Science.gov

Sample records for all-atom molecular dynamics

  1. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.

    PubMed

    Erban, Radek

    2016-02-01

    Molecular dynamics (MD) simulations of ions (K(+), Na(+), Ca(2+) and Cl(-)) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  2. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    PubMed

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  3. Human Inducible Hsp70: Structures, Dynamics, and Interdomain Communication from All-Atom Molecular Dynamics Simulations.

    PubMed

    Nicolaï, Adrien; Senet, Patrick; Delarue, Patrice; Ripoll, Daniel R

    2010-08-10

    The 70 kDa human heat shock protein is a major molecular chaperone involved in de novo folding of proteins in vivo and refolding of proteins under stress conditions. Hsp70 is related to several "misfolding diseases" and other major pathologies, such as cancer, and is a target for new therapies. Hsp70 is comprised of two main domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate protein binding domain (SBD). The chaperone function of Hsp70 is based on an allosteric mechanism. Binding of ATP in NBD decreases the affinity of the substrate for SBD, and hydrolysis of ATP is promoted by binding of polypeptide segments in the SBD. No complete structure of human Hsp70 is known. Here, we report two models of human Hsp70, constructed by homology with Saccharomyces cerevisiae cochaperone protein Hsp110 (open model) and with Escherichia coli 70 kDa DnaK (closed model) and relaxed for several tens to hundreds of nanoseconds by using all-atom molecular dynamics simulations in explicit solvent. We obtain two stable states, Hsp70 with SBD open and SBD closed, which agree with experimental and structural information for ATP-Hsp70 and ADP-Hsp70, respectively. The dynamics of the transition from the open to closed states is investigated with a coarse-grained model and normal-mode analysis. The results show that the conformational change between the two states can be represented by a relatively small number of collective modes which involved major conformational changes in the two domains. These modes provide a mechanistic representation of the communication between NBD and SBD and allow us to identify subdomains and residues that appear to have a critical role in the conformational change mechanism that guides the chaperoning cycle of Hsp70.

  4. Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.

    PubMed

    Henry, Eric R; Best, Robert B; Eaton, William A

    2013-10-29

    Advances in computing have enabled microsecond all-atom molecular dynamics trajectories of protein folding that can be used to compare with and test critical assumptions of theoretical models. We show that recent simulations by the Shaw group (10, 11, 14, 15) are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain, with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter, is remarkably similar to the distribution in the molecular dynamics trajectories.

  5. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

    PubMed Central

    2016-01-01

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  6. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

    PubMed

    Higo, Junichi; Umezawa, Koji

    2014-01-01

    We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

  7. Ab initio folding of proteins using all-atom discrete molecular dynamics

    PubMed Central

    Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

    2008-01-01

    Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374

  8. High-throughput all-atom molecular dynamics simulations using distributed computing.

    PubMed

    Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G

    2010-03-22

    Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

  9. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    PubMed

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  10. All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer

    PubMed Central

    Perlmutter, Jason D.; Drasler, William J.; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N.

    2011-01-01

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native and functional state for longer periods than detergents do. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles, with a mass of ~40 kDa and a Rg of ~2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. While AAMD simulations result in cohesive and stable particles over a 45-ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond timescale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations, and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows higher-resolution characterization of a configuration determined by a long-timescale simulation. An excellent agreement is observed between MD models and experimental, small angle neutron scattering data. The MD data provides new insights into the structure and dynamics of A8-35 particles, possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes. PMID:21806035

  11. All-atom molecular dynamics simulation of a photosystem I/detergent complex

    SciTech Connect

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2014-09-18

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  12. All-atom molecular dynamics simulation of a photosystem i/detergent complex.

    PubMed

    Harris, Bradley J; Cheng, Xiaolin; Frymier, Paul

    2014-10-09

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  13. All-atom molecular dynamics of virus capsids as drug targets

    DOE PAGES

    Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

    2016-04-29

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

  14. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  15. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    NASA Astrophysics Data System (ADS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  16. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    PubMed

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods. Copyright © 2012 Wiley Periodicals, Inc.

  17. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    SciTech Connect

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  18. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore.

    PubMed

    Di Marino, Daniele; Bonome, Emma Letizia; Tramontano, Anna; Chinappi, Mauro

    2015-08-06

    Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  19. 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

  20. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.

    PubMed

    Zhao, Gongpu; Perilla, Juan R; Yufenyuy, Ernest L; Meng, Xin; Chen, Bo; Ning, Jiying; Ahn, Jinwoo; Gronenborn, Angela M; Schulten, Klaus; Aiken, Christopher; Zhang, Peijun

    2013-05-30

    Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.

  1. All-atom molecular dynamics studies of the full-length β-amyloid peptides

    NASA Astrophysics Data System (ADS)

    Luttmann, Edgar; Fels, Gregor

    2006-03-01

    β-Amyloid peptides are believed to play an essential role in Alzheimer's disease (AD), due to their sedimentation in the form of β-amyloid aggregates in the brain of AD-patients, and the in vitro neurotoxicity of oligomeric aggregates. The monomeric peptides come in different lengths of 39-43 residues, of which the 42 alloform seems to be most strongly associated with AD-symptoms. Structural information on these peptides to date comes from NMR studies in acidic solutions, organic solvents, or on shorter fragments of the peptide. In addition X-ray and solid-state NMR investigations of amyloid fibrils yield insight into the structure of the final aggregate and therefore define the endpoint of any conformational change of an Aβ-monomer along the aggregation process. The conformational changes necessary to connect the experimentally known conformations are not yet understood and this process is an active field of research. In this paper, we report results from all-atom molecular dynamics simulations based on experimental data from four different peptides of 40 amino acids and two peptides consisting of 42 amino acids. The simulations allow for the analysis of intramolecular interactions and the role of structural features. In particular, they show the appearance of β-turn in the region between amino acid 21 and 33, forming a hook-like shape as it is known to exist in the fibrillar Aβ-structures. This folding does not depend on the formation of a salt bridge between Asp-23 and Lys-28 but requires the Aβ(1-42) as such structure was not observed in the shorter system Aβ(1-40).

  2. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    PubMed

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  3. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.

    PubMed

    Euston, Stephen R

    2010-10-11

    The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

  4. Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study.

    PubMed

    Das, Atanu; Mukhopadhyay, Chaitali

    2007-10-28

    We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide-ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.

  5. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  6. Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.

    PubMed

    Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki

    2016-08-01

    Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA(+) ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named 'the ADP model' and 'the ATP model', where ADP and ATP are bound to AAA1 in the AAA(+) ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results.

  7. Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations

    PubMed Central

    Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki

    2016-01-01

    Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA+ ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named ‘the ADP model’ and ‘the ATP model’, where ADP and ATP are bound to AAA1 in the AAA+ ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455

  8. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations.

    PubMed

    Cota, Junio; Oliveira, Leandro C; Damásio, André R L; Citadini, Ana P; Hoffmam, Zaira B; Alvarez, Thabata M; Codima, Carla A; Leite, Vitor B P; Pastore, Glaucia; de Oliveira-Neto, Mario; Murakami, Mario T; Ruller, Roberto; Squina, Fabio M

    2013-08-01

    Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes.

  9. Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics.

    PubMed

    Nash, Jessica A; Singh, Abhishek; Li, Nan K; Yingling, Yaroslava G

    2015-12-22

    The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

  10. Understanding thermal phases in atomic detail by all-atom molecular-dynamics simulation of a phospholipid bilayer.

    PubMed

    Ogata, Koji; Uchida, Waka; Nakamura, Shinichiro

    2014-12-11

    All-atom molecular dynamics (MD) simulations were used to investigate the thermal phase behavior of two hydrated phospholipids, namely, DPPC and DPPE, at the atomic level. The trajectories in the MD simulations clearly identified the structures of DPPC in the crystalline (Lc), gel (Lβ), ripple (Pβ), and liquid-crystalline (Lα) phases and those of DPPE in the Lc and Lα phases. The physicochemical and structural properties of these phases agree well with the experimental results. Moreover, the structural transformations between phases were observed. In the Lβ phase, forces are directed in opposite directions in the upper and lower layers of the bilayer. These forces, which are due to the thermal motion of each monolayer, strongly influence the series of phase transitions from Lβ to Pβ. The MD simulations in this work can provide an understanding of the dynamics of the lipid bilayer in each thermal phase and suggest the mechanism that generates the Pβ phase.

  11. Two-dimensional NMR and All-atom Molecular Dynamics of Cytochrome P450 CYP119 Reveal Hidden Conformational Substates*

    PubMed Central

    Lampe, Jed N.; Brandman, Relly; Sivaramakrishnan, Santhosh; de Montellano, Paul R. Ortiz

    2010-01-01

    Cytochrome P450 enzymes are versatile catalysts involved in a wide variety of biological processes from hormonal regulation and antibiotic synthesis to drug metabolism. A hallmark of their versatility is their promiscuous nature, allowing them to recognize a wide variety of chemically diverse substrates. However, the molecular details of this promiscuity have remained elusive. Here, we have utilized two-dimensional heteronuclear single quantum coherence NMR spectroscopy to examine a series of mutants site-specific labeled with the unnatural amino acid, [13C]p-methoxyphenylalanine, in conjunction with all-atom molecular dynamics simulations to examine substrate and inhibitor binding to CYP119, a P450 from Sulfolobus acidocaldarius. The results suggest that tight binding hydrophobic ligands tend to lock the enzyme into a single conformational substate, whereas weak binding low affinity ligands bind loosely in the active site, resulting in a distribution of localized conformers. Furthermore, the molecular dynamics simulations suggest that the ligand-free enzyme samples ligand-bound conformations of the enzyme and, therefore, that ligand binding may proceed largely through a process of conformational selection rather than induced fit. PMID:20097757

  12. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

    PubMed Central

    Chen, Wei; Shen, Jana K.

    2014-01-01

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

  13. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    PubMed

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma.

  14. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations

    SciTech Connect

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-05-03

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.

  15. Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

    SciTech Connect

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2015-12-15

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.

  16. Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study

    PubMed Central

    Thøgersen, Lea; Schiøtt, Birgit; Vosegaard, Thomas; Nielsen, Niels Chr.; Tajkhorshid, Emad

    2008-01-01

    We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-μs CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 μs is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the α-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer. PMID:18676652

  17. Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

    DOE PAGES

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2015-12-15

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigatingmore » protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

  18. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations

    DOE PAGES

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; ...

    2016-05-03

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up amore » CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.« less

  19. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations*

    PubMed Central

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-01-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  20. Multi-step formation of a hemifusion diaphragm for vesicle fusion revealed by all-atom molecular dynamics simulations.

    PubMed

    Tsai, Hui-Hsu Gavin; Chang, Che-Ming; Lee, Jian-Bin

    2014-06-01

    Membrane fusion is essential for intracellular trafficking and virus infection, but the molecular mechanisms underlying the fusion process remain poorly understood. In this study, we employed all-atom molecular dynamics simulations to investigate the membrane fusion mechanism using vesicle models which were pre-bound by inter-vesicle Ca(2+)-lipid clusters to approximate Ca(2+)-catalyzed fusion. Our results show that the formation of the hemifusion diaphragm for vesicle fusion is a multi-step event. This result contrasts with the assumptions made in most continuum models. The neighboring hemifused states are separated by an energy barrier on the energy landscape. The hemifusion diaphragm is much thinner than the planar lipid bilayers. The thinning of the hemifusion diaphragm during its formation results in the opening of a fusion pore for vesicle fusion. This work provides new insights into the formation of the hemifusion diaphragm and thus increases understanding of the molecular mechanism of membrane fusion. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Fluctuating hydrodynamics for multiscale simulation of inhomogeneous fluids: mapping all-atom molecular dynamics to capillary waves.

    PubMed

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

    2011-07-28

    We introduce a multiscale framework to simulate inhomogeneous fluids by coarse-graining an all-atom molecular dynamics (MD) trajectory onto sequential snapshots of hydrodynamic fields. We show that the field representation of an atomistic trajectory is quantitatively described by a dynamic field-theoretic model that couples hydrodynamic fluctuations with a Ginzburg-Landau free energy. For liquid-vapor interfaces of argon and water, the parameters of the field model can be adjusted to reproduce the bulk compressibility and surface tension calculated from the positions and forces of atoms in an MD simulation. These optimized parameters also enable the field model to reproduce the static and dynamic capillary wave spectra calculated from atomistic coordinates at the liquid-vapor interface. In addition, we show that a density-dependent gradient coefficient in the Ginzburg-Landau free energy enables bulk and interfacial fluctuations to be controlled separately. For water, this additional degree of freedom is necessary to capture both the bulk compressibility and surface tension emergent from the atomistic trajectory. The proposed multiscale framework illustrates that bottom-up coarse-graining and top-down phenomenology can be integrated with quantitative consistency to simulate the interfacial fluctuations in nanoscale transport processes.

  2. Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution.

    PubMed

    Roussel, Guillaume; Michaux, Catherine; Perpète, Eric A

    2014-10-01

    Sodium dodecyl sulfate (SDS) is a well-known anionic detergent widely used in both experimental and theoretical investigations. Many molecular dynamics (MD) simulation have been performed on the SDS molecule at coarse-grained (CG), united-atom (UA), and all-atom (AA) resolutions. However, these simulations are usually based on general parameters determined from large sets of molecules, and as a result, peculiar molecular specificities are often poorly represented. In addition, the parameters (ideal bond lengths, angles, dihedrals and charge distribution) differ according to the resolution, highlighting a lack of coherence. We therefore propose a new set of parameters for CG, UA, and AA resolutions based on a high quantum mechanics (QM) level optimization of the detergent structure and the charge distribution. For the first time, QM-optimized parameters were directly applied to build the AA, UA, and CG model of the SDS molecule, leading to a more coherent description. As a test case, MD simulations were then performed on SDS preformed micelles as previous experimental and theoretical investigations allow direct comparison with our new sets of parameters. While all three models yield similar macromolecular properties (size, shape, and accessible surface) perfectly matching previous results, the attribution of more coherent parameters to SDS enables the description of the specific interactions inside and outside the micelle. These more consistent parameters can now be used to accurately describe new multi-scale systems involving the SDS molecule.

  3. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

    PubMed

    Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

    2016-11-08

    Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

  4. Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation.

    PubMed

    Konermann, Lars

    2017-08-31

    Molecular dynamics (MD) simulations have become a key tool for examining the properties of electrosprayed protein ions. Traditional force fields employ static charges on titratable sites, whereas in reality, protons are highly mobile in gas-phase proteins. Earlier studies tackled this problem by adjusting charge patterns during MD runs. Within those algorithms, proton redistribution was subject to energy minimization, taking into account electrostatic and proton affinity contributions. However, those earlier approaches described (de)protonated moieties as point charges, neglecting charge solvation, which is highly prevalent in the gas phase. Here, we describe a mobile proton algorithm that considers the electrostatic contributions from all atoms, such that charge solvation is explicitly included. MD runs were broken down into 50 ps fixed-charge segments. After each segment, the electrostatics was reanalyzed and protons were redistributed. Challenges associated with computational cost were overcome by devising a streamlined method for electrostatic calculations. Avidin (a 504-residue protein complex) maintained a nativelike fold over 200 ns. Proton transfer and side chain rearrangements produced extensive salt bridge networks at the protein surface. The mobile proton technique introduced here should pave the way toward future studies on protein folding, unfolding, collapse, and subunit dissociation in the gas phase.

  5. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils

    NASA Astrophysics Data System (ADS)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2016-11-01

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

  6. Membrane binding and insertion of a pHLIP peptide studied by all-atom molecular dynamics simulations.

    PubMed

    Deng, Yonghua; Qian, Zhenyu; Luo, Yin; Zhang, Yun; Mu, Yuguang; Wei, Guanghong

    2013-07-12

    Recent experiments in function mechanism study reported that a pH low-insertion peptide (pHLIP) can insert into a zwitterionic palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer at acidic pH while binding to the bilayer surface at basic pH. However, the atomic details of the pH-dependent interaction of pHLIP with a POPC bilayer are not well understood. In this study, we investigate the detailed interactions of pHLIP with a POPC bilayer at acidic and basic pH conditions as those used in function mechanism study, using all-atom molecular dynamics (MD) simulations. Simulations have been performed by employing the initial configurations, where pHLIP is placed in aqueous solution, parallel to bilayer surface (system S), partially-inserted (system P), or fully-inserted (system F) in POPC bilayers. On the basis of multiple 200-ns MD simulations, we found (1) pHLIP in system S can spontaneously insert into a POPC bilayer at acidic pH, while binding to the membrane surface at basic pH; (2) pHLIP in system P can insert deep into a POPC bilayer at acidic pH, while it has a tendency to exit, and stays at bilayer surface at basic pH; (3) pHLIP in system F keeps in an α-helical structure at acidic pH while partially unfolding at basic pH. This study provides at atomic-level the pH-induced insertion of pHLIP into POPC bilayer.

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

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-07

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

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

    NASA Astrophysics Data System (ADS)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-01

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

  9. 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.

  10. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

    NASA Astrophysics Data System (ADS)

    Wallace, Jason A.; Shen, Jana K.

    2012-11-01

    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.

  11. 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.

  12. 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

  13. Differential dynamics of the serotonin1A receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation.

    PubMed

    Patra, Swarna M; Chakraborty, Sudip; Shahane, Ganesh; Prasanna, Xavier; Sengupta, Durba; Maiti, Prabal K; Chattopadhyay, Amitabha

    2015-01-01

    The serotonin1A receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin1A receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3 μs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin1A receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin1A receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.

  14. All-Atom Multiscale Molecular Dynamics Theory and Simulation of Self-Assembly, Energy Transfer and Structural Transition in Nanosystems

    NASA Astrophysics Data System (ADS)

    Espinosa Duran, John Michael

    The study of nanosystems and their emergent properties requires the development of multiscale computational models, theories and methods that preserve atomic and femtosecond resolution, to reveal details that cannot be resolved experimentally today. Considering this, three long time scale phenomena were studied using molecular dynamics and multiscale methods: self-assembly of organic molecules on graphite, energy transfer in nanosystems, and structural transition in vault nanoparticles. Molecular dynamics simulations of the self-assembly of alkoxybenzonitriles with different tail lengths on graphite were performed to learn about intermolecular interactions and phases exhibited by self-organized materials. This is important for the design of ordered self-assembled organic photovoltaic materials with greater efficiency than the disordered blends. Simulations revealed surface dynamical behaviors that cannot be resolved experimentally today due to the lack of spatiotemporal resolution. Atom-resolved structures predicted by simulations agreed with scanning tunneling microscopy images and unit cell measurements. Then, a multiscale theory based on the energy density as a field variable is developed to study energy transfer in nanoscale systems. For applications like photothermal microscopy or cancer phototherapy is required to understand how the energy is transferred to/from nanosystems. This multiscale theory could be applied in this context and here is tested for cubic nanoparticles immersed in water for energy being transferred to/from the nanoparticle. The theory predicts the energy transfer dynamics and reveals phenomena that cannot be described by current phenomenological theories. Finally, temperature-triggered structural transitions were revealed for vault nanoparticles using molecular dynamics and multiscale simulations. Vault is a football-shaped supramolecular assembly very distinct from the commonly observed icosahedral viruses. It has very promising

  15. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    SciTech Connect

    Calero, Carles; Stanley, H.; Franzese, Giancarlo

    2016-04-27

    Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water–lipid HBs as the hydration decreases. Lastly, our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

  16. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics.

    PubMed

    Calero, Carles; Stanley, H Eugene; Franzese, Giancarlo

    2016-04-27

    Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water-water and water-lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water-lipids HBs last longer than water-water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water-water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water-lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

  17. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    PubMed Central

    Calero, Carles; Stanley, H. Eugene; Franzese, Giancarlo

    2016-01-01

    Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels. PMID:28773441

  18. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

    PubMed

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-07

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  19. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

    PubMed Central

    2011-01-01

    Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions. Results Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA) or in combination with α-helix (BRCT repeats) or β-sheet (WW domain) fail to differentiate pThr/pSer. Conclusions Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors. PMID:21612598

  20. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

    PubMed

    Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

    2016-06-16

    Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

  1. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    DOE PAGES

    Calero, Carles; Stanley, H.; Franzese, Giancarlo

    2016-04-27

    Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confinedmore » in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water–lipid HBs as the hydration decreases. Lastly, our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.« less

  2. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    PubMed

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

  3. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

    PubMed Central

    2015-01-01

    We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically

  4. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-08

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups.

