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Sample records for channel molecular dynamics

  1. Molecular Dynamical Study on Ion Channeling through Peptide Nanotube

    NASA Astrophysics Data System (ADS)

    Sumiya, Norihito; Igami, Daiki; Takeda, Kyozaburo

    2011-12-01

    We theoretically study the possibility of ion channeling through peptide nanotubes (PNTs). After designing the minimal peptide nanorings (PNRs) and their aggregated form (peptide nanotubes, PNT) computationally, we carry out molecular dynamics (MD) calculations for cation channeling. The present MD calculations show that cation channeling through PNTs occurs. Furthermore, inter-ring hydrogen bonds (HBs) survive and maintain the tubular form of PNTs during cation channeling. We introduce mobility such that cation channeling can be evaluated quantitatively. As the ionic radius of the cation becomes smaller, the effective relaxation time τ becomes larger. Accordingly, mobilities of 10-2˜10-3[cm2/volt/sec] are calculated. In contrast, when an anion (F-) passes through the PNT, the inter-ring HBs are broken, thus inducing breakdown of the peptide backbone. Consequently, H atoms from the broken HBs surround the channeling anion (F-) and halt its motion.

  2. Molecular dynamics insights into human aquaporin 2 water channel.

    PubMed

    Binesh, A R; Kamali, R

    2015-12-01

    In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820

  3. 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.

  4. Generalized Langevin models of molecular dynamics simulations with applications to ion channels

    NASA Astrophysics Data System (ADS)

    Gordon, Dan; Krishnamurthy, Vikram; Chung, Shin-Ho

    2009-10-01

    We present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile is determined for the ion(s) in the channel, and the distribution of random and frictional forces is measured over discrete segments of the ion channel. The parameters thus determined are used in stochastic dynamics simulations based on the nonlinear generalized Langevin equation. We first provide the theoretical basis of this procedure, which we refer to as "distributional molecular dynamics," and detail the methods for estimating the parameters from molecular dynamics to be used in stochastic dynamics. We test the technique by applying it to study the dynamics of ion permeation across the gramicidin pore. Given the known difficulty in modeling the conduction of ions in gramicidin using classical molecular dynamics, there is a degree of uncertainty regarding the validity of the MD-derived potential of mean force (PMF) for gramicidin. Using our techniques and systematically changing the PMF, we are able to reverse engineer a modified PMF which gives a current-voltage curve closely matching experimental results.

  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. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.

    PubMed

    Oakes, V; Furini, S; Domene, C

    2016-01-01

    The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs. PMID:27586285

  7. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Nguyen, Thuy Hien; Pohorille, Andrew

    2014-12-01

    Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.

  8. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance.

    PubMed

    Wilson, Michael A; Nguyen, Thuy Hien; Pohorille, Andrew

    2014-12-14

    Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation. PMID:25494790

  9. Molecular dynamics simulations reveal highly permeable oxygen exit channels shared with water uptake channels in photosystem II.

    PubMed

    Vassiliev, Serguei; Zaraiskaya, Tatiana; Bruce, Doug

    2013-10-01

    Photosystem II (PSII) catalyzes the oxidation of water in the conversion of light energy into chemical energy in photosynthesis. Water delivery and oxygen removal from the oxygen evolving complex (OEC), buried deep within PSII, are critical requirements to facilitate the reaction and minimize reactive oxygen damage. It has often been assumed that water and oxygen travel through separate channels within PSII, as demonstrated in cytochrome c oxidase. This study describes all-atom molecular dynamics simulations of PSII designed to investigate channels by fully characterizing the distribution and permeation of both water and oxygen. Interestingly, most channels found in PSII were permeable to both oxygen and water, however individual channels exhibited different energetic barriers for the two solutes. Several routes for oxygen diffusion within PSII with low energy permeation barriers were found, ensuring its fast removal from the OEC. In contrast, all routes for water showed significant energy barriers, corresponding to a much slower permeation rate for water through PSII. Two major factors were responsible for this selectivity: (1) hydrogen bonds between water and channel amino acids, and (2) steric restraints. Our results reveal the presence of a shared network of channels in PSII optimized to both facilitate the quick removal of oxygen and effectively restrict the water supply to the OEC to help stabilize and protect it from small water soluble inhibitors. PMID:23816955

  10. Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase

    PubMed Central

    Watanabe, Go; Nakajima, Daisuke; Hiroshima, Akinori; Suzuki, Haruo; Yoneda, Shigetaka

    2015-01-01

    A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue, dimethylglycine. The spatial region including the protein was divided into small rectangular cells. The average number of the water molecules locating within each cell was calculated based on the simulation trajectory. The clusters of the cells filled with water molecules were used to determine the water channels. The narrowness of the channels, the average hydropathy indices of the residues of the channels, and the number of migration events of water molecules through the channels were consistent with the selective transport hypothesis whereby tunnel T3 is the pathway for the exit of the iminium intermediate of the enzyme reaction. PMID:27493862

  11. 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

  12. Binding and Channeling of Alternative Substrates in the Enzyme DmpFG: a Molecular Dynamics Study

    PubMed Central

    Smith, Natalie E.; Vrielink, Alice; Attwood, Paul V.; Corry, Ben

    2014-01-01

    DmpFG is a bifunctional enzyme comprised of an aldolase subunit, DmpG, and a dehydrogenase subunit, DmpF. The aldehyde intermediate produced by the aldolase is channeled directly through a buried molecular channel in the protein structure from the aldolase to the dehydrogenase active site. In this study, we have investigated the binding of a series of progressively larger substrates to the aldolase, DmpG, using molecular dynamics. All substrates investigated are easily accommodated within the active site, binding with free energy values comparable to the physiological substrate 4-hydroxy-2-ketovalerate. Subsequently, umbrella sampling was utilized to obtain free energy surfaces for the aldehyde intermediates (which would be generated from the aldolase reaction on each of these substrates) to move through the channel to the dehydrogenase DmpF. Small substrates were channeled with limited barriers in an energetically feasible process. We show that the barriers preventing bulky intermediates such as benzaldehyde from moving through the wild-type protein can be removed by selective mutation of channel-lining residues, demonstrating the potential for tailoring this enzyme to allow its use for the synthesis of specific chemical products. Furthermore, positions of transient escape routes in this flexible channel were determined. PMID:24739167

  13. Lateral Fenestrations in K(+)-Channels Explored Using Molecular Dynamics Simulations.

    PubMed

    Jorgensen, Christian; Darré, Leonardo; Oakes, Victoria; Torella, Rubben; Pryde, David; Domene, Carmen

    2016-07-01

    Potassium channels are of paramount physiological and pathological importance and therefore constitute significant drug targets. One of the keys to rationalize the way drugs modulate ion channels is to understand the ability of such small molecules to access their respective binding sites, from which they can exert an activating or inhibitory effect. Many computational studies have probed the energetics of ion permeation, and the mechanisms of voltage gating, but little is known about the role of fenestrations as possible mediators of drug entry in potassium channels. To explore the existence, structure, and conformational dynamics of transmembrane fenestrations accessible by drugs in potassium channels, molecular dynamics simulation trajectories were analyzed from three potassium channels: the open state voltage-gated channel Kv1.2, the G protein-gated inward rectifying channel GIRK2 (Kir3.2), and the human two-pore domain TWIK-1 (K2P1.1). The main results of this work were the identification of the sequence identity of four main lateral fenestrations of similar length and with bottleneck radius in the range of 0.9-2.4 Å for this set of potassium channels. It was found that the fenestrations in Kv1.2 and Kir3.2 remain closed to the passage of molecules larger than water. In contrast, in the TWIK-1 channel, both open and closed fenestrations are sampled throughout the simulation, with bottleneck radius shown to correlate with the random entry of lipid membrane molecules into the aperture of the fenestrations. Druggability scoring function analysis of the fenestration regions suggests that Kv and Kir channels studied are not druggable in practice due to steric constraining of the fenestration bottleneck. A high (>50%) fenestration sequence identity was found in each potassium channel subfamily studied, Kv1, Kir3, and K2P1. Finally, the reported fenestration sequence of TWIK-1 compared favorably with another channel, K2P channel TREK-2, reported to possess open

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

    PubMed Central

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

    2011-01-01

    Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent 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 nonconducting. 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. PMID:21575573

  15. Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels.

    PubMed

    Saam, Jan; Ivanov, Igor; Walther, Matthias; Holzhütter, Hermann-Georg; Kuhn, Hartmut

    2007-08-14

    Cells contain numerous enzymes that use molecular oxygen for their reactions. Often, their active sites are buried deeply inside the protein, which raises the question whether there are specific access channels guiding oxygen to the site of catalysis. Choosing 12/15-lipoxygenase as a typical example for such oxygen-dependent enzymes, we determined the oxygen distribution within the protein and defined potential routes for oxygen access. For this purpose, we have applied an integrated strategy of structural modeling, molecular dynamics simulations, site-directed mutagenesis, and kinetic measurements. First, we computed the 3D free-energy distribution for oxygen, which led to identification of four oxygen channels in the protein. All channels connect the protein surface with a region of high oxygen affinity at the active site. This region is localized opposite to the nonheme iron providing a structural explanation for the reaction specificity of this lipoxygenase isoform. The catalytically most relevant path can be obstructed by L367F exchange, which leads to a strongly increased Michaelis constant for oxygen. The blocking mechanism is explained in detail by reordering the hydrogen-bonding network of water molecules. Our results provide strong evidence that the main route for oxygen access to the active site of the enzyme follows a channel formed by transiently interconnected cavities whereby the opening and closure are governed by side chain dynamics. PMID:17675410

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

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

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

  17. Molecular dynamics study of free energy profiles for organic cations in gramicidin A channels.

    PubMed Central

    Hao, Y; Pear, M R; Busath, D D

    1997-01-01

    The free energy profiles for four organic cations in right-handed single-helix gramicidin A dimers were computed by using umbrella sampling molecular dynamics with CHARMM. Ion-water column translocations were facilitated by using a novel "water-tunnel" approach. The overlapping pieces of free energy profile for adjacent windows were selected from three trajectories that differed in initial ion rotation and were aligned by the method of umbrella potential differences. Neglected long-range electrostatic energies from the bulk water and the bilayer were computed with DelPhi and added to the profile. The approach was corroborated for the formamidinium-guanidinium pair by using perturbation dynamics at axial positions 0, 6, 12, and 15 A from the channel center. The barrier to ethylammonium entry was prohibitive at 21 kcal/mol, whereas for methylammonium it was 5.5 kcal/mol, and the profile was quite flat through the channel, roughly consistent with conductance measurements. The profile for formamidinium was very similar to that of methylammonium. Guanidinium had a high entry barrier (deltaF = +8.6 kcal/mol) and a narrow deep central well (deltaF = -2.6 kcal/mol), qualitatively consistent with predictions from voltage-dependent potassium current block measurements. Its deep central well, contrasting with the flat profile for formamidinium, was verified with perturbation dynamics and was correlated with its high propensity to form hydrogen bonds with the channel at the dimer junction (not shared by the other three cations). Analysis of the ensemble average radial forces on the ions demonstrates that all four ions undergo compressive forces in the channel that are at maximum at the center of the monomer and relieved at the dimer junction, illustrating increased flexibility of the channel walls in the center of the channel. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:9336167

