For comprehensive and current results, perform a real-time search at Science.gov.

1

Analytic Potentials and Molecular Dynamics Simulations

NSDL National Science Digital Library

This tutorial, created by Donald W. Brenner at North Carolina State University, explains the role of "atomistic simulation in enabling nanotechnology." The tutorial is divided into six sections: "Case Study: Fullene Nanogear," "Molecular Dynamics," "Historical Perspective," "The Nuts and Bolts," "Potential Energy Functions," and "More Examples." Simply click the "forward" and "back" buttons to navigate the tutorial. Images, equations, and graphs help visitors along in understanding the material. This is a useful resource for teachers to use in the classroom or as part of an assignment, and for students studying nanotechnology and nanofabrication.

Brenner, Donald W.

2008-08-27

2

Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, that influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the C$\\mu$MD method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\\mu$MD method to the paradigmatic case of urea crystall...

Perego, Claudio; Parrinello, Michele

2015-01-01

3

Molecular Dynamics Simulations of Supported Pt Nanoclusters with Sutton-Chen Potentials

Molecular Dynamics Simulations of Supported Pt Nanoclusters with Sutton-Chen Potentials Jeffrey M dynamics simulation based on the Sutton-Chen potential to model Pt10 nanoparticles supported on a [110] -Al2O3 surface. Results are compared to previous density functional theory/molecular dynamics (DFT

Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group

4

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change

de Groot, Bert

5

Dynamic parameterization and ladder operators for the Kratzer molecular potential

NASA Astrophysics Data System (ADS)

Introducing independent parameters k and \\delta to represent the strength of the attractive and repulsive components, respectively, we write the Kratzer molecular potential as V\\left( k,\\delta \\right)=({{\\hbar }^{2}}/2\\;m)(-k/r+\\delta (\\delta -1)/{{r}^{2}}). This parameterisation is not only natural, but also convenient for the construction of ladder operators for the system. Adopting the straightforward method of deriving recurrence relations among confluent hypergeometric functions, we construct seven pairs of ladder operators for the Kratzer potential system. Detailed analysis of the laddering actions of these operators is given to show that they connect eigenstates of equal energy but belong to a hierarchy of Kratzer potential systems corresponding to different values of the parameters k and \\delta . Significantly, it is pointed out that it may not be possible to construct, in the position representation, a ladder operator which would connect different eigenstates belonging to the same potential V(k,\\delta ). Transition to the hydrogen atom case is discussed. A number (14 altogether) of functional relations among the confluent hypergeometric functions have been derived and reported separately in an appendix.

Babynanda Devi, O.; Amuba Singh, C.

2014-09-01

6

We present a new, nondestructive, method for determining chemical potentials in Monte Carlo and molecular dynamics simulations. The method estimates a value for the chemical potential such that one has a balance between fictitious successful creation and destruction trials in which the Monte Carlo method is used to determine success or failure of the creation\\/destruction attempts; we thus call the

Patrick J. Fay; John R. Ray; Ralph J. Wolf

1994-01-01

7

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

Ladd, A.J.C.

1988-08-01

8

Molecular dynamics studies for the new refrigerant R152a with simple model potentials

The new refrigerant R152a (CH3-CHF2) is modelled as a fluid of homonuclear two-centre Lennard-Jones molecules with a point dipole along the axis. This 2CLJD potential has four parameters which were determined by using results of previous and new molecular dynamics simulations for 2CLJD molecules of elongation L* = 0·505 and different reduced dipole moments ?*. For each of these dipole

Carlos Vega; Berthold Saager; Johann Fischer

1989-01-01

9

NASA Astrophysics Data System (ADS)

An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient.

Starrett, C. E.; Daligault, J.; Saumon, D.

2015-01-01

10

NASA Astrophysics Data System (ADS)

The mechanical elongation of a finite gold nanowire has been studied by molecular dynamics simulations using different semiempirical potentials for transition metals. These potentials have been widely used to study the mechanical properties of finite metal clusters. Combining with density functional theory calculations along several atomic-configuration trajectories predicted by different semiempirical potentials, the authors conclude that the second-moment approximation of the tight-binding scheme (TB-SMA) potential is the most suitable one to describe the energetics of finite Au clusters. They find that for the selected geometries of Au wires studied in this work, the ductile elongation of Au nanowires along the [001] direction predicted by the TB-SMA potential is largely independent of temperature in the range of 0.01-298K. The elongation leads to the formation of monatomic chains, as has been observed experimentally. The calculated force-versus-elongation curve is remarkably consistent with available experimental results.

Pu, Qing; Leng, Yongsheng; Tsetseris, Leonidas; Park, Harold S.; Pantelides, Sokrates T.; Cummings, Peter T.

2007-04-01

11

The mechanical elongation of a finite gold nanowire has been studied by molecular dynamics simulations using different semiempirical potentials for transition metals. These potentials have been widely used to study the mechanical properties of finite metal clusters. Combining with density functional theory calculations along several atomic-configuration trajectories predicted by different semiempirical potentials, the authors conclude that the second-moment approximation of the tight-binding scheme (TB-SMA) potential is the most suitable one to describe the energetics of finite Au clusters. They find that for the selected geometries of Au wires studied in this work, the ductile elongation of Au nanowires along the [001] direction predicted by the TB-SMA potential is largely independent of temperature in the range of 0.01-298 K. The elongation leads to the formation of monatomic chains, as has been observed experimentally. The calculated force-versus-elongation curve is remarkably consistent with available experimental results. PMID:17444732

Pu, Qing; Leng, Yongsheng; Tsetseris, Leonidas; Park, Harold S; Pantelides, Sokrates T; Cummings, Peter T

2007-04-14

12

Simulations of spiral galaxies with an active potential: molecular cloud formation and gas dynamics

We describe simulations of the response of a gaseous disc to an active spiral potential. The potential is derived from an N-body calculation and leads to a multi-armed time-evolving pattern. The gas forms long spiral arms typical of grand design galaxies, although the spiral pattern is asymmetric. The primary difference from a grand-design spiral galaxy, which has a consistent 2/4-armed pattern, is that instead of passing through the spiral arms, gas generally falls into a developing potential minimum and is released only when the local minimum dissolves. In this case, the densest gas is coincident with the spiral potential, rather than offset as in the grand-design spirals. We would there fore expect no offset between the spiral shock and star formation, and no obvious co-rotation radius. Spurs which occur in grand-design spirals when large clumps are sheared off leaving the spiral arms, are rare in the active, time-evolving spiral reported here. Instead, large branches are formed from spiral arms when the underlying spiral potential is dissolving due to the N-body dynamics. We find that the molecular cloud mass spectrum for the active potential is similar to that for clouds in grand design calculations, depending primarily on the ambient pressure rather than the nature of the potential. The largest molecular clouds occur when spiral arms collide, rather than by agglomeration within a spiral arm.

Clare Dobbs; Ian Bonnell

2008-01-23

13

We present a new, nondestructive, method for determining chemical potentials in Monte Carlo and molecular dynamics simulations. The method estimates a value for the chemical potential such that one has a balance between fictitious successful creation and destruction trials in which the Monte Carlo method is used to determine success or failure of the creation/destruction attempts; we thus call the method a detailed balance method. The method allows one to obtain estimates of the chemical potential for a given species in any closed ensemble simulation; the closed ensemble is paired with a natural'' open ensemble for the purpose of obtaining creation and destruction probabilities. We present results for the Lennard-Jones system and also for an embedded atom model of liquid palladium, and compare to previous results in the literature for these two systems. We are able to obtain an accurate estimate of the chemical potential for the Lennard-Jones system at higher densities than reported in the literature.

Fay, P.J.; Ray, J.R. (Department of Physics and Astronomy, Kinard Laboratory of Physics, Clemson University, Clemson, South Carolina 29634-1911 (United States)); Wolf, R.J. (Savannah River Technology Center, Westinghouse Savannah River Company, Aiken, South Carolina 29808 (United States))

1994-02-01

14

Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000?ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000?ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential. PMID:25054066

Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep

2014-01-01

15

Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000?ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000?ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential. PMID:25054066

Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep

2014-01-01

16

NASA Astrophysics Data System (ADS)

Empirical potentials have a strong effect on the hybridization and structure of amorphous carbon and are of great importance in molecular dynamics (MD) simulations. In this work, amorphous carbon at densities ranging from 2.0 to 3.2 g/cm3 was modeled by a liquid quenching method using Tersoff, 2nd REBO, and ReaxFF empirical potentials. The hybridization, structure and radial distribution function G(r) of carbon atoms were analyzed as a function of the three potentials mentioned above. The ReaxFF potential is capable to model the change of the structure of amorphous carbon and MD results are in a good agreement with experimental results and density function theory (DFT) at low density of 2.6 g/cm3 and below. The 2nd REBO potential can be used when amorphous carbon has a very low density of 2.4 g/cm3 and below. Considering the computational efficiency, the Tersoff potential is recommended to model amorphous carbon at a high density of 2.6 g/cm3 and above. In addition, the influence of the quenching time on the hybridization content obtained with the three potentials is discussed.

Li, Longqiu; Xu, Ming; Song, Wenping; Ovcharenko, Andrey; Zhang, Guangyu; Jia, Ding

2013-12-01

17

The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated by a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.

Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

2014-09-01

18

NASA Astrophysics Data System (ADS)

Molecular dynamics calculation was performed to simulate nano-Focused Ion Beam (FIB) processing on a Silicon surface. A combination of potential functions of impacting ion and target atoms was evaluated, and the influence of computational domain along the lateral directions was estimated. The target Silicon atoms on (100) surface of Si crystal were described by Tersoff potential. Ion-beam source was represented by Ga ions, where the optimal potential of the Ga ion was chosen by comparing Lennard-Jones, Tersoff, and ZBL (Ziegler, Biersack and Littmark) potentials. The initial velocity of ion was 3.327×105 m/sec at 40 keV. First, for the evaluation of combined potential functions of Si atoms and Ga ion, a small computation volume (2.58 nm × 2.58 nm × 51.99 nm) consisting of 19200 Si atoms was chosen with a single Ga ion impacting on Si (100) surface. On the combination of Tersoff potential for Si atom, and ZBL potential for Ga ion, the depth of the combination was found to be in good agreement with the depth of SRIM. Next, the influences of computational domain in lateral direction were evaluated by a larger region with a combination of potentials where the computational volume was (8.55 nm × 8.55 nm × 51.99 nm) constructed by 196608 Si atoms. Consequently, the energy transfer along lateral computational length was faster in larger region than in smaller region, and the entire initial energy of Ga ion was transmitted to the target material.

Satake, S.; Inoue, N.; Taniguchi, J.; Shibahara, M.

2008-03-01

19

Second-moment interatomic potential for gold and its application to molecular-dynamics simulations

NASA Astrophysics Data System (ADS)

We have obtained a new interatomic potential for Au in the framework of the second-moment approximation to the tight-binding model by fitting the total energy of the metal as a function of the volume computed by first-principles calculations. The scheme was validated by calculating the bulk modulus, elastic constants, vacancy formation energy and relaxed surface energies of Au, which were found to be in fair agreement with experiment. We also have performed molecular-dynamics simulations at various temperatures and we have determined the temperature dependence of the lattice constant, mean-square displacements, as well as the phonon density of states and the phonon dispersion curves of the metal. The agreement with the available experimental data is much better than previous works based on the same approximation.

Chamati, H.; Papanicolaou, N. I.

2004-11-01

20

The Matsuoka-Clementi-Yoshimine (MCY) configuration interaction potential for rigid water-water interactions has been extended to include the intramolecular vibrations. The extended potential (MCYL), using no empirical parameters other than the atomic masses, electron charge, and Planck constant, is used in a molecular-dynamics simulation study of the static and dynamic properties of liquid water. Among the properties studied are internal energy, heat

G. C. Lie; E. Clementi

1986-01-01

21

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. PMID:19090563

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

22

NASA Astrophysics Data System (ADS)

We show that the hybrid quantum mechanical/effective fragment potential (QM/EFP) can be a very effective and practical quantum mechanical molecular dynamics method, when it is properly combined with well-developed traditional molecular dynamics (MD) techniques. QM/EFP-MD simulations on intra-molecular proton transfer of glycine with 290 EFP waters yielded accurate free energy change and reaction barrier of the zwitterion ? neutral form conversion. Water rearrangements turned out to be the main driving force of the proton transfer.

Choi, Cheol Ho; Re, Suyong; Feig, Michael; Sugita, Yuji

2012-06-01

23

NASA Astrophysics Data System (ADS)

The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li , J. Chem. Phys.JCPSA60021-960610.1063/1.2786449 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm3 and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm3 isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.

Shvab, I.; Sadus, Richard J.

2012-05-01

24

The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li et al., J. Chem. Phys. 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm^{3} and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm^{3} isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models. PMID:23004769

Shvab, I; Sadus, Richard J

2012-05-01

25

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of $r_{s}=0.912$.

Hua Y. Geng

2014-12-19

26

Implementing molecular dynamics on hybrid high performance computers—Three-body potentials

NASA Astrophysics Data System (ADS)

The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to use accelerators efficiently to improve the performance of molecular dynamics (MD) codes employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algorithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.