  5. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  6. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  7. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-01

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  8. Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.

    PubMed

    Wambo, Thierry O; Chen, Liao Y; McHardy, Stanton F; Tsin, Andrew T

    2016-01-01

    Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases.

  9. All-atom molecular dynamics study of EAK16 peptide: the effect of pH on single-chain conformation, dimerization and self-assembly behavior.

    PubMed

    Emamyari, Soheila; Fazli, Hossein

    2014-05-01

    Single-chain equilibrium conformation and dimerization of the three types of ionic EAK16 peptide are studied under three pH conditions using all-atom molecular dynamics simulations. It is found that both the single-chain conformation and the dimerization process of EAK16-IV are considerably different from those of the two other types, EAK16-I and EAK16-II. The value of pH is found to have a stronger effect on the single-chain conformation and dimerization of EAK16-IV. It is shown that in addition to the charge pattern on the peptide chains, the size of the side chains of the charged amino acids plays role in the conformation of the peptide chains and their dimerization. The results shed light on the pH-dependent self-assembly behavior of EAK16 peptide in the bulk solution, which has been reported in the literature.

  10. Uncovering the microscopic mechanism of strand exchange during RecA mediated homologous recombination using all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shankla, Manish; Yoo, Jejoong; Aksimentiev, Aleksei

    2012-02-01

    Homologous recombination (HR) is a key step during the repair process of double-stranded DNA (dsDNA) breakage. RecA is a protein that mediates HR in bacteria. RecA monomers polymerize on a single-stranded DNA (ssDNA) separated from the broken dsDNA to form a helical filament, thus allowing strand exchange to occur. Recent crystal structures depict each RecA monomer in contact with three contiguous nucleotides called DNA triplets. Surprisingly, the conformation of each triplet is similar to that of a triplet in B-form DNA. However, in the filament the neighboring triplets are separated by loops of the RecA proteins. Single molecule experiments demonstrated that strand exchange propagation occurs in 3 base-pair increments. However, the temporal resolution of the experiments was insufficient to determine the exact molecular mechanism of the triplet propagation. Using all-atom molecular dynamics simulations, we investigated the effect of both the RecA protein and the conformation of the bound ssDNA fragment on the stability of the duplex DNA intermediate formed during the strand-exchange process. Specifically, we report simulations of force-induced unzipping of duplex DNA in the presence and absence of the RecA filament that explored the effect of the triplet ladder conformation.

  11. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    DOE PAGES

    Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

    2017-01-16

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

  12. Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions.

    PubMed

    Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-05-21

    Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system.

  13. Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics.

    PubMed

    Marin-Gonzalez, Alberto; Vilhena, J G; Perez, Ruben; Moreno-Herrero, Fernando

    2017-07-03

    Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.

  14. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

    2017-03-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to  ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning’s theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1{{k}\\text{B}}T . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  15. All-atom molecular dynamics simulations of an artificial sodium channel in a lipid bilayer: the effect of water solvation/desolvation of the sodium ion.

    PubMed

    Skelton, A A; Khedkar, V M; Fried, J R

    2016-01-01

    All-atom molecular dynamics is used to investigate the transport of Na(+) across a 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayer facilitated by a diazacrown hydraphile. Specifically, the free energy of Na(+) passing through the bilayer is calculated using the adaptive biasing force method to study the free energy associated with the increase in Na(+) transport in the presence of the hydraphile molecule. The results show that water interaction greatly influences Na(+) transport through the lipid bilayer as water is pulled through the bilayer with Na(+) forming a water channel. The hydraphile causes a reduction in the free energy barrier for the transport of Na(+) through the head group part of the lipid bilayer since it complexes the Na(+) reducing the necessity for water to be complexed and, therefore, dragged through with Na(+), an energetically unfavorable process. The free energy associated with Na(+) being desolvated within the bilayer is significantly decreased in the presence of the hydraphile molecule; the hydraphile increases the number of solvation states of Na(+) that can be adopted, and this increase in the number of available configurations provides an entropic explanation for the success of the hydraphile.

  16. Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach.

    PubMed

    Sahoo, Bikash Ranjan; Fujiwara, Toshimichi

    2016-12-20

    Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1.15 M salt). Comparative analysis in the ground and intermediate state conformations reveals substantial inter-HAMP interactions in the intermediate state with uniform clockwise (+10° to +30°) and counterclockwise (-20° to -40°) rotations in the α1 helix and the α2 helix of the monomer, respectively. Low temperature and low salt environments (283 K and 0.15 M) significantly affect srII-htrII binding affinity in both states with unusual helix bending. The distinguished control cable, knob-into-holes packing and piston-like movements in HAMP helices are found in the intermediate state complex. The N-terminal htrII (159 residues) coupled with srII yields a binding energy (ΔGbind) of -309.22, -436.53 and -331.11 kJ mol(-1) in the MM/PBSA calculation for the NphtrII homodimer, the NpsrII-htrII ground state conformation and the NpsrII-htrII intermediate state conformation, respectively. Only the HAMP1 domain shows a very low ΔGbind value (-21.03 kJ mol(-1)) for the ground state in comparison to that for the intermediate state (-54.68 kJ mol(-1)). The structural analysis highlights the key residues that include Y199(srII), T189(srII), E43(htrII), T86(htrII), M100(htrII), E116(htrII), E126(htrII) and S130(htrII) for complex stabilization and signal transduction.

  17. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations

    PubMed Central

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-01-01

    In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of

  18. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    PubMed

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  19. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

    PubMed

    De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

    2014-12-09

    A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

  20. Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: a combined dynamic fluorescence and all-atom molecular dynamics simulation study.

    PubMed

    Guchhait, Biswajit; Biswas, Ranjit; Ghorai, Pradip K

    2013-03-28

    Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements.

  1. All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC.

    PubMed

    Xu, Wu; Amire-Brahimi, Benjamin; Xie, Xiao-Jun; Huang, Liying; Ji, Jun-Yuan

    2014-08-01

    The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable 'CDK8 submodule' consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop, as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate

  2. All-atomic Molecular Dynamic Studies of Human CDK8: Insight into the A-loop, Point Mutations and Binding with Its Partner CycC

    PubMed Central

    Xu, Wu; Amire-Brahimi, Benjamin; Xie, Xiao-Jun; Huang, Liying; Ji, Jun-Yuan

    2014-01-01

    The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable ‘CDK8 submodule’ consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate

  3. All-atom simulations of crowding effects on ubiquitin dynamics.

    PubMed

    Abriata, Luciano A; Spiga, Enrico; Dal Peraro, Matteo

    2013-08-01

    It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L⁻¹ solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (∼0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.

  4. Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2).

    PubMed

    Slochower, David R; Huwe, Peter J; Radhakrishnan, Ravi; Janmey, Paul A

    2013-07-18

    Molecular dynamics calculations have been used to determine the structure of phosphatidylinositol 4,5 bisphosphate (PIP2) at the quantum level and to quantify the propensity for PIP2 to bind two physiologically relevant divalent cations, Mg(2+) and Ca(2+). We performed a geometry optimization at the Hartree-Fock 6-31+G(d) level of theory in vacuum and with a polarized continuum dielectric to determine the conformation of the phospholipid headgroup in the presence of water and its partial charge distribution. The angle between the headgroup and the acyl chains is nearly perpendicular, suggesting that in the absence of other interactions the inositol ring would lie flat along the cytoplasmic surface of the plasma membrane. Next, we employed hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the protonation state of PIP2 and its interactions with magnesium or calcium. We test the hypothesis suggested by prior experiments that binding of magnesium to PIP2 is mediated by a water molecule that is absent when calcium binds. These results may explain the selective ability of calcium to induce the formation of PIP2 clusters and phase separation from other lipids.

  5. All-atom molecular dynamics study of a spherical micelle composed of N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) block copolymers: a potential carrier of drug delivery systems for cancer.

    PubMed

    Kuramochi, Hiroshi; Andoh, Yoshimichi; Yoshii, Noriyuki; Okazaki, Susumu

    2009-11-19

    An all-atom molecular dynamics simulation of a spherical micelle composed of amphiphilic N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) (PEG-PBLG-Ac) block copolymers was performed in aqueous solution at 298.15 K and 1 atm. Such copolymers have received considerable attention as carriers in drug delivery systems. In this study, we used copolymers consisting of 11 EG units and 9 BLG units as models. Starting from the copolymers arranged spherically, the calculation predicted an equilibrium state consisting of a slightly elliptical micelle structure with a hydrophobic PBLG inner core and a hydrophilic PEG outer shell. The micelle structure was dynamically stable during the simulation, with the PEG blocks showing a compact helical conformation and the PBLG blocks an alpha-helix form. Multiple hydrogen bonds with solvent water molecules stabilized the helical conformation of the PEG blocks, leading to their hydration as shown by longer residence times of water molecules near the PEG ether oxygen atoms compared with that of bulk water. Some water molecules have also been found distributed within the hydrophobic core; they showed continuous exchange with bulk water during the simulation. Those molecules existed mostly as a cluster in spaces between the copolymers, forming hydrogen bonds among themselves as well as with the hydrophobic core through hydrophilic groups such as esters and amides. The water molecules forming hydrogen bonds with the micelle may play an important role in the stabilization of the micelle structure.

  6. A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent.

    PubMed

    Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

    2013-05-14

    We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.

  7. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  8. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

    PubMed

    Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

    2015-05-12

    Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

  9. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  10. All-atom contact model for understanding protein dynamics from crystallographic B-factors.

    PubMed

    Li, Da-Wei; Brüschweiler, Rafael

    2009-04-22

    An all-atom local contact model is described that can be used to predict protein motions underlying isotropic crystallographic B-factors. It uses a mean-field approximation to represent the motion of an atom in a harmonic potential generated by the surrounding atoms resting at their equilibrium positions. Based on a 400-ns molecular dynamics simulation of ubiquitin in explicit water, it is found that each surrounding atom stiffens the spring constant by a term that on average scales exponentially with the interatomic distance. This model combines features of the local density model by Halle and the local contact model by Zhang and Brüschweiler. When applied to a nonredundant set of 98 ultra-high resolution protein structures, an average correlation coefficient of 0.75 is obtained for all atoms. The systematic inclusion of crystal contact contributions and fraying effects is found to enhance the performance substantially. Because the computational cost of the local contact model scales linearly with the number of protein atoms, it is applicable to proteins of any size for the prediction of B-factors of both backbone and side-chain atoms. The model performs as well as or better than several other models tested, such as rigid-body motional models, the local density model, and various forms of the elastic network model. It is concluded that at the currently achievable level of accuracy, collective intramolecular motions are not essential for the interpretation of B-factors.

  11. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

    PubMed

    Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-28

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  12. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    NASA Astrophysics Data System (ADS)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  13. Computational analysis of Amsacrine resistance in human topoisomerase II alpha mutants (R487K and E571K) using homology modeling, docking and all-atom molecular dynamics simulation in explicit solvent.

    PubMed

    Sader, Safaa; Wu, Chun

    2017-03-01

    Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide. This wild type complex was used to build the ternary complex with R487K and E571K mutants. Three 500ns molecular dynamics simulations were performed on complex systems of wild type and two mutants. The detailed energetic, structural and dynamic analysis were performed on the simulation data. Our binding data indicated a significant impairment of Amsacrine binding energy in the two mutants compared with the wild type. The order of weakening (R487K>E571K) was in agreement with the order of experimental drug resistance fold (R489K>E571K). Our binding energy decomposition further indicated that weakening of the ligand-protein interaction rather than the ligand-DNA interaction was the major contributor of the binding energy difference between R487K and E571K. In addition, key residues contributing to the binding energy (ΔG) or the decrease of the binding energy (ΔΔG) were identified through the energy decomposition analysis. The change in ligand binding pose, dynamics of protein, DNA and ligand upon the mutations were thoroughly analyzed and discussed. Deciphering the molecular basis of drug resistance is crucial to overcome drug resistance using rational drug design. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

    PubMed

    Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing

    2017-03-20

    The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

  15. All-Atom Molecular-Level Analysis of the Ballistic-Impact-Induced Densification and Devitrification of Fused Silica

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Snipes, J. S.; Ramaswami, S.; Yavari, R.; Barsoum, R. S.

    2015-08-01

    All-atom molecular-level computations are carried out to infer the dynamic response and material microstructure/topology changes of fused silica subjected to ballistic impact by a hard projectile. The analysis was focused on the investigation of specific aspects of the dynamic response and of the microstructural changes such as the deformation of highly sheared and densified regions and the conversion of amorphous fused silica to SiO2 crystalline allotropic modifications (in particular, α-quartz and stishovite). The microstructural changes in question were determined by carrying out a post-processing atom-coordination procedure. This procedure suggested the formation of stishovite (and perhaps α-quartz) within fused silica during ballistic impact. To rationalize the findings obtained, the all-atom molecular-level computational analysis is complemented by a series of quantum-mechanics density functional theory (DFT) computations. The latter computations enable determination of the relative potential energies of the fused silica, α-quartz, and stishovite under ambient pressure (i.e., under their natural densities) as well as under imposed (as high as 50 GPa) pressures (i.e., under higher densities) and shear strains. In addition, the transition states associated with various fused-silica devitrification processes were identified. The results obtained are found to be in good agreement with their respective experimental counterparts.

  16. The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A

    NASA Astrophysics Data System (ADS)

    Linhananta, Apichart; Zhou, Yaoqi

    2002-11-01

    Protein topology, which refers to the arrangement of secondary structures of proteins, has been extensively investigated to examine its role in protein folding. However, recent studies show that topology alone cannot account for the variation of folding behaviors observed in some proteins of the same structural family. In a recent work, we showed that the native structure of the second β hairpin of protein G predicts a folding mechanism that is different from topology-based models. Here, we continue to examine how much one can learn about folding mechanism from native structure. This work focuses on fragment B of Staphylococcal protein A (BpA) - a three-helix (H1, H2, and H3) bundle protein. Using a recently developed all-atom (except nonpolar hydrogen) Gō model interacting with simple discontinuous potentials, the folding of the model BpA was observed in 112 out of 249 trajectories within 50 h of CPU times on a Pentium PC (1 GHz). The model successfully captured several specific properties of BpA that have been observed experimentally. These include the higher stability of H3 compared to H1 and H2, and the higher stability of the H2-H3 microdomain compared to the H1-H2 microdomain. These specific details were not produced by a topology-based square-well model of BpA. Thus, the result further supports the important role of sidechain packing in determining the specific pathway of protein folding. Additional 96 000 short simulations were performed to locate the transition states of the two folding pathways. The limitation of the Gō model and its possible improvement are also discussed.

  17. Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations.

    PubMed

    Strom, Alexander M; Fehling, Samuel C; Bhattacharyya, Sudeep; Hati, Sanchita

    2014-05-01

    Coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. To evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-tRNA synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-tRNA synthetases--Escherichia coli methionyl-tRNA synthetase, Thermus thermophilus leucyl-tRNA synthetase, and Enterococcus faecium prolyl-tRNA synthetase. In the present study, comparison of predicted dynamics based on B-factor and overlap calculations revealed that coarse-grained methods are comparable to the all-atom simulations in depicting the intrinsic global dynamics of the three enzymes. However, the principal component analyses of the motions obtained from the all-atom molecular dynamics simulations provide a superior description of the local fluctuations of these enzymes. In particular, the all-atom model was able to capture the functionally relevant substrate-induced dynamical changes in prolyl-tRNA synthetase. The alteration in the coupled dynamics between the catalytically important proline-binding loop and its neighboring structural elements due to substrate binding has been characterized and reported for the first time. Taken together, the study portrays comparable and contrasting situations in studying the functional dynamics of large multi-domain aminoacyl-tRNA synthetases using coarse-grained and all-atom simulation methods.

  18. Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations

    NASA Astrophysics Data System (ADS)

    Zhang, Rong; Wu, Wen-juan

    2010-10-01

    An all-atom dimethyl sulfoxide (DMSO) and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H ··· O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of (DMSO)m·S=O···HW-OW·(H2O)n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.

  19. Dynamic performance of duolayers at the air/water interface. 2. Mechanistic insights from all-atom simulations.

    PubMed

    Christofferson, Andrew J; Yiapanis, George; Leung, Andy H M; Prime, Emma L; Tran, Diana N H; Qiao, Greg G; Solomon, David H; Yarovsky, Irene

    2014-09-18

    The novel duolayer system, comprising a monolayer of ethylene glycol monooctadecyl ether (C18E1) and the water-soluble polymer poly(vinylpyrrolidone) (PVP), has been shown to resist forces such as wind stress to a greater degree than the C18E1 monolayer alone. This paper reports all-atom molecular dynamics simulations comparing the monolayer (C18E1 alone) and duolayer systems under an applied force parallel to the air/water interface. The simulations show that, due to the presence of PVP at the interface, the duolayer film exhibits an increase in chain tilt, ordering, and density, as well as a lower lateral velocity compared to the monolayer. These results provide a molecular rationale for the improved performance of the duolayer system under wind conditions, as well as an atomic-level explanation for the observed efficacy of the duolayer system as an evaporation suppressant, which may serve as a useful guide for future development for thin films where resistance to external perturbation is desirable.

  20. From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations.

    PubMed

    Schwierz, Nadine; Frost, Christina V; Geissler, Phillip L; Zacharias, Martin

    2017-02-02

    Secondary nucleation pathways in which existing amyloid fibrils catalyze the formation of new aggregates and neurotoxic oligomers are of immediate importance for the onset and progression of Alzheimer's disease. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to study surface-activated secondary nucleation pathways at the extended lateral β-sheet surface of a preformed Aβ9-40 filament. Calculation of free-energy profiles allows us to determine binding free energies and conformational intermediates for nucleation complexes consisting of 1-4 Aβ peptides. In addition, we combine the free-energy profiles with position-dependent diffusion profiles to extract complementary kinetic information and macroscopic growth rates. Single monomers bind to the β-sheet surface in a disordered, hydrophobically collapsed conformation, whereas dimers and larger oligomers can retain a cross-β conformation resembling a more ordered fibril structure. The association processes during secondary nucleation follow a dock/lock mechanism consisting of a fast initial encounter phase (docking) and a slow structural rearrangement phase (locking). The major driving forces for surface-activated secondary nucleation are the release of a large number of hydration water molecules and the formation of hydrophobic interface contacts, the latter being in contrast to the elongation process at filament tips, which is dominated by the formation of stable and highly specific interface hydrogen bonds. The calculated binding free energies and the association rates for the attachment of Aβ monomers and oligomers to the extended lateral β-sheet surface of the filament seed are higher compared to those for elongation at the filament tips, indicating that secondary nucleation pathways can become important once a critical concentration of filaments has formed.

  1. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  2. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  3. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation.

    PubMed

    Zheng, Wenjun; Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant--while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  4. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    PubMed

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  5. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  6. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    DOE PAGES

    Perilla, Juan R.; Schulten, Klaus

    2017-07-19

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

  7. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Perilla, Juan R.; Schulten, Klaus

    2017-07-01

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

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

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    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. PMID:26926570

  9. 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.

  10. 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.

  11. Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches.

    PubMed

    Mozolewska, Magdalena A; Krupa, Paweł; Scheraga, Harold A; Liwo, Adam

    2015-08-01

    The iron-sulfur protein 1 (Isu1) and the J-type co-chaperone Jac1 from yeast are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ-shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105 , L109 , and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1-12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N(95), T(98), P(102), H(112), V(159), L(167), and A(170) of Jac1, not yet tested experimentally, were also found to be important in binding.

  12. Molecular modeling of the binding modes of the Iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

    PubMed Central

    Mozolewska, Magdalena A.; Krupa, Paweł; Scheraga, Harold A.; Liwo, Adam

    2015-01-01

    The Iron sulfur protein 1 (Isu1) from yeast, and the J-type co-chaperone Jac1, are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the “Γ” shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105, L109, and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J. Mol. Biol. 2012, 417, 1–12). These residues were also found, by UNRES/MD simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N95, T98, P102, H112, V159, L167 and A170 of Jac1, not yet tested experimentally, were also found important in binding. PMID:25973573

  13. Microtubule Elasticity: Connecting All-Atom Simulations with Continuum Mechanics

    NASA Astrophysics Data System (ADS)

    Sept, David; Mackintosh, Fred C.