  18. Molecular dynamics study of free energy profiles for organic cations in gramicidin A channels.

    PubMed

    Hao, Y; Pear, M R; Busath, D D

    1997-10-01

    The free energy profiles for four organic cations in right-handed single-helix gramicidin A dimers were computed by using umbrella sampling molecular dynamics with CHARMM. Ion-water column translocations were facilitated by using a novel "water-tunnel" approach. The overlapping pieces of free energy profile for adjacent windows were selected from three trajectories that differed in initial ion rotation and were aligned by the method of umbrella potential differences. Neglected long-range electrostatic energies from the bulk water and the bilayer were computed with DelPhi and added to the profile. The approach was corroborated for the formamidinium-guanidinium pair by using perturbation dynamics at axial positions 0, 6, 12, and 15 A from the channel center. The barrier to ethylammonium entry was prohibitive at 21 kcal/mol, whereas for methylammonium it was 5.5 kcal/mol, and the profile was quite flat through the channel, roughly consistent with conductance measurements. The profile for formamidinium was very similar to that of methylammonium. Guanidinium had a high entry barrier (deltaF = +8.6 kcal/mol) and a narrow deep central well (deltaF = -2.6 kcal/mol), qualitatively consistent with predictions from voltage-dependent potassium current block measurements. Its deep central well, contrasting with the flat profile for formamidinium, was verified with perturbation dynamics and was correlated with its high propensity to form hydrogen bonds with the channel at the dimer junction (not shared by the other three cations). Analysis of the ensemble average radial forces on the ions demonstrates that all four ions undergo compressive forces in the channel that are at maximum at the center of the monomer and relieved at the dimer junction, illustrating increased flexibility of the channel walls in the center of the channel. PMID:9336167

  19. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating.

    PubMed

    Yoo, Jejoong; Aksimentiev, Aleksei

    2015-12-01

    DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels. PMID:26551518

  20. Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

    PubMed Central

    Ulmschneider, Martin B.; Bagnéris, Claire; McCusker, Emily C.; DeCaen, Paul G.; Delling, Markus; Clapham, David E.; Ulmschneider, Jakob P.; Wallace, B. A.

    2013-01-01

    The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel’s full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate. PMID:23542377

  1. [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. PMID:17633536

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

    PubMed

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

    2015-03-24

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

  3. Molecular dynamics

    SciTech Connect

    Ladd, A.J.C.

    1988-08-01

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

  4. 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.

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

    PubMed

    Hedger, George; Sansom, Mark S P

    2016-10-01

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

  6. 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

  7. Molecular Dynamics of Ionic Transport and Electrokinetic Effects in Realistic Silica Channels

    SciTech Connect

    Christian D. Lorenz; Paul S. Crozier; Joshua A. Anderson; Alex Travesset

    2008-04-28

    Silica is one of the most widely used inorganic materials in experiments and applications involving aqueous solutions of biomolecules, nanoparticles, etc. In this paper, we construct a detailed atomistic model of a silica interface that captures the essential experimentally known properties of a silica interface. We then perform all-atom molecular dynamics simulations of a silica nanochannel subjected to either an external pressure or an electric field and provide an atomistic description of ionic transport and both electro-osmotic flow and streaming currents for a solution of monovalent (0.4 M NaCl) as well as divalent (0.2 and 1.0 M CaCl{sub 2}) salts. Our results allow a detailed investigation of {zeta}-potentials, Stern layer conductance, charge inversion, ionic mobilities, as well as continuum theories and Onsager relations. We conclude with a discussion on the implications of our results for silica nanopore experiments and micro- and nanofluidic devices.

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

    PubMed Central

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

    2009-01-01

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

  9. 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

  10. Molecular dynamics simulations of irradiation of α-Fe thin films with energetic Fe ions under channeling conditions

    NASA Astrophysics Data System (ADS)

    Aliaga, M. J.; Prokhodtseva, A.; Schaeublin, R.; Caturla, M. J.

    2014-09-01

    Using molecular dynamics simulations with recent interatomic potentials developed for Fe, we have studied the defects in thin films of pure bcc Fe induced by the displacement cascade produced by Fe atoms of 50, 100, and 150 keV impinging under a channeling incident angle of 6° to a [0 0 1] direction. The thin films have a thickness between 40 and 100 nm, to reproduce the thickness of the samples used in transmission electron microscope in situ measurements during irradiation. In the simulations we focus mostly on the effect of channeling and free surfaces on damage production. The results are compared to bulk cascades. The comparison shows that the primary damage in thin films of pure Fe is quite different from that originated in the volume of the material. The presence of near surfaces can lead to a variety of events that do not occur in bulk collisional cascades, such as the production of craters and the glide of self-interstitial defects to the surface. Additionally, in the range of energies and the incident angle used, channeling is a predominant effect that significantly reduces damage compared to bulk cascades.

  11. Towards further understanding of stacking fault tetrahedron absorption and defect-free channels - A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Fan, Haidong; El-Awady, Jaafar A.; Wang, Qingyuan

    2015-03-01

    The mechanisms leading to stacking fault tetrahedron (SFT) absorption via interactions with dislocations, and subsequent formation of plastic flow localization in defect-free channels, which were frequently observed in irradiated materials in transmission electron microscopy experiments, are still unclear. To address this, screw dislocation interactions with SFTs in copper were investigated using molecular dynamics (MD) simulations. The interaction details reveal that a screw dislocation can fully absorb an SFT through the thermally activated transformation of Lomer-Cottrell lock into Lomer dislocations. After absorption, almost all the vacancies in the SFT are transferred into Lomer dislocations, which are able to move transversely under complex loading conditions. As a result, SFTs can be removed from the material (for SFTs near surface) or from defect-free channels (for SFTs in the bulk) with the aid of Lomer dislocations. In addition, it was shown that this absorption process is favorable only at high temperature, low applied shear stress and/or high SFT density. These results are in good agreement with in situ TEM observations. The current simulations and analyses provide useful insights into the formation mechanisms of defect-free channels in irradiated materials.

  12. Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach.

    PubMed

    Khavani, Mohammad; Izadyar, Mohammad; Housaindokht, Mohammad Reza

    2015-10-14

    In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups. PMID:26366633

  13. Molecular Mechanism of TRP Channels

    PubMed Central

    Zheng, Jie

    2013-01-01

    Transient receptor potential (TRP) channels are cellular sensors for a wide spectrum of physical and chemical stimuli. They are involved in the formation of sight, hearing, touch, smell, taste, temperature, and pain sensation. TRP channels also play fundamental roles in cell signaling and allow the host cell to respond to benign or harmful environmental changes. As TRP channel activation is controlled by very diverse processes and, in many cases, exhibits complex polymodal properties, understanding how each TRP channel responds to its unique forms of activation energy is both crucial and challenging. The past two decades witnessed significant advances in understanding the molecular mechanisms that underlie TRP channels activation. This review focuses on our current understanding of the molecular determinants for TRP channel activation. PMID:23720286

  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. 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.

  16. A Molecular Dynamics-Decorated Finite Element Method (MDeFEM) Framework for Simulating the Gating of Mechanosensitive Channels

    NASA Astrophysics Data System (ADS)

    Chen, Xi; Tang, Yuye; Cao, Guoxin; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

    2007-03-01

    The gating pathways of mechanosensitive channels of large conductance (MscL) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness. The interactions between various continuum components are derived from atomistic energy calculations. The structural variations along the gating pathway are consistent with previous analyses based on structural models and biased molecular-dynamics simulations. Upon membrane bending, there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation. Compared to popular all-atom simulations, the MDeFEM framework offers a unique alternative to bridge detailed intermolecular interactions and biological processes occurring at large spatial and timescales. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction.

  17. Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.

    PubMed

    Oliveira, A Sofia F; Damas, João M; Baptista, António M; Soares, Cláudio M

    2014-12-01

    Cytochrome c oxidases (Ccoxs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes couple dioxygen (O2) reduction to the generation of a transmembrane electrochemical proton gradient. Despite decades of research and the availability of a large amount of structural and biochemical data available for the A-type Ccox family, little is known about the channel(s) used by O2 to travel from the solvent/membrane to the heme a3-CuB binuclear center (BNC). Moreover, the identification of all possible O2 channels as well as the atomic details of O2 diffusion is essential for the understanding of the working mechanisms of the A-type Ccox. In this work, we determined the O2 distribution within Ccox from Rhodobacter sphaeroides, in the fully reduced state, in order to identify and characterize all the putative O2 channels leading towards the BNC. For that, we use an integrated strategy combining atomistic molecular dynamics (MD) simulations (with and without explicit O2 molecules) and implicit ligand sampling (ILS) calculations. Based on the 3D free energy map for O2 inside Ccox, three channels were identified, all starting in the membrane hydrophobic region and connecting the surface of the protein to the BNC. One of these channels corresponds to the pathway inferred from the X-ray data available, whereas the other two are alternative routes for O2 to reach the BNC. Both alternative O2 channels start in the membrane spanning region and terminate close to Y288I. These channels are a combination of multiple transiently interconnected hydrophobic cavities, whose opening and closure is regulated by the thermal fluctuations of the lining residues. Furthermore, our results show that, in this Ccox, the most likely (energetically preferred) routes for O2 to reach the BNC are the alternative channels, rather than the X-ray inferred pathway. PMID:25474152

  18. Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

    PubMed Central

    Oliveira, A. Sofia F.; Damas, João M.; Baptista, António M.; Soares, Cláudio M.

