Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

PubMed

Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

2016-02-23

The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in that it initially involves transitions to surfaces with fewer, less favorable contacts compared with those seen in the fully formed complex. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

NASA Astrophysics Data System (ADS)

Pullara, Filippo; Ignacio, J., General

2015-10-01

Standard Molecular Dynamics simulations (MD) are usually performed under periodic boundary conditions using the well-established "Ewald summation". This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells—important in many biological activities, such as protein cooperativity and physiological/pathological aggregation—are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p) interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum). When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.

Early adaptation to altered gravitational environments in the squirrel monkey

NASA Technical Reports Server (NTRS)

Fuller, C. A.

1985-01-01

The feeding behavior of two squirrel monkeys flown in Spacelab 3 is compared to that of six monkeys exposed to 1.5 G through centrifugation. The monkeys in the centrifugation study were housed unrestrained in cages, maintained at 25 C + or - 1 C, exposed to a 12:12 light/dark cycle, and had unrestrained access to food and water. The Spacelab monkeys were maintained at 26 C, exposed to a 12:12 light/dark cycle and had unlimited food and water. It is observed that the centrifuge rats displayed a change in feeding behavior for 4 days prior to resuming a normal pattern; one Spacelab monkey exhibited a 6 day depression before recover to control levels, and the feeding pattern of the second monkey was not influenced by the environment. It is noted that the effect of an altered dynamic environment is variable on the feeding behavior of individual monkeys.

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

NASA Astrophysics Data System (ADS)

Minges, Alexander; Ciupka, Daniel; Winkler, Christian; Höppner, Astrid; Gohlke, Holger; Groth, Georg

2017-03-01

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.

A field evaluation of real-life motor vehicle accidents: presence of unrestrained objects and their association with distribution and severity of patient injuries.

PubMed

Staff, Trine; Eken, Torsten; Hansen, Trond Boye; Steen, Petter Andreas; Søvik, Signe

2012-03-01

Moving objects may pose an added threat to car occupants in motor vehicle accidents (MVAs). However, to our knowledge, there have only been two case studies published on the subject. For the present study, accident reports and photo documentation from MVAs were collected on-scene by dedicated paramedics. Emergency medical service personnel on-scene were interviewed as necessary. Potentially harmful unrestrained objects in the involved motor vehicles (MVs) were identified and categorised by type, weight and hardness. Seatback offset by unrestrained objects was noted. The patient injury distribution (Abbreviated Injury Scale (AIS) body regions) and severity (AIS severity scores and New Injury Severity Score (NISS) scores) were retrospectively determined from hospital and autopsy records, and their potential relationship to unrestrained objects was explored. A total of 190 accidents involving 338 MVs and 618 individuals were included. In total, 327 individuals (53%) were injured, and 61 (10%) died. 37 of 61 were not autopsied. The mean NISS was 17 (median 8, interquartile range (IQR) 1-27). Unrestrained objects were reported for 133 motor vehicles (39%) involving 293 individuals. 35% of the unrestrained objects found in the passenger compartment weighed >2 kg. In the boot, 32% of objects weighed >20 kg. Seatback offset associated with unrestrained objects was found for 45 individuals (15%). Unrestrained objects originally located in the boot (heavy luggage, groceries and tyres were the most frequently reported) had moved into the passenger compartment on impact in 27 cases, 24 of which were associated with seatback offset. An in-depth analysis was performed on 24 patients whose injuries were highly likely to be associated with unrestrained objects, as indicated by accident reports and medical documentation. Nineteen (79%) were involved in frontal collisions, and 12 (50%) died on-scene. The mean NISS was 51.7 (median 51, IQR 27-75) in the 17 (71%) patients with seatback offset and 37.2 (median 41, IQR 22.5-50) in the 7 (29%) without seatback offset. Seatback offset was associated with more severe head and thoracic injuries and an increased incidence of abdominal and pelvic injuries. Patients injured by unrestrained objects while sitting in unharmed car seats predominantly suffered head, cervical spine and thoracic injuries. Our results indicate a need for public information campaigns. The development of car backseats that can better sustain hits from heavy objects in the cargo boot is an important area for the motor vehicle production industry to explore. Copyright © 2011 Elsevier Ltd. All rights reserved.

Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity.

PubMed

Silva, Daniel-Adriano; Domínguez-Ramírez, Lenin; Rojo-Domínguez, Arturo; Sosa-Peinado, Alejandro

2011-07-01

The molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G-protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L-lysine, L-arginine, L-ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr-14 and Phe-52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation-π interaction with Tyr-14 and Phe-52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand-dependent conformational plasticity not explained by the previous crystallographic data. Copyright © 2011 Wiley-Liss, Inc.

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.

PubMed

Procacci, Piero

2016-06-01

In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non-covalent bonding in drug-receptor systems. I show that most of the pitfalls and entanglements for the binding free energy evaluation in computer simulations are rooted in the equilibrium assumption that is implicit in the reversible method. These critical issues can be resolved by using a non-equilibrium variant of the alchemical method in molecular dynamics simulations, relying on the production of many independent trajectories with a continuous dynamical evolution of an externally driven alchemical coordinate, completing the decoupling of the ligand in a matter of a few tens of picoseconds rather than nanoseconds. The absolute binding free energy can be recovered from the annihilation work distributions by applying an unbiased unidirectional free energy estimate, on the assumption that any observed work distribution is given by a mixture of normal distributions, whose components are identical in either direction of the non-equilibrium process, with weights regulated by the Crooks theorem. I finally show that the inherent reliability and accuracy of the unidirectional estimate of the decoupling free energies, based on the production of a few hundreds of non-equilibrium independent sub-nanosecond unrestrained alchemical annihilation processes, is a direct consequence of the funnel-like shape of the free energy surface in molecular recognition. An application of the technique to a real drug-receptor system is presented in the companion paper.

Peptide crystal simulations reveal hidden dynamics

PubMed Central

Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

2013-01-01

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

Unrestrained swelling of uranium-nitride fuel irradiated at temperatures ranging from 1100 to 1400 K (1980 to 2520 R)

NASA Technical Reports Server (NTRS)

Rohal, R. G.; Tambling, T. N.

1973-01-01

Six fuel pins were assembled, encapsulated, and irradiated in the Plum Brook Reactor. The fuel pins employed uranium mononitride (UN) in a stainless steel (type 304L) clad. The pins were irradiated for approximately 4000 hours to burnups of about 2.0 atom percent uranium. The average clad surface temperature during irradiation was about 1100 K (1980 deg R). Since stainless steel has a very low creep strength relative to that of UN at this temperature, these tests simulated unrestrained swelling of UN. The tests indicated that at 1 percent uranium atom burnup the unrestrained diametrical swelling of UN is about 0.5, 0.8, and 1.0 percent at 1223, 1264, and 1306 K (2200, deg 2273 deg, and 2350 deg R), respectively. The tests also indicated that the irradiation induced swelling of unrestrained UN fuel pellets appears to be isotropic.

Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case

PubMed Central

García-Fandiño, Rebeca; Bernadó, Pau; Ayuso-Tejedor, Sara; Sancho, Javier; Orozco, Modesto

2012-01-01

The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the thermal unfolding process and that it has the properties of an “activated” form of the native state, where thermal fluctuations in the loops break loop-loop contacts. The unrestrained loops gain then kinetic energy corrupting short secondary structure elements without corrupting the core of the protein. The MD-derived ensembles agree with experimental observables and draw a picture of the intermediate state inconsistent with a well-defined structure and characteristic of a typical partially disordered protein. Our results allow us to speculate that proteins with a well packed core connected by long loops might behave as partially disordered proteins under native conditions, or alternatively behave as three state folders. Small details in the sequence, easily tunable by evolution, can yield to one or the other type of proteins. PMID:22927805

Effects of Sound on the Behavior of Wild, Unrestrained Fish Schools.

PubMed

Roberts, Louise; Cheesman, Samuel; Hawkins, Anthony D

2016-01-01

To assess and manage the impact of man-made sounds on fish, we need information on how behavior is affected. Here, wild unrestrained pelagic fish schools were observed under quiet conditions using sonar. Fish were exposed to synthetic piling sounds at different levels using custom-built sound projectors, and behavioral changes were examined. In some cases, the depth of schools changed after noise playback; full dispersal of schools was also evident. The methods we developed for examining the behavior of unrestrained fish to sound exposure have proved successful and may allow further testing of the relationship between responsiveness and sound level.

Population shuffling between ground and high energy excited states

PubMed Central

Sabo, T Michael; Trent, John O; Lee, Donghan

2015-01-01

Stochastic processes powered by thermal energy lead to protein motions traversing time-scales from picoseconds to seconds. Fundamental to protein functionality is the utilization of these dynamics for tasks such as catalysis, folding, and allostery. A hierarchy of motion is hypothesized to connect and synergize fast and slow dynamics toward performing these essential activities. Population shuffling predicts a “top-down” temporal hierarchy, where slow time-scale conformational interconversion leads to a shuffling of the free energy landscape for fast time-scale events. Until now, population shuffling was only applied to interconverting ground states. Here, we extend the framework of population shuffling to be applicable for a system interconverting between low energy ground and high energy excited states, such as the SH3 domain mutants G48M and A39V/N53P/V55L from the Fyn tyrosine kinase, providing another tool for accessing the structural dynamics of high energy excited states. Our results indicate that the higher energy gauche− rotameric state for the leucine χ2 dihedral angle contributes significantly to the distribution of rotameric states in both the major and minor forms of the SH3 domain. These findings are corroborated with unrestrained molecular dynamics (MD) simulations on both the major and minor states of the SH3 domain demonstrating high correlations between experimental and back-calculated leucine χ2 rotameric populations. Taken together, we demonstrate how fast time-scale rotameric side-chain population distributions can be extracted from slow time-scale conformational exchange data further extending the scope and the applicability of the population shuffling model. PMID:26316263

Population shuffling between ground and high energy excited states.

PubMed

Sabo, T Michael; Trent, John O; Lee, Donghan

2015-11-01

Stochastic processes powered by thermal energy lead to protein motions traversing time-scales from picoseconds to seconds. Fundamental to protein functionality is the utilization of these dynamics for tasks such as catalysis, folding, and allostery. A hierarchy of motion is hypothesized to connect and synergize fast and slow dynamics toward performing these essential activities. Population shuffling predicts a "top-down" temporal hierarchy, where slow time-scale conformational interconversion leads to a shuffling of the free energy landscape for fast time-scale events. Until now, population shuffling was only applied to interconverting ground states. Here, we extend the framework of population shuffling to be applicable for a system interconverting between low energy ground and high energy excited states, such as the SH3 domain mutants G48M and A39V/N53P/V55L from the Fyn tyrosine kinase, providing another tool for accessing the structural dynamics of high energy excited states. Our results indicate that the higher energy gauche - rotameric state for the leucine χ2 dihedral angle contributes significantly to the distribution of rotameric states in both the major and minor forms of the SH3 domain. These findings are corroborated with unrestrained molecular dynamics (MD) simulations on both the major and minor states of the SH3 domain demonstrating high correlations between experimental and back-calculated leucine χ2 rotameric populations. Taken together, we demonstrate how fast time-scale rotameric side-chain population distributions can be extracted from slow time-scale conformational exchange data further extending the scope and the applicability of the population shuffling model. © 2015 The Protein Society.

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

PubMed

Spasic, Aleksandar; Kennedy, Scott D; Needham, Laura; Manoharan, Muthiah; Kierzek, Ryszard; Turner, Douglas H; Mathews, David H

2018-05-01

The RNA "GAGU" duplex, (5'GAC GAGU GUCA) 2 , contains the internal loop (5'-GAGU-3') 2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans -Watson-Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2'- endo conformation. This differs markedly from the internal loops, (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-UAGG-3') 2 , which all have cis -Watson-Crick/Watson-Crick AG "imino" pairs flanked by cis -Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-U AG G-3') 2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5'-UAGG-3') 2 , equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5'-GAGU-3') 2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5'-GAGU-3') 2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed. © 2018 Spasic et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Renal parameter estimates in unrestrained dogs

NASA Technical Reports Server (NTRS)

Rader, R. D.; Stevens, C. M.

1974-01-01

A mathematical formulation has been developed to describe the hemodynamic parameters of a conceptualized kidney model. The model was developed by considering regional pressure drops and regional storage capacities within the renal vasculature. Estimation of renal artery compliance, pre- and postglomerular resistance, and glomerular filtration pressure is feasible by considering mean levels and time derivatives of abdominal aortic pressure and renal artery flow. Changes in the smooth muscle tone of the renal vessels induced by exogenous angiotensin amide, acetylcholine, and by the anaesthetic agent halothane were estimated by use of the model. By employing totally implanted telemetry, the technique was applied on unrestrained dogs to measure renal resistive and compliant parameters while the dogs were being subjected to obedience training, to avoidance reaction, and to unrestrained caging.

Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution.

PubMed

Jas, Gouri S; Middaugh, C Russell; Kuczera, Krzysztof

2016-07-21

Chaotropes like urea and guanidinium chloride (GdmCl) tend to destabilize, and kosmotropes like proline tend to stabilize folded structures of peptides and proteins. Here, we combine fluorescence anisotropy decay measurements and molecular dynamics simulations to gain a microscopic understanding of the molecular mechanism for shifting conformational preferences in aqueous, GdmCl, urea, and proline solutions of a simple model dipeptide, N-acetyl-tryptophan-amide (NATA). Measured anisotropy decay of NATA as a function of temperature, pH, and cosolvent concentrations showed reorientations moderately slower in GdmCl and urea and substantially slower in proline compared to those of aqueous environment. A small change in pH significantly slows orientation time in water and GdmCl and less markedly in urea. Computationally, we use molecular dynamics with dihedral restraints to separately analyze the motions and interactions of the representative NATA conformers in the four different solvent environments. This novel analysis provides a dissection of the observed overall diffusion rates into contributions from individual dipeptide conformations. The variation of rotational diffusion rates with conformation are quite large. Population-weighted averaging or using properties of the major cluster reproduces the dynamical features of the full unrestrained dynamics. Additionally, we correlate the observable diffusion rates with microscopic features of conformer size, shape, and solvation. This analysis uncovered underlying differences in detailed atomistic behavior of the three cosolvents-urea, GdmCl, and proline. For both urea and the pure water system we find good agreement with hydrodynamic theory, with diffusion rates primarily correlated with conformer size and shape. In contrast, for GdmCl and proline solutions, the variation in conformer diffusion rates was mostly determined by specific interactions with the cosolvents. We also find preferences for different molecular shapes by the three cosolvents, with increased preferential solvation of smaller and more spherical conformers by urea and larger and more elongated conformers by GdmCl and proline. Additionally, our results provide a basis for a simple approximate model of the effects of pH lowering on dipeptide conformational equilibria. The translational diffusion rates of NATA are less sensitive to conformations, but variation with solvation strength is similar to rotational diffusion. Our results, combining experiment and simulation, show that we can identify the individual peptide conformers with definite microscopic properties of shape, size, and solvation, that are responsible for producing physical observables, such as translational and orientational diffusion in the complex solvent environments of denaturants and osmolytes.

Child passenger safety practices in the U.S.: disparities in light of updated recommendations.

PubMed

Macy, Michelle L; Freed, Gary L

2012-09-01

Children are best protected in motor vehicle collisions when properly using the appropriate restraint and sitting in a rear row. Racial and ethnic disparities have been reported in injury statistics and use of any restraint; however, predictors of safety seat use, being unrestrained, and sitting in the front seat have not been explored previously. To determine factors associated with child passenger safety practices by race/ethnicity in a national sample of child passengers aged <13 years. Secondary analysis conducted in 2011 of the 2007, 2008, and 2009 National Survey of the Use of Booster Seats in which child passenger restraint use was observed directly. Age-stratified, survey-weighted chi-square and logistic regression analyses were conducted. Restraint use was observed for 21,476 children aged <13 years. A decline in child safety seat use and increase in being unrestrained were observed with increasing child age. In multivariate analyses, race/ethnicity, unrestrained drivers, and sitting in the front seat were associated with lower odds of child safety seat use among children aged <8 years. Older child age was associated with sitting in the front seat and being unrestrained. The presence of multiple child passengers was associated with lower odds of sitting in the front but higher odds of being unrestrained. Few children use the recommended child passenger restraints. Understanding the reasons for the suboptimal child passenger restraint practices identified in this study is essential for the development of effective programs to reduce or eliminate preventable motor vehicle collision-related injuries. Copyright © 2012 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Respiratory monitoring by inductive plethysmography in unrestrained subjects using position sensor-adjusted calibration.

PubMed

Brüllmann, Gregor; Fritsch, Karsten; Thurnheer, Robert; Bloch, Konrad E

2010-01-01

Portable respiratory inductive plethysmography (RIP) is promising for noninvasive monitoring of breathing patterns in unrestrained subjects. However, its use has been hampered by requiring recalibration after changes in body position. To facilitate RIP application in unrestrained subjects, we developed a technique for adjustment of RIP calibration using position sensor feedback. Five healthy subjects and 12 patients with lung disease were monitored by portable RIP with sensors incorporated within a body garment. Unrestrained individuals were studied during 40-60 min while supine, sitting and upright/walking. Position was changed repeatedly every 5-10 min. Initial qualitative diagnostic calibration followed by volume scaling in absolute units during 20 breaths in different positions by flow meter provided position-specific volume-motion coefficients for RIP. These were applied during subsequent monitoring in corresponding positions according to feedback from 4 accelerometers placed at the chest and thigh. Accuracy of RIP was evaluated by face mask pneumotachography. Position sensor feedback allowed accurate adjustment of RIP calibration during repeated position changes in subjects and patients as reflected in a minor mean difference (bias) in breath-by-breath tidal volumes estimated by RIP and flow meter of 0.02 liters (not significant) and limits of agreement (+/-2 SD) of +/-19% (2,917 comparisons). An average of 10 breaths improved precision of RIP (limits of agreement +/-14%). RIP calibration incorporating position sensor feedback greatly enhances the application of RIP as a valuable, unobtrusive tool to investigate respiratory physiology and ventilatory limitation in unrestrained healthy subjects and patients with lung disease during everyday activities including position changes. Copyright 2009 S. Karger AG, Basel.

United States’ Strategy and Strategic Partnerships - Understanding Others’ Perspective

DTIC Science & Technology

2011-03-16

context that this paper seeks to delineate the way forward, based on a strategic approach that cultivates meaningful partnerships and fosters...delineate the way forward, based on a strategic approach that cultivates meaningful partnerships and fosters unrestrained cooperation among all...region.3 Such awareness would afford adoption of a regional approach that mitigates acrimony and cultivates unrestrained cooperation; amongst the

Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution.

PubMed

Haensele, Elke; Mele, Nawel; Miljak, Marija; Read, Christopher M; Whitley, David C; Banting, Lee; Delépée, Carla; Sopkova-de Oliveira Santos, Jana; Lepailleur, Alban; Bureau, Ronan; Essex, Jonathan W; Clark, Timothy

2017-02-27

Conformation and dynamics of the vasoconstrictive peptides human urotensin II (UII) and urotensin related peptide (URP) have been investigated by both unrestrained and enhanced-sampling molecular-dynamics (MD) simulations and NMR spectroscopy. These peptides are natural ligands of the G-protein coupled urotensin II receptor (UTR) and have been linked to mammalian pathophysiology. UII and URP cannot be characterized by a single structure but exist as an equilibrium of two main classes of ring conformations, open and folded, with rapidly interchanging subtypes. The open states are characterized by turns of various types centered at K 8 Y 9 or F 6 W 7 predominantly with no or only sparsely populated transannular hydrogen bonds. The folded conformations show multiple turns stabilized by highly populated transannular hydrogen bonds comprising centers F 6 W 7 K 8 or W 7 K 8 Y 9 . Some of these conformations have not been characterized previously. The equilibrium populations that are experimentally difficult to access were estimated by replica-exchange MD simulations and validated by comparison of experimental NMR data with chemical shifts calculated with density-functional theory. UII exhibits approximately 72% open:28% folded conformations in aqueous solution. URP shows very similar ring conformations as UII but differs in an open:folded equilibrium shifted further toward open conformations (86:14) possibly arising from the absence of folded N-terminal tail-ring interaction. The results suggest that the different biological effects of UII and URP are not caused by differences in ring conformations but rather by different interactions with UTR.

A twin study of differences in the response of plasma ghrelin to a milkshake preload in restrained eaters

PubMed Central

Myhre, Rachel; Kratz, Mario; Goldberg, Jack; Polivy, Janet; Melhorn, Susan; Buchwald, Dedra; Cummings, David E.; Schur, Ellen A.

2014-01-01

Background Genetic, physiological, and psychological factors can affect food intake, but twin studies can distinguish inherited from environmental contributors. We examined the influence of attempted cognitive control of eating (“restrained eating”) on levels of appetite-regulating hormones. Methods Sixteen female, monozygotic twin pairs, discordant for Restraint Scale score (i.e., one twin a restrained eater with score > 15 whereas the co-twin was unrestrained), were selected from the University of Washington Twin Registry. Serial plasma ghrelin concentrations were monitored during meals and a preload study paradigm involving intake of a milkshake followed by an ad libitum ice cream “taste test.” Results Body weight, body mass index, resting energy expenditure, and fasting leptin levels were very similar between restrained and unrestrained twins. In a preload study, twins ate similar amounts of ice cream shortly after drinking identical milkshakes (mean ±SD; restrained 239 ±158 vs. unrestrained 228 ±132 kilocalories; P = 0.83). However, ghrelin concentrations during the preload study were significantly higher (P = 0.03) in restrained twins than in their unrestrained co-twins. Regardless of restraint status, ghrelin levels prior to the preload study were prospectively and positively associated with ice cream intake (P = 0.001). Conclusions Compared to their unrestrained co-twins, restrained twins had higher endogenous ghrelin levels during a preload study, but ate similar amounts. This finding is consistent with exertion of cognitive control relative to the state of physiologic appetite stimulation. Moreover, these findings in twins suggest that higher ghrelin levels result from restrained eating behavior and not from genetic predisposition. PMID:24534168

Hierarchical control of two-dimensional gaze saccades

PubMed Central

Optican, Lance M.; Blohm, Gunnar; Lefèvre, Philippe

2014-01-01

Coordinating the movements of different body parts is a challenging process for the central nervous system because of several problems. Four of these main difficulties are: first, moving one part can move others; second, the parts can have different dynamics; third, some parts can have different motor goals; and fourth, some parts may be perturbed by outside forces. Here, we propose a novel approach for the control of linked systems with feedback loops for each part. The proximal parts have separate goals, but critically the most distal part has only the common goal. We apply this new control policy to eye-head coordination in two-dimensions, specifically head-unrestrained gaze saccades. Paradoxically, the hierarchical structure has controllers for the gaze and the head, but not for the eye (the most distal part). Our simulations demonstrate that the proposed control structure reproduces much of the published empirical data about gaze movements, e.g., it compensates for perturbations, accurately reaches goals for gaze and head from arbitrary initial positions, simulates the nine relationships of the head-unrestrained main sequence, and reproduces observations from lesion and single-unit recording experiments. We conclude by showing how our model can be easily extended to control structures with more linked segments, such as the control of coordinated eye on head on trunk movements. PMID:24062206

Documentation of incidental factors affecting the home healthcare work environment.

PubMed

Sitzman, Kathleen L; Leiss, Jack K

2009-10-01

Working conditions related to unrestrained pets, unruly children, clutter, and poor lighting during home healthcare visits are considered normal aspects of care providers' jobs. To date, there has been no documentation related to how often these factors are present in the home healthcare setting during home visits. In this study, 833 home healthcare nurses practicing in North Carolina answered a questionnaire that included items related to how often unrestrained pets, unruly children, poor lighting, and clutter existed in the homes they visited. Results showed that one-third to one-half of the respondents usually or always visited homes with unrestrained pets, clutter, or poor lighting and few nurses usually or always visited homes with uncontrolled children. Better understanding of the prevalence of these factors will facilitate further study related to their effects on safety, efficiency, and job satisfaction for home healthcare workers.

An evolution strategy for lunar nuclear surface power

NASA Technical Reports Server (NTRS)

Mason, Lee S.

1992-01-01

The production and transmission of electric power for a permanently inhabited lunar base poses a significant challenge which can best be met through an evolution strategy. Nuclear systems offer the best opportunity for evolution in terms of both life and performance. Applicable nuclear power technology options include isotope systems (either radioisotope thermoelectric generators or dynamic isotope power systems) and reactor systems with either static (thermoelectric or thermionic) or dynamic (Brayton, Stirling, Rankine) conversion. A power system integration approach that takes evolution into account would benefit by reduced development and operations cost, progressive flight experience, and simplified logistics, and would permit unrestrained base expansion. For the purposes of defining a nuclear power system evolution strategy, the lunar base development shall consist of four phases: precursor, emplacement, consolidation, and operations.

Proteolytic enzyme engineering: a tool for wool.

PubMed

Araújo, Rita; Silva, Carla; Machado, Raul; Casal, Margarida; Cunha, António M; Rodriguez-Cabello, José Carlos; Cavaco-Paulo, Artur

2009-06-08

One of the goals of protein engineering is to tailor the structure of enzymes to optimize industrial bioprocesses. In the present work, we present the construction of a novel high molecular weight subtilisin, based on the fusion of the DNA sequences coding for Bacillus subtilis prosubtilisin E and for an elastin-like polymer (ELP). The resulting fusion protein was biologically produced in Escherichia coli , purified and used for wool finishing assays. When compared to the commercial protease Esperase, the recombinant subtilisinE-VPAVG(220) activity was restricted to the cuticle of wool, allowing a significant reduction of pilling, weight loss and tensile strength loss of wool fibers. Here we report, for the first time, the microbial production of a functionalized high molecular weight protease for controlled enzymatic hydrolysis of wool surface. This original process overcomes the unrestrained diffusion and extended fiber damage which are the major obstacles for the use of proteases for wool finishing applications.

The Effect of Booster Seat Use on Pediatric Injuries in Motor Vehicle Frontal Crashes.

PubMed

Caskey, Sean; Hammond, Joshua; Peck, Jeffery; Sardelli, Matthew; Atkinson, Theresa

2018-04-20

Motor vehicle crashes are a significant source of pediatric mortality and morbidity. Studies indicate that booster seats significantly improve seat belt fit for children who have not attained a height of 145 cm (4' 9"). This study examined injuries occurring in booster age children up to age 12, as the majority of children do not attain 145 cm until this age. The purpose of the study was to identify differences in injuries due to the type of restraint used, with attention to musculoskeletal injuries. Vehicle and occupant data were obtained from a publically available statistical sample of tow-away crashes. Frontal crashes over an 8-year period were examined. A data set of cases was created involving children ages 5 to 12 years who were unrestrained, restrained using the vehicle's lap and shoulder belt, and restrained using a booster seat with the vehicle's lap and shoulder seat belt. Injury severity, frequency, and patterns of distribution were compared. Unrestrained children experienced moderate to severe injuries 3.8 to 19 times more frequently than children using restraints. There were more injuries to the head and face in unrestrained versus restrained children, but the head and face was the most frequently injured region for all groups. There were no serious cervical spine injuries reported for any group. Lower extremity fractures were not observed in booster seat users but occurred at similar rates in both unrestrained and seat belt restrained children. These fractures occurred in older children who were involved in more severe crashes. Unrestrained children were more likely to experience moderate and severe injuries than restrained children. The data sample suggests that booster use may reduce the risk of extremity fracture, as there were no extremity fractures in children restrained with booster seats. This work provides evidence for the efficacy of booster use for preventing orthopaedic injury in children. This evidence can be used to inform parents and establish recommendations for best practices in transporting children.

The impact of caloric preloading on attempts at food and eating-related thought suppression in restrained and unrestrained eaters.

PubMed

O'Connell, Cara; Larkin, Kevin; Mizes, J Scott; Fremouw, William

2005-07-01

The current study examined the impact of dietary restraint and caloric preload on thought suppression in a sample of 64 college females classified as either restrained or unrestrained eaters. Participants engaged in a 60-min laboratory session. One half of the participants were preloaded with a high-calorie milkshake and all participants were randomly assigned to a food and eating-related thought suppression condition or a no suppression control condition. Food-related thoughts were assessed with a digital counter and verbal references to food were tracked with an audio recorder. Restrained participants instructed to suppress food-related thoughts demonstrated significantly more food and eating-related thoughts than unrestrained participants. Preloading was associated with an increase in the frequency of indirect mentions to food and eating. Although the hypothesized "rebound" effect did not occur for any study groups, these findings indicate that both restraint status and preloading impact food and eating-related thoughts. Copyright 2005 by Wiley Periodicals, Inc

Anatomic and functional imaging of tagged molecules in animals

DOEpatents

Weisenberger, Andrew G [Yorktown, VA; Majewski, Stanislaw [Grafton, VA; Paulus, Michael J [Knoxville, TN; Gleason, Shaun S [Knoxville, VA

2007-04-24

A novel functional imaging system for use in the imaging of unrestrained and non-anesthetized small animals or other subjects and a method for acquiring such images and further registering them with anatomical X-ray images previously or subsequently acquired. The apparatus comprises a combination of an IR laser profilometry system and gamma, PET and/or SPECT, imaging system, all mounted on a rotating gantry, that permits simultaneous acquisition of positional and orientational information and functional images of an unrestrained subject that are registered, i.e. integrated, using image processing software to produce a functional image of the subject without the use of restraints or anesthesia. The functional image thus obtained can be registered with a previously or subsequently obtained X-ray CT image of the subject. The use of the system described herein permits functional imaging of a subject in an unrestrained/non-anesthetized condition thereby reducing the stress on the subject and eliminating any potential interference with the functional testing that such stress might induce.

Vital signs: restraint use and motor vehicle occupant death rates among children aged 0-12 years - United States, 2002-2011.

PubMed

Sauber-Schatz, Erin K; West, Bethany A; Bergen, Gwen

2014-02-07

Motor vehicle crashes are a leading cause of death among children in the United States. Age- and size-appropriate child restraint use is the most effective method for reducing these deaths. CDC analyzed 2002–2011 data from the Fatality Analysis Reporting System to determine the number and rate of motor-vehicle occupant deaths, and the proportion of unrestrained child deaths among children aged <1 year, 1–3 years , 4–7 years, 8–12 years, and for all children aged 0–12 years. Age group–specific death rates and proportions of unrestrained child motor vehicle deaths for 2009–2010 were further stratified by race/ethnicity. Motor vehicle occupant death rates for children declined significantly from 2002 to 2011. However, one third (33%) of children who died in 2011 were unrestrained. Compared with white children for 2009–2010, black children had significantly higher death rates, and black and Hispanic children both had significantly higher proportions of unrestrained child deaths. Motor vehicle occupant deaths among children in the United States have declined in the past decade, but more deaths could be prevented if restraints were always used. Effective interventions, including child passenger restraint laws (with child safety seat/ booster seat coverage through at least age 8 years) and child safety seat distribution plus education programs, can increase restraint use and reduce child motor vehicle deaths.

Vital Signs: Restraint Use and Motor Vehicle Occupant Death Rates Among Children Aged 0–12 Years — United States, 2002–2011

PubMed Central

Sauber-Schatz, Erin K.; West, Bethany A.; Bergen, Gwen

2014-01-01

Background Motor vehicle crashes are a leading cause of death among children in the United States. Age- and size-appropriate child restraint use is the most effective method for reducing these deaths. Methods CDC analyzed 2002–2011 data from the Fatality Analysis Reporting System to determine the number and rate of motor-vehicle occupant deaths, and the proportion of unrestrained child deaths among children aged <1 year, 1–3 years, 4–7 years, 8–12 years, and for all children aged 0–12 years. Age group–specific death rates and proportions of unrestrained child motor vehicle deaths for 2009–2010 were further stratified by race/ethnicity. Results Motor vehicle occupant death rates for children declined significantly from 2002 to 2011. However, one third (33%) of children who died in 2011 were unrestrained. Compared with white children for 2009–2010, black children had significantly higher death rates, and black and Hispanic children both had significantly higher proportions of unrestrained child deaths. Conclusions Motor vehicle occupant deaths among children in the United States have declined in the past decade, but more deaths could be prevented if restraints were always used. Implications for Public Health Effective interventions, including child passenger restraint laws (with child safety seat/booster seat coverage through at least age 8 years) and child safety seat distribution plus education programs, can increase restraint use and reduce child motor vehicle deaths. PMID:24500292

Cognitive load, stress, and disinhibited eating.

PubMed

Lattimore, Paul; Maxwell, Linda

2004-11-01

The impact of cognitive distraction on eating behaviour was examined in restrained and unrestrained eaters. It was predicted that restrained eaters would eat more than unrestrained eaters following high cognitive load when it involves processing of ego-threat information independent of self-reported anxiety. There were 119 female participants randomly allocated to one of four experimental conditions whereby cognitive load and ego threat were manipulated using modified colour-naming Stroop (CNS) tasks. Anxiety ratings were made prior to and following experimental tasks. After performing Stroop tasks, participants consumed snack foods ad libitum. Restrained eaters consumed significantly more food when high cognitive load was ego threatening than when it involved processing and memorisation of colour nouns and consumed significantly more than unrestrained eaters in a high cognitive load ego-threat condition. Posttask anxiety was greater than baseline across all conditions. Task difficulty was greater under high cognitive load than low cognitive load as indicated by Stroop response times. These results indicated that the escape theory of disinhibited eating is conceptually subsumed by a more generalisable limited cognitive capacity model.

A high-throughput assay for quantifying appetite and digestive dynamics.

PubMed

Jordi, Josua; Guggiana-Nilo, Drago; Soucy, Edward; Song, Erin Yue; Lei Wee, Caroline; Engert, Florian

2015-08-15

Food intake and digestion are vital functions, and their dysregulation is fundamental for many human diseases. Current methods do not support their dynamic quantification on large scales in unrestrained vertebrates. Here, we combine an infrared macroscope with fluorescently labeled food to quantify feeding behavior and intestinal nutrient metabolism with high temporal resolution, sensitivity, and throughput in naturally behaving zebrafish larvae. Using this method and rate-based modeling, we demonstrate that zebrafish larvae match nutrient intake to their bodily demand and that larvae adjust their digestion rate, according to the ingested meal size. Such adaptive feedback mechanisms make this model system amenable to identify potential chemical modulators. As proof of concept, we demonstrate that nicotine, l-lysine, ghrelin, and insulin have analogous impact on food intake as in mammals. Consequently, the method presented here will promote large-scale translational research of food intake and digestive function in a naturally behaving vertebrate. Copyright © 2015 the American Physiological Society.

A high-throughput assay for quantifying appetite and digestive dynamics

PubMed Central

Guggiana-Nilo, Drago; Soucy, Edward; Song, Erin Yue; Lei Wee, Caroline; Engert, Florian

2015-01-01

Food intake and digestion are vital functions, and their dysregulation is fundamental for many human diseases. Current methods do not support their dynamic quantification on large scales in unrestrained vertebrates. Here, we combine an infrared macroscope with fluorescently labeled food to quantify feeding behavior and intestinal nutrient metabolism with high temporal resolution, sensitivity, and throughput in naturally behaving zebrafish larvae. Using this method and rate-based modeling, we demonstrate that zebrafish larvae match nutrient intake to their bodily demand and that larvae adjust their digestion rate, according to the ingested meal size. Such adaptive feedback mechanisms make this model system amenable to identify potential chemical modulators. As proof of concept, we demonstrate that nicotine, l-lysine, ghrelin, and insulin have analogous impact on food intake as in mammals. Consequently, the method presented here will promote large-scale translational research of food intake and digestive function in a naturally behaving vertebrate. PMID:26108871

Motor Vehicle Crashes, Medical Outcomes, and Hospital Charges Among Children Aged 1-12 Years - Crash Outcome Data Evaluation System, 11 States, 2005-2008.

PubMed

Sauber-Schatz, Erin K; Thomas, Andrea M; Cook, Lawrence J

2015-10-02

Motor vehicle crashes are a leading cause of death among children. Age- and size-appropriate restraint use is an effective way to prevent motor vehicle-related injuries and deaths. However, children are not always properly restrained while riding in a motor vehicle, and some are not restrained at all, which increases their risk for injury and death in a crash. 2005-2008. The Crash Outcome Data Evaluation System (CODES) is a multistate program facilitated by the National Highway Traffic Safety Administration to probabilistically link police crash reports and hospital databases for traffic safety analyses. Eleven participating states (Connecticut, Georgia, Kentucky, Maryland, Minnesota, Missouri, Nebraska, New York, Ohio, South Carolina, and Utah) submitted data to CODES during the reporting period. Descriptive analysis was used to describe drivers and child passengers involved in motor vehicle crashes and to summarize crash and medical outcomes. Odds ratios and 95% confidence intervals were used to compare a child passenger's likelihood of sustaining specific types of injuries by restraint status (optimal, suboptimal, or unrestrained) and seating location (front or back seat). Because of data constraints, optimal restraint use was defined as a car seat or booster seat use for children aged 1-7 years and seat belt use for children aged 8-12 years. Suboptimal restraint use was defined as seat belt use for children aged 1-7 years. Unrestrained was defined as no use of car seat, booster seat, or seat belt for children aged 1-12 years. Optimal restraint use in the back seat declined with child's age (1 year: 95.9%, 5 years: 95.4%, 7 years: 94.7%, 8 years: 77.4%, 10 years: 67.5%, 12 years: 54.7%). Child restraint use was associated with driver restraint use; 41.3% of children riding with unrestrained drivers also were unrestrained compared with 2.2% of children riding with restrained drivers. Child restraint use also was associated with impaired driving due to alcohol or drug use; 16.4% children riding with drivers suspected of alcohol or drug use were unrestrained compared with 2.9% of children riding with drivers not suspected of such use. Optimally restrained and suboptimally restrained children were less likely to sustain a traumatic brain injury than unrestrained children. The 90th percentile hospital charges for children aged 4-7 years who were in motor vehicle crashes were $1,630.00 and $1,958.00 for those optimally restrained in a back seat and front seat, respectively; $2,035.91 and $3,696.00 for those suboptimally restrained in a back seat and front seat, respectively; and $9,956.60 and $11,143.85 for those unrestrained in a back seat and front seat, respectively. Proper car seat, booster seat, and seat belt use among children in the back seat prevents injuries and deaths, as well as averts hospital charges. However, the number, severity, and cost of injuries among children in crashes who were not optimally restrained or who were seated in a front seat indicates the need for improvements in proper use of age- and size-appropriate car seats, booster seats, and seat belts in the back seat. Effective interventions for increasing proper child restraint use could be universally implemented by states and communities to prevent motor vehicle-related injuries among children and their resulting costs.

Optimization of protein-protein docking for predicting Fc-protein interactions.

PubMed

Agostino, Mark; Mancera, Ricardo L; Ramsland, Paul A; Fernández-Recio, Juan

2016-11-01

The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc-protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc-protein complexes are available, numerous others have not yet been determined. Protein-protein docking could be used to investigate Fc-protein complexes; however, improved approaches are necessary to efficiently model such cases. In this study, a docking-based structural bioinformatics approach is developed for predicting the structures of Fc-protein complexes. Based on the available set of X-ray structures of Fc-protein complexes, three regions of the Fc, loosely corresponding to three turns within the structure, were defined as containing the essential features for protein recognition and used as restraints to filter the initial docking search. Rescoring the filtered poses with an optimal scoring strategy provided a success rate of approximately 80% of the test cases examined within the top ranked 20 poses, compared to approximately 20% by the initial unrestrained docking. The developed docking protocol provides a significant improvement over the initial unrestrained docking and will be valuable for predicting the structures of currently undetermined Fc-protein complexes, as well as in the design of peptides and proteins that target Fc. Copyright © 2016 John Wiley & Sons, Ltd.