    2010-01-01

    The mechanical properties of microtubules have been extensively studied using a wide range of biophysical techniques, seeking to understand the mechanics of these cylindrical polymers. Here we develop a method for connecting all-atom molecular dynamics simulations with continuum mechanics and show how this can be applied to understand microtubule mechanics. Our coarse-graining technique applied to the microscopic simulation system yields consistent predictions for the Young’s modulus and persistence length of microtubules, while clearly demonstrating how binding of the drug Taxol decreases the stiffness of microtubules. The techniques we develop should be widely applicable to other macromolecular systems.

  14. An all-atom simulation study of the ordering of liquid squalane near a solid surface

    NASA Astrophysics Data System (ADS)

    Tsige, Mesfin; Patnaik, Soumya S.

    2008-05-01

    An all-atom molecular dynamics study using the OPLS force field has been carried out to obtain new insights in to the orientation and ordering of liquid squalane near a solid surface. As observed in previous experiments, the squalane molecules closest to a SiO 2 substrate are found to be tightly bound with their molecular axis preferentially parallel to the interface. Unlike linear alkanes, the squalane molecules are also found to lie preferentially parallel to the liquid/vapor interface. The simulation results predict that the molecular plane orientation of the squalane molecules changes from mainly parallel to perpendicular to the substrate in going further away from the substrate.

  15. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    SciTech Connect

    Okumura, Hisashi

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  16. Folding of proteins with an all-atom Go-model.

    PubMed

    Wu, L; Zhang, J; Qin, M; Liu, F; Wang, W

    2008-06-21

    The Go-like potential at a residual level has been successfully applied to the folding of proteins in many previous works. However, taking into consideration more detailed structural information in the atomic level, the definition of contacts used in these traditional Go-models may not be suitable for all-atom simulations. Here, in this work, we develop a rational definition of contacts considering the screening effect in the crowded intramolecular environment. In such a scheme, a large amount of screened atom pairs are excluded and the number of contacts is decreased compared to the case of the traditional definition. These contacts defined by such a new definition are compatible with the all-atom representation of protein structures. To verify the rationality of the new definition of contacts, the folding of proteins CI2 and SH3 is simulated by all-atom molecular dynamics simulations. A high folding cooperativity and good correlation of the simulated Phi-values with those obtained experimentally, especially for CI2, are found. This suggests that the all-atom Go-model is improved compared to the traditional Go-model. Based on the comparison of the Phi-values, the roles of side chains in the folding are discussed, and it is concluded that the side-chain structures are more important for local contacts in determining the transition state structures. Moreover, the relations between side chain and backbone orderings are also discussed.

  17. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  18. An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

    PubMed Central

    Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

    2012-01-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  19. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals.

    PubMed

    Kaushik, Ananth P; Clancy, Paulette

    2012-03-21

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.

  20. Nonequilibrium molecular dynamics

    SciTech Connect

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

    1990-11-01

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

  1. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.

    PubMed

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

    2016-12-01

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

  2. Substructured multibody molecular dynamics.

    SciTech Connect

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

    2006-11-01

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

  3. Viral structural transitions: an all-atom multiscale theory.

    PubMed

    Miao, Yinglong; Ortoleva, Peter J

    2006-12-07

    An all-atom theory of viral structural transitions (STs) is developed based on a multiscale analysis of the N-atom Liouville equation. The approach yields an understanding of viral STs from first principles and a calibrated interatomic force field. To carry out the multiscale analysis, we introduce slow variables characterizing the whole-virus dynamics. Use of the "nanocanonical ensemble" technique and the fundamental hypothesis of statistical mechanics (i.e., the equivalence of long-time and ensemble averages) is shown to imply a Fokker-Planck equation yielding the coarse-grained evolution of the slow variables. As viral STs occur on long time scales, transition state theory is used to estimate the energy barrier of transition between free energy wells implied by observed hysteresis in viral STs. Its application to Nudaurelia capensis omega virus provides an upper bound on the free energy barrier when a single dilatational order parameter is used. The long time scale of viral STs is shown to follow from the aggregate effect of inertia, energy barrier, and entropic effects. Our formulation can be generalized for multiple order parameter models to account for lower free energy barrier pathways for transition. The theory with its all-atom description can be applied to nonviral nanoparticles as well.

  4. Accelerating molecular dynamic simulation on graphics processing units.

    PubMed

    Friedrichs, Mark S; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L; Ensign, Daniel L; Bruns, Christopher M; Pande, Vijay S

    2009-04-30

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. (c) 2009 Wiley Periodicals, Inc.

  5. Equipartition Principle for Internal Coordinate Molecular Dynamics.

    PubMed

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

    2012-08-14

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

  6. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik

    2015-01-01

    Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.

  7. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik R

    2008-01-01

    Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.

  8. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.

    PubMed

    Luo, Zhonglin; Ding, Jiandong; Zhou, Yaoqi

    2008-06-14

    This paper examines the folding mechanism of an individual beta-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel beta-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single beta-hairpin in literature is confirmed to be useful in describing beta-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, beta1-beta2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of beta2-beta3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent.

  9. Physics-based all-atom modeling of RNA energetics and structure.

    PubMed

    Smith, Louis G; Zhao, Jianbo; Mathews, David H; Turner, Douglas H

    2017-09-01

    The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422. © 2017 Wiley Periodicals, Inc.

  10. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    PubMed

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-24

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.

  11. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

    PubMed Central

    Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

    2016-01-01

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

  12. Multiscale reactive molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  13. Multiscale reactive molecular dynamics

    PubMed Central

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

    2012-01-01

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

  14. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Schroeder, Daniel V.

    2015-03-01

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

  15. Microsecond Molecular Dynamics Simulations of Lipid Mixing

    PubMed Central

    2015-01-01

    Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736

  16. Introduction to Accelerated Molecular Dynamics

    SciTech Connect

    Perez, Danny

    2012-07-10

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

  17. Molecular Dynamics Calculations

    NASA Technical Reports Server (NTRS)

    1996-01-01

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

  18. Coarse-grained protein molecular dynamics simulations.

    PubMed

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-14

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

  19. Coarse-grained protein molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-01

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

  20. Molecular origin of limiting shear stress of elastohydrodynamic lubrication oil film studied by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Washizu, Hitoshi; Ohmori, Toshihide; Suzuki, Atsushi

    2017-06-01

    All-atom molecular dynamics simulations of an elastohydrodynamic lubrication oil film are performed to study the effect of pressure. Fluid molecules of n-hexane are confined between two solid plates under a constant normal force of 0.1-8.0 GPa. Traction simulations are performed by applying relative sliding motion to the solid plates. A transition in the traction behavior is observed around 0.5-2.0 GPa, which corresponds to the viscoelastic region to the plastic-elastic region, which are experimentally observed. This phase transition is related to the suppression of the fluctuation in molecular motion.

  1. Attosecond Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Martin, Fernando

    2015-05-01

    The development of attosecond laser pulses allows one to probe the inner working of atoms, molecules and surfaces on the timescale of the electronic response. In molecules, attosecond pump-probe spectroscopy enables investigations of the prompt charge redistribution and localization that accompany photo-excitation processes, where a molecule is lifted from the ground Born-Oppenheimer potential energy surface to one or more excited surfaces, and where subsequent photochemistry evolves on femto- and attosecond timescales. In this talk I will present a few theoretical examples of realistic molecular attosecond pump-probe experiments in which simple molecules are ionized with a single attosecond pulse (or a train of attosecond pulses) and are subsequently probed by one or several infrared or xuv few-cycle pulses. The evolution of the electronic and nuclear densities in the photo-excited molecule or remaining molecular ions is calculated with attosecond time-resolution and is visualized by varying the delay between the pump and probe pulses. The results of these calculations allow us to explain several experimental observations as well as to guide future experimental efforts to uncover ultrafast electron and nuclear dynamics in molecules.

  2. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension.

    PubMed

    Sonne, Jacob; Jensen, Morten Ø; Hansen, Flemming Y; Hemmingsen, Lars; Peters, Günther H

    2007-06-15

    Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.

  3. A hybrid all-atom/coarse grain model for multiscale simulations of DNA.

    PubMed

    Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio

    2011-10-28

    Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulations. Our method allows us to forthrightly link a state-of-the-art force field for AA simulations of DNA with a CG representation developed by our group. We show that no modification is needed for any of the existing residues (neither AA nor CG). Only the bonding parameters at the hybrid interface are enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems, which are studied by molecular dynamics simulations using an implicit solvent. The simplicity of the approach potentially permits us to study the effect of mutations/modifications as well as DNA binding molecules at the atomistic level within a significantly larger DNA scaffold considered at the CG level. Since all the interactions are computed within the same classical Hamiltonian, the extension to a quantum/classical/coarse-grain multilayer approach using QM/MM modules implemented in widely used simulation packages is straightforward.

  4. VMD: visual molecular dynamics.

    PubMed

    Humphrey, W; Dalke, A; Schulten, K

    1996-02-01

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

  5. Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics.

    PubMed

    Vila Verde, Ana; Beltramo, Peter J; Maranas, Janna K

    2011-05-17

    We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.

  6. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

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

  7. MDplot: Visualise Molecular Dynamics.

    PubMed

    Margreitter, Christian; Oostenbrink, Chris

    2017-05-10

    The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

  8. Molecular Dynamics Trajectory Compression with a Coarse-Grained Model

    PubMed Central

    Cheng, Yi-Ming; Gopal, Srinivasa Murthy; Law, Sean M.; Feig, Michael

    2012-01-01

    Molecular dynamics trajectories are very data-intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data is about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory. PMID:22025759

  9. Folding of Small Proteins Using Constrained Molecular Dynamics

    PubMed Central

    Balaraman, Gouthaman S.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

    2011-01-01

    The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched towards “native-like” structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement. It is computationally expensive to perform all-atom simulations of protein folding because the processes occur on a timescale of microseconds. Compared to the all-atom MD simulation, constrained MD methods have the advantage that stable dynamics can be achieved for larger time steps and the number of degrees of freedom is an order of magnitude smaller, leading to a decrease in computational cost. We have developed a generalized constrained MD method that allows the user to “freeze and thaw” torsional degrees of freedom as fit for the problem studied. We have used this method to perform all-torsion constrained MD in implicit solvent coupled with the replica exchange method to study folding of small proteins with various secondary structural motifs such as, α-helix (polyalanine, WALP16), β-turn (1E0Q), and a mixed motif protein (Trp-cage). We demonstrate that constrained MD replica exchange method exhibits a wider conformational search than all-atom MD with increased enrichment of near native structures. “Hierarchical” constrained MD simulations, where the partially formed helical regions in the initial stretch of the all-torsion folding simulation trajectory of Trp-cage were frozen, showed a better sampling of near native structures than all-torsion constrained MD simulations. This is in agreement with the zipping-and-assembly folding model put forth by Dill and coworkers for folding proteins. The use of hierarchical “freeze and thaw” clustering schemes in constrained MD simulation can be used to sample conformations that contribute significantly to folding of proteins. PMID:21591767

  10. Molecular dynamics with quantum fluctuations

    SciTech Connect

    Georgescu, Ionut; Mandelshtam, Vladimir A.

    2010-09-01

    A quantum dynamics approach, called Gaussian molecular dynamics, is introduced. As in the centroid molecular dynamics, the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the variational Gaussian wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short-time limit and is computationally very efficient.

  11. Nanoscale deicing by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

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

  12. Dissipative particle dynamics with an effective pair potential from integral equation theory of molecular liquids.

    PubMed

    Kobryn, Alexander E; Nikolić, Dragan; Lyubimova, Olga; Gusarov, Sergey; Kovalenko, Andriy

    2014-10-16

    We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency.

  13. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

    PubMed

    Zheng, Wenjun

    2014-07-01

    The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins.

  14. Molecular dynamics of silicon indentation

    NASA Astrophysics Data System (ADS)

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

    1993-04-01

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

  15. Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model.

    PubMed

    Genheden, Samuel

    2016-01-12

    The solvation free energy is an essential quantity in force field development and in numerous applications. Here, we present the estimation of solvation free energies in polar (water, hexanol, octanol, and nonanol) and in apolar (hexane, octane, and nonane) media. The estimates are produced using molecular dynamics simulations employing a simple all-atom/coarse-grained hybrid model (AA/ELBA) and are therefore very efficient. More than 150 solutes were taken from the Minnesota solvation database and represent small, organic molecules. The mean absolute deviation for the different solvents ranges between 2.0 and 4.1 kJ/mol, and the correlation coefficient ranges between 0.78 and 0.99, indicating that the predictions are accurate. Outliers are identified, and potential avenues for improvements are discussed. Furthermore, partition coefficients between water and the organic solvents were estimated, and the percentage of the predictions that has the correct sign ranges between 74% (for octane) and 92% (for octanol and hexanol). Finally, membrane/water partition coefficients are replaced with hexane/water and octanol/water partition coefficients, and the latter is found to be as accurate as the expensive membrane calculations, indicating a wider application area.

  16. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.

    PubMed

    Shimada, J; Kussell, E L; Shakhnovich, E I

    2001-04-20

    We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding, all side-chain and backbone torsions, and uses a Go potential. In this study, we focus on the 46 residue alpha/beta protein crambin and two of its structural components, the helix and helix hairpin. For a wide range of temperatures, we recorded multiple folding events of these three structures from random coils to native conformations that differ by less than 1 A C(alpha) dRMS from their crystal structure coordinates. The thermodynamics and kinetic mechanism of the helix-coil transition obtained from our simulation shows excellent agreement with currently available experimental and molecular dynamics data. Based on insights obtained from folding its smaller structural components, a possible folding mechanism for crambin is proposed. We observed that the folding occurs via a cooperative, first order-like process, and that many folding pathways to the native state exist. One particular sequence of events constitutes a "fast-folding" pathway where kinetic traps are avoided. At very low temperatures, a kinetic trap arising from the incorrect packing of side-chains was observed. These results demonstrate that folding to the native state can be observed in a reasonable amount of time on desktop computers even when an all-atom representation is used, provided the energetics sufficiently stabilize the native state.

  17. Local elasticity of strained DNA studied by all-atom simulations

    NASA Astrophysics Data System (ADS)

    Mazur, Alexey K.

    2011-08-01

    Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

  18. Molecular dynamics studies of interfacial water at the alumina surface.

    SciTech Connect

    Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David

    2011-01-01

    Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.

  19. Molecular modelling and molecular dynamics of CFTR.

    PubMed

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

    2017-01-01

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

  20. Modeling Molecular Dynamics from Simulations

    SciTech Connect

    Hinrichs, Nina Singhal

    2009-01-28

    Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.

  1. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

    PubMed Central

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-01-01

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

  2. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    PubMed

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  3. Molecular dynamics simulation of pyridine

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

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

  4. Integration methods for molecular dynamics

    SciTech Connect

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

    1996-12-31

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

  5. Linear-scaling first-principles molecular dynamics of complex biological systems with the Conquest code

    NASA Astrophysics Data System (ADS)

    Otsuka, Takao; Taiji, Makoto; Bowler, David R.; Miyazaki, Tsuyoshi

    2016-11-01

    The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. In this paper, we show that all-atom molecular dynamics simulations of complex biological systems based on DFT are now possible using our linear-scaling DFT code Conquest. We first overview the calculation methods used in Conquest and explain the method introduced recently to realise efficient and robust first-principles molecular dynamics (FPMD) with O(N) DFT. Then, we show that we can perform reliable all-atom FPMD simulations of a hydrated DNA model containing about 3400 atoms. We also report that the velocity scaling method is both reliable and useful for controlling the temperature of the FPMD simulation of this system. From these results, we conclude that reliable FPMD simulations of complex biological systems are now possible with Conquest.

  6. GAS PHASE MOLECULAR DYNAMICS

    SciTech Connect

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

    1999-06-09

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

  7. Molecular-dynamics simulation of thin-film growth

    NASA Astrophysics Data System (ADS)

    Schneider, M.; Schuller, I. K.; Rahman, A.

    1987-01-01

    The epitaxial growth of thin films has been studied by molecular-dynamics computer simulation. In these simulations atoms are projected towards a temperature-controlled substrate, and the equations of motion of all atoms are solved for a given interaction potential. The calculations give insight into the microscopic structure of thin films, the dynamics of the adsorption process, and they help answer the way in which substrate temperature, form of the substrate, flux of impinging atoms, and form of the interaction potential, affect epitaxial growth. Simulations were performed for monatomic and binary systems with spherically symmetric atomic interactions, and for systems in which the atoms are interacting via a three-body potential to simulate the epitaxial growth of silicon.

  8. Beyond modeling: all-atom olfactory receptor model simulations.

    PubMed

    Lai, Peter C; Crasto, Chiquito J

    2012-01-01

    Olfactory receptors (ORs) are a type of GTP-binding protein-coupled receptor (GPCR). These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level beyond inferences that are drawn merely from static docking. Here we have shown the specific advantages of simulating the dynamic environment associated with OR-odorant interactions. We present a rigorous protocol which ranges from the creation of a computationally derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.

  9. Dynamic molecular graphs: "hopping" structures.

    PubMed

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

    2014-05-05

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

  10. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  11. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  12. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    PubMed

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  13. Sampling Kinetic Protein Folding Pathways using All-Atom Models

    NASA Astrophysics Data System (ADS)

    Bolhuis, P. G.

    This chapter summarizes several computational strategies to study the kinetics of two-state protein folding using all atom models. After explaining the background of two state folding using energy landscapes I introduce common protein models and computational tools to study folding thermodynamics and kinetics. Free energy landscapes are able to capture the thermodynamics of two-state protein folding, and several methods for efficient sampling of these landscapes are presented. An accurate estimate of folding kinetics, the main topic of this chapter, is more difficult to achieve. I argue that path sampling methods are well suited to overcome the problems connected to the sampling of folding kinetics. Some of the major issues are illustrated in the case study on the folding of the GB1 hairpin.

  14. Molecular basis of the initial platelet adhesion in arterial thrombosis: molecular dynamics simulations.

    PubMed

    Li, Jian; Zhang, Lin; Sun, Yan

    2012-07-01

    Molecular interactions between the von Willebrand factor (VWF) A1 domain and glycoprotein Ibα (GPIbα) promote the initial adhesion of platelets and subsequent arterial thrombus formation. However, little is understood about the interactions at a molecular level. Therefore, the binding dynamics and involved molecular interactions between VWF A1 domain and GPIbα in both water and physiological saline are investigated using molecular dynamics simulations and all-atom models. Faster binding is observed in water than that in physiological saline, and patches of opposite charges are observed at the binding interface. Moreover, molecular mechanics-Poisson-Boltzmann surface area analysis indicates that the binding is promoted by the long-range electrostatic interactions and then maintained by hydrophobic interactions. For the initial binding, the hot spots include the residues E14, E128, D175, D83, E151, D106, D63, E5, D18, E225, D235 in GPIbα, and K608, K569, K644, R571, K572, R636, K599 in VWF A1 domain. For the final complex formation, however, 72% of the favorable contributions are from hydrophobic interactions. The results provided molecular insight into the initial platelet adhesion. The hot spots identified would be beneficial for developing novel drugs for thrombotic diseases. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

  16. Combining Optimal Control Theory and Molecular Dynamics for Protein Folding

    PubMed Central

    Arkun, Yaman; Gur, Mert

    2012-01-01

    A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the atoms. In turn, MD simulation provides an all-atom conformation whose positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization - MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages. PMID:22238629

  17. Combining optimal control theory and molecular dynamics for protein folding.

    PubMed

    Arkun, Yaman; Gur, Mert

    2012-01-01

    A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  18. Oleuropein: Molecular Dynamics and Computation.