    2014-01-01

    Cytochrome c oxidases (Ccoxs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes couple dioxygen (O2) reduction to the generation of a transmembrane electrochemical proton gradient. Despite decades of research and the availability of a large amount of structural and biochemical data available for the A-type Ccox family, little is known about the channel(s) used by O2 to travel from the solvent/membrane to the heme a3-CuB binuclear center (BNC). Moreover, the identification of all possible O2 channels as well as the atomic details of O2 diffusion is essential for the understanding of the working mechanisms of the A-type Ccox. In this work, we determined the O2 distribution within Ccox from Rhodobacter sphaeroides, in the fully reduced state, in order to identify and characterize all the putative O2 channels leading towards the BNC. For that, we use an integrated strategy combining atomistic molecular dynamics (MD) simulations (with and without explicit O2 molecules) and implicit ligand sampling (ILS) calculations. Based on the 3D free energy map for O2 inside Ccox, three channels were identified, all starting in the membrane hydrophobic region and connecting the surface of the protein to the BNC. One of these channels corresponds to the pathway inferred from the X-ray data available, whereas the other two are alternative routes for O2 to reach the BNC. Both alternative O2 channels start in the membrane spanning region and terminate close to Y288I. These channels are a combination of multiple transiently interconnected hydrophobic cavities, whose opening and closure is regulated by the thermal fluctuations of the lining residues. Furthermore, our results show that, in this Ccox, the most likely (energetically preferred) routes for O2 to reach the BNC are the alternative channels, rather than the X-ray inferred pathway. PMID:25474152

  19. Accelerated molecular dynamics methods

    SciTech Connect

    Perez, Danny

    2011-01-04

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

  20. Molecular physiology of EAAT anion channels.

    PubMed

    Fahlke, Christoph; Kortzak, Daniel; Machtens, Jan-Philipp

    2016-03-01

    Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system. After release from presynaptic nerve terminals, glutamate is quickly removed from the synaptic cleft by a family of five glutamate transporters, the so-called excitatory amino acid transporters (EAAT1-5). EAATs are prototypic members of the growing number of dual-function transport proteins: they are not only glutamate transporters, but also anion channels. Whereas the mechanisms underlying secondary active glutamate transport are well understood at the functional and at the structural level, mechanisms and cellular roles of EAAT anion conduction have remained elusive for many years. Recently, molecular dynamics simulations combined with simulation-guided mutagenesis and experimental analysis identified a novel anion-conducting conformation, which accounts for all experimental data on EAAT anion currents reported so far. We here review recent findings on how EAATs accommodate a transporter and a channel in one single protein. PMID:26687113

  1. Molecular assembly and dynamics of fluorescent protein-tagged single KCa1.1 channel in expression system and vascular smooth muscle cells.

    PubMed

    Yamamura, Hisao; Ikeda, Chikako; Suzuki, Yoshiaki; Ohya, Susumu; Imaizumi, Yuji

    2012-04-15

    The large-conductance Ca(2+)-activated K(+) (K(Ca)1.1, BK) channel has pivotal roles in the regulation of vascular tone. To clarify the molecular dynamics of BK channels and their functionally coupled protein on the membrane surface, we examined single-molecule imaging of fluorescent-labeled BK subunits in the plasma membrane using total internal reflection fluorescence (TIRF) microscopy. The dynamic mobility of yellow fluorescent protein (YFP)-tagged BKα subunit (BKα-YFP) expressed in human embryo kidney 293 (HEK) cells was detected in TIRF regions at the level of individual channels and their clusters on the plasma membrane with a diffusion coefficient of 6.7 × 10(3) nm(2)/s. When BKα-YFP was coexpressed with cyan fluorescent protein (CFP)-tagged BKβ1 subunit (BKβ1-CFP) in HEK cells, the mobility was reduced by ∼50%. Fluorescent image analyses suggest that green fluorescent protein (GFP)-tagged BKα subunit (BKα-GFP) expressed in vascular smooth muscle cells (VSMCs), at low density, preferentially formed a heterotetrameric molecular assembly with native BKα subunits, rather than homotetrameric BKα-GFP. Movement of BKα-YFP in VSMCs (0.29 × 10(3) nm(2)/s) was far more restricted than BKα-YFP/BKβ1-CFP in HEK cells (2.5 × 10(3) nm(2)/s). Actin disruption by pretreatment with cytochalasin D in VSMCs appeared to increase the mobile behavior of BKα-YFP, which was then significantly reduced by addition of jasplakinolide. Most BKα-YFP colocalized with caveolin 1 (Cav1)-CFP in VSMCs, but unexpectedly not frequently in HEK cells. Fluorescence resonance energy transfer analyses showed the direct interaction between BKα-YFP and Cav1-CFP, particularly in VSMCs. These results, obtained by single molecule imaging in living cells, indicate that the dynamics of BKα molecules on the membrane surface are strongly restricted or regulated by its auxiliary β-subunit, cytoskeleton, and direct interaction with Cav1 in VSMCs. PMID:22301058

  2. 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.

  3. 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.

  4. Molecular pharmacology of the CFTR Cl- channel.

    PubMed

    Hwang, T C; Sheppard, D N

    1999-11-01

    Dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel is associated with a wide spectrum of disease. In the search for modulators of CFTR, pharmacological agents that interact directly with the CFTR Cl- channel have been identified. Some agents stimulate CFTR by interacting with the nucleotide-binding domains that control channel gating, whereas others inhibit CFTR by binding within the channel pore and preventing Cl- permeation. Knowledge of the molecular pharmacology of CFTR might lead to new treatments for diseases caused by the dysfunction of CFTR. PMID:10542444

  5. 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.

  6. Superposition State Molecular Dynamics.

    PubMed

    Venkatnathan, Arun; Voth, Gregory A

    2005-01-01

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

  7. Molecular Biophysics of Orai Store-Operated Ca2+ Channels

    PubMed Central

    Amcheslavsky, Anna; Wood, Mona L.; Yeromin, Andriy V.; Parker, Ian; Freites, J. Alfredo; Tobias, Douglas J.; Cahalan, Michael D.

    2015-01-01

    Upon endoplasmic reticulum Ca2+ store depletion, Orai channels in the plasma membrane are activated directly by endoplasmic reticulum-resident STIM proteins to generate the Ca2+-selective, Ca2+ release-activated Ca2+ (CRAC) current. After the molecular identification of Orai, a plethora of functional and biochemical studies sought to compare Orai homologs, determine their stoichiometry, identify structural domains responsible for the biophysical fingerprint of the CRAC current, identify the physiological functions, and investigate Orai homologs as potential therapeutic targets. Subsequently, the solved crystal structure of Drosophila Orai (dOrai) substantiated many findings from structure-function studies, but also revealed an unexpected hexameric structure. In this review, we explore Orai channels as elucidated by functional and biochemical studies, analyze the dOrai crystal structure and its implications for Orai channel function, and present newly available information from molecular dynamics simulations that shed light on Orai channel gating and permeation. PMID:25606672

  8. Computational Studies of Molecular Permeation through Connexin26 Channels.

    PubMed

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

    2016-02-01

    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. PMID:26840724

  9. The VDAC channel: Molecular basis for selectivity.

    PubMed

    Colombini, Marco

    2016-10-01

    The voltage dependent anion-selective channel, VDAC, is the major permeability pathway by which molecules and ion cross the mitochondrial outer membrane. This pathway has evolved to optimize the flow of these substances and to control this flow by a gating process that is influenced by a variety of factors including transmembrane voltage. The permeation pathway formed through the membrane by VDAC is complex. Small ion flow is primarily influenced by the charged surface of the inner walls of the channel. Channel closure changes this landscape resulting in a change from a channel that favors anions to one that favors cations. Molecular ions interact more intimately with the inner walls of the channel and are selected by their 3-dimensional structure, not merely by their size and charge. Molecular ions typically found in cells are greatly favored over those that are not. For these larger structures the channel may form a low-energy translocation path that complements the structure of the permeant. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:26826035

  10. Open boundary molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  11. Molecular Dynamics of Acetylcholinesterase

    SciTech Connect

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

    2002-06-01

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

  12. Single-molecular artificial transmembrane water channels.

    PubMed

    Hu, Xiao-Bo; Chen, Zhenxia; Tang, Gangfeng; Hou, Jun-Li; Li, Zhan-Ting

    2012-05-23

    Hydrazide-appended pillar[5]arene derivatives have been synthesized. X-ray crystal structure analysis and (1)H NMR studies revealed that the molecules adopt unique tubular conformations. Inserting the molecules into the lipid membranes of vesicles leads to the transport of water through the channels produced by single molecules, as supported by dynamic light scattering and cryo-SEM experiments. The channels exhibit the transport activity at a very low channel to lipid ratio (0.027 mol %), and a water permeability of 8.6 × 10(-10) cm s(-1) is realized. In addition, like natural water channel proteins, the artificial systems also block the transport of protons. PMID:22574988

  13. 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.

  14. Multiscale reactive molecular dynamics

    PubMed Central

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

    2012-01-01

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

  15. 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.

  16. Transmembrane dynamics of the Thr-5 phosphorylated sarcolipin pentameric channel.

    PubMed

    Cao, Yipeng; Wu, Xue; Wang, Xinyu; Sun, Haiying; Lee, Imshik

    2016-08-15

    Sarcolipin (SLN), an important membrane protein expressed in the sarcoplasmic reticulum (SR), regulates muscle contractions in cardiac and skeletal muscle. The phosphorylation at amino acid Thr5 of the SLN protein modulates the amount of Ca(2+) that passes through the SR. Using molecular dynamics simulation, we evaluated the phosphorylation at Thr5 of pentameric SLN (phospho-SLN) channel's energy barrier and pore characteristics by calculating the potential of mean force (PMF) along the channel pore and determining the diffusion coefficient. The results indicate that pentameric phospho-SLN promotes penetration of monovalent and divalent ions through the channel. The analysis of PMF, pore radius and diffusion coefficient indicates that Leu21 is the hydrophobic gate of the pentameric SLN channel. In the channel, water molecules near the Leu21 pore demonstrated a clear hydrated-dehydrated transition; however, the mutation of Leu21 to an Alanine (L21A) destroyed the hydrated-dehydrated transitions. These water-dynamic behaviors and PMF confirm that Leu21 is the key residue that regulates the ion permeability of the pentameric SLN channel. These results provide the structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SLN channel. PMID:27378083

  17. 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.

  18. 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

  19. Molecular Modeling of the Structural and Dynamical Changes in Calcium Channel TRPV5 Induced by the African-Specific A563T Variation.

    PubMed

    Wang, Lingyun; Holmes, Ross P; Peng, Ji-Bin

    2016-03-01

    Transient receptor potential cation channels, vanilloid subfamily, member 5 (TRPV5) plays a key role in active Ca(2+) reabsorption in the kidney. Variations in TRPV5 occur at high frequency in African populations and may contribute to their higher efficiency of Ca(2+) reabsorption. One of the African specific variations, A563T, exhibits increased Ca(2+) transport ability. However, it is unclear how this variation influences the channel pore. On the basis of the structure of TRPV1, a TRPV5 model was generated to simulate the structural and dynamical changes induced by the A563T variation. On the basis of this model, amino acid residue 563 interacts with V540, which is one residue away from the key residue, D542, involved in Ca(2+) selectivity and Mg(2+) blockade. The A563T variation increases secondary structure stability and reduces dynamical motion of D542. In addition, the A563T variation alters the electrostatic potential of the outer surface of the pore. Differences in contact between selective filter residues and residue 563 and in electrostatic potential between the two TRPV5 variants were also observed in another model derived from an alternative alignment in the selective filters between TRPV5 and TRPV1. These findings indicate that the A563T variation induces structural, dynamical, and electrostatic changes in the TRPV5 pore, providing structural insight into the functional alterations associated with the A563T variation. PMID:26837804

  20. Molecular dynamics simulations

    SciTech Connect

    Alder, B.J.