Brown, W. Michael; Yamada, Masako

2013-12-01

27

properties of crystalline and amorphous aluminum nitride Priya Vashishta,1,a Rajiv K. Kalia,1 Aiichiro Nakano ceramic materials, only AlN and beryllium oxide have high thermal conductivity. Aluminum nitrideInteraction potential for aluminum nitride: A molecular dynamics study of mechanical and thermal

Southern California, University of

28

Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline and amorphous silicon carbide Priya Vashishta,a Rajiv K. Kalia Silicon carbide SiC has been proposed for a wide range of technological applications

Southern California, University of

29

Molecular Dynamics Demonstration Model

NSDL National Science Digital Library

The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small time steps dt, the system's total energy should be approximately conserved. Users can select various initial configurations using the drop down menu. Ejs Molecular Dynamics Demonstration model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the js_stp_md_MolecularDynamicsDemo.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer models. Additional Ejs models for statistical mechanics are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Christian, Wolfgang

2008-11-15

30

NSDL National Science Digital Library

The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt, the system's total energy should be approximately conserved. The Molecular Dynamics model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_stp_md_MolecularDynamics.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer models. Additional Ejs models for classical mechanics are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Christian, Wolfgang

2008-11-16

31

NASA Astrophysics Data System (ADS)

Results from molecular dynamics simulations often need to be further processed to understand the physics on a larger scale. This paper considers the definitions of momentum and energy fluxes obtained from a control-volume approach. To assess the validity of these defined quantities, two consistency criteria are proposed. As examples, the embedded atom potential and the Tersoff potential are considered. The consistency is verified using analytical and numerical methods.

Wu, Xiaojie; Li, Xiantao

2015-01-01

32

Monoacylglycerol lipase (MAGL) is one of the key enzymes of the endocannabinoid system (ECS). It hydrolyzes one of the major endocannabinoid, 2-arachidonoylglycerol (2-AG), an endogenous full agonist at G protein coupled cannabinoid receptors CB1 and CB2. Numerous studies showed that MGL inhibitors are potentially useful for the treatment of pain, inflammation, cancer and CNS disorders. These provocative findings suggested that pharmacological inhibition of MAGL function may confer significant therapeutic benefits. In this study, we presented hybrid ligand and structure-based approaches to obtain a novel set of virtual leads as MAGL inhibitors. The constraints used in this study, were Glide score, binding free energy estimates and ADME properties to screen the ZINC database, containing approximately 21 million compounds. A total of seven virtual hits were obtained, which showed significant binding affinity towards MAGL protein. Ligand, ZINC24092691 was employed in complex form with the protein MAGL, for molecular dynamics simulation study, because of its excellent glide score, binding free energy and ADME properties. The RMSD of ZINC24092691 was observed to stay at 0.1 nm (1 Å) in most of the trajectories, which further confirmed its ability to inhibit the protein MAGL. The hits were then evaluated for their ability to inhibit human MAGL. The compound ZINC24092691 displayed the noteworthy inhibitory activity reducing MAGL activity to 21.15% at 100 nM concentration, with an IC50 value of 10 nM. PMID:25011912

Afzal, Obaid; Kumar, Suresh; Kumar, Rajiv; Firoz, Ahmad; Jaggi, Manu; Bawa, Sandhya

2014-08-15

33

An interatomic potential model for Si-Br systems has been developed for performing classical molecular dynamics (MD) simulations. This model enables us to simulate atomic-scale reaction dynamics during Si etching processes by Br{sup +}-containing plasmas such as HBr and Br{sub 2} plasmas, which are frequently utilized in state-of-the-art techniques for the fabrication of semiconductor devices. Our potential form is based on the well-known Stillinger-Weber potential function, and the model parameters were systematically determined from a database of potential energies obtained from ab initio quantum-chemical calculations using GAUSSIAN03. For parameter fitting, we propose an improved linear scheme that does not require any complicated nonlinear fitting as that in previous studies [H. Ohta and S. Hamaguchi, J. Chem. Phys. 115, 6679 (2001)]. In this paper, we present the potential derivation and simulation results of bombardment of a Si(100) surface using a monoenergetic Br{sup +} beam.

Ohta, H.; Iwakawa, A.; Eriguchi, K.; Ono, K. [Department of Aeronautics and Astronautics, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501 (Japan)

2008-10-01

34

Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations, both classical and Car-Parrinello, have been carried out to investigate ubiquinone (UQ), a proton mediator in both oxidative and photo-phosphorylation. The main objectives have been to follow the dynamics of methoxy groups, conformation of the tail with respect to the ring, hydration and hydrogen bond structure around UQ. The methoxy groups are found to be able to rotate fairly freely. The tail in both UQ and UQ - is approximately perpendicular to the ring plane. Only weak hydrogen bonds are formed between the neutral form of ubiquinone and water molecules in the solvent, while the anionic form shows a distinct solute-solvent hydrogen bond structure. We also conclude that anionic UQ can be accurately modelled by molecular mechanics methods, but the conformation of the methoxy groups in neutral UQ can hardly be properly modelled using a standard force field.

Nilsson, J. Arvid; Lyubartsev, Alexander; Eriksson, Leif A.; Laaksonen, Aatto

35

?-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, ?-hemolysin is the principal component in several biotechnological applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technology for DNA sequencing. Through large-scale molecular dynamics simulations, we studied the permeability of the ?-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of ?300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water solution of KCl. Monitoring the fluctuations of the pore structure revealed an asymmetric, on average, cross section of the ?-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of ?-hemolysin and a set of electrostatic potential maps. The selectivity of ?-hemolysin to Cl? was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quantitative agreement with available experimental data. Analyzing trajectories of all water molecule, we computed the ?-hemolysin's osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the ?-hemolysin channel. PMID:15764651

Aksimentiev, Aleksij; Schulten, Klaus

2005-01-01

36

Protein aggregation into insoluble fibrillar structures known as amyloid characterizes several neurodegenerative diseases, including Alzheimer's, Huntington's and Creutzfeldt-Jakob. Transthyretin (TTR), a homotetrameric plasma protein, is known to be the causative agent of amyloid pathologies such as FAP (familial amyloid polyneuropathy), FAC (familial amyloid cardiomiopathy) and SSA (senile systemic amyloidosis). It is generally accepted that TTR tetramer dissociation and monomer partial unfolding precedes amyloid fibril formation. To explore the TTR unfolding landscape and to identify potential intermediate conformations with high tendency for amyloid formation, we have performed molecular dynamics unfolding simulations of WT-TTR and L55P-TTR, a highly amyloidogenic TTR variant. Our simulations in explicit water allow the identification of events that clearly discriminate the unfolding behavior of WT and L55P-TTR. Analysis of the simulation trajectories show that (i) the L55P monomers unfold earlier and to a larger extent than the WT; (ii) the single alpha-helix in the TTR monomer completely unfolds in most of the L55P simulations while remain folded in WT simulations; (iii) L55P forms, early in the simulations, aggregation-prone conformations characterized by full displacement of strands C and D from the main beta-sandwich core of the monomer; (iv) L55P shows, late in the simulations, severe loss of the H-bond network and consequent destabilization of the CBEF beta-sheet of the beta-sandwich; (v) WT forms aggregation-compatible conformations only late in the simulations and upon extensive unfolding of the monomer. These results clearly show that, in comparison with WT, L55P-TTR does present a much higher probability of forming transient conformations compatible with aggregation and amyloid formation. PMID:19937650

Rodrigues, J Rui; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

2010-02-01

37

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

Guarini, E.; Barocchi, F. [Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Sampoli, M. [Dipartimento di Energetica, Universita di Firenze, via S. Marta 3, I-50139 Firenze (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Venturi, G. [CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Bafile, U. [Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino (Italy)

2007-10-19

38

Schistosomiasis, a disease caused by helminth parasites of genus Schistosoma. Its treatment intensively depends on single drug, praziquantel which increases the risk of development of drug-resistant parasite. Inhibitors of human HDAC are profoundly reported as novel anti-cancer drugs and used as new anit-parasitic agents. Schistosoma monsoni class I HDACs are expressed in all stages of life cycle and indicating that this enzyme is most likely a major target for the designing specific inhibitors. In order to find novel target for the treatment of Schistosomiasis, three dimensional structure of SmHDAC1 was generated, using homology modelling. Features of the generated structure, was then deduced with respect to conformation of peptide backbone, local compatibility of the generated structure in terms of energy and molecular dynamics study. Considering these features of the generated structure, we selected all the class 1 inhibitors reported so far, which showed interactions with HDACs. Virtual screening was done using reported inhibitors (70) and using SmHDAC1 and HsHDAC1 as the targets. On the basis of binding affinity and IC50 value, 24th ligand was selected for the molecular docking purpose. In this study, out of all the reported inhibitors, 24th inhibitor (N,8-dihydroxy-8-(naphthalen-2-yl) octanamide zinc id- ZINC13474421) showed better binding with SmHDAC1 (-8.1 kcal/mol) as compared to HsHDAC1 (-6.4 kcal/mol) in terms of binding energy and supported by IC50 value. This paper throws light on the reliable model for further structure based drug designing, concerning SmHDAC1 of S. mansoni. Molecular docking studies highlighted advantages of comparative in silico interaction studies of SmHDAC1 and HsHDAC1. N,8-dihydroxy-8-(naphthalen-2-yl) octanamide can further use for the clinical trial. PMID:25663090

Singh, Raghvendra; Pandey, Paras Nath

2015-03-01

39

Molecular dynamics simulations of the ceramic compound zirconolite (CaZrTi?O?), a potential crystalline wasteform host for plutonium, were carried out for ideal and experimental crystalline forms and a simulated molten ...

Rich, Sarah Celeste

2008-01-01

40

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations are performed to investigate the temperature relaxation between electrons and ions in a fully ionized, dense hydrogen plasma. We used HM (J. P. Hansen and I. R. McDonald) potential and introduced a truncated Coulomb interaction, which can avoid Coulomb catastrophe by choosing an appropriate cutting radius. The calculated results are compared with those from theoretical models (LS, GMS, BPS), whose applicability is also discussed. The effect of the interaction between ions and electrons on the temperature relaxation process is also investigated in the strong collision region. Finally, we discuss the effect of exchange interaction of electrons to the temperature relaxation.

Ma, Qian; Dai, Jiayu; Kang, Dongdong; Zhao, Zengxiu; Yuan, Jianmin; Zhao, Xueqing

2014-12-01

41

Accelerated molecular dynamics methods

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

Perez, Danny [Los Alamos National Laboratory

2011-01-04

42

Molecular dynamics simulations.

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 ?s-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. PMID:25330956

Lindahl, Erik

2015-01-01

43

NASA Astrophysics Data System (ADS)

It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900–1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100–2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860–2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C=C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Perhaps remarkably, but apparently because of electrostatic repulsion, the direction of rotation is the same for both reactions.

Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li; Allen, Roland E.

2015-02-01

44

Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N-H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the C?C double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis. PMID:25188903

Dorotíková, Sandra; Plevová, Kristína; Bu?inský, Lukáš; Mal?ek, Michal; Herich, Peter; Kucková, Lenka; Bobeni?ová, Miroslava; Šoralová, Stanislava; Kožíšek, Jozef; Fronc, Marek; Milata, Viktor; Dvoranová, Dana

2014-10-01

45

NASA Astrophysics Data System (ADS)

Molecular dynamics simulation of annular flow boiling in a nanochannel is numerically investigated. In this research, an annular flow model is developed to predict the superheated flow boiling heat transfer characteristics in a nanochannel. To characterize the forced annular boiling flow in a nanochannel, an external driving force overrightarrow {F}_{{ext}} ranging from 1 to 12 PN (PN = pico newton) is applied along the flow direction to inlet fluid particles during the simulation. Based on an annular flow model analysis, it is found that saturation condition and superheat degree have great influences on the liquid-vapor interface. Also, the results show that due to the relatively strong influence of the surface tension in small channels, the interface between the liquid film and the vapor core is fairly smooth, and the mean velocity along the stream-wise direction does not change anymore. Also, it is found that the heat flux values depend on the boundary conditions. Finally, the Green-Kubo formula is used to calculate the thermal conductivity of liquid Argon. The simulations predict thermal conductivity of liquid Argon quite well.

Semiromi, D. Toghraie; Azimian, A. R.

2012-01-01

46

NASA Astrophysics Data System (ADS)

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

47

NASA Astrophysics Data System (ADS)

A new pair-potential energy function of ammonia has been determined via the inversion of reduced viscosity collision integrals and fitted to obtain a Hartree-Fock dispersion (HFD)-like potential form. The pair-potential reproduces the second virial coefficient, viscosity, thermal conductivity, and self-diffusion coefficient of ammonia in a good accordance with experimental data over wide ranges of temperatures. Molecular dynamics (MD) simulation has been also performed to obtain pressure, self-diffusion coefficient, and radial distribution function of fluid ammonia at different temperatures and densities using the calculated HFD-like pair-potential. To take higher-body forces into account, three-body potential of Hauschild and Prausnitz (1993) [19] extended as a function of density and temperature and used with the HFD-like potential to improve the prediction of the pressures of fluid ammonia without requiring an expensive three-body calculation. The results are in a good agreement with experiment and literature values.

Abbaspour, Mohsen

2011-11-01

48

Molecular dynamics simulation of aluminium diffusion in decagonal quasicrystals

Molecular dynamics simulation of aluminium diffusion in decagonal quasicrystals Stephen Hocker- tigated by molecular dynamics simulations. Results obtained with newly developed EAM potentials are determined with molecular statics simulations. The qualitative behaviour of the dynamics is also confirmed

GÃ¤hler, Franz

49

The dynamics of structural relaxation of NO doped Kr solids on electronic excitation of the NO molecule has been characterized by molecular dynamics simulations and by normal and hyperspherical mode analysis, with special emphasis on the effects of the anisotropy of the Kr-NO interaction which has been modeled by ab initio potential energy surfaces (PESs). The time evolution of the

Juan Carlos Castro Palacio; Jesús Rubayo-Soneira; Andrea Lombardi; Vincenzo Aquilanti

2008-01-01

50

Molecular Dynamics modeling of O2/Pt(111) gas-surface interaction using the ReaxFF potential

NASA Astrophysics Data System (ADS)

We studied adsorption dynamics of O2 on Pt(111) using Molecular Dynamics (MD) simulations with the ab initio based reactive force field ReaxFF. We found good quantitative agreement with the experimental data at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF Potential Energy Surface (PES) and the progressive suppression of a steering mechanism as the translational kinetic energy (or the molecule's rotational energy) is increased. In the energy range between 0.1 eV and 0.4 eV, the sticking probability increases, similarly to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3, due to an overall less attractive ReaxFF PES compared to experiments and DFT.

Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana

2011-05-01

51

Molecular Dynamics Replicated Data Model

NSDL National Science Digital Library

The Molecular Dynamics Replicated Data Model implements a parallel computer program that uses a 3D Lennard-Jones potential truncated at a distance of three molecular diameters. Each thread computes a portion of the force on each atom and these contributions are summed to compute the total acceleration using the Verlet ODE algorithm. Allocating memory for each thread's avoids the problem of parallel threads simultaneously writing to array elements. The Molecular Dynamics Replicated Data Model was developed using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive.

Christian, Wolfgang

2013-08-30

52

NASA Astrophysics Data System (ADS)

We present a many-body interatomic potential for Pt within the second-moment approximation of the tight-binding model by fitting to the volume dependence of the total energy of the metal, computed by first-principles augmented-plane-wave calculations. This was used, in conjuction with molecular-dynamics simulations, to study the diffusion of Pt adatoms and dimers on Pt(111) surface. The diffusion coefficient of the adatoms and dimers was computed and was found to present Arrhenius behavior. The migration energies and pre-exponential factors for hopping diffusion mechanism were determined as well and compared with experimental data obtained by scanning tunnelling microscopy, field ion microscopy methods and previous calculations. Both quantities were found to be in good agreement with measurements. At high temperatures we have also investigated a concerted exchange adatom diffusion mechanism, where there is a participation of two surface atoms belonging to nearest-neighbour rows.

Papanicolaou, N. I.; Panagiotides, N.

53

NASA Astrophysics Data System (ADS)

Density Functional Theory calculations and Molecular Dynamics with a recently developed potential for W-He were used to evaluate the thermal stability of helium-vacancy clusters (nHe.mv) as well as pure interstitial helium clusters in tungsten. The stability of such objects results from a competitive process between thermal emission of vacancies, self interstitial atoms (SIAs) and helium, depending on the helium-to-vacancy ratio in mixed clusters or helium number in pure interstitial helium clusters. We investigated in particular the thermodynamics and kinetics of self trapping and trap mutation, i.e. the emission of one SIA along with the creation of one vacancy from a vacancy-helium or pure helium object.

Boisse, J.; Domain, C.; Becquart, C. S.

2014-12-01

54

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid. PMID:18624470

Uline, Mark J; Corti, David S

2008-07-01

55

Molecular modeling of hydrate-clathrates via ab initio, cell potential, and dynamic methods

High level ab initio quantum mechanical calculations were used to determine the intermolecular potential energy surface between argon and water, corrected for many- body interactions, to predict monovariant and invariant ...

Anderson, Brian, Ph. D. Massachusetts Institute of Technology

2005-01-01

56

Molecular Dynamics modeling of O2\\/Pt(111) gas-surface interaction using the ReaxFF potential

We studied adsorption dynamics of O2 on Pt(111) using Molecular Dynamics (MD) simulations with the ab initio based reactive force field ReaxFF. We found good quantitative agreement with the experimental data at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence

Paolo Valentini; Thomas E. Schwartzentruber; Ioana Cozmuta

2011-01-01

57

Substructured multibody molecular dynamics.

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.

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

58

Over the years, many techniques for studying molecular reaction dynamics have been developed and fine-tuned to probe chemical dynamics at an ever-increasing level of detail. Unfortunately, this progress has frequently come at the price of high experimental cost and great complexity. In this regard experiments employing direct absorption have a distinct advantage in that they are comparatively simple in setup

Liam M. Duffy

2005-01-01

59

Over the years, many techniques for studying molecular reaction dynamics have been developed and fine-tuned to probe chemical dynamics at an ever-increasing level of detail. Unfortunately, this progress has frequently come at the price of high experimental cost and great complexity. In this regard experiments employing direct absorption have a distinct advantage in that they are comparatively simple in setup

Liam M. Duffy; Liam M

2005-01-01

60

In the present study, we have performed combined molecular dynamics and potential of mean force (PMF) simulations to determine the enzyme-substrate (ES) binding pathway and the corresponding free energy profiles for wild-type butyrylcholinesterase (BChE) binding with (-)/(+)-cocaine and for the A328W/Y332G mutant binding with (-)-cocaine. According to the PMF simulations, for each ES binding system, the substrate first binds with the enzyme at a peripheral anionic site around the entrance of the active-site gorge to form the first ES complex (ES1-like) during the binding process. Further evolution from the ES1-like complex to the nonprereactive ES complex is nearly barrierless, with a free energy barrier lower than 1.0 kcal/mol. So, the nonprereactive ES binding process should be very fast. The rate-determining step of the entire ES binding process is the subsequent evolution from the nonprereactive ES complex to the prereactive ES complex. Further accounting for the entire ES binding process, the PMF-based simulations qualitatively reproduced the relative order of the experimentally derived binding free energies (?G(bind)), although the simulations systematically overestimated the magnitude of the binding affinity and systematically underestimated the differences between the ?G(bind) values. The obtained structural and energetic insights into the entire ES binding process provide a valuable base for future rational design of high-activity mutants of BChE as candidates for an enzyme therapy for cocaine overdose and abuse. PMID:21902185

Huang, Xiaoqin; Zheng, Fang; Zhan, Chang-Guo

2011-09-29

61

We calculate potentials of mean force (PMFs) and mean first passage times for a surfactant to escape a micelle, for both ionic sodium dodecyl sulfate (SDS) and nonionic ethoxylated alcohol (C12E5) micelles using both atomistic and coarse-grained molecular dynamics (MD) simulations. The PMFs are obtained by umbrella sampling and used in a Smoluchowski first-passage-time theory to obtain the times for a surfactant to escape a micelle. The calculated mean first passage time for an SDS molecule to break away from a micelle (with an aggregation number of 60) is around 2 ?s, which is consistent with previous experimental measurements of the "fast relaxation time" for exchange of surfactants between the micellar phase and the bulk solvent. The corresponding escape time calculated for a nonionic ethoxylated alcohol C12E5, with the same tail length as SDS, is 60 ?s, which is significantly longer than for SDS primarily because the PMF for surfactant desorption is about 3kT smaller than for C12E5. We also show that two coarse-grained (CG) force fields, MARTINI and SDK, give predictions similar to the atomistic CHARMM force field for the nonionic C12E5 surfactant, but for the ionic SDS surfactant, the CG simulations give a PMF similar to that obtained with CHARMM only if long-range electrostatic interactions are included in the CG simulations, rather than using a shifted truncated electrostatic interaction. We also calculate that the mean first passage time for an SDS and a C12E5 to escape from a latex binder surface is of the order of milliseconds, which is more than 100 times longer than the time for escape from the micelle, indicating that in latex waterborne coatings, SDS and C12E5 surfactants likely bind preferentially to the latex polymer interface rather than form micelles, at least at low surfactant concentrations. PMID:25560633

Yuan, Fang; Wang, Shihu; Larson, Ronald G

2015-02-01

62

Articaine, as a local anesthetic drug has been simulated in neutral and charged forms, and its interaction with the dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane is investigated by molecular dynamics simulation using GROMACS software. In order to obtain the optimum location of the drug molecules, as they penetrate into the membrane, umbrella sampling is applied and the free energy is calculated. The effect of protein binding to DMPC membrane on the process of drug diffusion through the membrane is considered. Five simulation systems are designed and by applying the potential of mean force, the molecular dynamics simulation on the system is performed. In light of the obtained results, the electrostatic potential, variation of lipid bilayer's order parameter and the diffusion coefficient of drug are discussed. PMID:23798311

Amjad-Iranagh, Sepideh; Yousefpour, Abbas; Haghighi, Parto; Modarress, Hamid

2013-09-01

63

We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence

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

2006-01-01

64

NAMD Scalable Molecular Dynamics

NSDL National Science Digital Library

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.

65

FPGA Acceleration of Discrete Molecular Dynamics Simulation

' & $ % FPGA Acceleration of Discrete Molecular Dynamics Simulation Joshua Model Thesis submitted UNIVERSITY COLLEGE OF ENGINEERING Thesis FPGA Acceleration of Discrete Molecular Dynamics Simulation Acceleration of Discrete Molecular Dynamics Simulation Joshua Model ABSTRACT Molecular dynamics simulation

Herbordt, Martin

66

We demonstrate a validation of the intermolecular pair potential model of SiH(4), which is constructed from ab initio molecular-orbital calculations and expressed as the sum of the exponential and the London dispersion terms. The saturated liquid densities of SiH(4) are calculated for temperatures from 100 to 225 K by molecular-dynamics (MD) simulation. The average deviation between the experiment and the MD simulation using the present potential model is 3.9%, while the deviations exceed 10% for other well-known potential models such as the five-center Lennard-Jones (LJ) model. Subsequently, the shear viscosity, the thermal conductivity, and the self-diffusion coefficient of liquid SiH(4) are calculated by an equilibrium MD simulation with the Green-Kubo formula from 100 to 225 K. The average deviations from experiment are 11.8% and 13.7% for the shear viscosity and the thermal conductivity, respectively. Comparing the present model with an empirical one-center LJ model, it turns out that the rotational energy transfer through the intermolecular potential energy, which comes from the anisotropic potential energy, plays an important role in the thermal conductivity of liquid SiH(4). These results indicate that the present intermolecular potential model has an ability to give realistic pictures for liquid SiH(4) through molecular simulations. PMID:16008456

Sakiyama, Yukinori; Takagi, Shu; Matsumoto, Yoichiro

2005-06-15

67

Effect of pressure on molecular photodissociation in matrices: Molecular dynamics simulations of Cl molecular dynamics simulations were carried out. The potentials used were accurate enough to reproduce, in Xe R. Alimi Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics

Apkarian, V. Ara

68

The dependence of spallation neutron production double-differential cross sections on the density of the quantum molecular dynamics potential is investigated in p+Al, Fe, Zr, and Pb reactions at 1.2 GeV. It is shown that the cascade component of the neutron spectra is largely unaffected by the parameters of the density-dependent potential. As for the evaporative part (<20 MeV), some differences are marked only for Pb. Calculated results with a Skyrme-type equation of state of K=300 MeV reproduce the neutron spectra for the reactions under study.

Abdel-Waged, Khaled [Umm Al-Qura University, Faculty of Applied Science, Physics Department, Makkah Unit 126, P.O. Box 7047 (Saudi Arabia)

2006-09-15

69

NASA Astrophysics Data System (ADS)

The parameter sets of the ReaxFF potential distributed with the open source, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code, is validated for simulating crystal RDX. These parameters are used to model crystal RDX and obtain its unit cell size and bulk modulus. It is seen that the parameters supplied with LAMMPS (5-April, 2011 release) do not reproduce the unit cell size and bulk modulus of crystal RDX as reported by experiments and by other simulations using the ReaxFF potential. The simulation method and relevant parts of the LAMMPS code implementing the method has been earlier validated for Cu. We conclude that either the parameter sets provided with the LAMMPS distribution or its implementation of the ReaxFF potential are not suitable for modeling crystal RDX.

Warrier, M.; Pahari, P.; Chaturvedi, S.

2012-07-01

70

NASA Astrophysics Data System (ADS)

Over the years, many techniques for studying molecular reaction dynamics have been developed and fine-tuned to probe chemical dynamics at an ever-increasing level of detail. Unfortunately, this progress has frequently come at the price of high experimental cost and great complexity. In this regard experiments employing direct absorption have a distinct advantage in that they are comparatively simple in setup and they probe nascent product distributions directly. Even though the low product number densities in molecular-beam experiments put severe constraints on the noise and sensitivity requirements of detectors, Nesbitt and co-workers [J. Chem. Phys. 86, 3151 (1987); Rev. Sci. Instrum. 58, 807 (1987); J. Chem. Phys. 85, 4890 (1986); J. Chem. Phys. 107, 5661 (1997); Chem. Phys. Lett. 258, 207 (1996)] have demonstrated the use of direct infrared absorption in a variety of molecular reaction dynamics studies. In analogous experiments, this article explores the use of millimeter- and submillimeter-wavelength radiation in direct absorption experiments in a molecular beam. The comparatively simple and inexpensive setup demonstrates the utility of combining new commercial solid-state millimeter/submillimeter-wavelength sources with hot-electron bolometer detectors to directly probe parent and product hyperfine rovibronic levels and their Doppler-resolved velocity distributions in a molecular beam. For example, in open-shell products with nuclear spin, the ultrahigh energy resolution of the rotational spectroscopy easily resolves nuclear quadrupole hyperfine structure and lambda doublets in both ground and excited spin-orbit states as well as in ground and excited vibrational levels. Two molecular beam examples are given: (1) detection of "hyper-rovibronic" structure in ClO (?? =3/2,1/22, ? =0-8, J =1 1/2-7 1/2, ?,F) following the mode-specific photodissociation of OClO (AA22?XB12, ?1=14-15), and (2) coherent transient absorption of HCN following the 266 nm photodissociation of sym-triazine/argon clusters.

Duffy, Liam M.

2005-09-01

71

An n-body potential is constructed for the Cu-Ti-Hf ternary metal system under a recently proposed formalism named long-range empirical potential. Applying the proven relevant Cu-Ti-Hf potential, molecular dynamics simulations are carried out using solid solution model to compare the relative stability of the crystalline solid solution versus its disordered counterpart as a function of solute concentration. The simulation results not only reveal that the physical origin of the crystal-to-amorphous transition is the collapse of the crystalline lattice, while the solute atoms exceed the critical value, but also predict a region in the composition triangle energetically favored for the Cu-Ti-Hf ternary metallic glass formation. Interestingly, the prediction directly from the n-body potential is supported by the experimental observations and is in accordance with the so-called structural difference rule. PMID:20597519

Liang, S H; Dai, Y; Li, J H; Liu, B X

2010-07-29

72

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419

Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R.; Pujol, Céline; Sankaran, Banu; Bliska, James B.; Amaro, Rommie E.; Goulding, Celia W.