    PubMed

    Gentile, Luigi; Uccella, Nicola A; Sivakumar, Ganapathy

    2017-09-11

    Olive oil and table olive biophenols have been shown to significantly enrich the hedonic-sensory and nutritional quality of the Mediterranean diet. Oleuropein is one of the predominate biophenols in green olives and leaves, which not only has noteworthy free-radical quenching activity but also putatively reduces the incidence of various cancers. Clinical trials suggest that the consumption of extra virgin olive oil reduces the risk of several degenerative diseases. The oleuropein-based bioactives in olive oil could reduce tumor necrosis factor α, interleukin-1β and nitric oxide. Therefore, olive bioactives quality should be preserved and even improved due to their disease-fighting properties. Understanding the molecular dynamics of oleuropein is crucial to increase olive oil and table olive quality. The objective of this review is to provide the molecular dynamics and computational mapping of oleuropein. It is a biophenol-secoiridoid expressing different functionalities such as two π-bonds, two esters, two acetals, one catechol, and four hexose hydroxyls within 540 mw. The molecular bond sequential breaking mechanisms were analyzed through unimolecular reactions under electron spray ionization, collision activated dissociations, and fast atom bombardment mass spectrometry. The oleuropein solvent-free reactivity is leading to glucose loss and bioactive aglycone-dialdehydes via secoiridoid ring opening. Oleuropein electron distribution revealed that the free-radical non-polar processes occur from its highest occupied molecular orbital, while the lowest unoccupied molecular orbital is clearly devoted to nucleophilic and base site reactivity. This molecular dynamics and computational mapping of oleuropein could contribute to the engineering of olive-based biomedicine and/or functional food. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  19. Effect of Calcium and Magnesium on Phosphatidylserine Membranes: Experiments and All-Atomic Simulations

    PubMed Central

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-01-01

    It is known that phosphatidylserine (PS−) lipids have a very similar affinity for Ca2+ and Mg2+ cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca2+ or Mg2+ induces very different aggregation behavior for PS− liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca2+ or Mg2+ cations. These puzzling results suggest that although these two cations have a similar affinity for PS− lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS− membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca2+ and Mg2+ cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca2+ cations present a peak at a distance ∼2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg2+ cations has two different peaks, located a few angstroms before and after the Ca2+ peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca2+ and Mg2+, respectively. PMID:22824273

  20. Effect of calcium and magnesium on phosphatidylserine membranes: experiments and all-atomic simulations.

    PubMed

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-05-02

    It is known that phosphatidylserine (PS(-)) lipids have a very similar affinity for Ca(2+) and Mg(2+) cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca(2+) or Mg(2+) induces very different aggregation behavior for PS(-) liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca(2+) or Mg(2+) cations. These puzzling results suggest that although these two cations have a similar affinity for PS(-) lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS(-) membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca(2+) and Mg(2+) cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca(2+) cations present a peak at a distance ~2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg(2+) cations has two different peaks, located a few angstroms before and after the Ca(2+) peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca(2+) and Mg(2

  1. Benchmarking all-atom simulations using hydrogen exchange

    SciTech Connect

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-10-27

    We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.

  2. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations

    PubMed Central

    Lai, Peter C.; Crasto, Chiquito J.

    2012-01-01

    Olfactory receptors (ORs) are a type of GTP-binding protein-coupled receptor (GPCR). These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level beyond inferences that are drawn merely from static docking. Here we have shown the specific advantages of simulating the dynamic environment associated with OR-odorant interactions. We present a rigorous protocol which ranges from the creation of a computationally derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs. PMID:22563330

  3. Benchmarking all-atom simulations using hydrogen exchange

    DOE PAGES

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; ...

    2014-10-27

    We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability andmore » H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.« less

  4. Benchmarking all-atom simulations using hydrogen exchange

    PubMed Central

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413

  5. Available Instruments for Analyzing Molecular Dynamics Trajectories

    PubMed Central

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

    2016-01-01

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

  6. Hidden Markov models from molecular dynamics simulations on DNA.

    PubMed

    Thayer, Kelly M; Beveridge, D L

    2002-06-25

    An enhanced bioinformatics tool incorporating the participation of molecular structure as well as sequence in protein DNA recognition is proposed and tested. Boltzmann probability models of sequence-dependent DNA structure from all-atom molecular dynamics simulations were obtained and incorporated into hidden Markov models (HMMs) that can recognize molecular structural signals as well as sequence in protein-DNA binding sites on a genome. The binding of catabolite activator protein (CAP) to cognate DNA sequences was used as a prototype case for implementation and testing of the method. The results indicate that even HMMs based on probabilistic roll/tilt dinucleotide models of sequence-dependent DNA structure have some capability to discriminate between known CAP binding and nonbinding sites and to predict putative CAP binding sites in unknowns. Restricting HMMs to sequence only in regions of strong consensus in which the protein makes base specific contacts with the cognate DNA further improved the discriminatory capabilities of the HMMs. Comparison of results with controls based on sequence only indicates that extending the definition of consensus from sequence to structure improves the transferability of the HMMs, and provides further supportive evidence of a role for dynamical molecular structure as well as sequence in genomic regulatory mechanisms.

  7. Virus capsid dissolution studied by microsecond molecular dynamics simulations.

    PubMed

    Larsson, Daniel S D; Liljas, Lars; van der Spoel, David

    2012-01-01

    Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.

  8. Novel methods for molecular dynamics simulations.

    PubMed

    Elber, R

    1996-04-01

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

  9. Molecular dynamics studies of Hsp90 with ADP: Protein-ligand binding dynamics

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kazutomo; Takagi, Hiroyuki; Takasu, Masako; Saito, Hiroaki; Nagao, Hidemi

    2013-02-01

    Ligand binding to a protein molecule plays a key role in the function of many proteins. We performed all-atom model molecular dynamics (MD) simulations of the N-terminal domain of human Hsp90 in complex with ADP, and calculated a free energy profile for ligand binding with thermodynamic integration method. The free energy profile as a function of the distance between the centers of mass of the N-terminal domain of Hsp90 and ADP was calculated using the results of the binding-distance constrained MD simulations. The free energy profile was fit to a harmonic oscillator. We obtained spring constant k = 3.84kJ/molṡnm2 = 9.17×10-1kcal/molṡÅ2. This result indicates that the dynamics of the ligand binding to the protein molecule is about 1,000 times slower than that of the covalent bond.

  10. Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks.

    PubMed

    Cieplak, Marek; Thompson, Damien

    2008-06-21

    A coarse-grained molecular dynamics (MD) model is developed to study the multivalent, or multisite, binding of small functionalized dendrimer molecules to beta-cyclodextrin-terminated self-assembled monolayers, the so-called "molecular printboards" used to print "ink" molecules on surfaces with a high degree of positional control and specificity. Some current and future bionanotechnology applications are in the creation of nanoparticle assemblies, directed protein assembly, platforms for biosensing, and cell:surface attachment. The coarse-grained model allows us to probe up to microsecond timescales and model ink diffusion, crucial for the application of the printboard in, for example, medical diagnostics. Recent all-atom MD simulations identified and quantified the molecular strain limiting the stability of nanopatterns created with small dendrimer inks, and explained the different patterns obtained experimentally with different dendrimer inks. In the present work, the all-atom simulations are "scaled up" to longer timescales via coarse graining, without incurring significant additional computational expense, and, crucially, without significant loss in atom-scale detail, the coarse-grained MD simulations yielding properties similar to those obtained from the all-atom simulations. The anchoring of the ink molecules to the monolayer is of multivalent nature and the degree of multivalency shows a sharp dependence on temperature, control of temperature thus providing a further operational "switch" for directed molecular assembly. The computational protocol developed can, in principle, be extended to model any multivalent assembly, for example, virus-cell complexation.

  11. Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek; Thompson, Damien

    2008-06-01

    A coarse-grained molecular dynamics (MD) model is developed to study the multivalent, or multisite, binding of small functionalized dendrimer molecules to β-cyclodextrin-terminated self-assembled monolayers, the so-called ``molecular printboards'' used to print ``ink'' molecules on surfaces with a high degree of positional control and specificity. Some current and future bionanotechnology applications are in the creation of nanoparticle assemblies, directed protein assembly, platforms for biosensing, and cell:surface attachment. The coarse-grained model allows us to probe up to microsecond timescales and model ink diffusion, crucial for the application of the printboard in, for example, medical diagnostics. Recent all-atom MD simulations identified and quantified the molecular strain limiting the stability of nanopatterns created with small dendrimer inks, and explained the different patterns obtained experimentally with different dendrimer inks. In the present work, the all-atom simulations are ``scaled up'' to longer timescales via coarse graining, without incurring significant additional computational expense, and, crucially, without significant loss in atom-scale detail, the coarse-grained MD simulations yielding properties similar to those obtained from the all-atom simulations. The anchoring of the ink molecules to the monolayer is of multivalent nature and the degree of multivalency shows a sharp dependence on temperature, control of temperature thus providing a further operational ``switch'' for directed molecular assembly. The computational protocol developed can, in principle, be extended to model any multivalent assembly, for example, virus-cell complexation.

  12. A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

    PubMed Central

    Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

    2016-01-01

    For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently

  13. Scalable Molecular Dynamics with NAMD

    PubMed Central

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

    2008-01-01

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

  14. Scalable molecular dynamics with NAMD.

    PubMed

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

    2005-12-01

    NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.

  15. Recovering position-dependent diffusion from biased molecular dynamics simulations

    SciTech Connect

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

  16. Recovering position-dependent diffusion from biased molecular dynamics simulations.

    PubMed

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica(®) package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories.

  17. Better, Cheaper, Faster Molecular Dynamics

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  18. Better, Cheaper, Faster Molecular Dynamics

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  19. The Digital Material: Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Bailey, Nicholas P.; Cretegny, Thierry; Dolgert, Andrew J.; Myers, Christopher R.; Schiøtz, Jakob; Sethna, James P.

    2001-03-01

    We announce the release of the molecular dynamics component of the Digital Material. The Digital Material is our multiscale modeling software infrastructure, designed for flexibility, extensibility, and for compatibility between simulations on disparate length scales. We illustrate how we use the high-level scripting language Python to control our low-level numerical kernals, and to interface them with standard visualization and data repository tools. Our use of design-patterns methodology leads us to decompose the MD simulation into a few weakly-coupled classes, such as AtomsMover, NeighborLocator, Potential, Constraint, and BoundaryConditions.

  20. Non-Equilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ciccotti, Giovanni; Kapral, Raymond; Sergi, Alessandro

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

  1. Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

    SciTech Connect

    Chaudhari, Mangesh I.; You, Xinli; Pratt, Lawrence R.; Rempe, Susan B.

    2015-11-24

    Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

  2. Molecular dynamics of interface rupture

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

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

  3. Molecular dynamics of interface rupture

    NASA Astrophysics Data System (ADS)

    Koplik, Joel; Banavar, Jayanth R.

    1993-03-01

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

  4. Molecular dynamics of interface rupture

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

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

  5. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

    PubMed

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  6. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    SciTech Connect

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan; Jain, Abhinandan

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  7. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    PubMed Central

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

    2016-01-01

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  8. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

    2016-01-01

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  9. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

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

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

    PubMed Central

    2013-01-01

    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. PMID:24198735

  11. Folding peptides and proteins with all-atom physics: methods and applications

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2008-03-01

    Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re

  12. Petascale molecular dynamics simulation using the fast multipole method on K computer

    NASA Astrophysics Data System (ADS)

    Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto

    2014-10-01

    In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods.

  13. Nonadiabatic Molecular Dynamics with Trajectories

    NASA Astrophysics Data System (ADS)

    Tavernelli, Ivano

    2012-02-01

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

  14. Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

    DTIC Science & Technology

    2015-01-01

    Maximum 200 Words) The minimum energy configuration for Molecular Dynamics (MD) simulations is found for a carbon nanotube (CNT)/polymer... Carbon Nanotubes (CNTs), Molecular Dynamics Simulations 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT... Carbon Nanotubes ,” Macromolecules, Volume 39, Number 16, pp. 5194-5205, July 2006. 6. “VMD-Visual Molecular Dynamics ,” March 2014, http

  15. Molecular dynamics simulation of benzene

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

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

  16. Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations.

    PubMed

    Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan

    2013-05-09

    Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly.

  17. Uncertainty quantification in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rizzi, Francesco

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

  18. Molecular dynamics of membrane proteins.

    SciTech Connect

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

    2004-10-01

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

  19. GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting

    PubMed Central

    McGreevy, Ryan; Isralewitz, Barry

    2014-01-01

    Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-a-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods. PMID:25340325

  20. GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.

    PubMed

    Stone, John E; McGreevy, Ryan; Isralewitz, Barry; Schulten, Klaus

    2014-01-01

    Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-à-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.

  1. Molecular dynamics study of the M412 intermediate of bacteriorhodopsin.

    PubMed Central

    Xu, D; Sheves, M; Schulten, K

    1995-01-01

    Molecular dynamics simulations have been carried out to study the M412 intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L550 intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M412 intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR568 obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein. The structures of the L550 intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M412 intermediate actually comprises a series of conformations involving 1) a motion of retinal; 2) protein conformational changes; and 3) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group. (1) turns the retinal Schiff base nitrogen from an early orientation toward Asp-85 to a late orientation toward Asp-96; (2) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; (3) adds two water molecules to the three water molecules existing in the cytoplasmic channel at the bR568 stage and forms a proton conduction pathway. The conformational change (2) of the protein involves a 60 degrees bent of the cytoplasmic side of helix F and is induced through a break of a hydrogen bond between Tyr-185 and a water-side group complex in the counterion region. Images FIGURE 3 FIGURE 8 FIGURE 9 FIGURE 10 FIGURE 11 FIGURE 12 FIGURE 14 FIGURE 15 FIGURE 16 PMID:8599681

  2. Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

    NASA Astrophysics Data System (ADS)

    Genheden, Samuel

    2017-09-01

    We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

  3. All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics.

    PubMed

    Gangupomu, Vamshi K; Abrams, Cameron F

    2010-11-17

    The 27-residue membrane-spanning domain (MSD) of the HIV-1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus, in particular a conserved GXXXG motif and a midspan arginine. However, structure-based explanations for the roles of these and other MSD features remain unclear. Using molecular dynamics and metadynamics calculations of an all-atom, explicit solvent, and membrane-anchored model, we study the conformational variability of the HIV-1 gp41 MSD. We find that the MSD peptide assumes a stable tilted α-helical conformation in the membrane. However, when the side chain of the midspan Arg (694) "snorkels" to the outer leaflet of the viral membrane, the MSD assumes a metastable conformation where the highly-conserved N-terminal core (between Lys(681) and Arg(694) and containing the GXXXG motif) unfolds. In contrast, when the Arg(694) side chain snorkels to the inner leaflet, the MSD peptide assumes a metastable conformation consistent with experimental observations where the peptide kinks at Phe(697) to facilitate Arg(694) snorkeling. Both of these models suggest specific ways that gp41 may destabilize viral membrane, priming the virus for fusion with a target cell.

  4. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  5. Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect.

    PubMed

    Landström, Jens; Widmalm, Göran

    2010-01-26

    An atomistic all-atom molecular dynamics simulation of the trisaccharide beta-D-ManpNAc-(1-->4)[alpha-D-Glcp-(1-->3)]-alpha-L-Rhap-OMe with explicit solvent molecules has been carried out. The trisaccharide represents a model for the branching region of the O-chain polysaccharide of a strain from Aeromonas salmonicida. The extensive MD simulations having a 1-micros duration revealed a conformational dynamics process on the nanosecond time scale, that is, a 'time window' not extensively investigated for carbohydrates to date. The results obtained from the MD simulation underscore the predictive power of molecular simulations in studies of biomolecular systems and also explain an unusual nuclear Overhauser effect originating from conformational exchange. 2009 Elsevier Ltd. All rights reserved.

  6. Dynamical Localization in Molecular Systems.

    NASA Astrophysics Data System (ADS)

    Wang, Xidi

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

  7. Methods for molecular dynamics simulations of protein folding/unfolding in solution.

    PubMed

    Beck, David A C; Daggett, Valerie

    2004-09-01

    All atom molecular dynamics simulations have become a standard method for mapping equilibrium protein dynamics and non-equilibrium events like folding and unfolding. Here, we present detailed methods for performing such simulations. Generic protocols for minimization, solvation, simulation, and analysis derived from previous studies are also presented. As a measure of validation, our water model is compared with experiment. An example of current applications of these methods, simulations of the ultrafast folding protein Engrailed Homeodomain are presented including the experimental evidence used to verify their results. Ultrafast folders are an invaluable tool for studying protein behavior as folding and unfolding events measured by experiment occur on timescales accessible with the high-resolution molecular dynamics methods we describe. Finally, to demonstrate the prospect of these methods for folding proteins, a temperature quench simulation of a thermal unfolding intermediate of the Engrailed Homeodomain is described.

  8. Mechanism resulting in chemical imbalance due to cellular damage associated with mechanoporation: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Sliozberg, Yelena R.; Chantawansri, Tanya L.

    2016-05-01

    To elucidate the mechanism of ion transport through a transmembrane pore, all-atom molecular dynamics simulations were employed. A model membrane where a pore connects the intra- and extra-cellular compartment was considered. Pores with radii of 1.5 nm or less exhibited resealing over the course of 135 ns simulations, and ionic disturbance is minimal. Ion transport through a larger pore (2 nm radius) leads to a substantial change in the intra- and extra-cellular ionic concentrations. The influx of Na+ and Cl- ions down their concentration gradients is greater than the efflux of K+ leading to an osmotic influx of water.

  9. Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; van der Maarel, Johan R. C.

    2008-03-01

    All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

  10. Study of thermal scattering for organic tissues through molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ramos, Ricardo; Cantargi, Florencia; Marquez Damian, Jose Ignacio; Gonçalves-Carralves, Manuel Sztejnberg

    2017-09-01

    Boron Neutron Capture Therapy (BNCT) is an experimental therapy for tumors which is based on the nuclear reaction that occurs when 10B is irradiated with thermal neutrons. Calculations for BNCT with Monte Carlo N-Particle (MCNP) take into account the thermal scattering treatment for hydrogen bound in bulk water for any organic tissue. However, in these tissues, hydrogen is also present in macromolecules (protein, lipids, etc.) and in confined water. Thermal scattering cross section for hydrogen in an organic tissue can be determined by calculating the scattering law S(α,β). This function can be obtained with the nuclear data processing system NJOY from the vibrational frequency spectrum of an atom in a molecular system. We performed calculations of the frequency spectrum from molecular dynamics simulations using the program GROMACS. Systems composed of a peptide in a water box were considered, with different proportions of water molecules. All-atom potentials for modeling this molecules were used in order to represent the internal vibrational normal modes for the atoms of hydrogen. The results showed several internal normal modes that in the case of hydrogen bound in bulk water do not appear.

  11. Molecular Dynamics Simulation of Supercritical Spray Phenomena

    DTIC Science & Technology

    2008-09-26

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

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

    PubMed

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

    2015-05-21

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

  13. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    PubMed

    Na, Hyuntae; Jernigan, Robert L; Song, Guang

    2015-10-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  14. Conformational Dynamics of RNA-Peptide Binding: A Molecular Dynamics Simulation Study

    PubMed Central

    Mu, Yuguang; Stock, Gerhard

    2006-01-01

    Molecular dynamics simulations of the binding of the heterochiral tripeptide KkN to the transactivation responsive (TAR) RNA of HIV-1 is presented, using an all-atom force field with explicit water. To obtain starting structures for the TAR-KkN complex, semirigid docking calculations were performed that employ an NMR structure of free TAR RNA. The molecular dynamics simulations show that the starting structures in which KkN binds to the major groove of TAR (as it is the case for the Tat-TAR complex of HIV-1) are unstable. On the other hand, the minor-groove starting structures are found to lead to several binding modes, which are stabilized by a complex interplay of stacking, hydrogen bonding, and electrostatic interactions. Although the ligand does not occupy the binding position of Tat protein, it is shown to hinder the interhelical motion of free TAR RNA. The latter is presumably necessary to achieve the conformational change of TAR RNA to bind Tat protein. Considering the time evolution of the trajectories, the binding process is found to be ligand-induced and cooperative. That is, the conformational rearrangement only occurs in the presence of the ligand and the concerted motion of the ligand and a large part of the RNA binding site is necessary to achieve the final low-energy binding state. PMID:16239331

  15. The liquid structure of tetrachloroethene: Molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials

    NASA Astrophysics Data System (ADS)

    Gereben, Orsolya; Pusztai, László

    2013-10-01

    The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ˜11 Å and a very small third one at ˜16 Å can be found as well, without preference for any axis or plane orientation.

  16. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

  17. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

    PubMed

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-10-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

  18. All-atom ab initio native structure prediction of a mixed fold (1FME): a comparison of structural and folding characteristics of various beta beta alpha miniproteins.