Dimerization of the EphA1 Receptor Tyrosine Kinase Transmembrane Domain: Insights into the Mechanism of Receptor Activation

PubMed Central

2014-01-01

EphA1 is a receptor tyrosine kinase (RTK) that plays a key role in developmental processes, including guidance of the migration of axons and cells in the nervous system. EphA1, in common with other RTKs, contains an N-terminal extracellular domain, a single transmembrane (TM) α-helix, and a C-terminal intracellular kinase domain. The TM helix forms a dimer, as seen in recent NMR studies. We have modeled the EphA1 TM dimer using a multiscale approach combining coarse-grain (CG) and atomistic molecular dynamics (MD) simulations. The one-dimensional potential of mean force (PMF) for this system, based on interhelix separation, has been calculated using CG MD simulations. This provides a view of the free energy landscape for helix–helix interactions of the TM dimer in a lipid bilayer. The resulting PMF profiles suggest two states, consistent with a rotation-coupled activation mechanism. The more stable state corresponds to a right-handed helix dimer interacting via an N-terminal glycine zipper motif, consistent with a recent NMR structure (2K1K). A second metastable state corresponds to a structure in which the glycine zipper motif is not involved. Analysis of unrestrained CG MD simulations based on representative models from the PMF calculations or on the NMR structure reveals possible pathways of interconversion between these two states, involving helix rotations about their long axes. This suggests that the interaction of TM helices in EphA1 dimers may be intrinsically dynamic. This provides a potential mechanism for signaling whereby extracellular events drive a shift in the repopulation of the underlying TM helix dimer energy landscape. PMID:25286141

Urinary excretion values in 2-day food-deprived, unrestrained chimpanzees.

NASA Technical Reports Server (NTRS)

Mcnew, J. J.; Sabbot, I. M.; Hoshizaki, T.; Mandell, A. J.; Spooner, C. E.; Marcus, I.; Adey, W. R.

1972-01-01

A study was conducted to determine the baseline 24-hr urinary excretion values in the young, unrestrained chimpanzee, and also changes in urinary values, if any, induced by the two-day food deprivation stress. Urine was analyzed for volume, osmolarity, creatinine, creatine, urea nitrogen, 17-hydroxycorticosteroids (17-OHCS), 3-methoxy-4-hydroxymandelic acid (VMA), calcium, and inorganic phosphorus. Significant increases due to food deprivation stress were observed for volume, creatine, urea nitrogen, 17-OHCS, VMA, and phosphorus values, with significant decreases in osmolarity and calcium. All values approached normal levels by the second poststress day. No significant changes were observed in creatinine. A comparison is drawn between human and chimpanzee adaptation to stress.

A Study of Airline Passenger Susceptibility to Atmospheric Turbulence Hazard

NASA Technical Reports Server (NTRS)

Stewart, Eric C.

2000-01-01

A simple, generic, simulation math model of a commercial airliner has been developed to study the susceptibility of unrestrained passengers to large, discrete gust encounters. The math model simulates the longitudinal motion to vertical gusts and includes (1) motion of an unrestrained passenger in the rear cabin, (2) fuselage flexibility, (3) the lag in the downwash from the wing to the tail, and (4) unsteady lift effects. Airplane and passenger response contours are calculated for a matrix of gust amplitudes and gust lengths of a simulated mountain rotor. A comparison of the model-predicted responses to data from three accidents indicates that the accelerations in actual accidents are sometimes much larger than the simulated gust encounters.

A far-field radio-frequency experimental exposure system with unrestrained mice.

PubMed

Hansen, Jared W; Asif, Sajid; Singelmann, Lauren; Khan, Muhammad Saeed; Ghosh, Sumit; Gustad, Tom; Doetkott, Curt; Braaten, Benjamin D; Ewert, Daniel L

2015-01-01

Many studies have been performed on exploring the effects of radio-frequency (RF) energy on biological function in vivo. In particular, gene expression results have been inconclusive due, in part, to a lack of a standardized experimental procedure. This research describes a new far field RF exposure system for unrestrained murine models that reduces experimental error. The experimental procedure includes the materials used, the creation of a patch antenna, the uncertainty analysis of the equipment, characterization of the test room, experimental equipment used and setup, power density and specific absorption rate experiment, and discussion. The result of this research is an experimental exposure system to be applied to future biological studies.

Digital live-tracking 3-dimensional minisensors for recording head orientation during image acquisition.

PubMed

de Paula, Leonardo Koerich; Ackerman, James L; Carvalho, Felipe de Assis Ribeiro; Eidson, Lindsey; Cevidanes, Lucia Helena Soares

2012-01-01

Our objective was to test the value of minisensors for recording unrestrained head position with 6 degrees of freedom during 3-dimensional stereophotogrammetry. Four 3-dimensional pictures (3dMD, Atlanta, Ga) were taken of 20 volunteers as follows: (1) in unrestrained head position, (2) a repeat of picture 1, (3) in unrestrained head position wearing a headset with 3-dimensional live tracking sensors (3-D Guidance trackSTAR; Ascension Technology, Burlington, Vt), and (4) a repeat of picture 3. The sensors were used to track the x, y, and z coordinates (pitch, roll, and yaw) of the head in space. The patients were seated in front of a mirror and asked to stand and take a walk between each acquisition. Eight landmarks were identified in each 3-dimensional picture (nasion, tip of nose, subnasale, right and left lip commissures, midpoints of upper and lower lip vermilions, soft-tissue B-point). The distances between correspondent landmarks were measured between pictures 1 and 2 and 3 and 4 with software. The Student t test was used to test differences between unrestrained head position with and without sensors. Interlandmark distances for pictures 1 and 2 (head position without the sensors) and pictures 3 and 4 (head position with sensors) were consistent for all landmarks, indicating that roll, pitch, and yaw of the head are controlled independently of the sensors. However, interlandmark distances were on average 17.34 ± 0.32 mm between pictures 1 and 2. Between pictures 3 and 4, the distances averaged 6.17 ± 0.15 mm. All interlandmark distances were significantly different between the 2 methods (P <0.001). The use of 3-dimensional live-tracking sensors aids the reproducibility of patient head positioning during repeated or follow-up acquisitions of 3-dimensional stereophotogrammetry. Even with sensors, differences in spatial head position between acquisitions still require additional registration procedures. Copyright © 2012 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Epidemic as a natural process.

PubMed

Koivu-Jolma, Mikko; Annila, Arto

2018-05-01

Mathematical epidemiology is a well-recognized discipline to model infectious diseases. It also provides guidance for public health officials to limit outbreaks. Nevertheless, epidemics take societies by surprise every now and then, for example, when the Ebola virus epidemic raged seemingly unrestrained in Western Africa. We provide insight to this capricious character of nature by describing the epidemic as a natural process, i.e., a phenomenon governed by thermodynamics. Our account, based on statistical mechanics of open systems, clarifies that it is impossible to predict accurately epidemic courses because everything depends on everything else. Nonetheless, the thermodynamic theory yields a comprehensive and analytical view of the epidemic. The tenet subsumes various processes in a scale-free manner from the molecular to the societal levels. The holistic view accentuates overarching procedures in arresting and eradicating epidemics. Copyright © 2018 Elsevier Inc. All rights reserved.

Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase.

PubMed

Goyal, Puja; Lu, Jianxun; Yang, Shuo; Gunner, M R; Cui, Qiang

2013-11-19

Cytochrome c oxidase contributes to the transmembrane proton gradient by removing two protons from the high-pH side of the membrane each time the binuclear center active site is reduced. One proton goes to the binuclear center, whereas the other is pumped to the low-pH periplasmic space. Glutamate 286 (Glu286) has been proposed to serve as a transiently deprotonated proton donor. Using unrestrained atomistic molecular dynamics simulations, we show that the size of and water distribution in the hydrophobic cavity that holds Glu286 is controlled by the protonation state of the propionic acid of heme a3, a group on the proton outlet pathway. Protonation of the propionate disrupts hydrogen bonding to two side chains, allowing a loop to swing open. Continuum electrostatics and atomistic free-energy perturbation calculations show that the resultant changes in hydration and electrostatic interactions lower the Glu proton affinity by at least 5 kcal/mol. These changes in the internal hydration level occur in the absence of major conformational transitions and serve to stabilize needed transient intermediates in proton transport. The trigger is not the protonation of the Glu of interest, but rather the protonation of a residue ∼10 Å away. Thus, unlike local water penetration to stabilize a new charge, this finding represents a specific role for water molecules in the protein interior, mediating proton transfers and facilitating ion transport.

Working harder to obtain more snack foods when wanting to eat less.

PubMed

Giesen, Janneke C A H; Havermans, Remco C; Nederkoorn, Chantal; Strafaci, Silvana; Jansen, Anita

2009-01-01

This study investigates individual differences in the reinforcing value of snack food. More specifically, it was investigated whether differences in restraint status are associated with differences in working for high-caloric snack food. Thirty-six unrestrained non-dieters, twenty restrained non-dieters and fifteen current dieters performed a concurrent schedules task in which they had the option to work for points for either snack food or fruit and vegetables. By progressively increasing the "price" of the snack foods (i.e., the amount of work required to obtain extra snack points) the relative reinforcing value of snack food was determined. As hypothesized, restrained non-dieters worked harder and current dieters worked less hard to obtain snack food as compared to unrestrained non-dieters.

Relationship of Dieting and Restrained Eating to Self-Reported Caloric Intake in Female College Freshmen

PubMed Central

Goldstein, Stephanie P.; Katterman, Shawn N.; Lowe, Michael R.

2012-01-01

Evidence indicates that restrained eaters do not eat less than unrestrained eaters in the natural environment. However, no study has examined caloric intake in those who are currently dieting to lose, or avoid gaining, weight. The current study examined caloric intake using 24-hour food recalls among individuals dieting to lose weight, dieting to avoid weight gain, restrained nondieters, and unrestrained nondieters. Participants were 246 female college students participating in a weight gain prevention trial. The predicted significant difference in caloric intake across the four groups was found for beverage but not for food intake. Results reinforce past literature indicating that dieting/restraint status does not reflect hypo-caloric intake in naturalistic settings. PMID:23557829

An analysis of risk-taking behavior among adolescent blunt trauma patients.

PubMed

Foley, David S; Draus, John M; Santos, Ariel P; Franklin, Glen A

2009-05-01

The impact of risk-taking behavior among adolescent blunt trauma patients is not fully appreciated. This study examined the relationship between adolescent risk-taking behaviors, the resultant injury severity, and outcome for blunt trauma. Between January 2000 and December 2005, data were collected on adolescent blunt trauma patients (12-18 years) admitted to either a Level I adult trauma center or large urban pediatric hospital. Five groups of risk-taking behavior were examined: ATV riders, drug and alcohol users, unhelmeted motorcyclists, unhelmeted extreme sports participants and unrestrained motor vehicle occupants. Demographic data, mechanism of injury, injury severity, hospital course and outcomes were evaluated for each group. A total of 2030 adolescents were admitted following blunt trauma; 723 adolescents (36%) were engaged in risk-taking behavior at the time of their injury. Most patients were male (68%). Unrestrained MVA occupants were the most frequently encountered risk takers (37%); among this subset, most were unrestrained passengers (74%). Head injuries were frequent (22%) among risk takers. When compared to non-risk-takers, there were no significant age, race, gender, or ISS differences. However, a significantly higher number of positive head CT scans were found among risk-taking adolescents (22%, p < 0.05). Mortality was low (3%). Risk-taking behavior is prevalent among adolescent blunt trauma patients. Improved injury prevention strategies are needed to discourage these behaviors during adolescence.

Air bags and passenger fatality according to passenger age and restraint use.

PubMed

Cummings, Peter; Koepsell, Thomas D; Rivara, Frederick P; McKnight, Barbara; Mack, Christopher

2002-09-01

Some children have been killed by air bags, leading to advice that young children should not sit in front of an active air bag. We conducted a case-control study to estimate the association of passenger air bag presence with death, according to passenger age and seat belt use. We used data from crashes on U.S. public roads in 1992 through 1998. Cases (N = 20,987) were front seat passengers who died, and controls (N = 69,277) were a sample of survivors. Among restrained passengers, the adjusted relative risk of death for those with a passenger air bag was 0.79 (95% confidence interval [CI] = 0.66-0.94); for children 12 years or younger, the adjusted relative risk was 1.04 (0.65-1.67) [corrected], and for adults 20 years or older it was 0.75 (0.62-0.91) [corrected]. Among unrestrained passengers, the adjusted relative risk was 1.03 (CI = 0.81-1.30); for children 12 years or younger the adjusted relative risk was 1.37 (0.84-2.21) [corrected], and for adults 20 years or older it was 0.96 (0.75-1.24). Passenger air bags may be a hazard to unrestrained children and of little benefit to unrestrained adults. Our results support the advice that children younger than 13 years should not sit in front of an active air bag.

Effect of head and neck position on intrathoracic pressure and arterial blood gas values in Dutch Warmblood riding horses during moderate exercise.

PubMed

Sleutjens, Janneke; Smiet, Esmee; van Weeren, René; van der Kolk, Johannes; Back, Willem; Wijnberg, Inge D

2012-04-01

To evaluate the effect of various head and neck positions on intrathoracic pressure and arterial oxygenation during exercise in horses. 7 healthy Dutch Warmblood riding horses. The horses were evaluated with the head and neck in the following predefined positions: position 1, free and unrestrained; position 2, neck raised with the bridge of the nose aligned vertically; position 4, neck lowered and extremely flexed with the nose pointing toward the pectoral muscles; position 5, neck raised and extended with the bridge of the nose in front of a vertical line perpendicular to the ground surface; and position 7, neck lowered and flexed with the nose pointing towards the carpus. The standard exercise protocol consisted of trotting for 10 minutes, cantering for 4 minutes, trotting again for 5 minutes, and walking for 5 minutes. An esophageal balloon catheter was used to indirectly measure intrathoracic pressure. Arterial blood samples were obtained for measurement of Pao(2), Paco(2), and arterial oxygen saturation. Compared with when horses were in the unrestrained position, inspiratory intrathoracic pressure became more negative during the first trot (all positions), canter and second trot (position 4), and walk (positions 4 and 5). Compared with when horses were in position 1, intrathoracic pressure difference increased in positions 4, 2, 7, and 5; Pao(2) increased in position 5; and arterial oxygen saturation increased in positions 4 and 7. Position 4 was particularly influential on intrathoracic pressure during exercise in horses. The effects detected may have been caused by a dynamic upper airway obstruction and may be more profound in horses with upper airway disease.

Stress-induced release of GUT peptides in young women classified as restrained or unrestrained eaters.

PubMed

Hilterscheid, Esther; Laessle, Reinhold

2015-12-01

Basal release of GUT peptides has been found to be altered in restrained eaters. Stress-induced secretion, however, has not yet been described, but could be a biological basis of overeating that exposes restrained eaters to a higher risk of becoming obese. The aim of the present study was to compare restrained and unrestrained eaters with respect to stress-induced release of the GUT peptides ghrelin and PYY. 46 young women were studied. Blood sampling for peptides was done before and after the Trier Social Stress Test. Ghrelin secretion after stress was significantly elevated in the restrained eaters, whereas no significant differences were detected for PYY. Stress-induced release of GUT peptides can be interpreted as a cause as well as a consequence of restrained eating.

Sleep-wake cycle of an unrestrained isolated chimpanzee under entrained and free running conditions.

NASA Technical Reports Server (NTRS)

Mcnew, J. J.; Burson, R. C.; Hoshizaki, T.; Adey, W. R.

1972-01-01

Biorhythmic patterns of EEG activity - the sleep-wake cycle and the sleep cycle - were investigated in an unrestrained chimpanzee subjected to 30 days of isolation in a 4-ft cubical cage placed in a high performance sound isolation chamber. The animal received 10 days of 12 hours of light and 12 hours of dark, then 10 days of continuous light, followed by 10 more days of 12 hours of light and 12 hours of dark. The circadian sleep-wake rhythm and the wake and sleep phases of this rhythm during entrained and free running conditions were analyzed in terms of duration. The awake and nonREM sleep and REM sleep stages were also analyzed. In addition, the mean duration of the sleep cycle of the sleep phase was computed.

Relationship of dieting and restrained eating to self-reported caloric intake in female college freshmen.

PubMed

Goldstein, Stephanie P; Katterman, Shawn N; Lowe, Michael R

2013-04-01

Evidence indicates that restrained eaters do not eat less than unrestrained eaters in the natural environment. However, no study has examined caloric intake in those who are currently dieting to lose, or avoid gaining, weight. The current study examined caloric intake using 24-hour food recalls among individuals dieting to lose weight, dieting to avoid weight gain, restrained nondieters, and unrestrained nondieters. Participants were 246 female college students participating in a weight gain prevention trial. The predicted significant difference in caloric intake across the four groups was found for beverage but not for food intake. Results reinforce past literature indicating that dieting/restraint status does not reflect hypo-caloric intake in naturalistic settings. Copyright © 2012 Elsevier Ltd. All rights reserved.

p53 on the crossroad between regeneration and cancer.

PubMed

Charni, Meital; Aloni-Grinstein, Ronit; Molchadsky, Alina; Rotter, Varda

2017-01-01

Regeneration and tumorigenesis share common molecular pathways, nevertheless the outcome of regeneration is life, whereas tumorigenesis leads to death. Although the process of regeneration is strictly controlled, malignant transformation is unrestrained. In this review, we discuss the involvement of TP53, the major tumor-suppressor gene, in the regeneration process. We point to the role of p53 as coordinator assuring that regeneration will not shift to carcinogenesis. The fluctuation in p53 activity during the regeneration process permits a tight control. On one hand, its inhibition at the initial stages allows massive proliferation, on the other its induction at advanced steps of regeneration is essential for preservation of robustness and fidelity of the regeneration process. A better understanding of the role of p53 in regulation of regeneration may open new opportunities for implementation of TP53-based therapies, currently available for cancer patients, in regenerative medicine.

Environmental assessment for the Satellite Power System (SPS): Studies of honey bees exposed to 2.45 GHz continuous wave electromagnetic energy

NASA Technical Reports Server (NTRS)

Gary, N. E.; Westerdahl, B. B.

1980-01-01

Post treatment brood development was normal and teratological effects were not detected at exposures of 3 to 50 mw sq cm for 30 minutes. Post treatment survival, longevity, orientation, navigation, and memory of adult bees were also normal after exposures of 3 to 50 mw sq cm for 30 minutes. Post treatment longevity of confined bees in the laboratory was normal after exposures of 3 to 50 mw sq cm for 24 hours. Thermoregulation of brood nest, foraging activity, brood rearing, and social interaction were not affected by chronic exposure to 1 mw sq cm during 28 days. In dynamic behavioral bioassays the frequency of entry and duration of activity of unrestrained, foraging adult bees was identical in microwave exposed areas versus control areas.

Underutilization of occupant restraint systems in motor vehicle injury crashes: A quantitative analysis from Qatar.

PubMed

El-Menyar, Ayman; Consunji, Rafael; Asim, Mohammad; Abdelrahman, Husham; Zarour, Ahmad; Parchani, Ashok; Peralta, Ruben; Al-Thani, Hassan

2016-01-01

Restraint systems (seat belts and airbags) are important tools that improve vehicle occupant safety during motor vehicle crashes (MVCs). We aimed to identify the pattern and impact of the utilization of passenger restraint systems on the outcomes of MVC victims in Qatar. A retrospective study was conducted for all admitted patients who sustained MVC-related injuries between March 2011 and March 2014 inclusive. Out of 2,730 road traffic injury cases, 1,830 (67%) sustained MVC-related injuries, of whom 88% were young males, 70% were expatriates, and 53% were drivers. The use of seat belts and airbags was documented in 26 and 2.5% of cases, respectively. Unrestrained passengers had greater injury severity scores, longer hospital stays, and higher rates of pneumonia and mortality compared to restrained passengers (P = .001 for all). There were 311 (17%) ejected cases. Seat belt use was significantly lower and the mortality rate was 3-fold higher in the ejected group compared to the nonejected group (P = .001). The overall mortality was 8.3%. On multivariate regression analysis, predictors of not using a seat belt were being a front seat passenger, driver, or Qatari national and young age. Unrestrained males had a 3-fold increase in mortality in comparison to unrestrained females. The risk of severe injury (relative risk [RR] = 1.82, 95% confidence interval [CI], 1.49-2.26, P = .001) and death (RR = 4.13, 95% CI, 2.31-7.38, P = .001) was significantly greater among unrestrained passengers. The nonuse of seat belts is associated with worse outcomes during MVCs in Qatar. Our study highlights the lower rate of seat belt compliance in young car occupants that results in more severe injuries, longer hospital stays, and higher mortality rates. Therefore, we recommend more effective seat belt awareness and education campaigns, the enforcement of current seat belt laws, their extension to all vehicle occupants, and the adoption of proven interventions that will assure sustained behavioral changes toward improvements in seat belt use in Qatar.

Spatiotemporal dynamics of the hedonic processing of chocolate images in individuals with and without trait chocolate craving.

PubMed

Asmaro, Deyar; Jaspers-Fayer, Fern; Sramko, Valery; Taake, Isabel; Carolan, Patrick; Liotti, Mario

2012-06-01

The spatiotemporal dynamics of the hedonic response to chocolate images was investigated in healthy participants high and low in trait-chocolate craving employing high-density ERPs. There were two sessions: (1) before and (2) after satiety for chocolate. Among cravers, chocolate stimuli evoked a positive amplitude ERP enhancement over the anterior frontal scalp (250-350 ms) that was not modified by satiety and that source localized to the left lateral orbitofrontal cortex. Chocolate stimuli also elicited a later LPP over the posterior scalp (360-560 ms) which was of similar amplitude for high and low chocolate cravers, independent of satiety. Unexpectedly, in non-cravers, chocolate stimuli elicited an earlier (100-250 ms) negative ERP modulation over the frontomedial scalp, which disappeared after eating chocolate to satiety. These results confirm the role of OFC in unrestrained appetitive responses to chocolate in cravers, and suggest top-down influences from cognitive control mechanisms when attempting to restrain the urge to eat chocolate in non-cravers. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

PubMed

Olson, Mark A; Lee, Michael S

2014-01-01

A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.

Special issue : child safety

DOT National Transportation Integrated Search

1999-10-02

Despite extensive publicity aimed at getting children restrained and riding in rear seats, observational surveys in three states show many children still ride unrestrained, improperly restrained, or in the front seats of cars equipped with passenger ...

Volume changes in unrestrained structural lightweight concrete.

DOT National Transportation Integrated Search

1964-08-01

In this study a comparator-type measuring system was developed to accurately determine volume change characteristics of one structural lightweight concrete. The specific properties studied were the coefficient of linear thermal expansion and unrestra...

The influence of occupant anthropometry and seat position on ejection risk in a rollover.

PubMed

Atkinson, Theresa; Fras, Andrew; Telehowski, Paul

2010-08-01

During rollover crashes, ejection increases an occupant's risk of severe to fatal injury as compared to risks for those retained in the vehicle. The current study examined whether occupant anthropometry might influence ejection risk. Factors such as restraint use/disuse, seating position, vehicle type, and roll direction were also considered in the analysis. The current study examined occupant ejections in 10 years of National Automotive Sampling System (NASS) single-event rollovers of passenger vehicles and light trucks. Statistical analysis of unweighted and weighted ejection data was carried out. No statistically significant differences in ejection rates were found based on occupant height, age, or body mass index. Drivers were ejected significantly more frequently than other occupants: 62 percent of unrestrained drivers were ejected vs. 51 percent unrestrained right front occupants. Second row unrestrained occupants were ejected at rates similar to right front-seated occupants. There were no significant differences in ejection rates for near- vs. far-side occupants. These data suggest that assessment of ejection prevention systems using either a 50th or 5th percentile adult anthropomorphic test dummy (ATD) might provide a reasonable measure of system function for a broad range of occupants. They also support the development of ejection mitigation technologies that extend beyond the first row to protect occupants in rear seat positions. Future studies should consider potential interaction effects (i.e., occupant size and vehicle dimensions) and the influence of occupant size on ejection risk in non-single-event rollovers.

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

PubMed Central

Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori

2012-01-01

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395

The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids.

PubMed

Li, Li; Szostak, Jack W

2014-02-19

The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.

Exploring Relationships between North American Urban Form and Rates of Urban CO2 Emissions: A System Dynamics Approach

NASA Astrophysics Data System (ADS)

Emmi, P. C.; Forster, C. B.; Mills, J. I.; Call, B. D.; Sabula, J.; Klewicki, J. C.; Pataki, D. E.; Peterson, T. R.

2004-12-01

Cities are the locus of North America's most intense consumption of fossil fuels. Thus the rate and character of urbanization influence the rate of urban CO2 released into the global atmosphere. The rate of rural-to-urban land conversion, and changes in the population density of urban land, are influenced by coupled changes in urban demographics and the local economy. Urban sprawl (a rapid expansion of urban land with low population densities) is governed by a self-reinforcing feedback effect between urban transportation infrastructure investments (road building) and urban land development where road building begets new urban neighborhoods that, in turn, induce more road building that begets additional new neighborhoods. If unrestrained, this feedback effect leads to the unrestrained expansion of urban sprawl, urban vehicular travel and traffic congestion. This self-reinforcing feedback loop forms a key dynamic that controls the rate at which CO2-emitting fossil fuels are burned for transportation, electricity production, heating, and commercial/industrial processes. In a rapidly sprawling city residents must travel increasingly greater distances between work, shopping, and home while commercial service vehicles must travel to increasingly remote residential locations. The increasing number of vehicle trips and vehicle miles traveled, combined with the growing prevalence of ever-lower density urban land development, leads to a rapid increase in mobile and stationary CO2 emissions. A more compact and punctuated form of urban development with higher-density and mixed-use urban activity centers leads to reduced CO2 emissions. Those who shape urban development policy are often unconcerned by increasing CO2 emissions unless they can be linked to: (1) local concerns about criteria air pollutant emissions and air quality, (2) the dependency of federal infrastructure funding on meeting ambient air quality standards, and (3) the consequences of human exposure to health risks associated with declining air quality. The dynamic simulation of urban systems demonstrates that a suite of policies can be found to diminish sprawl and defeat traffic congestion thereby safeguarding the vitality a city. A systems thinking approach, facilitated by a community engagement process, has further enabled community opinion leaders and policy makers to map the key features, linkages and feedbacks of a complex, CO2-emitting urban ecosystem. A corresponding lumped-parameter, simulation model provides a framework for decision makers and stakeholders to explore the consequences of alternative options for managing urban growth, sprawl and congestion while also reducing CO2 emissions.

Kinetic Shapes: Analysis, Verification, and Applications.

PubMed

Handz̆ić, Ismet; Reed, Kyle B

2014-06-01

A circular shape placed on an incline will roll; similarly, an irregularly shaped object, such as the Archimedean spiral, will roll on a flat surface when a force is applied to its axle. This rolling is dependent on the specific shape and the applied force (magnitude and location). In this paper, we derive formulas that define the behavior of irregular 2D and 3D shapes on a flat plane when a weight is applied to the shape's axle. These kinetic shape (KS) formulas also define and predict shapes that exert given ground reaction forces when a known weight is applied at the axle rotation point. Three 2D KS design examples are physically verified statically with good correlation to predicted values. Motion simulations of unrestrained 2D KS yielded expected results in shape dynamics and self-stabilization. We also put forth practical application ideas and research for 2D and 3D KS such as in robotics and gait rehabilitation.

Saccades to future ball location reveal memory-based prediction in a virtual-reality interception task.

PubMed

Diaz, Gabriel; Cooper, Joseph; Rothkopf, Constantin; Hayhoe, Mary

2013-01-16

Despite general agreement that prediction is a central aspect of perception, there is relatively little evidence concerning the basis on which visual predictions are made. Although both saccadic and pursuit eye-movements reveal knowledge of the future position of a moving visual target, in many of these studies targets move along simple trajectories through a fronto-parallel plane. Here, using a naturalistic and racquet-based interception task in a virtual environment, we demonstrate that subjects make accurate predictions of visual target motion, even when targets follow trajectories determined by the complex dynamics of physical interactions and the head and body are unrestrained. Furthermore, we found that, following a change in ball elasticity, subjects were able to accurately adjust their prebounce predictions of the ball's post-bounce trajectory. This suggests that prediction is guided by experience-based models of how information in the visual image will change over time.

Saccades to future ball location reveal memory-based prediction in a virtual-reality interception task

PubMed Central

Diaz, Gabriel; Cooper, Joseph; Rothkopf, Constantin; Hayhoe, Mary

2013-01-01

Despite general agreement that prediction is a central aspect of perception, there is relatively little evidence concerning the basis on which visual predictions are made. Although both saccadic and pursuit eye-movements reveal knowledge of the future position of a moving visual target, in many of these studies targets move along simple trajectories through a fronto-parallel plane. Here, using a naturalistic and racquet-based interception task in a virtual environment, we demonstrate that subjects make accurate predictions of visual target motion, even when targets follow trajectories determined by the complex dynamics of physical interactions and the head and body are unrestrained. Furthermore, we found that, following a change in ball elasticity, subjects were able to accurately adjust their prebounce predictions of the ball's post-bounce trajectory. This suggests that prediction is guided by experience-based models of how information in the visual image will change over time. PMID:23325347

Effect of a 30-day isolation stress on calcium, phosphorus and other excretory products in an unrestrained chimpanzee.

NASA Technical Reports Server (NTRS)

Sabbot, I. M.; Mcnew, J. J.; Hoshizaki, T.; Sedgwick, C. J.; Adey, W. R.

1972-01-01

An unrestrained chimpanzee was studied in an isolation chamber and in his home cage environment. The study consisted of 49 urine collection days (14 days pre-, 5 days post- and 30 days of isolation), and then of 10 days in the home cage. Dietary intake, urine and fecal data were obtained. The effect of isolation on various excretory parameters was studied. Urine samples were analyzed for volume, osmolarity, creatinine, creatine, urea-N, 17-hydroxy corticosteroids, VMA, calcium and inorganic phosphorus. One way analyses of variance performed on the urinary excretion parameters showed all except creatinine excretion to vary significantly during periods of the study. The changes observed in calcium and phosphorus were highly significant. The data suggests that the calcium to phosphorus excretion ratio might serve as a physiological stress indicator of Selye's adaptation syndrome (period of resistance).

Remote and chronic access to the third cerebral ventricle of the unrestrained prepubertal rhesus monkey.

PubMed

Gay, V L; Mikuma, N; Plant, T M

1993-03-01

One channel of a commercially available standard-size three-channel fluid swivel was modified to permit continuous access to the brain of unrestrained prepubertal rhesus monkeys via a continuous length of small-bore Teflon tube originating from a swivel device on top of the animal's cage and terminating in the third cerebral ventricle. This system was employed to achieve continuous access to the third cerebroventricle in four monkeys for periods of up to 12 mo. The value of the system for studies of the neurochemical control of hypothalamic-releasing factor secretion was established by monitoring adenohypophysial responses to neurotransmitter receptor agonists infused into the third ventricle. Specifically, repetitive infusions of morphine (30 micrograms/infusion) elicited a robust train of prolactin discharges, and third ventricular administration of N-methyl-DL-aspartic acid (NMA; 20 micrograms) resulted in striking discharges of LH.

Radiotelemetry recording of electroencephalogram in piglets during rest.

PubMed

Saito, Toshiyuki; Watanabe, Yasuko; Nemoto, Tetsu; Kasuya, Etsuko; Sakumoto, Ryosuke

2005-04-13

A wireless recording system was developed to study the electroencephalogram (EEG) in unrestrained, male Landrace piglets. Under general anesthesia, ball-tipped silver/silver chloride electrodes for EEG recording were implanted onto the dura matter of the parietal and frontal cortex of the piglets. A pair of miniature preamplifiers and transmitters was then mounted on the surface of the skull. To examine whether other bioelectrical activities interfere with the EEG measurements, an electrocardiogram (ECG) or electromyogram (EMG) of the neck was simultaneously recorded with the EEG. Next, wire electrodes for recording movement of the eyelid were implanted with EEG electrodes, and EEG and eyelid movements were simultaneously measured. Power spectral analysis using a Fast Fourier Transformation (FFT) algorithm indicates that EEG was successfully recorded in unrestrained piglets, at rest, during the daytime in the absence of interference from ECG, EMG or eyelid movements. These data indicate the feasibility of using our radiotelemetry system for measurement of EEG under these conditions.

Real-time landmark-based unrestrained animal tracking system for motion-corrected PET/SPECT imaging

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

J.S. Goddard; S.S. Gleason; M.J. Paulus

2003-08-01

Oak Ridge National Laboratory (ORNL) and Jefferson Lab and are collaborating to develop a new high-resolution single photon emission tomography (SPECT) instrument to image unrestrained laboratory animals. This technology development will allow functional imaging studies to be performed on the animals without the use of anesthetic agents. This technology development could have eventual clinical applications for performing functional imaging studies on patients that cannot remain still (Parkinson's patients, Alzheimer's patients, small children, etc.) during a PET or SPECT scan. A key component of this new device is the position tracking apparatus. The tracking apparatus is an integral part of themore » gantry and designed to measure the spatial position of the animal at a rate of 10-15 frames per second with sub-millimeter accuracy. Initial work focuses on brain studies where anesthetic agents or physical restraint can significantly impact physiologic processes.« less

Impact of airbags on a Level I trauma center: injury patterns, infectious morbidity, and hospital costs.

PubMed

Williams, Regan F; Fabian, Timothy C; Fischer, Peter E; Zarzaur, Ben L; Magnotti, Louis J; Croce, Martin A

2008-05-01

To date, no study has evaluated the potential impact of supplemental restraint use on resource use at a Level I trauma center. We hypothesized that airbag use would be related to decreased injury severity of motor vehicle collision survivors admitted to a Level I trauma center, leading to a decrease in infectious morbidity and hospital resource use. Using the trauma registry, motor vehicle collision victims admitted during an 11-year period were identified. Restraint groups were defined as unrestrained (reference group), seatbelt only, airbag only, or airbag and seatbelt. Multivariable logistic regression was used to determine the relationship between restraint type and injury patterns. Other outcomes measured included prevalence of ventilator-associated pneumonia and bacteremia, hospital length of stay, days in the ICU, and hospital mortality. A total of 14,390 patients (unrestrained, n = 7,881; airbag only, n = 692; seatbelt only, n = 4,909; airbag and seatbelt, n = 908) had restraint data available. Both airbag and seatbelt use were associated with a substantial reduction in injury to the brain, face, cervical spine, thorax, and abdomen. The largest reduction occurred when these restraints were used in combination. The only injury associated with airbag deployment was extremity fractures. Compared with unrestrained persons, any restraint use was associated with substantially reduced injury severity, significant infectious morbidity, and resource use. Airbags are associated with reduced in-hospital mortality. Airbags are also associated with decreased injury severity, substantial infectious morbidity, and resource use. Cost savings from reduced resource use associated with supplemental restraints could be tremendous.

Interactions between gaze-evoked blinks and gaze shifts in monkeys.

PubMed

Gandhi, Neeraj J

2012-02-01

Rapid eyelid closure, or a blink, often accompanies head-restrained and head-unrestrained gaze shifts. This study examines the interactions between such gaze-evoked blinks and gaze shifts in monkeys. Blink probability increases with gaze amplitude and at a faster rate for head-unrestrained movements. Across animals, blink likelihood is inversely correlated with the average gaze velocity of large-amplitude control movements. Gaze-evoked blinks induce robust perturbations in eye velocity. Peak and average velocities are reduced, duration is increased, but accuracy is preserved. The temporal features of the perturbation depend on factors such as the time of blink relative to gaze onset, inherent velocity kinematics of control movements, and perhaps initial eye-in-head position. Although variable across animals, the initial effect is a reduction in eye velocity, followed by a reacceleration that yields two or more peaks in its waveform. Interestingly, head velocity is not attenuated; instead, it peaks slightly later and with a larger magnitude. Gaze latency is slightly reduced on trials with gaze-evoked blinks, although the effect was more variable during head-unrestrained movements; no reduction in head latency is observed. Preliminary data also demonstrate a similar perturbation of gaze-evoked blinks during vertical saccades. The results are compared with previously reported effects of reflexive blinks (evoked by air-puff delivered to one eye or supraorbital nerve stimulation) and discussed in terms of effects of blinks on saccadic suppression, neural correlates of the altered eye velocity signals, and implications on the hypothesis that the attenuation in eye velocity is produced by a head movement command.

Activity of long-lead burst neurons in pontine reticular formation during head-unrestrained gaze shifts.

PubMed

Walton, Mark M G; Freedman, Edward G

2014-01-01

Primates explore a visual scene through a succession of saccades. Much of what is known about the neural circuitry that generates these movements has come from neurophysiological studies using subjects with their heads restrained. Horizontal saccades and the horizontal components of oblique saccades are associated with high-frequency bursts of spikes in medium-lead burst neurons (MLBs) and long-lead burst neurons (LLBNs) in the paramedian pontine reticular formation. For LLBNs, the high-frequency burst is preceded by a low-frequency prelude that begins 12-150 ms before saccade onset. In terms of the lead time between the onset of prelude activity and saccade onset, the anatomical projections, and the movement field characteristics, LLBNs are a heterogeneous group of neurons. Whether this heterogeneity is endemic of multiple functional subclasses is an open question. One possibility is that some may carry signals related to head movement. We recorded from LLBNs while monkeys performed head-unrestrained gaze shifts, during which the kinematics of the eye and head components were dissociable. Many cells had peak firing rates that never exceeded 200 spikes/s for gaze shifts of any vector. The activity of these low-frequency cells often persisted beyond the end of the gaze shift and was usually related to head-movement kinematics. A subset was tested during head-unrestrained pursuit and showed clear modulation in the absence of saccades. These "low-frequency" cells were intermingled with MLBs and traditional LLBNs and may represent a separate functional class carrying signals related to head movement.

Free energy profile of RNA hairpins: a molecular dynamics simulation study.

