain in the prototypical Shaker potassium channel. We introduced pairs of cysteines, one in S4 and the other in S5, and examined proximity changes between each pair of cysteines during activation, using Cd2+ and copper-phenanthroline, which crosslink the cysteines with metal and disulphide bridges, respectively. Modelling of the results suggests a novel mechanism: in the resting state, the top of the S3b-S4 voltage sensor paddle lies close to the top of S5 of the adjacent subunit, but moves towards the top of S5 of its own subunit during depolarization--this motion is accompanied by a reorientation of S4 charges to the extracellular phase.

  16. Dynamics, flexibility, and allostery in molecular chaperonins.

    PubMed

    Skjærven, Lars; Cuellar, Jorge; Martinez, Aurora; Valpuesta, José María

    2015-09-14

    The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements.

  17. 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.

  18. Fundamental frequency from classical molecular dynamics.

    PubMed

    Yamada, Tomonori; Aida, Misako

    2015-02-07

    We give a theoretical validation for calculating fundamental frequencies of a molecule from classical molecular dynamics (MD) when its anharmonicity is small enough to be treated by perturbation theory. We specifically give concrete answers to the following questions: (1) What is the appropriate initial condition of classical MD to calculate the fundamental frequency? (2) From that condition, how accurately can we extract fundamental frequencies of a molecule? (3) What is the benefit of using ab initio MD for frequency calculations? Our analytical approaches to those questions are classical and quantum normal form theories. As numerical examples we perform two types of MD to calculate fundamental frequencies of H2O with MP2/aug-cc-pVTZ: one is based on the quartic force field and the other one is direct ab initio MD, where the potential energies and the gradients are calculated on the fly. From those calculations, we show comparisons of the frequencies from MD with the post vibrational self-consistent field calculations, second- and fourth-order perturbation theories, and experiments. We also apply direct ab initio MD to frequency calculations of C-H vibrational modes of tetracene and naphthalene. We conclude that MD can give the same accuracy in fundamental frequency calculation as second-order perturbation theory but the computational cost is lower for large molecules.

  19. Molecular Dynamics Simulations of Ferroelectric Phase Transitions

    NASA Astrophysics Data System (ADS)

    Yu, Rici; Krakauer, Henry

    1997-03-01

    Based on an analysis of the wavevector dependence of the lattice instabilities in KNbO_3, we proposed a real-space chain-like instability and a scenario of sequential freezing out or onset of coherence of these instabilities, which qualitatively explains the sequence of observed temperature-dependent ferroelectric phases.(R. Yu and H. Krakauer, Phys. Rev. Lett. 74), 4067 (1995). We suggested that this chain-like instability should also be found in BaTiO_3, and this has been subsequently confirmed by Ghosez et al.(P. Ghosez et al.), Proc. 4th Williamsburg Workshop on First-Principles Calculations for Ferroelectrics, to be published We will present molecular dynamics simulations on BaTiO_3, using effective Hamiltonians constructed from first-principles calculations,(W. Zhong, D. Vanderbilt, and K. M. Rabe, Phys. Rev. Lett. 73), 1861 (1994). that reproduce the essential features of diffuse x-ray scattering measurements in the cubic, tetragonal, orthorhombic, and rhombohedral phases. The good agreement supports the interpretation of real-space chain-formation. Simulations for KNbO3 may also be reported.

  20. Direct anharmonic correction method by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang

    2017-04-01

    The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.

  1. Integrating influenza antigenic dynamics with molecular evolution

    PubMed Central

    Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

    2014-01-01

    Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547

  2. Molecular dynamics simulation of fractal aggregate diffusion

    NASA Astrophysics Data System (ADS)

    Pranami, Gaurav; Lamm, Monica H.; Vigil, R. Dennis

    2010-11-01

    The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)10.1088/0305-4470/27/9/012] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D) , but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the aggregate mass and fractal dimension. Using this result, it is possible to compute infinite dilution diffusion coefficients (Do) for aggregates of arbitrary size and fractal dimension, and it was found that Do∝Np-1/df , as is often assumed by investigators simulating Brownian aggregation of fractal aggregates. The ratio of hydrodynamic radius to radius of gyration is computed and shown to be independent of mass for aggregates of fixed fractal dimension, thus enabling an estimate of the diffusion coefficient for a fractal aggregate based on its radius of gyration.

  3. 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.

  4. Molecular Dynamics Study of Helicobacter pylori Urease.

    PubMed

    Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M

    2014-05-13

    Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

  5. The Dynamic Behavior of the P2X4 Ion Channel in the Closed Conformation.

    PubMed

    Pierdominici-Sottile, Gustavo; Moffatt, Luciano; Palma, Juliana

    2016-12-20

    We present the results of a detailed molecular dynamics study of the closed form of the P2X4 receptor. The fluctuations observed in the simulations were compared with the changes that occur in the transition from the closed to the open structure. To get further insight on the opening mechanism, the actual displacements were decomposed into interchain motions and intrachain deformations. This analysis revealed that the iris-like expansion of the transmembrane helices mainly results from interchain motions that already take place in the closed conformation. However, these movements cannot reach the amplitude required for the opening of the channel because they are impeded by interactions occurring around the ATP binding pocket. This suggests that the union of ATP produces distortions in the chains that eliminate the restrictions on the interchain displacements, leading to the opening of the pore.

  6. Computer simulations of channel meandering and the formation of point bars: Linking channel dynamics to the preserved stratigraphy

    NASA Astrophysics Data System (ADS)

    Sun, T.; Covault, J. A.; Pyrcz, M.; Sullivan, M.

    2012-12-01

    Meandering rivers are probably one of the most recognizable geomorphic features on earth. As they meander across alluvial and delta plains, channels migrate laterally and develop point bars, splays, levees and other geomorphic and sedimentary features that compose substantial portions of the fill within many sedimentary basins. These basins can include hydrocarbon producing fields. Therefore, a good understanding of the processes of meandering channels and their associated deposits is critical for exploiting these reservoirs in the subsurface. In the past couple of decades, significant progress has been made in our understanding of the morphodynamics of channel meandering. Basic fluid dynamics and sediment transport (Ikeda and Parker, 1981; Howard, 1992) has shown that many characteristic features of meandering rivers, such as the meandering wavelength, growth rate and downstream migration rate, can be predicted quantitatively. As a result, a number of variations and improvement of the theory have emerged (e.g., Blondeaux and Seminara, 1985; Parker and Andrews, 1985, 1986; and Sun et al., 2001a, b).The main improvements include the recognition of so called "bar-bend" interactions, where the development of bars on the channel bed and their interactions with the channel bend is recognized as a primary cause for meandering channels to develop greater complexity than the classic goose-neck meander bend shapes, such as compound bend. Recently, Sun and others have shown that the spatial patterns of width variations in meandering channels can be explained by an extrinsic periodic flow variations coupled with the intrinsic bend instability dynamics. In contrast to the significant improvement of our understanding of channel meandering, little work has been done to link the geomorphic features of meandering channels to the geometry and heterogeneity of the deposits they form and ultimately preserves. A computer simulation model based on the work of Sun and others (1996, 2001

  7. Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies

    PubMed Central

    2013-01-01

    Background PQS (PseudomonasQuinolone Signal) and its precursor HHQ are signal molecules of the P. aeruginosa quorum sensing system. They explicate their role in mammalian pathogenicity by binding to the receptor PqsR that induces virulence factor production and biofilm formation. The enzyme PqsD catalyses the biosynthesis of HHQ. Results Enzyme kinetic analysis and surface plasmon resonance (SPR) biosensor experiments were used to determine mechanism and substrate order of the biosynthesis. Comparative analysis led to the identification of domains involved in functionality of PqsD. A kinetic cycle was set up and molecular dynamics (MD) simulations were used to study the molecular bases of the kinetics of PqsD. Trajectory analysis, pocket volume measurements, binding energy estimations and decompositions ensured insights into the binding mode of the substrates anthraniloyl-CoA and β-ketodecanoic acid. Conclusions Enzyme kinetics and SPR experiments hint at a ping-pong mechanism for PqsD with ACoA as first substrate. Trajectory analysis of different PqsD complexes evidenced ligand-dependent induced-fit motions affecting the modified ACoA funnel access to the exposure of a secondary channel. A tunnel-network is formed in which Ser317 plays an important role by binding to both substrates. Mutagenesis experiments resulting in the inactive S317F mutant confirmed the importance of this residue. Two binding modes for β-ketodecanoic acid were identified with distinct catalytic mechanism preferences. PMID:23916145

  8. Diffusion, molecular separation, and drug delivery from lipid mesophases with tunable water channels.

    PubMed

    Negrini, Renata; Mezzenga, Raffaele

    2012-11-27

    Lyotropic liquid crystals characterized by a bicontinuous cubic phase (BCP) have a structure characterized by interpenetrated water channels following triply periodic minimal surfaces, which can be stable in excess water conditions and thus suitable in a multitude of applications. The control of the water channels size in these systems has a direct impact on their use for drug delivery, crystallization, and membrane separation processes. In this work we carry out systematic diffusion studies to show how the control on the water channel dimensions directly correlates with the release and separation performance of bicontinuous cubic phases. Specifically, we tune the water channels diameter of the monolinolein/water system by adding different amounts of sucrose stearate, which, having hydration-enhancing properties, can shift the boundaries of the phase diagram. We then design a model bicontinuous cubic phase lipidic membrane of the Im3m space group, having a sugar ester to monolinolein ratio of 20%, and we follow the diffusion within its water channels, by using molecules that differ systematically in size and molecular conformation, and we demonstrate, for each class of molecules, a diffusion-enhanced process upon increase of the water channel diameter. Finally, we also show the ability of the bicontinuous cubic phase to efficiently and selectively separate nanoparticles of a target size, by choosing an amount of sucrose stearate for which the water channel diameter and the nanoparticle dimensions match, demonstrating the possible use of these systems as filtering membranes of tunable molecular cutoff.

  9. Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis

    PubMed Central

    Hamacher, Kay; Greiner, Timo; Ogata, Hiroyuki; Van Etten, James L.; Gebhardt, Manuela; Villarreal, Luis P.; Cosentino, Cristian; Moroni, Anna; Thiel, Gerhard

    2012-01-01

    Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K+ channels. To determine if these viral K+ channels are the product of molecular piracy from their hosts, we compared the sequences of the K+ channel pore modules from seven phycodnaviruses to the K+ channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K+ channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K+ channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K+ channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K+ channels in algae and perhaps even all cellular organisms. PMID:22685610

  10. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

    PubMed

    Hamacher, Kay; Greiner, Timo; Ogata, Hiroyuki; Van Etten, James L; Gebhardt, Manuela; Villarreal, Luis P; Cosentino, Cristian; Moroni, Anna; Thiel, Gerhard

    2012-01-01

    Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

  11. Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs)

    PubMed Central

    Dreyer, Ingo; Gomez-Porras, Judith Lucia; Riaño-Pachón, Diego Mauricio; Hedrich, Rainer; Geiger, Dietmar

    2012-01-01

    Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general. PMID:23226151

  12. Ultrafast Molecular Dynamics Studied with Vacuum Ultraviolet Pulses

    NASA Astrophysics Data System (ADS)

    Wright, Travis William

    Studying the ultrafast dynamics of small molecules can serve as the first step in understanding the dynamics in larger chemically and biologically relevant molecules. To make direct comparisons with existing computational techniques, the photons used in pump-probe spectroscopy must make perturbative transitions between the electronic states of isolated small molecules. In this dissertation experimental investigations of ultrafast dynamics in electronic excitations of neutral ethylene and carbon dioxide are discussed. These experiments are performed using VUV/XUV femtosecond pulses as pump and probe. To make photons with sufficient energy for single photon transitions, VUV and XUV light is generated by high harmonic generation (HHG) using a high pulse energy (≈30--40 mJ) Ti:sapphire femtosecond laser. Sufficient flux must be generated to enable splitting of the HHG light into pump and probe arms. The system produces >1010 photons per shot, corresponding to nearly 10 MW of peak power in the XUV. Using a high flux of high energy photons creates a unique set of challenges when designing a detector capable of performing pump-probe experiments. A velocity map imaging (VMI) detector has been designed to address these challenges, and has become a successful tool facilitating studies into molecular dynamics that were not possible before its implementation. The emphasis on using high energy, single photon transitions allowed theoretical calculations to be directly compared to experimental yields for the first time. This comparison resolved a long standing issue in the excited state lifetime of ethylene, and provided a confirmation of the branching ratio between the two nonadiabatic relaxation pathways that return ethylene back to its ground state from the pi*. The participation of the 3s Rydberg state has also been measured by collecting the time resolved photoelectron spectrum during the dynamics on ethylene's pi* excited state, confirming calculations predicting the

  13. Molecular biology and biophysical properties of ion channel gating pores.

    PubMed

    Moreau, Adrien; Gosselin-Badaroudine, Pascal; Chahine, Mohamed

    2014-11-01

    The voltage sensitive domain (VSD) is a pivotal structure of voltage-gated ion channels (VGICs) and plays an essential role in the generation of electrochemical signals by neurons, striated muscle cells, and endocrine cells. The VSD is not unique to VGICs. Recent studies have shown that a VSD regulates a phosphatase. Similarly, Hv1, a voltage-sensitive protein that lacks an apparent pore domain, is a self-contained voltage sensor that operates as an H⁺ channel. VSDs are formed by four transmembrane helices (S1-S4). The S4 helix is positively charged due to the presence of arginine and lysine residues. It is surrounded by two water crevices that extend into the membrane from both the extracellular and intracellular milieus. A hydrophobic septum disrupts communication between these water crevices thus preventing the permeation of ions. The septum is maintained by interactions between the charged residues of the S4 segment and the gating charge transfer center. Mutating the charged residue of the S4 segment allows the water crevices to communicate and generate gating pore or omega pore. Gating pore currents have been reported to underlie several neuronal and striated muscle channelopathies. Depending on which charged residue on the S4 segment is mutated, gating pores are permeant either at depolarized or hyperpolarized voltages. Gating pores are cation selective and seem to converge toward Eisenmann's first or second selectivity sequences. Most gating pores are blocked by guanidine derivatives as well as trivalent and quadrivalent cations. Gating pores can be used to study the movement of the voltage sensor and could serve as targets for novel small therapeutic molecules.

  14. 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.

  15. STRUCTURE AND DYNAMICS OF QUIESCENT FILAMENT CHANNELS OBSERVED BY HINODE/XRT AND STEREO/EUVI

    SciTech Connect

    Su Yingna; Van Ballegooijen, Adriaan; Golub, Leon

    2010-09-20

    We present a study of the structure and dynamics of quiescent filament channels observed by Hinode/XRT and STEREO/EUVI at the solar minimum 23/24 from 2006 November to 2008 December. For 12 channels identified on the solar disk (Group I channels), we find that the morphology of the structure on the two sides of the channel is asymmetric in both X-rays and EUV: the eastern side has curved features while the western side has straight features. We interpret the results in terms of a magnetic flux rope model. The asymmetry in the morphology is due to the variation in axial flux of the flux rope along the channel, which causes the field lines from one polarity to turn into the flux rope (curved feature), while the field lines from the other polarity are connected to very distant sources (straight). For most of the 68 channels identified by cavities at the east and west limbs (Group II channels), the asymmetry cannot be clearly identified, which is likely due to the fact that the axial flux may be relatively constant along such channels. Corresponding cavities are identified only for 5 of the 12 Group I channels, while Group II channels are identified for all of the 68 cavity pairs. The studied filament channels are often observed as dark channels in X-rays and EUV. Sheared loops within Group I channels are often seen in X-rays, but are rarely seen in Group II channels as shown in the X-ray Telescope daily synoptic observations. A survey of the dynamics of studied filament channels shows that filament eruptions occur at an average rate of 1.4 filament eruptions per channel per solar rotation.

  16. Role of chaos in quantum communication through a dynamical dephasing channel

    SciTech Connect

    Barreto Lemos, Gabriela; Benenti, Giuliano

    2010-06-15

    In this article we treat the subject of chaotic environments with few degrees of freedom in quantum communication by investigating a conservative dynamical map as a model of a dephasing quantum channel. When the channel's dynamics is chaotic, we investigate the model's semi-classical limit and show that the entropy exchange grows at a constant rate which depends on a single parameter (the interaction strength), analogous to stochastic models of dephasing channels. We analyze memory effects in the channel and present strong physical arguments to support that the present model is forgetful in the chaotic regime while memory effects in general cannot be ignored when channel dynamics is regular. In order to render the nonchaotic channel forgetful, it becomes necessary to apply a reset to the channel and this reset can efficiently be modeled by application of a chaotic map. We may then refer to encoding theorems (valid in the case of forgetful channels) to present evidence of a transition from noiseless to noisy channel due to the environment's transition from regular to chaotic dynamics.

  17. Capacity and Delay Spread in Multilayer Diffusion-Based Molecular Communication (DBMC) Channel.

    PubMed

    Md Mustam, Saizalmursidi; Syed-Yusof, Sharifah K; Zubair, Suleiman

    2016-10-01

    In nanoscale communication, diffusion-based molecular communication (DBMC) in which information is encoded into molecule patterns by a transmitter nanomachine, has emerged as a promising communication system, particularly for biomedical and healthcare applications. Although, numerous studies have been conducted to evaluate and analyze DBMC systems, investigation on DBMC system through a multilayer channel has received less attention. The aims of this paper are to formulate channel characteristics and to evaluate the performance of multilayer DBMC channel in terms of delay spread and capacity. In this paper, the propagation of molecules over an n- layer channel is assumed to follow the Brownian motion and subjected to Fick's law of diffusion. Fourier transform is used to convert time to frequency domain functions. Besides, the multilayer channel is considered as a linear and deterministic channel. For the performance evaluation, the air-water-blood plasma medium representing the simplified multilayer diffusion model in the respiratory system was chosen. It was found that a high channel capacity can be achieved with wide transmission bandwidth, short transmission distance, and high averaged transmitted power. In addition, the findings showed that channel delay spread increases as both the transmission distance, and the pulse duration increased. By setting the symbol duration greater than the pulse duration or delay spread, an inter-symbol interference problem due to previous molecules transmission can be mitigated. These findings can be used as a guide in the development and fabrication of future artificial nanocommunication and nanonetworks systems involving multilayer transmission medium.

  18. Molecular determinants of anion selectivity in the cystic fibrosis transmembrane conductance regulator chloride channel pore.

    PubMed Central

    Linsdell, P; Evagelidis, A; Hanrahan, J W

    2000-01-01

    Ionic selectivity in many cation channels is achieved over a short region of the pore known as the selectivity filter, the molecular determinants of which have been identified in Ca(2+), Na(+), and K(+) channels. However, a filter controlling selectivity among different anions has not previously been identified in any Cl(-) channel. In fact, because Cl(-) channels are only weakly selective among small anions, and because their selectivity has proved so resistant to site-directed mutagenesis, the very existence of a discrete anion selectivity filter has been called into question. Here we show that mutation of a putative pore-lining phenylalanine residue, F337, in the sixth membrane-spanning region of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel, dramatically alters the relative permeabilities of different anions in the channel. Specifically, mutations that reduce the size of the amino acid side chain present at this position virtually abolish the relationship between anion permeability and hydration energy, a relationship that characterizes the anion selectivity not only of wild-type CFTR, but of most classes of Cl(-) channels. These results suggest that the pore of CFTR may indeed contain a specialized region, analogous to the selectivity filter of cation channels, at which discrimination between different permeant anions takes place. Because F337 is adjacent to another amino acid residue, T338, which also affects anion selectivity in CFTR, we suggest that selectivity is predominantly determined over a physically discrete region of the pore located near these important residues. PMID:10827976

  19. Dynamic evolution process of turbulent channel flow after opposition control

    NASA Astrophysics Data System (ADS)

    Ge, Mingwei; Tian, De; Yongqian, Liu

    2017-02-01

    Dynamic evolution of turbulent channel flow after application of opposition control (OC), together with the mechanism of drag reduction, is studied through direct numerical simulation (DNS). In the simulation, the pressure gradient is kept constant, and the flow rate increases due to drag reduction. In the transport of mean kinetic energy (MKE), one part of the energy from the external pressure is dissipated by the mean shear, and the other part is transported to the turbulent kinetic energy (TKE) through a TKE production term (TKP). It is found that the increase of MKE is mainly induced by the reduction of TKP that is directly affected by OC. Further analysis shows that the suppression of the redistribution term of TKE in the wall normal direction plays a key role in drag reduction, which represses the wall normal velocity fluctuation and then reduces TKP through the attenuation of its main production term. When OC is suddenly applied, an acute imbalance of energy in space is induced by the wall blowing and suction. Both the skin-friction and TKP terms exhibit a transient growth in the initial phase of OC, which can be attributed to the local effect of and <-u‧v‧> in the viscous sublayer. Project supported by the National Natural Science Foundation of China (Grant No. 11402088 and Grant No. 51376062) , State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources (Grant No. LAPS15005), and ‘the Fundamental Research Funds for the Central Universities’ (Grant No.2014MS33).

  20. Molecular Dynamics Simulation of Disordered Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2004-02-27

    The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.