2011-01-01

73

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419

Torres, Rodrigo; Swift, Robert V; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R; Pujol, Céline; Sankaran, Banu; Bliska, James B; Amaro, Rommie E; Goulding, Celia W

2011-01-01

74

Brittle and ductile fracture of semiconductor nanowires --molecular dynamics simulations

Brittle and ductile fracture of semiconductor nanowires -- molecular dynamics simulations Keonwook is studied by Molecular Dynamics simulations using sev- eral inter-atomic potential models. While someÂ15, 11Â21 May 2007, 2169Â2189 #12;Contents 1 Introduction 3 2 Molecular dynamics simulations 4 2

Cai, Wei

75

Molecular Dynamics Calculations

NASA Technical Reports Server (NTRS)

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 winning videos in a competition held at the meeting of the American Physical Society's Division of Fluid Dynamics, held in Atlanta, Georgia, in November 1994. Of great interest was the result that in every shock there were a few high-speed precursor particles racing ahead of the shock, carrying information about its impending arrival. Most recently, Dr. Woo has been applying molecular dynamics techniques to the problem of determining the drag produced by the space station truss structure as it flies through the thin residual atmosphere of low-Earth orbit. This problem is made difficult by the complex structure of the truss and by the extreme supersonic nature of the flow. A fully filled section of the truss has already been examined, and drag predictions have been made. Molecular dynamics techniques promise to make realistic drag calculations possible even for very complex partially filled truss segments flying at arbitrary angles.

1996-01-01

76

Scalable Molecular Dynamics with NAMD

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

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

77

NASA Astrophysics Data System (ADS)

Excited-state quantum mechanics/molecular mechanics molecular dynamics simulations are performed, to examine the solvent effects on the fluorescence spectra of aqueous formaldehyde. For that purpose, the analytical energy gradient has been derived and implemented for the linear-response time-dependent density functional theory (TDDFT) combined with the effective fragment potential (EFP) method. The EFP method is an efficient ab initio based polarizable model that describes the explicit solvent effects on electronic excitations, in the present work within a hybrid TDDFT/EFP scheme. The new method is applied to the excited-state MD of aqueous formaldehyde in the n-?* state. The calculated ?*?n transition energy and solvatochromic shift are in good agreement with other theoretical results.

Minezawa, Noriyuki; De Silva, Nuwan; Zahariev, Federico; Gordon, Mark S.

2011-02-01

78

Over the years, many techniques for studying molecular reaction dynamics have been developed and fine-tuned to probe chemical dynamics at an ever-increasing level of detail. Unfortunately, this progress has frequently come at the price of high experimental cost and great complexity. In this regard experiments employing direct absorption have a distinct advantage in that they are comparatively simple in setup and they probe nascent product distributions directly. Even though the low product number densities in molecular-beam experiments put severe constraints on the noise and sensitivity requirements of detectors, Nesbitt and co-workers [J. Chem. Phys. 86, 3151 (1987); Rev. Sci. Instrum. 58, 807 (1987); J. Chem. Phys. 85, 4890 (1986); J. Chem. Phys. 107, 5661 (1997); Chem. Phys. Lett. 258, 207 (1996)] have demonstrated the use of direct infrared absorption in a variety of molecular reaction dynamics studies. In analogous experiments, this article explores the use of millimeter- and submillimeter-wavelength radiation in direct absorption experiments in a molecular beam. The comparatively simple and inexpensive setup demonstrates the utility of combining new commercial solid-state millimeter (submillimeter)-wavelength sources with hot-electron bolometer detectors to directly probe parent and product hyperfine rovibronic levels and their Doppler-resolved velocity distributions in a molecular beam. For example, in open-shell products with nuclear spin, the ultrahigh energy resolution of the rotational spectroscopy easily resolves nuclear quadrupole hyperfine structure and lambda doublets in both ground and excited spin-orbit states as well as in ground and excited vibrational levels. Two molecular beam examples are given: (1) detection of 'hyper-rovibronic' structure in ClO ({sup 2}{pi}{sub {omega}}{sub =3/2l,12,{nu}}=0-8,J=1{sup 1/2})-7{sup 1/2}),{lambda},F) following the mode-specific photodissociation of OClO (A{sup 2}A{sub 2}<-X{sup 2}B{sub 1},{nu}{sub 1}=14-15), and (2) coherent transient absorption of HCN following the 266 nm photodissociation of sym-triazine/argon clusters.

Duffy, Liam M. [Department of Chemistry and Biochemistry, University of North Carolina Greensboro at Greensboro, North Carolina 27402-6170 (United States)

2005-09-15

79

Molecular dynamics simulations

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

Alder, B.J.

1985-07-01

80

One of the most stringent tests for chemical accuracy of a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation method would be to directly compare the calculated vibrational spectra with the corresponding experimental results. Here, the applicability of hybrid QM/effective fragment potential (EFP) to the simulations of methanol infrared spectra is investigated in detail. It is demonstrated that the QM/EFP simulations in combination with time correlation function theory yield not only the fundamental transition bands but also the major overtone and combination bands of methanol dissolved in water in both mid- and near-IR regions. This clearly indicates that the QM/EFP-molecular dynamics can be a viable way of obtaining an anharmonic infrared spectrum that provides information on solvatochromic frequency shifts and fluctuations, solute-solvent interaction-induced dephasing, and anharmonic coupling effects on vibrational spectra of aqueous solutions. We anticipate that the computational protocol developed here can be effectively used to simulate both one- and two-dimensional vibrational spectra of biomolecules and chemically reactive systems in condensed phases. PMID:22913548

Ghosh, Manik Kumer; Lee, Jooyong; Choi, Cheol Ho; Cho, Minhaeng

2012-09-13

81

Virtual Molecular Dynamics Laboratory (VMDL)

NSDL National Science Digital Library

The Virtual Molecular Dynamics Laboratory is a software and curriculum package that enables students to work with research quality molecular dynamics simulations. Users can easily visualize atomic motion, manipulate atomic interactions, and quantitatively investigate the resulting macroscopic properties of biological, chemical, and physical systems.

Center for Polymer Studies

82

Molecular dynamics simulations of planar elongational flow in a nematic liquid crystal model system based on the Gay-Berne fluid were undertaken by applying the SLLOD equations of motion with an elongational velocity field or strain rate. In order to facilitate the simulation, Kraynik-Reinelt periodic boundary conditions allowing arbitrarily long simulations were used. A Lagrangian constraint algorithm was utilized to fix the director at different angles relative to the elongation direction, so that the various pressure tensor elements could be calculated as a function of this angle. This made it possible to obtain accurate values of the shear viscosities which were found to agree with results previously obtained by shear flow simulations. The torque needed to fix the director at various angles relative to the elongation direction was evaluated in order to determine the stable orientation of the director, where this torque is equal to zero. This orientation was found to be parallel to the elongation direction. It was also noted that the irreversible entropy production was minimal when the director attained this orientation. Since the simulated system was rather large and fairly long simulation runs were undertaken it was also possible to study the cross coupling between the strain rate and the order tensor. It turned out to be very weak at low strain rates but at higher strain rates it could lead to break down of the liquid crystalline order. PMID:25523414

Sarman, Sten; Laaksonen, Aatto

2015-01-21

83

Molecular Dynamics (MD) Gas Module

NSDL National Science Digital Library

This simulation consists of a single-component system of particles that interact as either ideal gas particles with no intermolecular potential or as Lennard-Jones Particles . The system runs NVT Molecular Dynamics utilizing the Berendsen Thermostat. The number of particles, volume and temperature are all user-modifiable variables. Additionally, one can select between non-interacting ideal gas particles or particles that interact via the Lennard-Jones Potential. The system can be changed between Argon and Krypton based on reduced unit variables. The average temperature and pressure are displayed on the screen. Additional information is also provided such simulation model/method description, detailed instructions for running the simulation, tutorials, sample questions, literature examples, and links to other relevant data.

Iacovella, Christopher R.

2007-12-10

84

Variational Molecular Dynamics

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. We show that within this framework it is possible to simulate on a small computer cluster conformational reactions as complex as protein folding, using state-of-the-art all-atom force fields in explicit solvent. The same approach also yields the potential of mean-force for reaction coordinates, the reaction rate and transition path time. For illustration and validation purposes, we test this method against the results of protein folding MD simulations which were obtained on the Anton supercomputer, using the same all-atom force field. We find that our approach yields consistent results at a computational cost which is many orders of magnitude smaller than that required by standard MD simulations.

S. a Beccara; P. Faccioli

2014-05-23

85

Non-relativistic de Broglie-Bohm theory describes particles moving under the guidance of the wave function. In de Broglie's original formulation, the particle dynamics is given by a first-order differential equation. In Bohm's reformulation, it is given by Newton's law of motion with an extra potential that depends on the wave function--the quantum potential--together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm's formulation of the de Broglie-Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.

Sheldon Goldstein; Ward Struyve

2014-11-05

86

NASA Astrophysics Data System (ADS)

Non-relativistic de Broglie–Bohm theory describes particles moving under the guidance of the wave function. In de Broglie?s original formulation, the particle dynamics is given by a first-order differential equation. In Bohm?s reformulation, it is given by Newton?s law of motion with an extra potential that depends on the wave function—the quantum potential—together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm?s formulation of the de Broglie–Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.

Goldstein, Sheldon; Struyve, Ward

2015-01-01

87

Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 ?m and 0.8 ?m regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.

Larcher, G.; Tran, H., E-mail: ha.tran@lisa.u-pec.fr; Schwell, M.; Chelin, P.; Landsheere, X.; Hartmann, J.-M. [Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA, CNRS UMR 7583), Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France)] [Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA, CNRS UMR 7583), Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France); Hu, S.-M. [Hefei National Laboratory for Sciences at Microscale, University of Science and Technology of China, 230026 Hefei (China)] [Hefei National Laboratory for Sciences at Microscale, University of Science and Technology of China, 230026 Hefei (China)

2014-02-28

88

Two-phase molecular dynamics simulations employing a Monte Carlo volume sampling method were performed using an ab initio based force field model parameterized to reproduce quantum-mechanical dimer energies for methanol and 1-propanol at temperatures approaching the critical temperature. The intermolecular potential models were used to obtain the binodal vapor-liquid phase dome at temperatures to within about 10 K of the critical temperature. The efficacy of two all-atom, site-site pair potential models, developed solely from the energy landscape obtained from high-level ab initio pair interactions, was tested for the first time. The first model was regressed from the ab initio landscape without point charges using a modified Morse potential to model the complete interactions; the second model included point charges to separate Coulombic and dispersion interactions. Both models produced equivalent phase domes and critical loci. The model results for the critical temperature, density, and pressure, in addition to the sub-critical equilibrium vapor and liquid densities and vapor pressures, are compared to experimental data. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here. PMID:22191893

Patel, Sonal; Wilding, W Vincent; Rowley, Richard L

2011-12-21

89

NASA Astrophysics Data System (ADS)

We have evaluated interatomic potentials of Cu, Au and Cu-Au 0953-8984/10/48/018/img9 ordered alloys in the framework of the second-moment approximation to the tight-binding theory by fitting to the volume dependence of the total energy of these materials computed by first-principles augmented-plane-wave calculations. We have applied this scheme to calculate the bulk modulus and elastic constants of the pure elements and alloys and we have obtained a good agreement with experiment. We also have performed molecular-dynamics simulations at various temperatures, deducing the temperature dependence of the lattice constants and the atomic mean square displacements, as well as the phonon density of states and the phonon-dispersion curves of the ordered alloys. A satisfactory accuracy was obtained, comparable to previous works based on the same approximation, but resulting from fitting to various experimental quantities.

Papanicolaou, N. I.; Kallinteris, G. C.; Evangelakis, G. A.; Papaconstantopoulos, D. A.; Mehl, M. J.

1998-12-01

90

Reactive Force Field & Molecular Dynamics Simulations

: Parallel reactive molecular dynamics (MD) RMD ReaxFF Â· Applications: 1. Combustion of aluminum Â· Large scale (multimillion atoms) Â· Long time (nanosecond) #12;Reactive force field (RMD & ReaxFF (ReaxFF) #12;Classification of ReaxFF Potential Bonded Non-bonded E = Elp + Eover + Eunder + Ebond

Southern California, University of

91

VMD: Visual molecular dynamics

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

William Humphrey; Andrew Dalke; Klaus Schulten

1996-01-01

92

MDLab: A Molecular Dynamics Simulation Prototyping Environment

MDLab: A Molecular Dynamics Simulation Prototyping Environment Trevor Cickovski1 ,Santanu; Simulation], 83.10.Mj [Molecular dynamics, Brownian dynamics], 83.10.Rs [Computer simulation of molecular submitted to Elsevier 10 July 2009 #12;1 Introduction Molecular dynamics (MD) simulation propagates

Izaguirre, JesÃºs A.