    1985-07-01

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

  1. VMD: visual molecular dynamics.

    PubMed

    Humphrey, W; Dalke, A; Schulten, K

    1996-02-01

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

  2. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

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

  3. 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. PMID:26827925

  4. 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. PMID:26308210

  5. Exploring the Dynamics of the TWIK-1 Channel.

    PubMed

    Oakes, Victoria; Furini, Simone; Pryde, David; Domene, Carmen

    2016-08-23

    Potassium channels in the two-pore domain family (K2P) have various structural attributes that differ from those of other K(+) channels, including a dimeric assembly constituted of nonidentical domains and an expansive extracellular cap. Crystallization of the prototypical K2P channel, TWIK-1, finally revealed the structure of these characteristics in atomic detail, allowing computational studies to be undertaken. In this study, we performed molecular-dynamics simulations for a cumulative time of ∼1 μs to discern the mechanism of ion transport throughout TWIK-1. We observed the free passage of ions beneath the extracellular cap and identified multiple high-occupancy sites in close proximity to charged residues on the protein surface. Despite the overall topological similarity of the x-ray structure of the selectivity filter to other K(+) channels, the structure diverges significantly in molecular-dynamics simulations as a consequence of nonconserved residues in both pore domains contributing to the selectivity filter (T118 and L228). The behavior of such residues has been linked to channel inactivation and the phenomenon of dynamic selectivity, where TWIK-1 displays robust Na(+) inward flux in response to subphysiological K(+) concentrations. PMID:27558721

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

    PubMed

    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 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. PMID:21179205

  7. Molecular photoionization dynamics

    SciTech Connect

    Dehmer, Joseph L.

    1982-05-01

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

  8. Dynamic-domain-decomposition parallel molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    1997-05-01

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

  9. Thermal transpiration: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    T, Joe Francis; Sathian, Sarith P.

    2014-12-01

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

  10. 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.

  11. Molecular candidates for cardiac stretch-activated ion channels

    PubMed Central

    Reed, Alistair; Kohl, Peter; Peyronnet, Rémi

    2014-01-01

    The heart is a mechanically-active organ that dynamically senses its own mechanical environment. This environment is constantly changing, on a beat-by-beat basis, with additional modulation by respiratory activity and changes in posture or physical activity, and further overlaid with more slowly occurring physiological (e.g. pregnancy, endurance training) or pathological challenges (e.g. pressure or volume overload). Far from being a simple pump, the heart detects changes in mechanical demand and adjusts its performance accordingly, both via heart rate and stroke volume alteration. Many of the underlying regulatory processes are encoded intracardially, and are thus maintained even in heart transplant recipients. Over the last three decades, molecular substrates of cardiac mechanosensitivity have gained increasing recognition in the scientific and clinical communities. Nonetheless, the processes underlying this phenomenon are still poorly understood. Stretch-activated ion channels (SAC) have been identified as one contributor to mechanosensitive autoregulation of the heartbeat. They also appear to play important roles in the development of cardiac pathologies – most notably stretch-induced arrhythmias. As recently discovered, some established cardiac drugs act, in part at least, via mechanotransduction pathways suggesting SAC as potential therapeutic targets. Clearly, identification of the molecular substrate of cardiac SAC is of clinical importance and a number of candidate proteins have been identified. At the same time, experimental studies have revealed variable–and at times contrasting–results regarding their function. Further complication arises from the fact that many ion channels that are not classically defined as SAC, including voltage and ligand-gated ion channels, can respond to mechanical stimulation. Here, we summarise what is known about the molecular substrate of the main candidates for cardiac SAC, before identifying potential further

  12. Molecular dynamics and protein function

    PubMed Central

    Karplus, M.; Kuriyan, J.

    2005-01-01

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

  13. A sampling of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sindhikara, Daniel Jon

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

  14. Gas Phase Molecular Dynamics

    SciTech Connect

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

    1999-05-21

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

  15. Integration methods for molecular dynamics

    SciTech Connect

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

    1996-12-31

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

  16. The molecular physiology of CRAC channels

    PubMed Central

    Prakriya, Murali

    2011-01-01

    Summary The Ca2+release-activated Ca2+ (CRAC) channel is a highly Ca2+-selective store-operated channel expressed in T cells, mast cells, and various other tissues. CRAC channels regulate critical cellular processes such as gene expression, motility, and the secretion of inflammatory mediators. The identification of Orai1, a key subunit of the CRAC channel pore, and STIM1, the endoplasmic reticulum (ER) Ca2+ sensor, have provided the tools to illuminate the mechanisms of regulation and the pore properties of CRAC channels. Recent evidence indicates that the activation of CRAC channels by store depletion involves a coordinated series of steps, which include the redistributions of STIM1 and Orai1, direct physical interactions between these proteins, and conformational changes in Orai1, culminating in channel activation. Additional studies have revealed that the high Ca2+ selectivity of CRAC channels arises from the presence of an intrapore Ca2+ binding site, the properties of which are finely honed to occlude the permeation of the much more prevalent Na+. Structure-function studies have led to the identification of the potential pore-binding sites for Ca2+, providing a firm framework for understanding the mechanisms of selectivity and gating of the CRAC channel. This review summarizes recent progress in understanding the mechanisms of CRAC channel activation, pore properties, and modulation. PMID:19754891

  17. Dynamical coupled-channel analysis at EBAC.

    SciTech Connect

    Lee, T.-S. H.; Physics

    2008-01-01

    In this contribution, the author reports on the dynamical coupled-channels analysis being pursued at the Excited Baryon Analysis Center (EBAC) of Jefferson Laboratory. EBAC was established in January 2006. Its objective is to extract the parameters associated with the excited states (N*) of the nucleon from the world data of meson production reactions, and to also develop theoretical interpretations of the extracted N* parameters.

  18. Morphological dynamics of an englacial channel

    NASA Astrophysics Data System (ADS)

    Vatne, Geir; Irvine-Fynn, Tristram D. L.

    2016-07-01

    in cut-and-closure channels to better understand their coupling to supraglacial meltwater sources and potential significance in cold-based glacier hydrology and ice dynamics.

  19. 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

  20. 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.

  1. Molecular dynamics investigation of nanoscale cavitation dynamics

    NASA Astrophysics Data System (ADS)

    Sasikumar, Kiran; Keblinski, Pawel

    2014-12-01

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

  2. MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.

    PubMed

    Petrek, Martin; Kosinová, Pavlína; Koca, Jaroslav; Otyepka, Michal

    2007-11-01

    We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. This algorithm has been made freely available on the Internet (http://mole.chemi.muni.cz/) and overcomes many of the shortcomings and limitations of the recently developed CAVER software. The core of our MOLE algorithm is a Dijkstra's path search algorithm, which is applied to a Voronoi mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit have demonstrated that the MOLE algorithm performs well. MOLE is thus a powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories in which analysis of a large number of snapshots is required. PMID:17997961

  3. Dynamic fracture toughness determined using molecular dynamics

    SciTech Connect

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

    2004-01-01

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

  4. Structure and dynamics of one-dimensional ionic solutions in biological transmembrane channels.

    PubMed Central

    Skerra, A; Brickmann, J

    1987-01-01

    The structure and dynamics of solvated alkali metal cations in transmembrane channels are treated using the molecular dynamics simulation technique. The simulations are based on a modified Fischer-Brickmann model (Fischer, W., and J. Brickmann, 1983, Biophys. Chem., 18:323-337) for gramicidin A-type channels. The trajectories of all particles in the channel as well as two-dimensional pair correlation functions are analyzed. It is found from the analysis of the stationary simulation state that one-dimensional solvation complexes are formed and that the number of water molecules in the channel varies for different alkali metal cations. PMID:2440485

  5. Fiftieth anniversary of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Melker, Alexander I.

    2007-04-01

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

  6. 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

  7. Molecular dynamics on vector computers

    NASA Astrophysics Data System (ADS)

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

    1985-10-01

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

  8. The dynamics of vortex streets in channels

    NASA Astrophysics Data System (ADS)

    Wang, Xiaolin; Alben, Silas

    2015-07-01

    We develop a model to numerically study the dynamics of vortex streets in channel flows. Previous work has studied the vortex wakes of specific vortex generators. Here, we study a wide range of vortex wakes including regular and reverse von Kármán streets with various strengths, geometries, and Reynolds numbers (Re) by applying a smoothed von Kármán street as an inflow condition. We find that the spatial structure of the inflow vortex street is maintained for the reverse von Kármán street and altered for the regular street. For regular streets, we identify a transition to asymmetric dynamics which happens when Re increases, or vortices are stronger, or vortex streets are compressed horizontally or extended vertically. We also determine the effects of these parameters on vortex street inversion.

  9. Molecular dynamics for dense matter

    NASA Astrophysics Data System (ADS)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

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

  10. 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.

  11. 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.

  12. 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

  13. Multisurface Adiabatic Reactive Molecular Dynamics.

    PubMed

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

    2014-04-01

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

  14. Molecular Dynamics Simulations of Polymers

    NASA Astrophysics Data System (ADS)

    Han, Jie

    1995-01-01

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

  15. 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.

  16. Radiation in molecular dynamic simulations

    SciTech Connect

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

    2008-10-13

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

  17. [Cardiac potassium channels: molecular structure, physiology, pathophysiology and therapeutic implications].

    PubMed

    Mironov, N Iu; Golitsyn, S P

    2013-01-01

    Potassium channels and currents play essential roles in cardiac repolarization. Potassium channel blockade by class III antiarrhythmic drugs prolongs cardiac repolarization and results in termination and prevention of cardiac arrhythmias. Excessive inhomogeneous repolarization prolongation may lead to electrical instability and proarrhythmia (Torsade de Pointes tachycardia). This review focuses on molecular structure, physiology, pathophysiology and therapeutic potential of potassium channels of cardiac conduction system and myocardium providing information on recent findings in pathogenesis of cardiac arrhythmias, including inherited genetic abnormalities, and future perspectives. PMID:24654438

  18. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

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

  19. A concurrent multiscale micromorphic molecular dynamics

    SciTech Connect

    Li, Shaofan Tong, Qi

    2015-04-21

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

  20. Molecular Na-channel excitability from statistical physics

    NASA Astrophysics Data System (ADS)

    Ramírez-Piscina, L.; Sancho, J. M.

    2014-12-01

    The excitable properties of the neural cell membrane is the driving mechanism of the neural pulses. Coordinated ionic fluxes across Na and K channels are the devices responsible of this function. Here we present a simple microscopic physical scenario which accounts for this phenomenology. The main elements are ions and channel doors that obey the standard formulation of statistical physics (overdamped Langevin equations) with appropriate nonlinear interacting potentials. From these equations we obtain the ionic flux and the dynamics of the membrane potential. We show that the excitable properties of the membrane are present in a single and simple Na channel. From this framework, additional microscopic information can be obtained, such as statistics of single-channels dynamics or the energetics of action potential events.