  1. Dynamic aspects of large woody debris in river channels

    NASA Astrophysics Data System (ADS)

    Vergaro, Alexandra; Caporali, Enrica; Becchi, Ignazio

    2015-04-01

    Large Woody Debris (LWD) are an integral component of the fluvial environment. They represent an environmental resource, but without doubt they represent also a risk factor for the amplification that could give to the destructive power of a flood event. While countless intervention in river channels have reintroduced wood in rivers with restoration and banks protection aims, during several flash flood events LWD have had a great part in catastrophic consequences, pointing out the urgency of an adequate risk assessment procedure. At present wood dynamics in rivers is not systematically considered within the procedures for the elaboration of hazard maps resulting in loss of prediction accuracy and underestimation of hazard impacts. The assessment inconsistency comes from the complexity of the question: several aspects in wood processes are not yet well known and the superposition of different physical phenomena results in great difficulty to predict critical scenarios. The presented research activity has been aimed to improve management skills for the assessment of the hydrologic risk associated to the presence of large woody debris in rivers, improving knowledge about LWD dynamic processes and proposing effective tools for monitoring and mapping river catchments vulnerability. Utilizing critical review of the published works, field surveys and experimental investigations LWD damaging potential has been analysed to support the identification of the exposed sites and the redaction of hazard maps, taking into account that a comprehensive procedure has to involve: a) Identification of the critical cross sections; b) Evaluation of wood availability in the river catchment; c) Prediction of hazard scenarios through the estimation of water discharge, wood recruitment and entrainment, wood transport and destination. Particularly, a survey sheets form for direct measurements has been implemented and tested in field to provide an investigation instruments for wood and river

  2. Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation.

    PubMed

    Danelon, Christophe; Suenaga, Atsushi; Winterhalter, Mathias; Yamato, Ichiro

    2003-07-01

    Ion current through single outer membrane protein F (OmpF) trimers was recorded and compared to molecular dynamics simulation. Unidirectional insertion was revealed from the asymmetry in channel conductance. Single trimer conductance showed particularly high values at low symmetrical salt solution. The conductance values of various alkali metal ion solutions were proportional to the monovalent cation mobility values in the bulk phase, LiClchannels favored permeation of alkali metal ions over chloride and suggested size preference for smaller cations. These results suggest that there are specific interactions between the permeating cation and charged residues lining the channel walls. This hypothesis was supported by computational study which predicted that monovalent cations bind to Asp113 at low concentration. Here, free energy calculations revealed that the affinity of the alkali metal ions to its binding site increased with their atomic radii, Li(+) approximately Na(+)channel increases the translocation rate of cations under applied voltage by increasing their local concentration relative to the bulk solution.

  3. Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels.

    PubMed Central

    Fu, Wei; Cui, Meng; Briggs, James M; Huang, Xiaoqin; Xiong, Bing; Zhang, Yingmin; Luo, Xiaomin; Shen, Jianhua; Ji, Ruyun; Jiang, Hualiang; Chen, Kaixian

    2002-01-01

    The recognition of the scorpion toxin maurotoxin (MTX) by the voltage-gated potassium (Kv1) channels, Kv1.1, Kv1.2, and Kv1.3, has been studied by means of Brownian dynamics (BD) simulations. All of the 35 available structures of MTX in the Protein Data Bank (http://www.rcsb.org/pdb) determined by nuclear magnetic resonance were considered during the simulations, which indicated that the conformation of MTX significantly affected both the recognition and the binding between MTX and the Kv1 channels. Comparing the top five highest-frequency structures of MTX binding to the Kv1 channels, we found that the Kv1.2 channel, with the highest docking frequencies and the lowest electrostatic interaction energies, was the most favorable for MTX binding, whereas Kv1.1 was intermediate, and Kv1.3 was the least favorable one. Among the 35 structures of MTX, the 10th structure docked into the binding site of the Kv1.2 channel with the highest probability and the most favorable electrostatic interactions. From the MTX-Kv1.2 binding model, we identified the critical residues for the recognition of these two proteins through triplet contact analyses. MTX locates around the extracellular mouth of the Kv1 channels, making contacts with its beta-sheets. Lys23, a conserved amino acid in the scorpion toxins, protrudes into the pore of the Kv1.2 channel and forms two hydrogen bonds with the conserved residues Gly401(D) and Tyr400(C) and one hydrophobic contact with Gly401(C) of the Kv1.2 channel. The critical triplet contacts for recognition between MTX and the Kv1.2 channel are Lys23(MTX)-Asp402(C)(Kv1), Lys27(MTX)-Asp378(D)(Kv1), and Lys30(MTX)-Asp402(A)(Kv1). In addition, six hydrogen-bonding interactions are formed between residues Lys23, Lys27, Lys30, and Tyr32 of MTX and residues Gly401, Tyr400, Asp402, Asp378, and Thr406 of Kv1.2. Many of them are formed by side chains of residues of MTX and backbone atoms of the Kv1.2 channel. Five hydrophobic contacts exist between residues Pro

  4. Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels.

    PubMed

    Fu, Wei; Cui, Meng; Briggs, James M; Huang, Xiaoqin; Xiong, Bing; Zhang, Yingmin; Luo, Xiaomin; Shen, Jianhua; Ji, Ruyun; Jiang, Hualiang; Chen, Kaixian

    2002-11-01

    The recognition of the scorpion toxin maurotoxin (MTX) by the voltage-gated potassium (Kv1) channels, Kv1.1, Kv1.2, and Kv1.3, has been studied by means of Brownian dynamics (BD) simulations. All of the 35 available structures of MTX in the Protein Data Bank (http://www.rcsb.org/pdb) determined by nuclear magnetic resonance were considered during the simulations, which indicated that the conformation of MTX significantly affected both the recognition and the binding between MTX and the Kv1 channels. Comparing the top five highest-frequency structures of MTX binding to the Kv1 channels, we found that the Kv1.2 channel, with the highest docking frequencies and the lowest electrostatic interaction energies, was the most favorable for MTX binding, whereas Kv1.1 was intermediate, and Kv1.3 was the least favorable one. Among the 35 structures of MTX, the 10th structure docked into the binding site of the Kv1.2 channel with the highest probability and the most favorable electrostatic interactions. From the MTX-Kv1.2 binding model, we identified the critical residues for the recognition of these two proteins through triplet contact analyses. MTX locates around the extracellular mouth of the Kv1 channels, making contacts with its beta-sheets. Lys23, a conserved amino acid in the scorpion toxins, protrudes into the pore of the Kv1.2 channel and forms two hydrogen bonds with the conserved residues Gly401(D) and Tyr400(C) and one hydrophobic contact with Gly401(C) of the Kv1.2 channel. The critical triplet contacts for recognition between MTX and the Kv1.2 channel are Lys23(MTX)-Asp402(C)(Kv1), Lys27(MTX)-Asp378(D)(Kv1), and Lys30(MTX)-Asp402(A)(Kv1). In addition, six hydrogen-bonding interactions are formed between residues Lys23, Lys27, Lys30, and Tyr32 of MTX and residues Gly401, Tyr400, Asp402, Asp378, and Thr406 of Kv1.2. Many of them are formed by side chains of residues of MTX and backbone atoms of the Kv1.2 channel. Five hydrophobic contacts exist between residues Pro

  5. Functional analysis and molecular modeling of a cloned urate transporter/channel.

    PubMed

    Leal-Pinto, E; Cohen, B E; Abramson, R G

    1999-05-01

    Recombinant protein, designated UAT, prepared from a cloned rat renal cDNA library functions as a selective voltage-sensitive urate transporter/channel when fused with lipid bilayers. Since we previously suggested that UAT may represent the mammalian electrogenic urate transporter, UAT has been functionally characterized in the presence and absence of potential channel blockers, several of which are known to block mammalian electrogenic urate transport. Two substrates, oxonate (a competitive uricase inhibitor) and pyrazinoate, that inhibit renal electrogenic urate transport also block UAT activity. Of note, oxonate selectively blocks from the cytoplasmic side of the channel while pyrazinoate only blocks from the channel's extracellular face. Like oxonate, anti-uricase (an electrogenic transport inhibitor) also selectively blocks channel activity from the cytoplasmic side. Adenosine blocks from the extracellular side exclusively while xanthine blocks from both sides. These effects are consistent with newly identified regions of homology to uricase and the adenosine A1/A3 receptor in UAT and localize these homologous regions to the cytoplasmic and extracellular faces of UAT, respectively. Additionally, computer analyses identified four putative alpha-helical transmembrane domains, two beta sheets, and blocks of homology to the E and B loops of aquaporin-1 within UAT. The experimental observations substantiate our proposal that UAT is the molecular representation of the renal electrogenic urate transporter and, in conjunction with computer algorithms, suggest a possible molecular structure for this unique channel.

  6. Ion Channels in Plant Bioenergetic Organelles, Chloroplasts and Mitochondria: From Molecular Identification to Function.

    PubMed

    Carraretto, Luca; Teardo, Enrico; Checchetto, Vanessa; Finazzi, Giovanni; Uozumi, Nobuyuki; Szabo, Ildiko

    2016-03-07

    Recent technical advances in electrophysiological measurements, organelle-targeted fluorescence imaging, and organelle proteomics have pushed the research of ion transport a step forward in the case of the plant bioenergetic organelles, chloroplasts and mitochondria, leading to the molecular identification and functional characterization of several ion transport systems in recent years. Here we focus on channels that mediate relatively high-rate ion and water flux and summarize the current knowledge in this field, focusing on targeting mechanisms, proteomics, electrophysiology, and physiological function. In addition, since chloroplasts evolved from a cyanobacterial ancestor, we give an overview of the information available about cyanobacterial ion channels and discuss the evolutionary origin of chloroplast channels. The recent molecular identification of some of these ion channels allowed their physiological functions to be studied using genetically modified Arabidopsis plants and cyanobacteria. The view is emerging that alteration of chloroplast and mitochondrial ion homeostasis leads to organelle dysfunction, which in turn significantly affects the energy metabolism of the whole organism. Clear-cut identification of genes encoding for channels in these organelles, however, remains a major challenge in this rapidly developing field. Multiple strategies including bioinformatics, cell biology, electrophysiology, use of organelle-targeted ion-sensitive probes, genetics, and identification of signals eliciting specific ion fluxes across organelle membranes should provide a better understanding of the physiological role of organellar channels and their contribution to signaling pathways in plants in the future.

  7. Structure and dynamics underlying elementary ligand binding events in human pacemaking channels

    PubMed Central

    Goldschen-Ohm, Marcel P; Klenchin, Vadim A; White, David S; Cowgill, John B; Cui, Qiang; Goldsmith, Randall H; Chanda, Baron

    2016-01-01

    Although molecular recognition is crucial for cellular signaling, mechanistic studies have relied primarily on ensemble measures that average over and thereby obscure underlying steps. Single-molecule observations that resolve these steps are lacking due to diffraction-limited resolution of single fluorophores at relevant concentrations. Here, we combined zero-mode waveguides with fluorescence resonance energy transfer (FRET) to directly observe binding at individual cyclic nucleotide-binding domains (CNBDs) from human pacemaker ion channels critical for heart and brain function. Our observations resolve the dynamics of multiple distinct steps underlying cyclic nucleotide regulation: a slow initial binding step that must select a 'receptive' conformation followed by a ligand-induced isomerization of the CNBD. X-ray structure of the apo CNBD and atomistic simulations reveal that the isomerization involves both local and global transitions. Our approach reveals fundamental mechanisms underpinning ligand regulation of pacemaker channels, and is generally applicable to weak-binding interactions governing a broad spectrum of signaling processes. DOI: http://dx.doi.org/10.7554/eLife.20797.001 PMID:27858593

  8. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    NASA Astrophysics Data System (ADS)

    Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

    2014-03-01

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  9. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    SciTech Connect

    Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  10. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

    PubMed

    Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  11. Capillary dynamics driven by molecular self-layering.

    PubMed

    Wu, Pingkeng; Nikolov, Alex; Wasan, Darsh

    2017-02-10

    Capillary dynamics is a ubiquitous everyday phenomenon. It has practical applications in diverse fields, including ink-jet printing, lab-on-a-chip, biotechnology, and coating. Understanding capillary dynamics requires essential knowledge on the molecular level of how fluid molecules interact with a solid substrate (the wall). Recent studies conducted with the surface force apparatus (SFA), atomic force microscope (AFM), and statistical mechanics simulation revealed that molecules/nanoparticles confined into the film/wall surfaces tend to self-layer into 2D layer/s and even 2D in-layer with increased confinement and fluid volume fraction. Here, the capillary rise dynamics of simple molecular fluids in cylindrical capillary is explained by the molecular self-layering model. The proposed model considers the role of the molecular shape on self-layering and its effect on the molecularly thin film viscosity in regards to the advancing (dynamic) contact angle. The model was tested to explain the capillary rise dynamics of fluids of spherical, cylindrical, and disk shape molecules in borosilicate glass capillaries. The good agreement between the capillary rise data and SFA data from the literature for simple fluid self-layering shows the validity of the present model. The present model provides new insights into the design of many applications where dynamic wetting is important because it reveals the significant impact of molecular self-layering close to the wall on dynamic wetting.

  12. Molecular heterogeneity of large-conductance calcium-activated potassium channels in canine intracardiac ganglia.

    PubMed

    Selga, Elisabet; Pérez-Serra, Alexandra; Moreno-Asso, Alba; Anderson, Seth; Thomas, Kristen; Desai, Mayurika; Brugada, Ramon; Pérez, Guillermo J; Scornik, Fabiana S

    2013-01-01

    Large conductance calcium-activated potassium (BK) channels are widely expressed in the nervous system. We have recently shown that principal neurons from canine intracardiac ganglia (ICG) express a paxilline- and TEA-sensitive BK current, which increases neuronal excitability. In the present work, we further explore the molecular constituents of the BK current in canine ICG. We found that the β1 and β4 regulatory subunits are expressed in ICG. Single channel voltage-dependence at different calcium concentrations suggested that association of the BKα with a particular β subunit was not enough to explain the channel activity in this tissue. Indeed, we detected the presence of several splice variants of the BKα subunit. In conclusion, BK channels in canine ICG may result from the arrangement of different BKα splice variants, plus accessory β subunits. The particular combinations expressed in canine IC neurons likely rule the excitatory role of BK current in this tissue.

  13. Molecular simulation of the interaction of kappa-conotoxin-PVIIA with the Shaker potassium channel pore.

    PubMed

    Moran, O

    2001-12-01

    Molecular simulation techniques were appplied to predict the interaction of the voltage-dependent Shaker potassium channel with the channel-blocking toxin kappa-conotoxin-PVIIA (PVIIA). A structural thee-dimensional model of the extracellular vestibule of the potassium channel was constructed based on structural homologies with the bacterial potassium channel Kcsa, whose structure has been solved by X-ray crystallography. The docking of the PVIIA molecule was obtained by a geometric recognition algorithm, yielding 100 possible conformations. A series of residue-residue distance restraints, predicted from mutation-cycle experiments, were used to select a small set of a plausible channel-toxin complex models among the resulting possible conformations. The four final conformations, with similar characteristics, can explain most of the single-point mutation experiments done with this system. The models of the Shaker-PVIIA interaction predict two clusters of amino acids, critical for the binding of the toxin to the channel. The first cluster is the amino acids R2, I3, Q6 and K7 that form the plug of the toxin that interacts with the entrance to the selectivity filter of the channel. The second cluster of residues, R22, F23, N24 and K25, interacts with a channel region near to the external entrance of the pore vestibule. The consistency of the obtained models and the experimental data indicate that the Shaker-PVIIA complex model is reasonable and can be used in further biological studies such as the rational design of blocking agents of potassium channels and the mutagenesis of both toxins and potassium channels.

  14. An Adaptive Channel Access Method for Dynamic Super Dense Wireless Sensor Networks.

    PubMed

    Lei, Chunyang; Bie, Hongxia; Fang, Gengfa; Zhang, Xuekun

    2015-12-03

    Super dense and distributed wireless sensor networks have become very popular with the development of small cell technology, Internet of Things (IoT), Machine-to-Machine (M2M) communications, Vehicular-to-Vehicular (V2V) communications and public safety networks. While densely deployed wireless networks provide one of the most important and sustainable solutions to improve the accuracy of sensing and spectral efficiency, a new channel access scheme needs to be designed to solve the channel congestion problem introduced by the high dynamics of competing nodes accessing the channel simultaneously. In this paper, we firstly analyzed the channel contention problem using a novel normalized channel contention analysis model which provides information on how to tune the contention window according to the state of channel contention. We then proposed an adaptive channel contention window tuning algorithm in which the contention window tuning rate is set dynamically based on the estimated channel contention level. Simulation results show that our proposed adaptive channel access algorithm based on fast contention window tuning can achieve more than 95 % of the theoretical optimal throughput and 0 . 97 of fairness index especially in dynamic and dense networks.

  15. Deformation localization and dislocation channel dynamics in neutron-irradiated austenitic stainless steels

    SciTech Connect

    Gussev, Maxim N.; Field, Kevin G.; Busby, Jeremy T.

    2015-02-24

    We investigated dynamics of deformation localization and dislocation channel formation in situ in a neutron irradiated AISI 304 austenitic stainless steel and a model 304-based austenitic alloy by combining several analytical techniques including optic microscopy and laser confocal microscopy, scanning electron microscopy, electron backscatter diffraction and transmission electron microscopy. Channel formation was observed at 70% of the formal tensile yield stress for both alloys. It was shown that triple junction points do not always serve as a source of dislocation channels; at stress levels below the yield stress, channels often formed near the middle of the grain boundary. For a single grain, the role of elastic stiffness value (Young modulus) in the channel formation was analyzed; it was shown that in the irradiated 304 steels the initial channels appeared in soft grains with a high Schmid factor located near stiff grains with high elastic stiffness. Moreover, the spatial organization of channels in a single grain was analyzed; it was shown that secondary channels operating in the same slip plane as primary channels often appeared at the middle or at one third of the way between primary channels. The twinning nature of dislocation channels was analyzed for grains of different orientation using TEM. Finally, it was shown that in the AISI 304 steel, channels were twin-free in grains oriented close to [001] and [101] of standard unit triangle; [111]-grains and grains oriented close to Schmid factor maximum contained deformation twins.

  16. Deformation localization and dislocation channel dynamics in neutron-irradiated austenitic stainless steels

    DOE PAGES

    Gussev, Maxim N.; Field, Kevin G.; Busby, Jeremy T.

    2015-02-24

    We investigated dynamics of deformation localization and dislocation channel formation in situ in a neutron irradiated AISI 304 austenitic stainless steel and a model 304-based austenitic alloy by combining several analytical techniques including optic microscopy and laser confocal microscopy, scanning electron microscopy, electron backscatter diffraction and transmission electron microscopy. Channel formation was observed at 70% of the formal tensile yield stress for both alloys. It was shown that triple junction points do not always serve as a source of dislocation channels; at stress levels below the yield stress, channels often formed near the middle of the grain boundary. For amore » single grain, the role of elastic stiffness value (Young modulus) in the channel formation was analyzed; it was shown that in the irradiated 304 steels the initial channels appeared in soft grains with a high Schmid factor located near stiff grains with high elastic stiffness. Moreover, the spatial organization of channels in a single grain was analyzed; it was shown that secondary channels operating in the same slip plane as primary channels often appeared at the middle or at one third of the way between primary channels. The twinning nature of dislocation channels was analyzed for grains of different orientation using TEM. Finally, it was shown that in the AISI 304 steel, channels were twin-free in grains oriented close to [001] and [101] of standard unit triangle; [111]-grains and grains oriented close to Schmid factor maximum contained deformation twins.« less

  17. Dynamical coupled-channels study of meson production reactions from EBAC@Jlab

    SciTech Connect

    Hiroyuki Kamano

    2011-10-01

    We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.

  18. Dynamical coupled-channels study of meson production reactions from EBACatJLab

    SciTech Connect

    Kamano, Hiroyuki

    2011-10-24

    We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.

  19. Molecular determinants of Kv1.5 channel block by diphenyl phosphine oxide-1.

    PubMed

    Du, Yi-mei; Zhang, Xiao-xian; Tu, Dan-na; Zhao, Ning; Liu, Yan-jie; Xiao, Hua; Sanguinetti, Michael C; Zou, Anruo; Liao, Yu-hua

    2010-06-01

    Kv1.5 channels conduct the ultra-rapid delayed rectifier current (I(Kur)) that contributes to action potential repolarization of human atrial myocytes. Block of these channels has been proposed as a treatment for atrial arrhythmias. Diphenyl phosphine oxide-1 (DPO-1) is a novel and potent inhibitor of Kv1.5 potassium channels. The present study was undertaken to characterize the mechanisms and molecular determinants of channel block by DPO-1. Experiments were carried out on wild-type and mutant Kv1.5 channels expressed in Xenopus laevis oocytes using the standard two microelectrode voltage clamp technique. DPO-1 blocked Kv1.5 current in oocytes with an IC(50) of 0.78+/-0.12 microM at +40 mV. Block was enhanced by higher rates of stimulation, consistent with preferential binding of the drug to the open state of the channel. Ala-scanning mutagenesis of the pore domain of Kv1.5 identified the residues Thr480, Leu499, Leu506, Ile508, Leu510 and Val514 as components of the putative binding site for DPO-1, partially overlapping the site previously defined for the Kv1.5 channel blockers AVE0118 and S0100176. Block of Kv1.5 by DPO-1 was significantly reduced in the presence of Kvbeta1.3.