PubMed

Deng, Nan-Jie; Cieplak, Piotr

2010-02-17

RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, the UUCG hairpin is known to be significantly more stable than UUUU. In this study, the calculations using AMBER force field give a qualitatively correct description for the folding of two RNA hairpins, as the calculated PMF confirms the global stability of the folded structures and the resulting relative folding free energy is in quantitative agreement with the experimental result. The hairpin stabilities are also correctly differentiated by the more rapid molecular mechanics-Poisson Boltzmann-surface area approach, but the relative free energy estimated from this method is overestimated. The free energy profile shows that the native state basin and the unfolded state plateau are separated by a wide shoulder region, which samples a variety of native-like structures with frayed terminal basepair. The calculated PMF lacks major barriers that are expected near the transition regions, and this is attributed to the limitation of the 1-D reaction coordinate. The PMF results are compared with other studies of small RNA hairpins using kinetics method and coarse grained models. The two RNA hairpins described by CHARMM27 are significantly more deformable than those represented by AMBER. Compared with the AMBER results, the CHARMM27 calculated DeltaG(fold) for the UUUU tetraloop is in better agreement with the experimental results. However, the CHARMM27 calculation does not confirm the global stability of the experimental UUCG structure; instead, the extended conformations are predicted to be thermodynamically stable in solution. This finding is further supported by separate unrestrained CHARMM27 simulations, in which the UUCG hairpin unfolds spontaneously within 10 ns. The instability of the UUCG hairpin originates from the loop region, and propagates to the stem. The results of this study provide a molecular picture of RNA hairpin unfolding and reveal problems in the force field descriptions for the conformational energy of certain RNA hairpin. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Pharyngeal diameter in various head and neck positions during exercise in sport horses

PubMed Central

2014-01-01

Background In equine athletes, dynamic stenotic disorders of the upper airways are often the cause for abnormal respiratory noises and/or poor performance. There are hypotheses, that head and neck flexion may influence the morphology and function of the upper airway and thus could even induce or deteriorate disorders of the upper respiratory tract. Especially the pharynx, without osseous or cartilaginous support is prone to changes in pressure and airflow during exercise. The objective of this study was to develop a method for measuring the pharyngeal diameter in horses during exercise, in order to analyse whether a change of head-neck position may have an impact on the pharyngeal diameter. Results Under the assumption that the width of the epiglottis remains constant in healthy horses, the newly developed method for calculating the pharyngeal diameter in horses during exercise is unsusceptible against changes of the viewing-angle and distance between the endoscope and the structures, which are to be assessed. The quotient of the width of the epiglottis and the perpendicular from a fixed point on the dorsal pharynx to the epiglottis could be used to determine the pharyngeal diameter. The percentage change of this quotient (pharynx-epiglottis-ratio; PE-ratio) in the unrestrained head-neck position against the reference position was significantly larger than that of any other combination of the head-neck positions investigated. A relation between the percentage change in PE-ratio and the degree of head and neck flexion could not be confirmed. Conclusions It could be shown, that the pharyngeal diameter is reduced through the contact position implemented by the rider in comparison to the unrestrained head and neck position. An alteration of the pharyngeal diameter depending on the degree of head and neck flexion (represented by ground and withers angle) could not be confirmed. PMID:24886465

The Free Energy Landscape of Pseudorotation in 3′–5′ and 2′–5′ Linked Nucleic Acids

PubMed Central

2014-01-01

The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2′-endo and C3′-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2′-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3′-endo state. However, at a 2′–5′ linkage, the minimum shifts to the C2′-endo conformation. The free energy of the C3′-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3′-endo to C2′-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2′–5′ linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations. PMID:24499340

Elucidation of interactions of Alzheimer amyloid beta peptides (Abeta40 and Abeta42) with insulin degrading enzyme: a molecular dynamics study.

PubMed

Bora, Ram Prasad; Prabhakar, Rajeev

2010-05-11

In this study, interactions of the two full-length Alzheimer amyloid beta peptides (Abeta40 and Abeta42) with the fully active form of insulin degrading enzyme (IDE) through unrestrained, all-atom MD simulations have been investigated. This enzyme is a Zn-containing metallopeptidase that catalyzes the degradation of the monomeric forms of these peptides, and this process is critical for preventing the progression of Alzheimer's disease (AD). The available X-ray structures of the free and small fragment-bound (Asp1-Glu3 and Lys16-Asp23 of Abeta40 and Asp1-Glu3 and Lys16-Glu22 of Abeta42) mutated forms of IDE and NMR structures of the full-length Abeta40 and Abeta42 have been used to build the starting structures for these simulations. The most representative structures derived from the Abeta40-IDE and Abeta42-IDE simulations accurately reproduced the locations of the active site Zn(2+) metal and small fragments of the substrates and their interactions with the enzyme from the X-ray structures. The remaining fragments of both the substrates were found to interact with IDE through several hydrogen bonding, pi-pi, CH-pi, and NH-pi interactions. In comparison to Abeta40, Abeta42 is more flexible and interacts through a smaller number (17-22) of hydrogen bonds in the catalytic chamber of IDE. Both the substrates adopted more beta-sheet character in the IDE environment, an observation that is in line with experiments. Their structural characteristics inside IDE are significantly different than the ones observed in aqueous solution. The atomistic level details provided by these simulations can help in the elucidation of binding and degrading mechanisms of the Abeta peptides by IDE.

A Comprehensive Method To Quantify Adaptations by Male and Female Mice With Hot Flashes Induced by the Neurokinin B Receptor Agonist Senktide.

PubMed

Krull, Ashley A; Larsen, Sarah A; Clifton, Donald K; Neal-Perry, Genevieve; Steiner, Robert A

2017-10-01

Vasomotor symptoms (VMS; or hot flashes) plague millions of reproductive-aged men and women who have natural or iatrogenic loss of sex steroid production. Many affected individuals are left without treatment options because of contraindications to hormone replacement therapy and the lack of equally effective nonhormonal alternatives. Moreover, development of safer, more effective therapies has been stymied by the lack of an animal model that recapitulates the hot-flash phenomenon and enables direct testing of hypotheses regarding the pathophysiology underlying hot flashes. To address these problems, we developed a murine model for hot flashes and a comprehensive method for measuring autonomic and behavioral thermoregulation in mice. We designed and constructed an instrument called a thermocline that produces a thermal gradient along which mice behaviorally adapt to a thermal challenge to their core body temperature set point while their thermal preference over time is tracked and recorded. We tested and validated this murine model for VMS by administration of a TRPV1 agonist and a neurokinin B receptor agonist, capsaicin and senktide, respectively, to unrestrained mice and observed their autonomic and behavioral responses. Following both treatments, the mice exhibited a VMS-like response characterized by a drop in core body temperature and cold-seeking behavior on the thermocline. Senktide also caused a rise in tail skin temperature and increased Fos expression in the median preoptic area, a hypothalamic temperature control center. This dynamic model may be used to fully explore the cellular and molecular bases for VMS and to develop and test new therapeutic options. Copyright © 2017 Endocrine Society.

A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity

PubMed Central

Lam, Sonia Y.; Yeung, Rachel C. Y.; Yu, Tsz-Ha; Sze, Kong-Hung; Wong, Kam-Bo

2011-01-01

Background Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. Methods and Findings Acylphosphatases have a unique structural feature that its conserved active-site arginine residue forms a salt-bridge with the C-terminal carboxyl group only in thermophilic acylphosphatases, but not in mesophilic acylphosphatases. We perturbed the local rigidity of this active-site residue by removing the salt-bridge in the thermophilic acylphosphatase and by introducing the salt-bridge in the mesophilic homologue. The mutagenesis design was confirmed by x-ray crystallography. Removing the salt-bridge in the thermophilic enzyme lowered the activation energy that decreased the activation enthalpy and entropy. Conversely, the introduction of the salt-bridge to the mesophilic homologue increased the activation energy and resulted in increases in both activation enthalpy and entropy. Revealed by molecular dynamics simulations, the unrestrained arginine residue can populate more rotamer conformations, and the loss of this conformational freedom upon the formation of transition state justified the observed reduction in activation entropy. Conclusions Our results support the conclusion that restricting the active-site flexibility entropically favors the enzymatic activity at high temperatures. However, the accompanying enthalpy-entropy compensation leads to a stronger temperature-dependency of the enzymatic activity, which explains the less active nature of the thermophilic enzymes at low temperatures. PMID:21423654

A rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity.

PubMed

Lam, Sonia Y; Yeung, Rachel C Y; Yu, Tsz-Ha; Sze, Kong-Hung; Wong, Kam-Bo

2011-03-01

Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. Acylphosphatases have a unique structural feature that its conserved active-site arginine residue forms a salt-bridge with the C-terminal carboxyl group only in thermophilic acylphosphatases, but not in mesophilic acylphosphatases. We perturbed the local rigidity of this active-site residue by removing the salt-bridge in the thermophilic acylphosphatase and by introducing the salt-bridge in the mesophilic homologue. The mutagenesis design was confirmed by x-ray crystallography. Removing the salt-bridge in the thermophilic enzyme lowered the activation energy that decreased the activation enthalpy and entropy. Conversely, the introduction of the salt-bridge to the mesophilic homologue increased the activation energy and resulted in increases in both activation enthalpy and entropy. Revealed by molecular dynamics simulations, the unrestrained arginine residue can populate more rotamer conformations, and the loss of this conformational freedom upon the formation of transition state justified the observed reduction in activation entropy. Our results support the conclusion that restricting the active-site flexibility entropically favors the enzymatic activity at high temperatures. However, the accompanying enthalpy-entropy compensation leads to a stronger temperature-dependency of the enzymatic activity, which explains the less active nature of the thermophilic enzymes at low temperatures.

Review and specification for shrinkage cracks of bridge decks : final report.

DOT National Transportation Integrated Search

2016-12-01

An existing standard method ASTM C157 is used to determine the length change or free shrinkage of an unrestrained concrete specimen. However, in bridge decks, the concrete is actually under restrained conditions, and thus free shrinkage test methods ...

Child Restraint Use and Driver Screening in Fatal Crashes Involving Drugs and Alcohol.

PubMed

Huang, Yanlan; Liu, Chang; Pressley, Joyce C

2016-09-01

There are reports that the incidence of alcohol-involved crashes has remained stable among fatally injured drivers while drug involvement has increased in recent years. Data from the Fatality Analysis Reporting System (FARS) from 2010 to 2013 were used to examine drug and alcohol status of drivers (N = 10 864) of 4-wheeled passenger vehicles involved in a fatal crash while transporting a passenger aged 0 to 14 years (N = 17 179). Mixed effect multivariable logistic regression used SAS GLIMMIX to control for clustering. Odds ratios are reported with 95% confidence intervals (CIs). Only 28.9% of drivers were screened for both alcohol and drugs, and 56.7% were not tested for either. The total proportion of unrestrained child passengers increased nearly linearly by age. Findings ranged as high as 70% for 13- to 14-year-olds with drivers positive for drugs and alcohol. In multivariable adjusted models, inappropriate child seating with drivers who tested positive was as follows: alcohol, 1.30 (95% CI, 0.92-1.82); drugs, 1.54 (95% CI, 1.24-1.92); and for both drugs and alcohol, 1.88 (95% CI, 1.38-2.55). More than one-fourth were unrestrained with drivers positive for cannabis (27.7%). Overall mortality was approximately triple for unrestrained versus restrained (33.5% vs 11.5%; P < .0001) and was higher in front-seated than rear-seated passengers (40.7% vs 31.5%; P < .0001). Passengers were less likely to be appropriately seated and to be restrained when transported by a driver positive for drugs and alcohol, but this finding varied according to passenger age and drug/alcohol category. Copyright © 2016 by the American Academy of Pediatrics.

Spatial transformations between superior colliculus visual and motor response fields during head-unrestrained gaze shifts.

PubMed

Sadeh, Morteza; Sajad, Amirsaman; Wang, Hongying; Yan, Xiaogang; Crawford, John Douglas

2015-12-01

We previously reported that visuomotor activity in the superior colliculus (SC)--a key midbrain structure for the generation of rapid eye movements--preferentially encodes target position relative to the eye (Te) during low-latency head-unrestrained gaze shifts (DeSouza et al., 2011). Here, we trained two monkeys to perform head-unrestrained gaze shifts after a variable post-stimulus delay (400-700 ms), to test whether temporally separated SC visual and motor responses show different spatial codes. Target positions, final gaze positions and various frames of reference (eye, head, and space) were dissociated through natural (untrained) trial-to-trial variations in behaviour. 3D eye and head orientations were recorded, and 2D response field data were fitted against multiple models by use of a statistical method reported previously (Keith et al., 2009). Of 60 neurons, 17 showed a visual response, 12 showed a motor response, and 31 showed both visual and motor responses. The combined visual response field population (n = 48) showed a significant preference for Te, which was also preferred in each visual subpopulation. In contrast, the motor response field population (n = 43) showed a preference for final (relative to initial) gaze position models, and the Te model was statistically eliminated in the motor-only population. There was also a significant shift of coding from the visual to motor response within visuomotor neurons. These data confirm that SC response fields are gaze-centred, and show a target-to-gaze transformation between visual and motor responses. Thus, visuomotor transformations can occur between, and even within, neurons within a single frame of reference and brain structure. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Child Restraint Use and Driver Screening in Fatal Crashes Involving Drugs and Alcohol

PubMed Central

Huang, Yanlan; Liu, Chang

2016-01-01

BACKGROUND: There are reports that the incidence of alcohol-involved crashes has remained stable among fatally injured drivers while drug involvement has increased in recent years. METHODS: Data from the Fatality Analysis Reporting System (FARS) from 2010 to 2013 were used to examine drug and alcohol status of drivers (N = 10 864) of 4-wheeled passenger vehicles involved in a fatal crash while transporting a passenger aged 0 to 14 years (N = 17 179). Mixed effect multivariable logistic regression used SAS GLIMMIX to control for clustering. Odds ratios are reported with 95% confidence intervals (CIs). RESULTS: Only 28.9% of drivers were screened for both alcohol and drugs, and 56.7% were not tested for either. The total proportion of unrestrained child passengers increased nearly linearly by age. Findings ranged as high as 70% for 13- to 14-year-olds with drivers positive for drugs and alcohol. In multivariable adjusted models, inappropriate child seating with drivers who tested positive was as follows: alcohol, 1.30 (95% CI, 0.92–1.82); drugs, 1.54 (95% CI, 1.24–1.92); and for both drugs and alcohol, 1.88 (95% CI, 1.38–2.55). More than one-fourth were unrestrained with drivers positive for cannabis (27.7%). Overall mortality was approximately triple for unrestrained versus restrained (33.5% vs 11.5%; P < .0001) and was higher in front-seated than rear-seated passengers (40.7% vs 31.5%; P < .0001). CONCLUSIONS: Passengers were less likely to be appropriately seated and to be restrained when transported by a driver positive for drugs and alcohol, but this finding varied according to passenger age and drug/alcohol category. PMID:27550984

Evaluation of rebound tonometry in red-eared slider turtles (Trachemys scripta elegans).

PubMed

Delgado, Cherlene; Mans, Christoph; McLellan, Gillian J; Bentley, Ellison; Sladky, Kurt K; Miller, Paul E

2014-07-01

To evaluate feasibility and accuracy of intraocular pressure (IOP) measurement by rebound tonometry in adult red-eared slider turtles and determine the effects of manual and chemical restraint on IOP. Seventeen adult red-eared slider turtles. Intraocular pressure was measured with TonoLab® and TonoVet® tonometers in conscious, unrestrained turtles. To evaluate the effects of manual restraint, turtles were restrained by digital pressure on the rostral head or proximal neck. The effect of two chemical restraint protocols (dexmedetomidine, ketamine, midazolam [DKM] and dexmedetomidine, ketamine [DK] subcutaneously) on IOP was evaluated. Triplicate TonoLab® and TonoVet® readings were compared with direct manometry in three ex vivo turtle eyes. TonoLab® correlated better with manometry at IOPs < 45 mmHg than TonoVet® (linear regression slopes of 0.89 and 0.30, respectively). Mean (±SD) IOP in unrestrained conscious turtles was significantly lower (P < 0.01) with TonoLab® (10.02 ± 0.66 mmHg) than with TonoVet® (11.32 ± 1.57 mmHg). Manual neck restraint caused a significant increase in IOP (+6.31 ± 5.59 mmHg), while manual rostral head restraint did not. Both chemical restraint protocols significantly reduced IOP (DKM: −1.0 ± 0.76 mmHg; DK: −1.79 ± 1.17) compared with measurements in conscious unrestrained turtles. Chemical and manual neck restraint affected IOP. Rostral head restraint had no significant effect on IOP and is, therefore, recommended as the appropriate restraint technique in red-eared slider turtles. TonoLab® measurements estimated actual IOP more accurately, within physiologic range, than measurements obtained using the TonoVet®. © 2013 American College of Veterinary Ophthalmologists.

EVALUATION OF REBOUND TONOMETRY IN RED-EARED SLIDER TURTLES (TRACHEMYS SCRIPTA ELEGANS)

PubMed Central

Delgado, Cherlene; Mans, Christoph; McLellan, Gillian J.; Bentley, Ellison; Sladky, Kurt K.; Miller, Paul E.

2013-01-01

Objective To evaluate feasibility and accuracy of intraocular pressure (IOP) measurement by rebound tonometry in adult red-eared slider turtles and determine the effects of manual and chemical restraint on IOP. Animal studied Seventeen adult red-eared slider turtles. Procedures IOP was measured with TonoLab® and TonoVet® tonometers in conscious, unrestrained turtles. To evaluate the effects of manual restraint, turtles were restrained by digital pressure on the rostral head or proximal neck. The effect of two chemical restraint protocols (dexmedetomidine, ketamine, midazolam [DKM] and dexmedetomidine, ketamine [DK] subcutaneously) on IOP was evaluated. Triplicate TonoLab® and TonoVet® readings were compared to direct manometry in 3 ex vivo turtle eyes. Results TonoLab® correlated better with manometry at IOPs <45 mm Hg than TonoVet® (linear regression slopes of 0.89 and 0.30 respectively). Mean (±SD) IOP in unrestrained conscious turtles was significantly lower (P<0.01) with TonoLab® (10.02 ± 0.66 mmHg) than with TonoVet® (11.32 ± 1.57 mmHg). Manual neck restraint caused a significant increase in IOP (+6.31 ± 5.59 mmHg), while manual rostral head restraint did not. Both chemical restraint protocols significantly reduced IOP (DKM: −1.0 ± 0.76 mmHg,; DK: −1.79 ± 1.17) compared to measurements in conscious unrestrained turtles. Conclusions Chemical and manual neck restraint affected IOP. Rostral head restraint had no significant effect on IOP and is, therefore, recommended as the appropriate restraint technique in red-eared-slider turtles. TonoLab® measurements estimated actual IOP more accurately, within physiologic range, than measurements obtained using the TonoVet®. PMID:25097909

Comparison of oxygen saturation values obtained from fingers on physically restrained or unrestrained sides of the body.

PubMed

Korhan, Esra Akin; Yönt, Gülendam Hakverdioğlu; Khorshid, Leyla

2011-01-01

The aim of this study was to compare semiexperimentally the pulse oximetry values obtained from a finger on restrained or unrestrained sides of the body. The pulse oximeter provides a noninvasive measurement of the oxygen saturation of hemoglobin in arterial blood. One of the procedures most frequently applied to patients in intensive care units is the application of physical restraint. Circulation problems are the most important complication in patients who are physically restrained. Evaluation of oxygen saturation from body parts in which circulation is impeded or has deteriorated can cause false results. The research sample consisted of 30 hospitalized patients who participated in the study voluntarily and who were concordant with the inclusion criteria of the study. Patient information and patient follow-up forms were used for data collection. Pulse oximetry values were measured simultaneously using OxiMax Nellcor finger sensors from fingers on the restrained and unrestrained sides of the body. Numeric and percentile distributions were used in evaluating the sociodemographic properties of patients. A significant difference was found between the oxygen saturation values obtained from a finger of an arm that had been physically restrained and a finger of an arm that had not been physically restrained. The mean oxygen saturation value measured from a finger of an arm that had been physically restrained was found to be 93.40 (SD, 2.97), and the mean oxygen saturation value measured from a finger of an arm that had not been physically restrained was found to be 95.53 (SD, 2.38). The results of this study indicate that nurses should use a finger of an arm that is not physically restrained when evaluating oxygen saturation values to evaluate them correctly.

Reducing nonuse of restraints by children ages 5 to 7 : traffic tech.

DOT National Transportation Integrated Search

2010-02-01

NHTSAs Misuse of Child Restraints study (DOT HS 809 : 671) identified high rates of unrestrained children of booster : seat age and weight. This project was undertaken in response : to those findings, selecting 5- to 7-year-olds to target be...

HYPERTENSIVE AND TACHYCARDIC RESPONSES TO ORAL TOLUENE IN THE RAT.

EPA Science Inventory

Little is known regarding the effects of toluene and other volatile organic compounds on autonomic processes. Such studies should be performed in unrestrained and undisturbed animals to avoid the effects of handling stress on processes regulated by the autonomic nervous system. T...

Body Temperature Versus Microclimate Selection in Heat Stressed Dairy Cows

USDA-ARS?s Scientific Manuscript database

The purpose of this study is to characterize the thermoregulatory responses of unrestrained heat-stressed dairy cows within a freestall environment using fan and spray configurations for cooling cows while lying or standing. An experimental treatment sprayed individual cows lying in freestalls from ...

Dog and cat bites: epidemiologic analyses suggest different prevention strategies.

PubMed Central

Patrick, G R; O'Rourke, K M

1998-01-01

OBJECTIVE: To examine the characteristics of reported dog and cat bite incidents in El Paso, Texas, and their implications for local bite prevention programs. METHODS: The authors reviewed a random sample of reported dog bites and all reported cat bites in El Paso, Texas, in 1995 using existing animal control surveillance data. RESULTS: The majority of cat bites (89.4%) were provoked, with females (57.5%) and adults (68.3%) more likely to be victims than males or children. In contrast, just under half of dog bites (44.6%) were provoked, with males (65.6%) and children (63%) more likely to be victims than females or adults. Dogs that had not been vaccinated for rabies were involved in 65% of dog bites and cats that had not been vaccinated for rabies were involved in 92% of cat bites. CONCLUSION: Effective bite prevention programs should address the finding that both restrained and unrestrained dogs may bite even when unprovoked and that unrestrained cats usually bite when provoked. PMID:9633872

"I feel fat": an experimental induction of body displacement in disordered eating.

PubMed

McFarlane, Traci; Urbszat, Dax; Olmsted, Marion P

2011-04-01

Body displacement, the theory that predicts that individuals with eating disorders will displace negative feelings about themselves onto their body, was tested experimentally in this study. Unrestrained eaters (n = 61), restrained eaters (n = 33), and individuals with eating disorders (n = 26) were randomly assigned to a control condition or an ineffectiveness induction. In the ineffectiveness condition participants were asked to recall and reflect on a past experience when they felt useless or incapable (i.e., ineffective). Results showed that individuals with eating disorders who were made to feel ineffective reported more implicit appearance/body concern than those in the control condition. Unrestrained and restrained eaters did not show this effect. This is the first experimental study to support body displacement theory. These data can be used clinically to educate and encourage patients with eating disorders to address thoughts and feelings related to ineffectiveness directly, instead of displacing this distress onto their body and potentially perpetuating their eating disorder. Copyright © 2011 Elsevier Ltd. All rights reserved.

Suppression of Neutrophil-Mediated Tissue Damage—A Novel Skill of Mesenchymal Stem Cells

PubMed Central

Jiang, Dongsheng; Muschhammer, Jana; Qi, Yu; Kügler, Andrea; De Vries, Juliane C.; Saffarzadeh, Mona; Sindrilaru, Anca; Beken, Seppe Vander; Wlaschek, Meinhard; Kluth, Mark A.; Ganss, Christoph; Frank, Natasha Y.; Frank, Markus H.; Preissner, Klaus T.; Scharffetter-Kochanek, Karin

2017-01-01

Mesenchymal stem cells (MSCs) are crucial for tissue homeostasis and regeneration. Though of prime interest, their potentially protective role on neutrophil-induced tissue damage, associated with high morbidity and mortality, has not been explored in sufficient detail. Here we report the therapeutic skill of MSCs to suppress unrestrained neutrophil activation and to attenuate severe tissue damage in a murine immune-complex mediated vasculitis model of unbalanced neutrophil activation. MSC-mediated neutrophil suppression was due to intercellular adhesion molecule 1-dependent engulfment of neutrophils by MSCs, decreasing overall neutrophil numbers. Similar to MSCs in their endogenous niche of murine and human vasculitis, therapeutically injected MSCs via upregulation of the extracellular superoxide dismutase (SOD3), reduced super-oxide anion concentrations and consequently prevented neutrophil death, neutrophil extracellular trap formation and spillage of matrix degrading neutrophil elastase, gelatinase and myeloperoxidase. SOD3-silenced MSCs did not exert tissue protective effects. Thus, MSCs hold substantial therapeutic promise to counteract tissue damage in conditions with unrestrained neutrophil activation. PMID:27299700

Self-enhancing effects of exposure to thin-body images.

PubMed

Joshi, Ramona; Herman, C Peter; Polivy, Janet

2004-04-01

This study examines the effect of thin-body media images on mood, self-esteem, and self-image ratings of restrained and unrestrained eaters. A secondary purpose was to examine whether these effects were influenced by exposure duration. Under the guise of a perception study, participants were exposed to thin-body or control advertisements (e.g., perfume bottles) for either 7 or 150 ms and then completed a questionnaire packet. Restrained eaters reported more favorable self-image and social self-esteem (but not appearance self-esteem) scores after exposure to thin-body images than after exposure to control advertisements. The self-image and social self-esteem scores of unrestrained eaters were unaffected by advertisement type, but their appearance self-esteem scores were lower after exposure to thin-body advertisements. No differences were found for mood ratings and total self-esteem. We discuss restraint status as a moderator of the effects of thin-body images on women's body image. Copyright 2004 by Wiley Periodicals, Inc. Int J Eat Disord 35: 333-341, 2004.

Study of an advanced transport airplane design concept known as Flatbed

NASA Technical Reports Server (NTRS)

Smethers, R. G.; Caldwell, E. W.; Warnock, W. E.; Wilson, J. M., Jr.

1980-01-01

The design concept and configuration of the Flatbed transport aircraft are presented. The Flatbed configuration combines into one frame, the ability to haul cargo, virtually unrestrained by cross sectional dimensions of the fuselage. The feasibility and capability of the Flatbed is discussed in depth.

RELATIONSHIP BETWEEN BEHAVIORAL AND AUTONOMIC THERMOREGULATION IN THE GUINEA PIG

EPA Science Inventory

The study was conducted to correlate the preferred thermal environment of the unrestrained guinea pig with the activity of its thermoregulatory effectors when maintained under a wide range of ambient temperatures (Ta). Eight male guinea pigs were used in a series of experiments o...

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0059: Molecular Dynamics Modeling Support

DTIC Science & Technology

2008-03-01

Molecular Dynamics Simulations 5 Theory: Equilibrium Molecular Dynamics Simulations 6 Theory: Non...Equilibrium Molecular Dynamics Simulations 8 Carbon Nanotube Simulations : Approach and results from equilibrium and non-equilibrium molecular dynamics ...touched from the perspective of molecular dynamics simulations . However, ordered systems such as “Carbon Nanotubes” have been investigated in terms

POWER SPECTRUM ANALYSIS AND TIME-DOMAIN ANALYSIS OF HRV RECORDED BY TELEMETRY IN UNRESTRAINED RATS. (R828046)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Is Restraint a Model of Binge Eating and Obesity?

ERIC Educational Resources Information Center

Lowe, Michael R.; And Others

Restraint theory assumes that restrained eating is functionally equivalent to dieting and that "restraint" accounts for the eating behavior of overweight individuals. This study evaluated both of these assumptions. In the first part of the study, normal weight women were divided into groups of unrestrained nondieters, restrained…

COMPARATIVE THERMOREGULATORY RESPONSE TO PASSIVE HEAT LOADING BY EXPOSURE TO RADIOFREQUENCY RADIATION

EPA Science Inventory

Colonic and tail skin temperature of the unrestrained Fischer rat were measured immediately after a 90 min exposure to 600 MHz radiofrequency radiation in a waveguide-type system. Ambient temperature (Ta) was maintained at either 20, 28, or 35 C. The specific absorption rate (SAR...

CRITICAL MECHANICAL PROPERTIES OF STRUCTURAL LIGHT-WEIGHT CONCRETE AND THE EFFECTS OF THESE PROPERTIES ON THE DESIGN OF THE PAVEMENT STRUCTURE.

DOT National Transportation Integrated Search

1965-01-01

In this study, critical mechanical properties of structural lightweight concrete were determined and utilized in the evaluation of a design of concrete pavements. Also presented are the critical mechanical properties resulting from unrestrained and r...

CARDIOVASCULAR AND THERMOREGULATORY RESPONSES OF UNRESTRAINED RATS EXPOSED TO FILTERED OR UNFILTERED DIESEL EXHAUST

EPA Science Inventory

Diesel exhaust (DE) has been associated with adverse cardiovascular and pulmonary health effects. The relative contributions of the gas-phase and particulate (PM) components of DE are less well understood. We exposed WKY rats with or without implanted radiotransmitters to air or ...

CARDIOVASCULAR RESPONSES IN UNRESTRAINED WKY-RATS TO INHALED ULTRAFINE CARBON PARTICLES

EPA Science Inventory

Abstract
This study provides evidence for adverse cardiac effects of inhaled ultrafine particles (UFPs) in healthy WKY rats. Short term exposure (24 h) with carbon UFPs (180 ?g?m ?) induced a moderate but significant heart rate increase of 18 bpm (4.8 %) in association with a ...

Social Learning Theory of Aggression.

ERIC Educational Resources Information Center

Bandura, Albert

1978-01-01

Suggests that violent activities occur not because of reduced self-control, but because cognitive skills and self-control are used through moral justifications and self-exonerative devices in the service of destructive causes. Threats to human welfare are generally brought about by deliberate acts of principle rather than by unrestrained acts of…

High-Mobility Multipurpose Wheeled Vehicle Rollover Accidents and Injuries to U.S. Army Soldiers by Reported Occupant Restraint Use, 1992-2013.

PubMed

Lo, Michael C; Giffin, Robert P; Pakulski, Kraig A; Davis, W Sumner; Bernstein, Stephen A; Wise, Daniel V

2017-05-01

The high-mobility multipurpose wheeled vehicle (HMMWV) is a light military tactical vehicle. During Operation Iraqi Freedom and Operation Enduring Freedom, the U.S. Army modified the HMMWV into a combat vehicle by adding vehicle armor, which made the vehicle more difficult to control and more likely to roll over. Consequently, reports of fatal rollover accidents involving up-armored HMMWVs began to accumulate during the up-armoring period (August 2003 to April 2005). Furthermore, the lack of occupant restraint use prevalent in a predominantly young, male, and enlisted military population compounded the injuries resulting from these accidents. In this retrospective case series analysis, we describe the characteristics of U.S. Army HMMWV rollover accidents, occupants, and injuries reported worldwide from fiscal year 1992 to 2013 based on reported occupant restraint use. We conducted all analyses using Microsoft Excel 2010 and SAS version 9.1. Because this analysis does not constitute human subjects research, no institutional review board review was required. First, we obtained U.S. Army HMMWV accident records from the U.S. Army Combat Readiness Center, and selected those records indicating a HMMWV rollover had occurred. Next, we successively deduplicated the records at the accident, vehicle, occupant, and injury levels for descriptive analysis of characteristics at each level. For each occupant position, we calculated relative, attributable, and population attributable risks of nonfatal and fatal injury based on reported occupant restraint use. Finally, we analyzed body part injured and nature of injury to characterize the injury patterns that HMMWV occupants in each position sustained based on restraint use. We performed a χ 2 test of homogeneity to assess differences in injury patterns between restrained and unrestrained occupants. A total of 819 U.S. Army HMMWV rollover accidents worldwide were reported from October 1991 through May 2013 involving 821 HMMWVs and 1,395 occupants (828 nonfatally injured, 151 fatally injured, and 416 noninjured). Thirty-five percent of more severe (class A and B) accidents involved the M1114 up-armored variant, whereas 32% of less severe (class C and D) accidents involved the M998 nonarmored variant. Unrestrained occupants were 20% more likely to be nonfatally injured and 5.6 times more likely to be fatally injured than were restrained occupants. Among unrestrained occupants, restraint use could have potentially saved 82% of lives lost. Among all occupants involved in a HMMWV rollover, an estimated 56% of fatalities could have been prevented by restraint use. Unrestrained drivers and vehicle commanders had greater than expected torso injuries, while restrained vehicle commanders and passengers had greater than expected upper extremity injuries. Unrestrained drivers had greater than expected fractures, whereas restrained drivers and vehicle commanders had greater than expected sprains/strains. While reporting bias may exist, nevertheless these results show that occupant restraint use confers substantial life-saving protection to HMMWV occupants in rollover accidents. Therefore, commanders, safety officers, and peers should continue to promote and enforce restraint use consistently during all Army ground operations and training involving HMMWVs. Doing so will save Soldiers' lives in rollover accidents during the remaining years of the HMMWV program. Reprint & Copyright © 2017 Association of Military Surgeons of the U.S.

Targeting inflammatory pathways in myocardial infarction

PubMed Central

Christia, Panagiota; Frangogiannis, Nikolaos G

2013-01-01

Acute cardiomyocyte necrosis in the infarcted heart generates Damage-Associated Molecular Patterns (DAMPs), activating complement and Toll-Like Receptor (TLR)/Interleukin (IL)-1 signaling, and triggering an intense inflammatory reaction. Infiltrating leukocytes clear the infarct from dead cells, while activating reparative pathways that lead to formation of a scar. As the infarct heals the ventricle remodels; the geometric, functional and molecular alterations associated with post-infarction remodeling are driven by the inflammatory cascade and are involved in the development of heart failure. Because unrestrained inflammation in the infarcted heart induces matrix degradation and cardiomyocyte apoptosis, timely suppression of the post-infarction inflammatory reaction may be crucial to protect the myocardium from dilative remodeling and progressive dysfunction. Inhibition and resolution of post-infarction inflammation involves mobilization of inhibitory mononuclear cell subsets and requires activation of endogenous STOP signals. Our manuscript discusses the basic cellular and molecular events involved in initiation, activation and resolution of the post-infarction inflammatory response, focusing on identification of therapeutic targets. The failure of anti-integrin approaches in patients with myocardial infarction and a growing body of experimental evidence suggest that inflammation may not increase ischemic cardiomyocyte death, but accentuates matrix degradation causing dilative remodeling. Given the pathophysiologic complexity of post-infarction remodeling, personalized biomarker-based approaches are needed to target patient subpopulations with dysregulated inflammatory and reparative responses. Inhibition of pro-inflammatory signals (such as IL-1 and Monocyte Chemoattractant Protein-1) may be effective in patients with defective resolution of post-infarction inflammation who exhibit progressive dilative remodeling. In contrast, patients with predominant hypertrophic/fibrotic responses may benefit from anti-TGF strategies. PMID:23772948

A concurrent multiscale micromorphic molecular dynamics

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

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

2015-04-21

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

All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

NASA Astrophysics Data System (ADS)

Woo, Sun Young; Lee, Hwankyu

2016-03-01

Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

PubMed

Woo, Sun Young; Lee, Hwankyu

2016-03-01

Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

Analysis of dual tree M-band wavelet transform based features for brain image classification.

PubMed

Ayalapogu, Ratna Raju; Pabboju, Suresh; Ramisetty, Rajeswara Rao

2018-04-29

The most complex organ in the human body is the brain. The unrestrained growth of cells in the brain is called a brain tumor. The cause of a brain tumor is still unknown and the survival rate is lower than other types of cancers. Hence, early detection is very important for proper treatment. In this study, an efficient computer-aided diagnosis (CAD) system is presented for brain image classification by analyzing MRI of the brain. At first, the MRI brain images of normal and abnormal categories are modeled by using the statistical features of dual tree m-band wavelet transform (DTMBWT). A maximum margin classifier, support vector machine (SVM) is then used for the classification and validated with k-fold approach. Results show that the system provides promising results on a repository of molecular brain neoplasia data (REMBRANDT) with 97.5% accuracy using 4 th level statistical features of DTMBWT. Viewing the experimental results, we conclude that the system gives a satisfactory performance for the brain image classification. © 2018 International Society for Magnetic Resonance in Medicine.

A Test of the Abstinence Violation Effect.

ERIC Educational Resources Information Center

Ruderman, Audrey J.

According to the abstinence violation effect, highly controlled drinkers tend to overindulge following an initial slip. To investigate this relapse model, 47 male college students, ranging in age from 21 to 46, were assigned either to an unrestrained or a restrained drinker group according to their scores on the Restrained Drinking Scale. Subjects…

Infant activity and sleep behaviors in a maternal and infant home visiting project among rural, Southern, African American women

USDA-ARS?s Scientific Manuscript database

Background: Physical inactivity and inadequate amounts of sleep are two potential causes for excessive weight gain in infancy. Thus, parents and caregivers of infants need to be educated about decreasing infant sedentary behavior, increasing infant unrestrained floor time, as well as age specific r...

A Survey of Turkish Pre-Service Science Teachers' Attitudes toward the Environment

ERIC Educational Resources Information Center

Özsoy, Sibel

2012-01-01

Problem Statement: Increasing global population and unrestrained consumption of natural resources has resulted in increasing pollution, poor air and water quality and the extinction of animal and plant species. Today, environmental problems are experienced worldwide and threatening the continuity of human life. For the sake of human beings,…

The American Ornithologists' Union and bird conservation: recommitment to the revolution

Treesearch

John W. Fitzpatrick

2005-01-01

Exactly one hundred years ago, with North America in full-fledged environmental crisis, prominent members of the American Ornithologists' Union (AOU) participated in major political and social upheaval. A century of unrestrained exploitation had reached catastrophic proportions, with Passenger Pigeons and Eskimo Curlews representing only the tip of an iceberg....

Selective Moral Disengagement in the Exercise of Moral Agency.

ERIC Educational Resources Information Center

Bandura, Albert

2002-01-01

Addresses the issue of selective moral disengagement in the exercise of moral agency. Argues that moral functioning is governed by self-reactive selfhood rather than by dispassionate abstract reasoning. Concludes that the massive threats to human welfare stem mainly from deliberate acts of principle rather than from unrestrained acts of impulse.…

Fatality reduction by safety belts for front-seat occupants of cars and light trucks : updated and expanded estimates based on 1986-99 FARS data

DOT National Transportation Integrated Search

2000-12-01

The National Highway Traffic Safety Administration estimated in 1984 that manual 3-point safety belts : reduce the fatality risk of front-seat occupants of passenger cars by 45 percent relative to the unrestrained : occupant. The agency still relies ...

Effects of exposure to unrealistic promises about dieting: are unrealistic expectations about dieting inspirational?

PubMed

Trottier, Kathryn; Polivy, Janet; Herman, C Peter

2005-03-01

The false-hope syndrome suggests that unrealistic expectations about dieting set dieters up for failure and then promote renewed efforts at weight loss. Many dieters believe the inflated promises typical of diet advertisements, which may be the source of at least some of their unrealistic expectations. Diet advertisements promoting unrealistic expectations were expected to inspire restrained eaters to diet and lead to enhanced self-perceptions, relative to more circumspect advertisements. Female undergraduates rated their expectations in response to a control advertisement or to advertisements containing realistic, moderately unrealistic, or highly unrealistic promises of dieting. Participants then rated their self-perceptions and participated in an apparent "taste-test". Restrained eaters had higher expectations for themselves than did unrestrained eaters, and restrained and unrestrained eaters had similar expectations concerning dieting for others. Those who viewed the advertisements containing unrealistic expectations ate fewer cookies ad libitum than did those who viewed the realistic or control advertisements. This finding is consistent with the suggestion that unrealistic expectations contribute to the decision to change oneself. (c) 2005 by Wiley Periodicals, Inc.

How restrained eaters perceive the amount they eat.