  1. Dynamics and energetics of water permeation through the aquaporin channel.

    PubMed

    Vidossich, Pietro; Cascella, Michele; Carloni, Paolo

    2004-06-01

    Structural properties of water inside bovine aquaporin-1 are investigated by molecular simulation. The calculations, which are based on the recently determined X-ray structure at 2.2 A resolution (Sui et al., Nature 2001;414:872-878), are carried out on one monomeric subunit immersed in a water-n-octane-water bilayer. Molecular dynamics (MD) simulations suggest that His182, a fully conserved residue in the channel pore, is protonated in the delta position. Furthermore, they reveal a highly ordered water structure in the channel, induced by the electrostatic properties of the protein. Multiple-steering MD simulations are used to calculate the free-energy of water diffusion. To the best of our knowledge, this represents the first free-energy calculation based on the new, high-resolution structure of the pore. The calculated barrier is 2.5 kcal/mol, and it is associated to water permeation through the Asn-Pro-Ala (NPA) region of the pore, where water molecules are only hydrogen-bonded with themselves. These findings are fully consistent with those based on the previous MD studies on the human protein (de Groot and Grubmüller, Science 2001;294:2353-2357). PMID:15146490

  2. 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

  3. Molecular dynamics simulation of benzene

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

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

  4. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

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

    2015-03-01

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

  5. Molecular Basis of Functional Myocardial Potassium Channel Diversity.

    PubMed

    Nerbonne, Jeanne M

    2016-06-01

    Multiple types of voltage-gated K(+) and non-voltage-gated K(+) currents have been distinguished in mammalian cardiac myocytes based on differences in time-dependent and voltage-dependent properties and pharmacologic sensitivities. Many of the genes encoding voltage-gated K(+) (Kv) and non-voltage-gated K(+) (Kir and K2P) channel pore-forming and accessory subunits are expressed in the heart, and a variety of approaches have been, and continue to be, used to define the molecular determinants of native cardiac K(+) channels and to explore the molecular mechanisms controlling the diversity, regulation, and remodeling of these channels in the normal and diseased myocardium. PMID:27261820

  6. 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

    1995-05-01

    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. PMID:7727450

  7. 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.

  8. Langevin stabilization of molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2001-02-01

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

  9. Extended Molecular Dynamics Methods for Vortex Dynamics in Nano-structured Superconductors

    NASA Astrophysics Data System (ADS)

    Kato, Masaru; Sato, Osamu

    Using improved molecular dynamics simulation method, we study vortex dynamics in nano-scaled superconductors. Heat generations during vortex motion, heat transfer in superconductors, and entropy forces to vortices are incorporated. Also quasi-particle relaxations after vortex motion, and their attractive "retarded" forces to other vortices are incorporated using the condensation-energy field. We show the time development of formation of vortex channel flow in a superconducting Corbino-disk.

  10. Molecular dynamics of fluids and droplets in patterned nanochannels

    NASA Astrophysics Data System (ADS)

    Cieplak, M.

    2008-07-01

    Molecular dynamics studies of chain molecule fluids in nanochannels reveal new kinds of stationary flows when the walls of the channel are patterned chemically. In the single-fluid case, the patterning is shown to give rise to spatial switching between Poiseuille-like and plug-flow behaviours. In the two-fluid case, such that the two immiscible fluids wet different patches of a chemically patterned channel, the velocity field of the individual components is modulated in a way that is phase shifted relative to the single-fluid case. When the channel is homogeneous and wetting to one fluid component but non-wetting to the other then the resulting coating of the channel walls provides dissipation and thus stabilises flow of the other component. Wettability and geometrical patterning of substrates gives rise to a lotus-like effect in a rolling motion of nanodroplets along the substrate.

  11. 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

  12. 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

  13. Molecular dynamics on APE100

    NASA Astrophysics Data System (ADS)

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

    1995-09-01

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

  14. Dynamics of riboswitches: Molecular simulations.

    PubMed

    Sanbonmatsu, Karissa Y

    2014-10-01

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

  15. 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.

  16. WATER TEMPERATURE DYNAMICS IN EXPERIMENTAL FIELD CHANNELS: ANALYSIS AND MODELING

    EPA Science Inventory

    This study is on water temperature dynamics in the shallow field channels of the USEPA Monticello Ecological Research Station (MERS). The hydraulic and temperature environment in the MERS channels was measured and simulated to provide some background for several biological studie...

  17. The dynamics of small excitable ion channel clusters

    NASA Astrophysics Data System (ADS)

    Shuai, J. W.; Jung, P.

    2006-06-01

    Through computational modeling we predict that small sodium ion channel clusters on small patches of membrane can encode electric signals most efficiently at certain magic cluster sizes. We show that this effect can be traced back to algebraic features of small integers and are universal for channels with a simple gating dynamics. We further explore physiologic conditions under which such effects can occur.

  18. Molecular Mapping of General Anesthetic Sites in a Voltage-Gated Ion Channel

    PubMed Central

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

    2011-01-01

    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. PMID:21961587

  19. Time-Dependent Molecular Reaction Dynamics

    SciTech Connect

    Oehrn, Yngve

    2007-11-29

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

  20. Cystic Fibrosis Transmembrane Conductance Regulator: Using Differential Reactivity toward Channel-Permeant and Channel-Impermeant Thiol-Reactive Probes To Test a Molecular Model for the Pore†

    PubMed Central

    2009-01-01

    The sixth transmembrane segment (TM6) of the CFTR chloride channel has been intensively investigated. The effects of amino acid substitutions and chemical modification of engineered cysteines (cysteine scanning) on channel properties strongly suggest that TM6 is a key component of the anion-conducting pore, but previous cysteine-scanning studies of TM6 have produced conflicting results. Our aim was to resolve these conflicts by combining a screening strategy based on multiple, thiol-directed probes with molecular modeling of the pore. CFTR constructs were screened for reactivity toward both channel-permeant and channel-impermeant thiol-directed reagents, and patterns of reactivity in TM6 were mapped onto two new, molecular models of the CFTR pore: one based on homology modeling using Sav1866 as the template and a second derived from the first by molecular dynamics simulation. Comparison of the pattern of cysteine reactivity with model predictions suggests that nonreactive sites are those where the TM6 side chains are occluded by other TMs. Reactive sites, in contrast, are generally situated such that the respective amino acid side chains either project into the predicted pore or lie within a predicted extracellular loop. Sites where engineered cysteines react with both channel-permeant and channel-impermeant probes occupy the outermost extent of TM6 or the predicted TM5−6 loop. Sites where cysteine reactivity is limited to channel-permeant probes occupy more cytoplasmic locations. The results provide an initial validation of two, new molecular models for CFTR and suggest that molecular dynamics simulation will be a useful tool for unraveling the structural basis of anion conduction by CFTR. PMID:19754156

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Parallel Molecular Dynamics Program for Molecules

    Energy Science and Technology Software Center (ESTSC)

    1995-03-07

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

  6. Molecular dynamics studies on nanoscale gas transport

    NASA Astrophysics Data System (ADS)

    Barisik, Murat

    wall force penetration region at different flow conditions. Shear stress results are utilized to calculate the tangential momentum accommodation coefficient (TMAC) between argon gas and FCC walls. The TMAC value is shown to he independent of the now properties and Knudsen number in all simulations. Velocity profiles show distinct deviations from the kinetic theory based solutions inside the wall force penetration depth, while they match the linearized Boltzmann equation solution outside these zones. Afterwards, surface effects are studied as a function of the surface-gas potential strength ratio (epsilon wf/epsilonff) for the shear driven argon gas flows in the early transition and tree molecular flow regimes. Results show that increased epsilonwf/epsilon ff results in increased gas density, leading towards monolayer adsorption on surfaces. The near wall velocity profile shows reduced gas slip, and eventually velocity stick with increased epsilonwf/epsilon ff. Similarly, using MD predicted shear stress values and kinetic theory, TMAC are calculated as a function of epsilonwf/epsilon ff and TMAC values are shown to be independent of the Knudsen number. Results indicate emergence of the wall force field penetration depth as an additional length scale for gas flows in nano-channels, breaking the dynamic similarity between rarefied and nano-scale gas flows solely based on the Knudsen and Mach numbers.

  7. Molecular diversity and functional evolution of scorpion potassium channel toxins.

    PubMed

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

    2011-02-01

    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 (IC(50), 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 (IC(50), 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

  8. 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

  9. Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics

    NASA Astrophysics Data System (ADS)

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

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

  10. Molecular dynamics: A stitch in time

    NASA Astrophysics Data System (ADS)

    Deupi, Xavier

    2014-01-01

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

  11. 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.

  12. Dynamic molecular crystals with switchable physical properties.

    PubMed

    Sato, Osamu

    2016-06-21

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

  13. 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.

  14. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

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

    2015-01-01

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

  15. Surface dynamics of voltage-gated ion channels.

    PubMed

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

    2016-07-01

    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

  16. 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).

  17. 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

  18. 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. PMID:17090069

  19. Molecular dynamic simulations of ocular tablet dissolution.

    PubMed

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

    2013-11-25

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

  20. Local dynamic subgrid-scale models in channel flow

    NASA Astrophysics Data System (ADS)

    Cabot, William H.

    1994-12-01

    The dynamic subgrid-scale (SGS) model has given good results in the large-eddy simulation (LES) of homogeneous isotropic or shear flow, and in the LES of channel flow, using averaging in two or three homogeneous directions (the DA model). In order to simulate flows in general, complex geometries (with few or no homogeneous directions), the dynamic SGS model needs to be applied at a local level in a numerically stable way. Channel flow, which is inhomogeneous and wall-bounded flow in only one direction, provides a good initial test for local SGS models. Tests of the dynamic localization model were performed previously in channel flow using a pseudospectral code and good results were obtained. Numerical instability due to persistently negative eddy viscosity was avoided by either constraining the eddy viscosity to be positive or by limiting the time that eddy viscosities could remain negative by co-evolving the SGS kinetic energy (the DLk model). The DLk model, however, was too expensive to run in the pseudospectral code due to a large near-wall term in the auxiliary SGS kinetic energy (k) equation. One objective was then to implement the DLk model in a second-order central finite difference channel code, in which the auxiliary k equation could be integrated implicitly in time at great reduction in cost, and to assess its performance in comparison with the plane-averaged dynamic model or with no model at all, and with direct numerical simulation (DNS) and/or experimental data. Other local dynamic SGS models have been proposed recently, e.g., constrained dynamic models with random backscatter, and with eddy viscosity terms that are averaged in time over material path lines rather than in space. Another objective was to incorporate and test these models in channel flow.

  1. Local dynamic subgrid-scale models in channel flow

    NASA Technical Reports Server (NTRS)

    Cabot, William H.

    1994-01-01

    The dynamic subgrid-scale (SGS) model has given good results in the large-eddy simulation (LES) of homogeneous isotropic or shear flow, and in the LES of channel flow, using averaging in two or three homogeneous directions (the DA model). In order to simulate flows in general, complex geometries (with few or no homogeneous directions), the dynamic SGS model needs to be applied at a local level in a numerically stable way. Channel flow, which is inhomogeneous and wall-bounded flow in only one direction, provides a good initial test for local SGS models. Tests of the dynamic localization model were performed previously in channel flow using a pseudospectral code and good results were obtained. Numerical instability due to persistently negative eddy viscosity was avoided by either constraining the eddy viscosity to be positive or by limiting the time that eddy viscosities could remain negative by co-evolving the SGS kinetic energy (the DLk model). The DLk model, however, was too expensive to run in the pseudospectral code due to a large near-wall term in the auxiliary SGS kinetic energy (k) equation. One objective was then to implement the DLk model in a second-order central finite difference channel code, in which the auxiliary k equation could be integrated implicitly in time at great reduction in cost, and to assess its performance in comparison with the plane-averaged dynamic model or with no model at all, and with direct numerical simulation (DNS) and/or experimental data. Other local dynamic SGS models have been proposed recently, e.g., constrained dynamic models with random backscatter, and with eddy viscosity terms that are averaged in time over material path lines rather than in space. Another objective was to incorporate and test these models in channel flow.