  20. A molecular framework for temperature-dependent gating of ion channels

    PubMed Central

    Chowdhury, Sandipan; Jarecki, Brian W.; Chanda, Baron

    2014-01-01

    Summary Perception of heat or cold in higher organisms is mediated by specialized ion channels whose gating is exquisitely sensitive to temperature. The physicochemical underpinnings of this temperature-sensitive gating have proven difficult to parse. Here, we took a bottom-up protein design approach, and rationally engineered ion channels to activate in response to thermal stimuli. By varying amino acid polarities at sites undergoing state-dependent changes in solvation, we were able to systematically confer temperature-sensitivity to a canonical voltage-gated ion channel. Our results imply that the specific heat capacity change during channel gating is a major determinant of thermo-sensitive gating. We also show that reduction of gating charges amplifies temperature-sensitivity of designer channels which accounts for low voltage-sensitivity in all known temperature-gated ion channels. These emerging principles suggest a plausible molecular mechanism for temperature-dependent gating that reconcile how ion channels with an overall conserved transmembrane architecture may exhibit a wide range of temperature-sensing phenotypes. PMID:25156949

  1. Cloning and molecular characterization of a putative voltage-gated sodium channel gene in the crayfish.

    PubMed

    Coskun, Cagil; Purali, Nuhan

    2016-06-01

    Voltage-gated sodium channel genes and associated proteins have been cloned and studied in many mammalian and invertebrate species. However, there is no data available about the sodium channel gene(s) in the crayfish, although the animal has frequently been used as a model to investigate various aspects of neural cellular and circuit function. In the present work, by using RNA extracts from crayfish abdominal ganglia samples, the complete open reading frame of a putative sodium channel gene has firstly been cloned and molecular properties of the associated peptide have been analyzed. The open reading frame of the gene has a length of 5793 bp that encodes for the synthesis of a peptide, with 1930 amino acids, that is 82% similar to the α-peptide of a sodium channel in a neighboring species, Cancer borealis. The transmembrane topology analysis of the crayfish peptide indicated a pattern of four folding domains with several transmembrane segments, as observed in other known voltage-gated sodium channels. Upon analysis of the obtained sequence, functional regions of the putative sodium channel responsible for the selectivity filter, inactivation gate, voltage sensor, and phosphorylation have been predicted. The expression level of the putative sodium channel gene, as defined by a qPCR method, was measured and found to be the highest in nervous tissue.

  2. Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Garate, J.-A.; English, Niall J.; MacElroy, J. M. D.

    2011-02-01

    Water self-diffusion within human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of external ac and dc electric fields. The computed diffusive (pd) and osmotic (pf) permeabilities under zero-field conditions are (0.718 ± 0.24) × 10-14 cm3 s-1 and (2.94 ± 0.47) × 10-14 cm3 s-1, respectively; our pf agrees with the experimental value of (1.50 ± 0.6) × 10-14 cm3 s-1. A gating mechanism has been proposed in which side-chain dynamics of residue H201, located in the selectivity filter, play an essential role. In addition, for nonequilibrium MD in external fields, it was found that water dipole orientation within the constriction region of the channel is affected by electric fields (e-fields) and that this governs the permeability. It was also found that the rate of side-chain flipping motion of residue H201 is increased in the presence of e-fields, which influences water conductivity further.

  3. Dynamical analysis of highly excited molecular spectra

    SciTech Connect

    Kellman, M.E.

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  4. Nucleation of carbon nanostructures: Molecular dynamics with reactive potentials

    NASA Astrophysics Data System (ADS)

    Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.

    2016-11-01

    In this paper, we present our first results in the study of the details of nucleation in the homogeneous carbon gas phase using computer calculations with molecular dynamics methods. Direct and controlled molecular-dynamics approaches are used and two reactive potentials (ReaxFF and AIREBO) are compared. The calculations have shown that the nucleation process in the AIREBO model is going more actively than in the ReaxFF one.

  5. Special issue on ultrafast electron and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Hishikawa, Akiyoshi; Martin, Fernando; Vrakking, Marc

    2013-07-01

    Your invitation to submit. Journal of Physics. B: Atomic Molecular and Optical Physics (JPhysB) is delighted to announce a forthcoming special issue on ultrafast electron and molecular dynamics to appear in 2014, and invites you to submit a paper. Within the last decade, a number of novel approaches have emerged, both experimental and theoretical, that allow the investigation of (time-resolved) molecular dynamics in novel ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain. Along the way, particular types of molecular dynamics, such as dynamics around conical intersections, have gained an increased prominence, sparked by an emerging realization about the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of some of the most important developments in the field, while at the same time indicating how studies of (time-resolved) molecular dynamics are likely to evolve in the coming

  6. Pore helices play a dynamic role as integrators of domain motion during Kv11.1 channel inactivation gating.

    PubMed

    Perry, Matthew D; Ng, Chai Ann; Vandenberg, Jamie I

    2013-04-19

    Proteins that form ion-selective pores in the membrane of cells are integral to many rapid signaling processes, including regulating the rhythm of the heartbeat. In potassium channels, the selectivity filter is critical for both endowing an exquisite selectivity for potassium ions, as well as for controlling the flow of ions through the pore. Subtle rearrangements in the complex hydrogen-bond network that link the selectivity filter to the surrounding pore helices differentiate conducting (open) from nonconducting (inactivated) conformations of the channel. Recent studies suggest that beyond the selectivity filter, inactivation involves widespread rearrangements of the channel protein. Here, we use rate equilibrium free energy relationship analysis to probe the structural changes that occur during selectivity filter gating in Kv11.1 channels, at near atomic resolution. We show that the pore helix plays a crucial dynamic role as a bidirectional interface during selectivity filter gating. We also define the molecular bases of the energetic coupling between the pore helix and outer helix of the pore domain that occurs early in the transition from open to inactivated states, as well as the coupling between the pore helix and inner helix late in the transition. Our data demonstrate that the pore helices are more than just static structural elements supporting the integrity of the selectivity filter; instead they play a crucial dynamic role during selectivity filter gating.

  7. Elucidation of molecular dynamics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...

  8. Attosecond molecular dynamics: fact or fiction?

    NASA Astrophysics Data System (ADS)

    Lépine, Franck; Ivanov, Misha Y.; Vrakking, Marc J. J.

    2014-03-01

    The emerging application of attosecond techniques to molecular systems allows the role of electronic coherence in the control of chemical reactions to be investigated. Prompt ionization of molecules by an attosecond pulse may induce charge migration across a molecular structure on attosecond to few-femtosecond timescales, thereby possibly determining the subsequent relaxation pathways that a molecule may take. We discuss how proposals for this 'charge-directed reactivity' fit within the current understanding of quantum control and review the current state of the art of attosecond molecular science. Specifically, we review the role of electronic coherence and coupling of the electronic and nuclear degrees of freedom in high-harmonic spectroscopy and in the first attosecond pump-probe experiments on molecular systems.

  9. 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.

  10. Competition between abstraction and exchange channels in H + HCN reaction: Full-dimensional quantum dynamics

    SciTech Connect

    Jiang, Bin; Guo, Hua

    2013-12-14

    Dynamics of the title reaction is investigated on an ab initio based potential energy surface using a full-dimensional quantum wave packet method within the centrifugal sudden approximation. It is shown that the reaction between H and HCN leads to both the hydrogen exchange and hydrogen abstraction channels. The exchange channel has a lower threshold and larger cross section than the abstraction channel. It also has more oscillations due apparently to quantum resonances. Both channels are affected by long-lived resonances supported by potential wells. Comparison with experimental cross sections indicates underestimation of the abstraction barrier height.

  11. Non-Equilibrium Dynamics of Nano-channel Confined DNA: A Brownian Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Aniket; Huang, Aiqun; Reisner, Walter

    We carry out Brownian dynamics (BD) simulation for a semi-flexible polymer chain characterized by a contour length Na and a persistence length lp confined inside a rectangular nanochannel to study its compression and retraction dynamics while being pushed on one end at a constant velocity by a ``nano-dozer''. We study the evolution of one dimensional concentration profile c (x , t) and the chain extension R along the channel axis (x-axis) during both the contracting as well as the retracting phases as a function of the velocity of the nano-dozer, both in steady states and in transients. Furthermore, we measure the transverse fluctuations of the chain under contraction and retraction, and the amplitude of the density profile, and compare these simulation results with those obtained from an analytical model proposed by Khorshid et al. Our studies are guided by recent experimental results by Khorshid et al. (Phys. Rev. Lett, 113, 268104 (2014)) and provide further justification to use a one dimensional PDE approach to understand the non-equilibrium dynamics of confined polymers.

  12. Theoretical analysis of selectivity mechanisms in molecular transport through channels and nanopores

    SciTech Connect

    Agah, Shaghayegh; Pasquali, Matteo; Kolomeisky, Anatoly B.

    2015-01-28

    Selectivity is one of the most fundamental concepts in natural sciences, and it is also critically important in various technological, industrial, and medical applications. Although there are many experimental methods that allow to separate molecules, frequently they are expensive and not efficient. Recently, a new method of separation of chemical mixtures based on utilization of channels and nanopores has been proposed and successfully tested in several systems. However, mechanisms of selectivity in the molecular transport during the translocation are still not well understood. Here, we develop a simple theoretical approach to explain the origin of selectivity in molecular fluxes through channels. Our method utilizes discrete-state stochastic models that take into account all relevant chemical transitions and can be solved analytically. More specifically, we analyze channels with one and two binding sites employed for separating mixtures of two types of molecules. The effects of the symmetry and the strength of the molecular-pore interactions are examined. It is found that for one-site binding channels, the differences in the strength of interactions for two species drive the separation. At the same time, in more realistic two-site systems, the symmetry of interaction potential becomes also important. The most efficient separation is predicted when the specific binding site is located near the entrance to the nanopore. In addition, the selectivity is higher for large entrance rates into the channel. It is also found that the molecular transport is more selective for repulsive interactions than for attractive interactions. The physical-chemical origin of the observed phenomena is discussed.

  13. Immunomodulation of voltage-dependent K+ channels in macrophages: molecular and biophysical consequences.

    PubMed

    Villalonga, Núria; David, Miren; Bielanska, Joanna; Vicente, Rubén; Comes, Núria; Valenzuela, Carmen; Felipe, Antonio

    2010-02-01

    Voltage-dependent potassium (K(v)) channels play a pivotal role in the modulation of macrophage physiology. Macrophages are professional antigen-presenting cells and produce inflammatory and immunoactive substances that modulate the immune response. Blockage of K(v) channels by specific antagonists decreases macrophage cytokine production and inhibits proliferation. Numerous pharmacological agents exert their effects on specific target cells by modifying the activity of their plasma membrane ion channels. Investigation of the mechanisms involved in the regulation of potassium ion conduction is, therefore, essential to the understanding of potassium channel functions in the immune response to infection and inflammation. Here, we demonstrate that the biophysical properties of voltage-dependent K(+) currents are modified upon activation or immunosuppression in macrophages. This regulation is in accordance with changes in the molecular characteristics of the heterotetrameric K(v)1.3/K(v)1.5 channels, which generate the main K(v) in macrophages. An increase in K(+) current amplitude in lipopolysaccharide-activated macrophages is characterized by a faster C-type inactivation, a greater percentage of cumulative inactivation, and a more effective margatoxin (MgTx) inhibition than control cells. These biophysical parameters are related to an increase in K(v)1.3 subunits in the K(v)1.3/K(v)1.5 hybrid channel. In contrast, dexamethasone decreased the C-type inactivation, the cumulative inactivation, and the sensitivity to MgTx concomitantly with a decrease in K(v)1.3 expression. Neither of these treatments apparently altered the expression of K(v)1.5. Our results demonstrate that the immunomodulation of macrophages triggers molecular and biophysical consequences in K(v)1.3/K(v)1.5 hybrid channels by altering the subunit stoichiometry.

  14. Analysis of nanoscale two-phase flow of argon using molecular dynamics

    SciTech Connect

    Verma, Abhishek Kumar; Kumar, Rakesh

    2014-12-09

    Two phase flows through micro and nanochannels have attracted a lot of attention because of their immense applicability to many advanced fields such as MEMS/NEMS, electronic cooling, bioengineering etc. In this work, a molecular dynamics simulation method is employed to study the condensation process of superheated argon vapor force driven flow through a nanochannel combining fluid flow and heat transfer. A simple and effective particle insertion method is proposed to model phase change of argon based on non-periodic boundary conditions in the simulation domain. Starting from a crystalline solid wall of channel, the condensation process evolves from a transient unsteady state where we study the influence of different wall temperatures and fluid wall interactions on interfacial and heat transport properties of two phase flows. Subsequently, we analyzed transient temperature, density and velocity fields across the channel and their dependency on varying wall temperature and fluid wall interaction, after a dynamic equilibrium is achieved in phase transition. Quasi-steady nonequilibrium temperature profile, heat flux and interfacial thermal resistance were analyzed. The results demonstrate that the molecular dynamics method, with the proposed particle insertion method, effectively solves unsteady nonequilibrium two phase flows at nanoscale resolutions whose interphase between liquid and vapor phase is typically of the order of a few molecular diameters.

  15. Analysis of nanoscale two-phase flow of argon using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Verma, Abhishek Kumar; Kumar, Rakesh

    2014-12-01

    Two phase flows through micro and nanochannels have attracted a lot of attention because of their immense applicability to many advanced fields such as MEMS/NEMS, electronic cooling, bioengineering etc. In this work, a molecular dynamics simulation method is employed to study the condensation process of superheated argon vapor force driven flow through a nanochannel combining fluid flow and heat transfer. A simple and effective particle insertion method is proposed to model phase change of argon based on non-periodic boundary conditions in the simulation domain. Starting from a crystalline solid wall of channel, the condensation process evolves from a transient unsteady state where we study the influence of different wall temperatures and fluid wall interactions on interfacial and heat transport properties of two phase flows. Subsequently, we analyzed transient temperature, density and velocity fields across the channel and their dependency on varying wall temperature and fluid wall interaction, after a dynamic equilibrium is achieved in phase transition. Quasi-steady nonequilibrium temperature profile, heat flux and interfacial thermal resistance were analyzed. The results demonstrate that the molecular dynamics method, with the proposed particle insertion method, effectively solves unsteady nonequilibrium two phase flows at nanoscale resolutions whose interphase between liquid and vapor phase is typically of the order of a few molecular diameters.

  16. Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl.

    PubMed

    Tachikawa, Hiroto

    2006-10-07

    Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.

  17. Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto

    2006-10-01

    Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl-+H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH ⋯H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.

  18. Investigation of water droplet dynamics in PEM fuel cell gas channels

    NASA Astrophysics Data System (ADS)

    Gopalan, Preethi

    Water management in Proton Exchange Membrane Fuel Cell (PEMFC) has remained one of the most important issues that need to be addressed before its commercialization in automotive applications. Accumulation of water on the gas diffusion layer (GDL) surface in a PEMFC introduces a barrier for transport of reactant gases through the GDL to the catalyst layer. Despite the fact that the channel geometry is one of the key design parameters of a fluidic system, very limited research is available to study the effect of microchannel geometry on the two-phase flow structure. In this study, the droplet-wall dynamics and two-phase pressure drop across the water droplet present in a typical PEMFC channel, were examined in auto-competitive gas channel designs (0.4 x 0.7 mm channel cross section). The liquid water flow pattern inside the gas channel was analyzed for different air velocities. Experimental data was analyzed using the Concus-Finn condition to determine the wettability characteristics in the corner region. It was confirmed that the channel angle along with the air velocity and the channel material influences the water distribution and holdup within the channel. Dynamic contact angle emerged as an important parameter in controlling the droplet-wall interaction. Experiments were also performed to understand how the inlet location of the liquid droplet on the GDL surface affects the droplet dynamic behavior in the system. It was found that droplets emerging near the channel wall or under the land lead to corner filling of the channel. Improvements in the channel design has been proposed based on the artificial channel roughness created to act as capillary grooves to transport the liquid water away from the land area. For droplets emerging near the center of the channel, beside the filling and no-filling behavior reported in the literature, a new droplet jumping behavior was observed. As droplets grew and touched the sidewalls, they jumped off to the sidewall leaving the

  19. The Computer Simulation of Liquids by Molecular Dynamics.

    ERIC Educational Resources Information Center

    Smith, W.

    1987-01-01

    Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)

  20. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study.

    PubMed

    Sankararamakrishnan, R; Samsom, M S

    1994-12-01

    The pore-lining M2 helix of the nicotinic acetylcholine receptor exhibits a pronounced kink when the corresponding ion channel is in a closed conformation [N. Unwin (1993) Journal of Molecular Biology, Vol. 229, pp. 1101-1124]. We have performed molecular dynamics simulations of isolated 22-residue M2 helices in order to identify a possible molecular origin of this kink. In order to sample a wide range of conformational space, a simulated annealing protocol was used to generate five initial M2 helix structures, each of which was subsequently used as the basis of 300 ps MD simulations. Two helix sequences (M2 alpha and M2 delta) were studied in this manner, resulting in a total of ten 300 ps trajectories. Kinked helices present in the trajectories were identified and energy minimized to yield a total of five different stable kinked structures. For comparison, a similar molecular dynamics simulation of a Leu23 helix yielded no stable kinked structures. In four of the five kinked helices, the kink was stabilized by H bonds between the helix backbone and polar side-chain atoms. Comparison with data from the literature on site-directed mutagenesis of M2 residues suggests that such polar side-chain to main-chain H bonds may also contribute to kinking of M2 helices in the intact channel protein.

  1. 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.

  2. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.

    PubMed

    Makarov, G I; Makarova, T M; Sumbatyan, N V; Bogdanov, A A

    2016-12-01

    The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.

  3. Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure.

    PubMed

    Aguilella-Arzo, M; Aguilella, V M

    2010-04-01

    We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.

  4. Fluorescent protein-scorpion toxin chimera is a convenient molecular tool for studies of potassium channels

    PubMed Central

    Kuzmenkov, Alexey I.; Nekrasova, Oksana V.; Kudryashova, Kseniya S.; Peigneur, Steve; Tytgat, Jan; Stepanov, Alexey V.; Kirpichnikov, Mikhail P.; Grishin, Eugene V.; Feofanov, Alexey V.; Vassilevski, Alexander A.

    2016-01-01

    Ion channels play a central role in a host of physiological and pathological processes and are the second largest target for existing drugs. There is an increasing need for reliable tools to detect and visualize particular ion channels, but existing solutions suffer from a number of limitations such as high price, poor specificity, and complicated protocols. As an alternative, we produced recombinant chimeric constructs (FP-Tx) consisting of fluorescent proteins (FP) fused with potassium channel toxins from scorpion venom (Tx). In particular, we used two FP, eGFP and TagRFP, and two Tx, OSK1 and AgTx2, to create eGFP-OSK1 and RFP-AgTx2. We show that these chimeras largely retain the high affinity of natural toxins and display selectivity to particular ion channel subtypes. FP-Tx are displaced by other potassium channel blockers and can be used as an imaging tool in ion channel ligand screening setups. We believe FP-Tx chimeras represent a new efficient molecular tool for neurobiology. PMID:27650866

  5. Broad pore channels as molecular highways in nanoporous catalysts: Multiscale modeling, optimization and applications

    NASA Astrophysics Data System (ADS)

    Wang, Gang

    Porous catalysts are widely used in many applications, ranging from petroleum refining to fuel cells and emission control. Nanoporous catalysts like zeolites often have an extremely large internal surface area (e.g., 1000m 2/g), which is beneficial because catalytic reactions occur on the surface. However, their small pore size leads to slow molecular transport and pore blocking, limiting the efficient use of the catalytic material. This indicates that, apart from the nanopores where reactions actually occur, a "distribution" network of broad pore channels is needed for molecules to quickly move in and out of the catalyst. Despite considerable experimental efforts in the introduction of broad pore channels into nanoporous catalysts in a controllable way, the following generic question remains: which broad pore channel network should be included in a nanoporous catalyst for optimal catalyst performance? To this end, model-based optimizations were used to optimize hierarchically structured porous catalysts, containing both broad pore channels and nanopores. Extensive optimizations showed that, for a single, isothermal reaction, the nanoporous walls (i.e., the nanoporous catalytic material between two neighboring broad pore channels) should be sufficiently thin so that diffusion limitations vanish inside them. It was found that the optimal catalytic performance is dictated by the generalized distributor Thiele modulus, which is defined in a way analogous to the generalized Thiele modulus, but using the molecular diffusivity in the broad pore channels, rather than the effective diffusivity in the nanopores. The use of hierarchically structured porous catalysts was demonstrated for power plant deNOx catalysis and autothermal reforming of methane. For deNOx catalysis, overall catalytic activity in a mesoporous deNOx catalyst with a median pore size of 32.5 nm could be increased by a factor of 1.8-2.8 simply by introducing 8-22mum broad pore channels (occupying 20-40% of

  6. Interfacial Molecular Searching Using Forager Dynamics

    NASA Astrophysics Data System (ADS)

    Monserud, Jon H.; Schwartz, Daniel K.

    2016-03-01

    Many biological and technological systems employ efficient non-Brownian intermittent search strategies where localized searches alternate with long flights. Coincidentally, molecular species exhibit intermittent behavior at the solid-liquid interface, where periods of slow motion are punctuated by fast flights through the liquid phase. Single-molecule tracking was used here to observe the interfacial search process of DNA for complementary DNA. Measured search times were qualitatively consistent with an intermittent-flight model, and ˜10 times faster than equivalent Brownian searches, suggesting that molecular searches for reactive sites benefit from similar efficiencies as biological organisms.

  7. Force fields for classical molecular dynamics.

    PubMed

    Monticelli, Luca; Tieleman, D Peter

    2013-01-01

    In this chapter we review the basic features and the principles underlying molecular mechanics force fields commonly used in molecular modeling of biological macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization philosophies are then presented, followed by a section on force field validation. We conclude with a brief overview on future perspectives for the development of classical force fields.