PubMed

Jansen, A

1996-09-01

The cognitive model of binge eating states that it is the awareness of a broken diet that disinhibits the restrained eater. It is, according to that model, the perception of having overeaten that triggers disinhibited eating. However, although the perception of the amount eaten plays a central role in cognitive restraint theory, it has never directly been tested how restrained subjects perceive the amount of food they eat. In the present studies, participants were given ad libitum access to large amounts of palatable food and both their perception of the amount eaten and their estimated caloric intake were compared with the amount they actually ate. The restrained participants in these studies ate more than the unrestrained participants. In the first and second studies, the restrained participants consumed 571 and 372 'forbidden' calories respectively, without having the feeling that they had eaten very much, let alone too much. Moreover in both studies, the restrained eaters underestimated their caloric intake, whereas unrestrained eaters estimated their caloric intake quite well. The potential implications of the present findings for the cognitive restraint model are discussed.

Contribution of the frontal eye field to gaze shifts in the head-unrestrained rhesus monkey: neuronal activity.

PubMed

Knight, T A

2012-12-06

The frontal eye field (FEF) has a strong influence on saccadic eye movements with the head restrained. With the head unrestrained, eye saccades combine with head movements to produce large gaze shifts, and microstimulation of the FEF evokes both eye and head movements. To test whether the dorsomedial FEF provides commands for the entire gaze shift or its separate eye and head components, we recorded extracellular single-unit activity in monkeys trained to make large head-unrestrained gaze shifts. We recorded 80 units active during gaze shifts, and closely examined 26 of these that discharged a burst of action potentials that preceded horizontal gaze movements. These units were movement or visuomovement related and most exhibited open movement fields with respect to amplitude. To reveal the relations of burst parameters to gaze, eye, and/or head movement metrics, we used behavioral dissociations of gaze, eye, and head movements and linear regression analyses. The burst number of spikes (NOS) was strongly correlated with movement amplitude and burst temporal parameters were strongly correlated with movement temporal metrics for eight gaze-related burst neurons and five saccade-related burst neurons. For the remaining 13 neurons, the NOS was strongly correlated with the head movement amplitude, but burst temporal parameters were most strongly correlated with eye movement temporal metrics (head-eye-related burst neurons, HEBNs). These results suggest that FEF units do not encode a command for the unified gaze shift only; instead, different units may carry signals related to the overall gaze shift or its eye and/or head components. Moreover, the HEBNs exhibit bursts whose magnitude and timing may encode a head displacement signal and a signal that influences the timing of the eye saccade, thereby serving as a mechanism for coordinating the eye and head movements of a gaze shift. Copyright © 2012 IBRO. Published by Elsevier Ltd. All rights reserved.

The Impact of Child Safety Restraint Status and Age in Motor Vehicle Collisions in Predicting Type and Severity of Bone Fractures and Traumatic Injuries.

PubMed

Loftis, Christopher M; Sawyer, Jeffrey R; Eubanks, James W; Kelly, Derek M

2017-12-01

Although morbidity and mortality in children increases in motor vehicle collisions (MVC) if child restraints are not used, no data exist correlating specific injuries with proper or improper use of safety restraints or age. The purpose of this study was to evaluate correlations between childhood MVC injuries, age, and restraint status. A medical record search for pediatric patients involved in a MVC was conducted at a pediatric hospital (level 1 trauma). Charts were reviewed for demographics and injury-specific information. Patients were grouped by age, restraint use, and injuries. Nine hundred sixty-seven patients ≤12 years (average age 6.39 y) were identified. Being properly restrained was most common in all age groups except the 4- to 8-year age group in which being improperly restrained was most common. Unrestrained patients were most commonly found in the 9- to 12-year age group. A statistically significant difference was not observed for orthopaedic injuries among the restraint groups, but internal thoracic injuries, open head wound, and open upper extremity wounds were significantly more common in improperly or unrestrained patients. Improperly restrained infants had a significantly higher rate of intracranial bleeds and abrasions than those properly restrained. Unrestrained and improperly restrained 9- to 12-year olds had significantly more open head, open upper extremity, and vascular injuries. When comparing injury types with age groups, upper extremity fractures, femoral fractures, dislocations, and spinal fractures were found to be significantly higher in older children. Preventing orthopaedic injuries in older children may be accomplished by changes in regulations or automotive safety equipment. Rear-facing child safety seats could possibly be improved to prevent head trauma in the youngest patients. There is a continued need to reinforce the importance of proper use of child safety devices to parents. Knowledge of the patient's age, along with restraint status, might aid in diagnosis of less obvious MCV injuries. Level III.

Tidal regime dictates the cascading consumptive and nonconsumptive effects of multiple predators on a marsh plant.

PubMed

Kimbro, David L

2012-02-01

Prey perception of predators can dictate how prey behaviorally balance the need to avoid being eaten with the need to consume resources, and this perception and consequent behavior can be strongly influenced by physical processes. Physical factors, however, can also alter the density and diversity of predators that pursue prey. Thus, it remains uncertain to what extent variable risk perception and antipredator behavior vs. variation in predator consumption of prey underlie prey-resource dynamics and give rise to large-scale patterns in natural systems. In an experimental food web where tidal inundation of marsh controls which predators access prey, crab and conch (predators) influenced the survivorship and antipredator behavior of snails (prey) irrespective of whether tidal inundation occurred on a diurnal or mixed semidiurnal schedule. Specifically, cues of either predator caused snails to ascend marsh leaves; snail survivorship was reduced more by unrestrained crabs than by unrestrained conchs; and snail survivorship was lowest with multiple predators than with any single predator despite interference. In contrast to these tidally consistent direct consumptive and nonconsumptive effects, indirect predator effects differed with tidal regime: snail grazing of marsh leaves in the presence of predators increased in the diurnal tide but decreased in the mixed semidiurnal tidal schedule, overwhelming the differences in snail density that resulted from direct predation. In addition, results suggest that snails may increase their foraging to compensate for stress-induced metabolic demand in the presence of predator cues. Patterns from natural marshes spanning a tidal inundation gradient (from diurnal to mixed semidiurnal tides) across 400 km of coastline were consistent with experimental results: despite minimal spatial variation in densities of predators, snails, abiotic stressors, and marsh productivity, snail grazing on marsh plants increased and plant biomass decreased on shorelines exposed to a diurnal tide. Because both the field and experimental results can be explained by tidal-induced variation in risk perception and snail behavior rather than by changes in snail density, this study reinforces the importance of nonconsumptive predator effects in complex natural systems and at large spatial scales.

Cardiovascular adaptations during long-term altered gravity

NASA Technical Reports Server (NTRS)

Popovic, V. P.

1982-01-01

Cardiovascular studies were performed on unrestrained, unanesthetized rats and on the same animals in head-down hypokinetic conditions as well as during readaptation of the same animals to free activity. Possible circulatory mechanisms that evolved in mammals during long-lasting gravity exposure are considered. These mechanisms are likely to be affected during exposure to 0-g forces.

76 FR 17334 - Special Conditions: Boeing Model 747-2G4B Airplane; Certification of Cooktops

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-29

..., include with your comments a self-addressed, stamped postcard on which you have written the docket number. We will stamp the date on the postcard and mail it back to you. Background On July 20, 2010... the presence of relatively unrestrained hot cookware and heated food, which may represent...

Experimental Test of Spatial Updating Models for Monkey Eye-Head Gaze Shifts

PubMed Central

Van Grootel, Tom J.; Van der Willigen, Robert F.; Van Opstal, A. John

2012-01-01

How the brain maintains an accurate and stable representation of visual target locations despite the occurrence of saccadic gaze shifts is a classical problem in oculomotor research. Here we test and dissociate the predictions of different conceptual models for head-unrestrained gaze-localization behavior of macaque monkeys. We adopted the double-step paradigm with rapid eye-head gaze shifts to measure localization accuracy in response to flashed visual stimuli in darkness. We presented the second target flash either before (static), or during (dynamic) the first gaze displacement. In the dynamic case the brief visual flash induced a small retinal streak of up to about 20 deg at an unpredictable moment and retinal location during the eye-head gaze shift, which provides serious challenges for the gaze-control system. However, for both stimulus conditions, monkeys localized the flashed targets with accurate gaze shifts, which rules out several models of visuomotor control. First, these findings exclude the possibility that gaze-shift programming relies on retinal inputs only. Instead, they support the notion that accurate eye-head motor feedback updates the gaze-saccade coordinates. Second, in dynamic trials the visuomotor system cannot rely on the coordinates of the planned first eye-head saccade either, which rules out remapping on the basis of a predictive corollary gaze-displacement signal. Finally, because gaze-related head movements were also goal-directed, requiring continuous access to eye-in-head position, we propose that our results best support a dynamic feedback scheme for spatial updating in which visuomotor control incorporates accurate signals about instantaneous eye- and head positions rather than relative eye- and head displacements. PMID:23118883

Structural response and gas dynamics of an airship exposed to a nuclear detonation. Final report

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

Gilstad, D.A.; Weeber, C.G.; Kviljord, A.

1960-04-25

Four Model ZSG-3 airships, U. S. Navy Bureau of Aeronautics Nos. 40, 46, 77, and 92, participated during Operation Plumbbob to determine the response characteristics of the Model ZSG-3 airship when subjected to a nuclear detonation in order to establish criteria for safe escape distances for airship delivery of antisubmarine warfare special weapons. Restrained response data for 0.40-psi overpressure input were obtained during Shot Franklin with the ZSG-3 No. 77 moored tail to the blast. Unrestrained response data for 0.75-psi overpressure input were obtained during Shot Stokes with the ZSG-3 No. 40 free ballooned, tail to the blast, 300 feetmore » aboveground. The first airship exposed to overpressure experienced a structural failure of the nose cone when it was rammed into the mooring mast, together with a tear of the forward ballonet which necessitated deflation of the envelope. The second airship broke in half and crashed following a circumferential failure of the envelope originating at the bottom of the envelope, forward of the car.« less

Mechanism of delayed intracranial hypertension after cerebroventricular infusions in conscious rats

NASA Technical Reports Server (NTRS)

Morrow, B. A.; Holt, M. R.; Starcevic, V. P.; Keil, L. C.; Severs, W. B.

1992-01-01

Prior studies showed that cerebroventricular infusions of artificial cerebrospinal fluid, 8 microliter/min for 10 min, followed by a 10 min rest and a 24 h infusion of 0.5 microliters/min, raised cerebrospinal fluid pressure (CSFp) of conscious, unrestrained rats after about 2 h. Here, we report that the 10 min infusion alone evoked a delayed, prolonged rise in CSFp. Pressure during the infusion itself rose and recovered quickly, as is usually reported. Pressure/volume tests, used to calculate resistance to outflow (Ro) and compliance (C), revealed that infusions increased Ro and decreased C, after a delay (P less than 0.05). The rise in CSFp after infusion was blocked by pretreatment with acetazolamide + ouabain (P less than 0.05), but the delayed changes in Ro and C were unaffected. We suggest that the 10 min infusion of a sterile, balanced salt solution has a primary effect that increases Ro; as CSF synthesis continues, C is exhausted and the delayed rise in CSFp ensues. This non-traumatic method of raising CSFp may be a useful method to study intracranial fluid dynamics.

Environmental assessment for the Satellite Power System (SPS): studies of honey bees exposed to 2. 45 GHz continuous-wave electromagnetic energy

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

Gary, N E; Westerdahl, B B

1980-12-01

A system for small animal exposure was developed for treating honey bees, Apis mellifera L., in brood and adult stages, with 2.45 GHz continuous wave microwaves at selected power densities and exposure times. Post-treatment brood development was normal and teratological effects were not detected at exposures of 3 to 50 mw/cm/sup 2/ for 30 minutes. Post-treatment survival, longevity, orientation, navigation, and memory of adult bees were also normal after exposures of 3 to 50 mw/cm/sup 2/ for 30 minutes. Post-treatment longevity of confined bees in the laboratory was normal after exposures of 3 to 50 mw/cm/sup 2/ for 24 hours.more » Thermoregulation of brood nest, foraging activity, brood rearing, and social interaction were not affected by chronic exposure to 1 mw/cm/sup 2/ during 28 days. In dynamic behavioral bioassays the frequency of entry and duration of activity of unrestrained, foraging adult bees was identical in microwave-exposed (5 to 40 mw/cm/sup 2/) areas versus control areas.« less

Low-Noise Implantable Electrode

NASA Technical Reports Server (NTRS)

Lund, G. F.

1982-01-01

New implantable electrocardiogram electrode much less sensitive than previous designs to spurious biological potentials. Designed in novel "pocket" configuration, new electrode is intended as sensor for radiotelemetry of biological parameters in experiments on unrestrained subjects. Electrode is esentially squashed cylinder that admits body fluid into interior. Cylinder and electrical lead are made of stainless steel. Spot welding and crimping are used for assembly, rather than soldering.

Volcanic Tremors in the Third Circuit: First Amendment Freedom of Speech Protections through Common Law Authority.

ERIC Educational Resources Information Center

Sanders, Wayne C.

The authority of the First Amendment may transcend the strictures of its original wording, which limits it to proscriptions of federal government suppression of speech. Attempts by some courts to extend First Amendment authority to the workplace is clearly related to the growing criticism of unrestrained managerial dismissal power. The first major…

75 FR 35 - Special Conditions: Airbus Model A318-112 Airplane (S/N 3886); Certification of a Cooktop

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-04

..., include with your comments a self-addressed, stamped postcard on which the docket number appears. We will stamp the date on the postcard and mail it back to you. Background On December 5, 2008, Bizjet... sources and the presence of relatively unrestrained hot cookware and heated food. These may represent...

Hemodynamic alterations in chronically conscious unrestrained diabetic rats

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

Carbonell, L.F.; Salmon, M.G.; Garcia-Estan, J.

1987-05-01

Important cardiovascular dysfunctions have been described in streptozotocin (STZ)-diabetic rats. To determine the influence of these changes on the hemodynamic state and whether insulin treatment can avoid them, different hemodynamic parameters, obtained by the thermodilution method, were studied in STZ-induced (65 mg/kg) diabetic male Wistar rats, as well as in age-control, weight-control, and insulin-treated diabetic ones. Plasma volume was measured by dilution of radioiodinated (/sup 125/I) human serum albumin. All rats were examined in the conscious, unrestrained state 12 wk after induction of diabetes or acidified saline (pH 4.5) injection. At 12 wk of diabetic state most important findings weremore » normotension, high blood volume, bradycardia, increase in stroke volume, cardiac output, and cardiosomatic ratio, and decrease in total peripheral resistance and cardiac contractility and relaxation (dP/dt/sub max/ and dP/dt/sub min/ of left ventricular pressure curves). The insulin-treated diabetic rats did not show any hemodynamic differences when compared with the control animals. These results suggest that important hemodynamic alterations are present in the chronic diabetic states, possibly conditioning congestive heart failure. These alterations can be prevented by insulin treatment.« less

Predictors of restraint use among child occupants.

PubMed

Benedetti, Marco; Klinich, Kathleen D; Manary, Miriam A; Flannagan, Carol A

2017-11-17

The objective of this study was to identify factors that predict restraint use and optimal restraint use among children aged 0 to 13 years. The data set is a national sample of police-reported crashes for years 2010-2014 in which type of child restraint is recorded. The data set was supplemented with demographic census data linked by driver ZIP code, as well as a score for the state child restraint law during the year of the crash relative to best practice recommendations for protecting child occupants. Analysis used linear regression techniques. The main predictor of unrestrained child occupants was the presence of an unrestrained driver. Among restrained children, children had 1.66 (95% confidence interval, 1.27, 2.17) times higher odds of using the recommended type of restraint system if the state law at the time of the crash included requirements based on best practice recommendations. Children are more likely to ride in the recommended type of child restraint when their state's child restraint law includes wording that follows best practice recommendations for child occupant protection. However, state child restraint law requirements do not influence when caregivers fail to use an occupant restraint for their child passengers.

X-Ray based Lung Function measurement-a sensitive technique to quantify lung function in allergic airway inflammation mouse models

NASA Astrophysics Data System (ADS)

Dullin, C.; Markus, M. A.; Larsson, E.; Tromba, G.; Hülsmann, S.; Alves, F.

2016-11-01

In mice, along with the assessment of eosinophils, lung function measurements, most commonly carried out by plethysmography, are essential to monitor the course of allergic airway inflammation, to examine therapy efficacy and to correlate animal with patient data. To date, plethysmography techniques either use intubation and/or restraining of the mice and are thus invasive, or are limited in their sensitivity. We present a novel unrestrained lung function method based on low-dose planar cinematic x-ray imaging (X-Ray Lung Function, XLF) and demonstrate its performance in monitoring OVA induced experimental allergic airway inflammation in mice and an improved assessment of the efficacy of the common treatment dexamethasone. We further show that XLF is more sensitive than unrestrained whole body plethysmography (UWBP) and that conventional broncho-alveolar lavage and histology provide only limited information of the efficacy of a treatment when compared to XLF. Our results highlight the fact that a multi-parametric imaging approach as delivered by XLF is needed to address the combined cellular, anatomical and functional effects that occur during the course of asthma and in response to therapy.

Triggers of Eating in Everyday Life

PubMed Central

Tomiyama, A. Janet; Mann, Traci; Comer, Lisa

2009-01-01

Understanding the triggers of eating in everyday life is crucial for the creation of interventions to promote healthy eating and to prevent overeating. Here, the proximal predictors of eating are explored in a natural setting. Research from laboratory settings suggests that restrained eaters overeat after experiencing anxiety, distraction, and the presence of positive or negative moods, but not hunger; whereas the only factor that triggers eating in unrestrained eaters is hunger. In this study, 137 female participants reported hourly for two days on these potential predictors and their eating using electronic diaries, allowing us to establish the relationships between these factors while participants went about their normal daily activities. The main outcome variables were the number of servings eaten and whether or not food was eaten. Contrary to findings from laboratory settings, in everyday life restrained eaters (1) did not overeat in response to anxiety; (2) ate less in the presence of positive or negative moods; and (3) ate more in response to hunger. The relationships between these factors and eating among unrestrained eaters were closer to those found in laboratory settings. In conclusion, predictors of eating must be studied in everyday life to develop successful interventions. PMID:18773931

Catch-up saccades in head-unrestrained conditions reveal that saccade amplitude is corrected using an internal model of target movement

PubMed Central

Daye, Pierre M.; Blohm, Gunnar; Lefèvre, Phillippe

2014-01-01

This study analyzes how human participants combine saccadic and pursuit gaze movements when they track an oscillating target moving along a randomly oriented straight line with the head free to move. We found that to track the moving target appropriately, participants triggered more saccades with increasing target oscillation frequency to compensate for imperfect tracking gains. Our sinusoidal paradigm allowed us to show that saccade amplitude was better correlated with internal estimates of position and velocity error at saccade onset than with those parameters 100 ms before saccade onset as head-restrained studies have shown. An analysis of saccadic onset time revealed that most of the saccades were triggered when the target was accelerating. Finally, we found that most saccades were triggered when small position errors were combined with large velocity errors at saccade onset. This could explain why saccade amplitude was better correlated with velocity error than with position error. Therefore, our results indicate that the triggering mechanism of head-unrestrained catch-up saccades combines position and velocity error at saccade onset to program and correct saccade amplitude rather than using sensory information 100 ms before saccade onset. PMID:24424378

The role of memory in the relationship between attention toward thin-ideal media and body dissatisfaction.

PubMed

Jiang, Michelle Y W; Vartanian, Lenny R

2016-03-01

This study examined the causal relationship between attention and memory bias toward thin-body images, and the indirect effect of attending to thin-body images on women's body dissatisfaction via memory. In a 2 (restrained vs. unrestrained eaters) × 2 (long vs. short exposure) quasi-experimental design, female participants (n = 90) were shown images of thin models for either 7 s or 150 ms, and then completed a measure of body dissatisfaction and a recognition test to assess their memory for the images. Both restrained and unrestrained eaters in the long exposure condition had better recognition memory for images of thin models than did those in the short exposure condition. Better recognition memory for images of thin models was associated with lower body dissatisfaction. Finally, exposure duration to images of thin models had an indirect effect on body dissatisfaction through recognition memory. These findings suggest that memory for body-related information may be more critical in influencing women's body image than merely the exposure itself, and that targeting memory bias might enhance the effectiveness of cognitive bias modification programs.

Residual Strength Analyses of Riveted Lap-Splice Joints

NASA Technical Reports Server (NTRS)

Seshadri, B. R.; Newman, J. C., Jr.

2000-01-01

The objective of this paper was to analyze the crack-linkup behavior in riveted-stiffened lap-splice joint panels with small multiple-site damage (MSD) cracks at several adjacent rivet holes. Analyses are based on the STAGS (STructural Analysis of General Shells) code with the critical crack-tip-opening angle (CTOA) fracture criterion. To account for high constraint around a crack front, the "plane strain core" option in STAGS was used. The importance of modeling rivet flexibility with fastener elements that accurately model load transfer across the joint is discussed. Fastener holes are not modeled but rivet connectivity is accounted for by attaching rivets to the sheet on one side of the cracks that simulated both the rivet diameter and MSD cracks. Residual strength analyses made on 2024-T3 alloy (1.6-mm thick) riveted-lap-splice joints with a lead crack and various size MSD cracks were compared with test data from Boeing Airplane Company. Analyses were conducted for both restrained and unrestrained buckling conditions. Comparison of results from these analyses and results from lap-splice-joint test panels, which were partially restrained against buckling indicate that the test results were bounded by the failure loads predicted by the analyses with restrained and unrestrained conditions.

Regional differences in hyoid muscle activity and length-dynamics during mammalian head-shaking

PubMed Central

Wentzel, Sarah E.; Konow, Nicolai; German, Rebecca Z.

2010-01-01

The sternohyoid (SH) and geniohyoid (GH) are antagonist strap-muscles that are active during a number of different behaviors, including sucking, intraoral transport, swallowing, breathing, and extension/flexion of the neck. Because these muscles have served different functions through the evolutionary history of vertebrates, it is quite likely they will have complex patterns of electrical activity and muscle fiber contraction. Different regions of the sternohyoid exhibit different contraction and activity patterns during a swallow. We examined the dynamics of the sternohyoid and geniohyoid muscles during an unrestrained, and vigorous head-shake behavior in an animal model of human head, neck and hyolingual movement. A gentle touch to infant pig ears elicited a head shake of several head revolutions. Using sonomicrometry and intramuscular EMG we measured regional (within) muscle strain and activity in SH and GH. We found that EMG was consistent across three regions (anterior, belly and posterior) of each muscle. Changes in muscle length however, were more complex. In the SH, mid-belly length-change occurred out of phase with the anterior and posterior end-regions, but with a zero-lag timing; the anterior region shortened prior to the posterior. In the GH, the anterior region shortened prior to, and out of phase with the mid-belly and posterior regions. Head-shaking is a relatively simple reflex behavior, yet the underlying patterns of muscle length-dynamics and EMG activity are not. The regional complexity in SH and GH, similar to regionalization of SH during swallowing, suggests that these ‘simple hyoid strap muscles’ are more complex than textbooks often suggest. PMID:21370479

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

Joshua Vermaas | NREL

Science.gov Websites

molecular dynamics simulations to explore biological interfaces, such as those found at the cell membrane or in lignocellulosic biomass. In particular, molecular dynamics can see in molecular detail the research toward fruitful results. Areas of Expertise Molecular dynamics Compound parameterization

Bioengineering and Coordination of Regulatory Networks and Intracellular Complexes to Maximize Hydrogen Production by Phototrophic Microorganisms

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

Tabita, F. Robert

2013-07-30

In this study, the Principal Investigator, F.R. Tabita has teamed up with J. C. Liao from UCLA. This project's main goal is to manipulate regulatory networks in phototrophic bacteria to affect and maximize the production of large amounts of hydrogen gas under conditions where wild-type organisms are constrained by inherent regulatory mechanisms from allowing this to occur. Unrestrained production of hydrogen has been achieved and this will allow for the potential utilization of waste materials as a feed stock to support hydrogen production. By further understanding the means by which regulatory networks interact, this study will seek to maximize themore » ability of currently available “unrestrained” organisms to produce hydrogen. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Moreover, due to their great metabolic versatility, such organisms highly regulate these processes in the cell and since virtually all such capabilities are dispensable, excellent experimental systems to study aspects of molecular control and biochemistry/physiology are available.« less

Molecular Dynamics Analysis of Lysozyme Protein in Ethanol- Water Mixed Solvent

DTIC Science & Technology

2012-01-01

molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different concentrations of water-ethanol mixtures as...understood. This work focuses on detailed molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different...using GROMACS molecular dynamics simulation (MD) code. Compared to water environment, the lysozyme structure showed remarkable changes in water

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Injuries to Occupants of U.S. Army High Mobility Multipurpose Wheeled Vehicles in Rollover Accidents, 1989-2007

DTIC Science & Technology

2013-04-02

This research conducted on occupant injuries in U.S. Army High Mobility Multipurpose Wheeled Vehicle (HMMWV) rollover accidents was presented at the ...12  1 Introduction The High Mobility Multipurpose Wheeled Vehicle (HMMWV) is...Soldiers may experience the full impact of jarring forces and/or projectile forces of unrestrained equipment. Rollovers are especially hazardous to

The Impact of Overeating on Mood Among Unrestrained College Females

DTIC Science & Technology

2005-11-28

term caloric restriction, although those participants scoring high on this scale may not be in a hypocaloric state (Gorman & Allison, 1995...nervosa (Garner et al., 1983). The subscales of the EDI include: Drive for Thinness (DT; excessive concern with dieting , preoccupation with weight...Wadden, T.A. (2001). Restrictive dieting versus “undieting”: Effects on eating regulation in obese clinic attenders. Addictive Behaviors, 26, 253-266

Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

DTIC Science & Technology

2009-11-01

dynamics of the complex predicted by multiple molecular dynamics simulations , and discuss further structural optimization to achieve better in vivo efficacy...complex with BoNTAe and the dynamics of the complex predicted by multiple molecular dynamics simulations (MMDSs). On the basis of the 3D model, we discuss...is unlimited whereas AHP exhibited 54% inhibition under the same conditions (Table 1). Computer Simulation Twenty different molecular dynamics

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)

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

DTIC Science & Technology

2010-01-01

formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage...ad hoc force term in the SGLD model. Introduction Molecular dynamics (MD) simulations of small proteins provide insight into the mechanisms and... molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All

Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

DTIC Science & Technology

2008-07-17

Membrane insertion profiles of peptides probed by molecular dynamics simulations In-Chul Yeh,* Mark A. Olson,# Michael S. Lee,*#§ and Anders...a methodology based on molecular dynamics simulation techniques to probe the insertion profiles of small peptides across the membrane interface. The...profiles of peptides probed by molecular dynamics simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Parallel Fast Multipole Method For Molecular Dynamics

DTIC Science & Technology

2007-06-01

Parallel Fast Multipole Method For Molecular Dynamics THESIS Reid G. Ormseth, Captain, USAF AFIT/GAP/ENP/07-J02 DEPARTMENT OF THE AIR FORCE AIR...the United States Government. AFIT/GAP/ENP/07-J02 Parallel Fast Multipole Method For Molecular Dynamics THESIS Presented to the Faculty Department of...has also been provided by ‘The Art of Molecular Dynamics Simulation ’ by Dennis Rapaport. This work is the clearest treatment of the Fast Multipole

Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a Membrane Bilayer

DTIC Science & Technology

2008-07-01

Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a Membrane Bilayer Mark A. Olson1, In...presents replica-exchange molecular dynamics simulations of the folding and insertion of a 16- residue Ebola virus fusion peptide into a membrane...separate calculated structures into conformational basins. 2.1 Simulation models Molecular dynamics simulations were performed using the all-atom

Improvised Incendiary Devices: Risk Assessment, Threats, Vulnerabilities and Consequences

DTIC Science & Technology

2006-09-01

terrorism, Baird substitutes “the unlawful use of force and violence ” with “the use of incendiary attacks” to intimidate or coerce a government, the...targeting of noncombatants; political motivation; violence with 35 ALF/ELF, Arson Around with Auntie A.L.F: Your Guide for Putting the Heat on Animal...contends that future pyro-terrorist attacks will lean toward unrestrained violence for maximum psychological impact and challenge the conventional

Visual–Motor Transformations Within Frontal Eye Fields During Head-Unrestrained Gaze Shifts in the Monkey

PubMed Central

Sajad, Amirsaman; Sadeh, Morteza; Keith, Gerald P.; Yan, Xiaogang; Wang, Hongying; Crawford, John Douglas

2015-01-01

A fundamental question in sensorimotor control concerns the transformation of spatial signals from the retina into eye and head motor commands required for accurate gaze shifts. Here, we investigated these transformations by identifying the spatial codes embedded in visually evoked and movement-related responses in the frontal eye fields (FEFs) during head-unrestrained gaze shifts. Monkeys made delayed gaze shifts to the remembered location of briefly presented visual stimuli, with delay serving to dissociate visual and movement responses. A statistical analysis of nonparametric model fits to response field data from 57 neurons (38 with visual and 49 with movement activities) eliminated most effector-specific, head-fixed, and space-fixed models, but confirmed the dominance of eye-centered codes observed in head-restrained studies. More importantly, the visual response encoded target location, whereas the movement response mainly encoded the final position of the imminent gaze shift (including gaze errors). This spatiotemporal distinction between target and gaze coding was present not only at the population level, but even at the single-cell level. We propose that an imperfect visual–motor transformation occurs during the brief memory interval between perception and action, and further transformations from the FEF's eye-centered gaze motor code to effector-specific codes in motor frames occur downstream in the subcortical areas. PMID:25491118

"Just looking at food makes me gain weight": experimental induction of thought-shape fusion in eating-disordered and non-eating-disordered women.

PubMed

Coelho, Jennifer S; Carter, Jacqueline C; McFarlane, Traci; Polivy, Janet

2008-02-01

Thought-shape fusion (TSF) is a cognitive distortion that can be induced experimentally and is associated with eating pathology. The current study was conducted in order to elucidate the effects of TSF induction in females with eating disorders (n=35), as well as in restrained eaters (n=38) and unrestrained eaters (n=39). It was hypothesized that TSF induction would result in anxiety, guilt, increased feelings of fatness, perceived weight gain and feelings of moral wrong-doing relative to an anxiety and control induction. It was further hypothesized that restrained eaters and individuals with eating disorders would exhibit a stronger reaction to a TSF induction than would unrestrained eaters. The results indicated that, as predicted, TSF can be induced in individuals both with and without eating disorders, and individuals with eating disorders reported the highest levels of "state" TSF after the induction relative to the non-clinical controls. However, contrary to expectations, restrained eaters reported higher levels of perceived weight gain and moral wrong-doing after the anxiety induction (but not the TSF induction) relative to the control induction. Potential mechanisms for this pattern of results are discussed, and the clinical implications of research on TSF are also considered.

Electromyographic analysis of rotator cuff muscles in patients with rotator cuff tendinopathy: A systematic review.

PubMed

de Oliveira, Fábio Carlos Lucas; Bouyer, Laurent Julien; Ager, Amanda L; Roy, Jean-Sébastien

2017-08-01

The shoulder is inherently an unstable joint which heavily relies on the neuromuscular activation of the rotator cuff (RC) complex for stability during movement. Currently, there is no consensus regarding how the activity of RC muscles is affected among individuals with a RC tendinopathy (RCTe). This study reviewed the evidence of studies comparing the electromyographic (EMG) activity of any RC muscle of shoulders with a symptomatic RCTe to asymptomatic shoulders. Eight databases were searched. Data from 343 participants (201 symptomatic and 209 asymptomatic shoulders) were analyzed from 10 out of 402 included studies. Strong evidence for the infraspinatus and supraspinatus during isometric contractions and limited evidence for the supraspinatus and infraspinatus during isokinetic contractions suggest that the muscular activity is not altered among individuals with a RCTe during these types of contraction. Very limited evidence indicates reduced muscle activity for the infraspinatus and subscapularis in the presence of a RCTe during isotonic contractions, and no alterations for the supraspinatus or teres minor were identified. Lastly, conflicting to moderate evidence suggests alterations in RC muscle activity during unrestrained movements and swimming. These findings indicate that EMG deficits associated with a RCTe can best be appreciated during unrestrained movements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Coordination of eye and head components of movements evoked by stimulation of the paramedian pontine reticular formation.

PubMed

Gandhi, Neeraj J; Barton, Ellen J; Sparks, David L

2008-07-01

Constant frequency microstimulation of the paramedian pontine reticular formation (PPRF) in head-restrained monkeys evokes a constant velocity eye movement. Since the PPRF receives significant projections from structures that control coordinated eye-head movements, we asked whether stimulation of the pontine reticular formation in the head-unrestrained animal generates a combined eye-head movement or only an eye movement. Microstimulation of most sites yielded a constant-velocity gaze shift executed as a coordinated eye-head movement, although eye-only movements were evoked from some sites. The eye and head contributions to the stimulation-evoked movements varied across stimulation sites and were drastically different from the lawful relationship observed for visually-guided gaze shifts. These results indicate that the microstimulation activated elements that issued movement commands to the extraocular and, for most sites, neck motoneurons. In addition, the stimulation-evoked changes in gaze were similar in the head-restrained and head-unrestrained conditions despite the assortment of eye and head contributions, suggesting that the vestibulo-ocular reflex (VOR) gain must be near unity during the coordinated eye-head movements evoked by stimulation of the PPRF. These findings contrast the attenuation of VOR gain associated with visually-guided gaze shifts and suggest that the vestibulo-ocular pathway processes volitional and PPRF stimulation-evoked gaze shifts differently.

Next generation extended Lagrangian first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Niklasson, Anders M. N.

2017-08-01

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Next generation extended Lagrangian first principles molecular dynamics.

PubMed

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

The Design, Synthesis, and Study of Solid-State Molecular Rotors: Structure/Function Relationships for Condensed-Phase Anisotropic Dynamics

NASA Astrophysics Data System (ADS)

Vogelsberg, Cortnie Sue

Amphidynamic crystals are an extremely promising platform for the development of artificial molecular machines and stimuli-responsive materials. In analogy to skeletal muscle, their function will rely upon the collective operation of many densely packed molecular machines (i.e. actin-bound myosin) that are self-assembled in a highly organized anisotropic medium. By choosing lattice-forming elements and moving "parts" with specific functionalities, individual molecular machines may be synthesized and self-assembled in order to carry out desirable functions. In recent years, efforts in the design of amphidynamic materials based on molecular gyroscopes and compasses have shown that a certain amount of free volume is essential to facilitate internal rotation and reorientation within a crystal. In order to further establish structure/function relationships to advance the development of increasingly complex molecular machinery, molecular rotors and a molecular "spinning" top were synthesized and incorporated into a variety of solid-state architectures with different degrees of periodicity, dimensionality, and free volume. Specifically, lamellar molecular crystals, hierarchically ordered periodic mesoporous organosilicas, and metal-organic frameworks were targeted for the development of solid-state molecular machines. Using an array of solid-state nuclear magnetic resonance spectroscopy techniques, the dynamic properties of these novel molecular machine assemblies were determined and correlated with their corresponding structural features. It was found that architecture type has a profound influence on functional dynamics. The study of layered molecular crystals, composed of either molecular rotors or "spinning" tops, probed functional dynamics within dense, highly organized environments. From their study, it was discovered that: 1) crystallographically distinct sites may be utilized to differentiate machine function, 2) halogen bonding interactions are sufficiently strong to direct an assembly of molecular machines, 3) the relative flexibility of the crystal environment proximate to a dynamic component may have a significant effect on its function, and, 4) molecular machines, which possess both solid-state photochemical reactivity and dynamics may show complex reaction kinetics if the correlation time of the dynamic process and the lifetime of the excited state occur on the same time scale and the dynamic moiety inherently participates as a reaction intermediate. The study of periodic mesoporous organosilica with hierarchical order probed molecular dynamics within 2D layers of molecular rotors, organized in only one dimension and with ca. 50% exposed to the mesopore free volume. From their study, it was discovered that: 1) molecular rotors, which comprise the layers of the mesopore walls, form a 2D rotational glass, 2) rotator dynamics within the 2D rotational glass undergo a transition to a 2D rotational fluid, and, 3) a 2D rotational glass transition may be exploited to develop hyper-sensitive thermally activated molecular machines. The study of a metal-organic framework assembled from molecular rotors probed dynamics in a periodic three-dimensional free-volume environment, without the presence of close contacts. From the study of this solid-state material, it was determined that: 1) the intrinsic electronic barrier is one of the few factors, which may affect functional dynamics in a true free-volume environment, and, 2) molecular machines with dynamic barriers <

Chronic Myeloid Leukemia in the Era of Tyrosine Kinase Inhibitors: An Evolving Paradigm of Molecularly Targeted Therapy.

PubMed

Ali, Mohamed A M

2016-08-01

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm, characterized by the unrestrained expansion of pluripotent hematopoietic stem cells. CML was the first malignancy in which a unique chromosomal abnormality was identified and a pathophysiologic association was suggested. The hallmark of CML is a reciprocal chromosomal translocation between the long arms of chromosomes 9 and 22, t(9; 22)(q34; q11), creating a derivative 9q+ and a shortened 22q-. The latter, known as the Philadelphia (Ph) chromosome, harbors the breakpoint cluster region-abelson (BCR-ABL) fusion gene, encoding the constitutively active BCR-ABL tyrosine kinase that is necessary and sufficient for initiating CML. The successful implementation of tyrosine kinase inhibitors (TKIs) for the treatment of CML remains a flagship for molecularly targeted therapy in cancer. TKIs have changed the clinical course of CML; however, some patients nonetheless demonstrate primary or secondary resistance to such therapy and require an alternative therapeutic strategy. Therefore, the assessment of early response to treatment with TKIs has become an important tool in the clinical monitoring of CML patients. Although mutations in the BCR-ABL have proven to be the most prominent mechanism of resistance to TKIs, other mechanisms-either rendering the leukemic cells still dependent on BCR-ABL activity or supporting oncogenic properties of the leukemic cells independent of BCR-ABL signaling-have been identified. This article provides an overview of the current understanding of CML pathogenesis; recommendations for diagnostic tools, treatment strategies, and management guidelines; and highlights the BCR-ABL-dependent and -independent mechanisms that contribute to the development of resistance to TKIs.

Inflammasome and Autophagy Regulation: A Two-way Street

PubMed Central

Qian, Sun; Fan, Jie; Billiar, Timothy R; Scott, Melanie J

2017-01-01

Inflammation plays a significant role in protecting hosts against pathogens. Inflammation induced by noninfectious endogenous agents can be detrimental and, if excessive, can result in organ and tissue damage. The inflammasome is a major innate immune pathway that can be activated via both exogenous pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs). Inflammasome activation involves formation and oligomerization of a protein complex including a nucleotide oligomerization domain (NOD)-like receptor (NLR), an adaptor protein and pro-caspase-1. This then allows cleavage and activation of caspase-1, followed by downstream cleavage and release of proinflammatory cytokines interleukin (IL)-1β and IL-18 from innate immune cells. Hyperinflammation caused by unrestrained inflammasome activation is linked with multiple inflammatory diseases, including inflammatory bowel disease, Alzheimer’s disease and multiple sclerosis. So there is an understandable rush to understand mechanisms that regulate such potent inflammatory pathways. Autophagy has now been identified as a main regulator of inflammasomes. Autophagy is a vital intracellular process involved in cellular homeostasis, recycling and removal of damaged organelles (eg, mitochondria) and intracellular pathogens. Autophagy is regulated by proteins that are important in endosomal/phagosomal pathways, as well as by specific autophagy proteins coded for by autophagy-related genes. Cytosolic components are surrounded and contained by a double-membraned vesicle, which then fuses with lysosomes to enable degradation of the contents. Autophagic removal of intracellular DAMPs, inflammasome components or cytokines can reduce inflammasome activation. Similarly, inflammasomes can regulate the autophagic process, allowing for a two-way mutual regulation of inflammation that may hold the key for treatment of multiple diseases. PMID:28741645

On the nature of motor planning variables during arm pointing movement: Compositeness and speed dependence.