  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 signature of molecular association in methanol

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  4. Dynamic signature of molecular association in methanol.

    PubMed

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

    2016-07-01

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

  5. Molecular scale dynamics of large ring polymers.

    PubMed

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

    2014-10-17

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

  6. Numerical methods for molecular dynamics

    SciTech Connect

    Skeel, R.D.

    1991-01-01

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

  7. Molecular Dynamics Simulations of Hexadecane/Silicalite Interfaces

    SciTech Connect

    Grest, G.S.; Webb, E.B.

    1999-01-20

    The interface between liquid hexadecane and the (010) surface of silicalite was studied by molecular dynamics. The structure of molecules in the interracial region is influenced by the presence of pore mouths on the silicalite surface. For this surface, whose pores are the entrances to straight channels, the concentration profile for partially absorbed molecules is peaked around 10 monomers inside the zeolite. No preference to enter or exit the zeolite based on absorption length is observed except for very small or very large absorption lengths. We also found no preferential conformation of the unabsorbed tails for partially absorbed molecules.

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

    PubMed

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

    2016-02-01

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

  9. 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.

  10. 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.

  11. Molecular identity of dendritic voltage-gated sodium channels.

    PubMed

    Lorincz, Andrea; Nusser, Zoltan

    2010-05-14

    Active invasion of the dendritic tree by action potentials (APs) generated in the axon is essential for associative synaptic plasticity and neuronal ensemble formation. In cortical pyramidal cells (PCs), this AP back-propagation is supported by dendritic voltage-gated Na+ (Nav) channels, whose molecular identity is unknown. Using a highly sensitive electron microscopic immunogold technique, we revealed the presence of the Nav1.6 subunit in hippocampal CA1 PC proximal and distal dendrites. Here, the subunit density is lower by a factor of 35 to 80 than that found in axon initial segments. A gradual decrease in Nav1.6 density along the proximodistal axis of the dendritic tree was also detected without any labeling in dendritic spines. Our results reveal the characteristic subcellular distribution of the Nav1.6 subunit, identifying this molecule as a key substrate enabling dendritic excitability. PMID:20466935

  12. 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.

  13. 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.

  14. Non-equilibrium dynamics contribute to ion selectivity in the KcsA channel.

    PubMed

    Ngo, Van; Stefanovski, Darko; 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 dynamics calculations of nuclear stimulated desorption

    SciTech Connect

    Glikman, E.; Kelson, I. ); Doan, N.V. )

    1991-09-01

    Molecular dynamics calculations of nuclear stimulated desorption are carried out for a palladium crystal containing radioactive palladium atoms. The total desorption probability from various sites are computed, as well as the angular distribution of the desorbing atoms. The implications of the results to different experimental scenarios are discussed.

  16. 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.

  17. Optimizing replica exchange moves for molecular dynamics.

    PubMed

    Nadler, Walter; Hansmann, Ulrich H E

    2007-11-01

    We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method. PMID:18233794

  18. 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.

  19. Molecular Dynamics Simulations of Graphene Oxide Frameworks

    SciTech Connect

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

    2013-01-01

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

  20. Molecular dynamics of PLK1 during mitosis

    PubMed Central

    Schmucker, Stephane; Sumara, Izabela

    2014-01-01

    Polo-like kinase 1 (PLK1) is a key regulator of eukaryotic cell division. During mitosis, dynamic regulation of PLK1 is crucial for its roles in centrosome maturation, spindle assembly, microtubule–kinetochore attachment, and cytokinesis. Similar to other members of the PLK family, the molecular architecture of PLK1 protein is characterized by 2 domains—the kinase domain and the regulatory substrate-binding domain (polo-box domain)—that cooperate and control PLK1 function during mitosis. Mitotic cells employ many layers of regulation to activate and target PLK1 to different cellular structures in a timely manner. During the last decade, numerous studies have shed light on the precise molecular mechanisms orchestrating the mitotic activity of PLK1 in time and space. This review aims to discuss available data and concepts related to regulation of the molecular dynamics of human PLK1 during mitotic progression. PMID:27308323

  1. Molecular dynamics simulations of weak detonations.

    PubMed

    Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie

    2011-12-01

    Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055

  2. Erosive dynamics of channels incised by subsurface water flow

    NASA Astrophysics Data System (ADS)

    Lobkovsky, Alexander E.; Smith, Braunen E.; Kudrolli, Arshad; Mohrig, David C.; Rothman, Daniel H.

    2007-09-01

    We propose a dynamical model for channels incised into an erodible bed by subsurface water flow. The model is validated by the time-resolved topographic measurements of channel growth in a laboratory-scale experiment. Surface heights in the experiment are measured via a novel laser-aided imaging technique. The erosion rate in the model is composed of diffusive and advective components as well as a simple driving term due to the seeping water. Steady driving conditions may exist whenever channels are incised into a flat and level erodible bed by a water table replenished via steady (on average) rainfall. Under such steady driving conditions, the model predicts an asymptotically self-similar growing shape for the channel transects. Conversely, given a transect shape that evolved under steady driving conditions and an estimate of the erosion rate at the bottom of the channel, granular transport coefficients can be inferred from the static channel shape. We report an estimate of these transport coefficients for a system of ravines incised into unconsolidated sand in the Apalachicola River basin, Florida.

  3. 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.

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

    PubMed Central

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

    2013-01-01

    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. PMID:24305683

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

    PubMed

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

    2013-01-01

    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. PMID:24305683

  6. Dynamic properties of microemulsions in the single-phase channels.

    PubMed

    Wolf, Lukas; Hoffmann, Heinz; Richter, Walter; Teshigawara, Takashi; Okamoto, Tohru

    2011-09-29

    We have studied the dynamic and rheological properties in the single-phase channels of a microemulsion system with a mixed anionic/nonionic surfactant system and decane from the aqueous to the oil phase. One isotropic channel, called the "upper" channel, begins at the L(3) phase (sponge-like phase) of the binary surfactant mixture on the water side and passes with a shallow minimum for the surfactant composition to the oil side. The other "lower" single-phase channel begins at the micellar L(1) phase and ends in the middle of the phase diagram. Both isotropic channels are separated by a huge anisotropic single phase L(α) channel that reaches from the water side to 90% of oil in the solvent mixture. The structural relaxation time of the viscous fluids could be measured with electric birefringence (EB) measurements, where a signal is caused by the deformation of the internal nanostructure of the fluids by an electric field. For the L(3) phase, the EB signal can be fitted with a single time constant. With increasing oil in the upper channel, the main structural relaxation time passes over a maximum and correlates with the viscosity. Obviously, this time constant controls the viscosity of the fluid (η(o) = G'·τ). It is remarkable that the longest structural relaxation time increases three decades, and the viscosity increases two decades when 10% of oil is solubilized into the L(3) phase. Conductivity data imply that the fluid in the upper channel has a bicontinuous structure from the L(3) phase to the microemulsion with only 10% oil. In this oil range, the conductivity decreases three decades, and the electric birefringence signals are complicated because of a superposition of up to three processes. For higher oil ratios, the structure obviously changes to a HIPE (high internal phase emulsion) structure with water droplets in the oil matrix. PMID:21842905

  7. 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.

  8. 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

  9. Exciton dynamics in perturbed vibronic molecular aggregates.

    PubMed

    Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V

    2016-07-01

    A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840

  10. Molecular dynamics simulations of shallow nitrogen and silicon implantation into diamond

    NASA Astrophysics Data System (ADS)

    Lehtinen, Ossi; Naydenov, Boris; Börner, Pia; Melentjevic, Kristina; Müller, Christoph; McGuinness, Liam Paul; Pezzagna, Sebastien; Meijer, Jan; Kaiser, Ute; Jelezko, Fedor

    2016-01-01

    A solid understanding of the implantation process of N and Si ions into diamond is needed for the controlled creation of shallow color centers for quantum computing, simulation, and sensing applications. Here, molecular dynamics simulations of the shallow implantation of N and Si ions into diamond is simulated at 100-5000 eV kinetic energies and different angles of incidence. We find that ion channeling is an important effect with an onset energy depending on the crystal orientation. Consequently, the molecular dynamics simulations produce improved predictions as compared to standard Monte Carlo simulations. When implanting in a channeling direction, the spatial distribution of the channeled ions becomes markedly narrow, allowing a higher degree of control over the location of the nitrogen vacancy (NV-) centers. A contamination layer on the ion entry surface reduces the fraction of channeled ions. A comparison to an experimentally determined depth profile based on a NMR signal from protons yields a quantitative agreement, validating the simulation approach.

  11. 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

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

    PubMed

    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

  13. 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

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

    PubMed

    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

  15. Molecular dynamics studies of polyurethane nanocomposite hydrogels

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  16. Molecular dynamics study of cyclohexane interconversion

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Chandler, David

    1990-12-01

    Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.

  17. Molecular dynamics at constant Cauchy stress

    NASA Astrophysics Data System (ADS)

    Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio

    2016-05-01

    The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.

  18. Molecular dynamics at constant Cauchy stress.

    PubMed

    Miller, Ronald E; Tadmor, Ellad B; Gibson, Joshua S; Bernstein, Noam; Pavia, Fabio

    2016-05-14

    The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress. PMID:27179471

  19. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  20. Molecular dynamics simulations of the Cx26 hemichannel: Evaluation of structural models with Brownian dynamics

    PubMed Central

    Kwon, Taekyung; Harris, Andrew L.; Rossi, Angelo

    2011-01-01

    The recently published crystal structure of the Cx26 gap junction channel provides a unique opportunity for elucidation of the structure of the conductive connexin pore and the molecular determinants of its ion permeation properties (conductance, current–voltage [I-V] relations, and charge selectivity). However, the crystal structure was incomplete, most notably lacking the coordinates of the N-terminal methionine residue, which resides within the pore, and also lacking two cytosolic domains. To allow computational studies for comparison with the known channel properties, we completed the structure. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) simulations of the completed and the published Cx26 hemichannel crystal structure indicate that the pore is too narrow to permit significant ion flux. The GCMC/BD simulations predict marked inward current rectification and almost perfect anion selectivity, both inconsistent with known channel properties. The completed structure was refined by all-atom molecular dynamics (MD) simulations (220 ns total) in an explicit solvent and POPC membrane system. These MD simulations produced an equilibrated structure with a larger minimal pore diameter, which decreased the height of the permeation barrier formed by the N terminus. GCMC/BD simulations of the MD-equilibrated structure yielded more appropriate single-channel conductance and less anion/cation selectivity. However, the simulations much more closely matched experimentally determined I-V relations when the charge effects of specific co- and posttranslational modifications of Cx26 previously identified by mass spectrometry were incorporated. We conclude that the average equilibrated structure obtained after MD simulations more closely represents the open Cx26 hemichannel structure than does the crystal structure, and that co- and posttranslational modifications of Cx26 hemichannels are likely to play an important physiological role by defining the conductance and ion

  1. Nanoindentation of Zr by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.

    2015-12-01

    Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.