  8. Gas Diffusion in Polyethylene Terepthalate By Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Butler, Simon; Adolf, David

    2006-03-01

    Molecular dynamics simulations of the diffusion of small penetrants through PET have been performed utilising the anisotropic united atom model [1] and a virtual liquid technique. [2] The accuracy and reliability of these two approaches has been assessed in terms of the improvement in equation of state behaviour and of diffusion co-efficients and solubilities. The effect of the diffusion of nitrogen, carbon dioxide, and oxygen on the local dynamics of PET have been investigated as a result. Attention has been focused on the dual mode effect [3] observed during mixed gas diffusion. [1] Molecular dynamics calculation of the equation of state of alkanes, J. Chem. Phys. 93, 6 (1990) [2] Kikuchi, Kuwajima, Fukada, Novel method to estimate the solubility of small molecules in cis-polyisoprene by molecular dynamics simulations, J. Chem. Phys, 115, 13 (2001) [3] Lewis, Duckett, Ward, Fairclough, Ryan, The barrier properties of polyethylene terephthalate to mixtures of oxygen, carbon dioxide and nitrogen, Polymer, 1631, 44 (2003)

  9. First principles molecular dynamics without self-consistent field optimization

    SciTech Connect

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-28

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

  10. First principles molecular dynamics without self-consistent field optimization.

    PubMed

    Souvatzis, Petros; Niklasson, Anders M N

    2014-01-28

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

  11. Increasing the molecular contacts between maurotoxin and Kv1.2 channel augments ligand affinity.

    PubMed

    M'Barek, Sarrah; Chagot, Benjamin; Andreotti, Nicolas; Visan, Violeta; Mansuelle, Pascal; Grissmer, Stephan; Marrakchi, Mohamed; El Ayeb, Mohamed; Sampieri, François; Darbon, Hervé; Fajloun, Ziad; De Waard, Michel; Sabatier, Jean-Marc

    2005-08-15

    Scorpion toxins interact with their target ion channels through multiple molecular contacts. Because a "gain of function" approach has never been described to evaluate the importance of the molecular contacts in defining toxin affinity, we experimentally examined whether increasing the molecular contacts between a toxin and an ion channel directly impacts toxin affinity. For this purpose, we focused on two scorpion peptides, the well-characterized maurotoxin with its variant Pi1-like disulfide bridging (MTX(Pi1)), used as a molecular template, and butantoxin (BuTX), used as an N-terminal domain provider. BuTX is found to be 60-fold less potent than MTX(Pi1) in blocking Kv1.2 (IC(50) values of 165 nM for BuTX versus 2.8 nM for MTX(Pi1)). Removal of its N-terminal domain (nine residues) further decreases BuTX affinity for Kv1.2 by 5.6-fold, which is in agreement with docking simulation data showing the importance of this domain in BuTX-Kv1.2 interaction. Transfer of the BuTX N-terminal domain to MTX(Pi1) results in a chimera with five disulfide bridges (BuTX-MTX(Pi1)) that exhibits 22-fold greater affinity for Kv1.2 than MTX(Pi1) itself, in spite of the lower affinity of BuTX as compared to MTX(Pi1). Docking experiments performed with the 3-D structure of BuTX-MTX(Pi1) in solution, as solved by (1)H-NMR, reveal that the N-terminal domain of BuTX participates in the increased affinity for Kv1.2 through additional molecular contacts. Altogether, the data indicate that acting on molecular contacts between a toxin and a channel is an efficient strategy to modulate toxin affinity.

  12. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

    2009-04-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(χ, θe, varphie) MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and (θe, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hν = 19 eV, where direct PI is the only channel opened, and hν = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

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

    PubMed

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

    2017-03-07

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

  14. A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit

    NASA Astrophysics Data System (ADS)

    Smith, Edward

    2016-11-01

    What happens to turbulent motions below the Kolmogorov length scale? In order to explore this question, a 300 million molecule Molecular Dynamics (MD) simulation is presented for the minimal Couette channel in which turbulence can be sustained. The regeneration cycle and turbulent statistics show excellent agreement to continuum based computational fluid dynamics (CFD) at Re=400. As MD requires only Newton's laws and a form of inter-molecular potential, it captures a much greater range of phenomena without requiring the assumptions of Newton's law of viscosity, thermodynamic equilibrium, fluid isotropy or the limitation of grid resolution. The fundamental nature of MD means it is uniquely placed to explore the nature of turbulent transport. A number of unique insights from MD are presented, including energy budgets, sub-grid turbulent energy spectra, probability density functions, Lagrangian statistics and fluid wall interactions. EPSRC Post Doctoral Prize Fellowship.

  15. Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

    PubMed

    Yang, Jianjun; Tse, John S

    2011-11-17

    The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.

  16. Discotic columnar liquid crystal studied in the bulk and nanoconfined states by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Busselez, Rémi; Cerclier, Carole V.; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis

    2014-10-01

    A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes.

  17. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Garate, José-A.

    2016-08-01

    An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ˜0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

  18. Tuning Piezo ion channels to detect molecular-scale movements relevant for fine touch

    NASA Astrophysics Data System (ADS)

    Poole, Kate; Herget, Regina; Lapatsina, Liudmila; Ngo, Ha-Duong; Lewin, Gary R.

    2014-03-01

    In sensory neurons, mechanotransduction is sensitive, fast and requires mechanosensitive ion channels. Here we develop a new method to directly monitor mechanotransduction at defined regions of the cell-substrate interface. We show that molecular-scale (~13 nm) displacements are sufficient to gate mechanosensitive currents in mouse touch receptors. Using neurons from knockout mice, we show that displacement thresholds increase by one order of magnitude in the absence of stomatin-like protein 3 (STOML3). Piezo1 is the founding member of a class of mammalian stretch-activated ion channels, and we show that STOML3, but not other stomatin-domain proteins, brings the activation threshold for Piezo1 and Piezo2 currents down to ~10 nm. Structure-function experiments localize the Piezo modulatory activity of STOML3 to the stomatin domain, and higher-order scaffolds are a prerequisite for function. STOML3 is the first potent modulator of Piezo channels that tunes the sensitivity of mechanically gated channels to detect molecular-scale stimuli relevant for fine touch.

  19. Regulation of K+ channel activities in plants: from physiological to molecular aspects.

    PubMed

    Chérel, Isabelle

    2004-02-01

    Plant voltage-gated channels belonging to the Shaker family participate in sustained K+ transport processes at the cell and whole plant levels, such as K+ uptake from the soil solution, long-distance K+ transport in the xylem and phloem, and K+ fluxes in guard cells during stomatal movements. The attention here is focused on the regulation of these transport systems by protein-protein interactions. Clues to the identity of the regulatory mechanisms have been provided by electrophysiological approaches in planta or in heterologous systems, and through analogies with their animal counterparts. It has been shown that, like their animal homologues, plant voltage-gated channels can assemble as homo- or heterotetramers associating polypeptides encoded by different Shaker genes, and that they can bind auxiliary subunits homologous to those identified in mammals. Furthermore, several regulatory processes (involving, for example, protein kinases and phosphatases, G proteins, 14-3-3s, or syntaxins) might be common to plant and animal Shakers. However, the molecular identification of plant channel partners is still at its beginning. This paper reviews current knowledge on plant K+ channel regulation at the physiological and molecular levels, in the light of the corresponding knowledge in animal cells, and discusses perspectives for the deciphering of regulatory networks in the future.

  20. The molecular architecture of dihydropyrindine receptor/L-type Ca2+ channel complex

    PubMed Central

    Hu, Hongli; Wang, Zhao; Wei, Risheng; Fan, Guizhen; Wang, Qiongling; Zhang, Kaiming; Yin, Chang-Cheng

    2015-01-01

    Dihydropyridine receptor (DHPR), an L-type Ca2+ channel complex, plays an essential role in muscle contraction, secretion, integration of synaptic input in neurons and synaptic transmission. The molecular architecture of DHPR complex remains elusive. Here we present a 15-Å resolution cryo-electron microscopy structure of the skeletal DHPR/L-type Ca2+ channel complex. The DHPR has an asymmetrical main body joined by a hook-like extension. The main body is composed of a “trapezoid” and a “tetrahedroid”. Homologous crystal structure docking and site-specific antibody labelling revealed that the α1 and α2 subunits are located in the “trapezoid” and the β subunit is located in the “tetrahedroid”. This structure revealed the molecular architecture of a eukaryotic Ca2+ channel complex. Furthermore, this structure provides structural insights into the key elements of DHPR involved in physical coupling with the RyR/Ca2+ release channel and shed light onto the mechanism of excitation-contraction coupling. PMID:25667046

  1. Alpine Channel and Floodplain Dynamics in the Lake Tahoe Region, California

    NASA Astrophysics Data System (ADS)

    Liquori, M.; Chris, B.; Parris, A.; Heins, A.; Stofleth, J.; Wickland, M.

    2006-12-01

    Alpine floodplains provide diverse habitat components for terrestrial and aquatic species, and strongly influence bank stability and channel migration processes. They also present complex restoration challenges. Several systems in the Lake Tahoe region have been diagnosed with incised channel conditions that generate excessive mobile sediment from eroding banks, degrade riparian vegetation communities, and diminish floodplain wetland abundance and quality. Conventional efforts to restore these systems focus on reconnecting floodplains, primarily through channel or floodplain modifications designed to reestablish floodplain inundation frequency near a Q1.5 level. Recent observations along lower Squaw Creek and the Upper Truckee River suggest that human impacts and climate-induced shifts over the 20th Century appear to significantly change the processes and dynamics between channels and floodplains. Our observations highlight differences in alpine settings as compared with lowland environments. Increased rain-on-snow frequency appears to increase the importance of avulsion and channel widening processes over channel meander processes. Loss of channel sinuosity, increases in depth and changes in channel shape appear to follow rain-on-snow events. These changes affect the overall sediment transport regime, even as snowmelt duration continues to exert the primary influence over dominant discharge relationships. During floods, discontinuous, proximal deposition of coarse sediment replaces uniform, distal deposition of finer sediments, altering the structure of the channel bed and floodplain. Early snowmelt from developed hillslopes saturates floodplains even in the absence of regular flooding, potentially negating or eliminating the restorative benefit of increased flood frequency. These results suggest that effective long-term restoration strategies cannot rely on historic sinuosity patterns or simple flood frequency metrics, but must begin to understand how changes in

  2. Flood plain and channel dynamics of the Quinault and Queets Rivers, Washington, USA

    USGS Publications Warehouse

    O'Connor, J. E.; Jones, M.A.; Haluska, T.L.

    2003-01-01

    Observations from this study and previous studies on the Queets River show that channel and flood-plain dynamics and morphology are affected by interactions between flow, sediment, and standing and entrained wood, some of which likely involve time frames similar to 200–500-year flood-plain half-lives. On the upper Quinault River and Queets River, log jams promote bar growth and consequent channel shifting, short-distance avulsions, and meander cutoffs, resulting in mobile and wide active channels. On the lower Quinault River, large portions of the channel are stable and flow within vegetated flood plains. However, locally, channel-spanning log jams have caused channel avulsions within reaches that have been subsequently mobile for several decades. In all three reaches, log jams appear to be areas of conifer germination and growth that may later further influence channel and flood-plain conditions on long time scales by forming flood-plain areas resistant to channel migration and by providing key members of future log jams. Appreciation of these processes and dynamics and associated temporal and spatial scales is necessary to formulate effective long-term approaches to managing fluvial ecosystems in forested environments.

  3. Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

    SciTech Connect

    Luchko, T.; Simmerling, C.; Gusarov, S.; Roe, D.R., Case, D.A.; Tuszynski, J.; Kovalenko, A.

    2010-02-01

    We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multiple time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package and is illustrated here on alanine-dipeptide and protein-G.

  4. Molecular Dynamics Simulations of Network Glasses

    NASA Astrophysics Data System (ADS)

    Drabold, David A.

    The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References

  5. Electron-Nuclear Dynamics of Molecular Systems

    DTIC Science & Technology

    1994-04-18

    approach with a completely general form of trial function yields the time - dependent Schr ~ dinger equation . Restricting the...dynamical equations approximating the time - dependent SchrOdinger equation . These equations govern the time evolution of the relevant state vector parameters... equations that apprximate the Apuit 18, 1994 time - dependent Schradinger equation and govern the time evolution of

  6. Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Hou, Tingjun; Zhang, Wei; Xu, Xiaojie

    2002-01-01

    We have performed docking and molecular dynamics simulations of hydroxamates complexed with human gelatinase-A (MMP-2) to gain insight into the structural and energetic preferences of these inhibitors. The study was conducted on a selected set of eleven compounds with variation in structure and activity. Molecular dynamics simulations were performed at 300 K for 100 ps with equilibration for 50 ps. The structural analyses of the trajectories indicate that the coordinate bond interactions, the hydrogen bond interactions, the van der Waals interactions as well as the hydrophobic interactions between ligand and receptor are responsible simultaneously for the preference of inhibition and potency. The ligand hydroxamate group is coordinated to the catalytic zinc ion and form stable hydrogen bonds with the carbonyl oxygen of Gly 162. The P1' group makes extensive van der Waals and hydrophobic contacts with the nonpolar side chains of several residues in the S1' subsite, including Leu 197, Val 198, Leu 218 and Tyr 223. Moreover, four to eight hydrogen bonds between hydroxamates and MMP-2 are formed to stabilize the inhibitors in the active site. Compared with the P2' and P3' groups, the P1' groups of inhibitors are oriented regularly, which is produced by the restrain of the S1' subsite. From the relationship between the length of the nonpolar P1' group and the biological activity, we confirm that MMP-2 has a pocket-like S1' subsite, not a channel-like S1' subsite proposed by Kiyama (Kiyama, R. et al., J. Med. Chem. 42 (1999), 1723). The energetic analyses show that the experimental binding free energies can be well correlated with the interactions between the inhibitors and their environments, which could be used as a simple score function to evaluate the binding affinities for other similar hydroxamates. The validity of the force field parameters and the MD simulations can be fully testified by the satisfactory agreements between the experimental structure

  7. Molecular Characterization of the Role of a Calcium Channel in Plant Development

    SciTech Connect

    Karen S. Schumaker

    2004-12-21

    A stimulus-induced change in cellular Ca2+ levels is a critical component of energy transduction in plant and animal development. Demonstrating Ca2+'s involvement in any developmental process requires identification of mechanisms that regulate these Ca2+ changes. In plants, biochemical studies have implicated the activity of Ca2+ channels in increases in cellular Ca2+ levels; however, molecular evidence for these transporters is lacking. Our studies used the mosses Physcomitrella patens and Funaria hygrometrica to establish a role for Ca2+ in hormone-induced morphogenesis and to use this developmental process to identify transporters responsible for increasing cytosolic Ca2+ levels. Using 1,4-dihydropyridines (DHPs), molecules that block Ca2+ movement through voltage-dependent channels in animal cells, we have shown that Ca2+ is important early in the transition from filamentous to meristematic-like growth that occurs in response to the plant hormone cytokinin. In addition to inhibiting moss growth (see below), these Ca2+ channel blockers prevent Ca2+ transport into moss cells (Schumaker and Gizinski, 1993) and bind specifically to two proteins in the moss plasma membrane (Schumaker and Gizinski, 1994; 1996; Dietrich et al., unpublished results). We used tandem mass spectrometry of the partially purified DHP-binding proteins with the goal of identifying the putative Ca2+ channel and providing sequence information for studies to understand channel expression, regulation, structure, and function during development. In addition, we used insertional mutagenesis to identify additional components of the pathway underlying hormone-induced morphogenesis.

  8. Molecular identity of axonal sodium channels in human cortical pyramidal cells

    PubMed Central

    Tian, Cuiping; Wang, Kaiyan; Ke, Wei; Guo, Hui; Shu, Yousheng

    2014-01-01

    Studies in rodents revealed that selective accumulation of Na+ channel subtypes at the axon initial segment (AIS) determines action potential (AP) initiation and backpropagation in cortical pyramidal cells (PCs); however, in human cortex, the molecular identity of Na+ channels distributed at PC axons, including the AIS and the nodes of Ranvier, remains unclear. We performed immunostaining experiments in human cortical tissues removed surgically to cure brain diseases. We found strong immunosignals of Na+ channels and two channel subtypes, NaV1.2 and NaV1.6, at the AIS of human cortical PCs. Although both channel subtypes were expressed along the entire AIS, the peak immunosignals of NaV1.2 and NaV1.6 were found at proximal and distal AIS regions, respectively. Surprisingly, in addition to the presence of NaV1.6 at the nodes of Ranvier, NaV1.2 was also found in a subpopulation of nodes in the adult human cortex, different from the absence of NaV1.2 in myelinated axons in rodents. NaV1.1 immunosignals were not detected at either the AIS or the nodes of Ranvier of PCs; however, they were expressed at interneuron axons with different distribution patterns. Further experiments revealed that parvalbumin-positive GABAergic axon cartridges selectively innervated distal AIS regions with relatively high immunosignals of NaV1.6 but not the proximal NaV1.2-enriched compartments, suggesting an important role of axo-axonic cells in regulating AP initiation in human PCs. Together, our results show that both NaV1.2 and NaV1.6 (but not NaV1.1) channel subtypes are expressed at the AIS and the nodes of Ranvier in adult human cortical PCs, suggesting that these channel subtypes control neuronal excitability and signal conduction in PC axons. PMID:25294986

  9. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    SciTech Connect

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  10. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    DOE PAGES

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; ...

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of themore » substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  11. Dynamic NHERF interaction with TRPC4/5 proteins is required for channel gating by diacylglycerol

    PubMed Central

    Storch, Ursula; Forst, Anna-Lena; Pardatscher, Franziska; Erdogmus, Serap; Philipp, Maximilian; Gregoritza, Manuel; Mederos y Schnitzler, Michael; Gudermann, Thomas

    2017-01-01

    The activation mechanism of the classical transient receptor potential channels TRPC4 and -5 via the Gq/11 protein-phospholipase C (PLC) signaling pathway has remained elusive so far. In contrast to all other TRPC channels, the PLC product diacylglycerol (DAG) is not sufficient for channel activation, whereas TRPC4/5 channel activity is potentiated by phosphatidylinositol 4,5-bisphosphate (PIP2) depletion. As a characteristic structural feature, TRPC4/5 channels contain a C-terminal PDZ-binding motif allowing for binding of the scaffolding proteins Na+/H+ exchanger regulatory factor (NHERF) 1 and 2. PKC inhibition or the exchange of threonine for alanine in the C-terminal PDZ-binding motif conferred DAG sensitivity to the channel. Altogether, we present a DAG-mediated activation mechanism for TRPC4/5 channels tightly regulated by NHERF1/2 interaction. PIP2 depletion evokes a C-terminal conformational change of TRPC5 proteins leading to dynamic dissociation of NHERF1/2 from the C terminus of TRPC5 as a prerequisite for DAG sensitivity. We show that NHERF proteins are direct regulators of ion channel activity and that DAG sensitivity is a distinctive hallmark of TRPC channels. PMID:27994151

  12. Molecular identification of an N-type Ca2+ channel in saccular hair cells.

    PubMed

    Ramakrishnan, N A; Drescher, M J; Sheikhali, S A; Khan, K M; Hatfield, J S; Dickson, M J; Drescher, D G

    2006-01-01

    We report new molecular evidence for the presence of an N-type (Ca(v)2.2, alpha1B) voltage-gated Ca(2+) channel in hair cells of the saccular epithelium of the rainbow trout. The Ca(v)2.2 amino-acid sequence shows 68% and 63% identity compared with chick and human Ca(v)2.2, respectively. This channel reveals features that are characteristic of an N-type Ca(2+) channel: an omega-conotoxin GVIA binding domain, G(betagamma) binding regions, and a synaptic protein interaction site. Immunohistochemical studies with a custom antibody show that immunoreactivity for the Ca(v)2.2 is concentrated in the basolateral and apical regions of hair cells. Whereas trout brain and saccular macula express an 11-amino-acid insert in the second G(betagamma) binding domain of the Ca(v)2.2 I-II loop, isolated hair cells appear not to express this variant. We constructed fusion polypeptides representing portions of the I-II loop, beta1 and beta2a auxiliary subunits, the II-III loop, and syntaxin, and examined their intermolecular interactions via immunoprecipitation and surface plasmon resonance. The I-II loop polypeptides bound both beta1 and beta2a subunits with a preference for beta1, and the II-III loop exhibited Ca(2+)-dependent syntaxin binding. We demonstrated syntaxin immunoreactivity near afferent endings in hair cells, at hair-cell apices, and in efferent endings on hair cells, the former two sites consistent with binding of syntaxin to Ca(v)2.2. The present molecular characterization of the Ca(v)2.2 channel provides novel biochemical evidence for an N-type channel in hair cells, and details molecular interactions of this channel that reflect hair-cell function, such as spontaneous activity and vesicular trafficking. The current work, to our knowledge, represents the first demonstration of a putative N-type channel in hair cells as documented by tissue-specific antibody immunoreactivity and hair-cell-specific cDNA sequence.

  13. Dynamic expression of genes encoding subunits of inward rectifier potassium (Kir) channels in the yellow fever mosquito Aedes aegypti.

    PubMed

    Yang, Zhongxia; Statler, Bethanie-Michelle; Calkins, Travis L; Alfaro, Edna; Esquivel, Carlos J; Rouhier, Matthew F; Denton, Jerod S; Piermarini, Peter M

    2017-02-01

    Inward rectifier potassium (Kir) channels play fundamental roles in neuromuscular, epithelial, and endocrine function in mammals. Recent research in insects suggests that Kir channels play critical roles in the development, immune function, and excretory physiology of fruit flies and/or mosquitoes. Moreover, our group has demonstrated that mosquito Kir channels may serve as valuable targets for the development of novel insecticides. Here we characterize the molecular expression of 5 mRNAs encoding Kir channel subunits in the yellow fever mosquito, Aedes aegypti: Kir1, Kir2A-c, Kir2B, Kir2B', and Kir3. We demonstrate that 1) Kir mRNA expression is dynamic in whole mosquitoes, Malpighian tubules, and the midgut during development from 4th instar larvae to adult females, 2) Kir2B and Kir3 mRNA levels are reduced in 4th instar larvae when reared in water containing an elevated concentration (50mM) of KCl, but not NaCl, and 3) Kir mRNAs are differentially expressed in the Malpighian tubules, midgut, and ovaries within 24h after blood feeding. Furthermore, we provide the first characterization of Kir mRNA expression in the anal papillae of 4th instar larval mosquitoes, which indicates that Kir2A-c is the most abundant. Altogether, the data provide the first comprehensive characterization of Kir mRNA expression in Ae. aegypti and offer insights into the putative physiological roles of Kir subunits in this important disease vector.