93

Stochastic molecular dynamics: A combined Monte Carlo and molecular dynamics technique techniques--Monte Carlo and molecular dynamics--has their own advantage. The molecular dynamics method can to cover the important states of the system in an efficient manner. In recent years the molecular dynamics

Attard, Phil

94

Molecular dynamics simulations of supramolecular polymer rheology

Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential

Zhenlong Li; Hadrian Djohari; Elena E. Dormidontova

2010-01-01

95

interaction potential models for pure alkanes D. K. Dysthe,a) A. H. Fuchs, and B. Rousseau Laboratoire de of the fluid.7 We therefore find it timely to evaluate the alkane models that are most frequently used and most

Dysthe, Dag Kristian

96

NASA Astrophysics Data System (ADS)

A molecular dynamics calculation on aqueous solution of urea has been carried out using constant temperature technique. The total number of molecules was 216, one of which was urea and the temperature was set to 298.15 K and an experimental value was used for the density. For water-water interaction, the MCY (Matsuoka-Clementi-Yoshimine) potential was used, whereas a new potential function was determined for urea-water interaction from SCF LCAO calculations for more than 800 different dimeric configurations with an STO-3G basis set and subsequent multiparameter fitting of the MO results thus obtained to an appropriate functional form by a nonlinear optimization method. The molecular dynamics calculation has been carried out up to 64 000 time steps and from the final 40 000 time steps, thermodynamic quantities, structural and energetic distribution functions, and time-dependent properties were obtained. The original water structure in the vicinity of urea molecule is slightly changed energetically by incorporation of the urea molecule. However, this energy difference is insignificant for the whole system. Instead of the possibility to form strong hydrogen bonding as estimated from the potential function, it is found that urea molecule could enter into the water structure without any appreciable distortion. This fact was confirmed by the angular dependence of any distribution function around the urea molecule. The hydrophilic region does not show a large energetic stabilization between water molecules and the system is stabilized slightly by including urea-water interaction. In contrast to this, the energy for water molecules in the hydrophobic region (above and below the plane containing urea molecule) becomes lower than that of pure water, although this region is small and water molecules cannot form a strong hydrogen bond with urea. This fact reveals that the role of each functional region, which may be either hydrophobic or hydrophilic, is similar to that of alcohol in aqueous solution, although the whole hydration structure of urea molecule is somewhat different from that of alcohol. Reflecting strong interaction of urea-water, the diffusion coefficient for shell water molecules in the vicinity of urea (within 5 Å from urea molecule) becomes smaller by 10%. Moreover, the hydration structure around urea continues for a long time (16 ps), though the energetic relaxation time is very short.

Tanaka, H.; Touhara, Hidekazu; Nakanishi, Koichiro; Watanabe, Nobuatsu

1984-05-01

97

State-dependent molecular dynamics.

This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics. PMID:25302703

Yang, Ciann-Dong; Weng, Hung-Jen

2014-01-01

98

Quantum dynamics via adiabatic ab initio centroid molecular dynamics

NASA Astrophysics Data System (ADS)

The ab initio path integral simulation method is combined with centroid molecular dynamics. This unification, and thus extension of these basic techniques, allows for the investigation of the real-time quantum dynamics in chemically complex many-body systems. The theory underlying the proposed ab initio centroid molecular dynamics (AICMD) technique is presented in detail. The real-time propagation of the nuclei is obtained in the quasiclassical approximation within the framework of centroid path integrals. Concurrently, the forces acting on the nuclei are computed from "on the fly" electronic structure calculations based on first-principle techniques such as, e.g., Hohenberg—Kohn—Sham density functional theory. AICMD can be considered as a quasiclassical generalization of standard Car—Parrinello ab initio molecular dynamics. At the same time, AICMD preserves the virtues of the ab initio path integral technique to generate exact time-independent quantum equilibrium averages. AICMD is well suited to investigate, in a quasiclassical sense, the real-time evolution of molecular quantum systems with complex interactions which cannot be satisfactorily represented by simple model potentials. In particular, the method permits the simulation of the dynamics of chemical reactions including quantum effects. AICMD is applicable to isolated systems in the gas phase such as molecules, clusters or complexes as well as to condensed matter, i.e. molecular liquids or solids.

Marx, Dominik; Tuckerman, Mark E.; Martyna, Glenn J.

1999-05-01

99

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

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

1999-05-21

100

FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS

this problem by creating an explicitly designed FPGA-coprocessor that can be integrated into generic' & $ % FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS YONGFENG GU Dissertation submitted;BOSTON UNIVERSITY COLLEGE OF ENGINEERING Dissertation FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS

Herbordt, Martin

101

Molecular dynamics simulation of zirconia melting

The melting point for the tetragonal and cubic phases of zirconia (ZrO2) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical\\u000a Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over\\u000a the tetragonal phase at high temperatures, ReaxFF also gives approximately the

Sergio Davis; Anatoly B. Belonoshko; Anders Rosengren; Adri C. T. van Duin; Börje Johansson

2010-01-01

102

Grand canonical Molecular Dynamics Simulations

For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.

Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K

2011-01-01

103

A Fast Recursive Algorithm Molecular Dynamics Simulation

A Fast Recursive Algorithm for Molecular Dynamics Simulation A. Jain Jet Propulsion Laboratory: Molecular dynamics, algorithms, simulation. #12; Running head: A Fast Algorithm for MD Simulation Please Pasadena, CA 91109 2 #12; A Fast Recursive Algorithm for Molecular Dynamics Simulation A. Jain, N. Vaidehi

104

Saliency Guided Summarization of Molecular Dynamics Simulations

Saliency Guided Summarization of Molecular Dynamics Simulations Robert Patro1 , Cheuk Yiu Ip1,ipcy,varshney}@cs.umd.edu Abstract We present a novel method to measure saliency in molecular dynamics simulation data. This saliency exceedingly long timescale molecular dynamics simulations, does not necessarily mean that we are better

Varshney, Amitabh

105

Molecular dynamics investigation of nanoscale cavitation dynamics.

We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ?90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ?20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse. PMID:25527949

Sasikumar, Kiran; Keblinski, Pawel

2014-12-21

106

Molecular dynamics investigation of nanoscale cavitation dynamics

NASA Astrophysics Data System (ADS)

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

Sasikumar, Kiran; Keblinski, Pawel

2014-12-01

107

Ab initio molecular dynamics of hypervelocity chemistry

NASA Astrophysics Data System (ADS)

Resolving chemical dynamics of decomposition of energetic molecules is crucial for understanding detonation initiation in energetic materials and predicting their sensitivity to shock and impact stimuli. We employ Born-Oppenheimer molecular dynamics driven by density-functional methods to identify possible decomposition pathways in nitric esters (including pentaerythritol tetranitrate) and to understand the effect of collision orientation and velocity. Studies of the potential energy surface in the bond-breaking region, unimolecular decomposition, and binary hypervelocity collisions of model nitric esters (methyl and ethyl nitrates) will be reported. Methodological challenges in describing extensive changes in the electronic structure that accompany decomposition will be discussed.

Schweigert, Igor; Dunlap, Brett

2009-03-01

108

Molecular Dynamics Performance JS Model

NSDL National Science Digital Library

The Molecular Dynamics Performance JavaScript Model computes the trajectory of particles acted on by a Lennard-Jones force. This simulation was designed to test the speed of JavaScript for a computationally intensive model. The user can vary the number of particles, the number of frames per second displayed on the computer monitor, and the requested number of Verlet steps between frames. The actual number of Verlet steps per frame is shown. This number will be less than the requested number of steps on slow processors. The Molecular Dynamics Performance JS Model was developed using the Easy Java Simulations (EJS) version 5. It is distributed as a ready-to-run html page and requires only a browser with JavaScript support.

Christian, Wolfgang; Franciscouembre

2013-09-06

109

Molecular Dynamics Adiabatic Piston Model

NSDL National Science Digital Library

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for the article by Eric Gislason and has been approved by the authors and the AJP editor. Initially the piston is held (locked) in place, and the pressures of the gases on each side of the piston are different. When the piston is released it undergoes oscillations that are damped due to collisions of the particles with the piston, and it finally ends up at rest. The final pressures of the two gases are equal, but the final temperatures are typically different. All particles in the Molecular Dynamics Adiabatic Piston model have unit mass and interact through pairwise Leonard-Jones forces. Gas particles interact with the container walls via a spring (Hooke's law) force and this particle-wall interaction is used to move the piston and to compute the pressure. The temperature is computed from the average kinetic energy. The piston position and the temperature and pressure are shown as functions of time in additional windows. The Molecular Dynamics Adiabatic Piston model was created using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_md_AdiabaticPiston.jar file will run the program if Java is installed.

Christian, Wolfgang

2010-07-13

110

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

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

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

2012-01-01

111

Solute sampling of explicit bulk-phase aqueous environments in grand canonical (GC) ensemble simulations suffer from poor convergence due to low insertion probabilities of the solutes. To address this, we developed an iterative procedure involving Grand Canonical-like Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Each iteration involves GCMC of both the solutes and water followed by MD, with the excess chemical potential (?ex) of both the solute and the water oscillated to attain their target concentrations in the simulation system. By periodically varying the ?ex of the water and solutes over the GCMC-MD iterations, solute exchange probabilities and the spatial distributions of the solutes improved. The utility of the oscillating-?ex GCMC-MD method is indicated by its ability to approximate the hydration free energy (HFE) of the individual solutes in aqueous solution as well as in dilute aqueous mixtures of multiple solutes. For seven organic solutes: benzene, propane, acetaldehyde, methanol, formamide, acetate, and methylammonium, the average ?ex of the solutes and the water converged close to their respective HFEs in both 1 M standard state and dilute aqueous mixture systems. The oscillating-?ex GCMC methodology is also able to drive solute sampling in proteins in aqueous environments as shown using the occluded binding pocket of the T4 lysozyme L99A mutant as a model system. The approach was shown to satisfactorily reproduce the free energy of binding of benzene as well as sample the functional group requirements of the occluded pocket consistent with the crystal structures of known ligands bound to the L99A mutant as well as their relative binding affinities. PMID:24932136

Lakkaraju, Sirish Kaushik; Raman, E Prabhu; Yu, Wenbo; MacKerell, Alexander D

2014-06-10

112

From molecular dynamics to Brownian dynamics

Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane. PMID:25002825

Erban, Radek

2014-01-01

113

NMR investigations of molecular dynamics

NASA Astrophysics Data System (ADS)

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Palmer, Arthur

2011-03-01

114

Molecular dynamics studies of aromatic hydrocarbon liquids

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

McLaughlin, E.; Gupta, S.

1990-01-01

115

The "Collisions Cube" Molecular Dynamics Simulator.

ERIC Educational Resources Information Center

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)

Nash, John J.; Smith, Paul E.

1995-01-01

116

Molecular Dynamics Simulations of Polymers

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from orientational autocorrelation functions of PS-d_3 were found to agree with NMR measurements.

Han, Jie

1995-01-01

117

Better, Cheaper, Faster Molecular Dynamics

NASA Technical Reports Server (NTRS)

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.

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

2001-01-01

118

Molecular dynamics simulation of surface roughness effects on nanoscale flows

In the present study, a molecular based scheme has been developed for simulating of surface roughness effects on nano- and micro- scale flows. In micro channel flow, there are some differences on the flow friction between roughness and cavitations which are not well studied. In the presented approach, based on the Molecular Dynamics Simulation (MD), the Lennard–Jones potential is used

Reza Kamali; Ali Kharazmi

2011-01-01

119

The rotation of F1Fo-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane Fo domain, which is coupled to the ATP-producing F1 domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the “locked” and “open” conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F1Fo-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode. PMID:22942277

Gohlke, Holger; Schlieper, Daniel; Groth, Georg

2012-01-01

120

Anomalous molecular dynamics in the vicinity of a conical intersection

NASA Astrophysics Data System (ADS)

Conical intersections between molecular electronic potential energy surfaces can greatly affect molecular dynamics and chemical properties. Molecular gauge theory is capable of explaining many of these often unexpected phenomena deriving from the physics of the conical intersection. Here we will give an example of anomalous dynamics in the paradigm E × ? Jahn-Teller model, which does not allow for a simple explanation in terms of standard molecular gauge theory. By introducing a dual gauge theory, we unwind this surprising behavior by identifying it with an intrinsic spin Hall effect. Thus, this work link knowledge of condensed-matter theories with non-adiabatic molecular dynamics. Furthermore, via ab initio calculations of potential energy surfaces, the findings are as well demonstrated to appear in a realistic system such as the Li3 molecule.

Larson, J.; Nour Ghassemi, E.; Larson, Å.

2013-02-01

121

Molecular Dynamics Simulations of Crystal Copper: Bulk Modulus and Shocks

NASA Astrophysics Data System (ADS)

Molecular dynamics is used to study the response of single crystal copper target to impacts by single crystal copper at velocities in the range 1 km/s to 3 km/s. The Embedded Atom Method (EAM) potential by Foiles et al. for Cu [1] was used in the simulation. The potential and its implementation in the open source, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) [2] was verified by reproducing the experimental values of bulk modulus of Cu. The shock velocity (us) as a function of particle velocity (up) matches published experimental and molecular dynamic simulations results.

Warrier, M.; Rawat, S.; Chaturvedi, S.

2011-07-01

122

Radiation in molecular dynamic simulations

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

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

2008-10-13

123

Molecular dynamics simulation of zirconia melting

NASA Astrophysics Data System (ADS)

The melting point for the tetragonal and cubic phases of zirconia (ZrO2) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over the tetragonal phase at high temperatures, ReaxFF also gives approximately the correct melting point, around 2900 K, whereas the Lewis-Catlow estimate is above 6000 K.