  2. New faster CHARMM molecular dynamics engine

    PubMed Central

    Hynninen, Antti-Pekka; Crowley, Michael F

    2014-01-01

    We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199

  3. Molecular dynamics modelling of solidification in metals

    SciTech Connect

    Boercker, D.B.; Belak, J.; Glosli, J.

    1997-12-31

    Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.

  4. Molecular crowding and protein enzymatic dynamics.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2012-05-21

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

  5. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  6. Optimally designed fields for controlling molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rabitz, Herschel

    1991-10-01

    This research concerns the development of molecular control theory techniques for designing optical fields capable of manipulating molecular dynamic phenomena. Although is has been long recognized that lasers should be capable of manipulating dynamic events, many frustrating years of intuitively driven laboratory studies only serve to illustrate the point that the task is complex and defies intuition. The principal new component in the present research is the recognition that this problem falls into the category of control theory and its inherent complexities require the use of modern control theory tools largely developed in the engineering disciplines. Thus, the research has initiated a transfer of the control theory concepts to the molecular scale. Although much contained effort will be needed to fully develop these concepts, the research in this grant set forth the basic components of the theory and carried out illustrative studies involving the design of optical fields capable of controlling rotational, vibrational and electronic degrees of freedom. Optimal control within the quantum mechanical molecular realm represents a frontier area with many possible ultimate applications. At this stage, the theoretical tools need to be joined with merging laboratory optical pulse shaping capabilities to illustrate the power of the concepts.

  7. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  8. Dynamic Maintenance and Visualization of Molecular Surfaces

    SciTech Connect

    Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N

    2004-12-16

    Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.

  9. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  10. Polymer Fluid Dynamics: Continuum and Molecular Approaches.

    PubMed

    Bird, R B; Giacomin, A J

    2016-06-01

    To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems. PMID:27276553

  11. Application of optimal prediction to molecular dynamics

    SciTech Connect

    Barber IV, John Letherman

    2004-12-01

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

  12. 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

  13. Effect of entrance channel on dynamics of heavy ions collision

    NASA Astrophysics Data System (ADS)

    Naderi, D.

    2016-01-01

    A combined dynamical model using concept of dinuclear systems (DNS) and one-dimensional (1D) Langevin equations was applied to investigate the effect of entrance channel on dynamics of heavy ions collision. The 30Si+170Er, 16O+184W and 19F+181Ta reactions which formed the compound nucleus 200Pb have been considered to study this effect. We studied these reactions dynamically and calculated the ratio of evaporation residue cross-section to fusion cross-section (σER/σFus) as a tool for investigation of entrance channel effect. Results of combined model are compared with available experimental data and results of 1D Langevin equations. Obtained results based on combined model are in better agreement with experimental data in comparison with results of Langevin equations. We concluded for 30Si+170Er and 19F+181Ta reactions the results of combined model that support the quasi-fission process are different relative to Langevin dynamical approach, whereas for 16O+184W system the two models give similar results.

  14. Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.

    PubMed

    Paquet, Eric; Viktor, Herna L

    2015-01-01

    Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

  15. 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

  16. The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel.

    PubMed

    Meng, Xuan-Yu; Liu, Shengtang; Cui, Meng; Zhou, Ruhong; Logothetis, Diomedes E

    2016-01-01

    Inwardly rectifying K(+) (Kir) channels, serving as natural molecular nanomachines, transport potassium ions across the plasma membrane of the cell. Along the ion permeation pathway, three relatively narrow regions (the selectivity filter (SF), the inner helix bundle crossing (HBC), and the cytosolic G loop) may serve as gates to control ion permeation. Our previous molecular dynamics simulations based on the crystal structure of a Kir3.1 chimera revealed the possible gating mechanism of the G loop gate. Here, we introduced a proline mutation in the inner helix and obtained a channel model of the open HBC gate. The open HBC gate reaches 0.6 nm in diameter, which allows partial hydrated K(+) ions to pass through. During the gating process, both the transmembrane helices TM1 and TM2 cooperatively rotate in a counterclockwise direction (viewed from the extracellular side) with the aid of the phospholipid PIP2. Only when all the transmembrane helices adopt a counterclockwise rotation, the HBC gate can be stabilized in the open state. We estimate that introduction of the proline mutation decreases the energy required to open the HBC gate by about 1.4 kcal/mol (ΔΔG). PMID:27439597

  17. The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel

    PubMed Central

    Meng, Xuan-Yu; Liu, Shengtang; Cui, Meng; Zhou, Ruhong; Logothetis, Diomedes E.

    2016-01-01

    Inwardly rectifying K+ (Kir) channels, serving as natural molecular nanomachines, transport potassium ions across the plasma membrane of the cell. Along the ion permeation pathway, three relatively narrow regions (the selectivity filter (SF), the inner helix bundle crossing (HBC), and the cytosolic G loop) may serve as gates to control ion permeation. Our previous molecular dynamics simulations based on the crystal structure of a Kir3.1 chimera revealed the possible gating mechanism of the G loop gate. Here, we introduced a proline mutation in the inner helix and obtained a channel model of the open HBC gate. The open HBC gate reaches 0.6 nm in diameter, which allows partial hydrated K+ ions to pass through. During the gating process, both the transmembrane helices TM1 and TM2 cooperatively rotate in a counterclockwise direction (viewed from the extracellular side) with the aid of the phospholipid PIP2. Only when all the transmembrane helices adopt a counterclockwise rotation, the HBC gate can be stabilized in the open state. We estimate that introduction of the proline mutation decreases the energy required to open the HBC gate by about 1.4 kcal/mol (ΔΔG). PMID:27439597

  18. 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.

  19. Dynamic Propagation Channel Characterization and Modeling for Human Body Communication

    PubMed Central

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

    2012-01-01

    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. PMID:23250278

  20. 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.

  1. Stochastic dynamics of electrical membrane with voltage-dependent ion channel fluctuations

    NASA Astrophysics Data System (ADS)

    Qian, Hong; Zhang, Xue-Juan; Qian, Min

    2014-04-01

    A Brownian-ratchet-like stochastic theory for the electrochemical membrane system of Hodgkin-Huxley (HH) is developed. The system is characterized by a continuous variable Q_m(t) , representing mobile membrane charge density, and a discrete variable Kt representing ion channel conformational dynamics. A Nernst-Planck-Nyquist-Johnson-type equilibrium is obtained when multiple conducting ions have a common reversal potential. Detailed balance yields a previously unknown relation between the channel switching rates and membrane capacitance, bypassing an Eyring-type explicit treatment of gating charge kinetics. From a molecular structural standpoint, the membrane charge Qm is a more natural dynamic variable than the potential Vm; our formalism treats Qm-dependent conformational transition rates \\lambda_{ij} as intrinsic parameters. Therefore, in principle, \\lambda_{ij} vs. Vm is experimental-protocol-dependent, e.g., different from voltage or charge clamping measurements. For constant membrane capacitance per unit area Cm and neglecting the membrane potential induced by gating charges, V_m=Q_m/C_m , and HH's formalism is recovered. The presence of two types of ions, with different channels and reversal potentials, gives rise to a nonequilibrium steady state with positive entropy production ep. For rapidly fluctuating channels, an expression for ep is obtained.

  2. Symmetry Reduced Dynamics of Charged Molecular Strands

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

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

  3. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  4. Dynamical coupled channel calculation of pion and omega meson production

    SciTech Connect

    Paris, Mark

    2009-01-01

    A dynamical coupled channel approach is used to study $\\pi$ and $\\omega$--meson production induced by pions and photons scattering from the proton. Six-channels are used to fit unpolarized and polarized scattering data including $\\pi N$, $\\eta N$, $\\pi\\Delta$, $\\sigma N$, $\\rho N$, $\\omega N$. Bare parameters in an effective hadronic Lagrangian are fixed in $\\chi^2$-fits to data from $\\pi N \\to \\pi N$, $\\gamma N \\to \\pi N$, $\\pi^- p \\to \\omega n$, and $\\gamma p \\to \\omega p$ reactions at center-of-mass energies from threshold to $E < 2.0$ GeV. The $T$ matrix determined in these fits is used to calculate the photon beam asymmetry for $\\omega$-meson production and the $\\omega N \\to \\omega N$ total cross section and scattering lengths.

  5. 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)

  6. Partial synchronization in stochastic dynamical networks with switching communication channels

    NASA Astrophysics Data System (ADS)

    Huang, Chi; Ho, Daniel W. C.; Lu, Jianquan; Kurths, Jürgen

    2012-06-01

    In this paper, the partial synchronization problem of stochastic dynamical networks (SDNs) is investigated. Unlike the existing models, the SDN considered in this paper suffers from a class of communication constraint—only part of nodes' states can be transmitted. Thus, less nodes' states can be used to synchronize the SDN, which makes the analysis of the synchronization problem much harder. A set of channel matrices are introduced to reflect such kind of constraint. Furthermore, due to unpredictable environmental changes, the channel matrices can switch among some communication modes. The switching considered here is governed by a Markov process. To overcome the difficulty, a regrouping method is employed to derive our main results. The obtained conditions guarantee that partial synchronization can be achieved for SDNs under switching communication constraint. Finally, numerical examples are given to illustrate the effectiveness of the theoretical results and how the communication constraint influences synchronization result.

  7. Electronic continuum model for molecular dynamics simulations.

    PubMed

    Leontyev, I V; Stuchebrukhov, A A

    2009-02-28

    A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627

  8. Stochastic Event-Driven Molecular Dynamics

    SciTech Connect

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

    2008-02-01

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

  9. Molecular dynamics in high electric fields

    NASA Astrophysics Data System (ADS)

    Apostol, M.; Cune, L. C.

    2016-06-01

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

  10. Molecular dynamics studies of aromatic hydrocarbon liquids

    SciTech Connect

    McLaughlin, E.; Gupta, S.