    PubMed

    Kim, Eunae; Jang, Soonmin; Pak, Youngshang

    2009-11-21

    We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold beta beta alpha miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other beta beta alpha miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue beta beta alpha miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1-->Glu1 and Ile7-->Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I(') turn (1FME) was well reproduced with the present simulation.

  19. Time-Dependent Molecular Reaction Dynamics

    NASA Astrophysics Data System (ADS)

    Öhrn, Yngve

    2007-11-01

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

  20. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

    PubMed Central

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoît

    2015-01-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

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

    SciTech Connect

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

    2015-05-21

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

  2. Probing the Huntingtin 1-17 membrane anchor on a phospholipid bilayer by using all-atom simulations.

    PubMed

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S; Bechinger, Burkhard; Mousseau, Normand

    2015-03-10

    Mislocalization and aggregation of the huntingtin protein are related to Huntington's disease. Its first exon-more specifically the first 17 amino acids (Htt17)-is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin's activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties-order parameter, thickness, and area per lipid-of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions.

  3. Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations

    PubMed Central

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S.; Bechinger, Burkhard; Mousseau, Normand

    2015-01-01

    Mislocalization and aggregation of the huntingtin protein are related to Huntington’s disease. Its first exon—more specifically the first 17 amino acids (Htt17)—is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin’s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties—order parameter, thickness, and area per lipid—of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions. PMID:25762330

  4. Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field.

    PubMed

    MacCallum, Justin L; Tieleman, D Peter

    2003-11-30

    We calculated the free energy of solvation of the neutral analogs of 18 amino acid side-chains (not including glycine and proline) using the OPLS all-atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid.

  5. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    PubMed Central

    Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Huang, Jian-Ming; Juwita, Ratna

    2013-01-01

    Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC), lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC) lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications. PMID:23571494

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

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

  7. A comprehensive molecular dynamics approach to protein retention modeling in ion exchange chromatography.

    PubMed

    Lang, Katharina M H; Kittelmann, Jörg; Dürr, Cathrin; Osberghaus, Anna; Hubbuch, Jürgen

    2015-02-13

    In downstream processing, the underlying adsorption mechanism of biomolecules to adsorbent material are still subject of extensive research. One approach to more mechanistic understanding is simulating this adsorption process and hereby the possibility to identify the parameters with strongest impact. So far this method was applied with all-atom molecular dynamics simulations of two model proteins on one cation exchanger. In this work we developed a molecular dynamics tool to simulate protein-adsorber interaction for various proteins on an anion exchanger and ran gradient elution experiments to relate the simulation results to experimental data. We were able to show that simulation results yield similar results as experimental data regarding retention behavior as well as binding orientation. We could identify arginines in case of cation exchangers and aspartic acids in case of anion exchangers as major contributors to binding.

  8. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    PubMed

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. (c) 2004 American Institute of Physics.

  9. Molecular dynamics on hypercube parallel computers

    NASA Astrophysics Data System (ADS)

    Smith, W.

    1991-03-01

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

  10. Systematic Coarse-graining of Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Voth, Gregory

    2015-03-01

    Coarse-grained (CG) models can provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms that are correlated over distance scales of many covalent bond lengths and at long time scales. Systematic variational coarse-graining methods based on information from molecular dynamics simulations of finer-grained (e.g., all-atom) models provide attractive tools for the systematic development of CG models. Examples include the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, and results from the former theory will be presented in this talk. In addition, a new approach will be presented that is appropriate for the ``ultra coarse-grained'' (UCG) regime, e.g., at a coarse-grained resolution that is much coarser than one amino acid residue per CG particle in a protein. At this level of coarse-graining, one is faced with the possible existence of multiple metastable states ``within'' the CG sites for a given UCG model configuration. I will therefore describe newer systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain aspects of this work connect back to single-state force matching and open up new avenues for method development. This general body of theory and algorithm provides a formal statistical mechanical basis for the coarse-graining of fine-grained molecular dynamics simulation data at various levels of CG resolution. Representative applications will be described as time allows.

  11. 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.

  12. Molecular ions, Rydberg spectroscopy and dynamics

    SciTech Connect

    Jungen, Ch.

    2015-01-22

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

  13. Molecular Dynamics Simulations of Simple Liquids

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  14. 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.

  15. 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.

  16. Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

    Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C; Roux, Benoît

    2013-10-01

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

  18. Molecular dynamics simulations of nanostructures

    NASA Astrophysics Data System (ADS)

    Yuan, Zaoshi

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

  19. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

  20. An Evolutionary Strategy for All-Atom Folding of the 60-Amino-Acid Bacterial Ribosomal Protein L20

    PubMed Central

    Schug, A.; Wenzel, W.

    2006-01-01

    We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of “native content” in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence. PMID:16565067

  1. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.

    PubMed

    Orzechowski, Marek; Tama, Florence

    2008-12-15

    A methodology for flexible fitting of all-atom high-resolution structures into low-resolution cryoelectron microscopy (cryo-EM) maps is presented. Flexibility of the modeled structure is simulated by classical molecular dynamics and an additional effective potential is introduced to enhance the fitting process. The additional potential is proportional to the correlation coefficient between the experimental cryo-EM map and a synthetic map generated for an all-atom structure being fitted to the map. The additional forces are calculated as a gradient of the correlation coefficient. During the molecular dynamics simulations under the additional forces, the molecule undergoes a conformational transition that maximizes the correlation coefficient, which results in a high-accuracy fit of all-atom structure into a cryo-EM map. Using five test proteins that exhibit structural rearrangement during their biological activity, we demonstrate performance of our method. We also test our method on the experimental cryo-EM of elongation factor G and show that the model obtained is comparable to previous studies. In addition, we show that overfitting can be avoided by assessing the quality of the fitted model in terms of correlation coefficient and secondary structure preservation.

  2. Self-assembly of Spherical Macroions in Solution: A Coarse-grained Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Liu, Zhuonan; Liu, Tianbo; Tsige, Mesfin

    2015-03-01

    Macroions (such as polyoxometalates) in solution can form a stable hollow spherical super-molecular structure called blackberry when they have moderate surface charge density and size (1-10 nm). Depending on the surface charge density of macroions, the size of the blackberry can be from 20 to more than 100 nm. Other macroions such as dendrimers can also self-assemble into similar super-molecular structure in solution. Existing theories such as Debye-Hückel and DLVO theories cannot explain this phenomenon and we are not aware of any other theory that can explain this. Previous studies using all-atom Molecular Dynamics simulations have shown identical macroions forming oligomers mediated by counterions. Due to the limitations in all-atom simulation and available computational capabilities, these studies handled only small systems with simple macroions, leading to less conclusive but still relevant results on the self-assembly behavior. To overcome these limitations, in this work large-scale coarse-grained modeling of macroions in solution is used. In order to understand the origin of the attractive force that is responsible for the self-assembly of macroions, different types of macroions in different solution conditions are studied. This work was supported by NSF Grant DMR0847580.

  3. Modeling hybrid perovskites by molecular dynamics.

    PubMed

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

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

  4. Modeling hybrid perovskites by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

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

  5. Molecular dynamics simulations: advances and applications

    PubMed Central

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

    2015-01-01

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

  6. Targeting HIV-1 Envelope Proteins Using a Fragment Discovery All-Atom Computational Algorithm.

    PubMed

    Peters, Michael H

    2017-04-01

    HIV viral envelope proteins are targets for small inhibitor molecules aimed at disrupting the cellular entry process. Potential peptide-class inhibitor molecules (rDNA drugs) have been previously identified, with mixed results, through biomimicry and phage display experimental methods. Here we describe a new approach based on computational fragment discovery. The method has the potential to not only optimize peptide binding affinity but also to rapidly produce alternative inhibitors against mutated strains. A comprehensive, all-atom implicit solvent method is used to bombard the C-heptad repeat unit of HIV-1 target envelope protein GP41 with single D-amino acid residues as they exist in their native state. A nascent peptide computational search process then identifies potential favorable sequences of attached ligands based on four peptide bond criteria. Finally, dynamic simulations of nascent peptides attached to host targets help refine potential peptide inhibitors for experimental HIV-1 challenge assays and testing. Initial testing of the method was done using 64,000 total ligands of D-amino acid residues at a total computational time of 0.05 microseconds per ligand, which resulted in several thousand attached ligands. Peptide bond criteria search employing three of the four bond constraints with a tolerance of 20 percent, resulted in four potential peptide inhibitors of 5 to 6 residues in length. Only one of the four peptides demonstrated IC50 values and partial viral inhibition based on cell challenge assays using CEM-SS host cells. That peptide inhibitor also computationally demonstrated long-time attachment and stability to a helical groove in its C-heptad target. This initial testing of peptide fragment discovery against HIV-1 has helped us refine the protocols and identify key areas of improvement. Our methods demonstrate the potential to design efficient peptide inhibitors to viral target proteins based on an all-atom dynamic simulation and using a ligand

  7. Molecular Dynamics Studies of Matrix Metalloproteases.

    PubMed

    Díaz, Natalia; Suárez, Dimas

    2017-01-01

    Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.

  8. Dynamic molecular crystals with switchable physical properties.

    PubMed

    Sato, Osamu

    2016-06-21

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

  9. New ways to boost molecular dynamics simulations.

    PubMed

    Krieger, Elmar; Vriend, Gert

    2015-05-15

    We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  10. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  11. A real-time all-atom structural search engine for proteins.

    PubMed

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

    2014-07-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

  12. 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.

  13. Dynamics of excited molecular states

    NASA Astrophysics Data System (ADS)

    Meyer, Hans-Dieter

    2005-01-01

    The photo-excitation or photo-ionization of a polyatomic molecule is typically accompanied by a strong excitation of the vibrational modes. In particular when a conical intersection of the electronic potential energy surfaces involved lies within or close to the Frank-Condon zone, the nuclear motion becomes very complicated, often chaotic, and the spectra become irregular and dense. An accurate simulation of the dynamics of such excited molecules requires firstly that the multi-dimensional and multi-state potential energy surface - or a reliable model thereof - can be determined. Secondly, the multi-dimensional quantum dynamics have to be solved. This is a very difficult task, because of the high dimensionality of the problem (6 to 30 degrees of freedom, say). The multi-configuration time-dependent Hartree (MCTDH) method has proven to be very useful for the study of such problems. In fact, an accurate treatment of the quantal dynamics of molecules like the allene cation (C3 H+4, 15D), the butatriene cation (C4 H+4, 18D), or the pyrazine molecule (C4N2H4, 24D) in their full dimensionality, is - up to date - only possible with MCTDH. (The acronym n D denotes the dimensionality.) The construction of the vibronic model Hamiltonian and the MCTDH method will be briefly discussed. After this, the excited state dynamics of the butatriene and pyrazine molecules will be discussed.

  14. Molecular dynamics simulations of substitutional diffusion

    DOE PAGES

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

    2016-12-18

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

  15. Molecular dynamics simulations of substitutional diffusion

    SciTech Connect

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

    2016-12-18

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

  16. Discrete Molecular Dynamics Simulation of Biomolecules

    NASA Astrophysics Data System (ADS)

    Ding, Feng

    2011-10-01

    Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.

  17. Liouville-von Neumann molecular dynamics.

    PubMed

    Jakowski, Jacek; Morokuma, Keiji

    2009-06-14

    We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C(2) and retinal system.

  18. Liouville-von Neumann molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jakowski, Jacek; Morokuma, Keiji

    2009-06-01

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

  19. Wavelet Analysis for Molecular Dynamics

    DTIC Science & Technology

    2015-06-01

    factor of 1,000. Ultra-high-molecular-weight polyethylene offers a classic example of the scale challenge: despite its simple chemical makeup , CnH2n+2...below, but also disconnected graphs from individual molecules . 6 Linear homopolymers can be ordered to have block tridiagonal structure where each...solutions for this simple system; r̃(0)1 = √ 2rOH , r̃ (0) 2 = 0, which leads to a symmetric linear molecule , and r̃(0)1 = 0, r̃ (0) 2 = rOH √ 4+2mO

  20. 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

  1. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.

    PubMed

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

    2017-02-21

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

  2. Dynamic signature of molecular association in methanol.

    PubMed

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

    2016-07-07

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

  3. Molecular scale dynamics of large ring polymers.

    PubMed

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

    2014-10-17

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

  4. Molecular Scale Dynamics of Large Ring Polymers

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  5. Molecular dynamic simulations of ocular tablet dissolution.

    PubMed

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

    2013-11-25

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

  6. Understanding Modularity in Molecular Networks Requires Dynamics

    PubMed Central

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

    2014-01-01

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

  7. Mechanisms of the self-assembly of EAK16-family peptides into fibrillar and globular structures: molecular dynamics simulations from nano- to micro-seconds.

    PubMed

    Emamyari, Soheila; Kargar, Faezeh; Sheikh-Hasani, Vahid; Emadi, Saeed; Fazli, Hossein

    2015-05-01

    The self-assembly of EAK16-family peptides in a bulk solution was studied using a combination of all-atom and coarse-grained molecular dynamics simulations. In addition, specified concentrations of EAK16 peptides were induced to form fibrillary or globular assemblies in vitro. The results show that the combination of all-atom molecular dynamics simulations on the single- and double-chain levels and coarse-grained simulations on the many-chain level predicts the experimental observations reasonably well. At neutral pH conditions, EAK16-I and EAK16-II assemble into fibrillary structures, whereas EAK16-IV aggregates into globular assemblies. Mechanisms of the formation of fibrillar and globular assemblies are described using the simulation results.

  8. Numerical methods for molecular dynamics

    SciTech Connect

    Skeel, R.D.

    1991-01-01

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

  9. Semiclassical guided optimal control of molecular dynamics

    SciTech Connect

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

    2005-10-15

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

  10. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

    PubMed Central

    2012-01-01

    In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We combine aMD with the inherent power of graphics processor units (GPUs) and apply the implementation to the bovine pancreatic trypsin inhibitor (BPTI). A 500 ns aMD simulation is compared to a previous millisecond unbiased brute force MD simulation carried out on BPTI, showing that the same conformational space is sampled by both approaches. To our knowledge, this represents the first implementation of aMD on GPUs and also the longest aMD simulation of a biomolecule run to date. Our implementation is available to the community in the latest release of the Amber software suite (v12), providing routine access to millisecond events sampled from dynamics simulations using off the shelf hardware. PMID:22984356

  11. Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates.

    PubMed

    Ghoufi, A; Morineau, D; Lefort, R; Malfreyt, P

    2010-10-12

    Many interesting physical phenomena occur on length and time scales that are not accessible by atomistic molecular simulations. By introducing a coarse graining of the degrees of freedom, coarse-grained (CG) models allow ther study of larger scale systems for longer times. Coarse-grained force fields have been mostly derived for large molecules, including polymeric materials and proteins. By contrast, there exist no satisfactory CG potentials for mesostructured porous solid materials in the literature. This issue has become critical among a growing number of studies on confinement effects on fluid properties, which require both long time and large scale simulations and the conservation of a sufficient level of atomistic description to account for interfacial phenomena. In this paper, we present a general multiscale procedure to derive a hybrid coarse grained/all atoms force field CG/AA model for mesoporous systems. The method is applied to mesostructured MCM-41 molecular sieves, while the parameters of the mesoscopic interaction potentials are obtained and validated from the computation of the adsorption isotherm of methanol by grand canonical molecular dynamic simulation.

  12. Molecular dynamics simulations of highly cross-linked polymer networks: prediction of thermal and mechanical properties

    NASA Astrophysics Data System (ADS)

    Shenogina, Natalia; Tsige, Mesfin; Mukhopadhyay, Sharmila; Patnaik, Soumya

    2012-02-01

    We use all-atom molecular dynamics (MD) simulations to predict the mechanical and thermal properties of thermosetting polymers. Atomistic simulation is a promising tool which can provide detailed structure-property relationships of densely cross-linked polymer networks. In this work we study the thermo-mechanical properties of thermosetting polymers based on amine curing agents and epoxy resins and have focused on the DGEBA/DETDA epoxy system. At first we describe the modeling approach to construction of realistic all-atom models of densely cross-linked polymer matrices. Subsequently, a series of atomistic simulations was carried out to examine the simulation cell size effect as well as the role of cross-linking density and chain length of the resin strands on thermo-mechanical properties at different temperatures. Two different methods were used to deform the polymer networks. Both static and dynamic approaches to calculating the mechanical properties were considered and the thermo-mechanical properties obtained from our simulations were found in reasonable agreement with experimental values.

  13. Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

    PubMed Central

    Yu, Hang; Schulten, Klaus

    2013-01-01

    Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy. PMID:23382665

  14. 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

  15. Composition Dependence of Dynamic Heterogeneity Time- and Length Scales in [Omim][BF4]/Water Binary Mixtures: Molecular Dynamics Simulation Study.

    PubMed

    Pal, Tamisra; Biswas, Ranjit

    2015-12-24

    Composition dependence of four-point dynamic susceptibilities, overlap functions, and other dynamic heterogeneity (DH) parameters have been investigated by using all-atom molecular dynamics simulations for aqueous solutions of the ionic liquid (IL), 1-octyl-3-methyl imidazolium tetrafluoroborate ([Omim][BF4]) covering the pure-to-pure range. Upon addition of water in the IL, the DH time scales become faster and the four-point dynamic susceptibility time scale softens. Evidences for jump motions for both water and ions have been found from the simulated single particle displacements that show strong deviation from Gaussian distribution. Estimated dynamic correlation length for water reflects effects of IL, whereas those for ions remain largely insensitive to the mixture composition. Simulated structural aspects and DH time scales provide microscopic explanations to the existing experimental observations from time-resolved fluorescence and Kerr spectroscopic measurements.

  16. Molecular Dynamics Simulations of Liquid-Crystalline Dendritic Architectures

    NASA Astrophysics Data System (ADS)

    Bourgogne, C.; Bury, I.; Gehringer, L.; Zelcer, A.; Cukiernik, F.; Terazzi, E.; Donnio, B.; Guillon, D.

    We report here a few examples of the self-organization behaviour of some novel materials based on liquid-crystalline dendritic architectures. The original design of the molecules imposes the use of all-atomic methods to model correctly every intra- and intermolecular effects. The selected materials are octopus dendrimers with block anisotropic side-arms, segmented amphiphilic block codendrimers, multicore and star-shaped oligomers, and multi-functionalized manganese clusters. The molecular organization in lamellar or columnar phases occurs due to soft/rigid parts self-recognition, hydrogen-bonding networks or from the molecular shape intrinsically.

  17. Tricationic Ionic Liquids: Structural and Dynamical Properties via Molecular Dynamics Simulations.

    PubMed

    Sedghamiz, Elaheh; Moosavi, Majid

    2017-03-02

    Three imidazolium-based linear tricationic ionic liquids (LTILs) have been simulated to study their structural and dynamical properties and obtain a fundamental understanding of the molecular basis of the microscopic and macroscopic properties of their bulk liquid phase. The effects of temperature and alkyl chain length on the physiochemical, transport, and structural properties of these LTILs have been investigated. A nonpolarizable all-atom force field, which is a refined version of the Canongia Lopes and Paudua force field, was adopted for the simulations. Densities, mean square displacements, self-diffusivities, viscosities, electrical conductivities, and transference numbers have been presented for various ions from MD simulations. The detailed microscopic structures have been discussed in terms of radial distribution functions and spatial distribution functions. The results show that, similar to that in monocationic and dicationic ILs (MILs and DILs, respectively), the anions are mainly organized around the imidazolium rings. The diffusion coefficients of the studied LTILs are smaller than those of both MILs and DILs, with comparable viscosities. Unlike those of MILs and DILs, the diffusion coefficients of the cations and anions of the studied LTILs increase with an increase in the length of the alkyl chain between the rings for LTIL-1 and LTIL-2 but then decrease for LTIL-3, which is in a good agreement with the trend of viscosity data. The calculated transference numbers show that, similar to that in MILs and DILs, cations have a major role in carrying electric current in LTILs, but this role increases from MILs to LTILs.

  18. Water network dynamics at the critical moment of a peptide's beta-turn formation: a molecular dynamics study.

    PubMed

    Karvounis, George; Nerukh, Dmitry; Glen, Robert C

    2004-09-08

    All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of beta-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.