PubMed

Vu, Van Hoan; Isableu, Brice; Berret, Bastien

2016-07-22

The purpose of this study was to investigate the nature of the variables and rules underlying the planning of unrestrained 3D arm reaching. To identify whether the brain uses kinematic, dynamic and energetic values in an isolated manner or combines them in a flexible way, we examined the effects of speed variations upon the chosen arm trajectories during free arm movements. Within the optimal control framework, we uncovered which (possibly composite) optimality criterion underlays at best the empirical data. Fifteen participants were asked to perform free-endpoint reaching movements from a specific arm configuration at slow, normal and fast speeds. Experimental results revealed that prominent features of observed motor behaviors were significantly speed-dependent, such as the chosen reach endpoint and the final arm posture. Nevertheless, participants exhibited different arm trajectories and various degrees of speed dependence of their reaching behavior. These inter-individual differences were addressed using a numerical inverse optimal control methodology. Simulation results revealed that a weighted combination of kinematic, energetic and dynamic cost functions was required to account for all the critical features of the participants' behavior. Furthermore, no evidence for the existence of a speed-dependent tuning of these weights was found, thereby suggesting subject-specific but speed-invariant weightings of kinematic, energetic and dynamic variables during the motor planning process of free arm movements. This suggested that the inter-individual difference of arm trajectories and speed dependence was not only due to anthropometric singularities but also to critical differences in the composition of the subjective cost function. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto

2013-07-01

The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.

Surface induced molecular dynamics of thin lipid films confined to submicron cavities: A 1H multiple-quantum NMR study

NASA Astrophysics Data System (ADS)

Jagadeesh, B.; Prabhakar, A.; Demco, D. E.; Buda, A.; Blümich, B.

2005-03-01

The dynamics and molecular order of thin lipid (lecithin) films confined to 200, 100 and 20 nm cylindrical pores with varying surface coverage, were investigated by 1H multiple-quantum NMR. The results show that the molecular dynamics in the surface controlled layers are less hindered compared to those in the bulk. Dynamic heterogeneity among terminal CH 3 groups is evident. Enhanced dynamic freedom is observed for films with area per molecule, ˜ 128 Å 2. The results are discussed in terms of changes in the lipid molecular organization with respect to surface concentration, its plausible motional modes and dynamic heterogeneity.

The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations

PubMed Central

Boršnik, Urban; Miller, Benjamin T.; Brooks, Bernard R.; Janežič, Dušanka

2011-01-01

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Biomedical Analyses, Tolerance, and Mitigation of Acute and Chronic Trauma

DTIC Science & Technology

2012-07-01

aligned such that in one group the heads were constrained to rotate in the mid-sagittal line and in the other group head was angulated about all three...the restrained than in the unrestrained groups indicating the role of posture on trauma. Uniaxial force gages introduced into the C5-C6...directions for future experimental design. Tests conducted on the Hybrid-III ATD with both curved and straightened lumbar spines demonstrated that

Irradiation behavior of U 6Mn-Al dispersion fuel elements

NASA Astrophysics Data System (ADS)

Meyer, M. K.; Wiencek, T. C.; Hayes, S. L.; Hofman, G. L.

2000-02-01

Irradiation testing of U 6Mn-Al dispersion fuel miniplates was conducted in the Oak Ridge Research Reactor (ORR). Post-irradiation examination showed that U 6Mn in an unrestrained plate configuration performs similarly to U 6Fe under irradiation, forming extensive and interlinked fission gas bubbles at a fission density of approximately 3×10 27 m-3. Fuel plate failure occurs by fission gas pressure driven `pillowing' on continued irradiation.

Clonidine and Cortical Plasticity: Possible Evidence for Noradrenergic Involvement.

DTIC Science & Technology

1984-10-31

Recording, MHPG, Development of CNS, Plasticity. INTRODUCTION Temporary closure of one eye for even a short duration during a three week to three...bottom line shows the daily schedule of injections along with the cycle of general illumination in the colony. EiLug.2- Composite ocular dominance...Neureaci., 4 (1984) 1354. 1360. 15. DEGRELL, I., VENNER , K., KUMMER, P., and STOCK, G., Monoamine metabolites in the CSF of conscious unrestrained cats

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-01

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

How Dynamic Visualization Technology Can Support Molecular Reasoning

ERIC Educational Resources Information Center

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

PubMed

Galindo-Murillo, Rodrigo; Roe, Daniel R; Cheatham, Thomas E

2015-05-01

The structure and dynamics of DNA are critically related to its function. Molecular dynamics simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Molecular dynamics simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale molecular dynamics performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. These molecular dynamics simulations-including one of the longest simulations of DNA published to date at ~44μs-surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale. We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. With access to large-scale GPU resources or the specialized MD engine "Anton" it is possible for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. This article is part of a Special Issue entitled: Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Molecular motors interacting with their own tracks

NASA Astrophysics Data System (ADS)

Artyomov, Max N.; Morozov, Alexander Yu.; Kolomeisky, Anatoly B.

2008-04-01

Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state “burnt-bridge” models. Molecular motors are viewed as diffusing particles that can asymmetrically break or rebuild periodically distributed weak links when passing over them. Our explicit calculations of dynamic properties show that coupling the transport of the unbiased molecular motor with the bridge-burning mechanism leads to a directed motion that lowers fluctuations and produces a dynamic transition in the limit of low concentration of weak links. Interaction between the backward biased molecular motor and the bridge-burning mechanism yields a complex dynamic behavior. For the reversible dissociation the backward motion of the molecular motor is slowed down. There is a change in the direction of the molecular motor’s motion for some range of parameters. The molecular motor also experiences nonmonotonic fluctuations due to the action of two opposing mechanisms: the reduced activity after the burned sites and locking of large fluctuations. Large spatial fluctuations are observed when two mechanisms are comparable. The properties of the molecular motor are different for the irreversible burning of bridges where the velocity and fluctuations are suppressed for some concentration range, and the dynamic transition is also observed. Dynamics of the system is discussed in terms of the effective driving forces and transitions between different diffusional regimes.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

NASA Astrophysics Data System (ADS)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

Advanced Polymer Network Structures

DTIC Science & Technology

2016-02-01

double networks in a single step was identified from coarse-grained molecular dynamics simulations of polymer solvents bearing rigid side chains dissolved...in a polymer network. Coarse-grained molecular dynamics simulations also explored the mechanical behavior of traditional double networks and...DRI), polymer networks, polymer gels, molecular dynamics simulations , double networks 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

PubMed Central

2017-01-01

Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular biodynamers are commonly produced in aqueous media under mild or even physiological conditions to suit their biorelated applications. In contrast to static biopolymers emphasizing structural stability and unity by using irreversible covalent bonds, molecular biodynamers are seeking relative structural adaptability and diversity through the formation of reversible covalent bonds. Based on these considerations, molecular biodynamers are capable of reorganizing their monomers, generating, identifying, and amplifying the fittest structures in response to environmental factors. Hence, molecular biodynamers have received considerable research attention over the past decades. Accordingly, the construction of molecular biodynamers through equilibrium polymerization of nucleobase-, carbohydrate- or amino-acid-based monomers can lead to the fabrication of dynamic analogues of nucleic acids (DyNAs), polysaccharides (glycodynamers), or proteins (dynamic proteoids), respectively. In this Account, we summarize recent advances in developing different types of molecular biodynamers as structural or functional biomimetics of biopolymers, including DyNAs, glycodynamers, and dynamic proteoids. We introduce how chemists utilize various reversible reactions to generate molecular biodynamers with specific sequences and well-ordered structures in aqueous medium. We also discuss and list their potential applications in various research fields, such as drug delivery, drug discovery, gene sensing, cancer diagnosis, and treatment. PMID:28169527

Molecular dynamics simulations of large macromolecular complexes.

PubMed

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

2015-04-01

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Generalized Green's function molecular dynamics for canonical ensemble simulations

NASA Astrophysics Data System (ADS)

Coluci, V. R.; Dantas, S. O.; Tewary, V. K.

2018-05-01

The need of small integration time steps (˜1 fs) in conventional molecular dynamics simulations is an important issue that inhibits the study of physical, chemical, and biological systems in real timescales. Additionally, to simulate those systems in contact with a thermal bath, thermostating techniques are usually applied. In this work, we generalize the Green's function molecular dynamics technique to allow simulations within the canonical ensemble. By applying this technique to one-dimensional systems, we were able to correctly describe important thermodynamic properties such as the temperature fluctuations, the temperature distribution, and the velocity autocorrelation function. We show that the proposed technique also allows the use of time steps one order of magnitude larger than those typically used in conventional molecular dynamics simulations. We expect that this technique can be used in long-timescale molecular dynamics simulations.

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

PubMed

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

2014-01-01

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

Molecular Dynamics Simulations and XAFS (MD-XAFS)

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

Schenter, Gregory K.; Fulton, John L.

2017-01-20

MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

Chimpanzee sleep stages.

NASA Technical Reports Server (NTRS)

Freemon, F. R.; Mcnew, J. J.; Adey, W. R.

1971-01-01

The electroencephalogram and electro-oculogram of two unrestrained juvenile chimpanzees was monitored for 7 consecutive nights using telemetry methods. Of the sleeping time, 23% was spent in the rapid eye movement of REM type of sleep, whereas 8, 4, 15, and 10% were spent in non-REM stages 1 through 4, respectively. Seven to nine periods of REM sleep occurred per night. The average time from the beginning of one REM period to the beginning of the next was approximately 85 min.

Non-effect of hexamethonium, a ganglionic blocker, on the response of ileal apolipoprotein A-IV mRNA following a massive small bowel resection in rats.

PubMed

Sonoyama, K; Fujiwara, R; Kasai, T

2000-06-01

An intravenous infusion of hexamethonium, a ganglionic blocker, did not affect the increase in the apolipoprotein A-IV mRNA level in the residual ileum following a massive small bowel resection in unrestrained conscious rats. The result suggests that upregulation of the apolipoprotein A-IV gene in the residual ileum is not mediated by a neural pathway, including the nicotinic synapse route.

Techniques for chronic monitoring of brain activity in freely moving sheep using wireless EEG recording.

PubMed

Perentos, N; Nicol, A U; Martins, A Q; Stewart, J E; Taylor, P; Morton, A J

2017-03-01

Large mammals with complex central nervous systems offer new possibilities for translational research into basic brain function. Techniques for monitoring brain activity in large mammals, however, are not as well developed as they are in rodents. We have developed a method for chronic monitoring of electroencephalographic (EEG) activity in unrestrained sheep. We describe the methods for behavioural training prior to implantation, surgical procedures for implantation, a protocol for reliable anaesthesia and recovery, methods for EEG data collection, as well as data pertaining to suitability and longevity of different types of electrodes. Sheep tolerated all procedures well, and surgical complications were minimal. Electrode types used included epidural and subdural screws, intracortical needles and subdural disk electrodes, with the latter producing the best and most reliable results. The implants yielded longitudinal EEG data of consistent quality for periods of at least a year, and in some cases up to 2 years. This is the first detailed methodology to be described for chronic brain function monitoring in freely moving unrestrained sheep. The developed method will be particularly useful in chronic investigations of brain activity during normal behaviour that can include sleep, learning and memory. As well, within the context of disease, the method can be used to monitor brain pathology or the progress of therapeutic trials in transgenic or natural disease models in sheep. Copyright © 2016 Elsevier B.V. All rights reserved.

Driver seat belt use indicates decreased risk for child passengers in a motor vehicle crash.

PubMed

Olsen, Cody S; Cook, Lawrence J; Keenan, Heather T; Olson, Lenora M

2010-03-01

We examined the association between driver restraint use and child emergency department (ED) evaluation following a motor vehicle crash (MVC). This cohort study included child passengers aged 0-12 years riding with an adult driver aged 21 years or older involved in a MVC in Utah from 1999 to 2004. The 6 years of Utah MVC records were probabilistically linked to statewide Utah ED records. We estimated the relative risk of ED evaluation following a MVC for children riding with restrained versus unrestrained drivers. Generalized estimating equations were used to calculate relative risks adjusted for child, driver, and crash characteristics. Six percent (6%) of children riding with restrained adult drivers were evaluated in the ED compared to twenty-two percent (22%) of children riding with unrestrained adult drivers following a MVC (relative risk 0.29, 95% confidence interval 0.26-0.32). After adjusting for child, vehicle, and crash characteristics, the relative risk of child ED evaluation associated with driver restraint remained significant (relative risk 0.82, 95% confidence interval 0.72-0.94). Driver restraint use was associated with child restraint use, less alcohol/drug involvement, and lower relative risk of severe collision types (head-on, rollover). Driver seat belt use is associated with decreased risk of ED evaluation for child passengers in the event of a MVC. Copyright 2009 Elsevier Ltd. All rights reserved.

Visual-Motor Transformations Within Frontal Eye Fields During Head-Unrestrained Gaze Shifts in the Monkey.

PubMed

Sajad, Amirsaman; Sadeh, Morteza; Keith, Gerald P; Yan, Xiaogang; Wang, Hongying; Crawford, John Douglas

2015-10-01

A fundamental question in sensorimotor control concerns the transformation of spatial signals from the retina into eye and head motor commands required for accurate gaze shifts. Here, we investigated these transformations by identifying the spatial codes embedded in visually evoked and movement-related responses in the frontal eye fields (FEFs) during head-unrestrained gaze shifts. Monkeys made delayed gaze shifts to the remembered location of briefly presented visual stimuli, with delay serving to dissociate visual and movement responses. A statistical analysis of nonparametric model fits to response field data from 57 neurons (38 with visual and 49 with movement activities) eliminated most effector-specific, head-fixed, and space-fixed models, but confirmed the dominance of eye-centered codes observed in head-restrained studies. More importantly, the visual response encoded target location, whereas the movement response mainly encoded the final position of the imminent gaze shift (including gaze errors). This spatiotemporal distinction between target and gaze coding was present not only at the population level, but even at the single-cell level. We propose that an imperfect visual-motor transformation occurs during the brief memory interval between perception and action, and further transformations from the FEF's eye-centered gaze motor code to effector-specific codes in motor frames occur downstream in the subcortical areas. © The Author 2014. Published by Oxford University Press.

The energetic, physiological, and behavioral response of lemon sharks (Negaprion brevirostris) to simulated longline capture.

PubMed

Bouyoucos, Ian A; Suski, Cory D; Mandelman, John W; Brooks, Edward J

2017-05-01

Commercial fisheries bycatch is a considerable threat to elasmobranch population recovery, and techniques to mitigate sub-lethal consequences can be improved with data on the energetic, physiological, and behavioral response of individuals to capture. This study sought to estimate the effects of simulated longline capture on the behavior, energy use, and physiological stress of juvenile lemon sharks (Negaprion brevirostris). Captive sharks equipped with acceleration biologgers were subjected to 1h of simulated longline capture. Swimming behaviors were identified from acceleration data using a machine-learning algorithm, energetic costs were estimated using accelerometer-calibrated relationships and respirometry, and physiological stress was quantified with point-of-care blood analyzers. During capture, sharks exhibited nine-fold increases in the frequency of burst swimming, 98% reductions in resting, and swam as often as unrestrained sharks. Aerobic metabolic rates during capture were 8% higher than for unrestrained sharks, and accounted for a 57.7% increase in activity costs when excess post-exercise oxygen consumption was included. Lastly, sharks exhibited significant increases in blood lactate and glucose, but no change in blood pH after 1h of capture. Therefore, these results provide preliminary insight into the behavioral and energetic responses of sharks to capture, and have implications for mitigating sub-lethal consequences of capture for sharks as commercial longline bycatch. Copyright © 2017 Elsevier Inc. All rights reserved.

Restraint use among northwest American Indian children traveling in motor vehicles.

PubMed

Lapidus, Jodi A; Smith, Nicole H; Ebel, Beth E; Romero, Francine C

2005-11-01

We sought to estimate motor vehicle passenger restraint use among Northwest American Indian children 8 years old or younger and to determine factors associated with using proper (i.e., age and weight appropriate) passenger restraint systems. We surveyed vehicles driven by members of 6 tribes in Idaho, Oregon, and Washington. Associations between proper restraint and child, driver, and vehicle characteristics were analyzed using logistic regression for clustered data. We observed 775 children traveling in 574 vehicles; 41% were unrestrained. Proper restraint ranged from 63% among infant seat-eligible children to 11% among booster seat-eligible children and was associated with younger child's age (odds ratio (OR) per year = 0.60; 95% confidence interval (CI) = 0.48, 0.75), seating location (OR front vs rear=0.27; 95% CI=0.16, 0.44), driver seat belt use (OR=2.39; 95% CI=1.51, 3.80), and relationship (OR for nonparent vs parent=0.28; 95% CI=0.14, 0.58). More than half of drivers felt children could use an adult seat belt earlier than recommended guidelines, and 63% did not correctly identify whether their tribe had child safety seat laws. Children in these communities are inadequately restrained. Restraint use was exceedingly low among booster-eligible children and children riding with unrestrained adults. Interventions emphasizing appropriate restraint use and enforcement of passenger safety laws could reduce the risk of injury or death in motor vehicle accidents.

Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS

NASA Astrophysics Data System (ADS)

Fakhardji, W.; Gustafsson, M.

2017-02-01

We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.

Molecular System for the Division of Self-Propelled Oil Droplets by Component Feeding.

PubMed

Banno, Taisuke; Toyota, Taro

2015-06-30

Unique dynamics using inanimate molecular assemblies have drawn a great amount of attention for demonstrating prebiomimetic molecular systems. For the construction of an organized logic combining two fundamental dynamics of life, we demonstrate here a molecular system that exhibits both division and self-propelled motion using oil droplets. The key molecule of this molecular system is a novel cationic surfactant containing a five-membered acetal moiety, and the molecular system can feed the self-propelled oil droplet composed of a benzaldehyde derivative and an alkanol. The division dynamics of the self-propelled oil droplets were observed through the hydrolysis of the cationic surfactant in bulk solution. The mechanism of the current dynamics is argued to be based on the supply of "fresh" oil components in the moving oil droplets, which is induced by the Marangoni instability. We consider this molecular system to be a prototype of self-reproducing inanimate molecular assembly exhibiting self-propelled motion.

Identification of promising DNA GyrB inhibitors for Tuberculosis using pharmacophore-based virtual screening, molecular docking and molecular dynamics studies.

PubMed

Islam, Md Ataul; Pillay, Tahir S

2017-08-01

In this study, we searched for potential DNA GyrB inhibitors using pharmacophore-based virtual screening followed by molecular docking and molecular dynamics simulation approaches. For this purpose, a set of 248 DNA GyrB inhibitors was collected from the literature and a well-validated pharmacophore model was generated. The best pharmacophore model explained that two each of hydrogen bond acceptors and hydrophobicity regions were critical for inhibition of DNA GyrB. Good statistical results of the pharmacophore model indicated that the model was robust in nature. Virtual screening of molecular databases revealed three molecules as potential antimycobacterial agents. The final screened promising compounds were evaluated in molecular docking and molecular dynamics simulation studies. In the molecular dynamics studies, RMSD and RMSF values undoubtedly explained that the screened compounds formed stable complexes with DNA GyrB. Therefore, it can be concluded that the compounds identified may have potential for the treatment of TB. © 2017 John Wiley & Sons A/S.

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

PubMed

Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D

2015-01-01

Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.

Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

NASA Astrophysics Data System (ADS)

Asafi, M. S.; Yildirim, A.; Tekpinar, M.

2016-04-01

Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

Insight into the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

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

Corradini, Dario; Vuilleumier, Rodolphe, E-mail: rodolphe.vuilleumier@ens.fr; Sorbonne Universités, UPMC Univ. Paris 06, PASTEUR, 75005 Paris

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900–1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, wemore » present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture’s self-diffusion coefficients, viscosity, and ionic conductivity.« less

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

Molecular dynamics simulation and NMR investigation of the association of the β-blockers atenolol and propranolol with a chiral molecular micelle

NASA Astrophysics Data System (ADS)

Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

2015-08-01

Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

PubMed

Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

2018-06-01

Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆G binding  = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation ability, drug release and further development of novel liposome-based pH-responsive nano-drug delivery system with refined structural and chemical features of potential lipid molecule for formulation development.

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

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

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

NASA Astrophysics Data System (ADS)

Scukins, Arturs; Bardik, Vitaliy; Pavlov, Evgen; Nerukh, Dmitry

2015-05-01

Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Structural mechanisms of chaperone mediated protein disaggregation

PubMed Central

Sousa, Rui

2014-01-01

The ClpB/Hsp104 and Hsp70 classes of molecular chaperones use ATP hydrolysis to dissociate protein aggregates and complexes, and to move proteins through membranes. ClpB/Hsp104 are members of the AAA+ family of proteins which form ring-shaped hexamers. Loops lining the pore in the ring engage substrate proteins as extended polypeptides. Interdomain rotations and conformational changes in these loops coupled to ATP hydrolysis unfold and pull proteins through the pore. This provides a mechanism that progressively disrupts local secondary and tertiary structure in substrates, allowing these chaperones to dissociate stable aggregates such as β-sheet rich prions or coiled coil SNARE complexes. While the ClpB/Hsp104 mechanism appears to embody a true power-stroke in which an ATP powered conformational change in one protein is directly coupled to movement or structural change in another, the mechanism of force generation by Hsp70s is distinct and less well understood. Both active power-stroke and purely passive mechanisms in which Hsp70 captures spontaneous fluctuations in a substrate have been proposed, while a third proposed mechanism—entropic pulling—may be able to generate forces larger than seen in ATP-driven molecular motors without the conformational coupling required for a power-stroke. The disaggregase activity of these chaperones is required for thermotolerance, but unrestrained protein complex/aggregate dissociation is potentially detrimental. Disaggregating chaperones are strongly auto-repressed, and are regulated by co-chaperones which recruit them to protein substrates and activate the disaggregases via mechanisms involving either sequential transfer of substrate from one chaperone to another and/or simultaneous interaction of substrate with multiple chaperones. By effectively subjecting substrates to multiple levels of selection by multiple chaperones, this may insure that these potent disaggregases are only activated in the appropriate context. PMID:25988153

Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car Parrinello) molecular dynamics

NASA Astrophysics Data System (ADS)

Hammond, Philip S.; Wu, Yudong; Harris, Rebecca; Minehardt, Todd J.; Car, Roberto; Schmitt, Jeffrey D.

2005-01-01

A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Fuson, Michael M.

2017-01-01

Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

Nuclear Dynamics at Molecule–Metal Interfaces: A Pseudoparticle Perspective

DOE PAGES

Galperin, Michael; Nitzan, Abraham

2015-11-20

We discuss nuclear dynamics at molecule-metal interfaces including nonequilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we introduce gradient expansion to reduce the adiabatic nuclear dynamics (that is, nuclear dynamics on a single molecular potential surface) into its semiclassical form while maintaining the effect of the nonadiabatic electronic transitions between different molecular charge states. Finally, this yields a set of equations for the nuclear dynamics in the presence of these nonadiabatic transitions, which reproduce the surface-hopping formulation in the limit of small metal-molecule coupling (where broadening of the molecularmore » energy levels can be disregarded) and Ehrenfest dynamics (motion on the potential of mean force) when information on the different charging states is traced out.« less

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

NASA Astrophysics Data System (ADS)

Hamelberg, Donald; Mongan, John; McCammon, J. Andrew

2004-06-01

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

A centroid molecular dynamics study of liquid para-hydrogen and ortho-deuterium.

PubMed

Hone, Tyler D; Voth, Gregory A

2004-10-01

Centroid molecular dynamics (CMD) is applied to the study of collective and single-particle dynamics in liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The CMD results are compared with the results of classical molecular dynamics, quantum mode coupling theory, a maximum entropy analytic continuation approach, pair-product forward- backward semiclassical dynamics, and available experimental results. The self-diffusion constants are in excellent agreement with the experimental measurements for all systems studied. Furthermore, it is shown that the method is able to adequately describe both the single-particle and collective dynamics of quantum liquids. (c) 2004 American Institute of Physics

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

PubMed

Fogarty, Aoife C; Laage, Damien

2014-07-17

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

PubMed Central

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

How Dynamic Visualization Technology can Support Molecular Reasoning

NASA Astrophysics Data System (ADS)

Levy, Dalit

2013-10-01

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

Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics

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

Holian, B.L.; Voter, A.F.; Ravelo, R.

The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,`` which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations.

A Digital Program for Calculating the Interaction Between Flexible Structures, Unsteady Aerodynamics and Active Controls

NASA Technical Reports Server (NTRS)

Peele, E. L.; Adams, W. M., Jr.

1979-01-01

A computer program, ISAC, is described which calculates the stability and response of a flexible airplane equipped with active controls. The equations of motion relative to a fixed inertial coordinate system are formulated in terms of the airplane's rigid body motion and its unrestrained normal vibration modes. Unsteady aerodynamic forces are derived from a doublet lattice lifting surface theory. The theoretical basis for the program is briefly explained together with a description of input data and output results.

Nocturnal sleep in isolation-reared monkeys: evidence for enviromental independence.

PubMed

Reite, M; Short, R

1977-11-01

Thirteen all-night recordings were obtained from 3 infant pigtailed (Macaca nemestrina) monkeys raised on a cloth surrogate mother and under conditions of social isolation. Totally implantable biotelemetry systems were used to record the sleep physiology from the unrestrained animals. Sleep stages and night-to-night variability were virtually identical to values previously found in 8 mother-reared group-living infants. Sustained alterations in the early rearing enviroment, even though considerably modifying the organism's development, did not appear to result in differences in sleep organization.

Fatigue-Arrestor Bolts

NASA Technical Reports Server (NTRS)

Onstott, Joseph W.; Gilster, Mark; Rodriguez, Sergio; Larson, John E.; Wickham, Mark D.; Schoonover, Kevin E.

1995-01-01

Bolts that arrest (or, more precisely, retard) onset of fatigue cracking caused by inelastic strains developed. Specifically developed to be installed in flange holes of unrestrained rocket engine nozzle. Fanges sometimes used to bolt nozzle to test stand; however, when rocket engine operated without this restraint, region around bolt holes experience severe inelastic strains causing fatigue cracking. Interference fits introduce compressive preloads that retard fatigue by reducing ranges of strains. Principle of these fatigue-arrestor bolts also applicable to holes in plates made of other materials and/or used for different purposes.

Molecular dynamics simulation of low-energy recoil events in titanate pyrochlores

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

Dong, Liyuan; Setyawan, Wahyu; Li, Yuhong

2017-01-01

Molecular dynamics simulations of low-energy displacements in titanate pyrochlores have been carried out along three main directions, to determineE dfor A, Ti and O, corresponding defect configurations, and defect formation dynamics.

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Exploring GPCR-Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward.

PubMed

Sengupta, Durba; Prasanna, Xavier; Mohole, Madhura; Chattopadhyay, Amitabha

2018-06-07

Gprotein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions and their subsequent effects on GPCR structure, organization, and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association. In spite of several success stories, the methodologies in molecular dynamics simulations are still emerging. In this Feature Article, we provide a comprehensive overview of coarse-grain and atomistic molecular dynamics simulations of GPCR-lipid interaction in the context of experimental observations. In addition, we discuss the effect of secondary and tertiary structural constraints in coarse-grain simulations in the context of functional dynamics and structural plasticity of GPCRs. We envision that this comprehensive overview will help resolve differences in computational studies and provide a way forward.

Novel Breast Cancer Therapeutics Based on Bacterial Cupredoxin

DTIC Science & Technology

2008-09-01

M. and Lim, C. (1999) Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the...crowding has structural effects on the folded ensemble of polypeptides. energy landscape theory excluded volume effect molecular simulations protein... molecular simulations (51). Thermo- dynamic properties such as the radius of gyration (Rg), shape parameters ( and S) (11), and the fraction of native

Visualizing Energy on Target: Molecular Dynamics Simulations

DTIC Science & Technology

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide from Influenza A Virus

DTIC Science & Technology

2008-12-01

ABSTRACT The insertion of the M2 transmembrane peptide from influenza A virus into a membrane has been studied with molecular - dynamics simulations ...performed replica-exchange molecular - dynamics simulations with umbrella-sampling techniques to characterize the probability distribution and conformation...atomic- detailed molecular dynamics (MD) simulation techniques represent a valuable complementary methodology to inves- tigate membrane-insertion of

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

PubMed

van der Vaart, Arjan

2015-05-01

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

Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

NASA Astrophysics Data System (ADS)

Stolow, Albert

We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.

Perspective: A Dynamics-Based Classification of Ventricular Arrhythmias

PubMed Central

Weiss, James N.; Garfinkel, Alan; Karagueuzian, Hrayr S.; Nguyen, Thao P.; Olcese, Riccardo; Chen, Peng-Sheng; Qu, Zhilin

2015-01-01

Despite key advances in the clinical management of life-threatening ventricular arrhythmias, culminating with the development of implantable cardioverter-defibrillators and catheter ablation techniques, pharmacologic/biologic therapeutics have lagged behind. The fundamental issue is that biological targets are molecular factors. Diseases, however, represent emergent properties at the scale of the organism that result from dynamic interactions between multiple constantly changing molecular factors. For a pharmacologic/biologic therapy to be effective, it must target the dynamic processes that underlie the disease. Here we propose a classification of ventricular arrhythmias that is based on our current understanding of the dynamics occurring at the subcellular, cellular, tissue and organism scales, which cause arrhythmias by simultaneously generating arrhythmia triggers and exacerbating tissue vulnerability. The goal is to create a framework that systematically links these key dynamic factors together with fixed factors (structural and electrophysiological heterogeneity) synergistically promoting electrical dispersion and increased arrhythmia risk to molecular factors that can serve as biological targets. We classify ventricular arrhythmias into three primary dynamic categories related generally to unstable Ca cycling, reduced repolarization, and excess repolarization, respectively. The clinical syndromes, arrhythmia mechanisms, dynamic factors and what is known about their molecular counterparts are discussed. Based on this framework, we propose a computational-experimental strategy for exploring the links between molecular factors, fixed factors and dynamic factors that underlie life-threatening ventricular arrhythmias. The ultimate objective is to facilitate drug development by creating an in silico platform to evaluate and predict comprehensively how molecular interventions affect not only a single targeted arrhythmia, but all primary arrhythmia dynamics categories as well as normal cardiac excitation-contraction coupling. PMID:25769672

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

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

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

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

Elements of the cellular metabolic structure

PubMed Central

De la Fuente, Ildefonso M.

2015-01-01

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell. PMID:25988183

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

PubMed

Doshi, Urmi; Hamelberg, Donald

2014-04-03

Molecular dynamics simulations can provide valuable atomistic insights into biomolecular function. However, the accuracy of molecular simulations on general-purpose computers depends on the time scale of the events of interest. Advanced simulation methods, such as accelerated molecular dynamics, have shown tremendous promise in sampling the conformational dynamics of biomolecules, where standard molecular dynamics simulations are nonergodic. Here we present a sampling method based on accelerated molecular dynamics in which rotatable dihedral angles and nonbonded interactions are boosted separately. This method (RaMD-db) is a different implementation of the dual-boost accelerated molecular dynamics, introduced earlier. The advantage is that this method speeds up sampling of the conformational space of biomolecules in explicit solvent, as the degrees of freedom most relevant for conformational transitions are accelerated. We tested RaMD-db on one of the most difficult sampling problems - protein folding. Starting from fully extended polypeptide chains, two fast folding α-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed β-hairpin (Chignolin) were completely folded to their native structures in very short simulation time. Multiple folding/unfolding transitions could be observed in a single trajectory. Our results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent. RaMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.

A network of molecular switches controls the activation of the two-component response regulator NtrC

NASA Astrophysics Data System (ADS)

Vanatta, Dan K.; Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S.

2015-06-01

Recent successes in simulating protein structure and folding dynamics have demonstrated the power of molecular dynamics to predict the long timescale behaviour of proteins. Here, we extend and improve these methods to predict molecular switches that characterize conformational change pathways between the active and inactive state of nitrogen regulatory protein C (NtrC). By employing unbiased Markov state model-based molecular dynamics simulations, we construct a dynamic picture of the activation pathways of this key bacterial signalling protein that is consistent with experimental observations and predicts new mutants that could be used for validation of the mechanism. Moreover, these results suggest a novel mechanistic paradigm for conformational switching.

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

Development of a Computational Assay for the Estrogen Receptor

DTIC Science & Technology

2006-07-01

University Ashley Deline, Senior Thesis in chemistry, " Molecular Dynamic Simulations of a Glycoform and its Constituent Parts Related to Rheumatoid Arthritis...involves running a long molecular dynamics (MD) simulation of the uncoupled receptor in order to sample the protein’s unique conformations. The second...Receptor binding domain. * Performed several long molecular dynamics simulations (800 ps - 3 ns) on the ligand-ER system using ligands with known

In Silico Design of Smart Binders to Anthrax PA

DTIC Science & Technology

2012-09-01

nanosecond(ns) molecular dynamics simulation in the NPT ensemble (constant particle number, pressure, and temperature) at 300K, with the CHARMM force...protective antigen (PA). Before the docking runs, the DS23 peptide was simulated using molecular dynamics to generate an ensemble of structures...structure), we do not see a large amount of structural change when using molecular dynamics after Rosetta docking. We note that this RMSD does not take

In Silico Analyses of Substrate Interactions with Human Serum Paraoxonase 1

DTIC Science & Technology

2008-01-01

substrate interactions of HuPON1 remains elusive. In this study, we apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the...mod- eling; docking; molecular dynamics simulations ; binding free energy decomposition. 486 PROTEINS Published 2008 WILEY-LISS, INC. yThis article is a...apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the binding interactions of HuPON1 with representative substrates. The

Predictions of Crystal Structures from First Principles

DTIC Science & Technology

2007-06-01

RDX crystal in hoped that the problem could be resolved by the molecular dynamics simulations . The fully ab initio development of density functional... Molecular Dynamics Simulations of RDX i.e., without any use of experimental results (except that Crystal the geometry of monomers was derived from X-ray...applied in molecular dynamics simulations of the RDX system, due to its size, is intractable by any high-level ab crystal. We performed isothermal

Coarse-Grained Lattice Model Simulations of Sequence-Structure Fitness of a Ribosome-Inactivating Protein

DTIC Science & Technology

2007-11-05

limits of what is considered practical when applying all-atom molecular - dynamics simulation methods. Lattice models provide computationally robust...of expectation values from the density of states. All-atom molecular - dynamics simulations provide the most rigorous sampling method to generate con... molecular - dynamics simulations of protein folding,6–9 reported studies of computing a heat capacity or other calorimetric observables have been limited to

Driving simulation in the clinic: testing visual exploratory behavior in daily life activities in patients with visual field defects.

PubMed

Hamel, Johanna; Kraft, Antje; Ohl, Sven; De Beukelaer, Sophie; Audebert, Heinrich J; Brandt, Stephan A

2012-09-18

Patients suffering from homonymous hemianopia after infarction of the posterior cerebral artery (PCA) report different degrees of constraint in daily life, despite similar visual deficits. We assume this could be due to variable development of compensatory strategies such as altered visual scanning behavior. Scanning compensatory therapy (SCT) is studied as part of the visual training after infarction next to vision restoration therapy. SCT consists of learning to make larger eye movements into the blind field enlarging the visual field of search, which has been proven to be the most useful strategy(1), not only in natural search tasks but also in mastering daily life activities(2). Nevertheless, in clinical routine it is difficult to identify individual levels and training effects of compensatory behavior, since it requires measurement of eye movements in a head unrestrained condition. Studies demonstrated that unrestrained head movements alter the visual exploratory behavior compared to a head-restrained laboratory condition(3). Martin et al.(4) and Hayhoe et al.(5) showed that behavior demonstrated in a laboratory setting cannot be assigned easily to a natural condition. Hence, our goal was to develop a study set-up which uncovers different compensatory oculomotor strategies quickly in a realistic testing situation: Patients are tested in the clinical environment in a driving simulator. SILAB software (Wuerzburg Institute for Traffic Sciences GmbH (WIVW)) was used to program driving scenarios of varying complexity and recording the driver's performance. The software was combined with a head mounted infrared video pupil tracker, recording head- and eye-movements (EyeSeeCam, University of Munich Hospital, Clinical Neurosciences). The positioning of the patient in the driving simulator and the positioning, adjustment and calibration of the camera is demonstrated. Typical performances of a patient with and without compensatory strategy and a healthy control are illustrated in this pilot study. Different oculomotor behaviors (frequency and amplitude of eye- and head-movements) are evaluated very quickly during the drive itself by dynamic overlay pictures indicating where the subjects gaze is located on the screen, and by analyzing the data. Compensatory gaze behavior in a patient leads to a driving performance comparable to a healthy control, while the performance of a patient without compensatory behavior is significantly worse. The data of eye- and head-movement-behavior as well as driving performance are discussed with respect to different oculomotor strategies and in a broader context with respect to possible training effects throughout the testing session and implications on rehabilitation potential.

Molecular dynamics simulations: advances and applications

PubMed Central

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

2015-01-01

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions.

PubMed

Fogolari, Federico; Corazza, Alessandra; Varini, Nicola; Rotter, Matteo; Gumral, Devrim; Codutti, Luca; Rennella, Enrico; Viglino, Paolo; Bellotti, Vittorio; Esposito, Gennaro

2011-03-01

β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect. Copyright © 2010 Wiley-Liss, Inc.

Quantifying utricular stimulation during natural behavior

PubMed Central

Rivera, Angela R. V.; Davis, Julian; Grant, Wally; Blob, Richard W.; Peterson, Ellengene; Neiman, Alexander B.; Rowe, Michael

2012-01-01

The use of natural stimuli in neurophysiological studies has led to significant insights into the encoding strategies used by sensory neurons. To investigate these encoding strategies in vestibular receptors and neurons, we have developed a method for calculating the stimuli delivered to a vestibular organ, the utricle, during natural (unrestrained) behaviors, using the turtle as our experimental preparation. High-speed digital video sequences are used to calculate the dynamic gravito-inertial (GI) vector acting on the head during behavior. X-ray computed tomography (CT) scans are used to determine the orientation of the otoconial layer (OL) of the utricle within the head, and the calculated GI vectors are then rotated into the plane of the OL. Thus, the method allows us to quantify the spatio-temporal structure of stimuli to the OL during natural behaviors. In the future, these waveforms can be used as stimuli in neurophysiological experiments to understand how natural signals are encoded by vestibular receptors and neurons. We provide one example of the method which shows that turtle feeding behaviors can stimulate the utricle at frequencies higher than those typically used in vestibular studies. This method can be adapted to other species, to other vestibular end organs, and to other methods of quantifying head movements. PMID:22753360

Fluvial processes and passive rehabilitation of the Lisbon Bottom side-channel chute, Lower Missouri River

USGS Publications Warehouse

Jacobson, Robert B.; Laustrup, Mark S.; Chapman, Michael D.