  14. Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics

    NASA Astrophysics Data System (ADS)

    Ehrlicher, Allen

    2012-02-01

    Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.

  15. Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

    NASA Astrophysics Data System (ADS)

    McCammon, J. Andrew

    2002-03-01

    Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

  16. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    PubMed

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

    2015-02-13

    Biological transport is supported by 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 analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and 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 motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  17. 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.

  18. Molecular basis of proton block of L-type Ca2+ channels

    PubMed Central

    1996-01-01

    Hydrogen ions are important regulators of ion flux through voltage- gated Ca2+ channels but their site of action has been controversial. To identify molecular determinants of proton block of L-type Ca2+ channels, we combined site-directed mutagenesis and unitary current recordings from wild-type (WT) and mutant L-type Ca2+ channels expressed in Xenopus oocytes. WT channels in 150 mM K+ displayed two conductance states, deprotonated (140 pS) and protonated (45 pS), as found previously in native L-type Ca2+ channels. Proton block was altered in a unique fashion by mutation of each of the four P-region glutamates (EI-EIV) that form the locus of high affinity Ca2+ interaction. Glu(E)-->Gln(Q) substitution in either repeats I or III abolished the high-conductance state, as if the titration site had become permanently protonated. While the EIQ mutant displayed only an approximately 40 pS conductance, the EIIIQ mutant showed the approximately 40 pS conductance plus additional pH-sensitive transitions to an even lower conductance level. The EIVQ mutant exhibited the same deprotonated and protonated conductance states as WT, but with an accelerated rate of deprotonation. The EIIQ mutant was unusual in exhibiting three conductance states (approximately 145, 102, 50 pS, respectively). Occupancy of the low conductance state increased with external acidification, albeit much higher proton concentration was required than for WT. In contrast, the equilibrium between medium and high conductance levels was apparently pH-insensitive. We concluded that the protonation site in L-type Ca2+ channels lies within the pore and is formed by a combination of conserved P-region glutamates in repeats I, II, and III, acting in concert. EIV lies to the cytoplasmic side of the site but exerts an additional stabilizing influence on protonation, most likely via electrostatic interaction. These findings are likely to hold for all voltage-gated Ca2+ channels and provide a simple molecular explanation

  19. Sodium channel selectivity and conduction: prokaryotes have devised their own molecular strategy.

    PubMed

    Finol-Urdaneta, Rocio K; Wang, Yibo; Al-Sabi, Ahmed; Zhao, Chunfeng; Noskov, Sergei Y; French, Robert J

    2014-02-01

    Striking structural differences between voltage-gated sodium (Nav) channels from prokaryotes (homotetramers) and eukaryotes (asymmetric, four-domain proteins) suggest the likelihood of different molecular mechanisms for common functions. For these two channel families, our data show similar selectivity sequences among alkali cations (relative permeability, Pion/PNa) and asymmetric, bi-ionic reversal potentials when the Na/K gradient is reversed. We performed coordinated experimental and computational studies, respectively, on the prokaryotic Nav channels NaChBac and NavAb. NaChBac shows an "anomalous," nonmonotonic mole-fraction dependence in the presence of certain sodium-potassium mixtures; to our knowledge, no comparable observation has been reported for eukaryotic Nav channels. NaChBac's preferential selectivity for sodium is reduced either by partial titration of its highly charged selectivity filter, when extracellular pH is lowered from 7.4 to 5.8, or by perturbation-likely steric-associated with a nominally electro-neutral substitution in the selectivity filter (E191D). Although no single molecular feature or energetic parameter appears to dominate, our atomistic simulations, based on the published NavAb crystal structure, revealed factors that may contribute to the normally observed selectivity for Na over K. These include: (a) a thermodynamic penalty to exchange one K(+) for one Na(+) in the wild-type (WT) channel, increasing the relative likelihood of Na(+) occupying the binding site; (b) a small tendency toward weaker ion binding to the selectivity filter in Na-K mixtures, consistent with the higher conductance observed with both sodium and potassium present; and (c) integrated 1-D potentials of mean force for sodium or potassium movement that show less separation for the less selective E/D mutant than for WT. Overall, tight binding of a single favored ion to the selectivity filter, together with crucial inter-ion interactions within the pore, suggests

  20. Quantum and quasiclassical dynamics of the multi-channel H + H2S reaction

    NASA Astrophysics Data System (ADS)

    Qi, Ji; Lu, Dandan; Song, Hongwei; Li, Jun; Yang, Minghui

    2017-03-01

    The prototypical multi-channel reaction H + H2S → H2 + SH/H + H2S has been investigated using the full-dimensional quantum scattering and quasi-classical trajectory methods to unveil the underlying competition mechanism between different product channels and the mode specificity. This reaction favors the abstraction channel over the exchange channel. For both channels, excitations in the two stretching modes promote the reaction with nearly equal efficiency and are more efficient than the bending mode excitation. However, they are all less efficient than the translational energy. In addition, the experimentally observed non-Arrhenius temperature dependence of the thermal rate constants is reasonably reproduced by the quantum dynamics calculations, confirming that the non-Arrhenius behavior is caused by the pronounced quantum tunneling.

  1. Feedback channel in linear noiseless dynamic systems controlled over the packet erasure network

    NASA Astrophysics Data System (ADS)

    Farhadi, Alireza

    2015-08-01

    This paper is concerned with tracking state trajectory at remote controller, stability and performance of linear time-invariant noiseless dynamic systems with multiple observations over the packet erasure network subject to random packet dropout and transmission delay that does not necessarily use feedback channel full time. Three cases are considered in this paper: (1) without feedback channel, (2) with feedback channel intermittently and (3) with full time availability of feedback channel. For all three cases, coding strategies that result in reliable tracking of state trajectory at remote controller with asymptotically zero mean absolute estimation error are presented. Asymptotic mean absolute stability of the controlled system equipped with each of these coding strategies is shown; trade-offs between duty cycle for feedback channel use, transmission delay and performance, which is defined in terms of the settling time, are studied.

  2. Statistical characterization of the dynamic human body communication channel at 45 MHz.

    PubMed

    Nie, Zedong; Ma, Jingjing; Chen, Hong; Wang, Lei

    2013-01-01

    The dynamic human body communication (HBC) propagation channel at 45 MHz was statistical characterized in this paper. A large amount of measurement data has been gathered in practical environment with real activities -treadmill running at different speeds in a lab room. The received power between two lower legs was acquired from three volunteers, with more than 60,000 snap shot of data in total. The statistical analyses confirmed that the HBC propagation channel at 45 MHz followed the Gamma and Lognormal distributions at the slower (2 km/h and 4 km/h) and faster (6 km/h and 8 km/h) running activities, respectively. The channel is insensitive to body motion with the maximum average fade duration is 0.0413 s and the most averaging bad channel duration time being less than 60 ms with the percentage of the bad channel duration time being less than 4.35%.

  3. Molecular Basis of the Membrane Interaction of the β2e Subunit of Voltage-Gated Ca(2+) Channels.

    PubMed

    Kim, Dong-Il; Kang, Mooseok; Kim, Sangyeol; Lee, Juhwan; Park, Yongsoo; Chang, Iksoo; Suh, Byung-Chang

    2015-09-01

    The auxiliary β subunit plays an important role in the regulation of voltage-gated calcium (CaV) channels. Recently, it was revealed that β2e associates with the plasma membrane through an electrostatic interaction between N-terminal basic residues and anionic phospholipids. However, a molecular-level understanding of β-subunit membrane recruitment in structural detail has remained elusive. In this study, using a combination of site-directed mutagenesis, liposome-binding assays, and multiscale molecular-dynamics (MD) simulation, we developed a physical model of how the β2e subunit is recruited electrostatically to the plasma membrane. In a fluorescence resonance energy transfer assay with liposomes, binding of the N-terminal peptide (23 residues) to liposome was significantly increased in the presence of phosphatidylserine (PS) and phosphatidylinositol 4,5-bisphosphate (PIP2). A mutagenesis analysis suggested that two basic residues proximal to Met-1, Lys-2 (K2) and Trp-5 (W5), are more important for membrane binding of the β2e subunit than distal residues from the N-terminus. Our MD simulations revealed that a stretched binding mode of the N-terminus to PS is required for stable membrane attachment through polar and nonpolar interactions. This mode obtained from MD simulations is consistent with experimental results showing that K2A, W5A, and K2A/W5A mutants failed to be targeted to the plasma membrane. We also investigated the effects of a mutated β2e subunit on inactivation kinetics and regulation of CaV channels by PIP2. In experiments with voltage-sensing phosphatase (VSP), a double mutation in the N-terminus of β2e (K2A/W5A) increased the PIP2 sensitivity of CaV2.2 and CaV1.3 channels by ∼3-fold compared with wild-type β2e subunit. Together, our results suggest that membrane targeting of the β2e subunit is initiated from the nonspecific electrostatic insertion of N-terminal K2 and W5 residues into the membrane. The PS-β2e interaction observed here

  4. Molecular Basis of the Membrane Interaction of the β2e Subunit of Voltage-Gated Ca2+ Channels

    PubMed Central

    Kim, Dong-Il; Kang, Mooseok; Kim, Sangyeol; Lee, Juhwan; Park, Yongsoo; Chang, Iksoo; Suh, Byung-Chang

    2015-01-01

    The auxiliary β subunit plays an important role in the regulation of voltage-gated calcium (CaV) channels. Recently, it was revealed that β2e associates with the plasma membrane through an electrostatic interaction between N-terminal basic residues and anionic phospholipids. However, a molecular-level understanding of β-subunit membrane recruitment in structural detail has remained elusive. In this study, using a combination of site-directed mutagenesis, liposome-binding assays, and multiscale molecular-dynamics (MD) simulation, we developed a physical model of how the β2e subunit is recruited electrostatically to the plasma membrane. In a fluorescence resonance energy transfer assay with liposomes, binding of the N-terminal peptide (23 residues) to liposome was significantly increased in the presence of phosphatidylserine (PS) and phosphatidylinositol 4,5-bisphosphate (PIP2). A mutagenesis analysis suggested that two basic residues proximal to Met-1, Lys-2 (K2) and Trp-5 (W5), are more important for membrane binding of the β2e subunit than distal residues from the N-terminus. Our MD simulations revealed that a stretched binding mode of the N-terminus to PS is required for stable membrane attachment through polar and nonpolar interactions. This mode obtained from MD simulations is consistent with experimental results showing that K2A, W5A, and K2A/W5A mutants failed to be targeted to the plasma membrane. We also investigated the effects of a mutated β2e subunit on inactivation kinetics and regulation of CaV channels by PIP2. In experiments with voltage-sensing phosphatase (VSP), a double mutation in the N-terminus of β2e (K2A/W5A) increased the PIP2 sensitivity of CaV2.2 and CaV1.3 channels by ∼3-fold compared with wild-type β2e subunit. Together, our results suggest that membrane targeting of the β2e subunit is initiated from the nonspecific electrostatic insertion of N-terminal K2 and W5 residues into the membrane. The PS-β2e interaction observed here

  5. Multi-channel probes to understand fission dynamics

    SciTech Connect

    Mosby, Shea Morgan

    2016-04-15

    Explaining the origin of the elements is a major outstanding question in nuclear astrophysics. Observed elemental abundance distribution shows strong nuclear physics effects. In conclusion, neutron-induced reactions are important for nuclear astrophysics and applied fields in nuclear energy and security. LANSCE has a program to address many of these questions directly with neutron beams on (near-)stable nuclei. Increasing demand for correlated data to test details of fission models poses additional challenges. Possibilities exist to extend existing experimental efforts to radioactive beam facilities. Kinematic focusing from using inverse kinematics has potential to circumvent some challenges associated with measuring correlations between fission output channels.

  6. The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.

    PubMed

    Furukawa-Hagiya, Tomoka; Furuta, Tadaomi; Chiba, Shuntaro; Sohma, Yoshiro; Sakurai, Minoru

    2013-01-10

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a "closed-apo" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions.

  7. Molecular dynamics studies of pathways of water movement in cyanobacterial photosystem II

    SciTech Connect

    Gabdulkhakov, A. G. Kljashtorny, V. G.; Dontsova, M. V.

    2015-01-15

    Photosystem II (PSII) catalyzes the light-induced generation of oxygen from water. The oxygen-evolving complex is buried deep in the protein on the lumenal side of PSII, and water molecules need to pass through protein subunits to reach the active site—the manganese cluster. Previous studies on the elucidation of water channels in PSII were based on an analysis of the cavities in the static PSII structure determined by X-ray diffraction. In the present study, we perform molecular dynamics simulations of the water movement in the transport system of PSII.

  8. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels.

    PubMed Central

    Im, W; Seefeld, S; Roux, B

    2000-01-01

    A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (; Biophys. J. 77:139-153). The GCMC/BD algorithm is illustrated with simulations of simple test systems and of the OmpF porin of Escherichia coli. The approach provides a framework for simulating ion permeation in the context of detailed microscopic models. PMID:10920012

  9. State-to-state dynamics of molecular energy transfer

    SciTech Connect

    Gentry, W.R.; Giese, C.F.

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  10. AceCloud: Molecular Dynamics Simulations in the Cloud.

    PubMed

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  11. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    PubMed

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-07

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

  12. Trillion-atom molecular dynamics becomes a reality

    SciTech Connect

    Kadau, Kai; Germann, Timothy C

    2008-01-01

    By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.

  13. Nonholonomic Hamiltonian method for molecular dynamics simulations of reacting shocks

    NASA Astrophysics Data System (ADS)

    Bass, Joseph; Fahrenthold, Eric P.

    2017-01-01

    Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general the potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new nonholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations, and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted parameters.

  14. Electron-phonon interaction within classical molecular dynamics

    SciTech Connect

    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 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.

  15. Electron-phonon interaction within classical molecular dynamics

    DOE PAGES

    Tamm, A.; Samolyuk, G.; Correa, A. 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

  16. 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.

  17. 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.

  18. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

    PubMed Central

    Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus

    2014-01-01

    Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171

  19. Dynamic Mode Decomposition of Jet in Channel Crossflow

    NASA Astrophysics Data System (ADS)

    Wu, Zhao; Laurence, Dominique

    2016-11-01

    In this paper, the authors present a comparative analysis of Koopman modes computed from snap-shots of direct numerical simulations of a jet in channel crossflow (channel flow Re number = 3333, jet-to-crossflow velocity ratio = 1/6). The flow is complex due to interactions between the jet and the cross-flow, and contains geometry-dependent large-scale coherent structures; thus, the Koopman mode analysis provides a powerful tool for studying the spatial and spectral information of the flow. The Koopman modes are approximated by the DMD modes restricted to Krylov subspace, and the Koopman modes isolate structures associated with single frequency only. In this work, we address issues related to the physical interpretation of the DMD modes. The results show that the computed Koopman modes identify the relevant frequencies and the corresponding three-dimensional flow structures automatically. We present the selected DMD modes, which show big differences in the spatial structures and frequency. The shear layer vortices are separated from the horseshoe vortex. These modes have large amplitudes among all modes obtained. Acknowledging the IT Services at The University of Manchester, the use of ARCHER HPC allocated via UK EPSRC Turbulence Consortium (EPSRC Grant EP/L000261/1), the use of BlueGene/Q supercomputer sponsored by EDF R&D centre Chatou and Cedric Flageul.

  20. Static and dynamical properties of a hard-disk fluid confined to a narrow channel.

    PubMed

    Godfrey, M J; Moore, M A

    2014-03-01

    The thermodynamic properties of disks moving in a channel sufficiently narrow that they can collide only with their nearest neighbors can be solved exactly by determining the eigenvalues and eigenfunctions of an integral equation. Using it, we have determined the correlation length ξ of this system. We have developed an approximate solution which becomes exact in the high-density limit. It describes the system in terms of defects in the regular zigzag arrangement of disks found in the high-density limit. The correlation length is then effectively the spacing between the defects. The time scales for defect creation and annihilation are determined with the help of transition-state theory, as is the diffusion coefficient of the defects, and these results are found to be in good agreement with molecular dynamics simulations. On compressing the system with the Lubachevsky-Stillinger procedure, jammed states are obtained whose packing fractions ϕJ are a function of the compression rate γ. We find a quantitative explanation of this dependence by making use of the Kibble-Zurek hypothesis. We have also determined the point-to-set length scale ξPS for this system. At a packing fraction ϕ close to its largest value ϕmax, ξPS has a simple power law divergence, ξPS∼1/(1-ϕ/ϕmax), while ξ diverges much faster, ln(ξ)∼1/(1-ϕ/ϕmax).

  1. Contact line and contact angle dynamics in superhydrophobic channels.

    PubMed

    Zhang, Junfeng; Kwok, Daniel Y

    2006-05-23

    The dynamics of the wetting and movement of a three-phase contact line confined between two superhydrophobic surfaces were studied using a mean-field free-energy lattice Boltzmann model. Principle features of superhydrophobic surfaces, such as trapped vapor/air between rough microstructures, high contact angles, reduced contact angle hysteresis, and low resistance to fluid flow, were all observed. Movement of the three-phase contact line over a well-patterned superhydrophobic surface displays a periodic stick-jump-slip behavior, while the dynamic contact angle changes accordingly from maximum to minimum. Two regimes were found for the flow velocity as a function of surface roughness and can be related directly to the balance between driving force and flow resistance. This work provides a better understanding of dynamic wetting and fluid flow behaviors over superhydrophobic surfaces and hence could be useful in related applications.

  2. Imaging the molecular dynamics of dissociative electron attachment to water

    SciTech Connect

    Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali

    2009-10-19

    Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.

  3. Mesoscopic Dynamics of Biopolymers and Protein Molecular Machines

    NASA Astrophysics Data System (ADS)

    Kapral, Raymond

    2013-03-01

    The dynamics of biopolymers in solution and in crowded molecular environments, which mimic some features of the interior of a biochemical cell, will be discussed. In particular, the dynamics of protein machines that utilize chemical energy to effect cyclic conformational changes to carry out their catalytic functions will be described. The investigation of the dynamics of such complex systems requires knowledge of the time evolution on physically relevant long distance and time scales. This often necessitates a coarse grained or mesoscopic treatment of the dynamics. A hybrid particle-based mesoscopic dynamical method, which combines molecular dynamics for a coarse-grain model of the proteins with multiparticle collision dynamics for the solvent, will be described and utilized to study the dynamics of such systems. See, C. Echeverria, Y. Togashi, A. S. Mikhailov, and R. Kapral, Phys. Chem. Chem. Phys 13, 10527 (2011); C. Echeverria and R. Kapral, Phys. Chem. Chem. Phys., 14, 6755 (2012); J. M. Schofield, P. Inder and R. Kapral, J. Chem. Phys. 136, 205101 (2012). Work was supported in part by a grant from the Natural Sciences and Engineering Research Council of Canada.

  4. Molecular Basis of Regulating High Voltage-Activated Calcium Channels by S-Nitrosylation.

    PubMed

    Zhou, Meng-Hua; Bavencoffe, Alexis; Pan, Hui-Lin

    2015-12-18

    Nitric oxide (NO) is involved in a variety of physiological processes, such as vasoregulation and neurotransmission, and has a complex role in the regulation of pain transduction and synaptic transmission. We have shown previously that NO inhibits high voltage-activated Ca(2+) channels in primary sensory neurons and excitatory synaptic transmission in the spinal dorsal horn. However, the molecular mechanism involved in this inhibitory action remains unclear. In this study, we investigated the role of S-nitrosylation in the NO regulation of high voltage-activated Ca(2+) channels. The NO donor S-nitroso-N-acetyl-DL-penicillamine (SNAP) rapidly reduced N-type currents when Cav2.2 was coexpressed with the Cavβ1 or Cavβ3 subunits in HEK293 cells. In contrast, SNAP only slightly inhibited P/Q-type and L-type currents reconstituted with various Cavβ subunits. SNAP caused a depolarizing shift in voltage-dependent N-type channel activation, but it had no effect on Cav2.2 protein levels on the membrane surface. The inhibitory effect of SNAP on N-type currents was blocked by the sulfhydryl-specific modifying reagent methanethiosulfonate ethylammonium. Furthermore, the consensus motifs of S-nitrosylation were much more abundant in Cav2.2 than in Cav1.2 and Cav2.1. Site-directed mutagenesis studies showed that Cys-805, Cys-930, and Cys-1045 in the II-III intracellular loop, Cys-1835 and Cys-2145 in the C terminus of Cav2.2, and Cys-346 in the Cavβ3 subunit were nitrosylation sites mediating NO sensitivity of N-type channels. Our findings demonstrate that the consensus motifs of S-nitrosylation in cytoplasmically accessible sites are critically involved in post-translational regulation of N-type Ca(2+) channels by NO. S-Nitrosylation mediates the feedback regulation of N-type channels by NO.

  5. Molecular and functional significance of Ca2+-activated Cl− channels in pulmonary arterial smooth muscle

    PubMed Central

    Forrest, Abigail S.; Ayon, Ramon J.; Wiwchar, Michael; Angermann, Jeff E.; Pritchard, Harry A. T.; Singer, Cherie A.; Valencik, Maria L.; Britton, Fiona; Greenwood, Iain A.