  19. Reaction dynamics in polyatomic molecular systems

    SciTech Connect

    Miller, W.H.

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  20. Adaptively restrained molecular dynamics in LAMMPS

    NASA Astrophysics Data System (ADS)

    Kant Singh, Krishna; Redon, Stephane

    2017-07-01

    Adaptively restrained molecular dynamics (ARMD) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual simplicity of the approach, however, integrating it in existing molecular dynamics packages is non-trivial, in particular since implemented potentials should a priori be rewritten to take advantage of frozen particles and achieve a speed-up. In this paper, we present novel algorithms for integrating ARMD in LAMMPS, a popular multi-purpose molecular simulation package. In particular, we demonstrate how to enable ARMD in LAMMPS without having to re-implement all available force fields. The proposed algorithms are assessed on four different benchmarks, and show how they allow us to speed up simulations up to one order of magnitude.

  1. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    PubMed

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  2. MolProbity: all-atom structure validation for macromolecular crystallography.

    PubMed

    Chen, Vincent B; Arendall, W Bryan; Headd, Jeffrey J; Keedy, Daniel A; Immormino, Robert M; Kapral, Gary J; Murray, Laura W; Richardson, Jane S; Richardson, David C

    2010-01-01

    MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

  3. Free-energy function based on an all-atom model for proteins.

    PubMed

    Yoshidome, Takashi; Oda, Koji; Harano, Yuichi; Roth, Roland; Sugita, Yuji; Ikeguchi, Mitsunori; Kinoshita, Masahiro

    2009-12-01

    We have developed a free-energy function based on an all-atom model for proteins. It comprises two components, the hydration entropy (HE) and the total dehydration penalty (TDP). Upon a transition to a more compact structure, the number of accessible configurations arising from the translational displacement of water molecules in the system increases, leading to a water-entropy gain. To fully account for this effect, the HE is calculated using a statistical-mechanical theory applied to a molecular model for water. The TDP corresponds to the sum of the hydration energy and the protein intramolecular energy when a fully extended structure, which possesses the maximum number of hydrogen bonds with water molecules and no intramolecular hydrogen bonds, is chosen as the standard one. When a donor and an acceptor (e.g., N and O, respectively) are buried in the interior after the break of hydrogen bonds with water molecules, if they form an intramolecular hydrogen bond, no penalty is imposed. When a donor or an acceptor is buried with no intramolecular hydrogen bond formed, an energetic penalty is imposed. We examine all the donors and acceptors for backbone-backbone, backbone-side chain, and side chain-side chain intramolecular hydrogen bonds and calculate the TDP. Our free-energy function has been tested for three different decoy sets. It is better than any other physics-based or knowledge-based potential function in terms of the accuracy in discriminating the native fold from misfolded decoys and the achievement of high Z-scores.

  4. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    SciTech Connect

    Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  5. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    NASA Astrophysics Data System (ADS)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan

    2015-04-01

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  6. MolProbity: all-atom structure validation for macromolecular crystallography

    SciTech Connect

    Chen, Vincent B.; Arendall, W. Bryan III; Headd, Jeffrey J.; Keedy, Daniel A.; Immormino, Robert M.; Kapral, Gary J.; Murray, Laura W.; Richardson, Jane S.; Richardson, David C.

    2010-01-01

    MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

  7. Towards the prediction of order parameters from molecular dynamics simulations in proteins

    PubMed Central

    Perilla, Juan R.; Woolf, Thomas B.

    2012-01-01

    A molecular understanding of how protein function is related to protein structure requires an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies, and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter – a reduced descriptor for the major subset of degrees of freedom – that can be used to aid sampling for the large conformational change. We present a method to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that may be used to enhance sampling of intermediate states. PMID:22559464

  8. 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

  9. 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.

  10. Excited State Quantum-Classical Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Krstic, Predrag

    2005-05-01

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

  11. Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model.

    PubMed

    Mitomo, Daisuke; Nakamura, Hironori K; Ikeda, Kazuyoshi; Yamagishi, Akihiko; Higo, Junichi

    2006-09-01

    The src SH3 domain has been known to be a two-state folder near room temperature. However, in a previous study with an all-atom model simulation near room temperature, the transition state of this protein was not successfully detected on a free-energy profile using two axes: the radius of gyration (R(g)) and native contact reproduction ratio (Q value). In this study, we focused on an atom packing effect to characterize the transition state and tried another analysis to detect it. To explore the atom packing effect more efficiently, we introduced a charge-neutralized all-atom model, where all of the atoms in the protein and water molecules were treated explicitly, but their partial atomic charges were set to zero. Ten molecular dynamics simulations were performed starting from the native structure at 300 K, where the simulation length of each run was 90 ns, and the protein unfolded in all runs. The integrated trajectories (10 x 90 = 900 ns) were analyzed by a principal component analysis (PCA) and showed a clear free-energy barrier between folded- and unfolded-state conformational clusters in a conformational space generated by PCA. There were segments that largely deformed when the conformation passed through the free-energy barrier. These segments correlated well with the structural core regions characterized by large phi-values, and the atom-packing changes correlated with the conformational deformations. Interestingly, using the same simulation data, no significant barrier was found in a free-energy profile using the R(g) and Q values for the coordinate axes. These results suggest that the atom packing effect may be one of the most important determinants of the transition state.

  12. The MOLDY short-range molecular dynamics package

    NASA Astrophysics Data System (ADS)

    Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

    2011-12-01

    measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

  13. Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.

    PubMed

    McCullagh, Peter; Lake, Peter T; McCullagh, Martin

    2016-09-13

    An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.

  14. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

    PubMed

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

    2012-12-11

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

  15. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

    PubMed Central

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

    2012-01-01

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

  16. Dynamic assembly of molecularly imprinted polymer nanoparticles.

    PubMed

    Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei

    2017-09-11

    Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Dynamic strength of molecular adhesion bonds.

    PubMed

    Evans, E; Ritchie, K

    1997-04-01

    In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale

  18. Exciton dynamics in perturbed vibronic molecular aggregates

    PubMed Central

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

    2015-01-01

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

  19. Choice of timestep in molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Fincham, David

    1986-06-01

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

  20. Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

    PubMed

    Sieradzan, Adam K; Jakubowski, Rafał

    2017-03-30

    In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc.

  1. Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics.

    PubMed

    Wells, David B; Abramkina, Volha; Aksimentiev, Aleksei

    2007-09-28

    The transport of biomolecules across cell boundaries is central to cellular function. While structures of many membrane channels are known, the permeation mechanism is known only for a select few. Molecular dynamics (MD) is a computational method that can provide an accurate description of permeation events at the atomic level, which is required for understanding the transport mechanism. However, due to the relatively short time scales accessible to this method, it is of limited utility. Here, we present a method for all-atom simulation of electric field-driven transport of large solutes through membrane channels, which in tens of nanoseconds can provide a realistic account of a permeation event that would require a millisecond simulation using conventional MD. In this method, the average distribution of the electrostatic potential in a membrane channel under a transmembrane bias of interest is determined first from an all-atom MD simulation. This electrostatic potential, defined on a grid, is subsequently applied to a charged solute to steer its permeation through the membrane channel. We apply this method to investigate permeation of DNA strands, DNA hairpins, and alpha-helical peptides through alpha-hemolysin. To test the accuracy of the method, we computed the relative permeation rates of DNA strands having different sequences and global orientations. The results of the G-SMD simulations were found to be in good agreement in experiment.

  2. Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling.

    PubMed

    Pang, Yuan-Ping

    2014-09-26

    CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277K and 1atm with the first folding event occurring as early as 66.1ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers-an important step forward in quantitative biology. Copyright © 2014 The Author. Published by Elsevier Inc. All rights reserved.

  3. Mechanical properties of a complete microtubule revealed through molecular dynamics simulation.

    PubMed

    Wells, David B; Aksimentiev, Aleksei

    2010-07-21

    Microtubules (MTs) are the largest type of cellular filament, essential in processes ranging from mitosis and meiosis to flagellar motility. Many of the processes depend critically on the mechanical properties of the MT, but the elastic moduli, notably the Young's modulus, are not directly revealed in experiment, which instead measures either flexural rigidity or response to radial deformation. Molecular dynamics (MD) is a method that allows the mechanical properties of single biomolecules to be investigated through computation. Typically, MD requires an atomic resolution structure of the molecule, which is unavailable for many systems, including MTs. By combining structural information from cryo-electron microscopy and electron crystallography, we have constructed an all-atom model of a complete MT and used MD to determine its mechanical properties. The simulations revealed nonlinear axial stress-strain behavior featuring a pronounced softening under extension, a possible plastic deformation transition under radial compression, and a distinct asymmetry in response to the two senses of twist. This work demonstrates the possibility of combining different levels of structural information to produce all-atom models suitable for quantitative MD simulations, which extends the range of systems amenable to the MD method and should enable exciting advances in our microscopic knowledge of biology. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges.

    PubMed Central

    Sheldahl, C; Harvey, S C

    1999-01-01

    The results of an all-atom molecular dynamics simulation on a discoidal complex made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and a synthetic alpha-helical 18-mer peptide with an apolipoprotein-like charge distribution are presented. The system consists of 12 acetyl-18A-amide (Ac-18A-NH2) (. J. Biol. Chem. 260:10248-10255) molecules and 20 molecules of POPC in a bilayer, 10 in each leaflet, solvated in a sphere of water for a total of 28,522 atoms. The peptide molecules are oriented with their long axes normal to the bilayer (the "picket fence" orientation). This system is analogous to complexes formed in nascent high-density lipoprotein and to Ac-18A-NH2/phospholipid complexes observed experimentally. The simulation extended over 700 ps, with the last 493 ps used for analysis. The symmetry of this system allows for averaging over different helices to improve sampling, while maintaining explicit all-atom representation of all peptides. The complex is stable on the simulated time scale. Several possible salt bridges between and within helices were studied. A few salt bridge formations and disruptions were observed. Salt bridges provide specificity in interhelical interactions. PMID:10049304

  5. Molecular dynamics at constant Cauchy stress.

    PubMed

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

    2016-05-14

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

  6. Molecular dynamics studies of polyurethane nanocomposite hydrogels

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  7. Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

    PubMed

    Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

    2012-04-10

    To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

  8. Molecular dynamics modelling of solidification in metals

    SciTech Connect

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

    1997-12-31

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

  9. Vacuum Ultraviolet Studies of Molecular Dynamics

    DTIC Science & Technology

    1992-01-15

    the Journal of Chemical Physics . Vacuum Ultraviolet Studies of Molecular Dynamics Page 4 B. Quenching of S(’D) by N2...An article on this work has been published in the Journal of Chemical Physics . E. The 157 am Photodissoclation of OCS The photodissociation of OCS...angular momentum vectors are perpendicular to one another. A report of this work has been published in the Journal of Chemical Physics . Vacuum

  10. New faster CHARMM molecular dynamics engine

    PubMed Central

    Hynninen, Antti-Pekka; Crowley, Michael F

    2014-01-01

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

  11. Molecular crowding and protein enzymatic dynamics.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2012-05-21

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

  12. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

    NASA Astrophysics Data System (ADS)

    Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V.; Carloni, Paolo

    2006-04-01

    Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases.

  13. Reduced Cβ statistical potentials can outperform all-atom potentials in decoy identification

    PubMed Central

    Fitzgerald, James E.; Jha, Abhishek K.; Colubri, Andres; Sosnick, Tobin R.; Freed, Karl F.

    2007-01-01

    We developed a series of statistical potentials to recognize the native protein from decoys, particularly when using only a reduced representation in which each side chain is treated as a single Cβ atom. Beginning with a highly successful all-atom statistical potential, the Discrete Optimized Protein Energy function (DOPE), we considered the implications of including additional information in the all-atom statistical potential and subsequently reducing to the Cβ representation. One of the potentials includes interaction energies conditional on backbone geometries. A second potential separates sequence local from sequence nonlocal interactions and introduces a novel reference state for the sequence local interactions. The resultant potentials perform better than the original DOPE statistical potential in decoy identification. Moreover, even upon passing to a reduced Cβ representation, these statistical potentials outscore the original (all-atom) DOPE potential in identifying native states for sets of decoys. Interestingly, the backbone-dependent statistical potential is shown to retain nearly all of the information content of the all-atom representation in the Cβ representation. In addition, these new statistical potentials are combined with existing potentials to model hydrogen bonding, torsion energies, and solvation energies to produce even better performing potentials. The ability of the Cβ statistical potentials to accurately represent protein interactions bodes well for computational efficiency in protein folding calculations using reduced backbone representations, while the extensions to DOPE illustrate general principles for improving knowledge-based potentials. PMID:17893359

  14. Bead-Fourier path integral molecular dynamics.

    PubMed

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

    2003-06-01

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

  15. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

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

    2015-01-01

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

  16. Bead-Fourier path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2003-06-01

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

  17. Learning generative models of molecular dynamics

    PubMed Central

    2012-01-01

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

  18. Learning generative models of molecular dynamics.

    PubMed

    Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J

    2012-01-01

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

  19. Control-volume representation of molecular dynamics.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2012-05-01

    A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.

  20. Molecular dynamics studies of heterogeneous dynamics and dynamic crossover in supercooled atomic liquids

    PubMed Central

    Andersen, Hans C.

    2005-01-01

    Supercooled liquids near the glass transition exhibit the phenomenon of heterogeneous relaxation; at any specific time, a nominally homogeneous equilibrium fluid undergoes dynamic fluctuations in its structure on a molecular distance scale with rates that are very different in different regions of the sample. Several theoretical and simulation studies have suggested a change in the nature of the dynamics of fluids as they are supercooled, leading to the concept of a dynamic crossover that is often associated with mode coupling theory. Here, we will review the use of molecular dynamics computer simulation methods to investigate heterogeneous dynamics and dynamic crossovers in models of atomic liquids. PMID:15870201

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

    PubMed

    Nebgen, Ben; Prezhdo, Oleg V

    2016-09-15

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

  2. Selective Refinement and Molecular Dynamics Ranking Selection of Near-native Protein Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jiong; Zhang, Jingfen; Xu, Dong; Shang, Yi; Kosztin, Ioan

    2014-03-01

    In recent years in silico protein structure prediction reached a level where a variety of servers can generate large pools of near-native structures. However, the identification and further refinement of the best structures from the pool of decoys remain problematic. To address these issues, we have developed a selective refinement protocol (SRP), and a molecular dynamics (MD) simulation based ranking method (MDR). In SRP the refinement of structures is accomplished by using the relax mode of the Rosetta software package, subject to specific constraints determined by the type and complexity of the target. The final best models are selected with MDR by testing their relative stability against gradual heating during all atom MD simulations. We have implemented the selective refinement protocol and the MDR method in Mufold-MD, our fully automated protein structure prediction server. Mufold-MD was one of the top servers in the CASP10 competition.

  3. Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

    The contacts between the N-terminal domain of heat shock protein 90 (N-Hsp90) and ADP involve both direct and water-mediated hydrogen bonds in X-ray crystallographic structure. We perform all-atom molecular dynamics (MD) simulations of N-Hsp90 and ADP to investigate the changes of the hydrogen bond lengths during ADP dissociation. We show the difference between the hydrogen bonds in the crystal structure and MD simulations. Moreover, the N6 group of ADP does not contact with the Cγ group of Asp93, and the hydrogen bonds between Asn51 side chain and ADP are stable in the early step of ADP dissociation.

  4. Investigating the specificity of peptide adsorption on gold using molecular dynamics simulations.

    PubMed

    Verde, Ana Vila; Acres, Jacqueline M; Maranas, Janna K

    2009-08-10

    We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold surfaces modeled with dispersive interactions. We examine the dependence of adsorption on both identity of the amino acids and mobility of the peptides. Within the limitations of the approach, results indicate that when the peptides are solvated, adsorption requires both configurational changes and local flexibility of individual amino acids. This is achieved when peptides consist mostly of random coils or when their secondary structural motifs (helices, sheets) are short and connected by flexible hinges. In the absence of solvent, only affinity for the surface is required: mobility is not important. In combination, these results suggest the barrier to adsorption presented by displacement of water molecules requires conformational sampling enabled through mobility.

  5. Design and characterization of symmetric nucleic acids via molecular dynamics simulations.

    PubMed

    Pant, Pradeep; Afshan Shaikh, Saher; Jayaram, B

    2017-04-01

    Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.

  6. SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Le Grand, Scott; Götz, Andreas W.; Walker, Ross C.

    2013-02-01

    A new precision model is proposed for the acceleration of all-atom classical molecular dynamics (MD) simulations on graphics processing units (GPUs). This precision model replaces double precision arithmetic with fixed point integer arithmetic for the accumulation of force components as compared to a previously introduced model that uses mixed single/double precision arithmetic. This significantly boosts performance on modern GPU hardware without sacrificing numerical accuracy. We present an implementation for NVIDIA GPUs of both generalized Born implicit solvent simulations as well as explicit solvent simulations using the particle mesh Ewald (PME) algorithm for long-range electrostatics using this precision model. Tests demonstrate both the performance of this implementation as well as its numerical stability for constant energy and constant temperature biomolecular MD as compared to a double precision CPU implementation and double and mixed single/double precision GPU implementations.

  7. Molecular Dynamics Studies of Caspase-3

    PubMed Central

    Sulpizi, M.; Rothlisberger, U.; Carloni, P.

    2003-01-01

    Caspase-3 is a fundamental target for pharmaceutical interventions against a variety of diseases involving disregulated apoptosis. The enzyme is active as a dimer with two symmetry-related active sites, each featuring a Cys-His catalytic dyad and a selectivity loop, which recognizes the characteristic DEVD pattern of the substrate. Here, a molecular dynamics study of the enzyme in complex with two pentapeptide substrates DEVDG is presented, which provides a characterization of the dynamic properties of the active form in aqueous solution. The mobility of the substrate and that of the catalytic residues are rather low indicating a distinct preorganization effect of the Michaelis complex. An essential mode analysis permits us to identify coupled motions between the two monomers. In particular, it is found that the motions of the two active site loops are correlated and tend to steer the substrate toward the reactive center, suggesting that dimerization has a distinct effect on the dynamic properties of the active site regions. The selectivity loop of one monomer turns out to be correlated with the N-terminal region of the p12 subunit of the other monomer, an interaction that is also found to play a fundamental role in the electrostatic stabilization of the quaternary structure. To further characterize the specific influence of dimerization on the enzyme essential motions, a molecular dynamics analysis is also performed on the isolated monomer. PMID:12668429

  8. Folding and association of a homotetrameric protein complex in an all-atom Go model.

    PubMed

    Berhanu, W M; Jiang, P; Hansmann, U H E

    2013-01-01

    The 84-residue homotetrameric BBAT1 is one of the smallest stable protein complexes and therefore is a good test system to study the self-assembly of multimeric proteins. We have researched for this protein the interplay between the folding of monomers and their assembly into tetramers. Replica exchange molecular dynamics simulations relying on a Go model are compared with earlier simulations that use the physics-based coarse-grained UNRES model.

  9. Molecular dynamics simulations of magnetized dusty plasmas

    NASA Astrophysics Data System (ADS)

    Piel, Alexander; Reichstein, Torben; Wilms, Jochen

    2012-10-01

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

  10. Application of optimal prediction to molecular dynamics

    SciTech Connect

    Barber, IV, John Letherman

    2004-12-01

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

  11. Spectroscopy and molecular dynamics in nonpolar fluids

    NASA Astrophysics Data System (ADS)

    Everitt, Karl Frederick

    This thesis considers the mechanisms by which molecular dynamics in nonpolar liquids influences solvation dynamics and vibrational energy relaxation. We use semiclassical molecular dynamics simulations to calculate photon echo signals for two simple fluids. We demonstrate that two new observables are directly related to the relevant molecular quantity, the frequency- frequency time correlation function (TCF), in contrast to the commonly measured 3PEPS, which cannot be simply related to this TCF at short times. We also present a semianalytic photon echo theory, based on an ansatz which determines the full time dependence from the short time expansion coefficients of the TCF. We demonstrate that this theory accurately predicts most photon echo observables, even when the theory's gaussian approximation is not accurate. We also consider vibrational energy relaxation (VER) in liquid oxygen. Using semiclassical molecular dynamics simulations and an intermolecular potential from the literature, we evaluate the required quantity (the spectral density of a certain force-force TCF) using the same ansatz described above. We demonstrate numerically that this procedure is accurate. Approximately relating this semiclassical rate to the fully quantum mechanical VER rate, using one of the more accurate ``quantum corrections'' available in the literature, yields a result which is in order-of-magnitude agreement with the experimental VER rate. We also calculate the VER rate for liquid oxygen/argon mixtures. The rotations of the solvent near a vibrationally excited molecule, and of that molecule itself, have important consequences for the short-time dynamics of the force-force TCF. We propose a simple statistical model which quantitatively explains the mole- fraction dependence of the observed VER rate. Next, we demonstrate that a newly-developed model for oxygen very accurately describes the liquid, by comparing to experimental measures of microscopic structure and dynamics. We also

  12. Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity.