Davis, Sergio; Belonoshko, Anatoly B.; Rosengren, Anders; van Duin, Adri C. T.; Johansson, Börje

2010-10-01

124

Unified approach for molecular dynamics and density-functional theory

We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential approximation, thereby making possible the simulation of both covalently bonded and metallic systems. In addition it permits the application of density-functional theory to much larger systems than previously feasible. The new

R. Car; M. Parrinello

1985-01-01

125

Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA

Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA S.B. Sane* , T. Cagin computational methods has offered the potential for "molecular dynamics" simulations to predict the mechanical of temperature using molecular dynamics simulation techniques. There have been a few efforts to study

Ã?agin, Tahir

126

was predicted using non-equilibrium molecular dynamics simulations. The Stillinger-Weber potential for silicon predicted by molecular dynamics simulations for spherical pores (present study) as well as for cylindricalScaling laws for thermal conductivity of crystalline nanoporous silicon based on molecular dynamics

Pilon, Laurent

127

Molecular dynamics simulation of aluminium di#usion in decagonal quasicrystals

Molecular dynamics simulation of aluminium di#usion in decagonal quasicrystals Stephen HockerÂ tigated by molecular dynamics simulations. Results obtained with newly developed EAM potentials with molecular statics simulations. The qualitative behaviour of the dynamics is also confirmed by ab

GÃ¤hler, Franz

128

Application of optimal prediction to molecular dynamics

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

Barber IV, John Letherman

2004-12-01

129

Symmetry Reduced Dynamics of Charged Molecular Strands

NASA Astrophysics Data System (ADS)

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

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

2010-09-01

130

Molecular dynamics simulations of nanostructures

NASA Astrophysics Data System (ADS)

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 transitions are found from brittle cleavage to structural transformation-mediated brittle cleavage to ductile failure. Atomistic mechanisms of the unique nano-thermo-mechanical behavior are elucidated as a consequence of surface-structural relaxation, which in particular predicts spontaneous formation of a core/shell structure under tension. The phase diagram resolves controversies between previous experiments and theory, and the predicted `intrinsic' core/shell structure may find novel device applications. Generation of stacking faults (SFs) during the growth of NWs is a major concern for the efficiency of NW-based devices such as solar cells. MD simulation of a [111]-oriented gallium arsenide NW reveals an atomistic mechanism of SF generation. Spatial distribution of the adatom energy on the (111)B top surface exhibits a novel core/shell structure due to the contraction of atomic bonds at the sidewall surfaces, where SFs are preferentially nucleated in the shell. A nucleation growth model incorporating the core/shell mechanism suggests a size and growth-condition controlled approach for SF-free growth of NWs.

Yuan, Zaoshi

131

Optimal prediction in molecular dynamics

Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in order to reduce the number of particles to be tracked in the computations. We consider a model problem, which describes a surface coating process, and show how asymptotic methods can be employed to approximate the high dimensional conditional expectations, which arise in optimal prediction. The thus derived smaller system is compared to the original system in terms of statistical quantities, such as diffusion constants. The comparison is carried out by Monte-Carlo simulations, and it is shown under which conditions optimal prediction yields a valid approximation to the original system.

Benjamin Seibold

2008-08-22

132

NAMD2: Greater Scalability for Parallel Molecular Dynamics

Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application–domain programmers. The

Laxmikant Kalé; Robert Skeel; Milind Bhandarkar; Robert Brunner; Attila Gursoy; Neal Krawetz; James Phillips; Aritomo Shinozaki; Krishnan Varadarajan; Klaus Schulten

1999-01-01

133

Microcanonical Molecular Dynamic Simulations of Au Nanoclusters

In this paper, we study nanoparticles with constituent atoms ranging from dozens to hundreds of them. These types of particles display structural and magnetic properties that strongly depend on the number of constituents N. The metal clusters are important due their interesting properties when compared to bulk materials; hence they have potential technological applications. Specifically, we study the Au nanoclusters through classical molecular dynamics simulations; we analyze the total and potential energy as a function of time. Likewise, we study the geometrical structures of Au Nanocluster corresponding to the lowest energy states at 0 K. We consider the method of microcanonical ensemble, and we carry out computer simulations by operating the XMD software package and the atomistic configuration viewer AtomEye.

H., Karina L D Barturen; Rojas, Justo T

2010-01-01

134

For the first time, the binding of ropinirole hydrochloride (ROP) and aspirin (ASA) to human holo-transferrin (hTf) has been investigated by spectroscopic approaches (fluorescence quenching, synchronous fluorescence, time-resolved fluorescence, three-dimensional fluorescence, UV-vis absorption, circular dichroism, resonance light scattering), as well as zeta potential and molecular modeling techniques, under simulated physiological conditions. Fluorescence analysis was used to estimate the effect of the ROP and ASA drugs on the fluorescence of hTf as well as to define the binding and quenching properties of binary and ternary complexes. The synchronized fluorescence and three-dimensional fluorescence spectra demonstrated some micro-environmental and conformational changes around the Trp and Tyr residues with a faint red shift. Thermodynamic analysis displayed the van der Waals forces and hydrogen bonds interactions are the major acting forces in stabilizing the complexes. Steady-state and time-resolved fluorescence data revealed that the fluorescence quenching of complexes are static mechanism. The effect of the drugs aggregating on the hTf resulted in an enhancement of the resonance light scattering (RLS) intensity. The average binding distance between were computed according to the forster non-radiation energy transfer theory. The circular dichroism (CD) spectral examinations indicated that the binding of the drugs induced a conformational change of hTf. Measurements of the zeta potential indicated that the combination of electrostatic and hydrophobic interactions between ROP, ASA and hTf formed micelle-like clusters. The molecular modeling confirmed the experimental results. This study is expected to provide important insight into the interaction of hTf with ROP and ASA to use in various toxicological and therapeutic processes. PMID:22410420

Kabiri, Mona; Amiri-Tehranizadeh, Zeinab; Baratian, Ali; Saberi, Mohammad Reza; Chamani, Jamshidkhan

2012-01-01

135

Elastic constants of sodium from molecular dynamics

NASA Astrophysics Data System (ADS)

We have performed molecular-dynamics calculations of the adiabatic elastic constants of sodium at three different temperatures, T=198, 299, and 349 K. Our method uses fluctuation formulas appropriate for the microcanonical ensemble which contain the elastic constants. In the simulation we have used a first-principles potential to model the interaction between the sodium atoms. The results, including the shear modulus C44, show good agreement with experiment at all three temperatures. We have analyzed the contributions to the elastic constants from different types of terms appearing in the fluctuation formula and compared these contributions to other model-potential calculations. The volume dependence in the potential has considerable effect on the values of elastic constants. In comparison to some earlier calculations which employed pair potentials with no volume dependence, the fluctuation contributions to elastic constants C11 and C44 are noticeably large (20% of the value of the elastic constants in some cases). We find that the elastic constants do not change by much for the different potential-cutoff ranges employed: 17.85, 23.27, and 27.70 bohrs.

Çagin, Tahir; Ray, John R.

1988-01-01

136

Charmonium with an effective Morse molecular potential

NASA Astrophysics Data System (ADS)

The Morse molecular potential is used for the first time as an effective potential for the overall interaction in charmonium. This procedure allows the calculation of the rotational contributions of P states, the radii of five S states, and an absolute threshold for bound states. The calculation of the latter provides important information on the character of the recently found levels X(3915), X(3940), ?(4040), X(4050), X(4140), ?(4160), X(4160), X(4250), X(4260), X(4350), ?(4415), X(4430), and X(4660).

Everaldo de Souza, Mario

2014-11-01

137

Hydration dynamics in water clusters via quantum molecular dynamics simulations

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 the non-cavity type model. Relaxation associated with cavity collapse presents, however, unique dynamical signatures.

Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

2014-05-28

138

Molecular dynamics simulations of gold-catalyzed growth of silicon bulk crystals and nanowires

ARTICLES Molecular dynamics simulations of gold-catalyzed growth of silicon bulk crystals with AuÂSi liquids is studied by molecular dynamics simulations using an empirical potential fitted of the NW nucleation and growth mechanisms at the atomistic level. Atomistic simulations, such as molecular

Cai, Wei

139

First principles molecular dynamics without self-consistent field optimization

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

Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden)] [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2014-01-28

140

Hypervelocity-impact phenomena via molecular dynamics

NASA Astrophysics Data System (ADS)

Novel molecular-dynamics calculations have been carried out for a hypervelocity impact of a sphere of 683 atoms (a central atom surrounded by 23 coordination shells) hitting a rectangular plate composed of 8000 atoms (five close-packed planes thick). The ratio of the sphere diameter to the plate thickness was chosen to be approximately 2.4, with the velocity of the sphere chosen such that its kinetic energy was roughly 25 times its binding energy, relative to the bottom of the potential well. Under these conditions, the debris cloud generated by the ball after it penetrates the wall is composed mostly of vaporized material. These microscopic results scale hydrodynamically to macroscopic experiments of a lead sphere hitting a lead plate at 6.6 km/s. There are striking similarities between these atomistic calculations and continuum hydrodynamics simulations, as well as notable differences.

Holian, Brad Lee

1987-10-01

141

Hypervelocity-impact phenomena via molecular dynamics

Novel molecular-dynamics calculations have been carried out for a hypervelocity impact of a sphere of 683 atoms (a central atom surrounded by 23 coordination shells) hitting a rectangular plate composed of 8000 atoms (five close-packed planes thick). The ratio of the sphere diameter to the plate thickness was chosen to be approximately 2.4, with the velocity of the sphere chosen such that its kinetic energy was roughly 25 times its binding energy, relative to the bottom of the potential well. Under these conditions, the debris cloud generated by the ball after it penetrates the wall is composed mostly of vaporized material. These microscopic results scale hydrodynamically to macroscopic experiments of a lead sphere hitting a lead plate at u/sub p/ = 6.6 km/s. There are striking similarities between these atomistic calculations and continuum hydrodynamics simulations, as well as notable differences.

Holian, B.L.

1987-10-15

142

Thermal transpiration: A molecular dynamics study

NASA Astrophysics Data System (ADS)

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.

T, Joe Francis; Sathian, Sarith P.

2014-12-01

143

Imaging Ultrafast Dynamics in the Molecular Frame

NASA Astrophysics Data System (ADS)

Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) is a femtosecond photoelectron probe of Molecular Frame ultrafast dynamics in polyatomic molecules. TRCIS makes use of 3D particle timing-imaging detectors for full 3D recoil momentum vector determination of coincident photoions and photoelectrons as a function of time. One vector correlation is particularly interesting as it permits Time-Angle-Energy resolved photoelectron studies from the Molecular Frame rather than the lab frame point of view. An alternate approach to Molecular Frame ultrafast dynamics is to make use non-resonant laser field pre-alignment. Provided that the molecular dynamics are fast compared to rotational dephasing, this method also permits time-resolved Molecular Frame observations. We experimentally demonstrate both these approaches, comparing and contrasting their relative merits.

Stolow, Albert

2009-05-01

144

Phonostat: Thermostatting phonons in molecular dynamics simulations

Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a “phonostat” algorithm ...

Raghunathan, Rajamani

145

Molecular dynamics simulations of supramolecular polymer rheology

NASA Astrophysics Data System (ADS)

Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate ? and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.

Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.

2010-11-01

146

Molecular ions, Rydberg spectroscopy and dynamics

NASA Astrophysics Data System (ADS)

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.

Jungen, Ch.

2015-01-01

147

Molecular Dynamics Simulations of Simple Liquids

ERIC Educational Resources Information Center

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.

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

2004-01-01

148

Multiple time step integrators in ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

149

Multiple time step integrators in ab initio molecular dynamics

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

Luehr, Nathan; Martínez, Todd J. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States) [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); The PULSE Institute, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Markland, Thomas E. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)] [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

2014-02-28

150

Molecular-dynamics investigation of hydrogen hopping in palladium

Diffusive hopping of hydrogen in PdHx has been reexamined with molecular-dynamics (MD) simulations in order to clarify earlier results of Gillan. We obtain the same values for the diffusion coefficient and width Gammaq of the quasielastic neutron scattering function when Gillan's potentials are used, but go beyond Gillan in performing a statistical analysis of the jumps. The analysis shows that

J. W. Culvahouse; Peter M. Richards

1988-01-01

151

Molecular dynamics simulation of shell-symmetric Pd nanoclusters

The melting behaviour of Palladium (Pd) isolated shell-symmetric cubooctahedron and icosahedron nanoclusters, both consisting of 309 atoms, were simulated by Molecular Dynamics (MD) simulation, using the Sutton-Chen many-body potential (SC) for the interaction between the Pd atoms. The thermal, structural and dynamic properties were calculated for the Pd nanoclusters along the heating process. The cubooctahedron nanocluster melts around 1040 K,

Y. Pan; S. Huang; Z. Liu; W. Wang

2005-01-01

152

Molecular-Dynamics Simulations and Density Functional Theory

Molecular-Dynamics Simulations and Density Functional Theory Part 1 - Molecular-Dynamics Simulations 1. Introduction 2. Basics of Molecular-Dynamics Simulations 3. Analyzing the Results 4. Model Simulations of Liquids (Clarendon Press, Oxford 1987). Â· D. C. Rapaport, The Art of Molecular Dynamics

Duisburg-Essen, UniversitÃ¤t

153

Osmosis : a molecular dynamics computer simulation study

NASA Astrophysics Data System (ADS)

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..

Lion, Thomas

154

The Molecular Dynamic Simulation of neutral Argon By Michiel Bosch

The Molecular Dynamic Simulation of neutral Argon Particles By Michiel Bosch Bachelor of Science the Monte Carlo (MC) method. A few years later in 1956 the first Molecular Dynamic (MD) simulation......................................................................................................................... 5 2.1 Molecular Simulations Techniques

Luding, Stefan

155

A Review of Wave Packet Molecular Dynamics

Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple approximations enabling computationally feasibility. Wave packet molecular dynamics (WPMD) provides a simple framework for simulating time-dependent quantum plasmas. Here, this method is reviewed. The different variants of WPMD are shown and compared and their validity is discussed.

Paul E. Grabowski

2014-08-09

156

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

NASA Astrophysics Data System (ADS)

Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

2010-12-01

157

NVU dynamics. III. Simulating molecules at constant potential energy.