    2015-01-01

    Abstract Increased peripheral resistance of small distal pulmonary arteries is a hallmark signature of pulmonary hypertension (PH) and is believed to be the consequence of enhanced vasoconstriction to agonists, thickening of the arterial wall due to remodeling, and increased thrombosis. The elevation in arterial tone in PH is attributable, at least in part, to smooth muscle cells of PH patients being more depolarized and displaying higher intracellular Ca2+ levels than cells from normal subjects. It is now clear that downregulation of voltage-dependent K+ channels (e.g., Kv1.5) and increased expression and activity of voltage-dependent (Cav1.2) and voltage-independent (e.g., canonical and vanilloid transient receptor potential [TRPC and TRPV]) Ca2+ channels play an important role in the functional remodeling of pulmonary arteries in PH. This review focuses on an anion-permeable channel that is now considered a novel excitatory mechanism in the systemic and pulmonary circulations. It is permeable to Cl− and is activated by a rise in intracellular Ca2+ concentration (Ca2+-activated Cl− channel, or CaCC). The first section outlines the biophysical and pharmacological properties of the channel and ends with a description of the molecular candidate genes postulated to encode for CaCCs, with particular emphasis on the bestrophin and the newly discovered TMEM16 and anoctamin families of genes. The second section provides a review of the various sources of Ca2+ activating CaCCs, which include stimulation by mobilization from intracellular Ca2+ stores and Ca2+ entry through voltage-dependent and voltage-independent Ca2+ channels. The third and final section summarizes recent findings that suggest a potentially important role for CaCCs and the gene TMEM16A in PH. PMID:26064450

  6. Molecular characterization of genes encoding inward rectifier potassium (Kir) channels in the bed bug (Cimex lectularius).

    PubMed

    Mamidala, Praveen; Mittapelly, Priyanka; Jones, Susan C; Piermarini, Peter M; Mittapalli, Omprakash

    2013-04-01

    The molecular genetics of inward-rectifier potassium (Kir) channels in insects is poorly understood. To date, Kir channel genes have been characterized only from a few representative dipterans (i.e., fruit flies and mosquitoes). The goal of the present study was to characterize Kir channel cDNAs in a hemipteran, the bed bug (Cimex lectularius). Using our previously reported bed bug transcriptome (RNA-seq), we identified two cDNAs that encode putative Kir channels. One was a full-length cDNA that encodes a protein belonging to the insect 'Kir3' clade, which we designate as 'ClKir3'. The other was a partial cDNA that encodes a protein with similarity to both the insect 'Kir1' and 'Kir2' clades, which we designate as 'ClKir1/2'. Quantitative real-time PCR analysis revealed that ClKir1/2 and ClKir3 exhibited peak expression levels in late-instar nymphs and early-instar nymphs, respectively. Furthermore, ClKir3, but not ClKir1/2, showed tissue-specific expression in Malpighian tubules of adult bed bugs. Lastly, using an improved procedure for delivering double-stranded RNA (dsRNA) to male and female bed bugs (via the cervical membrane) we demonstrate rapid and systemic knockdown of ClKir3 transcripts. In conclusion, we demonstrate that the bed bug possesses at least two genes encoding Kir channels, and that RNAi is possible for at least Kir3, thereby offering a potential approach for elucidating the roles of Kir channel genes in bed bug physiology.

  7. Multiobjective Optimization of Low-Energy Trajectories Using Optimal Control on Dynamical Channels

    NASA Technical Reports Server (NTRS)

    Coffee, Thomas M.; Anderson, Rodney L.; Lo, Martin W.

    2011-01-01

    We introduce a computational method to design efficient low-energy trajectories by extracting initial solutions from dynamical channels formed by invariant manifolds, and improving these solutions through variational optimal control. We consider trajectories connecting two unstable periodic orbits in the circular restricted 3-body problem (CR3BP). Our method leverages dynamical channels to generate a range of solutions, and approximates the areto front for impulse and time of flight through a multiobjective optimization of these solutions based on primer vector theory. We demonstrate the application of our method to a libration orbit transfer in the Earth-Moon system.

  8. Molecular Dynamics Simulation of Fluid Transport in Nanoscale Pore of Porous Medium

    NASA Astrophysics Data System (ADS)

    Chu, Y.; Lu, J. F.; Lu, W. Q.

    2010-03-01

    In this paper, the Poiseuille water flow inside a nanosized channel style pore formed by two solid parallel walls is studied using molecular dynamics (MD) simulation. Alumina has been chosen as the material of the wall. The flow is initiated by applying a uniform external force on each water molecule inside the channel. Periodic boundary conditions are imposed for the simulation. 12-6 L-J potentials are chosen in the simulation to describe H2O-H2O molecule interactions as well as H2O-Al2O3 molecule interactions. The present work aims at finding that, in the process of hemodialysis, how the filtration velocity and slip boundaries inside the pore of a filtration membrane are affected by the magnitude of the applied external force and how the results are different from that of the simplified Kedem-Ketchalsky (1958) equations employing the present physical parameters.

  9. A restricted nonlinear-dynamics model for turbulent channel flows

    NASA Astrophysics Data System (ADS)

    Lozano-Durán, Adrián; Jiménez, Javier; Farrell, Brian F.; Ioannou, Petros J.; Nikolaidis, Marios A.; Constantinou, Navid C.

    2014-11-01

    The dynamics of the formation of very-large scale structure in turbulent plane Poiseuille flow is studied by restricting the nonlinearity in the Navier-Stokes (NS) equations to interactions between the streamwise-averaged flow and perturbations. Using comparisons with DNS, we show that this restricted nonlinear dynamics (RNL) supports essentially realistic turbulence at Reτ = 900 , despite the naturally occurring severe reduction in the set of streamwise wavenumbers supporting the turbulence. Using statistical diagnostics we verify that there are similar self-sustaining processes (SSP) underlying turbulence in the RNL and in the NS dynamics, separate manifestations of which operate in the buffer and outer layers. In the buffer layer, the SSP supports the familiar roll-streak mechanism of wall-bounded turbulence, while the outer-layer streaks in the RNL are probably the streamwise elongated structures referred to as VLSI. It is argued that the formation of the roll-streak structure is a universal mechanism that can be fruitfully studied in the minimal dynamics of RNL. Funded by Multiflow project of the ERC, Navid Constantinou acknowledges the support of the Alexander S. Onassis Public Benefit Foundation. Brian Farrell was supported by NSF AGS-1246929.

  10. Analyte distribution at channel intersections of electro-fluid-dynamic devices.

    PubMed

    Liu, Chang; Luo, Yong; Fang, Ning; Chen, David D Y

    2011-02-15

    Mass conservation is the guiding principle for analyte distribution at channel intersections of microfluidic devices, where analyte migration is mainly driven by an applied electric field, and in electro-fluid-dynamic (EFD) devices, where multiple fields and pressures can be applied simultaneously on the same channel network. This paper introduces another type of conservation, the conservation of effective volumetric flow rate, at channel intersections when the conductivity of the solution in the intersecting channels is maintained constant. This conservation principle provides an additional criterion needed to describe analyte migration in channels connecting to a common intersection and to predict how analyte is distributed into individual channels in the channel network of EFD devices, when multiple voltages and pressures are applied. The theoretical bases of effective volumetric flow rate balance are discussed, and the potential use of this principle in conjunction with the principle of mass conservation to predict the migration behavior of analytes is demonstrated. Junctions of different geometry in EFD devices are used to demonstrate the validity of these equations, and the measured velocities and numbers of microbeads in each channel agree with the predicted values.

  11. Applications of Langevin and Molecular Dynamics methods

    NASA Astrophysics Data System (ADS)

    Lomdahl, P. S.

    Computer simulation of complex nonlinear and disordered phenomena from materials science is rapidly becoming an active and new area serving as a guide for experiments and for testing of theoretical concepts. This is especially true when novel massively parallel computer systems and techniques are used on these problems. In particular the Langevin dynamics simulation technique has proven useful in situations where the time evolution of a system in contact with a heat bath is to be studied. The traditional way to study systems in contact with a heat bath has been via the Monte Carlo method. While this method has indeed been used successfully in many applications, it has difficulty addressing true dynamical questions. Large systems of coupled stochastic ODE's (or Langevin equations) are commonly the end result of a theoretical description of higher dimensional nonlinear systems in contact with a heat bath. The coupling is often local in nature, because it reflects local interactions formulated on a lattice, the lattice for example represents the underlying discreteness of a substrate of atoms or discrete k-values in Fourier space. The fundamental unit of parallelism thus has a direct analog in the physical system the authors are interested in. In these lecture notes the authors illustrate the use of Langevin stochastic simulation techniques on a number of nonlinear problems from materials science and condensed matter physics that have attracted attention in recent years. First, the authors review the idea behind the fluctuation-dissipation theorem which forms that basis for the numerical Langevin stochastic simulation scheme. The authors then show applications of the technique to various problems from condensed matter and materials science.

  12. Molecular packing and magnetic properties of lithium naphthalocyanine crystals: hollow channels enabling permeability and paramagnetic sensitivity to molecular oxygen

    PubMed Central

    Pandian, Ramasamy P.; Dolgos, Michelle; Marginean, Camelia; Woodward, Patrick M.; Hammel, P. Chris; Manoharan, Periakaruppan T.; Kuppusamy, Periannan

    2009-01-01

    The synthesis, structural framework, magnetic and oxygen-sensing properties of a lithium naphthalocyanine (LiNc) radical probe are presented. LiNc was synthesized in the form of a microcrystalline powder using a chemical method and characterized by electron paramagnetic resonance (EPR) spectroscopy, magnetic susceptibility, powder X-ray diffraction analysis, and mass spectrometry. X-Ray powder diffraction studies revealed a structural framework that possesses long, hollow channels running parallel to the packing direction. The channels measured approximately 5.0 × 5.4 Å2 in the two-dimensional plane perpendicular to the length of the channel, enabling diffusion of oxygen molecules (2.9 × 3.9 Å2) through the channel. The powdered LiNc exhibited a single, sharp EPR line under anoxic conditions, with a peak-to-peak linewidth of 630 mG at room temperature. The linewidth was sensitive to surrounding molecular oxygen, showing a linear increase in pO2 with an oxygen sensitivity of 31.2 mG per mmHg. The LiNc microcrystals can be further prepared as nano-sized crystals without the loss of its high oxygen-sensing properties. The thermal variation of the magnetic properties of LiNc, such as the EPR linewidth, EPR intensity and magnetic susceptibility revealed the existence of two different temperature regimes of magnetic coupling and hence differing columnar packing, both being one-dimensional antiferromagnetic chains but with differing magnitudes of exchange coupling constants. At a temperature of ∼50 K, LiNc crystals undergo a reversible phase transition. The high degree of oxygen-sensitivity of micro- and nano-sized crystals of LiNc, combined with excellent stability, should enable precise and accurate measurements of oxygen concentration in biological systems using EPR spectroscopy. PMID:19809598

  13. The neuron as a dynamic electrogenic machine: modulation of sodium-channel expression as a basis for functional plasticity in neurons.

    PubMed Central

    Waxman, S G

    2000-01-01

    Neurons signal each other via regenerative electrical impulses (action potentials) and thus can be thought of as electrogenic machines. Voltage-gated sodium channels produce the depolarizations necessary for action potential activity in most neurons and, in this respect, lie close to the heart of the electrogenic machinery. Although classical neurophysiological doctrine accorded 'the' sodium channel a crucial role in electrogenesis, it is now clear that nearly a dozen genes encode distinct sodium channels with different molecular structures and functional properties, and the majority of these channels are expressed within the mammalian nervous system. The transcription of these sodium-channel genes, and the deployment of the channels that they encode, can change significantly within neurons following various injuries. Moreover, the transcription of these genes and the deployment of various types of sodium channels within neurons of the normal nervous system can change markedly as neurons respond to changing milieus or physiological inputs. As a result of these changes in sodium-channel expression, the membranes of neurons may be retuned so as to alter their transductive and/or encoding properties. Neurons within the normal and injured nervous system can thus function as dynamic electrogenic machines with electroresponsive properties that change not only in response to pathological insults, but also in response to shifting functional needs. PMID:10724456

  14. Molecular Chaperone Calnexin Regulates the Function of Drosophila Sodium Channel Paralytic

    PubMed Central

    Xiao, Xi; Chen, Changyan; Yu, Tian-Ming; Ou, Jiayao; Rui, Menglong; Zhai, Yuanfen; He, Yijing; Xue, Lei; Ho, Margaret S.

    2017-01-01

    Neuronal activity mediated by voltage-gated channels provides the basis for higher-order behavioral tasks that orchestrate life. Chaperone-mediated regulation, one of the major means to control protein quality and function, is an essential route for controlling channel activity. Here we present evidence that Drosophila ER chaperone Calnexin colocalizes and interacts with the α subunit of sodium channel Paralytic. Co-immunoprecipitation analysis indicates that Calnexin interacts with Paralytic protein variants that contain glycosylation sites Asn313, 325, 343, 1463, and 1482. Downregulation of Calnexin expression results in a decrease in Paralytic protein levels, whereas overexpression of the Calnexin C-terminal calcium-binding domain triggers an increase reversely. Genetic analysis using adult climbing, seizure-induced paralysis, and neuromuscular junction indicates that lack of Calnexin expression enhances Paralytic-mediated locomotor deficits, suppresses Paralytic-mediated ghost bouton formation, and regulates minature excitatory junction potentials (mEJP) frequency and latency time. Taken together, our findings demonstrate a need for chaperone-mediated regulation on channel activity during locomotor control, providing the molecular basis for channlopathies such as epilepsy. PMID:28326013

  15. Molecular mechanisms of lipoic acid modulation of T-type calcium channels in pain pathway

    PubMed Central

    Lee, Woo Yong; Orestes, Peihan; Latham, Janelle; Naik, Ajit K.; Nelson, Michael T.; Vitko, Iuliia; Perez-Reyes, Edward; Jevtovic-Todorovic, Vesna; Todorovic, Slobodan M.

    2011-01-01

    α-Lipoic acid (1,2-dithiolane-3-pentanoic acid; lipoic acid) is an endogenous compound used to treat pain disorders in humans, but its mechanisms of analgesic action are not well understood. Here we show that lipoic acid selectively inhibited native CaV3.2 T-type calcium currents (T-currents) and diminished T-channel-dependent cellular excitability in acutely isolated rat sensory neurons. Lipoic acid locally injected into peripheral receptive fields of pain-sensing sensory neurons (nociceptors) in vivo decreased sensitivity to noxious thermal and mechanical stimuli in wild-type but not CaV3.2 knockout mice. Ensuing molecular studies demonstrated that lipoic acid inhibited recombinant CaV3.2 channels heterologously expressed in human embryonic kidney 293 cells by oxidating specific thiol residues on the cytoplasmic face of the channel. This study provides the first mechanistic demonstration of a nociceptive ion channel modulation that may contribute to the documented analgesic properties of lipoic acid in vivo. PMID:19641113

  16. Theory of multiexciton dynamics in molecular chains

    NASA Astrophysics Data System (ADS)

    Wang, Luxia; May, Volkhard

    2016-11-01

    Ultrafast and strong optical excitation of a molecular system is considered which is formed by a regular one-dimensional arrangement of identical molecules. As it is typical for zinc chlorine-type molecules the transition energy from the ground state to the first excited singlet state is assumed to be smaller than the energy difference between the first excited state and the following one. This enables the creation of many excitons without their immediate quenching due to exciton-exciton annihilation. As a first step into the field of dense Frenkel-exciton systems the present approach stays at a mean-field type of description and ignores vibrational contributions. The resulting nonlinear kinetic equations mix Rabi-type oscillations with those caused by energy transfer and suggest an excitation-dependent narrowing of the exciton band. The indication of this effect in the framework of a two-color pump-probe experiment and of the detection of photon emission is discussed.

  17. Molecular dynamics simulation of aqueous solutions of glycine betaine

    NASA Astrophysics Data System (ADS)

    Civera, Monica; Fornili, Arianna; Sironi, Maurizio; Fornili, Sandro L.

    2003-01-01

    Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine- N-oxide, a bioprotectant closely related to glycine betaine.

  18. 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.

  19. Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

    DTIC Science & Technology

    2008-07-17

    Medical Research and Materiel Command, Fort Detrick, Maryland #Department of Cell Biology and Biochemistry , U.S. Army Medical Research Institute of...Molecular dynamics of n- alkanes ," J. Comput. Phys., vol. 23, pp. 327-341, 1977. [24] S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M

  20. Reasoning with Atomic-Scale Molecular Dynamic Models

    ERIC Educational Resources Information Center

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  1. Optimizing legacy molecular dynamics software with directive-based offload

    SciTech Connect

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-05-14

    The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.

  2. Optimizing legacy molecular dynamics software with directive-based offload

    DOE PAGES

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; ...

    2015-05-14

    The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less

  3. 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

  4. 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.

  5. Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor

    PubMed Central

    Raharjo, Sentot Joko; Kikuchi, Takeshi

    2016-01-01

    Objective: Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor. Methods: Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software. Result: The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2. Conclusion: Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor. PMID:28077888

  6. Molecular Characterization of Neurally Expressing Genes in the Para Sodium Channel Gene Cluster of Drosophila

    PubMed Central

    Hong, C. S.; Ganetzky, B.

    1996-01-01

    To elucidate the mechanisms regulating expression of para, which encodes the major class of sodium channels in the Drosophila nervous system, we have tried to locate upstream cis-acting regulatory elements by mapping the transcriptional start site and analyzing the region immediately upstream of para in region 14D of the polytene chromosomes. From these studies, we have discovered that the region contains a cluster of neurally expressing genes. Here we report the molecular characterization of the genomic organization of the 14D region and the genes within this region, which are: calnexin (Cnx), actin related protein 14D (Arp14D), calcineurin A 14D (CnnA14D), and chromosome associated protein (Cap). The tight clustering of these genes, their neuronal expression patterns, and their potential functions related to expression, modulation, or regulation of sodium channels raise the possibility that these genes represent a functionally related group sharing some coordinate regulatory mechanism. PMID:8849894

  7. Comparison of gating dynamics of different IP3R channels with immune algorithm searching for channel parameter distributions

    NASA Astrophysics Data System (ADS)

    Cai, Xiuhong; Li, Xiang; Qi, Hong; Wei, Fang; Chen, Jianyong; Shuai, Jianwei

    2016-10-01

    The gating properties of the inositol 1, 4, 5-trisphosphate (IP3) receptor (IP3R) are determined by the binding and unbinding capability of Ca2+ ions and IP3 messengers. With the patch clamp experiments, the stationary properties have been discussed for Xenopus oocyte type-1 IP3R (Oo-IP3R1), type-3 IP3R (Oo-IP3R3) and Spodoptera frugiperda IP3R (Sf-IP3R). In this paper, in order to provide insights about the relation between the observed gating characteristics and the gating parameters in different IP3Rs, we apply the immune algorithm to fit the parameters of a modified DeYoung-Keizer model. By comparing the fitting parameter distributions of three IP3Rs, we suggest that the three types of IP3Rs have the similar open sensitivity in responding to IP3. The Oo-IP3R3 channel is easy to open in responding to low Ca2+ concentration, while Sf-IP3R channel is easily inhibited in responding to high Ca2+ concentration. We also show that the IP3 binding rate is not a sensitive parameter for stationary gating dynamics for three IP3Rs, but the inhibitory Ca2+ binding/unbinding rates are sensitive parameters for gating dynamics for both Oo-IP3R1 and Oo-IP3R3 channels. Such differences may be important in generating the spatially and temporally complex Ca2+ oscillations in cells. Our study also demonstrates that the immune algorithm can be applied for model parameter searching in biological systems.

  8. CFTR chloride channel is a molecular target of the natural cancer preventive agent resveratrol.

    PubMed

    Yang, Shuang; Yu, B O; Sui, Yujie; Zhang, Yaofang; Wang, Xue; Hou, Shuguang; Ma, Tonghui; Yang, Hong

    2013-09-01

    The naturally occurring polyphenol compound resveratrol (RES) has been receiving wide attention because of its variety of health benefits and favourable biological activities. Previous studies have shown that RES could induce intestinal chloride secretion in mouse jejunum and stimulate cAMP-dependent Cl- secretion in T84, primary cultured murine nasal septal and human sinonasal epithelial cells, but the precise molecular target is not clear. We therefore tested the hypothesis that RES may stimulate the activity of cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. Using cell-based fluorescent assays, transepithelial short-circuit current measurements and excised inside-out patch-clamp analysis; we found that RES dose-dependently potentiate CFTR Cl- channel activities, which was reversed by CFTR inhibitors CFTR(inh)-172 and GlyH101. Transepithelial Cl- secretion by CFTR-expressing FRT cells was stimulated by RES with half maximal concentration -80 microM. Intracellular cAMP content was not elevated by RES in FRT cells. Excised inside-out patch-clamp analysis indicated that RES significantly increased the chloride currents of CFTR. In ex vivo studies, RES stimulated the transmucosal chloride current of rat colon by short-circuit current assay. These data suggested that CFTR is a molecular target of RES. Our findings add a new molecular target to RES, and RES may represent a novel class of therapeutic lead compounds in treating CFTR-related diseases including CF and habitual constipation.

  9. Diversity dynamics: molecular phylogenies need the fossil record.

    PubMed

    Quental, Tiago B; Marshall, Charles R

    2010-08-01

    Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota.

  10. Molecular dynamics simulation of friction of hydrocarbon thin films

    SciTech Connect

    Tamura, Hiroyuki; Yoshida, Muneo; Kusakabe, Kenichi

    1999-10-26

    Molecular Dynamics (MD) simulations were performed to investigate the dynamic behavior of hydrocarbon molecules under shear conditions. Frictional properties of cyclohexane, n-hexane, and iso-hexane thin films confirmed between two solid surfaces were calculated. Because the affinity of the solid surfaces in these simulations is strong, slippages occurred at inner parts of the confined films, whereas no slippages were observed at the solid boundaries. The hexagonal closest packing structure was observed for the adsorbed cyclohexane molecular layers. The branched methyl groups in the iso-hexane molecules increase the shear stress between the molecular layers. For the n-hexane monolayer, molecules were observed to roll during the sliding simulations. Rolling of the n-hexane molecules decreased the shear stress.