    PubMed

    Bignon, Emmanuelle; Chan, Chen-Hui; Morell, Christophe; Monari, Antonio; Ravanat, Jean-Luc; Dumont, Elise

    2017-08-16

    Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding. Through all-atom dynamics, noncovalent interactions that stabilize the polyamine-DNA complex and prefigure the reactivity, leading to the low-barrier formation of deleterious DNA-polyamine cross-links, after one-electron oxidation of a guanine nucleobase, are unraveled. The binding strength is quantified from the obtained trajectories by molecular mechanics generalized Born surface area post-processing (MM-GBSA). The values of binding free energies provide the same affinity order, Put

  13. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

    SciTech Connect

    McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

    2014-09-01

    A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

  14. Polymer Fluid Dynamics: Continuum and Molecular Approaches.

    PubMed

    Bird, R B; Giacomin, A J

    2016-06-07

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

  15. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

    PubMed

    Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

    2015-05-12

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the

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

    DOE PAGES

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

    2015-02-25

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

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

    SciTech Connect

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

    2015-02-25

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

  18. Structural and Transport Properties of Tertiary Ammonium Triflate Ionic Liquids: A Molecular Dynamics Study.

    PubMed

    Nasrabadi, Amir Taghavi; Gelb, Lev D

    2017-03-02

    Ammonium-based protic ionic liquids (PILs) have shown promising physicochemical properties as proton conductors in polymer membrane fuel cells. In this work, molecular dynamics simulations are used to study the structural, dynamic, and transport properties of a series of tertiary ammonium triflate PILs. Nonpolarizable all-atom force fields were used, including two different models for the triflate anion. Previous simulation studies of these PILs have yielded poor results for transport properties due to unrealistically slow dynamics. To improve performance, polarization and charge-transfer effects were approximately accounted for by scaling all atomic partial charges by a uniform factor, γ. The optimum scaling factor γ = 0.69 was determined by comparing simulation results with available experimental data and found to be transferable between different ammonium cations and insensitive to both the temperature and choice of experimental data used for comparison. Simulations performed using optimized charge scaling showed that the transport properties significantly improved over previous studies. Both the self-diffusion coefficients and viscosity were in good agreement with experiment over the whole range of systems and temperatures studied. Simulated PIL densities were also in good agreement with experiment, although the thermal expansivity was underestimated. Structural analysis revealed a strong directionality in interionic interactions. Triflate anions preferentially approach the ammonium cation so as to form strong hydrogen bonds between sulfonate oxygen atoms and the acidic ammonium hydrogen. The ionic conductivity was somewhat underestimated, especially at lower temperatures. Analysis of conductivity data suggests that there is significant correlated motion of oppositely charged ions in these PILs, especially at short times. These results overall indicate that the transport properties of this class of PILs are accurately modeled by these force fields if charge

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

    NASA Astrophysics Data System (ADS)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

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

  20. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

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

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

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

    2012-01-01

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

  3. Molecular dynamics in high electric fields

    NASA Astrophysics Data System (ADS)

    Apostol, M.; Cune, L. C.

    2016-06-01

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

  4. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

    PubMed

    Das, Rhiju; Qian, Bin; Raman, Srivatsan; Vernon, Robert; Thompson, James; Bradley, Philip; Khare, Sagar; Tyka, Michael D; Bhat, Divya; Chivian, Dylan; Kim, David E; Sheffler, William H; Malmström, Lars; Wollacott, Andrew M; Wang, Chu; Andre, Ingemar; Baker, David

    2007-01-01

    We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template-based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near-atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions.

  5. Dynamic Molecular Invasion into Multiply Interlocked Catenane.

    PubMed

    Yamada, Yasuyuki; Ito, Ryohei; Ogino, Sayaka; Kato, Tatsuhisa; Tanaka, Kentaro

    2017-09-14

    A multiply interlocked catenane with a novel molecular topology was synthesized; a phthalocyanine bearing four peripheral crown ethers was quadruply interlocked with a cofacial porphyrin dimer bridged with four alkylammonium chains. The supramolecular conjugate has two nanospaces surrounded by a porphyrin, a phthalocyanine, and four alkyl chains to accommodate guest molecules. Because the phthalocyanine is movable along the alkyl chains, it acts as an adjustable wall, permitting the invasion of large molecules to the nanospaces without spoiling the affinity of the association. The dynamic molecular invasion allowed the intercalation of dianionic porphyrins into both the nanospaces with a high affinity. A photometric titration experiment revealed the two-step inclusion phenomenon. The multiply interlocked catenane complexed with three Cu2+ ions, and the spin-spin interaction was switched off by the intercalation of dianionic porphyrins. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  7. Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization

    NASA Astrophysics Data System (ADS)

    Arntsen, Christopher; Chen, Chen; Voth, Gregory A.

    2017-09-01

    We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.

  8. Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization.

    PubMed

    Arntsen, Christopher; Chen, Chen; Voth, Gregory A

    2017-09-01

    We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.

  9. Molecular Dynamics: New Frontier in Personalized Medicine.

    PubMed

    Sneha, P; Doss, C George Priya

    2016-01-01

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

  10. Exploring Hamiltonian dielectric solvent molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

    2014-09-01

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

  11. Exchange frequency in replica exchange molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2008-01-01

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

  12. 8B structure in Fermionic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  13. Molecular Dynamics Simulations of Interface Failure

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  14. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Y.T.

    1987-03-01

    Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.

  15. Molecular dynamics simulations of dense plasmas

    SciTech Connect

    Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.

    1993-12-31

    We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

  16. Charge transport network dynamics in molecular aggregates

    SciTech Connect

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

    2016-07-20

    Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ~100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed.

  17. Collective dynamics of interacting molecular motors.

    PubMed

    Campàs, O; Kafri, Y; Zeldovich, K B; Casademunt, J; Joanny, J-F

    2006-07-21

    The collective dynamics of N interacting processive molecular motors are considered theoretically when an external force is applied to the leading motor. We show, using a discrete lattice model, that the force-velocity curves strongly depend on the effective dynamic interactions between motors and differ significantly from those of a simple approach where the motors equally share the force. Moreover, they become essentially independent of the number of motors if N is large enough (N> or approximately 5 for conventional kinesin). We show that a two-state ratchet model has a very similar behavior to that of the coarse-grained lattice model with effective interactions. The general picture is unaffected by motor attachment and detachment events.

  18. Charge transport network dynamics in molecular aggregates

    PubMed Central

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

    2016-01-01

    Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ∼100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed. PMID:27439871

  19. Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking.

    PubMed

    Wroblewska, Liliana; Skolnick, Jeffrey

    2007-09-01

    Recent work has shown that physics-based, all-atom energy functions (AMBER, CHARMM, OPLS-AA) and local minimization, when used in scoring, are able to discriminate among native and decoy structures. Yet, there have been only few instances reported of the successful use of physics based potentials in the actual refinement of protein models from a starting conformation to one that ends in structures, which are closer to the native state. An energy function that has a global minimum energy in the protein's native state and a good correlation between energy and native-likeness should be able to drive model structures closer to their native structure during a conformational search. Here, the possible reasons for the discrepancy between the scoring and refinement results for the case of AMBER potential are examined. When the conformational search via molecular dynamics is driven by the AMBER potential for a large set of 150 nonhomologous proteins and their associated decoys, often the native minimum does not appear to be the lowest free energy state. Ways of correcting the potential function in order to make it more suitable for protein model refinement are proposed. Copyright 2007 Wiley Periodicals, Inc.

  20. The dependence of all-atom statistical potentials on structural training database.

    PubMed

    Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi

    2004-06-01

    An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 alpha-proteins and 271 beta-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP (atomic knowledge-based potential), and DFIRE (statistical potential based on distance-scaled finite ideal-gas reference state). These energy functions differ in the reference states used for energy derivation. The energy functions extracted from the different structural databases are used to select native structures from multiple decoys of 64 alpha-proteins and 28 beta-proteins. The performance in native structure selections indicates that the DFIRE-based energy function is mostly independent of the structural database whereas RAPDF and KBP have a significant dependence. The construction of two additional structural databases of alpha/beta and alpha + beta-proteins further confirmed the weak dependence of DFIRE on the structural databases of various structural classes. The possible source for the difference between the three all-atom statistical energy functions is that the physical reference state of ideal gas used in the DFIRE-based energy function is least dependent on the structural database.

  1. Structure prediction for CASP8 with all-atom refinement using Rosetta.

    PubMed

    Raman, Srivatsan; Vernon, Robert; Thompson, James; Tyka, Michael; Sadreyev, Ruslan; Pei, Jimin; Kim, David; Kellogg, Elizabeth; DiMaio, Frank; Lange, Oliver; Kinch, Lisa; Sheffler, Will; Kim, Bong-Hyun; Das, Rhiju; Grishin, Nick V; Baker, David

    2009-01-01

    We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.

  2. Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

    2012-04-01

    Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

  3. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.

    PubMed

    Yamamori, Yu; Kitao, Akio

    2013-10-14

    A new and efficient conformational sampling method, MuSTAR MD (Multi-scale Sampling using Temperature Accelerated and Replica exchange Molecular Dynamics), is proposed to calculate the free energy landscape on a space spanned by a set of collective variables. This method is an extension of temperature accelerated molecular dynamics and can also be considered as a variation of replica-exchange umbrella sampling. In the MuSTAR MD, each replica contains an all-atom fine-grained model, at least one coarse-grained model, and a model defined by the collective variables that interacts with the other models in the same replica through coupling energy terms. The coarse-grained model is introduced to drive efficient sampling of large conformational space and the fine-grained model can serve to conduct more accurate conformational sampling. The collective variable model serves not only to mediate the coarse- and fine-grained models, but also to enhance sampling efficiency by temperature acceleration. We have applied this method to Ala-dipeptide and examined the sampling efficiency of MuSTAR MD in the free energy landscape calculation compared to that for replica exchange molecular dynamics, replica exchange umbrella sampling, temperature accelerated molecular dynamics, and conventional MD. The results clearly indicate the advantage of sampling a relatively high energy conformational space, which is not sufficiently sampled with other methods. This feature is important in the investigation of transition pathways that go across energy barriers. MuSTAR MD was also applied to Met-enkephalin as a test case in which two Gō-like models were employed as the coarse-grained model.

  4. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  5. MDLab: a molecular dynamics simulation prototyping environment.

    PubMed

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

    2010-05-01

    Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Copyright 2009 Wiley Periodicals, Inc.

  6. Accelerated molecular dynamics simulations of protein folding.

    PubMed

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

  7. Flow and plasticity via nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G.

    1984-06-11

    The viscous flow of fluids and the plastic flow of solids, such as metals, are interesting from both the practical and the theoretical points of view. Atomistic molecular dynamics simulations provide a way of visualizing and understanding these flows in a detailed microscopic way. Simulations are necessarily carried out at relatively high rates of strain. For this reason they are ideally suited to the study of nonlinear flow phenomena: normal stresses induced by shear deformation, stress rotation, and the coupling of stress with heat flow, for instance. The simulations require appropriate boundary conditions, forces, and equations of motion. Newtonian mechanics is relatively inefficient for this simulation task. A modification, Nonequilibrium Molecular Dynamics, has been developed to simulate nonequilibrium flows. By now, many high-strain-rate rheological studies of flowing (viscous) fluids and (plastic) solids have been carried out. Here I describe the new methods used in the simulations and some results obtained in this way. A three-body shear-flow exercise is appended to make these ideas more concrete.

  8. Exact dynamic properties of molecular motors.

    PubMed

    Boon, N J; Hoyle, R B

    2012-08-28

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

  9. Exact dynamic properties of molecular motors

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  10. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  11. Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.

    PubMed

    Liu, Fu-Feng; Huang, Bo; Dong, Xiao-Yan; Sun, Yan

    2013-01-01

    Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1) in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154) of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137) in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.

  12. Molecular Basis for the Dissociation Dynamics of Protein A-Immunoglobulin G1 Complex

    PubMed Central

    Liu, Fu-Feng; Huang, Bo; Dong, Xiao-Yan; Sun, Yan

    2013-01-01

    Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1) in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154) of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137) in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex. PMID:23776704

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

    NASA Astrophysics Data System (ADS)

    Hung, Shih-Wei; Shiomi, Junichiro

    2015-11-01

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

  14. Dynamic transitions in molecular dynamics simulations of supercooled silicon

    NASA Astrophysics Data System (ADS)

    Mei, Xiaojun; Eapen, Jacob

    2013-04-01

    Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.

  15. Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.

    PubMed

    Luk, Hoi Ling; Feist, Johannes; Toppari, J Jussi; Groenhof, Gerrit

    2017-09-12

    When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.

  16. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

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

  17. Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

    NASA Astrophysics Data System (ADS)

    Mogurampelly, Santosh; Ganesan, Venkat

    2015-03-01

    Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

  18. Dual folding pathways of an α /β protein from all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wang, Zhi-Xiang; Wu, Chun; Duan, Yong

    2009-10-01

    Successful ab initio folding of proteins with both α-helix and β-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any α /β proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold α /β proteins with a force field emphasizing the balance between the two major secondary structures. Using our newly developed force field, we conducted extensive ab initio folding simulations on an α /β protein full sequence design (FSD) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-Born solvation model. In these simulations, the folding of FSD to the native state with high population (>64.2%) and high fidelity (Cα-Root Mean Square Deviation of 1.29 Å for the most sampled conformation when compared to the experimental structure) was achieved. The folding of FSD was found to follow two pathways. In the major pathway, the folding started from the formation of the helix. In the minor pathway, however, folding of the β-hairpin started first. Further examination revealed that the helix initiated from the C-terminus and propagated toward the N-terminus. The formation of the hydrophobic contacts coincided with the global folding. Therefore the hydrophobic force does not appear to be the driving force of the folding of this protein.

  19. Detecting Allosteric Networks Using Molecular Dynamics Simulation.

    PubMed

    Bowerman, S; Wereszczynski, J

    2016-01-01

    Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. © 2016 Elsevier Inc. All rights reserved.

  20. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

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

  1. Partial hydrodynamic representation of quantum molecular dynamics

    NASA Astrophysics Data System (ADS)

    Gu, Bing; Franco, Ignacio

    2017-05-01

    A hybrid method is proposed to propagate system-bath quantum dynamics that use both basis functions and coupled quantum trajectories. In it, the bath is represented with an ensemble of Bohmian trajectories while the system degrees of freedom are accounted through reduced density matrices. By retaining the Hilbert space structure for the system, the method is able to capture interference processes that are challenging to describe in Bohmian dynamics due to singularities that these processes introduce in the quantum potential. By adopting quantum trajectories to represent the bath, the method beats the exponential scaling of the computational cost with the bath size. This combination makes the method suitable for large-scale ground and excited state fully quantum molecular dynamics simulations. Equations of motion for the quantum trajectories and reduced density matrices are derived from the Schrödinger equation and a computational algorithm to solve these equations is proposed. Through computations in two-dimensional model systems, the method is shown to offer an accurate description of subsystem observables and of quantum decoherence, which is difficult to obtain when the quantum nature of the bath is ignored. The scaling of the method is demonstrated using a model with 21 degrees of freedom. The limit of independent trajectories is recovered when the mass of bath degrees of freedom is much larger than the one of the system, in agreement with mixed quantum-classical descriptions.

  2. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    SciTech Connect

    Turi, László

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  3. Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models.

    PubMed

    Genheden, Samuel; Eriksson, Leif A

    2016-09-13

    Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.

  4. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors.

    PubMed

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane-solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane-solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor.

  5. Molecular dynamics studies of nanofluidics and nanomechanics

    NASA Astrophysics Data System (ADS)

    Lee, Ki-Ho

    Developing a membrane that can successfully filter molecules such as hydrocarbons, oxygen, and carbon dioxide from gaseous mixtures is an important issue for the environmental and economic industries. This potential selectivity can be predicted from atomistic simulations of the diffusion and adsorption of gases into and within carbon nanotubes. The computational nanofluidics of hydrocarbons, oxygen, and carbon dioxide have been studied with molecular dynamics simulations in the work reported here. The interactions in the system are modeled by a classical reactive empirical bond-order potential coupled to Lennard-Jones and Coulombic potentials. The transport of gas molecules for long time periods is characterized by initial non-equilibrium states followed by equilibrium states. The non-equilibrium state is induced by the diffusive motion of gas molecules from one end of the nanotubes into the vacuum or low-pressure region at the other end of the nanotubes, and lasts until the gases are evenly distributed in the nanotubes. During the non-equilibrium state, the gas molecules move back and forth through the nanotubes. It is found that this behavior, the time needed for the attainment of equilibrium, and the molecular motions at the openings of the nanotubes are affected by the density (or pressure) of gas molecules both inside and outside of the carbon nanotubes. When the gas molecules reach the end of the nanotubes, the attractive force between the tube end and the gas molecules prevents the molecules from exiting. The mechanical properties of carbon nanotubes have extended the potential applications of nanoelectromechanical systems (HEMS) such as nano-switches, nanosensors, nano-actuators, and nano-tweezers. In this study, the bending motion from externally incident Ar atom impacts on nanotubes with one firmly-fixed end is examined with classical molecular dynamics simulations. The deformation of the carbon nanotubes in the direction perpendicular to their axis is

  6. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  7. All-atomic simulations on human telomeric G-quadruplex DNA binding with thioflavin T.

    PubMed

    Luo, Di; Mu, Yuguang

    2015-04-16

    Ligand-stabilized human telomeric G-quadruplex DNA is believed to be an anticancer agent, as it can impede the continuous elongation of telomeres by telomerase in cancer cells. In this study, five well-established human telomeric G-quadruplex DNA models were probed on their binding behaviors with thioflavin T (ThT) via both conventional molecular dynamics (MD) and well-tempered metadynamics (WT-MetaD) simulations. Novel dynamics and characteristic binding patterns were disclosed by the MD simulations. It was observed that the K(+) promoted parallel and hybridized human telomeric G-quadruplex conformations pose higher binding affinities to ThT than the Na(+) and K(+) promoted basket conformations. It is the end, sandwich, and base stacking driven by π-π interactions that are identified as the major binding mechanisms. As the most energy favorable binding mode, the sandwich stacking observed in (3 + 1) hybridized form 1 G-quadruplex conformation is triggered by reversible conformational change of the G-quadruplex. To further examine the free energy landscapes, WT-MetaD simulations were utilized on G-quadruplex-ThT systems. It is found that all of the major binding modes predicted by the MD simulations are confirmed by the WT-MetaD simulations. The results in this work not only accord with existing experimental findings, but also reinforce our understanding on the dynamics of G-quadruplexes and aid future drug developments for G-quadruplex stabilization ligands.

  8. Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle.

    PubMed

    Choe, Seungho; Chang, Rakwoo; Jeon, Jonggu; Violi, Angela

    2008-11-01

    This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide consisting of the first 25 residues from surfactant protein B. The nanoparticle model with a chemical formula C188H53 was generated using a computational code for combustion conditions. The nanoparticle has a carbon cage structure reminiscent of the buckyballs with open ends. A series of molecular-scale structural and dynamical properties of the surfactant film in the absence and presence of nanoparticle are analyzed, including radial distribution functions, mean-square displacements of lipids and nanoparticle, chain tilt angle, and the surfactant protein B peptide helix tilt angle. The results show that the nanoparticle affects the structure and packing of the lipids and peptide in the film, and it appears that the nanoparticle and peptide repel each other. The ability of the nanoparticle to translocate the surfactant film is one of the most important predictions of this study. The potential of mean force for dragging the particle through the film provides such information. The reported potential of mean force suggests that the nanoparticle can easily penetrate the monolayer but further translocation to the water phase is energetically prohibitive. The implication is that nanoparticles can interact with the lung surfactant, as supported by recent experimental data by Bakshi et al.