    1990-01-01

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

  11. Molecular Dynamics Simulations of the Photoactive Protein Nitrile Hydratase

    PubMed Central

    Kubiak, Karina; Nowak, Wieslaw

    2008-01-01

    Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, α and β. Hydrogen bonds between βArg-56 and αCys-114 sulfenic acid (αCEA114) are important to maintain the enzymatic activity. The enzyme may be inactivated by endogenous nitric oxide (NO) and activated by absorption of photons of wavelength λ < 630 nm. To explain the photosensitivity and to propose structural determinants of catalytic activity, differences in the dynamics of light-active and dark-inactive forms of NHase were investigated using molecular dynamics (MD) modeling. To this end, a new set of force field parameters for nonstandard NHase active sites have been developed. The dynamics of the photodissociated NO ligand in the enzyme channel was analyzed using the locally enhanced sampling method, as implemented in the MOIL MD package. A series of 1 ns trajectories of NHases shows that the protonation state of the active site affects the dynamics of the catalytic water and NO ligand close to the metal center. MD simulations support the catalytic mechanism in which a water molecule bound to the metal ion directly attacks the nitrile carbon. PMID:18234830

  12. 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.

  13. Molecular dynamics simulation for flow characteristics in nanochannels and single walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Yasuoka, H.; Imae, T.; Kaneda, M.; Suga, K.

    2014-08-01

    Flows in graphite-, diamond- and silicon-walled nanochannels are discussed by performing molecular dynamics simulations. Flows in carbon nanotubes (CNTs) and graphene- walled nanochannels are also investigated. It is found that the flow rate in the graphite-walled channel tends to be the largest because of its slippery wall structure by the short bond length and the high molecular density of the CNTs. The flow rate in the single walled CNT at a very narrow diameter tends to increase although such a tendency is not seen in the graphene-walled channel.

  14. Crystallization of nickel nanoclusters by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Chamati, H.; Gaminchev, K.

    2012-12-01

    We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.

  15. Molecular dynamics simulation of ice XII

    NASA Astrophysics Data System (ADS)

    Borzsák, István; Cummings, Peter T.

    1999-02-01

    Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.

  16. Thermostability of Enzymes from Molecular Dynamics Simulations.

    PubMed

    Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G

    2016-06-14

    Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810

  17. 8B structure in Fermionic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Henninger, K. R.; Neff, T.; Feldmeier, H.

    2015-04-01

    The structure of the light exotic nucleus 8B is investigated in the Fermionic Molecular Dynamics (FMD) model. The decay of 8B is responsible for almost the entire high- energy solar-neutrino flux, making structure calculations of 8B important for determining the solar core temperature. 8B is a proton halo candidate thought to exhibit clustering. FMD uses a wave-packet basis and is well-suited for modelling clustering and halos. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo.

  18. 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.

  19. 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.

  20. Molecular dynamics at constant temperature and pressure

    NASA Astrophysics Data System (ADS)

    Toxvaerd, S.

    1993-01-01

    Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.

  1. Charge transport network dynamics in molecular aggregates.

    PubMed

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

    2016-08-01

    Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, [Formula: see text] Simulations reveal the relevant timescale for local transfer integral decorrelation to be [Formula: see text]100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed. PMID:27439871

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2003-10-01

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

  4. Molecular dynamics simulation of liquid sulfur dioxide.

    PubMed

    Ribeiro, Mauro C C

    2006-05-01

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

  5. Attosecond vacuum UV coherent control of molecular dynamics

    PubMed Central

    Ranitovic, Predrag; Hogle, Craig W.; Rivière, Paula; Palacios, Alicia; Tong, Xiao-Ming; Toshima, Nobuyuki; González-Castrillo, Alberto; Martin, Leigh; Martín, Fernando; Murnane, Margaret M.; Kapteyn, Henry

    2014-01-01

    High harmonic light sources make it possible to access attosecond timescales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized; this is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep UV, which have not yet been synthesized. Here, we present a unique approach using attosecond vacuum UV pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born–Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipulate the ionization and dissociation channels. Furthermore, through advanced theory, we succeed in rigorously modeling multiscale electron and nuclear quantum control in a molecule. The observed richness and complexity of the dynamics, even in this very simplest of molecules, is both remarkable and daunting, and presents intriguing new possibilities for bridging the gap between attosecond physics and attochemistry. PMID:24395768

  6. Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Byutner, Oleksiy; Smith, Grant

    2001-03-01

    In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.

  7. 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.

  8. Fluid dynamics at transition regions of enhanced heat transfer channels

    NASA Astrophysics Data System (ADS)

    Case, Jennifer C.; Pohlman, Nicholas A.

    2012-11-01

    Helical wire coil inserts are used to enhance heat transfer in high heat flux cooling channels. Past research using temperature probes has sufficiently proven that wire coils increase heat transfer by factors of three to five through the disruption of the boundary layer in the channels. The coils are passive devices that are inexpensive to manufacture and easily integrate into existing heat exchangers given the limited pressure drop they produce. Most of the fluid mechanics research in flow over helical coils has focused on the dynamics and vortex structure in fully developed regions rather than the short transition region where the enhanced heat transfer is often expected. Understanding how the development of the flow occurs over the axial length of the cooling channel will determine minimum dimensions necessary for enhanced heat transfer. Results of particle-shadow velocimetry (PSV) measurements report on the flow velocities and turbulence that occurs in the transition regions at the beginning of wire coil inserts. The ability to relate parameters such as flow rate, wire diameter, coil pitch, and the total tube length will increase fundamental knowledge and will allow for more efficient heat exchanger designs. Funding provided by NIU's Undergraduate Special Opportunities in Artistry & Research grant program.

  9. Fluctuating supply and emplacement dynamic of channelized lava flows

    NASA Astrophysics Data System (ADS)

    Tarquini, Simone; de'Michieli Vitturi, Mattia

    2014-05-01

    The evolution of lava flows emplaced on Mount Etna (Italy) in September 2004 is examined in detail through the analysis of morphometric measurements of flow units. The growth of the main channelized flow is consistent with a layering of lava blankets which maintains the initial geometry of the channel (although levees are widened and raised), and is here explicitly related to the repeated overflow of lava pulses. A simple analytical model is introduced describing the evolution of the flow level in a channelized flow unit fed by a fluctuating supply. The model, named FLOWPULSE, shows that a fluctuation in the velocity of lava extrusion at the vent triggers the formation of pulses which become increasingly high the farther they are from the vent, and are invariably destined to overflow within a given distance. The FLOWPULSE simulations are in accordance with the observed morphology, characterized by a very flat initial profile followed by a massive increase in flow unit cross-section area between 600 and 700 m downflow. The modeled emplacement dynamics provides also an explanation for the observed substantial "loss" of the original flowing mass with increasing distance from the vent.

  10. 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

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

    PubMed

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

    2015-10-01

    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

  12. Exact dynamic properties of molecular motors

    NASA Astrophysics Data System (ADS)

    Boon, N. J.; Hoyle, R. B.

    2012-08-01

    Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

  13. 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.

  14. Exact dynamic properties of molecular motors.

    PubMed

    Boon, N J; Hoyle, R B

    2012-08-28

    Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)] on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods. PMID:22938213

  15. 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

  16. Stabilization and dynamics of edge flames in narrow channels

    NASA Astrophysics Data System (ADS)

    Bieri, Joanna A.

    The dynamics of edge flames in narrow channels is studied, first within the context of a reactive diffusive (or constant density) model and then in a variable density model which allows for the consideration of thermal expansion effects. Fuel and oxidizer, separated upstream by a thin plate of finite length, flow into a channel with a prescribed upstream velocity. At the end of the plate, the fuel and oxidizer mix and, when ignited, an edge flame is sustained at some distance from the tip of the plate. Typically, the flame, which is stabilized by heat conduction back to the cold plate, has a tribrachial structure. It consists of a leading edge, made up of lean and rich premixed segments, and an attached diffusion flame trailing behind. The flame can also have a hook-like shape, when one of the premixed branches is missing. This often happens for conditions away from stoichiometry and when the mass diffusivities of the fuel and oxidizer are unequal. Earlier work has determined the behavior of an edge flame in a mixing layer that develops downstream of a splitter plate with no boundaries in the lateral direction. This is relevant to the stabilization and liftoff of jet diffusion flames. The confined case has other possible applications, such as flames in mini-combustor systems, that have been recently tested experimentally. The objective in this work is to determine the effect that confinement has on the edge standoff distance, on the flame shape and on the flame stability. In particular, we examine the influence of channel width, wall temperature, and the effects of differential diffusion. We determine conditions under which the edge flame is stabilized near the tip of the splitter plate, is held near the tip but oscillates back and forth, or is blown-off. We consider a wide range of channel widths and boundary conditions at the walls.

  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. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  19. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  20. 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

  1. 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.

  2. Tethered Spectroscopic Probes Estimate Dynamic Distances with Subnanometer Resolution in Voltage-Dependent Potassium Channels

    PubMed Central

    Jarecki, Brian W.; Zheng, Suqing; Zhang, Leili; Li, Xiaoxun; Zhou, Xin; Cui, Qiang; Tang, Weiping; Chanda, Baron

    2013-01-01

    Measurements of inter- and intramolecular distances are important for monitoring structural changes and understanding protein interaction networks. Fluorescence resonance energy transfer and functionalized chemical spacers are the two predominantly used strategies to map short-range distances in living cells. Here, we describe the development of a hybrid approach that combines the key advantages of spectroscopic and chemical methods to estimate dynamic distance information from labeled proteins. Bifunctional spectroscopic probes were designed to make use of adaptable-anchor and length-varied spacers to estimate molecular distances by exploiting short-range collisional electron transfer. The spacers were calibrated using labeled polyproline peptides of defined lengths and validated by molecular simulations. This approach was extended to estimate distance restraints that enable us to evaluate the resting-state model of the Shaker potassium channel. PMID:24359744

  3. 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..

  4. Enhanced Fluid Mixing in Nanochannels: A Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Oliver, Eric C. J.; Slater, Gary W.

    2006-03-01

    The efficient mixing of fluids is of paramount importance in several applications such as lab-on-a-chip and microfluidic devices. The main limitation to efficiency is that on small scales where the Reynolds number of the flow is low, mixing is dominated by diffusion. Purely diffusive motion is very slow and is an inefficient mixing mechanism unless the channel width is extremely small. Starting with the basic result for diffusive mixing of a binary fluid in a Poiseuille flow we explore methods to enhance the level of mixing between the two fluid species. We simulate the system using Molecular Dynamics and model the fluids as assemblies of Lennard-Jones beads. In order to increase the rate of mixing we have forced lateral motion in the fluid using configurations of mid-stream posts. Specifically, posts set in a prism-like structure have proven to be extremely well suited to reducing the channel length required to achieve complete mixing. In order to measure efficiency we have proposed a mathematical function that quantifies the level mixing associated with a fluid element. Furthermore, we have developed a basic theory for the position of the mixing front in a flow with spatially dependent velocity and diffusion coefficient.

  5. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

    PubMed Central

    Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C.

    2013-01-01

    A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26–27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K+ channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K+ and Na+ concentration gradients and the electrostatic potential difference of living cells. PMID:24081985

  6. 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.

  7. 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

  8. 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.

  9. Development of semiclassical molecular dynamics simulation method.

    PubMed

    Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi

    2016-04-28

    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383

  10. Molecular Dynamics Simulation of Shock Induced Detonation

    NASA Astrophysics Data System (ADS)

    Tomar, Vikas; Zhou, Min

    2004-07-01

    This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.