  11. A specialized molecular motion opens the Hv1 voltage-gated proton channel

    PubMed Central

    Isacoff, Ehud Y.

    2015-01-01

    Summary The Hv1 proton channel is unique among voltage-gated channels for containing the pore and gate within its voltage-sensing domain (VSD). Opening of the pore has been proposed to include assembly of the selectivity filter between the third arginine (R3) of S4 and an aspartate of S1 (D1). We asked whether gating involves a motion of S1 using Ciona intestinalis Hv1. We find that channel opening is concomitant with solution access from the cytoplasm deep into the pore-lining face of S1. Voltage- and patch-clamp fluorometry show that this involves a motion of S1 relative to its surround. S1 motion, and the S4 motion that precedes it, are each influenced by residues on the other helix, suggesting a dynamic interaction between S1 and S4. Our findings suggest that the S1 of Hv1 has specialized to function as part of the channel's gate. PMID:25730777

  12. Multiscale equation-free algorithms for molecular dynamics

    NASA Astrophysics Data System (ADS)

    Abi Mansour, Andrew

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

  13. Bubble dynamics in a micro-channel with a virtual check valve

    NASA Astrophysics Data System (ADS)

    Chen, Rou; Zhu, Likun; Yu, Huidan (Whitney)

    2015-11-01

    Bubble dynamics plays a critical role in the design of a self-circulation and self-regulation gas generator with little or zero parasitic power consumption (Zhu et al, Microfluidics and Nanofluidics, 2011). We numerically study bubble dynamics in the micro-channel with a virtual check valve using lattice Boltzmann method. The lattice Boltzmann model has been validated through several static cases with a bubble sitting inside a liquid and on a solid surface with a triple contact among bubble, liquid, and solid. In this work, we simulate bubble transport driven via unbalanced capillary forces. Focus will be on the bubble merging phenomena between the moving bubble and a static bubble prior siting downstream in the channel with same and different sizes. By varying the size of the check valve, we study the effects of channel ratio between the check valve and channel on the dynamics of bubble-driven liquid circulation and seek for an optimal channel ratio to support experimental design. This research is supported by NSF Collaborative Research (1264739).

  14. Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.

    PubMed

    Markegard, Cade B; Mazaheripour, Amir; Jocson, Jonah-Micah; Burke, Anthony M; Dickson, Mary N; Gorodetsky, Alon A; Nguyen, Hung D

    2015-09-03

    Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.

  15. Crossed molecular beam studies of atmospheric chemical reaction dynamics

    SciTech Connect

    Zhang, Jingsong

    1993-04-01

    The dynamics of several elementary chemical reactions that are important in atmospheric chemistry are investigated. The reactive scattering of ground state chlorine or bromine atoms with ozone molecules and ground state chlorine atoms with nitrogen dioxide molecules is studied using a crossed molecular beams apparatus with a rotatable mass spectrometer detector. The Cl + O3 → ClO + O2 reaction has been studied at four collision energies ranging from 6 kcal/mole to 32 kcal/mole. The derived product center-of-mass angular and translational energy distributions show that the reaction has a direct reaction mechanism and that there is a strong repulsion on the exit channel. The ClO product is sideways and forward scattered with respect to the Cl atom, and the translational energy release is large. The Cl atom is most likely to attack the terminal oxygen atom of the ozone molecule. The Br + O3 → ClO + O2 reaction has been studied at five collision energies ranging from 5 kcal/mole to 26 kcal/mole. The derived product center-of-mass angular and translational energy distributions are quite similar to those in the Cl + O3 reaction. The Br + O3 reaction has a direct reaction mechanism similar to that of the Cl + O3 reaction. The electronic structure of the ozone molecule seems to play the central role in determining the reaction mechanism in atomic radical reactions with the ozone molecule. The Cl + NO2 → ClO + NO reaction has been studied at three collision energies ranging from 10.6 kcal/mole to 22.4 kcal/mole. The center-of-mass angular distribution has some forward-backward symmetry, and the product translational energy release is quite large. The reaction proceeds through a short-lived complex whose lifetime is less than one rotational period. The experimental results seem to show that the Cl atom mainly attacks the oxygen atom instead of the nitrogen atom of the NO2

  16. Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics.

    PubMed

    Wells, David B; Abramkina, Volha; Aksimentiev, Aleksei

    2007-09-28

    The transport of biomolecules across cell boundaries is central to cellular function. While structures of many membrane channels are known, the permeation mechanism is known only for a select few. Molecular dynamics (MD) is a computational method that can provide an accurate description of permeation events at the atomic level, which is required for understanding the transport mechanism. However, due to the relatively short time scales accessible to this method, it is of limited utility. Here, we present a method for all-atom simulation of electric field-driven transport of large solutes through membrane channels, which in tens of nanoseconds can provide a realistic account of a permeation event that would require a millisecond simulation using conventional MD. In this method, the average distribution of the electrostatic potential in a membrane channel under a transmembrane bias of interest is determined first from an all-atom MD simulation. This electrostatic potential, defined on a grid, is subsequently applied to a charged solute to steer its permeation through the membrane channel. We apply this method to investigate permeation of DNA strands, DNA hairpins, and alpha-helical peptides through alpha-hemolysin. To test the accuracy of the method, we computed the relative permeation rates of DNA strands having different sequences and global orientations. The results of the G-SMD simulations were found to be in good agreement in experiment.

  17. Reaction Ensemble Molecular Dynamics: Direct Simulation of the Dynamic Equilibrium Properties of Chemically Reacting Mixtures

    DTIC Science & Technology

    2006-09-01

    Therefore, dynamic quantities of reaction mixtures such as the velocity autocorrelation functions and the diffusion coefficients can be accurately...using the virial expression [25]. A standard NVT molecular dynamics method was em- ployed with the equations of motion solved using the Verlet leapfrog...configurational energy, pressure, and species concen- trations) are compared to quantities calculated by the RxMC approach. Second , the dynamic quantities

  18. The KATP channel is a molecular sensor of atrophy in skeletal muscle

    PubMed Central

    Tricarico, Domenico; Mele, Antonietta; Camerino, Giulia Maria; Bottinelli, Roberto; Brocca, Lorenza; Frigeri, Antonio; Svelto, Maria; George, Alfred L; Camerino, Diana Conte

    2010-01-01

    The involvement of ATP-sensitive K+ (KATP) channels in the atrophy of slow-twitch (MHC-I) soleus (SOL) and fast-twitch (MHC-IIa) flexor digitorum brevis (FDB) muscles was investigated in vivo in 14-day-hindlimb-unloaded (14-HU) rats, an animal model of disuse, and in vitro in drug-induced muscle atrophy. Patch-clamp and gene expression experiments were performed in combination with measurements of fibre diameters used as an index of atrophy, and with MHC labelling in 14-HU rats and controls. A down-regulation of KATP channel subunits Kir6.2, SUR1 and SUR2B with marked atrophy and incomplete phenotype transition were observed in SOL of 14-HU rats. The observed changes in KATP currents were well correlated with changes in fibre diameters and SUR1 expression, as well as with MHC-IIa expression. Half of the SOL fibres of 14-HU rats had reduced diameter and KATP currents and were labelled by MHC-I antibodies. Non-atrophic fibres were labelled by MHC-IIa (22%) antibodies and had enhanced KATP currents, or were labelled by MHC-I (28%) antibodies but had normal current. FDB was not affected in 14-HU rats and this is related to the high expression/activity of Kir6.2/SUR1 subunits characterizing this muscle phenotype. The long-term incubation of the control muscles in vitro with the KATP channel blocker glibenclamide (10−6m) reduced the KATP currents with atrophy and these effects were prevented by the KATP channel opener diazoxide (10−4m). The in vivo down-regulation of SUR1, and possibly of Kir6.2 and SUR2B, or their in vitro pharmacological blockade activates atrophic signalling in skeletal muscle. All these findings suggest a new role for the KATP channel as a molecular sensor of atrophy. PMID:20064856

  19. Molecular diversity of GABA-gated chloride channels in the rat anterior pituitary.

    PubMed

    Boué-Grabot, E; Dufy, B; Garret, M

    1995-12-15

    mRNA expression of GABA-gated Cl(-)-channels in rat antepituitary was evaluated by using an reverse-transcribed (RT)-polymerase chain reaction (RT-PCR) method with degenerate and specific oligonucleotides. The main result of our findings is that the antepituitary expresses mRNAs encoding alpha 4 and rho 1 GABA receptor subunits. These two subunits are believed to be, respectively, constituents of benzodiazepine-insensitive GABAA and GABAC receptors in the CNS. This molecular analysis is consistent with the pharmacological diversity of GABA receptors in pituitary cells.

  20. Molecular size of different neurotoxin receptors on the voltage-sensitive Na+ channel.

    PubMed

    Barhanin, J; Schmid, A; Lombet, A; Wheeler, K P; Lazdunski, M; Ellory, J C

    1983-01-25

    Measurements were made of the molecular sizes of two distinct receptors on the Na+ channel in rat brain synaptosomes that are specific for different neurotoxins. Radiation inactivation of the binding of radiolabeled derivatives of the toxins was consistent with Mr = 260,000 for the tetrodotoxin receptor and Mr = 266,000 for the receptor specific for two scorpion toxins, toxin II from Centruroides suffusus suffusus and toxin gamma from Tityus serrulatus serrulatus. Covalent cross-linking of the latter to its receptor similarly indicated Mr = 270,000. It seems most likely that these two distinct receptors reside on the same molecule.

  1. Molecular dynamic simulation of Ar-Kr mixture across a rough walled nanochannel: Velocity & temperature profiles

    NASA Astrophysics Data System (ADS)

    Pooja, Pathania, Y.; Ahluwalia, P. K.

    2015-05-01

    This paper presents the results from a molecular dynamics simulation of mixture of argon and krypton in the Poiseuille flow across a rough walled nanochannel. The roughness effect on liquid nanoflows has recently drawn attention The computational software used for carrying out the molecular dynamics simulations is LAMMPS. The fluid flow takes place between two parallel plates and is bounded by horizontal rough walls in one direction and periodic boundary conditions are imposed in the other two directions. Each fluid atom interacts with other fluid atoms and wall atoms through Leenard-Jones (LJ) potential with a cut off distance of 5.0. To derive the flow a constant force is applied whose value is varied from 0.1 to 0.3 and velocity profiles and temperature profiles are noted for these values of forces. The velocity profile and temperature profiles are also looked at different channel widths of nanochannel and at different densities of mixture. The velocity profile and temperature profile of rough walled nanochannel are compared with that of smooth walled nanochannel and it is concluded that mean velocity increases with increase in channel width, force applied and decrease in density also with introduction of roughness in the walls of nanochannel mean velocity again increases and results also agree with the analytical solution of a Poiseuille flow.

  2. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    PubMed Central

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  3. A random rotor molecule: Vibrational analysis and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.

    2012-12-01

    Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.

  4. Molecular dynamics computer simulation of permeation in solids

    SciTech Connect

    Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M.

    1997-12-31

    In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.

  5. Brownian dynamics study of ion transport in the vestibule of membrane channels.

    PubMed

    Li, S C; Hoyles, M; Kuyucak, S; Chung, S H

    1998-01-01

    Brownian dynamics simulations have been carried out to study the transport of ions in a vestibular geometry, which offers a more realistic shape for membrane channels than cylindrical tubes. Specifically, we consider a torus-shaped channel, for which the analytical solution of Poisson's equation is possible. The system is composed of the toroidal channel, with length and radius of the constricted region of 80 A and 4 A, respectively, and two reservoirs containing 50 sodium ions and 50 chloride ions. The positions of each of these ions executing Brownian motion under the influence of a stochastic force and a systematic electric force are determined at discrete time steps of 50 fs for up to 2.5 ns. All of the systematic forces acting on an ion due to the other ions, an external electric field, fixed charges in the channel protein, and the image charges induced at the water-protein boundary are explicitly included in the calculations. We find that the repulsive dielectric force arising from the induced surface charges plays a dominant role in channel dynamics. It expels an ion from the vestibule when it is deliberately put in it. Even in the presence of an applied electric potential of 100 mV, an ion cannot overcome this repulsive force and permeate the channel. Only when dipoles of a favorable orientation are placed along the sides of the transmembrane segment can an ion traverse the channel under the influence of a membrane potential. When the strength of the dipoles is further increased, an ion becomes detained in a potential well, and the driving force provided by the applied field is not sufficient to drive the ion out of the well. The trajectory of an ion navigating across the channel mostly remains close to the central axis of the pore lumen. Finally, we discuss the implications of these findings for the transport of ions across the membrane.

  6. Dynamics of elementary atomic and molecular processes in gases and plasmas

    NASA Astrophysics Data System (ADS)

    Shcheglov, V. A.

    The papers presented in this volume provide an overview of recent theoretical research in the dynamics of atomic-molecular processes in gas and plasma. The theory of bimolecular reactions is developed in the context of a statistical approach. Results of Monte Carlo calculations of two-channel chemical reactions are presented; the cross sections of a number of processes in nuclear, atomic, and molecular physics are calculated within the framework of the quantum theory of scattering. The discussion also covers the ionization of Rydberg atoms colliding with neutral particles, the bremsstrahlung effect associated with the resonance scattering of electrons by atoms, and the elementary process of three-level system decomposition. (No individual items are abstracted in this volume)

  7. Dynamical characterization of inactivation path in voltage-gated Na(+) ion channel by non-equilibrium response spectroscopy.

    PubMed

    Pal, Krishnendu; Gangopadhyay, Gautam

    2016-11-01

    Inactivation path of voltage gated sodium channel has been studied here under various voltage protocols as it is the main governing factor for the periodic occurrence and shape of the action potential. These voltage protocols actually serve as non-equilibrium response spectroscopic tools to study the ion channel in non-equilibrium environment. In contrast to a lot of effort in finding the crystal structure based molecular mechanism of closed-state(CSI) and open-state inactivation(OSI); here our approach is to understand the dynamical characterization of inactivation. The kinetic flux as well as energetic contribution of the closed and open- state inactivation path is compared here for voltage protocols, namely constant, pulsed and oscillating. The non-equilibrium thermodynamic quantities used in response to these voltage protocols serve as improved characterization tools for theoretical understanding which not only agrees with the previously known kinetic measurements but also predict the energetically optimum processes to sustain the auto-regulatory mechanism of action potential and the consequent inactivation steps needed. The time dependent voltage pattern governs the population of the conformational states which when couple with characteristic rate parameters, the CSI and OSI selectivity arise dynamically to control the inactivation path. Using constant, pulsed and continuous oscillating voltage protocols we have shown that during depolarization the OSI path is more favored path of inactivation however, in the hyper-polarized situation the CSI is favored. It is also shown that the re-factorisation of inactivated sodium channel to resting state occurs via CSI path. Here we have shown how the subtle energetic and entropic cost due to the change in the depolarization magnitude determines the optimum path of inactivation. It is shown that an efficient CSI and OSI dynamical profile in principle can characterize the open-state drug blocking phenomena.

  8. Special issue on ultrafast electron and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Martin, Fernando; Hishikawa, Akiyoshi; Vrakking, Marc

    2014-06-01

    In the last few years, the advent of novel experimental and theoretical approaches has made possible the investigation of (time-resolved) molecular dynamics in ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation (HHG) and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain, thus opening completely new avenues for imaging electronic and nuclear dynamics in molecules. Along the way, particular types of molecular dynamics, e.g., dynamics around conical intersections, have gained an increased prominence, sparked by the realization of the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. In the short term, this will allow one to uncover and control the dynamics of elementary chemical processes such as, e.g., ultrafast charge migration, proton transfer, isomerization or multiple ionization, and to address new key questions about the role of attosecond coherent electron dynamics in chemical reactivity. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules, including biomolecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of the current

  9. Selective excitation, relaxation, and energy channeling in molecular systems. Comprehensive progress report, April 1990--July 1993

    SciTech Connect

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems.

  10. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

    NASA Astrophysics Data System (ADS)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

    We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

  11. Ground based monitoring of channel and floodplain inundation dynamics

    NASA Astrophysics Data System (ADS)

    Nghia Hung, Nguyen; Thoss, Heiko; Güntner, Andreas; Apel, Heiko

    2010-05-01

    Monitoring of floodplain inundation is one of the key issues in respect to hydraulic model calibration, especially for 2-dimensional modeling of floodplains. While in recent years the use of remote sensing products for flood mapping have received a large boost by new techniques and platforms (LiDAR, SAR, optical system, both satellite and airborn) and proved to be a significant step forward in floodplain inundation model calibration, they are not the encompassing answer to the chronic lack of data of floodplain inundation. Due to the singular nature of floods and restrictions in sensor availability, overpass frequencies, unfavorable atmospheric conditions and difficulties in signal interpretation, remote sensing products usually provide only a short but spatially extensive view on the inundation process. In order to get a more encompassing picture of the inundation dynamics, time series of flood parameters have to be collected in the floodplains itself. In order to overcome the intrinsic problem of testing flood monitoring equipment in a short termed research project, an extensive ground-based flood monitoring system was established within the WISDOM (www.wisdom.caf.dlr.de) project in the Mekong Delta. Due to annual flood rhythm flood condition could be guaranteed within the projects duration. The test site Tam Nong in the Plain of Reeds in the Delta was equipped with 21 water level pressure gauges, 7 turbidity sensors and 2 GPS buoys, all designed to run autonomously for a period of 6 month and sampling data in short termed intervals. The collected data show a detailed picture of the inundation and sediment dynamics in the whole area including tidal influence and dike overtopping. This unique data set will be used in combination with spatial explicit water masks derived by remote sensing for 2D hydraulic model calibration.

  12. Molecular dynamics simulation and site-directed mutagenesis of alcohol acyltransferase: a proposed mechanism of catalysis.

    PubMed

    Morales-Quintana, Luis; Nuñez-Tobar, María Ximena; Moya-León, María Alejandra; Herrera, Raúl

    2013-10-28

    Aroma in Vasconcellea pubescens fruit is determined by esters, which are the products of catalysis by alcohol acyltransferase (VpAAT1). VpAAT1 protein structure displayed the conserved HxxxD motif facing the solvent channel in the center of the structure. To gain insight into the role of these catalytic residues, kinetic and site-directed mutagenesis studies were carried out in VpAAT1 protein. Based on dead-end inhibition studies, the kinetic could be described in terms of a ternary complex mechanism with the H166 residue as the catalytic base. Kinetic results showed the lowest Km value for hexanoyl-CoA. Additionally, the most favorable predicted substrate orientation was observed for hexanoyl-CoA, showing a coincidence between kinetic studies and molecular docking analysis. Substitutions H166A, D170A, D170N, and D170E were evaluated in silico. The solvent channel in all mutant structures was lost, showing large differences with the native structure. Molecular docking and molecular dynamics simulations were able to describe unfavored energies for the interaction of the mutant proteins with different alcohols and acyl-CoAs. Additionally, in vitro site-directed mutagenesis of H166 and D170 in VpAAT1 induced a loss of activity, confirming the functional role of both residues for the activity, H166 being directly involved in catalysis.

  13. Molecular dynamics simulation: A tool for exploration and discovery

    NASA Astrophysics Data System (ADS)

    Rapaport, Dennis C.

    2009-03-01

    The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).

  14. Ab initio molecular dynamics using hybrid density functionals.

    PubMed

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost

    2008-06-07

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  15. Ab initio molecular dynamics using hybrid density functionals

    NASA Astrophysics Data System (ADS)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  16. A Molecular Dynamics Simulation of Vesicle Deformation and Rupture in Confined Poiseuille Flow

    NASA Astrophysics Data System (ADS)

    Harman, Alison

    Vesicles are simple structures, but display complex, non-linear dynamics in fluid flow. I investigate the deformation of nanometer-sized vesicles, both fully-inflated and those with excess area, as they travel in tightly confined capillaries. By varying both channel size and flow strength, I simulate vesicles as they transition from steady-state to unstable shapes, and then rupture in strong flow fields. By employing a molecular dynamics model of the vesicle, fluid, and capillary system one is able to rupture the lipid bilayer of these vesicles. This is unique in that most other numerical methods for modelling vesicles are unable to show rupture. The rupture of fully-inflated vesicles is applicable to drug delivery in which the release of the encapsulated medicine needs to be controlled. The deformation and rupture of vesicles with excess area could be applicable to red blood cells which have similar rheological properties.

  17. The dynamics of a channel-fed lava flow on Pico Partido volcano, Lanzarote

    NASA Astrophysics Data System (ADS)

    Woodcock, Duncan; Harris, Andrew

    2006-09-01

    A short length of channel on Pico Partido volcano, Lanzarote, provides us the opportunity to examine the dynamics of lava flowing in a channel that extends over a sudden break in slope. The 1 2-m-wide, 0.5 2-m-deep channel was built during the 1730 1736 eruptions on Lanzarote and exhibits a sinuous, well-formed channel over a steep (11° slope) 100-m-long proximal section. Over-flow units comprising smooth pahoehoe sheet flow, as well as evidence on the inner channel walls for multiple (at least 11) flow levels, attest to unsteady flow in the channel. In addition, superelevation is apparent at each of the six bends along the proximal channel section. Superelevation results from banking of the lava as it moves around the bend thus causing preferential construction of the outer bank. As a result, the channel profile at each bend is asymmetric with an outer bank that is higher than the inner bank. Analysis of superelevation indicates flow velocities of ~8 m s 1. Our analysis of the superelevation features is based on an inertia-gravity balance, which we show is appropriate, even though the down-channel flow is in laminar flow. We use a viscosity-gravity balance model, together with the velocities calculated from superelevation, to obtain viscosities in the range 25 60 Pa s (assuming that the lava behaved as a Newtonian liquid). Estimated volume fluxes are in the range 7 12 m3 s 1. An apparent down-flow increase in derived volume flux may have resulted from variable supply or bulking up of the flow due to vesiculation. Where the channel moves over a sharp break in slope and onto slopes of ~6°, the channel becomes less well defined and widens considerably. At the break of slope, an elongate ridge extends across the channel. We speculate that this ridge was formed as a result of a reduction in velocity immediately below the break of slope to allow deposition of entrained material or accretion of lava to the channel bed as a result of a change in flow regime or depth.