2001-01-01

Multiple large floods in 1993-1997 on the Lower Missouri River carved a side-channel chute through the river bottom at Lisbon, Missouri. Although similar in some respects to engineered side-channel chutes designed for habitat rehabilitation projects, the Lisbon Bottom chute has been unique in that it was allowed to evolve for more than four years with minimal stabilization. During the wet years, 1996-1999, the chute was subjected to abnormally high discharges and passed as much as 20% of the total discharge of the Missouri River. Relatively unrestrained fluvial processes during this time created a wide channel with highly diverse habitats. The upper one-half of the chute established a shallow, braided channel morphology similar to the pre-managed Missouri River. The lower half established a dynamically migrating, single-thread channel, and an incipient flood plain. Compared to the adjacent navigation channel, the chute established substantial areas of shallow, slow-velocity aquatic habitat that is considered to be in short supply in the present-day Lower Missouri River. The shortterm biological benefits have been mixed: the chute has fewer waterbird and benthic macroinvertebrate taxa than adjacent riverine habitats, but greater numbers of fish species compared to the navigation channel.

Negligible Motion Artifacts in Scalp Electroencephalography (EEG) During Treadmill Walking.

PubMed

Nathan, Kevin; Contreras-Vidal, Jose L

2015-01-01

Recent mobile brain/body imaging (MoBI) techniques based on active electrode scalp electroencephalogram (EEG) allow the acquisition and real-time analysis of brain dynamics during active unrestrained motor behavior involving whole body movements such as treadmill walking, over-ground walking and other locomotive and non-locomotive tasks. Unfortunately, MoBI protocols are prone to physiological and non-physiological artifacts, including motion artifacts that may contaminate the EEG recordings. A few attempts have been made to quantify these artifacts during locomotion tasks but with inconclusive results due in part to methodological pitfalls. In this paper, we investigate the potential contributions of motion artifacts in scalp EEG during treadmill walking at three different speeds (1.5, 3.0, and 4.5 km/h) using a wireless 64 channel active EEG system and a wireless inertial sensor attached to the subject's head. The experimental setup was designed according to good measurement practices using state-of-the-art commercially available instruments, and the measurements were analyzed using Fourier analysis and wavelet coherence approaches. Contrary to prior claims, the subjects' motion did not significantly affect their EEG during treadmill walking although precaution should be taken when gait speeds approach 4.5 km/h. Overall, these findings suggest how MoBI methods may be safely deployed in neural, cognitive, and rehabilitation engineering applications.

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

NASA Astrophysics Data System (ADS)

Wang, Han; Zhang, Linfeng; Han, Jiequn; E, Weinan

2018-07-01

Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. DeePMD-kit is interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient. On the other end, DeePMD-kit is interfaced with high-performance classical molecular dynamics and quantum (path-integral) molecular dynamics packages, i.e., LAMMPS and the i-PI, respectively. Thus, upon training, the potential energy and force field models can be used to perform efficient molecular simulations for different purposes. As an example of the many potential applications of the package, we use DeePMD-kit to learn the interatomic potential energy and forces of a water model using data obtained from density functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information contained in the original model.

Theory of attosecond delays in molecular photoionization.

PubMed

Baykusheva, Denitsa; Wörner, Hans Jakob

2017-03-28

We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N 2 O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H 2 O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.

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.

Temporal attention for visual food stimuli in restrained eaters.

PubMed

Neimeijer, Renate A M; de Jong, Peter J; Roefs, Anne

2013-05-01

Although restrained eaters try to limit their food intake, they often fail and indulge in exactly those foods that they want to avoid. A possible explanation is a temporal attentional bias for food cues. It could be that for these people food stimuli are processed relatively efficiently and require less attentional resources to enter awareness. Once a food stimulus has captured attention, it may be preferentially processed and granted prioritized access to limited cognitive resources. This might help explain why restrained eaters often fail in their attempts to restrict their food intake. A Rapid Serial Visual Presentation task consisting of dual and single target trials with food and neutral pictures as targets and/or distractors was administered to restrained (n=40) and unrestrained (n=40) eaters to study temporal attentional bias. Results indicated that (1) food cues did not diminish the attentional blink in restrained eaters when presented as second target; (2) specifically restrained eaters showed an interference effect of identifying food targets on the identification of preceding neutral targets; (3) for both restrained and unrestrained eaters, food cues enhanced the attentional blink; (4) specifically in restrained eaters, food distractors elicited an attention blink in the single target trials. In restrained eaters, food cues get prioritized access to limited cognitive resources, even if this processing priority interferes with their current goals. This temporal attentional bias for food stimuli might help explain why restrained eaters typically have difficulties maintaining their diet rules. Copyright © 2012 Elsevier Ltd. All rights reserved.

Non-contact and Unrestrained Respiration Monitoring System for Sleeping Person Using Near-infrared Bright Spots Matrix Irradiation

NASA Astrophysics Data System (ADS)

Aoki, Hirooki; Aoki, Hiroichi; Nakajima, Masato

Measurement of biological information appears to be an effective method to obtain an understanding of health conditions measures to maintain and improve the health of elderly people. However, every conventional bioinstrumentation technique imposes a sense of restraint that results in aversion against measurements that would last over consecutive days. To solve this problem, we propose a system for monitoring the respiration of sleepers, and it uses a fiber grating vision sensor, which is a type of optical range finder, to achieve non-contact and unrestrained monitoring. The signals obtained by the system include the respiration rate, shifts of the ventilation, and the body movement interval of the sleeper. The information enables to investigate the stability of the sleeper throughout the night. We examined the measuring accuracy, validity, and effectiveness of our proposed system. And all-night monitoring performed at elderly care facility revealed that respiratory disturbances during sleep occurred in many of the residents and that sleep apnea is a common syndrome, especially among residents who have senile dementia or have had a stroke. We were able to carry out the all-night monitoring with this system for a total of about 370 times, according to our schedule, without experiencing any failure, accident, or interruption. Our proposed system is highly effective for monitoring elderly dementia patients who are likely to become uncooperative during measurement with existing monitoring methods that use certain amounts of restraint.

Evolution of restraint in a structured rock–paper–scissors community

PubMed Central

Nahum, Joshua R.; Harding, Brittany N.; Kerr, Benjamin

2011-01-01

It is not immediately clear how costly behavior that benefits others evolves by natural selection. By saving on inherent costs, individuals that do not contribute socially have a selective advantage over altruists if both types receive equal benefits. Restrained consumption of a common resource is a form of altruism. The cost of this kind of prudent behavior is that restrained individuals give up resources to less-restrained individuals. The benefit of restraint is that better resource management may prolong the persistence of the group. One way to dodge the problem of defection is for altruists to interact disproportionately with other altruists. With limited dispersal, restrained individuals persist because of interaction with like types, whereas it is the unrestrained individuals that must face the negative long-term consequences of their rapacity. Here, we study the evolution of restraint in a community of three competitors exhibiting a nontransitive (rock–paper–scissors) relationship. The nontransitivity ensures a form of negative feedback, whereby improvement in growth of one competitor has the counterintuitive consequence of lowering the density of that improved player. This negative feedback generates detrimental long-term consequences for unrestrained growth. Using both computer simulations and evolution experiments with a nontransitive community of Escherichia coli, we find that restrained growth can evolve under conditions of limited dispersal in which negative feedback is present. This research, thus, highlights a set of ecological conditions sufficient for the evolution of one form of altruism. PMID:21690371

Evolution of restraint in a structured rock-paper-scissors community.

PubMed

Nahum, Joshua R; Harding, Brittany N; Kerr, Benjamin

2011-06-28

It is not immediately clear how costly behavior that benefits others evolves by natural selection. By saving on inherent costs, individuals that do not contribute socially have a selective advantage over altruists if both types receive equal benefits. Restrained consumption of a common resource is a form of altruism. The cost of this kind of prudent behavior is that restrained individuals give up resources to less-restrained individuals. The benefit of restraint is that better resource management may prolong the persistence of the group. One way to dodge the problem of defection is for altruists to interact disproportionately with other altruists. With limited dispersal, restrained individuals persist because of interaction with like types, whereas it is the unrestrained individuals that must face the negative long-term consequences of their rapacity. Here, we study the evolution of restraint in a community of three competitors exhibiting a nontransitive (rock-paper-scissors) relationship. The nontransitivity ensures a form of negative feedback, whereby improvement in growth of one competitor has the counterintuitive consequence of lowering the density of that improved player. This negative feedback generates detrimental long-term consequences for unrestrained growth. Using both computer simulations and evolution experiments with a nontransitive community of Escherichia coli, we find that restrained growth can evolve under conditions of limited dispersal in which negative feedback is present. This research, thus, highlights a set of ecological conditions sufficient for the evolution of one form of altruism.

Restraint Use Among Northwest American Indian Children Traveling in Motor Vehicles

PubMed Central

Lapidus, Jodi A.; Smith, Nicole H.; Ebel, Beth E.; Romero, Francine C.

2005-01-01

Objectives. We sought to estimate motor vehicle passenger restraint use among Northwest American Indian children 8 years old or younger and to determine factors associated with using proper (i.e., age and weight appropriate) passenger restraint systems. Methods. We surveyed vehicles driven by members of 6 tribes in Idaho, Oregon, and Washington. Associations between proper restraint and child, driver, and vehicle characteristics were analyzed using logistic regression for clustered data. Results. We observed 775 children traveling in 574 vehicles; 41% were unrestrained. Proper restraint ranged from 63% among infant seat-eligible children to 11% among booster seat-eligible children and was associated with younger child’s age (odds ratio (OR) per year = 0.60; 95% confidence interval (CI) = 0.48, 0.75), seating location (OR front vs rear=0.27; 95% CI=0.16, 0.44), driver seat belt use (OR=2.39; 95% CI=1.51, 3.80), and relationship (OR for nonparent vs parent=0.28; 95% CI=0.14, 0.58). More than half of drivers felt children could use an adult seat belt earlier than recommended guidelines, and 63% did not correctly identify whether their tribe had child safety seat laws. Conclusions. Children in these communities are inadequately restrained. Restraint use was exceedingly low among booster-eligible children and children riding with unrestrained adults. Interventions emphasizing appropriate restraint use and enforcement of passenger safety laws could reduce the risk of injury or death in motor vehicle accidents. PMID:16195522

27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

USDA-ARS?s Scientific Manuscript database

DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

Diffusive molecular dynamics simulations of lithiation of silicon nanopillars

NASA Astrophysics Data System (ADS)

Mendez, J. P.; Ponga, M.; Ortiz, M.

2018-06-01

We report diffusive molecular dynamics simulations concerned with the lithiation of Si nano-pillars, i.e., nano-sized Si rods held at both ends by rigid supports. The duration of the lithiation process is of the order of milliseconds, well outside the range of molecular dynamics but readily accessible to diffusive molecular dynamics. The simulations predict an alloy Li15Si4 at the fully lithiated phase, exceedingly large and transient volume increments up to 300% due to the weakening of Sisbnd Si iterations, a crystalline-to-amorphous-to-lithiation phase transition governed by interface kinetics, high misfit strains and residual stresses resulting in surface cracks and severe structural degradation in the form of extensive porosity, among other effects.

Statistical errors in molecular dynamics averages

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

Schiferl, S.K.; Wallace, D.C.

1985-11-15

A molecular dynamics calculation produces a time-dependent fluctuating signal whose average is a thermodynamic quantity of interest. The average of the kinetic energy, for example, is proportional to the temperature. A procedure is described for determining when the molecular dynamics system is in equilibrium with respect to a given variable, according to the condition that the mean and the bandwidth of the signal should be sensibly constant in time. Confidence limits for the mean are obtained from an analysis of a finite length of the equilibrium signal. The role of serial correlation in this analysis is discussed. The occurence ofmore » unstable behavior in molecular dynamics data is noted, and a statistical test for a level shift is described.« less

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.

PubMed

Jiang, Ping; Yaşar, Fatih; Hansmann, Ulrich H E

2013-08-13

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β -sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β -sheet formed by the two chain ends.

Gromita: a fully integrated graphical user interface to gromacs 4.

PubMed

Sellis, Diamantis; Vlachakis, Dimitrios; Vlassi, Metaxia

2009-09-07

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

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.

Two Argonne scientists named 2012 AAAS fellows | Argonne National

Science.gov Websites

"contributions to understanding structural dynamics of molecular excited states with special . "I'm really interested in how molecules respond to light and how light could influence molecular is being honored for her "contributions to understanding structural dynamics of molecular

The Computer Simulation of Liquids by Molecular Dynamics.

ERIC Educational Resources Information Center

Smith, W.

1987-01-01

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

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

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

2015-05-01

Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

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

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

PubMed

Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

2018-05-17

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

Capillary waves' dynamics at the nanoscale

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Chacón, Enrique; Tarazona, Pedro

2008-12-01

We study the dynamics of thermally excited capillary waves (CW) at molecular scales, using molecular dynamics simulations of simple liquid slabs. The analysis is based on the Fourier modes of the liquid surface, constructed via the intrinsic sampling method (Chacón and Tarazona 2003 Phys. Rev. Lett. 91 166103). We obtain the time autocorrelation of the Fourier modes to get the frequency and damping rate Γd(q) of each mode, with wavenumber q. Continuum hydrodynamics predicts \\Gamma (q) \\propto q\\gamma (q) and thus provides a dynamic measure of the q-dependent surface tension, γd(q). The dynamical estimation is much more robust than the structural prediction based on the amplitude of the Fourier mode, γs(q). Using the optimal estimation of the intrinsic surface, we obtain quantitative agreement between the structural and dynamic pictures. Quite surprisingly, the hydrodynamic prediction for CW remains valid up to wavelengths of about four molecular diameters. Surface tension hydrodynamics break down at shorter scales, whereby a transition to a molecular diffusion regime is observed.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Stroop interference and food intake.

PubMed

Overduin, J; Jansen, A; Louwerse, E

1995-11-01

The Stroop task is aimed at assessing attentional bias. Words are displayed one by one on a computer screen and subjects are instructed to name the color in which every word is printed. The attentional bias is supposed to be reflected in the extent to which the word meanings interfere with the speed of color naming: The longer the color naming latency, the larger the attentional bias. Experiments using this task have demonstrated attentional bias for eating and body shape-related words in bulimic, anorexic, and restrained subjects. Explanations of these results have generally been formulated in terms of restricted food intake or emotional concerns about food and body shape-related themes. In contrast, in the present article it was proposed that Stroop interference might reflect a tendency either to withdraw or approach food or body shape-related stimuli. Fifty-one subjects (25 unrestrained, 26 restrained) were administered a Stroop task containing neutral, food, and body shape-related words. There were two conditions to which subjects were randomly allocated: the "appetizer" and "no-appetizer" condition. The appetizer was a bit of pudding to be ingested by the subject just before the Stroop task. Following the Stroop task an ice cream taste test was presented in which the subjects were allowed to eat as much as they liked. The amount of ice cream eaten was registered secretly. The results show that in unrestrained subjects Stroop interference for food words was found only in the appetizer condition. Restrained subjects, however, showed a permanent interference for food words. A significant correlation of .58 between Stroop food-word interference and ice cream intake was found only in unrestrained subjects. In restrained eaters the correlation was near 0. No effect of condition or restraint was found on Stroop body shape-word interference. The findings indicate that (1) ingestion of an appetizer seems to have evoked an attentional bias for food words in nonrestraints that correlated with food intake; (2) restrained eaters showed continuous attentional bias. This appears to support the urge-to-act explanation of Stroop interference. The lack of correlation between restraints' attentional bias and ad lib food intake could have been caused by inhibition of approach which is one of the characteristics of restrained eating: The present procedure seems not to have triggered disinhibited eating in these subjects. Among other things it is concluded that Stroop interference, as a measure of "craving" triggered by food cue, might be a useful aid in assessing the risk of relapse in treated binge eating patients.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

2007-01-01

The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

Time-resolved molecular imaging

NASA Astrophysics Data System (ADS)

Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

2016-06-01

Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

PubMed

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

2018-06-25

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

Elucidation of molecular dynamics of invasive species of rice

USDA-ARS?s Scientific Manuscript database

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

Multiscale Modeling of Multiphase Fluid Flow

DTIC Science & Technology

2016-08-01

the disparate time and length scales involved in modeling fluid flow and heat transfer. Molecular dynamics simulations were carried out to provide a...fluid dynamics methods were used to investigate the heat transfer process in open-cell micro-foam with phase change material; enhancement of natural...Computational fluid dynamics, Heat transfer, Phase change material in Micro-foam, Molecular Dynamics, Multiphase flow, Multiscale modeling, Natural

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

PubMed

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

2016-01-01

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

Girsanov reweighting for path ensembles and Markov state models

NASA Astrophysics Data System (ADS)

Donati, L.; Hartmann, C.; Keller, B. G.

2017-06-01

The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics.

Molecular dynamics in principal component space.

PubMed

Michielssens, Servaas; van Erp, Titus S; Kutzner, Carsten; Ceulemans, Arnout; de Groot, Bert L

2012-07-26

A molecular dynamics algorithm in principal component space is presented. It is demonstrated that sampling can be improved without changing the ensemble by assigning masses to the principal components proportional to the inverse square root of the eigenvalues. The setup of the simulation requires no prior knowledge of the system; a short initial MD simulation to extract the eigenvectors and eigenvalues suffices. Independent measures indicated a 6-7 times faster sampling compared to a regular molecular dynamics simulation.

Coarse-Grained Molecular Dynamics Simulation of Ionic Polymer Networks

DTIC Science & Technology

2008-07-01

AFRL-RX-WP-TP-2009-4198 COARSE-GRAINED MOLECULAR DYNAMICS SIMULATION OF IONIC POLYMER NETWORKS (Postprint) T.E. Dirama, V. Varshney, K.L...GRAINED MOLECULAR DYNAMICS SIMULATION OF IONIC POLYMER NETWORKS (Postprint) 5a. CONTRACT NUMBER FA8650-05-D-5807-0052 5b. GRANT NUMBER 5c...We studied two types of networks which differ only by one containing ionic pairs that amount to 7% of the total number of bonds present. The stress

Molecular Dynamics and Morphology of High Performance Elastomers and Fibers by Solid State NMR

DTIC Science & Technology

2016-06-30

Distribution Unlimited UU UU UU UU 30-06-2016 1-Sep-2015 31-May-2016 Final Report: Molecular Dynamics and Morphology of High - Performance Elastomers and...non peer-reviewed journals: Final Report: Molecular Dynamics and Morphology of High -Performance Elastomers and Fibers by Solid-State NMR Report Title...Kanbargi 0.50 0.50 1 PERCENT_SUPPORTEDNAME FTE Equivalent: Total Number: Sub Contractors (DD882) Names of Faculty Supported Names of Under Graduate

Prediction of Protein-Peptide Interactions: Application of the XPairIT to Anthrax Lethal Factor and Substrates

DTIC Science & Technology

2013-09-01

hydrogen bonds in Tyrosine-containing peptides. Dalkas et al[7] used docking and molecular dynamics simulations to study a variety of MAPKK-based... simulated using NAMD molecular dynamics and the CHARMM[20] forcefield at 300K and employing the Generalized Born Implicit Solvent (GBIS[21]) with the...which were reported in Section 2. Specifically, after a ~10ns molecular dynamics simulation in TIP3 explicit water, significant motion of domains III

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.

PubMed

Chen, Changjun; Huang, Yanzhao; Xiao, Yi

2013-01-01

Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of freedom in the molecule to environment temperature, like dihedrals in generalized coordinates or nonhydrogen atoms in Cartesian coordinate. After applying to ALA dipeptide model, we find that this modified molecular dynamics greatly enhances the sampling behavior in the conformational space and provides more information about the state-to-state transition, while conventional molecular dynamics fails to do so. Moreover, from the results of 16 independent 100 ns simulations by the new method, it shows that trpzip2 has one-half chances to reach the naive state in all the trajectories, which is greatly higher than conventional molecular dynamics. Such an improvement would provide a potential way for searching the conformational space or predicting the most stable states of peptides and proteins.

Impact of anisotropy on the structure and dynamics of ionic liquids: A computational study of 1-butyl-3-methyl-imidazolium trifluoroacetate

NASA Astrophysics Data System (ADS)

Schröder, C.; Rudas, T.; Neumayr, G.; Gansterer, W.; Steinhauser, O.

2007-07-01

The complex ionic network of 1-butyl-3-methyl-imidazolium trifluoroacetate was simulated by means of the molecular dynamics methods over a time period of 100ns. The influence of the anisotropy of the shape and charge distribution of both the cations and the anions on the local (molecular) and global (collective) structure and dynamics is analyzed. The distance-dependent g coefficients of the orientational probability function g(r,Ω) were found to be an excellent way to interpret local structure. Thereby, the combination and interrelation of individual g coefficients elucidate the mutual orientation. Dynamics at the molecular level is characterized by the time correlation function of the center-of-mass corrected molecular dipole moment μcm. Upon uniting the set of molecular dipoles to a single collective rotational dipole moment, MD, dynamics on a global level is studied. Decomposing into subsets of cations and anions respective self terms as well as the prominent cross term can be extracted. This decomposition also enables a detailed peak assignment in dielectric spectra.

Impact of anisotropy on the structure and dynamics of ionic liquids: a computational study of 1-butyl-3-methyl-imidazolium trifluoroacetate.

PubMed

Schröder, C; Rudas, T; Neumayr, G; Gansterer, W; Steinhauser, O

2007-07-28

The complex ionic network of 1-butyl-3-methyl-imidazolium trifluoroacetate was simulated by means of the molecular dynamics methods over a time period of 100 ns. The influence of the anisotropy of the shape and charge distribution of both the cations and the anions on the local (molecular) and global (collective) structure and dynamics is analyzed. The distance-dependent g coefficients of the orientational probability function g(r,Omega) were found to be an excellent way to interpret local structure. Thereby, the combination and interrelation of individual g coefficients elucidate the mutual orientation. Dynamics at the molecular level is characterized by the time correlation function of the center-of-mass corrected molecular dipole moment mucm. Upon uniting the set of molecular dipoles to a single collective rotational dipole moment, MD, dynamics on a global level is studied. Decomposing into subsets of cations and anions respective self terms as well as the prominent cross term can be extracted. This decomposition also enables a detailed peak assignment in dielectric spectra.

Optimizing legacy molecular dynamics software with directive-based offload

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Clustering molecular dynamics trajectories for optimizing docking experiments.

PubMed

De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Accelerating the use of molecular modeling in the high school classroom with VMD Lite.

PubMed

Lundquist, Karl; Herndon, Conner; Harty, Tyson H; Gumbart, James C

2016-01-01

It is often difficult for students to develop an intuition about molecular processes, which occur in a realm far different from day-to-day life. For example, thermal fluctuations take on hurricane-like proportions at the molecular scale. Students need a way to visualize realistic depictions of molecular processes to appreciate them. To this end, we have developed a simplified graphical interface to the widely used molecular visualization and analysis tool Visual Molecular Dynamics (VMD) called VMD lite. We demonstrate the use of VMD lite through a module on diffusion and the hydrophobic effect as they relate to membrane formation. Trajectories from molecular dynamics simulations, which students can interact with freely, illustrate the dynamical behavior of lipid molecules and water. VMD lite was tested by ∼70 students with overall positive reception. Remaining deficiencies in conceptual understanding were noted, however, and the module has been revised in response. © 2016 The International Union of Biochemistry and Molecular Biology.

Complementary study of molecular dynamics and domain sizes in heterogenous nanocomposites PBT/DA-C{sub 60} and PBT/TCNEO-C{sub 60}

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

Woźniak-Braszak, A., E-mail: abraszak@amu.edu.pl; Baranowski, M.; Jurga, K.

2014-05-28

A comprehensive study of molecular dynamics and structure in new heterogenous nanocomposites based on poly(butylene terephthalate) and nanoparticles C{sub 60} modified by n-decylamine or tetracyanoethylene oxide has been performed. The domain structure of new nanocomposites has been investigated by Fourier transform infrared spectroscopy, wide-angle X-ray scattering, and differential scanning calorimetry techniques. Solid-state {sup 1}H NMR techniques were used to study molecular dynamics and domain sizes in new nanocomposites. Information about the electronic properties of these nanocomposites was obtained by means of electron paramagnetic resonance method. It was shown that the structure and molecular dynamics of new nanocomposites were strongly dependentmore » on the properties and concentration of fullerene derivates.« less

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

NASA Astrophysics Data System (ADS)

Takada, Shoji

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

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

PubMed

Komeiji, Y; Yokoyama, H; Uebayasi, M; Taiji, M; Fukushige, T; Sugimoto, D; Takata, R; Shimizu, A; Itsukashi, K

1996-01-01

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

Sleep-enhancing effects of far-infrared radiation in rats

NASA Astrophysics Data System (ADS)

Honda, K.; Inoué, S.

1988-06-01

Unrestrained male rats continuously exposed to far-infrared radiation exhibited a significant increase in slow wave sleep (SWS) during the light period but not in the dark period. The change was largely due to the elevated occurrence of SWS episodes but not to the prolongation of their duration. Paradoxical sleep was not affected throughout the observation period except for a significant decrease at the end of the dark period. Thus the far-infrared radiation exerted a sleep modulatory effect closely related to the circadian activity-rest cycle.

Capillary Rise: Validity of the Dynamic Contact Angle Models.

PubMed

Wu, Pingkeng; Nikolov, Alex D; Wasan, Darsh T

2017-08-15

The classical Lucas-Washburn-Rideal (LWR) equation, using the equilibrium contact angle, predicts a faster capillary rise process than experiments in many cases. The major contributor to the faster prediction is believed to be the velocity dependent dynamic contact angle. In this work, we investigated the dynamic contact angle models for their ability to correct the dynamic contact angle effect in the capillary rise process. We conducted capillary rise experiments of various wetting liquids in borosilicate glass capillaries and compared the model predictions with our experimental data. The results show that the LWR equations modified by the molecular kinetic theory and hydrodynamic model provide good predictions on the capillary rise of all the testing liquids with fitting parameters, while the one modified by Joos' empirical equation works for specific liquids, such as silicone oils. The LWR equation modified by molecular self-layering model predicts well the capillary rise of carbon tetrachloride, octamethylcyclotetrasiloxane, and n-alkanes with the molecular diameter or measured solvation force data. The molecular self-layering model modified LWR equation also has good predictions on the capillary rise of silicone oils covering a wide range of bulk viscosities with the same key parameter W(0), which results from the molecular self-layering. The advantage of the molecular self-layering model over the other models reveals the importance of the layered molecularly thin wetting film ahead of the main meniscus in the energy dissipation associated with dynamic contact angle. The analysis of the capillary rise of silicone oils with a wide range of bulk viscosities provides new insights into the capillary dynamics of polymer melts.

Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

PubMed

Lehn, Jean-Marie

2012-01-01

Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

Monte Carlo and Molecular Dynamics in the Multicanonical Ensemble: Connections between Wang-Landau Sampling and Metadynamics

NASA Astrophysics Data System (ADS)

Vogel, Thomas; Perez, Danny; Junghans, Christoph

2014-03-01

We show direct formal relationships between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)] and statistical temperature molecular dynamics [PRL 97, 050601 (2006)], the major Monte Carlo and molecular dynamics work horses for sampling from a generalized, multicanonical ensemble. We aim at helping to consolidate the developments in the different areas by indicating how methodological advancements can be transferred in a straightforward way, avoiding the parallel, largely independent, developments tracks observed in the past.

III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic

A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

ERIC Educational Resources Information Center

Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

2010-01-01

As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

Avoiding Defect Nucleation during Equilibration in Molecular Dynamics Simulations with ReaxFF

DTIC Science & Technology

2015-04-01

respectively. All simulations are performed using the LAMMPS computer code.12 2 Fig. 1 a) Initial and b) final configurations of the molecular centers...Plimpton S. Fast parallel algorithms for short-range molecular dynamics. Comput J Phys. 1995;117:1–19. (Software available at http:// lammps .sandia.gov

Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods

PubMed Central

Johnston, Jennifer M.

2014-01-01

The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field. PMID:24158803

Dynamical photo-induced electronic properties of molecular junctions

NASA Astrophysics Data System (ADS)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics

DTIC Science & Technology

2011-05-04

pubs.acs.org/JPCB Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics Si-ping Han,†,‡ Adri C. T. van...ABSTRACT: We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molec- ular dynamics...with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.

PubMed

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F; Cohen, Itay; Henin, Rachel D; Hockla, Alexandra; Soares, Alexei S; Papo, Niv; Caulfield, Thomas R; Radisky, Evette S

2016-12-16

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular dynamics study of the structural and dynamic characteristics of the polyextremophilic short-chain dehydrogenase from the Thermococcus sibiricus archaeon and its homologues

NASA Astrophysics Data System (ADS)

Popinako, Anna V.; Antonov, Mikhail Yu.; Bezsudnova, Ekaterina Yu.; Prokopiev, Georgiy A.; Popov, Vladimir O.

2017-11-01

The study of structural adaptations of proteins from polyextremophilic organisms using computational molecular dynamics method is appealing because the obtained knowledge can be applied to construction of synthetic proteins with high activity and stability in polyextreme media which is useful for many industrial applications. To investigate molecular adaptations to high temperature, we have focused on a superthermostable short-chain dehydrogenase TsAdh319 from the Thermococcus sibiricus polyextremophilic archaeon and its closest structural homologues. Molecular dynamics method is widely used for molecular structure refinement, investigation of biological macromolecules motion, and, consequently, for interpreting the results of certain biophysical experiments. We performed molecular dynamics simulations of the proteins at different temperatures. Comparison of root mean square fluctuations (RMSF) of the atoms in thermophilic alcohol dehydrogenases (ADHs) at 300 K and 358 K revealed the existence of stable residues at 358 K. These residues surround the active site and form a "nucleus of rigidity" in thermophilic ADHs. The results of our studies suggest that the existence of the "nucleus of rigidity" is crucial for the stability of TsAdh319. Absence of the "nucleus of rigidity" in non-thermally stable proteins causes fluctuations throughout the protein, especially on the surface, triggering the process of denaturation at high temperatures.

Control of Mechanotransduction by Molecular Clutch Dynamics.

PubMed

Elosegui-Artola, Alberto; Trepat, Xavier; Roca-Cusachs, Pere

2018-05-01

The linkage of cells to their microenvironment is mediated by a series of bonds that dynamically engage and disengage, in what has been conceptualized as the molecular clutch model. Whereas this model has long been employed to describe actin cytoskeleton and cell migration dynamics, it has recently been proposed to also explain mechanotransduction (i.e., the process by which cells convert mechanical signals from their environment into biochemical signals). Here we review the current understanding on how cell dynamics and mechanotransduction are driven by molecular clutch dynamics and its master regulator, the force loading rate. Throughout this Review, we place a specific emphasis on the quantitative prediction of cell response enabled by combined experimental and theoretical approaches. Copyright © 2018 Elsevier Ltd. All rights reserved.

REPERTOIRE OF MESOSCOPIC CORTICAL ACTIVITY IS NOT REDUCED DURING ANESTHESIA

PubMed Central

HUDETZ, ANTHONY G.; VIZUETE, JEANNETTE A.; PILLAY, SIVESHIGAN; MASHOUR, GEORGE A.

2016-01-01

Consciousness has been linked to the repertoire of brain states at various spatiotemporal scales. Anesthesia is thought to modify consciousness by altering information integration in cortical and thalamocortical circuits. At a mesoscopic scale, neuronal populations in the cortex form synchronized ensembles whose characteristics are presumably state-dependent but this has not been rigorously tested. In this study, spontaneous neuronal activity was recorded with 64-contact microelectrode arrays in primary visual cortex of chronically instrumented, unrestrained rats under stepwise decreasing levels of desflurane anesthesia (8%, 6%, 4%, and 2% inhaled concentrations) and wakefulness (0% concentration). Negative phases of the local field potentials formed compact, spatially contiguous activity patterns (CAPs) that were not due to chance. The number of CAPs was 120% higher in wakefulness and deep anesthesia associated with burst-suppression than at intermediate levels of consciousness. The frequency distribution of CAP sizes followed a power–law with slope −1.5 in relatively deep anesthesia (8–6%) but deviated from that at the lighter levels. Temporal variance and entropy of CAP sizes were lowest in wakefulness (76% and 24% lower at 0% than at 8% desflurane, respectively) but changed little during recovery of consciousness. CAPs categorized by K-means clustering were conserved at all anesthesia levels and wakefulness, although their proportion changed in a state-dependent manner. These observations yield new knowledge about the dynamic landscape of ongoing population activity in sensory cortex at graded levels of anesthesia. The repertoire of population activity and self-organized criticality at the mesoscopic scale do not appear to contribute to anesthetic suppression of consciousness, which may instead depend on large-scale effects, more subtle dynamic properties, or changes outside of primary sensory cortex. PMID:27751957

Repertoire of mesoscopic cortical activity is not reduced during anesthesia.

PubMed

Hudetz, Anthony G; Vizuete, Jeannette A; Pillay, Siveshigan; Mashour, George A

2016-12-17

Consciousness has been linked to the repertoire of brain states at various spatiotemporal scales. Anesthesia is thought to modify consciousness by altering information integration in cortical and thalamocortical circuits. At a mesoscopic scale, neuronal populations in the cortex form synchronized ensembles whose characteristics are presumably state-dependent but this has not been rigorously tested. In this study, spontaneous neuronal activity was recorded with 64-contact microelectrode arrays in primary visual cortex of chronically instrumented, unrestrained rats under stepwise decreasing levels of desflurane anesthesia (8%, 6%, 4%, and 2% inhaled concentrations) and wakefulness (0% concentration). Negative phases of the local field potentials formed compact, spatially contiguous activity patterns (CAPs) that were not due to chance. The number of CAPs was 120% higher in wakefulness and deep anesthesia associated with burst-suppression than at intermediate levels of consciousness. The frequency distribution of CAP sizes followed a power-law with slope -1.5 in relatively deep anesthesia (8-6%) but deviated from that at the lighter levels. Temporal variance and entropy of CAP sizes were lowest in wakefulness (76% and 24% lower at 0% than at 8% desflurane, respectively) but changed little during recovery of consciousness. CAPs categorized by K-means clustering were conserved at all anesthesia levels and wakefulness, although their proportion changed in a state-dependent manner. These observations yield new knowledge about the dynamic landscape of ongoing population activity in sensory cortex at graded levels of anesthesia. The repertoire of population activity and self-organized criticality at the mesoscopic scale do not appear to contribute to anesthetic suppression of consciousness, which may instead depend on large-scale effects, more subtle dynamic properties, or changes outside of primary sensory cortex. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

Ab initio molecular dynamics in a finite homogeneous electric field.

PubMed

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Evaluation of a grid based molecular dynamics approach for polypeptide simulations.

PubMed

Merelli, Ivan; Morra, Giulia; Milanesi, Luciano

2007-09-01

Molecular dynamics is very important for biomedical research because it makes possible simulation of the behavior of a biological macromolecule in silico. However, molecular dynamics is computationally rather expensive: the simulation of some nanoseconds of dynamics for a large macromolecule such as a protein takes very long time, due to the high number of operations that are needed for solving the Newton's equations in the case of a system of thousands of atoms. In order to obtain biologically significant data, it is desirable to use high-performance computation resources to perform these simulations. Recently, a distributed computing approach based on replacing a single long simulation with many independent short trajectories has been introduced, which in many cases provides valuable results. This study concerns the development of an infrastructure to run molecular dynamics simulations on a grid platform in a distributed way. The implemented software allows the parallel submission of different simulations that are singularly short but together bring important biological information. Moreover, each simulation is divided into a chain of jobs to avoid data loss in case of system failure and to contain the dimension of each data transfer from the grid. The results confirm that the distributed approach on grid computing is particularly suitable for molecular dynamics simulations thanks to the elevated scalability.

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

PubMed

Karczyńska, Agnieszka S; Czaplewski, Cezary; Krupa, Paweł; Mozolewska, Magdalena A; Joo, Keehyoung; Lee, Jooyoung; Liwo, Adam

2017-12-05

Molecular simulations restrained to single or multiple templates are commonly used in protein-structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template-restrained canonical molecular dynamics (MD), multiplexed replica-exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse-grained UNRES force field on nine selected proteins, with pseudo-harmonic log-Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non-ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor-quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

PubMed

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms☆

PubMed Central

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-01-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins.

PubMed

Krishnan, Ranjani; Walton, Emily B; Van Vliet, Krystyn J

2009-11-01

As computational resources increase, molecular dynamics simulations of biomolecules are becoming an increasingly informative complement to experimental studies. In particular, it has now become feasible to use multiple initial molecular configurations to generate an ensemble of replicate production-run simulations that allows for more complete characterization of rare events such as ligand-receptor unbinding. However, there are currently no explicit guidelines for selecting an ensemble of initial configurations for replicate simulations. Here, we use clustering analysis and steered molecular dynamics simulations to demonstrate that the configurational changes accessible in molecular dynamics simulations of biomolecules do not necessarily correlate with observed rare-event properties. This informs selection of a representative set of initial configurations. We also employ statistical analysis to identify the minimum number of replicate simulations required to sufficiently sample a given biomolecular property distribution. Together, these results suggest a general procedure for generating an ensemble of replicate simulations that will maximize accurate characterization of rare-event property distributions in biomolecules.

Masses, luminosities and dynamics of galactic molecular clouds

NASA Technical Reports Server (NTRS)

Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.

1987-01-01

Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.

Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

DOE PAGES

Tringe, J. W.; Ileri, N.; Levie, H. W.; ...

2015-08-01

We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more » Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei.

PubMed

Grottesi, Alessandro; Sansom, Mark S P

2003-01-30

Toxins that block voltage-gated potassium (Kv) channels provide a possible template for improved homology models of the Kv pore. In assessing the interactions of Kv channels and their toxins it is important to determine the dynamic flexibility of the toxins. Multiple 10 ns duration molecular dynamics simulations combined with essential dynamics analysis have been used to explore the flexibility of four different Kv channel-blocking toxins. Three toxins (Tc1, AgTx and ChTx) share a common fold. They also share a common pattern of conformational dynamics, as revealed by essential dynamics analysis of the simulation results. This suggests that some aspects of dynamic behaviour are conserved across a single protein fold class. In each of these three toxins, the residue exhibiting minimum flexibility corresponds to a conserved lysine residue that is suggested to interact with the filter domain of the channel. Thus, comparative simulations reveal functionally important conservation of molecular dynamics as well as protein fold across a family of related toxins.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

PubMed

Bottaro, Sandro; Bussi, Giovanni; Kennedy, Scott D; Turner, Douglas H; Lindorff-Larsen, Kresten

2018-05-01

RNA molecules are key players in numerous cellular processes and are characterized by a complex relationship between structure, dynamics, and function. Despite their apparent simplicity, RNA oligonucleotides are very flexible molecules, and understanding their internal dynamics is particularly challenging using experimental data alone. We show how to reconstruct the conformational ensemble of four RNA tetranucleotides by combining atomistic molecular dynamics simulations with nuclear magnetic resonance spectroscopy data. The goal is achieved by reweighting simulations using a maximum entropy/Bayesian approach. In this way, we overcome problems of current simulation methods, as well as in interpreting ensemble- and time-averaged experimental data. We determine the populations of different conformational states by considering several nuclear magnetic resonance parameters and point toward properties that are not captured by state-of-the-art molecular force fields. Although our approach is applied on a set of model systems, it is fully general and may be used to study the conformational dynamics of flexible biomolecules and to detect inaccuracies in molecular dynamics force fields.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Nonadiabatic ab initio molecular dynamics with PME-ONIOM scheme of photoisomerization reaction between 1,3-cyclohexadiene and 1,3,5-cis-hexatriene in solution phase

NASA Astrophysics Data System (ADS)

Ohta, Ayumi; Kobayashi, Osamu; Danielache, Sebastian O.; Nanbu, Shinkoh

2017-03-01

The ultra-fast photoisomerization reactions between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) in both hexane and ethanol solvents were revealed by nonadiabatic ab initio molecular dynamics (AI-MD) with a particle-mesh Ewald summation method and our Own N-layered Integrated molecular Orbital and molecular Mechanics model (PME-ONIOM) scheme. Zhu-Nakamura version trajectory surface hopping method (ZN-TSH) was employed to treat the ultra-fast nonadiabatic decaying process. The results for hexane and ethanol simulations reasonably agree with experimental data. The high nonpolar-nonpolar affinity between CHD and the solvent was observed in hexane solvent, which definitely affected the excited state lifetimes, the product branching ratio of CHD:HT, and solute (CHD) dynamics. In ethanol solvent, however, the CHD solute was isomerized in the solvent cage caused by the first solvation shell. The photochemical dynamics in ethanol solvent results in the similar property to the process appeared in vacuo (isolated CHD dynamics).