  9. Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.

    PubMed

    Kukol, Andreas

    2009-03-10

    United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.

  10. All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.

    PubMed

    Vashisth, Harish; Abrams, Cameron F

    2010-07-16

    Type 1 insulin-like growth factor receptor (IGF1R) is a membrane-spanning glycoprotein of the insulin receptor family that has been implicated in a variety of cancers. The key questions related to molecular mechanisms governing ligand recognition by IGF1R remain unanswered, partly due to the lack of testable structural models of apo or ligand-bound receptor complexes. Using a homology model of the IGF1R ectodomain IGF1RDeltabeta, we present the first experimentally consistent all-atom structural models of IGF1/IGF1RDeltabeta and IGF2/IGF1RDeltabeta complexes. Our explicit-solvent molecular dynamics (MD) simulation of apo-IGF1RDeltabeta shows that it displays asymmetric flexibility mechanisms that result in one of two binding pockets accessible to growth factors IGF1 and IGF2, as demonstrated via an MD-assisted Monte Carlo docking procedure. Our MD-generated ensemble of structures of apo and IGF1-bound IGF1RDeltabeta agrees reasonably well with published small-angle X-ray scattering data. We observe simultaneous contacts of each growth factor with sites 1 and 2 of IGF1R, suggesting cross-linking of receptor subunits. Our models provide direct evidence in favor of suggested electrostatic complementarity between the C-domain (IGF1) and the cysteine-rich domain (IGF1R). Our IGF1/IGF1RDeltabeta model provides structural bases for the observation that a single IGF1 molecule binds to IGF1RDeltabeta at low concentrations in small-angle X-ray scattering studies. We also suggest new possible structural bases for differences in the affinities of insulin, IGF1, and IGF2 for their noncognate receptors.

  11. Nanodrop contact angles from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  12. Nonequilibrium molecular dynamics: The first 25 years

    SciTech Connect

    Hoover, W.G. |

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.

  13. Assessing Electrolyte Transport Properties with Molecular Dynamics

    DOE PAGES

    Jones, R. E.; Ward, D. K.; Gittleson, F. S.; ...

    2017-04-15

    Here in this work we use estimates of ionic transport properties obtained from molecular dynamics to rank lithium electrolytes of different compositions. We develop linear response methods to obtain the Onsager diffusivity matrix for all chemical species, its Fickian counterpart, and the mobilities of the ionic species. We apply these methods to the well-studied propylene carbonate/ethylene carbonate solvent with dissolved LiBF4 and O2. The results show that, over a range of lithium concentrations and carbonate mixtures, trends in the transport coefficients can be identified and optimal electrolytes can be selected for experimental focus; however, refinement of these estimation techniques ismore » necessary for a reliable ranking of a large set of electrolytes.« less

  14. Molecular dynamics simulation of aluminium melting

    NASA Astrophysics Data System (ADS)

    Novak, Jakob

    2016-06-01

    Solid-liquid phase transition has been simulated by the molecular dynamics method, using isobaric-isoenthalpic ensemble. For interatomic potential, glue potential has been selected. The original algorithm for bookkeeping of the information on neighbouring relationships of the atoms has been developed and used in this research. Time consumption for calculation of interatomic forces has been reduced from o(N2) to o(N) by the use of this algorithm. Calculations show that phase transition from solid to liquid occurs between 1,000 K and 1,300 K. The simulated temperature of phase transition is higher than the experimental value due to the absence of crystal defects. If constant heat flux is supplied, temperature decreases during melting because the superheated state becomes unstable. During the cooling process, no significant changes of the observed variables were detected due to the high cooling rate, which prevents crystallisation.

  15. Cell list algorithms for nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew; Fox, Ian; Saracino, Alexandra

    2016-06-01

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

  16. Classical Molecular Dynamics Simulation of Nuclear Fuel

    SciTech Connect

    Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

    2015-10-10

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

  17. Cluster production within antisymmetrized molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ono, Akira

    2016-06-01

    Clusters are quite important at various situations in heavy-ion collisions. Antisymmetrized molecular dynamics was improved to take into account the correlations to form light clusters, such as deuterons and α particles, and light nuclei composed of several clusters. The momentum fluctuations of emitted particles are also taken into account by a simple method. Formation of fragments and light clusters in a wide range of heavy-ion collisions was well described with a single set of model parameters. Fragmentation in a proton induced reaction was also well reproduced by introducing cluster correlations. Calculated results demonstrate strong impacts of clusters in various observables including those usually regarded as probes of the density dependence of symmetry energy.

  18. Ion mobility analysis of molecular dynamics.

    PubMed

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

    2014-01-01

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

  19. Molecular Dynamics Simulations of Hypervelocity Impacts

    NASA Astrophysics Data System (ADS)

    Owens, Eli T.; Bachlechner, Martina E.

    2007-03-01

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

  20. Molecular-dynamics simulations of lead clusters

    NASA Astrophysics Data System (ADS)

    Hendy, S. C.; Hall, B. D.

    2001-08-01

    Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.

  1. On the parallelization of molecular dynamics codes

    NASA Astrophysics Data System (ADS)

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

    2002-08-01

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

  2. Fiber lubrication: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Liu, Hongyi

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

  3. Molecular dynamics simulations and morphology analysis of TEM imaged PVDF nanofibers

    NASA Astrophysics Data System (ADS)

    Miao, Jiayuan; Reneker, Darrell; Tsige, Mesfin; Taylor, Philip

    With the goal of elucidating the structure of polyvinylidene fluoride (PVDF) nanofibers, all-atom molecular dynamics simulations were performed, and the results compared with structures observed in high resolution transmission electron microscopy (TEM) at the molecular level. Simulation shows that the stability of the β-phase component in a PVDF nanofiber is influenced by its thickness and processing history. When exposed to irradiation, as in a TEM observation, the structure is then further modified by the effects of chain scission. The transformation from the β phase into a paraelectric phase can explain the spindle formation and serpentine motion of molecular segments observed by Zhong et al. (Polymer, 54, 2013, 3745-3756) in irradiated PVDF nanofibers. From a comparison between simulated and experimental TEM images it was possible to identify numerous features that are useful in unveiling the inherent structure of PVDF nanofibers. The experimental TEM images appear to match well with those predicted by a model based on α-phase PVDF, while also being consistent with an alternative model (Nanoscale 2015, DOI: 10.1039/c5nr01619c). Work supported by the Petroleum Research Fund of the ACS.

  4. A new parallel method for molecular dynamics simulation of macromolecular systems

    SciTech Connect

    Plimpton, S.; Hendrickson, B.

    1994-08-01

    Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter-processor communication scales as N, the number of atoms, independent of P, the number of processors. Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this paper a new parallel method called force-decomposition for simulating macromolecular or small-molecule systems is presented. Its memory and communication costs scale as N/{radical}P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load-balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor.

  5. Molecular dynamics simulations of dotriacontane films supported on a SiO2 surface

    NASA Astrophysics Data System (ADS)

    Gutierrez, Sebastian; Araya, Raul; Perez-Acle, Tomas; Retamal, Maria Jose; Volkmann, Ulrich G.

    2011-03-01

    Dotriacontane (C32 H66 , C32) films supported on Si O2 surfaces were studied using very high-resolution ellipsometry, atomic force microscopy (AFM) and x-ray reflectivity techniques. For almost complete layers a model was proposed in which the C32/ Si O2 interfacial region is characterized by a parallel bilayer and perpendicular layers on top. Recent AFM measurements performed on samples forming sea-weed like structures, showed that for these particular perpendicular ``fractal like'' layers the heights are lower than the all-trans length of dotriacontane (42.5 AA). To gain insights on the internal molecular ordering and layering of C32 supported on Si O2 surfaces, we used all-atom molecular dynamics to simulate C32 films at different temperatures. Our results confirm the presence of the parallel bilayer suggesting the existence of a mixed layer on top, formed by molecules with both parallel and perpendicular segments. These findings suggest a different molecular architecture for sea-weed like structures of dotriacontane supported on Si O2 .

  6. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies

    PubMed Central

    Soler, Miguel A.; de Marco, Ario; Fortuna, Sara

    2016-01-01

    Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules. PMID:27721441

  7. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies

    NASA Astrophysics Data System (ADS)

    Soler, Miguel A.; De Marco, Ario; Fortuna, Sara

    2016-10-01

    Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules.

  8. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies.

    PubMed

    Soler, Miguel A; de Marco, Ario; Fortuna, Sara

    2016-10-10

    Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules.

  9. Molecular Dynamics Simulation of a RNA Aptasensor.

    PubMed

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

    2017-04-14

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

  10. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect

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

    1998-02-01

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

  11. An All-Atom Model of the Structure of Human Copper Transporter 1

    PubMed Central

    Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.

    2013-01-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840

  12. Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit.

    PubMed

    Liu, Li; Liu, Xiaofeng; Gong, Jiayu; Jiang, Hualiang; Li, Honglin

    2011-06-14

    All-atom normal mode analysis (NMA) is an efficient way to predict the collective motions in a given macromolecule, which is essential for the understanding of protein biological function and drug design. However, the calculations are limited in time scale mainly because the required diagonalization of the Hessian matrix by Householder-QR transformation is a computationally exhausting task. In this paper, we demonstrate the parallel computing power of the graphics processing unit (GPU) in NMA by mapping Householder-QR transformation onto GPU using Compute Unified Device Architecture (CUDA). The results revealed that the GPU-accelerated all-atom NMA could reduce the runtime of diagonalization significantly and achieved over 20× speedup over CPU-based NMA. In addition, we analyzed the influence of precision on both the performance and the accuracy of GPU. Although the performance of GPU with double precision is weaker than that with single precision in theory, more accurate results and an acceptable speedup of double precision were obtained in our approach by reducing the data transfer time to a minimum. Finally, the inherent drawbacks of GPU and the corresponding solution to deal with the limitation in computational scale are also discussed in this study.

  13. All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2016-11-01

    We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.

  14. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.

  15. An all-atom model of the structure of human copper transporter 1.

    PubMed

    Tsigelny, Igor F; Sharikov, Yuriy; Greenberg, Jerry P; Miller, Mark A; Kouznetsova, Valentina L; Larson, Christopher A; Howell, Stephen B

    2012-07-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin.

  16. All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5

    NASA Astrophysics Data System (ADS)

    Genheden, Samuel; Essex, Jonathan W.

    2016-11-01

    We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.

  17. All-Atom Folding and Characterization of the Free-Energy Landscape of the Villin Headpiece

    NASA Astrophysics Data System (ADS)

    Wenzel, Wolfgang

    2005-03-01

    The prediction of protein tertiary structure, in particular based on sequence information alone, remains one of the outstanding problems in biophysical chemistry. According to the thermodynamic hypothesis, the native conformation of a protein can be predicted as the global optimum of its free energy surface with stochastic optimization methods[1] orders of magnitude faster than by direct simulation of the folding process. We have recently developed an all-atom free energy forcefield[2]which implements a minimal thermodynamic model based on physical interactions . Using this forcefield we could reproducibly fold several proteins[3] ranging from 20-60 amino acids in length at the all atom level, among them the 36-amino acid, three helix villin headpiece. The conformations generated in the search can be used to construct a decoy tree, which completely characterizes the low energy conformations of the protein Consistent with the ``new paradigm'' for protein folding their analysis characterizes the folding funnel and its metastable branches. [1] W. Wenzel, K. Hamacher, PRL 59, 3003 (1999) [2] T. Herges, W. Wenzel, Biophysical J. 87, 3100 (2004) [3] A. Schug, W. Wenzel, PRL 91, 158102 (2003), EPL 67, 307 (2004), Proteins (in press), PRL (in press), JACS (in press)

  18. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Y.T.

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  19. Molecular-dynamic study of liquid ethylenediamine

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Y.T.

    1990-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation. 34 refs.

  1. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  2. A molecular dynamics approach to barrodiffusion

    NASA Astrophysics Data System (ADS)

    Cooley, James; Marciante, Mathieu; Murillo, Michael

    2016-10-01

    Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

  3. Molecular dynamics simulation in virus research

    PubMed Central

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

    2012-01-01

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

  4. Molecular dynamics simulation study of distribution and dynamics of aqueous solutions of uranyl ions: the effect of varying temperature and concentration.

    PubMed

    Chopra, Manish; Choudhury, Niharendu

    2015-11-07

    Investigating the characteristics of actinyl ions has been of great interest due to their direct relevance in the nuclear fuel cycle. All-atom molecular dynamics simulations have been employed to study the orientational structure and dynamics of aqueous solutions of uranyl ions of various concentrations. The orientational structure of water around a uranyl ion has been thoroughly investigated by calculating different orientational probability distributions corresponding to different molecular axes of water. The orientational distribution of water molecules in the first coordination shell of a uranyl ion is found to be markedly different from that in bulk water. Analysis of counterion distribution around the uranyl ion reveals the presence of nitrate ions along with water molecules in the first solvation shell. From the comparison of the number of coordinated water and nitrate ions at various uranyl nitrate concentrations, it is evident that these two species compete for occupying the first solvation shell of the uranyl ion. Orientational dynamics of water molecules about different molecular axes of water in the vicinity of uranyl ions have also been investigated and decreasing orientational mobility of water with increasing uranyl concentration has been found. However, it is observed that the orientational dynamics remains more or less the same whether we consider all the water molecules in the aqueous solution or only the solvation shell water molecules. The effect of temperature on the translational and orientational characteristics of the aqueous uranyl solutions has also been studied in detail.

  5. TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

    PubMed

    Li, Min; Liu, Fengjiao; Zhang, John Z H

    2016-12-13

    Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

  6. GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES

    SciTech Connect

    MUCKERMAN,J.T.

    1999-06-09

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

  7. Interfacial water on crystalline silica: A comparative molecular dynamics simulation study

    SciTech Connect

    Ho, Tuan A.; Argyris, D.; Cole, David; Striolo, Alberto

    2011-01-01

    All-atom molecular dynamics simulations were conducted to study the dynamics of aqueous electrolyte solutions confined in slit-shaped silica nanopores of various degrees of protonation. Five degrees of protonation were prepared by randomly removing surface hydrogen atoms from fully protonated crystalline silica surfaces. Aqueous electrolyte solutions containing NaCl or CsCl salt were simulated at ambient conditions. In all cases, the ionic concentration was 1 M. The results were quantified in terms of atomic density distributions within the pores, and the self-diffusion coefficient along the direction parallel to the pore surface. We found evidence for ion-specific properties that depend on ion surface, water ion, and only in some cases ion ion correlations. The degree of protonation strongly affects the structure, distribution, and the dynamic behavior of confined water and electrolytes. Cl ions adsorb on the surface at large degrees of protonation, and their behavior does not depend significantly on the cation type (either Na+ or Cs+ ions are present in the systems considered). The cations show significant ion-specific behavior. Na+ ions occupy different positions within the pore as the degree of protonation changes, while Cs+ ions mainly remain near the pore center at all conditions considered. For a given degree of protonation, the planar self-diffusion coefficient of Cs+ is always greater than that of Na+ ions. The results are useful for better understanding transport under confinement, including brine behavior in the subsurface, with important applications such as environmental remediation.

  8. Molecular dynamics studies on nanoscale gas transport

    NASA Astrophysics Data System (ADS)

    Barisik, Murat

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

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

    PubMed

    Vaidehi, Nagarajan; Jain, Abhinandan

    2015-01-29

    Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics.

  10. Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics

    PubMed Central

    2015-01-01

    Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406

  11. Molecular Dynamics Simulations of Tri-n-butyl-phosphate/n-Dodecane Mixture: Thermophysical Properties and Molecular Structure

    SciTech Connect

    de Almeida, Valmor F; Cui, Shengting; Khomami, Bamin

    2014-01-01

    Molecular dynamics simulations of tri-n-butyl-phosphate (TBP)/n-dodecane mixture in the liquid phase have been carried out using two recently developed TBP force field models (J. Phys. Chem. B 2012, 116, 305) in combination with the all-atom optimized potentials for liquid simulations (OPLS-AA) force field model for n-dodecane. Specifically, the electric dipole moment of TBP, mass density of the mixture, and the excess volume of mixing were computed with TBP mole fraction ranging from 0 to 1. It is found that the aforementioned force field models accurately predict the mass density of the mixture in the entire mole fraction range. Commensurate with experimental measurements, the electric dipole moment of the TBP was found to slightly increase with the mole fraction of TBP in the mixture. Also, in accord with experimental data, the excess volume of mixing is positive in the entire mole fraction range, peaking at TBP mole fraction range 0.3 0.5. Finally, a close examination of the spatial pair correlation functions between TBP molecules, and between TBP and n-dodecane molecules, revealed formation of TBP dimers through self-association at close distance, a phenomenon with ample experimental evidence.

  12. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

    PubMed

    Krokhotin, Andrey; Dokholyan, Nikolay V

    2015-01-01

    Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  14. A quantum molecular dynamics study of aqueous solvation dynamics

    NASA Astrophysics Data System (ADS)

    Videla, Pablo E.; Rossky, Peter J.; Laria, D.

    2013-10-01

    Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.

  15. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    SciTech Connect

    Pang, Yuan-Ping

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  16. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

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

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

    DTIC Science & Technology

    2014-08-30

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

  18. Molecular dynamics and spectra. II. Diatomic Raman

    NASA Astrophysics Data System (ADS)

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

    1981-07-01

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

  19. Thermal transpiration: A molecular dynamics study

    SciTech Connect

    T, Joe Francis; Sathian, Sarith P.

    2014-12-09

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

  20. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  1. Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields.

    PubMed

    Dahlgren, Markus K; Schyman, Patric; Tirado-Rives, Julian; Jorgensen, William L

    2013-05-24

    The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parametrization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and nonplanar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 °C) are also reported.

  2. Nonlinear Resonance Artifacts in Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

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

    1998-02-01

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

  3. 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…

  4. 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…

  5. Molecular dynamics simulations of glycoclusters and glycodendrimers.

    PubMed

    von der Lieth, Claus W; Frank, Martin; Lindhorst, Thisbe K

    2002-05-01

    Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.

  6. Molecular dynamics simulations of xDNA.

    PubMed

    Varghese, Mathew K; Thomas, Renjith; Unnikrishnan, N V; Sudarsanakumar, C

    2009-05-01

    xDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force-field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5' G xT A xC xG C xA xG T3').(xA5' C T xG C G xT A xC A3') was explored using a 22 ns molecular dynamics simulation in explicit solvent. During the simulation, the duplex retained its Watson-Crick base-pairing and double helical structure, with deviations from the starting B-form geometry towards A-form; the deviations are mainly in the backbone torsion angles and in the helical parameters. The sugar pucker of the residues were distributed among a variety of modes; C2' endo, C1' exo, O4' endo, C4' exo, C2' exo, and C3' endo. The enhanced stacking interactions on account of the modification in the bases could help to retain the duplex nature of the helix with minor deviations from the ideal geometry. In our simulation, the xDNA showed a reduced minor groove width and an enlarged major groove width in comparison with the NMR structure. Both the grooves are larger than that of standard B-DNA, but major groove width is larger than that of A-DNA with almost equal minor groove width. The enlarged groove widths and the possibility of additional hydration in the grooves makes xDNA a potential molecule for various applications. Copyright (c) 2009 Wiley Periodicals, Inc.

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

    SciTech Connect

    Silling, Stewart Andrew; Lehoucq, Richard B.

    2007-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-11-01

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

  9. Molecular dynamics simulation of fractal aggregate diffusion

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  10. Molecular Dynamics Simulations of Ferroelectric Phase Transitions

    NASA Astrophysics Data System (ADS)

    Yu, Rici; Krakauer, Henry

    1997-03-01

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

  11. Integrating influenza antigenic dynamics with molecular evolution

    PubMed Central

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

    2014-01-01

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

  12. Quantum molecular dynamics simulations of dense matter

    SciTech Connect

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

    1997-12-31

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

  13. Fundamental frequency from classical molecular dynamics.

    PubMed

    Yamada, Tomonori; Aida, Misako

    2015-02-07

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

  14. Molecular Dynamics Simulations of Coulomb Explosion

    SciTech Connect

    Bringa, E M

    2002-05-17

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

  15. Molecular chaperone-mediated nuclear protein dynamics.