This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, ibid. 135, 104102 (2011)], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nose?-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems. PMID:23277922

Ingebrigtsen, Trond S; Dyre, Jeppe C

2012-12-28

158

Molecular dynamics simulations on the hydration of fluoroalcohols

Molecular dynamics (MD) calculations have been carried out for aqueous solutions of isopropyl alcohol (IPA) and its fluorinated compounds, 1,1,1-trifluoro-2-propanol (TFIPA) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIPA). The simulated systems were canonical ensembles containing 216 molecules in each, one of which was alcohol and the temperature was set to 298.15 K. The MCY (Matsuoka–Clementi–Yoshimine) potential was used for water–water interaction, whereas new potential

Kenichi Kinugawa; Koichiro Nakanishi

1988-01-01

159

NASA Astrophysics Data System (ADS)

Background: Of the two sources of nonlocality in nucleon-nucleus and nucleus-nucleus interactions, knock-on exchange and dynamically generated, almost all papers referring to nonlocality mention only the first. Purpose: Our purpose is threefold: to demonstrate a method for including dynamical nonlocality, for which a simple prescription (like the Perey factor for exchange nonlocality) is unknown, within distorted wave Born approximation (DWBA) calculations; to identify signatures of dynamic nonlocality and illuminate the extent to which the presence of such nonlocality can influence the extraction of spectroscopic information from direct reactions, and more generally, to increase our understanding of nucleus-nucleus interactions. Methods: After reviewing existing indications of dynamically induced nonlocality, DWBA transfer calculations are presented which compare results involving dynamically nonlocal potentials with those involving their local equivalents. The dynamical nonlocal potentials are generated in situ by the presence of channel coupling and the local equivalents are generated by inversion of the corresponding coupled channel elastic S matrix. This method obviates the need for solving integro-differential equations for including nonlocal potentials in DWBA. Results: The coupling of nucleons to collective states of the target nucleus induces dynamical nonlocality in the nucleon-nucleus interaction that has a significant effect on (p ,d) reactions at energies relevant to spectroscopic studies. Conclusions: A method for studying the contribution of dynamically induced nonlocality in nuclear interactions has been demonstrated. Dynamically induced nonlocality should not be overlooked in the analysis of direct reactions. The method can also be applied to dynamic nonlocality due to projectile excitation.

Keeley, N.; Mackintosh, R. S.

2014-10-01

160

Theoretical analysis of dynamic processes for interacting molecular motors

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

161

Method of molecular dynamics in mechanics of deformable solids

NASA Astrophysics Data System (ADS)

The basic principles of the method of molecular dynamics are analyzed. Symplectic difference schemes for the numerical solution of molecular dynamics equations are considered. Stability is studied, and the errors in the energy conservation law, which are induced by using these schemes, are estimated. Equations of mechanics of continuous media are derived by means of averaging over the volume of an atomic system. Expressions for the stress tensor are obtained by using the virial principle and the method of averaging over the volume. The principles of construction of EAM and MEAM potentials of atomic interaction in crystals are analyzed. Two problems of fracture of copper-molybdenum composites are solved by the method of molecular dynamics.

Kiselev, S. P.

2014-05-01

162

Molecular dynamics studies of molecular diffusion in ice Ih

We performed molecular dynamics simulations of the diffusion of interstitial He and H2O in ice Ih and found diffusion hops for these interstitial molecules from a stable site to an adjacent site. By observing the jumps of these diffusing species, we determined the jump frequencies, the crystal orientation dependence of the diffusion coefficients, and the diffusion activation energies. Most jumps

Tomoko Ikeda-Fukazawa; Shinichiro Horikawa; Takeo Hondoh; Katsuyuki Kawamura

2002-01-01

163

Standard Potentials for Non-Even Dynamics

The notion of standard potentials is introduced for a general dynamics. This is a generalization of earlier works of Araki\\u000a and Moriya which is restricted to even dynamics.\\u000a \\u000a Most formulae in the present analysis are the same as the case of even dynamics: The time derivative of a local observable\\u000a is times the sum of commutators with all potentials, and

Huzihiro Araki

2006-01-01

164

Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated state complex reaction dynamics. This paper reports the first application of these new simulation methods1,2 to a real molecular system, the ultrafast photodis- sociation dynamics associated

Miller, William H.

165

Molecular dynamics simulations of ordered alkane chains physisorbed on graphite

Molecular dynamics simulations of ordered alkane chains physisorbed on graphite Reinhard Hentschke molecular axes oriented parallel to the substrate. Here we employ molecular dynamics (MD) simulations to obtain more details on the molecular order and dynamics within the alkane lamellae as a function

Peters, Achim

166

Molecular scale dynamics of large ring polymers.

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

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

167

Molecular dynamics simulation of Li surface erosion and bubble formation

Molecular dynamics simulation of Li surface erosion and bubble formation Z. Insepov *, A. Hassanein Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics devices. Molecular dynamics (MD) method is capable of studying important collision processes and providing

Harilal, S. S.

168

Neutron Star Crust and Molecular Dynamics Simulation

In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.

C. J. Horowitz; J. Hughto; A. Schneider; D. K. Berry

2011-09-23

169

Quantum molecular Dynamics Ronnie Kosloff

demolition if Monotonic Energy Change #12;#12;#12;#12;#12;40 :Chirp Pulses Husimi Plot Frequency Transform #12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;#12;Li2 nuclear dynamics on the E state #12

Kosloff, Ronnie

170

Modeling Propellant Combustion Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Currently, a first-principles theoretical model of self-sustained combustion of solid energetic materials does not exist and consequently the development of new propellants has to be approached from a strictly empirical viewpoint. Without a theoretical framework to guide it, this method remains expensive and time consuming and therefore inefficient. The benefits of a theoretical model are numerous. Primarily, it would offer a systematic way of understanding the seemingly unapproachable combination of physical and chemical reactions inherent in all combustion phenomena. The resulting predictive capabilities would serve as the underlying methods in the development of new propellants. Our model involves the three states of matter as frozen ozone(M.S. Miller, Materials Research Society, Fall meeting (1995).) melts and eventually vaporizes giving oxygen upon decomposition. However, much of the needed thermodynamic and transport properties are unavailable from experiments and therefore, we have appealed to molecular dynamics simulations. Using a Lennard-Jones potential we have been able to obtain thermodynamic and transport properties about the pure components and various mixtures of ozone and oxygen in each phase as well as at the interfaces.

Bembenek, Scott D.; Rice, Betsy M.; Miller, Martin S.

1998-03-01

171

Structural and dynamic properties of calcium aluminosilicate melts: A molecular dynamics study

NASA Astrophysics Data System (ADS)

The structural and dynamic properties of calcium aluminosilicate (CaO-Al2O3)1-x(SiO2)x melts with low silica content, namely, along the concentration ratio R = 1 are studied by classical molecular dynamics. An empirical potential has been developed here on the basis of our previous ab initio molecular dynamics. The new potential gives a description of the structural as well as the dynamics with a good accuracy. The self-intermediate scattering function and associated ?-relaxation times are analyzed within the mode-coupling theory. Our results indicate a decrease of the fragility whose structural origin is a reduction of the number of fivefold coordinated Al atoms and non-bridging oxygen.

Bouhadja, M.; Jakse, N.; Pasturel, A.

2013-06-01

172

Molecular dynamics calculations of nuclear stimulated desorption

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

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

1991-01-01

173

Molecular dynamics calculations of nuclear stimulated desorption

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

Glikman, E.; Kelson, I. (School of Physics and Astronomy, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel)); Doan, N.V. (Centre d'Etudes Nucleaires de Saclay, Cerem-Dtm-Srmp 91191 Gif-sur-Yvette Cedex (France))

1991-09-01

174

Dynamics and Molecular Evolution of Influenza

Dynamics and Molecular Evolution of Influenza Gunnar SigurÃ°sson Hlynur SigurgÃslason JÃ³n Ingi SveinbjÃ¶rnsson #12;The Orthomyxoviridae family Influenza is in the Orthomyxoviridae family. The family contains Influenza A,B,C and the following viruses: Isavirus Infectious salmon anemia virus Atlantic salmon

Goldschmidt, Christina

175

Reaction dynamics in polyatomic molecular systems

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.

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

176

Ab Initio Molecular Dynamics Simulations of Molecular Collisions of Nitromethane

Ab initio molecular dynamics simulations of bimolecular collisions of nitromethane, and collisions of one nitromethane molecule into a cluster of 12 nitromethane molecules have been performed. For the bimolecular simulations we have examined a variety of collision orientations and collision velocities between 6.5 and 12.0 km\\/s. The lowest dissociation threshold velocity found was 7.0 km\\/s for an anti-parallel collision orientation.

Dongqing Wei; Fan Zhang; Tom K. Woo

2002-01-01

177

Molecular Dynamics Simulations of Graphene Oxide Frameworks

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

Zhu, Pan [Rensselaer Polytechnic Institute (RPI)] [Rensselaer Polytechnic Institute (RPI); Sumpter, Bobby G [ORNL] [ORNL; Meunier, V. [Rensselaer Polytechnic Institute (RPI)] [Rensselaer Polytechnic Institute (RPI); Nicolai, Adrien [Rensselaer Polytechnic Institute (RPI)] [Rensselaer Polytechnic Institute (RPI)

2013-01-01

178

Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.

NASA Astrophysics Data System (ADS)

The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.

Fidelis, Krzysztof Andrzej

1990-08-01

179

Molecular dynamics and tunnelling in supramolecular complexes

NASA Astrophysics Data System (ADS)

Inelastic neutron scattering has been used to study molecular tunnelling and intramolecular vibrational modes in several inclusion complexes of calixarenes. In methyl-containing guest molecules the free rotor limit is approached, and the splitting of the librational modes appears to be very sensitive to the details of the particle motion. The experimental spectra are interpreted in the framework of different models, and the potential barriers obtained are compared with molecular mechanics calculations.

Caciuffo, R.; Amoretti, G.; Carlile, C. J.; Ferrero, C.; Geremia, S.; Paci, B.; Prager, M.; Ugozzoli, F.

1997-02-01

180

Warm dense matter through classical molecular dynamics

NASA Astrophysics Data System (ADS)

A classical Molecular Dynamics code has been developed to simulate dense plasmas i.e. neutral systems of interacting ions and electrons. Our goal is to design a tool that relies on a reduced set of microscopic mechanisms in order to obtain solutions of complex time dependent N-body problems and to allow an efficient description of the plasma states between classical high temperature systems to strongly coupled plasmas. Our present objective is an attempt to explore the behavior of such a classical approach for typical conditions of warm dense matter. We calculate the dynamic structure factor in warm dense beryllium by means of our molecular dynamics simulations. The results are then compared with those obtained within the framework of the random phase approximation (RPA).

Calisti, A.; Ferri, S.; Marciante, M.; Talin, B.

2014-12-01

181

A random rotor molecule: Vibrational analysis and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4??-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2?-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.

Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.

2012-12-01

182

A molecular dynamics study on uranium–plutonium mixed nitride

Molecular dynamic (MD) calculations were performed for the uranium–plutonium mixed nitride (U0.8Pu0.2)N in the temperature range 300–3000 K to evaluate the physicochemical properties of nitride fuels. The parameters of the interatomic potential were determined by fitting to the experimental values of the lattice parameters for UN and PuN. The lattice parameters, thermal expansion coefficient (?), compressibility (?), heat capacity, and

Ken Kurosaki; Kimihiko Yano; Kazuhiro Yamada; Masayoshi Uno; Shinsuke Yamanaka

2001-01-01

183

Molecular dynamics study for the thermal conductivity of diatomic liquid

The thermal conductivity of diatomic liquids was analyzed using a nonequilibrium molecular dynamics (NEMD) method. Five liquids, namely, O2, CO, CS2, Cl2 and Br2, were assumed. The two-center Lennard-Jones (2CLJ) model was used to express the intermolecular potential acting on liquid molecules. First, the equation of state of each liquid was obtained using MD simulation, and the critical temperature, density

Takashi Tokumasu; Kenjiro Kamijo

2004-01-01

184

Molecular dynamics simulation of diffusion of small atmospheric penetratesin polydimethylsiloxane

Motivated by the development of a microelectromechanical (MEMS) corrosion sensor which utilises a thin polydimethylsiloxane (PDMS) membrane as a permeable medium, molecular dynamics (MD) simulation is used to study the diffusion of CH4, N2 and O2 penetrates in uncrosslinked PDMS. Both PDMS and penetrates are modelled within the MD framework using a hybrid coarse-grained interatomic potential; the accuracy of this

Alexander Sudibjo; Douglas E. Spearot

2011-01-01

185

Molecular dynamics study of self-diffusion in bcc Fe

A semiempirical interatomic potential for Fe was used to calculate the diffusivity in bcc Fe assuming the vacancy and interstitial mechanisms of self-diffusion. Point-defect concentrations and diffusivities were obtained directly from molecular dynamics (MD) simulations. It was found that self-diffusion in bcc Fe is controlled by the vacancy mechanism at all temperatures. This result is due to the fact that

Mikhail I. Mendelev; Yuri Mishin

2009-01-01

186

Molecular-dynamics investigation of hydrogen hopping in palladium

Diffusive hopping of hydrogen in PdH\\/sub x\\/ has been reexamined with molecular-dynamics (MD) simulations in order to clarify earlier results of Gillan. We obtain the same values for the diffusion coefficient and width GAMMA\\/sub q\\/ of the quasielastic neutron scattering function when Gillan's potentials are used, but go beyond Gillan in performing a statistical analysis of the jumps. The analysis

J. W. Culvahouse; Peter Richards

1988-01-01

187

Grand Canonical Molecular Dynamic Simulations For Polar Systems

The purely molecular dynamical formulation of grand canonical ensemble of Pettitt and co-workers was extended to implement the Nosé-Hoover thermostat and introduce multiple fractional particles. The algorithm was applied to simulation of ?VT ensembles of TIP4P water and methanol molecules at 298 K. The procedure reproduced the experimental density of water for input chemical potential of ?24.0 kJ\\/mol, as well that of

Tatyana Kuznetsova; Bjørn Kvamme

2005-01-01

188

Molecular Dynamics Simulation of a Two-Dimensional Heisenberg Fluid

NASA Astrophysics Data System (ADS)

In this work we use numerical Monte Carlo and molecular dynamics to study a classical two-dimensional compressible magnetic fluid. The magnetic interactions are realized through a Yukawa-like potential while particles interact through Lenard-Jones forces. Our preliminary results point to a very rich phase transition picture. At high density the system seems to undergoes a transition, as suggested by the magnetization and susceptibility results.