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

Exciton dynamics of C60-based single-photon emitters explored by Hanbury Brown-Twiss scanning tunnelling microscopy.

PubMed

Merino, P; Große, C; Rosławska, A; Kuhnke, K; Kern, K

2015-09-29

Exciton creation and annihilation by charges are crucial processes for technologies relying on charge-exciton-photon conversion. Improvement of organic light sources or dye-sensitized solar cells requires methods to address exciton dynamics at the molecular scale. Near-field techniques have been instrumental for this purpose; however, characterizing exciton recombination with molecular resolution remained a challenge. Here, we study exciton dynamics by using scanning tunnelling microscopy to inject current with sub-molecular precision and Hanbury Brown-Twiss interferometry to measure photon correlations in the far-field electroluminescence. Controlled injection allows us to generate excitons in solid C60 and let them interact with charges during their lifetime. We demonstrate electrically driven single-photon emission from localized structural defects and determine exciton lifetimes in the picosecond range. Monitoring lifetime shortening and luminescence saturation for increasing carrier injection rates provides access to charge-exciton annihilation dynamics. Our approach introduces a unique way to study single quasi-particle dynamics on the ultimate molecular scale.

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

NASA Astrophysics Data System (ADS)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M. N.; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-01

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins.

PubMed

Walczewska-Szewc, Katarzyna; Deplazes, Evelyne; Corry, Ben

2015-07-14

Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for relatively simple systems. An example where this problem arises is in the simulation of dye-labeled proteins, which are now being widely used in the design and interpretation of Förster resonance energy transfer (FRET) experiments. In this study, MD simulations are used to characterize the motion of two commonly used FRET dyes attached to an immobilized chain of polyproline. Even in this simple system, the dyes exhibit complex behavior that is a mixture of fast and slow motions. Consequently, very long MD simulations are required to sufficiently sample the entire range of dye motion. Here, we compare the ability of enhanced sampling methods to reproduce the behavior of fluorescent labels on proteins. In particular, we compared Accelerated Molecular Dynamics (AMD), metadynamics, Replica Exchange Molecular Dynamics (REMD), and High Temperature Molecular Dynamics (HTMD) to equilibrium MD simulations. We find that, in our system, all of these methods improve the sampling of the dye motion, but the most significant improvement is achieved using REMD.

Optimizing legacy molecular dynamics software with directive-based offload

DOE PAGES

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

2015-05-14

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

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

PubMed

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

DOE PAGES

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; ...

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities aremore » treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Furthermore, both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.« less

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

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

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities aremore » treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Furthermore, both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.« less

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

PubMed Central

De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

Visualizing global properties of a molecular dynamics trajectory.

PubMed

Zhou, Hao; Li, Shangyang; Makowski, Lee

2016-01-01

Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule. © 2015 Wiley Periodicals, Inc.

Multigrid based First-Principles Molecular Dynamics

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

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

PubMed

Yoshioka, Sumie; Aso, Yukio; Kojima, Shigeo

2003-06-01

To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective.

PubMed

Momin, Mohamed; Xin, Yao; Hamelberg, Donald

2017-06-29

Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis-trans isomerization of a peptidyl-prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic. Here, we explore the conformational dynamics and free energy landscape of the SH2 domain of interleukin-2-inducible T-cell or tyrosine kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch and its binding pocket of the phosphotyrosine motif. We use multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs. We show that cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly coupled to the dynamics of the binding pocket of the phosphotyrosine motif, in agreement with previous NMR experiments. Unlike the cis state that is localized and less dynamic in a single free energy basin, the trans state samples two distinct conformations of the binding pocket-one that recognizes the phosphotyrosine motif and the other that is somewhat similar to that of the cis state. The results provide an atomic-level description of a less well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant subcellular processes and the identification of these elusive molecular switches in other proteins.

Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

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

Bowers, Geoffrey

United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

PubMed

Sakuraba, Shun; Asai, Kiyoshi; Kameda, Tomoshi

2015-11-05

The dimerization free energies of RNA-RNA duplexes are fundamental values that represent the structural stability of RNA complexes. We report a comparative analysis of RNA-RNA duplex dimerization free-energy changes upon mutations, estimated from a molecular dynamics simulation and experiments. A linear regression for nine pairs of double-stranded RNA sequences, six base pairs each, yielded a mean absolute deviation of 0.55 kcal/mol and an R(2) value of 0.97, indicating quantitative agreement between simulations and experimental data. The observed accuracy indicates that the molecular dynamics simulation with the current molecular force field is capable of estimating the thermodynamic properties of RNA molecules.

Modulation of ozone toxicity with changes in ambient temperature in the unanesthetized, unrestrained rat

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

Watkinson, W.P.; Wiester, M.J.

1991-03-15

Previous studies from this laboratory have demonstrated an attenuating effect of moderate decreases in body core temperature (T{sub co}) on the toxic response to xenobiotic agents. This study examined an additional modulating effect induced by changes in ambient temperature (T{sub a}). Male Fischer 344 rats were implanted with radiometry transmitters that permitted continuous monitoring of T{sub co}, activity, and electrocardiogram (ECG); heart rate (HR) was derived from the ECG signal. Animals were divided into nine treatment groups and continuously exposed to one of three concentrations of O{sub 3} for 48 hrs while maintained at one of three T{sub a}'s. O{submore » 3} exposure led to hypothermia and bradycardia at all three T{sub a}'s. Decreases in T{sub co} and HR ranged from 1.5C and 75 bpm in the high T{sub a} group to 6.1C and 250 bpm in the low T{sub a} group. The only lethalities occurred in the high O{sub 3}-low T{sub a} group. Following O{sub 3} exposure, rats were anesthetized with urethane, intubated, and their lungs were lavaged with warm saline. The number of cells/ml in lavage fluid increased proportionally with decreases in T{sub a} and increases in O{sub 3} concentration. Cellular debris and the ratio of white cells/alveolar macrophages increased with increases in O{sub 3}. These results demonstrate the profound impact of T{sub a} on T{sub co} and the subsequent toxic response in the conscious, unrestrained rat exposed to O{sub 3}.« less

Behavior and modeling of two-dimensional precedence effect in head-unrestrained cats

PubMed Central

Ruhland, Janet L.; Yin, Tom C. T.

2015-01-01

The precedence effect (PE) is an auditory illusion that occurs when listeners localize nearly coincident and similar sounds from different spatial locations, such as a direct sound and its echo. It has mostly been studied in humans and animals with immobile heads in the horizontal plane; speaker pairs were often symmetrically located in the frontal hemifield. The present study examined the PE in head-unrestrained cats for a variety of paired-sound conditions along the horizontal, vertical, and diagonal axes. Cats were trained with operant conditioning to direct their gaze to the perceived sound location. Stereotypical PE-like behaviors were observed for speaker pairs placed in azimuth or diagonally in the frontal hemifield as the interstimulus delay was varied. For speaker pairs in the median sagittal plane, no clear PE-like behavior occurred. Interestingly, when speakers were placed diagonally in front of the cat, certain PE-like behavior emerged along the vertical dimension. However, PE-like behavior was not observed when both speakers were located in the left hemifield. A Hodgkin-Huxley model was used to simulate responses of neurons in the medial superior olive (MSO) to sound pairs in azimuth. The novel simulation incorporated a low-threshold potassium current and frequency mismatches to generate internal delays. The model exhibited distinct PE-like behavior, such as summing localization and localization dominance. The simulation indicated that certain encoding of the PE could have occurred before information reaches the inferior colliculus, and MSO neurons with binaural inputs having mismatched characteristic frequencies may play an important role. PMID:26133795

Development of an imaging system for in vivo real-time monitoring of neuronal activity in deep brain of free-moving rats.

PubMed

Iijima, Norio; Miyamoto, Shinji; Matsumoto, Keisuke; Takumi, Ken; Ueta, Yoichi; Ozawa, Hitoshi

2017-09-01

We have newly developed a system that allows monitoring of the intensity of fluorescent signals from deep brains of rats transgenically modified to express enhanced green fluorescent protein (eGFP) via an optical fiber. One terminal of the optical fiber was connected to a blue semiconductor laser oscillator/green fluorescence detector. The other terminal was inserted into the vicinity of the eGFP-expressing neurons. Since the optical fiber was vulnerable to twisting stresses caused by animal movement, we also developed a cage in which the floor automatically turns, in response to the turning of the rat's head. This relieved the twisting stress on the optical fiber. The system then enabled real-time monitoring of fluorescence in awake and unrestrained rats over many hours. Using this system, we could continuously monitor eGFP-expression in arginine vasopressin-eGFP transgenic rats. Moreover, we observed an increase of eGFP-expression in the paraventricular nucleus under salt-loading conditions. We then performed in vivo imaging of eGFP-expressing GnRH neurons in the hypothalamus, via a bundle consisting of 3000 thin optical fibers. With the combination of the optical fiber bundle connection to the fluorescence microscope, and the special cage system, we were able to capture and retain images of eGFP-expressing neurons from free-moving rats. We believe that our newly developed method for monitoring and imaging eGFP-expression in deep brain neurons will be useful for analysis of neuronal functions in awake and unrestrained animals for long durations.

Neural correlates of restrained eaters' high susceptibility to food cues: An fMRI study.

PubMed

Wang, Yu; Dong, Debo; Todd, Jackson; Du, Jie; Yang, Zhou; Lu, Hui; Chen, Hong

2016-09-19

Many studies have reported that specific susceptibility to food cues plays an important role in disordered eating behavior. However, whether restraint status modulates the neural bases of attentional bias to different types of food cues remains unknown. Thus, functional magnetic resonance imaging (fMRI) was conducted in individuals (12 restraint eaters, 12 unrestraint eaters) exposed to high/low-energy food and neutral images while performing a two-choice oddball task. The results indicated that restrained eaters responded more quickly to high-energy food images than to neutral and low-energy food images. More notably, compared with unrestrained eaters, restrained eaters showed faster reaction times, hyper-activation in a much wider array of reward (e.g., insula/orbitofrontal cortex), attention (superior frontal gyrus) and visual processing (e.g., superior temporal gyrus) regions, and hypo-activation in cognitive control areas (e.g., anterior cingulate) in response to high-energy food cues. Furthermore, among restrained eaters, the longest reaction times were found for low-energy food images, and activation of the attention and visual-related cortex (e.g., superior parietal gyrus) in the low-neutral contrast condition was significantly stronger than in unrestrained eaters. These findings contribute to our understanding of susceptibility to food cues: in addition to the special sensitivity (attentional bias) to high-energy food images, restrained eaters may also be more sensitive (allocate more attentional resources) to low-energy food images. These potential neural bases of restrained eaters may help clarify why dieting to lose or maintain weight is so often unsuccessful. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Gaze pursuit responses in nucleus reticularis tegmenti pontis of head-unrestrained macaques.

PubMed

Suzuki, David A; Betelak, Kathleen F; Yee, Robert D

2009-01-01

Eye-head gaze pursuit-related activity was recorded in rostral portions of the nucleus reticularis tegmenti pontis (rNRTP) in alert macaques. The head was unrestrained in the horizontal plane, and macaques were trained to pursue a moving target either with their head, with the eyes stationary in the orbits, or with their eyes, with their head voluntarily held stationary in space. Head-pursuit-related modulations in rNRTP activity were observed with some cells exhibiting increases in firing rate with increases in head-pursuit frequency. For many units, this head-pursuit response appeared to saturate at higher frequencies (>0.6 Hz). The response phase re:peak head-pursuit velocity formed a continuum, containing cells that could encode head-pursuit velocity and those encoding head-pursuit acceleration. The latter cells did not exhibit head position-related activity. Sensitivities were calculated with respect to peak head-pursuit velocity and averaged 1.8 spikes/s/deg/s. Of the cells that were tested for both head- and eye-pursuit-related activity, 86% exhibited responses to both head- and eye-pursuit and therefore carried a putative gaze-pursuit signal. For these gaze-pursuit units, the ratio of head to eye response sensitivities averaged approximately 1.4. Pursuit eccentricity seemed to affect head-pursuit response amplitude even in the absence of a head position response per se. The results indicated that rNRTP is a strong candidate for the source of an active head-pursuit signal that projects to the cerebellum, specifically to the target-velocity and gaze-velocity Purkinje cells that have been observed in vermal lobules VI and VII.

Mechanisms of Normal and Abnormal Endometrial Bleeding

PubMed Central

Lockwood, Charles J.

2011-01-01

Expression of tissue factor (TF), the primary initiator of coagulation, is enhanced in decidualized human endometrial stromal cells (HESC) during the progesterone-dominated luteal phase. Progesterone also augments a second HESC hemostatic factor, plasminogen activator inhibitor-1 (PAI-1). In contrast, progestins inhibit HESC matrix metalloproteinase (MMP)-1, 3 and 9 expression to stabilize endometrial stromal and vascular extracellular matrix. Through these mechanisms decidualized endometrium is rendered both hemostatic and resistant to excess trophoblast invasion in the mid-luteal phase and throughout gestation to prevent hemorrhage and accreta. In non-fertile cycles, progesterone withdrawal results in decreased HESC TF and PAI-expression and increased MMP activity and inflammatory cytokine production promoting the controlled hemorrhage of menstruation and related tissue sloughing. In contrast to these well ordered biochemical processes, unpredictable endometrial bleeding associated with anovulation reflects absence of progestational effects on TF, PAI-1 and MMP activity as well as unrestrained angiogenesis rendering the endometrium non-hemostatic, proteolytic and highly vascular. Abnormal bleeding associated with long-term progestin-only contraceptives results not from impaired hemostasis but from unrestrained angiogenesis leading to large fragile endometrial vessels. This abnormal angiogenesis reflects progestational inhibition of endometrial blood flow promoting local hypoxia and generation of reactive oxygen species that increase production of angiogenic factors such as vascular endothelial growth factor (VEGF) in HESCs and Angiopoietin-2 (Ang-2) in endometrial endothelial cells while decreasing HESC expression of angiostatic, Ang-1. The resulting vessel fragility promotes bleeding. Aberrant angiogenesis also underlies abnormal bleeding associated with myomas and endometrial polyps however there are gaps in our understanding of this pathology. PMID:21499503

Effects of environmental and pharmacological manipulations on a novel delayed nonmatching-to-sample 'working memory' procedure in unrestrained rhesus monkeys.

PubMed

Hutsell, Blake A; Banks, Matthew L

2015-08-15

Working memory is a domain of 'executive function.' Delayed nonmatching-to-sample (DNMTS) procedures are commonly used to examine working memory in both human laboratory and preclinical studies. The aim was to develop an automated DNMTS procedure maintained by food pellets in rhesus monkeys using a touch-sensitive screen attached to the housing chamber. Specifically, the DNMTS procedure was a 2-stimulus, 2-choice recognition memory task employing unidimensional discriminative stimuli and randomized delay interval presentations. DNMTS maintained a delay-dependent decrease in discriminability that was independent of the retention interval distribution. Eliminating reinforcer availability during a single delay session or providing food pellets before the session did not systematically alter accuracy, but did reduce total choices. Increasing the intertrial interval enhanced accuracy at short delays. Acute Δ(9)-THC pretreatment produced delay interval-dependent changes in the forgetting function at doses that did not alter total choices. Acute methylphenidate pretreatment only decreased total choices. All monkeys were trained to perform NMTS at the 1s training delay within 60 days of initiating operant touch training. Furthermore, forgetting functions were reliably delay interval-dependent and stable over the experimental period (∼6 months). Consistent with previous studies, increasing the intertrial interval improved DNMTS performance, whereas Δ(9)-THC disrupted DNMTS performance independent of changes in total choices. Overall, the touchscreen-based DNMTS procedure described provides an efficient method for training and testing experimental manipulations on working memory in unrestrained rhesus monkeys. Copyright © 2015 Elsevier B.V. All rights reserved.

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

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

2016-07-14

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

Inhibition of Metalloprotease Botulinum Serotype A from a Pseudo-Peptide Binding Mode to a Small Molecule that is Active in Primary Neurons

DTIC Science & Technology

2007-02-16

a modeled binding mode for inhibitor 2-mercapto-3-phenylpropionyl-RATKML (Ki 330 nM) was generated, and required the use of a molecular dynamic ...2-mercapto-3-phenylpropionyl-RATKML (K(i) = 330 nM) was generated, and required the use of a molecular dynamic conformer of the enzyme displaying the...SiliconGraphicsOctane 2. Insight II (Accelrys, San Diego, CA) was used to build and inspect models. Energy refinement and molecular dynamics were performed using the

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

PubMed

Dalby, Andrew; Shamsir, Mohd Shahir

2015-01-01

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

PubMed Central

Dalby, Andrew; Shamsir, Mohd Shahir

2015-01-01

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation. PMID:26539292

AceCloud: Molecular Dynamics Simulations in the Cloud.

PubMed

Harvey, M J; De Fabritiis, G

2015-05-26

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

Substructured multibody molecular dynamics.

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

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James

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.

Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies

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

Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu

2016-03-28

We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.

Electronic Spectra from Molecular Dynamics: A Simple Approach.

DTIC Science & Technology

1983-10-01

82.30.Cr. 33.20K. S2.40.1s The authors provided phototypeset copy for this paper using REFER TlL EON, TOFF On UNIX I ELECTRONIC SPECTRA FROM MOLECULAR...Alamos National Laboratory Los Alamos, NM 87545 I. INTRODUCTION In this paper we show how molecular dynamics can be used in a simple manner to com...could equally use Monte Carlo or explicit integration over coordinates to compute equilibrium electronic absorption bands. How- ever, molecular

Crossed Molecular Beam Studies and Dynamics of Decomposition of Chemically Activated Radicals

DOE R&D Accomplishments Database

Lee, Y. T.

1973-09-01

The power of the crossed molecular beams method in the investigation of the dynamics of chemical reactions lies mainly in the direct observation of the consequences of single collisions of well controlled reactant molecules. The primary experimental observations which provide information on reaction dynamics are the measurements of angular and velocity distributions of reaction products.

Quantum dynamics of light-driven chiral molecular motors.

PubMed

Yamaki, Masahiro; Nakayama, Shin-ichiro; Hoki, Kunihito; Kono, Hirohiko; Fujimura, Yuichi

2009-03-21

The results of theoretical studies on quantum dynamics of light-driven molecular motors with internal rotation are presented. Characteristic features of chiral motors driven by a non-helical, linearly polarized electric field of light are explained on the basis of symmetry argument. The rotational potential of the chiral motor is characterized by a ratchet form. The asymmetric potential determines the directional motion: the rotational direction is toward the gentle slope of the asymmetric potential. This direction is called the intuitive direction. To confirm the unidirectional rotational motion, results of quantum dynamical calculations of randomly-oriented molecular motors are presented. A theoretical design of the smallest light-driven molecular machine is presented. The smallest chiral molecular machine has an optically driven engine and a running propeller on its body. The mechanisms of transmission of driving forces from the engine to the propeller are elucidated by using a quantum dynamical treatment. The results provide a principle for control of optically-driven molecular bevel gears. Temperature effects are discussed using the density operator formalism. An effective method for ultrafast control of rotational motions in any desired direction is presented with the help of a quantum control theory. In this method, visible or UV light pulses are applied to drive the motor via an electronic excited state. A method for driving a large molecular motor consisting of an aromatic hydrocarbon is presented. The molecular motor is operated by interactions between the induced dipole of the molecular motor and the electric field of light pulses.

GPCRs: What Can We Learn from Molecular Dynamics Simulations?

PubMed

Velgy, Naushad; Hedger, George; Biggin, Philip C

2018-01-01

Advances in the structural biology of G-protein Coupled Receptors have resulted in a significant step forward in our understanding of how this important class of drug targets function at the molecular level. However, it has also become apparent that they are very dynamic molecules, and moreover, that the underlying dynamics is crucial in shaping the response to different ligands. Molecular dynamics simulations can provide unique insight into the dynamic properties of GPCRs in a way that is complementary to many experimental approaches. In this chapter, we describe progress in three distinct areas that are particularly difficult to study with other techniques: atomic level investigation of the conformational changes that occur when moving between the various states that GPCRs can exist in, the pathways that ligands adopt during binding/unbinding events and finally, the influence of lipids on the conformational dynamics of GPCRs.

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport.

PubMed

Kaplan, Luke; Ierokomos, Athena; Chowdary, Praveen; Bryant, Zev; Cui, Bianxiao

2018-03-01

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors.

Nanoscopic length scale dependence of hydrogen bonded molecular associates’ dynamics in methanol

PubMed Central

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

2017-01-01

In a recent paper [C. E. Bertrand et al., J. Chem. Phys. 145, 014502 (2016)], we have shown that the collective dynamics of methanol shows a fast relaxation process related to the standard density-fluctuation heat mode and a slow non-Fickian mode originating from the hydrogen bonded molecular associates. Here we report on the length scale dependence of this slow relaxation process. Using quasielastic neutron scattering and molecular dynamics simulations, we show that the dynamics of the slow process is affected by the structuring of the associates, which is accessible through polarized neutron diffraction experiments. Using a series of partially deuterated samples, the dynamics of the associates is investigated and is found to have a similar time scale to the lifetime of hydrogen bonding in the system. Both the structural relaxation and the dynamics of the associates are thermally activated by the breaking of hydrogen bonding. PMID:28527447

Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping

NASA Astrophysics Data System (ADS)

Lu, Jianfeng; Zhou, Zhennan

2018-02-01

To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.

Solvated molecular dynamics of LiCN isomerization: All-atom argon solvent versus a generalized Langevin bath.

PubMed

Junginger, Andrej; Garcia-Muller, Pablo L; Borondo, F; Benito, R M; Hernandez, Rigoberto

2016-01-14

The reaction rate rises and falls with increasing density or friction when a molecule is activated by collisions with the solvent particles. This so-called Kramers turnover has recently been observed in the isomerization reaction of LiCN in an argon bath. In this paper, we demonstrate by direct comparison with those results that a reduced-dimensional (generalized) Langevin description gives rise to similar reaction dynamics as the corresponding (computationally expensive) full molecular dynamics calculations. We show that the density distributions within the Langevin description are in direct agreement with the full molecular dynamics results and that the turnover in the reaction rates is reproduced qualitatively and quantitatively at different temperatures.

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

PubMed

Hamelberg, Donald; Shen, Tongye; McCammon, J Andrew

2005-02-16

The presence of serine/threonine-proline motifs in proteins provides a conformational switching mechanism of the backbone through the cis/trans isomerization of the peptidyl-prolyl (omega) bond. The reversible phosphorylation of the serine/threonine modulates this switching in regulatory proteins to alter signaling and transcription. However, the mechanism is not well understood. This is partly because cis/trans isomerization is a very slow process and, hence, difficult to study. We have used our accelerated molecular dynamics method to study the cis/trans proline isomerization, preferred backbone conformation of a serine-proline motif, and the effects of phosphorylation of the serine residue. We demonstrate that, unlike normal molecular dynamics, the accelerated molecular dynamics allows for the system to escape very easily from the trans isomer to cis isomer, and vice versa. Moreover, for both the unphosphorylated and phosphorylated peptides, the statistical thermodynamic properties are recaptured, and the results are consistent with experimental values. Isomerization of the proline omega bond is shown to be asymmetric and strongly dependent on the psi backbone angle before and after phosphorylation. The rates of escape decrease after phosphorylation. Also, the alpha-helical backbone conformation is more favored after phosphorylation. This accelerated molecular dynamics approach provides a general approach for enhancing the conformational transitions of molecular systems without having prior knowledge of the location of the minima and barriers on the potential-energy landscape.

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium.

PubMed

Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

2017-12-01

The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium

NASA Astrophysics Data System (ADS)

Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

2017-07-01

The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Molecular dynamics simulations of substitutional diffusion

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

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

2016-12-18

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

Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion

USDA-ARS?s Scientific Manuscript database

Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

DTIC Science & Technology

2012-08-30

drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD) with Hamiltonian Replica Exchange and...conformations that are virtually identical to WT [10]. Molecular simulations that rigorously model the microscopic structure and thermodynamics PLOS...influenza neuraminidase (NA) that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD) with

Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2012-01-01

Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based “conformational selection” of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected residue clusters may be a rather general functional requirement encoded across molecular chaperones. The obtained insights may be useful in guiding discovery of allosteric Hsp90 inhibitors targeting protein interfaces with co-chaperones and protein binding clients. PMID:22624053

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

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

Hardy, David J., E-mail: dhardy@illinois.edu; Schulten, Klaus; Wolff, Matthew A.

2016-03-21

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

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

PubMed

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

2016-03-21

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

Nonadiabatic electron wavepacket dynamics behind molecular autoionization

NASA Astrophysics Data System (ADS)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Spörlein, Sebastian; Carstens, Heiko; Satzger, Helmut; Renner, Christian; Behrendt, Raymond; Moroder, Luis; Tavan, Paul; Zinth, Wolfgang; Wachtveitl, Josef

2002-06-01

Femtosecond time-resolved spectroscopy on model peptides with built-in light switches combined with computer simulation of light-triggered motions offers an attractive integrated approach toward the understanding of peptide conformational dynamics. It was applied to monitor the light-induced relaxation dynamics occurring on subnanosecond time scales in a peptide that was backbone-cyclized with an azobenzene derivative as optical switch and spectroscopic probe. The femtosecond spectra permit the clear distinguishing and characterization of the subpicosecond photoisomerization of the chromophore, the subsequent dissipation of vibrational energy, and the subnanosecond conformational relaxation of the peptide. The photochemical cis/trans-isomerization of the chromophore and the resulting peptide relaxations have been simulated with molecular dynamics calculations. The calculated reaction kinetics, as monitored by the energy content of the peptide, were found to match the spectroscopic data. Thus we verify that all-atom molecular dynamics simulations can quantitatively describe the subnanosecond conformational dynamics of peptides, strengthening confidence in corresponding predictions for longer time scales.

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions.

PubMed

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-20

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-01

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.

Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers

NASA Astrophysics Data System (ADS)

Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen

1999-06-01

Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.

Alignment dynamics of diffusive scalar gradient in a two-dimensional model flow

NASA Astrophysics Data System (ADS)

Gonzalez, M.

2018-04-01

The Lagrangian two-dimensional approach of scalar gradient kinematics is revisited accounting for molecular diffusion. Numerical simulations are performed in an analytic, parameterized model flow, which enables considering different regimes of scalar gradient dynamics. Attention is especially focused on the influence of molecular diffusion on Lagrangian statistical orientations and on the dynamics of scalar gradient alignment.

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

PubMed

Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V

2014-08-06

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation.

PubMed

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-08-15

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA.

The Influence of Fatty Acids on the GpA Dimer Interface by Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-01-01

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA. PMID:25196522

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

PubMed

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-07-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks

NASA Astrophysics Data System (ADS)

Fahrenthold, Eric; Bass, Joseph

2015-06-01

Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.

Nonlinear dynamics and damage induced properties of soft matter with application in oncology

NASA Astrophysics Data System (ADS)

Naimark, O.

2017-09-01

Molecular-morphological signs of oncogenesis could be linked to multiscale collective effects in molecular, cell and tissue related to defects (damage) dynamics. It was shown that nonlinear behavior of biological systems can be linked to the existence of characteristic collective open state modes providing the coherent expression dynamics. New type of criticality in nonequilibrium systems with defects—structural-scaling transition allows the definition of the `driving force' for a biological soft matter related to consolidated open states. The set of collective open states (breathers, autosolitons and blow-up modes) in the molecular ensembles provides the collective expression dynamics to attract the entire system (cell, tissue) toward a few preferred global states. The co-existence of three types of collective modes determines the multifractal scenario of biological soft matter dynamics. The appearance of `globally convergent' dynamics corresponding to the coherent behavior of multiscale blow-up open states (blow-up gene expression) leads to anomalous localized softening (blow-up localized damage) and the subjection of the cells (or tissue) to monofractal dynamics. This dynamics can be associated with cancer progression.

A human transcription factor in search mode.

PubMed

Hauser, Kevin; Essuman, Bernard; He, Yiqing; Coutsias, Evangelos; Garcia-Diaz, Miguel; Simmerling, Carlos

2016-01-08

Transcription factors (TF) can change shape to bind and recognize DNA, shifting the energy landscape from a weak binding, rapid search mode to a higher affinity recognition mode. However, the mechanism(s) driving this conformational change remains unresolved and in most cases high-resolution structures of the non-specific complexes are unavailable. Here, we investigate the conformational switch of the human mitochondrial transcription termination factor MTERF1, which has a modular, superhelical topology complementary to DNA. Our goal was to characterize the details of the non-specific search mode to complement the crystal structure of the specific binding complex, providing a basis for understanding the recognition mechanism. In the specific complex, MTERF1 binds a significantly distorted and unwound DNA structure, exhibiting a protein conformation incompatible with binding to B-form DNA. In contrast, our simulations of apo MTERF1 revealed significant flexibility, sampling structures with superhelical pitch and radius complementary to the major groove of B-DNA. Docking these structures to B-DNA followed by unrestrained MD simulations led to a stable complex in which MTERF1 was observed to undergo spontaneous diffusion on the DNA. Overall, the data support an MTERF1-DNA binding and recognition mechanism driven by intrinsic dynamics of the MTERF1 superhelical topology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

NASA Astrophysics Data System (ADS)

Kitao, Akio; Hirata, Fumio; Gō, Nobuhiro

1991-12-01

The effects of solvent on the conformation and dynamics of protein is studied by computer simulation. The dynamics is studied by focusing mainly on collective motions of the protein molecule. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water are applied to melittin, the major component of bee venom. To define collective motions principal, component analysis as well as normal mode analysis has been carried out. The principal components with large fluctuation amplitudes have a very good correspondence with the low-frequency normal modes. Trajectories of the molecular dynamics simulation are projected onto the principal axes. From the projected motions time correlation functions are calculated. The results indicate that the very-low-frequency modes, whose frequencies are less than ≈ 50 cm -1, are overdamping in water with relaxation times roushly twice as long as the period of the oscillatory motion. Effective Langevin mode analysis is carried out by using the friction coefficient matrix determined from the velocity correlation function calculated from the molecular dynamics trajectory in water. This analysis reproduces the results of the simulation in water reasonably well. The presence of the solvent water is found also to affect the shape of the potential energy surface in such a way that it produces many local minima with low-energy barriers in between, the envelope of which is given by the surface in vacuum. Inter-minimum transitions endow the conformational dynamics of proteins in water another diffusive character, which already exists in the intra-minimum collective motions.

Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.

PubMed

Zanchi, Fernando Berton; Caceres, Rafael Andrade; Stabeli, Rodrigo Guerino; de Azevedo, Walter Filgueira

2010-03-01

Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed.

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

System and method for generating motion corrected tomographic images

DOEpatents

Gleason, Shaun S [Knoxville, TN; Goddard, Jr., James S.

2012-05-01

A method and related system for generating motion corrected tomographic images includes the steps of illuminating a region of interest (ROI) to be imaged being part of an unrestrained live subject and having at least three spaced apart optical markers thereon. Simultaneous images are acquired from a first and a second camera of the markers from different angles. Motion data comprising 3D position and orientation of the markers relative to an initial reference position is then calculated. Motion corrected tomographic data obtained from the ROI using the motion data is then obtained, where motion corrected tomographic images obtained therefrom.

Chronic recording of regenerating VIIIth nerve axons with a sieve electrode

NASA Technical Reports Server (NTRS)

Mensinger, A. F.; Anderson, D. J.; Buchko, C. J.; Johnson, M. A.; Martin, D. C.; Tresco, P. A.; Silver, R. B.; Highstein, S. M.

2000-01-01

A micromachined silicon substrate sieve electrode was implanted within transected toadfish (Opsanus tau) otolith nerves. High fidelity, single unit neural activity was recorded from seven alert and unrestrained fish 30 to 60 days after implantation. Fibrous coatings of genetically engineered bioactive protein polymers and nerve guide tubes increased the number of axons regenerating through the electrode pores when compared with controls. Sieve electrodes have potential as permanent interfaces to the nervous system and to bridge missing connections between severed or damaged nerves and muscles. Recorded impulses might also be amplified and used to control prosthetic devices.

Two-dimensional unsteady lift problems in supersonic flight

NASA Technical Reports Server (NTRS)

Heaslet, Max A; Lomax, Harvard

1949-01-01

The variation of pressure distribution is calculated for a two-dimensional supersonic airfoil either experiencing a sudden angle-of-attack change or entering a sharp-edge gust. From these pressure distributions the indicial lift functions applicable to unsteady lift problems are determined for two cases. Results are presented which permit the determination of maximum increment in lift coefficient attained by an unrestrained airfoil during its flight through a gust. As an application of these results, the minimum altitude for safe flight through a specific gust is calculated for a particular supersonic wing of given strength and wing loading.

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

Molecular alignment and orientation with a hybrid Raman scattering technique

NASA Astrophysics Data System (ADS)

Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

2012-11-01

We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

PubMed

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

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

Thermal characterization assessment of rigid and flexible water models in a nanogap using molecular dynamics

NASA Astrophysics Data System (ADS)

Akıner, Tolga; Mason, Jeremy; Ertürk, Hakan

2017-11-01

The thermal properties of the TIP3P and TIP5P water models are investigated using equilibrium and non-equilibrium molecular dynamics techniques in the presence of solid surfaces. The performance of the non-equilibrium technique for rigid molecules is found to depend significantly on the distribution of atomic degrees of freedom. An improved approach to distribute atomic degrees of freedom is proposed for which the thermal conductivity of the TIP5P model agrees more closely with equilibrium molecular dynamics and experimental results than the existing state of the art.

Understanding the kinetics of ligand binding to globins with molecular dynamics simulations: the necessity of multiple state models.

PubMed

Estarellas Martin, Carolina; Seira Castan, Constantí; Luque Garriga, F Javier; Bidon-Chanal Badia, Axel

2015-10-01

Residue conformational changes and internal cavity migration processes play a key role in regulating the kinetics of ligand migration and binding events in globins. Molecular dynamics simulations have demonstrated their value in the study of these processes in different haemoglobins, but derivation of kinetic data demands the use of more complex techniques like enhanced sampling molecular dynamics methods. This review discusses the different methodologies that are currently applied to study the ligand migration process in globins and highlight those specially developed to derive kinetic data. Copyright © 2015 Elsevier Ltd. All rights reserved.

The dance of molecules: new dynamical perspectives on highly excited molecular vibrations.

PubMed

Kellman, Michael E; Tyng, Vivian

2007-04-01

At low energies, molecular vibrational motion is described by the normal modes model. This model breaks down at higher energy, with strong coupling between normal modes and onset of chaotic dynamics. New anharmonic modes are born in bifurcations, or branchings of the normal modes. Knowledge of these new modes is obtained through the window of frequency-domain spectroscopy, using techniques of nonlinear classical dynamics. It may soon be possible to "watch" molecular rearrangement reactions spectroscopically. Connections are being made with reaction rate theories, condensed phase systems, and motions of electrons in quantum dots.

General framework for constraints in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kneller, Gerald R.

2017-06-01

The article presents a theoretical framework for molecular dynamics simulations of complex systems subject to any combination of holonomic and non-holonomic constraints. Using the concept of constrained inverse matrices both the particle accelerations and the associated constraint forces can be determined from given external forces and kinematical conditions. The formalism enables in particular the construction of explicit kinematical conditions which lead to the well-known Nosé-Hoover type equations of motion for the simulation of non-standard molecular dynamics ensembles. Illustrations are given for a few examples and an outline is presented for a numerical implementation of the method.

Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

PubMed Central

Chng, Choon-Peng; Yang, Lee-Wei

2008-01-01

Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

Metal-organic frameworks with dynamic interlocked components

NASA Astrophysics Data System (ADS)

Vukotic, V. Nicholas; Harris, Kristopher J.; Zhu, Kelong; Schurko, Robert W.; Loeb, Stephen J.

2012-06-01

The dynamics of mechanically interlocked molecules such as rotaxanes and catenanes have been studied in solution as examples of rudimentary molecular switches and machines, but in this medium, the molecules are randomly dispersed and their motion incoherent. As a strategy for achieving a higher level of molecular organization, we have constructed a metal-organic framework material using a [2]rotaxane as the organic linker and binuclear Cu(II) units as the nodes. Activation of the as-synthesized material creates a void space inside the rigid framework that allows the soft macrocyclic ring of the [2]rotaxane to rotate rapidly, unimpeded by neighbouring molecular components. Variable-temperature 13C and 2H solid-state NMR experiments are used to characterize the nature and rate of the dynamic processes occurring inside this unique material. These results provide a blueprint for the future creation of solid-state molecular switches and molecular machines based on mechanically interlocked molecules.

Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

PubMed Central

Tambunan, Usman Sumo Friend; Nasution, Mochammad Arfin Fardiansyah; Azhima, Fauziah; Parikesit, Arli Aditya; Toepak, Erwin Prasetya; Idrus, Syarifuddin; Kerami, Djati

2017-01-01

Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever. PMID:28469408

Effect of PEO molecular weight on the miscibility and dynamics in epoxy/PEO blends.

PubMed

Lu, Shoudong; Zhang, Rongchun; Wang, Xiaoliang; Sun, Pingchuan; Lv, Weifeng; Liu, Qingjie; Jia, Ninghong

2015-11-01

In this work, the effect of poly(ethylene oxide) (PEO) molecular weight in blends of epoxy (ER) and PEO on the miscibility, inter-chain weak interactions and local dynamics were systematically investigated by multi-frequency temperature modulation DSC and solid-state NMR techniques. We found that the molecular weight (M(w)) of PEO was a crucial factor in controlling the miscibility, chain dynamics and hydrogen bonding interactions between PEO and ER. A critical PEO molecular weight (M(crit)) around 4.5k was found. PEO was well miscible with ER when the molecular weight was below M(crit), where the chain motion of PEO was restricted due to strong inter-chain hydrogen bonding interactions. However, for the blends with high molecular weight PEO (M(w) > M(crit)), the miscibility between PEO and ER was poor, and most of PEO chains were considerably mobile. Finally, polarization inversion spin exchange at magic angle (PISEMA) solid-state NMR experiment further revealed the different mobility of the PEO in ER/PEO blends with different molecular weight of PEO at molecular level. Based on the DSC and NMR results, a tentative model was proposed to illustrate the miscibility in ER/PEO blends.

Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

PubMed

Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

2012-11-28

Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

Circadian variations of adenosine and of its metabolism. Could adenosine be a molecular oscillator for circadian rhythms?

PubMed

Chagoya de Sánchez, V

1995-03-01

The present review describes the biological implications of the periodic changes of adenosine concentrations in different tissues of the rat. Adenosine is a purine molecule that could have been formed in the prebiotic chemical evolution and has been preserved. The rhythmicity of this molecule, as well as its metabolism and even the presence of specific receptors, suggests a regulatory role in eukaryotic cells and in multicellular organisms. Adenosine may be considered a chemical messenger and its action could take place at the level of the same cell (autocrine), the same tissue (paracrine), or on separate organs (endocrine). Exploration of the circadian variations of adenosine was planned considering the liver as an important tissue for purine formation, the blood as a vehicle among tissues, and the brain as the possible acceptor for hepatic adenosine or its metabolites. The rats used in these studies were adapted to a dark-light cycle of 12 h with an unrestrained feeding and drinking schedule. The metabolic control of adenosine concentration in the different tissues studied through the 24-h cycle is related to the activity of adenosine-metabolizing enzyme: 5'-nucleotidase adenosine deaminase, adenosine kinase, and S-adenosylhomocysteine hydrolase. Some possibilities of the factors modulating the activity of these enzymes are commented upon. The multiphysiological action of adenosine could be mediated by several actions: (i) by interaction with extracellular and intracellular receptors and (ii) through its metabolism modulating the methylation pathway, possibly inducing physiological lipoperoxidation, or participating in the energetic homeostasis of the cell. The physiological meaning of the circadian variations of adenosine and its metabolism was focused on: maintenance of the energetic homeostasis of the tissues, modulation of membrane structure and function, regulation of fasting and feeding metabolic pattern, and its participation in the sleep-wake cycle. From these considerations, we suggest that adenosine could be a molecular oscillator involved in the circadian pattern of biological activity in the rat.

Hypothalamic nutrient sensing activates a forebrain-hindbrain neuronal circuit to regulate glucose production in vivo.

PubMed

Lam, Carol K L; Chari, Madhu; Rutter, Guy A; Lam, Tony K T

2011-01-01

Hypothalamic nutrient sensing regulates glucose production, but the neuronal circuits involved remain largely unknown. Recent studies underscore the importance of N-methyl-d-aspartate (NMDA) receptors in the dorsal vagal complex in glucose regulation. These studies raise the possibility that hypothalamic nutrient sensing activates a forebrain-hindbrain NMDA-dependent circuit to regulate glucose production. We implanted bilateral catheters targeting the mediobasal hypothalamus (MBH) (forebrain) and dorsal vagal complex (DVC) (hindbrain) and performed intravenous catheterizations to the same rat for infusion and sampling purposes. This model enabled concurrent selective activation of MBH nutrient sensing by either MBH delivery of lactate or an adenovirus expressing the dominant negative form of AMPK (Ad-DN AMPK α2 [D¹⁵⁷A]) and inhibition of DVC NMDA receptors by either DVC delivery of NMDA receptor blocker MK-801 or an adenovirus expressing the shRNA of NR1 subunit of NMDA receptors (Ad-shRNA NR1). Tracer-dilution methodology and the pancreatic euglycemic clamp technique were performed to assess changes in glucose kinetics in the same conscious, unrestrained rat in vivo. MBH lactate or Ad-DN AMPK with DVC saline increased glucose infusion required to maintain euglycemia due to an inhibition of glucose production during the clamps. However, DVC MK-801 negated the ability of MBH lactate or Ad-DN AMPK to increase glucose infusion or lower glucose production. Molecular knockdown of DVC NR1 of NMDA receptor via Ad-shRNA NR1 injection also negated MBH Ad-DN AMPK to lower glucose production. Molecular and pharmacological inhibition of DVC NMDA receptors negated hypothalamic nutrient sensing mechanisms activated by lactate metabolism or AMPK inhibition to lower glucose production. Thus, DVC NMDA receptor is required for hypothalamic nutrient sensing to lower glucose production and that hypothalamic nutrient sensing activates a forebrain-hindbrain circuit to lower glucose production.

Role of wave packet width in quantum molecular dynamics in fusion reactions near barrier

NASA Astrophysics Data System (ADS)

Cao, X. G.; Ma, Y. G.; Zhang, G. Q.; Wang, H. W.; Anastasi, A.; Curciarello, F.; De Leo, V.

2014-05-01

The dynamical fusion process of 48Ca + 144Sm with different impact parameters near barrier is studied by an extended quantum molecular dynamics (EQMD) model, where width of wavepacket is dynamically treated based on variational principle. The time evolution of different energy components such as potential energy, kinetic energy, Coulomb energy and Pauli potential are analyzed when dynamical or fixed width is assumed in calculation. It is found that the dynamical wavepacket width can enhance the dissipation of incident energy and the fluctuations, which are important to form compound nuclei. Moreover, we compare the fusion barrier dependence on the incident energy when it is determined by both dynamical and fixed wavepacket width.

Molecular dynamics study of silicon carbide properties under external dynamic loading

NASA Astrophysics Data System (ADS)

Utkin, A. V.; Fomin, V. M.

2017-10-01

In this study, molecular dynamic simulations of high-velocity impact of a spherical 3C-SiC cluster, with a wide range of velocities (from 100 to 2600 m/s) and with a rigid wall, were performed. The analysis of the final structure shows that no structural phase transformation occurred in the material, despite the high pressure during the collision process.

Quantum electron-vibrational dynamics at finite temperature: Thermo field dynamics approach

NASA Astrophysics Data System (ADS)

Borrelli, Raffaele; Gelin, Maxim F.

2016-12-01

Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on the thermo field dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. A comparison with the theoretically equivalent density matrix formulation shows the key numerical advantages of the present approach. The solution of thermo field dynamics equations with a novel technique for the propagation of tensor trains (matrix product states) is discussed. Numerical applications to model spin-boson systems show that the present approach is a promising tool for the description of quantum dynamics of complex molecular systems at finite temperature.

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

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. While considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here in this paper, we examine the importance of substrate dynamics in the cleavage of Kunitz-BPTI protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4 Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals amore » dramatic conformational change in the substrate upon proteolysis. Using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning three orders of magnitude, we identify global and local dynamic features of substrates on the ns-μs timescale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substratelike and product-like states, linking substrate dynamics on the ns-μs timescale with large collective substrate motions on the much slower timescale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.« less

Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield.

PubMed

Bhadra, Pratiti; Pal, Debnath

2017-04-01

Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

The physics of interstellar shock waves

NASA Technical Reports Server (NTRS)

Shull, J. Michael; Draine, Bruce T.

1987-01-01

This review discusses the observations and theoretical models of interstellar shock waves, in both diffuse cloud and molecular cloud environments. It summarizes the relevant gas dynamics, atomic, molecular and grain processes, radiative transfer, and physics of radiative and magnetic precursors in shock models. It then describes the importance of shocks for observations, diagnostics, and global interstellar dynamics. It concludes with current research problems and data needs for atomic, molecular and grain physics.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

PubMed

Woolf, T B

1997-11-01

Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.

Molecular shear heating and vortex dynamics in thermostatted two dimensional Yukawa liquids

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

Gupta, Akanksha; Ganesh, Rajaraman, E-mail: ganesh@ipr.res.in; Joy, Ashwin

2016-07-15

It is well known that two-dimensional macroscale shear flows are susceptible to instabilities leading to macroscale vortical structures. The linear and nonlinear fate of such a macroscale flow in a strongly coupled medium is a fundamental problem. A popular example of a strongly coupled medium is a dusty plasma, often modelled as a Yukawa liquid. Recently, laboratory experiments and molecular dynamics (MD) studies of shear flows in strongly coupled Yukawa liquids indicated the occurrence of strong molecular shear heating, which is found to reduce the coupling strength exponentially leading to the destruction of macroscale vorticity. To understand the vortex dynamicsmore » of strongly coupled molecular fluids undergoing macroscale shear flows and molecular shear heating, MD simulation has been performed, which allows the macroscopic vortex dynamics to evolve, while at the same time “removes” the microscopically generated heat without using the velocity degrees of freedom. We demonstrate that by using a configurational thermostat in a novel way, the microscale heat generated by shear flow can be thermostatted out efficiently without compromising the large scale vortex dynamics. In the present work, using MD simulations, a comparative study of shear flow evolution in Yukawa liquids in the presence and absence of molecular or microscopic heating is presented for a prototype shear flow, namely, Kolmogorov flow.« less

3D-QSAR (CoMFA, CoMSIA), molecular docking and molecular dynamics simulations study of 6-aryl-5-cyano-pyrimidine derivatives to explore the structure requirements of LSD1 inhibitors.

PubMed

Ding, Lina; Wang, Zhi-Zheng; Sun, Xu-Dong; Yang, Jing; Ma, Chao-Ya; Li, Wen; Liu, Hong-Min

2017-08-01

Recently, Histone Lysine Specific Demethylase 1 (LSD1) was regarded as a promising anticancer target for the novel drug discovery. And several small molecules as LSD1 inhibitors in different structures have been reported. In this work, we carried out a molecular modeling study on the 6-aryl-5-cyano-pyrimidine fragment LSD1 inhibitors using three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. The results show that the best CoMFA model has q 2 =0.802, r 2 ncv =0.979, and the best CoMSIA model has q 2 =0.799, r 2 ncv =0.982. The electrostatic, hydrophobic and H-bond donor fields play important roles in the models. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300K. All the results can provide us more useful information for our further drug design. Copyright © 2017. Published by Elsevier Ltd.

Communication: Probing the interaction of infrared antenna arrays and molecular films with ultrafast quantum dynamics

NASA Astrophysics Data System (ADS)

Cohn, Bar; Prasad, Amit K.; Chuntonov, Lev

2018-04-01

Narrowband vibrational molecular transitions interacting with the broadband resonance of infrared plasmonic antennas lead to Fano lineshapes observed in linear (FTIR) and third-order (transient absorption and 2DIR) spectroscopic experiments. Both molecular and plasmonic components are inherently dissipative, and the effects associated with their coupling can be observed, in principle, when measuring the corresponding ultrafast quantum dynamics. We used 2DIR spectroscopy to study the waiting time evolution of quantum coherence excited in the carbonyl stretching modes of rhodium (acetylacetonato) dicarbonyl molecules, which were embedded in an 80 nm-thick polymer film spin-coated on an array of infrared half-wavelength gold antennas. Despite the pronounced Fano lineshapes obtained for the molecular transitions, and up to a four order of magnitude enhancement of the third-order signals, which taken together, indicate the coupling between the plasmonic and molecular transitions, the dynamics of the quantum coherence were identical to that obtained with 3 μm-thick film without the interaction with the plamson mode. This suggests that the coupling rate between the molecular and plasmonic excitations is significantly smaller than the relaxation rates of the molecular excitations monitored in the experiment. Here, the Fano lineshape, observed at the frequency of the molecular transition, can result from the mutual radiation damping of the molecular and plasmon modes.

Merging constitutional and motional covalent dynamics in reversible imine formation and exchange processes.

PubMed

Kovaříček, Petr; Lehn, Jean-Marie

2012-06-06

The formation and exchange processes of imines of salicylaldehyde, pyridine-2-carboxaldehyde, and benzaldehyde have been studied, showing that the former has features of particular interest for dynamic covalent chemistry, displaying high efficiency and fast rates. The monoimines formed with aliphatic α,ω-diamines display an internal exchange process of self-transimination type, inducing a local motion of either "stepping-in-place" or "single-step" type by bond interchange, whose rate decreases rapidly with the distance of the terminal amino groups. Control of the speed of the process over a wide range may be achieved by substituents, solvent composition, and temperature. These monoimines also undergo intermolecular exchange, thus merging motional and constitutional covalent behavior within the same molecule. With polyamines, the monoimines formed execute internal motions that have been characterized by extensive one-dimensional, two-dimensional, and EXSY proton NMR studies. In particular, with linear polyamines, nondirectional displacement occurs by shifting of the aldehyde residue along the polyamine chain serving as molecular track. Imines thus behave as simple prototypes of systems displaying relative motions of molecular moieties, a subject of high current interest in the investigation of synthetic and biological molecular motors. The motional processes described are of dynamic covalent nature and take place without change in molecular constitution. They thus represent a category of dynamic covalent motions, resulting from reversible covalent bond formation and dissociation. They extend dynamic covalent chemistry into the area of molecular motions. A major further step will be to achieve control of directionality. The results reported here for imines open wide perspectives, together with other chemical groups, for the implementation of such features in multifunctional molecules toward the design of molecular devices presenting a complex combination of motional and constitutional dynamic behaviors.

Melt-growth dynamics in CdTe crystals

DOE PAGES

Zhou, X. W.; Ward, D. K.; Wong, B. M.; ...

2012-06-01

We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potential capable of predicting both crystalline growth and property trends of many transitional structures encountered during the melt → crystal transformation. Here, we demonstrate successful molecular dynamics simulations of melt growth in CdTe using a BOP that significantly improves over other potentials on property trends of different phases. Our simulations result in a detailed understanding of defect formation during themore » melt growth process. Equally important, we show that the new BOP enables defect formation mechanisms to be studied at a scale level comparable to empirical molecular dynamics simulation methods with a fidelity level approaching quantum-mechanical methods.« less

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration.

PubMed

Furmanchuk, Al'ona; Isayev, Olexandr; Gorb, Leonid; Shishkin, Oleg V; Hovorun, Dmytro M; Leszczynski, Jerzy

2011-03-14

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.

Enzyme-free nucleic acid dynamical systems.

PubMed

Srinivas, Niranjan; Parkin, James; Seelig, Georg; Winfree, Erik; Soloveichik, David

2017-12-15

Chemistries exhibiting complex dynamics-from inorganic oscillators to gene regulatory networks-have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Futera, Zdenek; English, Niall J.

2017-07-01

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

Random Matrix Theory in molecular dynamics analysis.

PubMed

Palese, Luigi Leonardo

2015-01-01

It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes. Copyright © 2014 Elsevier B.V. All rights reserved.

Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

Desai, Tapan; Keblinski, Pawel

2003-03-01

SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport

PubMed Central

Kaplan, Luke; Ierokomos, Athena; Chowdary, Praveen; Bryant, Zev; Cui, Bianxiao

2018-01-01

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors. PMID:29536037

Dynamics in supercooled polyalcohols: Primary and secondary relaxation

NASA Astrophysics Data System (ADS)

Döß, A.; Paluch, M.; Sillescu, H.; Hinze, G.

2002-10-01

We have studied details of the molecular dynamics in a series of pure polyalcohols by means of dielectric spectroscopy and 2H nuclear magnetic resonance (NMR). From glycerol to threitol, xylitol and sorbitol a systematic change in the dynamics of the primary and secondary relaxation is found. With increasing molecular weight and fragility an increase in the width of the α-peak is observed. Details of the molecular reorientation process responsible for the α-relaxation were exploited by two-dimensional NMR experiments. It is found that in the same sequence of polyalcohols the appearance of the secondary relaxation changes gradually from a wing type scenario to a pronounced β-peak. From NMR experiments using selectively deuterated samples the molecular origin of the secondary relaxation could be elucidated in more detail.

Accurate protein structure modeling using sparse NMR data and homologous structure information.

PubMed

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

AKT-mediated stabilization of histone methyltransferase WHSC1 promotes prostate cancer metastasis

PubMed Central

Li, Ni; Xue, Wei; Yuan, Huairui; Dong, Baijun; Ding, Yufeng; Liu, Yongfeng; Jiang, Min; Kan, Shan; Sun, Tongyu; Ren, Jiale; Pan, Qiang; Li, Xiang; Zhang, Peiyuan; Wang, Yan; Wang, Xiaoming; Li, Qintong

2017-01-01

Loss of phosphatase and tensin homolog (PTEN) and activation of the PI3K/AKT signaling pathway are hallmarks of prostate cancer (PCa). However, these alterations alone are insufficient for cells to acquire metastatic traits. Here, we have shown that the histone dimethyl transferase WHSC1 critically drives indolent PTEN-null tumors to become metastatic PCa. In a PTEN-null murine PCa model, WHSC1 overexpression in prostate epithelium cooperated with Pten deletion to produce a metastasis-prone tumor. Conversely, genetic ablation of Whsc1 prevented tumor progression in PTEN-null mice. Molecular characterization revealed that increased AKT activity due to PTEN loss directly phosphorylates WHSC1 at S172, preventing WHSC1 degradation by CRL4Cdt2 E3 ligase. Increased WHSC1 expression transcriptionally upregulates expression of RICTOR, a pivotal component of mTOR complex 2 (mTORC2), to further enhance AKT activity. Therefore, the AKT/WHSC1/mTORC2 signaling cascade represents a vicious feedback loop that elicits unrestrained AKT signaling. Furthermore, we determined that WHSC1 positively regulates Rac1 transcription to increase tumor cell motility. The biological importance of a WHSC1-mediated signaling cascade is substantiated by patient sample analysis in which WHSC1 signaling is tightly correlated with disease progression and recurrence. Taken together, our findings highlight a pivotal link between an epigenetic regulator, WHSC1, and key intracellular signaling molecules, AKT, RICTOR, and Rac1, to drive PCa metastasis. PMID:28319045

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

PubMed

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

PubMed Central

2013-01-01

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176

POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

NASA Astrophysics Data System (ADS)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

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

PubMed

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

2014-10-14

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

Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

NASA Technical Reports Server (NTRS)

Menon, Madhu

1998-01-01

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

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

Barbante, Paolo; Frezzotti, Aldo; Gibelli, Livio

The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviationsmore » of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.« less

Extended Lagrangian Excited State Molecular Dynamics

DOE PAGES

Bjorgaard, Josiah August; Sheppard, Daniel Glen; Tretiak, Sergei; ...

2018-01-09

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both formore » the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).« less

Extended Lagrangian Excited State Molecular Dynamics

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

Bjorgaard, Josiah August; Sheppard, Daniel Glen; Tretiak, Sergei

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both formore » the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).« less

Extended Lagrangian Excited State Molecular Dynamics.

PubMed

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

PubMed

Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

2015-06-09

The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

Enhanced conformational sampling via novel variable transformations and very large time-step molecular dynamics

NASA Astrophysics Data System (ADS)

Tuckerman, Mark

2006-03-01

One of the computational grand challenge problems is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. If met, many important problems, most notably protein folding, could be significantly impacted. In this talk, two new approaches for addressing this problem will be presented. First, it will be shown how molecular dynamics can be combined with a novel variable transformation designed to warp configuration space in such a way that barriers are reduced and attractive basins stretched. This method rigorously preserves equilibrium properties while leading to very large enhancements in sampling efficiency. Extensions of this approach to the calculation/exploration of free energy surfaces will be discussed. Next, a new very large time-step molecular dynamics method will be introduced that overcomes the resonances which plague many molecular dynamics algorithms. The performance of the methods is demonstrated on a variety of systems including liquid water, long polymer chains simple protein models, and oligopeptides.

Dynamic properties of molecular motors in burnt-bridge models

NASA Astrophysics Data System (ADS)

Artyomov, Maxim N.; Morozov, Alexander Yu; Pronina, Ekaterina; Kolomeisky, Anatoly B.

2007-08-01

Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic 'burnt-bridge' models. The transport of the particles is viewed as an effective diffusion along one-dimensional lattices with periodically distributed weak links. When an unbiased random walker passes the weak link it can be destroyed ('burned') with probability p, providing a bias in the motion of the molecular motor. We present a theoretical approach that allows one to calculate exactly all dynamic properties of motor proteins, such as velocity and dispersion, under general conditions. It is found that dispersion is a decreasing function of the concentration of bridges, while the dependence of dispersion on the burning probability is more complex. Our calculations also show a gap in dispersion for very low concentrations of weak links or for very low burning probabilities which indicates a dynamic phase transition between unbiased and biased diffusion regimes. Theoretical findings are supported by Monte Carlo computer simulations.

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

NASA Astrophysics Data System (ADS)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.

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

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Molecular mechanisms of cryoprotection in aqueous proline: light scattering and molecular dynamics simulations.

PubMed

Troitzsch, R Z; Vass, H; Hossack, W J; Martyna, G J; Crain, J

2008-04-10

Free proline amino acid is a natural cryoprotectant expressed by numerous organisms under low-temperature stress. Previous reports have suggested that complex assemblies underlie its functional properties. We investigate here aqueous proline solutions as a function of temperature using combinations of Raman spectroscopy, Rayleigh-Brillouin light scattering, and molecular dynamics simulations with the view to revealing the molecular origins of the mixtures' functionality as a cryoprotectant. The evolution of the Brillouin frequency shifts and line widths with temperature shows that, above a critical proline concentration, the water-like dynamics is suppressed and viscoelastic behavior emerges: Here, the Landau-Placzek ratio also shows a temperature-independent maximum arising from concentration fluctuations. Molecular dynamics simulations reveal that the water-water correlations in the mixtures depend much more weakly on temperature than does bulk water. By contrast, the water OH Raman bands exhibit strong red-shifts on cooling similar to those seen in ices; however, no evidence of ice lattice phonons is observed in the low-frequency spectrum. We attribute this primarily to enhanced proline-water hydrogen bonding. In general, the picture that emerges is that aqueous proline is a heterogeneous mixture on molecular length scales (characterized by significant concentration fluctuations rather than well-defined aggregates). Simulations reveal that proline also appears to suppress the normal dependence of water structure on temperature and preserves the ambient-temperature correlations even in very cold solutions. The water structure in cold proline solutions therefore appears to be similar to that at a higher effective temperature. This, coupled with the emergence of glassy dynamics offers a molecular explanation for the functional properties of proline as a cryoprotectant without the need to invoke previously proposed complex aggregates.

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis*

PubMed Central

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.; Cohen, Itay; Henin, Rachel D.; Hockla, Alexandra; Soares, Alexei S.; Papo, Niv; Caulfield, Thomas R.; Radisky, Evette S.

2016-01-01

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis. PMID:27810896

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

DOE PAGES

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.; ...

2016-11-03

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. While considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here in this paper, we examine the importance of substrate dynamics in the cleavage of Kunitz-BPTI protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4 Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals amore » dramatic conformational change in the substrate upon proteolysis. Using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning three orders of magnitude, we identify global and local dynamic features of substrates on the ns-μs timescale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substratelike and product-like states, linking substrate dynamics on the ns-μs timescale with large collective substrate motions on the much slower timescale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.« less

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

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

NASA Astrophysics Data System (ADS)

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

2009-09-01

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

Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

NASA Astrophysics Data System (ADS)

Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A.; Bernardi, Anna; Colombo, Giorgio

2016-04-01

Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

Dynamics of crystalline acetanilide: Analysis using neutron scattering and computer simulation

NASA Astrophysics Data System (ADS)

Hayward, R. L.; Middendorf, H. D.; Wanderlingh, U.; Smith, J. C.

1995-04-01

The unusual temperature dependence of several optical spectroscopic vibrational bands in crystalline acetanilide has been interpreted as providing evidence for dynamic localization. Here we examine the vibrational dynamics of crystalline acetanilide over a spectral range of ˜20-4000 cm-1 using incoherent neutron scattering experiments, phonon normal mode calculations and molecular dynamics simulations. A molecular mechanics energy function is parametrized and used to perform the normal mode analyses in the full configurational space of the crystal i.e., including the intramolecular and intermolecular degrees of freedom. One- and multiphonon incoherent inelastic neutron scattering intensities are calculated from harmonic analyses in the first Brillouin zone and compared with the experimental data presented here. Phonon dispersion relations and mean-square atomic displacements are derived from the harmonic model and compared with data derived from coherent inelastic neutron scattering and neutron and x-ray diffraction. To examine the temperature effects on the vibrations the full, anharmonic potential function is used in molecular dynamics simulations of the crystal at 80, 140, and 300 K. Several, but not all, of the spectral features calculated from the molecular dynamics simulations exhibit temperature-dependent behavior in agreement with experiment. The significance of the results for the interpretation of the optical spectroscopic results and possible improvements to the model are discussed.

X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

DOE PAGES

Fang, Li; Xiong, Hui; Kukk, Edwin; ...

2017-05-19

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

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

Hua, Xin; Szymanski, Craig; Wang, Zhaoying

2016-01-01

Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics atmore » the molecular level.« less

Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling.

PubMed

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-17

Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.

Well-posed two-temperature constitutive equations for stable dense fluid shock waves using molecular dynamics and generalizations of Navier-Stokes-Fourier continuum mechanics.

PubMed

Hoover, Wm G; Hoover, Carol G

2010-04-01

Guided by molecular dynamics simulations, we generalize the Navier-Stokes-Fourier constitutive equations and the continuum motion equations to include both transverse and longitudinal temperatures. To do so we partition the contributions of the heat transfer, the work done, and the heat flux vector between the longitudinal and transverse temperatures. With shockwave boundary conditions time-dependent solutions of these equations converge to give stationary shockwave profiles. The profiles include anisotropic temperature and can be fitted to molecular dynamics results, demonstrating the utility and simplicity of a two-temperature description of far-from-equilibrium states.

Chemical reactivity and spectroscopy explored from QM/MM molecular dynamics simulations using the LIO code

NASA Astrophysics Data System (ADS)

Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.

2018-03-01

In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

NASA Astrophysics Data System (ADS)

Hudson, Brian D.; George, Ashley R.; Ford, Martyn G.; Livingstone, David J.

1992-04-01

Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Fatal dog attacks, 1989-1994.

PubMed

Sacks, J J; Lockwood, R; Hornreich, J; Sattin, R W

1996-06-01

To update data on fatal dog bites and see if past trends have continued. To merge data from vital records, the Humane Society of the United States, and searches of electronic news files. United States. U.S. residents dying in the U.S. from 1989 through 1994 from dog bites. We identified 109 dog bite-related fatalities, of which 57% were less than 10 years of age. The death rate for neonates was two orders of magnitude higher than for adults and the rate for children one order of magnitude higher. Of classifiable deaths, 22% involved an unrestrained dog off the owner's property, 18% involved a restrained dog on the owner's property, and 59% involved an unrestrained dog on the owner's property. Eleven attacks involved a sleeping infant; 19 dogs involved in fatal attacks had a prior history of aggression; and 19 of 20 classifiable deaths involved an unneutered dog. Pit bulls, the most commonly reported breed, were involved in 24 deaths; the next most commonly reported breeds were rottweilers (16) and German shepherds (10). The dog bite problem should be reconceptualized as a largely preventable epidemic. Breed-specific approaches to the control of dog bites do not address the issue that many breeds are involved in the problem and that most of the factors contributing to dog bites are related to the level of responsibility exercised by dog owners. To prevent dog bite-related deaths and injuries, we recommend public education about responsible dog ownership and dog bite prevention, stronger animal control laws, better resources for enforcement of these laws, and better reporting of bites. Anticipatory guidance by pediatric health care providers should address dog bite prevention.

Future Urban Climate Projection in A Tropical Megacity Based on Global and Regional Scenarios

NASA Astrophysics Data System (ADS)

Darmanto, N. S.; Varquez, A. C. G.; Kanda, M.

2017-12-01

Cities in Asian developing countries experience rapid transformation in urban morphology and energy consumption, which correspondingly affects urban climate. Weather Research and Forecasting (WRF) Model coupled with improved single-layer urban canopy model incorporating realistic distribution of urban parameters and anthropogenic heat emission (AHE) in the tropic Jakarta Greater Area was conducted. Simulation was conducted during the dry months from 2006 to 2015 and agreed well with point and satellite observation. The same technology coupled with pseudo global warming (PGW) method based on representative concentration pathways (RCP) scenario 2.6 and 8.5 was conducted to produce futuristic climate condition in 2050. Projected urban morphology and AHE in 2050s were constructed using regional urban growing model with shared socioeconomic pathways (SSP) among its inputs. Compact future urban configuration, based on SSP1, was coupled to RCP2.6. Unrestrained future urban configuration, based on SSP3, was coupled to RCP8.5. Results show that background warming from RCP 2.6 and 8.5 will increase background temperature by 0.55°C and 1.2°C throughout the region, respectively. Future projection of urban sprawl results to an additional 0.3°C and 0.5°C increase on average, with maximum increase of 1.1°C and 1.3°C due to urban effect for RCP2.6/compact and RCP8.5/unrestrained, respectively. Higher moisture content in urban area is indicated in the future due to higher evaporation. Change in urban roughness is likely affect slower wind velocity in urban area and sea breeze front inland penetration the future compare with current condition. Acknowledgement: This research was supported by the Environment Research and Technology Development Fund (S-14) of the Ministry of the Environment, Japan.

Matching the oculomotor drive during head-restrained and head-unrestrained gaze shifts in monkey.

PubMed

Bechara, Bernard P; Gandhi, Neeraj J

2010-08-01

High-frequency burst neurons in the pons provide the eye velocity command (equivalently, the primary oculomotor drive) to the abducens nucleus for generation of the horizontal component of both head-restrained (HR) and head-unrestrained (HU) gaze shifts. We sought to characterize how gaze and its eye-in-head component differ when an "identical" oculomotor drive is used to produce HR and HU movements. To address this objective, the activities of pontine burst neurons were recorded during horizontal HR and HU gaze shifts. The burst profile recorded on each HU trial was compared with the burst waveform of every HR trial obtained for the same neuron. The oculomotor drive was assumed to be comparable for the pair yielding the lowest root-mean-squared error. For matched pairs of HR and HU trials, the peak eye-in-head velocity was substantially smaller in the HU condition, and the reduction was usually greater than the peak head velocity of the HU trial. A time-varying attenuation index, defined as the difference in HR and HU eye velocity waveforms divided by head velocity [alpha = (H(hr) - E(hu))/H] was computed. The index was variable at the onset of the gaze shift, but it settled at values several times greater than 1. The index then decreased gradually during the movement and stabilized at 1 around the end of gaze shift. These results imply that substantial attenuation in eye velocity occurs, at least partially, downstream of the burst neurons. We speculate on the potential roles of burst-tonic neurons in the neural integrator and various cell types in the vestibular nuclei in mediating the attenuation in eye velocity in the presence of head movements.

Markerless rat head motion tracking using structured light for brain PET imaging of unrestrained awake small animals

NASA Astrophysics Data System (ADS)

Miranda, Alan; Staelens, Steven; Stroobants, Sigrid; Verhaeghe, Jeroen

2017-03-01

Preclinical positron emission tomography (PET) imaging in small animals is generally performed under anesthesia to immobilize the animal during scanning. More recently, for rat brain PET studies, methods to perform scans of unrestrained awake rats are being developed in order to avoid the unwanted effects of anesthesia on the brain response. Here, we investigate the use of a projected structure stereo camera to track the motion of the rat head during the PET scan. The motion information is then used to correct the PET data. The stereo camera calculates a 3D point cloud representation of the scene and the tracking is performed by point cloud matching using the iterative closest point algorithm. The main advantage of the proposed motion tracking is that no intervention, e.g. for marker attachment, is needed. A manually moved microDerenzo phantom experiment and 3 awake rat [18F]FDG experiments were performed to evaluate the proposed tracking method. The tracking accuracy was 0.33 mm rms. After motion correction image reconstruction, the microDerenzo phantom was recovered albeit with some loss of resolution. The reconstructed FWHM of the 2.5 and 3 mm rods increased with 0.94 and 0.51 mm respectively in comparison with the motion-free case. In the rat experiments, the average tracking success rate was 64.7%. The correlation of relative brain regional [18F]FDG uptake between the anesthesia and awake scan reconstructions was increased from on average 0.291 (not significant) before correction to 0.909 (p  <  0.0001) after motion correction. Markerless motion tracking using structured light can be successfully used for tracking of the rat head for motion correction in awake rat PET scans.

Gaze Pursuit Responses in Nucleus Reticularis Tegmenti Pontis of Head-Unrestrained Macaques

PubMed Central

Suzuki, David A.; Betelak, Kathleen F.; Yee, Robert D.

2009-01-01

Eye-head gaze pursuit–related activity was recorded in rostral portions of the nucleus reticularis tegmenti pontis (rNRTP) in alert macaques. The head was unrestrained in the horizontal plane, and macaques were trained to pursue a moving target either with their head, with the eyes stationary in the orbits, or with their eyes, with their head voluntarily held stationary in space. Head-pursuit–related modulations in rNRTP activity were observed with some cells exhibiting increases in firing rate with increases in head-pursuit frequency. For many units, this head-pursuit response appeared to saturate at higher frequencies (>0.6 Hz). The response phase re:peak head-pursuit velocity formed a continuum, containing cells that could encode head-pursuit velocity and those encoding head-pursuit acceleration. The latter cells did not exhibit head position–related activity. Sensitivities were calculated with respect to peak head-pursuit velocity and averaged 1.8 spikes/s/deg/s. Of the cells that were tested for both head- and eye-pursuit–related activity, 86% exhibited responses to both head- and eye-pursuit and therefore carried a putative gaze-pursuit signal. For these gaze-pursuit units, the ratio of head to eye response sensitivities averaged ∼1.4. Pursuit eccentricity seemed to affect head-pursuit response amplitude even in the absence of a head position response per se. The results indicated that rNRTP is a strong candidate for the source of an active head-pursuit signal that projects to the cerebellum, specifically to the target-velocity and gaze-velocity Purkinje cells that have been observed in vermal lobules VI and VII. PMID:18987125

Fatigue of reinforcing bars during hydro-demolition

NASA Astrophysics Data System (ADS)

Hyland, C. W. K.; Ouwejan, A.

2017-05-01

Reinforcing steel fractured during hydro-demolition of a reinforced concrete pier head due to low cycle flexural fatigue from vibration caused by impact of the high pressure water jet on the exposed length of the bars. Research into the fatigue performance of steel reinforcing steel tends to focus on the high cycle axial performance in reinforced concrete members and re-bending behaviour. However with the increasing use of hydro-demolition of concrete structures as part of remediation works care is required to ensure the steel reinforcement exposed to the high pressure jet of water is not going to suffer relatively low cycle flexural damage that may compromise the designed performance of the completed reinforced concrete structure. This paper describes the failure assessment, fatigue analysis, and metallographic examination that was undertaken. It was found that the rib to flank transition radius on the reinforcement steel was small enough to cause a significant stress concentration effect and was the location of fatigue crack growth. A relatively simple analysis using the maximum unrestrained cantilevered bar length and force exerted by the water jet was used to calculate the maximum expected bending moment. This was compared to the bending capacity at initiation of yielding at the rib flank transition accounting for stress concentration effects. This showed that the observed cyclic reversing ductile crack growth and fracture of the H25 bars was consistent with the loading applied. A method is proposed based on these observations to assess suitable limits for unrestrained bar lengths or maximum working offset of the water jet from the point of bar restraint when undertaking hydro-demolition work. The fatigue critical performance requirements of AS/NZS4671 500E bars are also therefore compared with those of BS4449:2005 and PN EN/ISO 15630-1:2011 for comparable 500C bars

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Todd, B. D.; Sadus, Richard J.

2004-12-01

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.

Exploring the Origin of Differential Binding Affinities of Human Tubulin Isotypes αβII, αβIII and αβIV for DAMA-Colchicine Using Homology Modelling, Molecular Docking and Molecular Dynamics Simulations

PubMed Central

Panda, Dulal; Kunwar, Ambarish

2016-01-01

Tubulin isotypes are found to play an important role in regulating microtubule dynamics. The isotype composition is also thought to contribute in the development of drug resistance as tubulin isotypes show differential binding affinities for various anti-cancer agents. Tubulin isotypes αβII, αβIII and αβIV show differential binding affinity for colchicine. However, the origin of differential binding affinity is not well understood at the molecular level. Here, we investigate the origin of differential binding affinity of a colchicine analogue N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) for human αβII, αβIII and αβIV isotypes, employing sequence analysis, homology modeling, molecular docking, molecular dynamics simulation and MM-GBSA binding free energy calculations. The sequence analysis study shows that the residue compositions are different in the colchicine binding pocket of αβII and αβIII, whereas no such difference is present in αβIV tubulin isotypes. Further, the molecular docking and molecular dynamics simulations results show that residue differences present at the colchicine binding pocket weaken the bonding interactions and the correct binding of DAMA-colchicine at the interface of αβII and αβIII tubulin isotypes. Post molecular dynamics simulation analysis suggests that these residue variations affect the structure and dynamics of αβII and αβIII tubulin isotypes, which in turn affect the binding of DAMA-colchicine. Further, the binding free-energy calculation shows that αβIV tubulin isotype has the highest binding free-energy and αβIII has the lowest binding free-energy for DAMA-colchicine. The order of binding free-energy for DAMA-colchicine is αβIV ≃ αβII >> αβIII. Thus, our computational approaches provide an insight into the effect of residue variations on differential binding of αβII, αβIII and αβIV tubulin isotypes with DAMA-colchicine and may help to design new analogues with higher binding affinities for tubulin isotypes. PMID:27227832

Model systems for single molecule polymer dynamics

PubMed Central

Latinwo, Folarin

2012-01-01

Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

De novo inference of protein function from coarse-grained dynamics.

PubMed

Bhadra, Pratiti; Pal, Debnath

2014-10-01

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. © 2014 Wiley Periodicals, Inc.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

PubMed

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

PubMed Central

Wallace, Jason A.; Shen, Jana K.

2012-01-01

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future. PMID:23163362

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

PubMed Central

Caulfield, Thomas R.; Devkota, Batsal; Rollins, Geoffrey C.

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. PMID:21716650

Investigations of FAK inhibitors: a combination of 3D-QSAR, docking, and molecular dynamics simulations studies.

PubMed

Cheng, Peng; Li, Jiaojiao; Wang, Juan; Zhang, Xiaoyun; Zhai, Honglin

2018-05-01

Focal adhesion kinase (FAK) is one kind of tyrosine kinases that modulates integrin and growth factor signaling pathways, which is a promising therapeutic target because of involving in cancer cell migration, proliferation, and survival. To investigate the mechanism between FAK and triazinic inhibitors and design high activity inhibitors, a molecular modeling integrated with 3D-QSAR, molecular docking, molecular dynamics simulations, and binding free energy calculations was performed. The optimum CoMFA and CoMSIA models showed good reliability and satisfactory predictability (with Q 2  = 0.663, R 2  = 0.987, [Formula: see text] = 0.921 and Q 2  = 0.670, R 2  = 0.981, [Formula: see text] = 0.953). Its contour maps could provide structural features to improve inhibitory activity. Furthermore, a good consistency between contour maps, docking, and molecular dynamics simulations strongly demonstrates that the molecular modeling is reliable. Based on it, we designed several new compounds and their inhibitory activities were validated by the molecular models. We expect our studies could bring new ideas to promote the development of novel inhibitors with higher inhibitory activity for FAK.

Multiscale geometric modeling of macromolecules II: Lagrangian representation

PubMed Central

Feng, Xin; Xia, Kelin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei

2013-01-01

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X-ray, NMR and cryo-EM, and theoretical/mathematical models, such as molecular dynamics, the Poisson-Boltzmann equation and the Nernst-Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger’s functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent-solute interaction, and ion channel dynamics, while our coarse resolution representations highlight the compatibility of protein-ligand bindings and possibility of protein-protein interactions. PMID:23813599