  18. An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations.

    PubMed

    Law, Richard J; Munson, Keith; Sachs, George; Lightstone, Felice C

    2008-09-15

    Gastric H,K-ATPase is an electroneutral transmembrane pump that moves protons from the cytoplasm of the parietal cell into the gastric lumen in exchange for potassium ions. The mechanism of transport against the established electrochemical gradients includes intermediate conformations in which the transferred ions are trapped (occluded) within the membrane domain of the pump. The pump cycle involves switching between the E1 and E2P states. Molecular dynamics simulations on homology models of the E2P and E1 states were performed to investigate the mechanism of K(+) movement in this enzyme. We performed separate E2P simulations with one K(+) in the luminal channel, one K(+) ion in the occlusion site, two K(+) ions in the occlusion site, and targeted molecular dynamics from E2P to E1 with two K(+) ions in the occlusion site. The models were inserted into a lipid bilayer system and were stable over the time course of the simulations, and K(+) ions in the channel moved to a consistent location near the center of the membrane domain, thus defining the occlusion site. The backbone carbonyl oxygen from residues 337 through 342 on the nonhelical turn of M4, as well as side-chain oxygen from E343, E795, and E820, participated in the ion occlusion. A single water molecule was stably bound between the two K(+) ions in the occlusion site, providing an additional ligand and partial shielding the positive charges from one another. Targeted molecular dynamics was used to transform the protein from the E2P to the E1 state (two K(+) ions to the cytoplasm). This simulation identified the separation of the water column in the entry channel as the likely gating mechanism on the luminal side. A hydrated exit channel also formed on the cytoplasmic side of the occlusion site during this simulation. Hence, water molecules became available to hydrate the ions. The movement of the M1M2 transmembrane segments, and the displacement of residues Q159, E160, Q110, and T152 during the

  19. Molecular, Biophysical, and Pharmacological Properties of Calcium-Activated Chloride Channels.

    PubMed

    Kamaleddin, Mohammad Amin

    2017-01-25

    Calcium-activated chloride channels (CaCCs) are a family of anionic transmembrane ion channels. They are mainly responsible for the movement of Cl(-) and other anions across the biological membranes and are widely expressed in different tissues. Due to the fact that Cl(-) flow into or out of the cell plays a crucial role in hyperpolarizing or depolarizing the cells, respectively, the impact of intracellular Ca(2+) concentration on these channels is attracting a lot of attentions. After summarizing the molecular, biophysical, and pharmacological properties of CaCCs, the role of CaCCs in normal cellular functions will be discussed, and I will emphasize how dysregulation of CaCCs in pathological conditions can account for different diseases. A better understanding of CaCCs and a pivotal regulatory role of Ca(2+) can shed more light on the therapeutic strategies for different neurological disorders that arise from chloride dysregulation, such as asthma, cystic fibrosis, and neuropathic pain. This article is protected by copyright. All rights reserved.

  20. Molecular interactions involved in proton-dependent gating in KcsA potassium channels

    PubMed Central

    Posson, David J.; Thompson, Ameer N.; McCoy, Jason G.

    2013-01-01

    The bacterial potassium channel KcsA is gated open by the binding of protons to amino acids on the intracellular side of the channel. We have identified, via channel mutagenesis and x-ray crystallography, two pH-sensing amino acids and a set of nearby residues involved in molecular interactions that influence gating. We found that the minimal mutation of one histidine (H25) and one glutamate (E118) near the cytoplasmic gate completely abolished pH-dependent gating. Mutation of nearby residues either alone or in pairs altered the channel’s response to pH. In addition, mutations of certain pairs of residues dramatically increased the energy barriers between the closed and open states. We proposed a Monod–Wyman–Changeux model for proton binding and pH-dependent gating in KcsA, where H25 is a “strong” sensor displaying a large shift in pKa between closed and open states, and E118 is a “weak” pH sensor. Modifying model parameters that are involved in either the intrinsic gating equilibrium or the pKa values of the pH-sensing residues was sufficient to capture the effects of all mutations. PMID:24218397

  1. Ground based monitoring of channel and floodplain inundation dynamics

    NASA Astrophysics Data System (ADS)

    Apel, H.; Hung, N. N.; Güntner, A.; Thoss, H.

    2009-12-01

    Monitoring of floodplain inundation is one of the key issues in respect to hydraulic model calibration, especially for 2-dimensional modeling of floodplains. While in recent years the use of remote sensing products for flood mapping have received a large boost by new techniques and platforms (LiDAR, SAR, optical system, both satellite and airborn) and proved to be a significant step forward in floodplain inundation model calibration, they are not the encompassing answer to the chronic lack of data of floodplain inundation. Due to the singular nature of floods and restrictions in sensor availability, overpass frequencies, unfavorable atmospheric conditions and difficulties in signal interpretation, remote sensing products usually provide only a short but spatially extensive view on the inundation process. In order to get a more encompassing picture of the inundation dynamics, time series of flood parameters have to be collected in the floodplains itself. In order to overcome the intrinsic problem of testing flood monitoring equipment in a short termed research project, an extensive ground-based flood monitoring system was established within the WISDOM (www.wisdom.caf.dlr.de) project in the Mekong Delta. Due to annual flood rhythm flood condition could be guaranteed within the projects duration. The test site Tam Nong in the Plain of Reeds in the Delta was equipped with 21 water level pressure gauges, 7 turbidity sensors and 2 GPS buoys, all designed to run autonomously for a period of 6 month and sampling data in short termed intervals. The equipment used range from cheap pressure sensors to rather expensive developments like the GPS buoys. Nevertheless, overall costs of the systems are comparatively low, especially in cost-benefit considerations. This is because they are developed for continuous monitoring, are modular in their sensor configuration and movable, i.e. reusable. The collected data show a detailed picture of the inundation and sediment dynamics in the

  2. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  3. Molecular dynamics of liquid lead near its melting point

    SciTech Connect

    Khusnutdinov, R. M.; Mokshin, A. V. Yul'met'ev, R. M.

    2009-03-15

    The molecular dynamics of liquid lead is simulated at T = 613 K using the following three models of an interparticle interaction potential: the Dzugutov pair potential and two multiparticle potentials (the 'glue' potential and the Gupta potential). One of the purposes of this work is to determine the optimal model potential of the interatomic interaction in liquid lead. The calculated structural static and dynamic characteristics are compared with the experimental data on X-ray and neutron scattering. On the whole, all three model potentials adequately reproduce the experimental data. The calculations using the Dzugutov pair potential are found to reproduce the structural properties and dynamics of liquid lead on the nanoscale best of all. The role of a multiparticle contribution to the glue and Gupta potentials is studied, and its effect on the dynamic properties of liquid lead in nanoregions is revealed. In particular, the neglect of this contribution is shown to noticeably decrease the acoustic-mode frequency.

  4. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    SciTech Connect

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-03-14

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  5. A molecular dynamics study of polymer/graphene interfacial systems

    SciTech Connect

    Rissanou, Anastassia N.; Harmandaris, Vagelis

    2014-05-15

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

  6. Anomalous flow behavior in nanochannels: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Murad, Sohail; Luo, Lin; Chu, Liang-Yin

    2010-06-01

    We report molecular dynamics simulations of flow of water in nanochannels with a range of surface wettability characteristics (hydrophobic to strongly hydrophilic) and driving forces (pressures). Our results show apparently anomalous behavior. At low pressures, the rate is higher in nanochannels with hydrophilic surfaces than that with hydrophobic surfaces; however, with high pressure driven flow we observe opposite trends. This apparently anomalous behavior can be explained on the basis of molecular thermodynamics and fluid mechanics considerations. Understanding such behavior is important in many nanofluidic devices such as nanoreactors, nanosensors, and nanochips that are increasingly being designed and used.

  7. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps.

    PubMed

    Ruggerone, Paolo; Vargiu, Attilio V; Collu, Francesca; Fischer, Nadine; Kandt, Christian

    2013-01-01

    Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  8. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    PubMed Central

    Ruggerone, Paolo; Vargiu, Attilio V.; Collu, Francesca; Fischer, Nadine; Kandt, Christian

    2013-01-01

    Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa. PMID:24688701

  9. Two-dimensional fluid dynamics in a sharply bent channel: Laminar flow, separation bubble, and vortex dynamics

    NASA Astrophysics Data System (ADS)

    Matsumoto, Daichi; Fukudome, Koji; Wada, Hirofumi

    2016-10-01

    Understanding the hydrodynamic properties of fluid flow in a curving pipe and channel is important for controlling the flow behavior in technologies and biomechanics. The nature of the resulting flow in a bent pipe is extremely complicated because of the presence of a cross-stream secondary flow. In an attempt to disentangle this complexity, we investigate the fluid dynamics in a bent channel via the direct numerical simulation of the Navier-Stokes equation in two spatial dimensions. We exploit the absence of secondary flow from our model and systematically investigate the flow structure along the channel as a function of both the bend angle and Reynolds number of the laminar-to-turbulent regime. We numerically suggest a scaling relation between the shape of the separation bubble and the flow conductance, and construct an integrated phase diagram.

  10. Mechanisms of cation permeation in cardiac sodium channel: description by dynamic pore model.

    PubMed Central

    Kurata, Y; Sato, R; Hisatome, I; Imanishi, S

    1999-01-01

    The selective permeability to monovalent metal cations, as well as the relationship between cation permeation and gating kinetics, was investigated for native tetrodotoxin-insensitive Na-channels in guinea pig ventricular myocytes using the whole-cell patch clamp technique. By the measurement of inward unidirectional currents and biionic reversal potentials, we demonstrate that the cardiac Na-channel is substantially permeable to all of the group Ia and IIIa cations tested, with the selectivity sequence Na(+) >/= Li(+) > Tl(+) > K(+) > Rb(+) > Cs(+). Current kinetics was little affected by the permeant cation species and concentrations tested (channel. The permeability ratios determined from biionic reversal potentials were concentration and orientation dependent: the selectivity to Na(+) increased with increasing internal [K(+)] or external [Tl(+)]. The dynamic pore model describing the conformational transition of the Na-channel pore between different selectivity states could account for all the experimental data, whereas conventional static pore models failed to fit the concentration-dependent permeability ratio data. We conclude that the dynamic pore mechanism, independent of the gating machinery, may play an important physiological role in regulating the selective permeability of native Na-channels. PMID:10512810

  11. Efficient massively parallel simulation of dynamic channel assignment schemes for wireless cellular communications

    NASA Technical Reports Server (NTRS)

    Greenberg, Albert G.; Lubachevsky, Boris D.; Nicol, David M.; Wright, Paul E.

    1994-01-01

    Fast, efficient parallel algorithms are presented for discrete event simulations of dynamic channel assignment schemes for wireless cellular communication networks. The driving events are call arrivals and departures, in continuous time, to cells geographically distributed across the service area. A dynamic channel assignment scheme decides which call arrivals to accept, and which channels to allocate to the accepted calls, attempting to minimize call blocking while ensuring co-channel interference is tolerably low. Specifically, the scheme ensures that the same channel is used concurrently at different cells only if the pairwise distances between those cells are sufficiently large. Much of the complexity of the system comes from ensuring this separation. The network is modeled as a system of interacting continuous time automata, each corresponding to a cell. To simulate the model, conservative methods are used; i.e., methods in which no errors occur in the course of the simulation and so no rollback or relaxation is needed. Implemented on a 16K processor MasPar MP-1, an elegant and simple technique provides speedups of about 15 times over an optimized serial simulation running on a high speed workstation. A drawback of this technique, typical of conservative methods, is that processor utilization is rather low. To overcome this, new methods were developed that exploit slackness in event dependencies over short intervals of time, thereby raising the utilization to above 50 percent and the speedup over the optimized serial code to about 120 times.

  12. Molecular and functional expression of high conductance Ca 2+ activated K+ channels in the eel intestinal epithelium.

    PubMed

    Lionetto, Maria G; Rizzello, Antonia; Giordano, Maria E; Maffia, Michele; De Nuccio, Francesco; Nicolardi, Giuseppe; Hoffmann, Else K; Schettino, Trifone

    2008-01-01

    Several types of K(+) channels have been identified in epithelial cells. Among them high conductance Ca(2+)-activated K(+) channels (BK channels) are of relevant importance for their involvement in regulatory volume decrease (RVD) response following hypotonic stress. The aim of the present work was to investigate the functional and molecular expression of BK in the eel intestine, which is a useful experimental model for cell volume regulation research. In the present paper using rat BK channel-specific primer, a RT-PCR signal of 696 pb cDNA was detected in eel intestine, whole nucleotide sequence showed high similarity (83%) to the alpha subunit of BK channel family. BK channel protein expression was verified by immunoblotting and confocal microscopy, while the functional role of BK channels in epithelial ion transport mechanisms and cell volume regulation was examined by electrophysiological and morphometric analysis on the intact tissue. BK(Ca) channels appeared to be localized along all the plasma membrane of the enterocytes; the apical part of the villi showed the most intense immunostaining. These channels were silent in basal condition, but were activated on both membranes (apical and basolateral) by increasing intracellular Ca(2+) concentration with the Ca(2+) ionophore ionomycin (1 microM). BK(Ca) channels were also activated on both membranes by hypotonic swelling of the epithelium and their inhibition by 100 nM iberiotoxin (specific BK(Ca) inhibitor) abolished the Regulatory Volume Decrease (RVD) of the intestinal cells after hypotonic swelling. In conclusion, our results demonstrated the molecular and functional expression of high conductance Ca(2+) -activated K(+) channels in eel intestine; the physiological role of these channels is mainly related to the RVD response of the epithelial cells following hypotonic swelling.

  13. Molecular Dynamics Simulations of Ibuprofen Release from pH-Gated Silica Nanochannels.

    PubMed

    Rodriguez, Javier; Elola, M Dolores

    2015-07-23

    The iboprufen delivery process from cylindrical silica pores of 3 nm diameter, with polyamine chains anchored at the pore outlets, was investigated by means of massive molecular dynamics simulations. Effects from pH were introduced by considering polyamine chains with different degrees of protonation. High, low, and intermediate pH environments were investigated. The increment of the acidity of the environment leads to a significant decrease of the pore aperture, yielding an effective diameter, for the lowest pH case, that is 3.5 times smaller than the one associated with the highest pH one. Using a biased sampling procedure, Gibbs free energy profiles for the ibuprofen delivery process were obtained. The joint analysis of the corresponding profiles, time evolution of the ibuprofen position within the channel, orientation of the molecule, and instantaneous effective diameter of the gate suggest a three-step mechanism for ibuprofen delivery. A complementary analysis of the translational mobility of ibuprofen along the axial direction of the channel revealed a subdiffusive dynamics in the low and intermediate pH cases. Deviations from Brownian diffusive dynamics are discussed and compared with direct experimental results.

  14. 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.

  15. A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

    ERIC Educational Resources Information Center

    Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

    2010-01-01

    As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

  16. Molecular docking study of the binding of aminopyridines within the K+ channel.

    PubMed

    Caballero, Norma Angélica; Meléndez, Francisco Javier; Niño, Alfonso; Muñoz-Caro, Camelia

    2007-05-01

    We present a molecular docking study aimed to identify the binding site of protonated aminopyridines for the blocking of voltage dependent K(+) channels. Several active aminopyridines are considered: 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, 3,4-diaminopyridine, and 4-aminoquinoleine. We apply the AutoDock force field with a lamarckian genetic algorithm, using atomic charges for the ligands derived from the electrostatic potential obtained at the B3LYP/cc-pVDZ level. We find a zone in the alpha-subunit of the K(+) channel bearing common binding sites. This zone corresponds to five amino acids comprised between residuals Thr107 and Ala111, in the KcsA K(+) channel (1J95 pdb structure). The 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, and 3,4-diaminopyridine bind to the carboxylic oxygens of Thr107 and Ala111. In all cases aminopyridines are perpendicular to the axis of the pore. 4-aminoquinoleine binds to the carboxylic oxygen of Ala111. Due to its large size, the molecular plane is parallel to the axis of the pore. The charge distributions and the structures of the binding complexes suggest that the interaction is driven by formation of several hydrogen bonds. We find 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, and 3,4-diaminopyridine with similar binding energy. Considering the standard error of the estimate of the AutoDock force field, this energy should lie, as a rough estimation, in the interval 3-7 kcal mol(-1). On the other hand, 4-aminoquinoleine seems to have a smaller binding energy.

  17. Probabilistic Evaluation of Anthropogenic Regulations In a Vegetated River Channel Using a Vegetation Dynamics Modeling

    NASA Astrophysics Data System (ADS)

    Miyamoto, Hitoshi

    2015-04-01

    Vegetation overgrowth in fluvial floodplains, gravel beds, and sand bars has been a serious engineering problem for riparian management in Japan. From the viewpoints of flood control and ecological conservation, it would be necessary to predict the vegetation dynamics accurately for long-term duration. In this research, we have developed a stochastic model for predicting the vegetation dynamics in fluvial floodplains with emphasis on the interaction with flood impacts. The model consists of the following four components: (i) long-term stochastic behavior of flow discharge, (ii) hydrodynamics in a channel with floodplain vegetation, (iii) variation of riverbed topography, and (iv) vegetation dynamics on floodplains. In the vegetation dynamics model, the flood discharge (i) is stochastically simulated using a filtered Poisson process, one of the conventional approaches in hydrological time-series generation. The component for vegetation dynamics (iv) includes the effects of tree growth, mortality by floods, and infant tree recruitment. Vegetation condition has been observed mainly before and after floods since 2008 at a field site located between 23-24 km from the river mouth in Kako River, Japan. The Kako River has the catchment area of 1,730 km2 and the main channel length of 96 km. This site is one of the vegetation overgrowth sites in the Kako River floodplains. The predominant tree species are willows and bamboos. In the field survey, the position, trunk diameter and height of each tree as well as the riverbed materials were measured after several flood events to investigate their impacts on the floodplain vegetation community. This presentation tries to examine effects of anthropogenic river regulations, i.e., thinning and cutting-down, in the vegetated channel in Kako River by using the vegetation dynamics model. Sensitivity of both the flood water level and the vegetation status in the channel is statistically evaluated in terms of the different cutting

  18. Application of two dimensional periodic molecular dynamics to interfaces.

    NASA Astrophysics Data System (ADS)

    Gay, David H.; Slater, Ben; Catlow, C. Richard A.

    1997-08-01

    We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.

  19. Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms

    SciTech Connect

    Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R

    2005-02-02

    Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.

  20. Molecular Dynamics Simulations of Gas Transport in Polymer Films

    NASA Astrophysics Data System (ADS)

    Whitley, David; Butler, Simon; Adolf, David

    2010-03-01

    Parallel molecular dynamics simulations have been carried out to determine the permeability of O2 and N2 through polyethylene terephthalate, polypropylene and cis(1-4) polybutadiene. The permeability of both mixed and unmixed gas penetrants is studied within films of these well known gas barrier polymers. Results are obtained either through the solubility and diffusion (i.e. P=D*S) or via the permeability directly. Encouraging results are obtained. Additional analysis focuses on ``unmixed/mixed gas'' intracomparisons of the simulated permeability data in addition to corresponding penetrant and host polymer local dynamics.

  1. Molecular dynamical simulations of melting behaviors of metal clusters

    SciTech Connect

    Hamid, Ilyar; Fang, Meng; Duan, Haiming

    2015-04-15

    The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.

  2. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

  3. A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations

    PubMed Central

    Mak, Terrence S. T.; Rachmuth, Guy; Lam, Kai-Pui; Poon, Chi-Sang

    2008-01-01

    Neuron-machine interfaces such as dynamic clamp and brain-implantable neuroprosthetic devices require real-time simulations of neuronal ion channel dynamics. Field Programmable Gate Array (FPGA) has emerged as a high-speed digital platform ideal for such application-specific computations. We propose an efficient and flexible component-based FPGA design framework for neuronal ion channel dynamics simulations, which overcomes certain limitations of the recently proposed memory-based approach. A parallel processing strategy is used to minimize computational delay, and a hardware-efficient factoring approach for calculating exponential and division functions in neuronal ion channel models is used to conserve resource consumption. Performances of the various FPGA design approaches are compared theoretically and experimentally in corresponding implementations of the AMPA and NMDA synaptic ion channel models. Our results suggest that the component-based design framework provides a more memory economic solution as well as more efficient logic utilization for large word lengths, whereas the memory-based approach may be suitable for time-critical applications where a higher throughput rate is desired. PMID:17190033

  4. A dipeptidyl aminopeptidase-like protein remodels gating charge dynamics in Kv4.2 channels.

    PubMed

    Dougherty, Kevin; Covarrubias, Manuel

    2006-12-01

    Dipeptidyl aminopeptidase-like proteins (DPLPs) interact with Kv4 channels and thereby induce a profound remodeling of activation and inactivation gating. DPLPs are constitutive components of the neuronal Kv4 channel complex, and recent observations have suggested the critical functional role of the single transmembrane segment of these proteins (Zagha, E., A. Ozaita, S.Y. Chang, M.S. Nadal, U. Lin, M.J. Saganich, T. McCormack, K.O. Akinsanya, S.Y. Qi, and B. Rudy. 2005. J. Biol. Chem. 280:18853-18861). However, the underlying mechanism of action is unknown. We hypothesized that a unique interaction between the Kv4.2 channel and a DPLP found in brain (DPPX-S) may remodel the channel's voltage-sensing domain. To test this hypothesis, we implemented a robust experimental system to measure Kv4.2 gating currents and