Correa, Eberth; Lima, A. B.; Costa, B. V.

2012-04-01

189

Molecular Dynamics Simulation of a Two Dimensional Heisenberg Fluid

NASA Astrophysics Data System (ADS)

In this work we use numerical Monte Carlo and Molecular Dynamics to study a classical two-dimensional compressible magnetic fluid. The magnetic interactions are realized through a Yukawa-like potential while particles interact through Lenard-Jones forces. Our preliminary results point to a very rich phase transition picture. At high density the system seems to undergo a magnetic transition, as suggested by the magnetization and susceptibility results.

Costa, B. V.; Lima, A. B.; Correa, E.

2012-02-01

190

Potential energy surfaces and reaction dynamics of polyatomic molecules

A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

Chang, Yan-Tyng.

1991-11-01

191

Polar solvation dynamics of lysozyme from molecular dynamics studies

NASA Astrophysics Data System (ADS)

The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the ?-helices and ?-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

2012-05-01

192

Looking Back Molecular-dynamics simulations require numerical methods

Looking Back Â· Molecular-dynamics simulations require numerical methods for the integration, Heun, and Runge-Kutta. However, these methods are not suitable for molecular-dynamics simulations. Â· Frequently used methods for the integration of the equations in a molecular-dynamics simulation are the Gear

Duisburg-Essen, UniversitÃ¤t

193

been observed by molecular dynamics simulations is that, once

been observed by molecular dynamics simulations is that, once the interface is removed (by removing microscopy and insights from molecular dynamics simulations are rapidly completing the picture of how clamp as the conformational agility observed by EM and by molecular dynamics simulations. As the role of DNA sliding clamps

Thompson, John N.

194

A molecular dynamics simulation of droplet evaporation Lorenzo Consolini 1

A molecular dynamics simulation of droplet evaporation Lorenzo Consolini 1 , Suresh K. Aggarwal A molecular dynamics (MD) simulation method is developed to study the evaporation of submicron droplets the ``vaporization'' process. Ã? 2003 Elsevier Science Ltd. All rights reserved. Keywords: Molecular dynamics

Aggarwal, Suresh K.

195

MOLECULAR DYNAMICS SIMULATION ON COMMODITY SHAREDMEMORY MULTIPROCESSOR SYSTEMS

MOLECULAR DYNAMICS SIMULATION ON COMMODITY SHAREDÂMEMORY MULTIPROCESSOR SYSTEMS WITH LIGHTWEIGHT@cco.caltech.edu {hli, tahir, wag}@wag.caltech.edu Keywords: molecular dynamics simulation, NÂbody probÂ lems, shared molecular dynamics to astrophysics. In all these applications, the basic approach to simulation is the same

Goddard III, William A.

196

TECHNICAL REPORT 022 "Molecular Dynamics Simulation of Vitreous Silica Structures"

TECHNICAL REPORT 022 1999 "Molecular Dynamics Simulation of Vitreous Silica Structures" N. T. Huff-Crystalline Solids MOLECULAR DYNAMICS SIMULATION OF VITREOUS SILICA STRUCTURES Norman T. Huff*, Owens Corning Science-74), California Institute of Technology, Pasadena, CA 91125 Abstract Molecular dynamics (MD) simulations can

Barr, Al

197

Computing thermomechanical properties of crosslinked epoxy by molecular dynamic simulations

Computing thermomechanical properties of crosslinked epoxy by molecular dynamic simulations Shaorui Keywords: Cross-linked epoxy Molecular dynamics simulation StructuralÂproperty correlation a b s t r a c t This paper reports the use of molecular dynamics simulations to study the thermomechanical properties

Chen, Wei

198

A PENALTY FUNCTION METHOD FOR CONSTRAINED MOLECULAR DYNAMICS SIMULATION

A PENALTY FUNCTION METHOD FOR CONSTRAINED MOLECULAR DYNAMICS SIMULATION By Ajith GunaratneÂ000 A PENALTY FUNCTION METHOD FOR CONSTRAINED MOLECULAR DYNAMICS SIMULATION AJITH GUNARATNE AND ZHIJUN WU FOR MOLECULAR DYNAMICS SIMULATION 1 that the new iterate can satisfy the constraints [3]. Depending

199

RESEARCH PAPER Molecular dynamics simulations of oscillatory Couette flows

RESEARCH PAPER Molecular dynamics simulations of oscillatory Couette flows with slip boundary-periodic flows of monatomic liquids is investigated using non-equilibrium molecular dynamics simulations Molecular dynamics simulation Ã Liquid flow Ã Nanofluidics Ã Slip length 1 Introduction The rational design

Priezjev, Nikolai V.

200

Molecular Dynamics simulations of enforced functional protein motions

Molecular Dynamics simulations of enforced functional protein motions Dissertation zur Erlangung;Contents 1 Introduction 7 2 Theory and Methods 17 2.1 Molecular Dynamics Simulations-Exchange Molecular Dynamics Simulations . . . . . . 25 2.4 Simulating force-induced transitions

GrÃ¤ter, Frauke

201

Molecular dynamics simulations of protein folding from the transition state

Molecular dynamics simulations of protein folding from the transition state JoÂ¨ rg Gsponer molecular dynamics (MD) simulations of unfolding. Sixty MD trajectories (for a total of about 7 s) were as in the denatured state. Molecular dynamics (MD) simulations of protein unfolding at high temperature with explicit

Caflisch, Amedeo

202

Molecular dynamics simulation of thermal conductivity of nanocrystalline composite films

Molecular dynamics simulation of thermal conductivity of nanocrystalline composite films N numerically using a molecular dynamics simulation. Results indicate that a reduction of 25% in the effective yielding values for ZT 6 1 at room temperature [4]. Using molecular dynamics, the present work explores

Walker, D. Greg

203

Molecular understanding of mutagenicity using potential energy methods

Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.

Broyde, S.; Shapiro, R.

1992-07-01

204

Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

NASA Technical Reports Server (NTRS)

Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

205

Application of two dimensional periodic molecular dynamics to interfaces.

NASA Astrophysics Data System (ADS)

We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.

Gay, David H.; Slater, Ben; Catlow, C. Richard A.

1997-08-01

206

Molecular Dynamics Simulations of Alpha-synuclein

NASA Astrophysics Data System (ADS)

We investigate the conformational dynamics of single alpha-synuclein proteins, which have been implicated in amyloid diseases such as Parkinson's and Alzheimer's disease, in solution using unconstrained and constrained all-atom, explicit solvent molecular dynamics simulations. The constraints on inter-residue separations are obtained from our single-molecule FRET measurements of eleven FRET pairs that span the protein. By comparing the simulation data satisfying different combinations of FRET constraints, we are able to identify those constraints that are most important in determining the radius of gyration and key features of the contact map of the protein.

Sammalkorpi, Maria; Schreck, Carl; Nath, Abhinav; Dewitt, David; Rhoades, Elizabeth; O'Hern, Corey

2011-03-01

207

Molecular dynamics studies of polyurethane nanocomposite hydrogels

NASA Astrophysics Data System (ADS)

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.

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

2013-10-01

208

Molecular dynamics simulation of disordered zircon

NASA Astrophysics Data System (ADS)

The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision for the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190 200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with an average connectivity of 2, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.

Devanathan, R.; Corrales, L. R.; Weber, W. J.; Chartier, A.; Meis, C.

2004-02-01

209

New faster CHARMM molecular dynamics engine.

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

Hynninen, Antti-Pekka; Crowley, Michael F

2014-02-15

210

is the use of classical molecular dynamics simulations with molecular mechanical forcefields.7Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics profiles. The dynamical effects are studied with the molecular dynamics with quantum transitions MDQT

Hammes-Schiffer, Sharon

211

Control-volume representation of molecular dynamics

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 (\\CV) conversion function $\\vartheta_{i}$, for each molecule $i$. The \\CV 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 (VA, Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, 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 non-equilibrium (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.

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

2012-05-24

212

Molecular dynamics simulation of strongly coupled QCD plasmas

The properties of a strongly interacting quark plasma are investigated by molecular dynamics method including non-abelian quark-quark potential. Our main goal is to study the thermalization process in this system. We find an interesting resonance-like behaviour: at a characteristic time close to the inverse plasma frequency the quark plasma is heated up substantially via energy transfer from quark potential energy into one particle kinetic energy. Color rotation mechanism enhances the effectivity of this heating process, leading to a very fast thermalization with high temperature.

P. Hartmann; Z. Donko; P. Levai; G. J. Kalman

2006-01-06

213

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

Yu H. G.; Muckerman, J.T.

2012-05-29

214

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

Andersen, Hans C.

2005-01-01

215

Evaluating data mining algorithms using molecular dynamics trajectories.

Molecular dynamics simulations provide a sample of a molecule's conformational space. Experiments on the mus time scale, resulting in large amounts of data, are nowadays routine. Data mining techniques such as classification provide a way to analyse such data. In this work, we evaluate and compare several classification algorithms using three data sets which resulted from computer simulations, of a potential enzyme mimetic biomolecule. We evaluated 65 classifiers available in the well-known data mining toolkit Weka, using 'classification' errors to assess algorithmic performance. Results suggest that: (i) 'meta' classifiers perform better than the other groups, when applied to molecular dynamics data sets; (ii) Random Forest and Rotation Forest are the best classifiers for all three data sets; and (iii) classification via clustering yields the highest classification error. Our findings are consistent with bibliographic evidence, suggesting a 'roadmap' for dealing with such data. PMID:24010266

Tatsis, Vasileios A; Tjortjis, Christos; Tzirakis, Panagiotis

2013-01-01

216

Dynamical nucleus-nucleus potential at short distances

The dynamical nucleus-nucleus potentials for fusion reactions {sup 40}Ca+{sup 40}Ca, {sup 48}Ca+{sup 208}Pb, and {sup 126}Sn+{sup 130}Te are studied with the improved quantum molecular dynamics model together with the extended Thomas-Fermi approximation for the kinetic energies of nuclei. The obtained fusion barrier for {sup 40}Ca+{sup 40}Ca is in good agreement with the extracted fusion barrier from the measured fusion excitation function, and the depths of the fusion pockets are close to the results of time-dependent Hartree-Fock calculations. The energy dependence of the fusion barrier is also investigated. The fusion pocket becomes shallow for a heavy fusion system and almost disappears for heavy nearly symmetric systems, and the obtained potential at short distances is higher than the adiabatic potential.

Jiang Yongying; Wang Ning [Department of Physics, Guangxi Normal University, Guilin 541004 (China); Li Zhuxia [China Institute of Atomic Energy, Beijing 102413 (China); Scheid, Werner [Institute for Theoretical Physics, Justus-Liebig-University, D-35392 Giessen (Germany)

2010-04-15

217

Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties December 2004) A molecular simulation method to study the dynamics of chemically reacting mixtures for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation

Lisal, Martin

218

Molecular Dynamics Simulations Using Temperature-Enhanced Essential Dynamics Replica Exchange

Molecular Dynamics Simulations Using Temperature-Enhanced Essential Dynamics Replica Exchange-Planck-Institute for Biophysical Chemistry, 37077 GoÂ¨ttingen, Germany ABSTRACT Today's standard molecular dynamics simulations, especially molecular dynamics (MD) simulations, have been increasingly applied to study structure

de Groot, Bert

219

Brittle dynamic fracture of crystalline cubic silicon carbide ,,3C-SiC... via molecular dynamics for three low-index crack surfaces, i.e., 110 , 111 , and 100 , in crystalline cubic silicon carbide 3C Institute of Physics. DOI: 10.1063/1.2135896 I. INTRODUCTION Potential applications of silicon carbide Si

Southern California, University of

220

Molecular dynamics simulations of structure and dynamics of organic molecular crystals.

A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment. PMID:20944862

Nemkevich, Alexandra; Bürgi, Hans-Beat; Spackman, Mark A; Corry, Ben

2010-12-01

221

(Molecular understanding of mutagenicity using potential energy methods)

The objective of our work has been, for many year, to elucidate on a molecular level at atomic resolution the structures of DNAs modified by highly mutagenic polycyclic aromatic amines and hydrocarbons, and their less mutagenic chemically related analogs and unmodified DNAs, as controls. The ultimate purpose of this undertaking is to obtain an understanding of the relationship DNA structures and mutagenicity. Our methods for elucidating structures are computational, but we keep in close contact with experimental developments, and have, very recently, been able to incorporate the first experimental information from NMR studies by other workers in our calculations. The specific computational methods we employ are minimized potential energy calculations using the torsion angle space program DUPLEX, developed and written by Dr. Brain Hingerty to yield static views. Molecular dynamics simulations of the important static structures with full solvation and salt are carried out with the program AMBER; this yields mobile views in a milieu that best mimics the natural environment of the cell. In addition, we have been developing new strategies for searching conformation space and building DNA duplexes from favored subunit structures. 30 refs., 12 figs.

Broyde, S.

1990-01-01

222

Role of wave packet width in quantum molecular dynamics in fusion reactions near barrier

NASA Astrophysics Data System (ADS)

The dynamical fusion process of 48Ca + 144Sm with different impact parameters near barrier is studied by an extended quantum molecular dynamics (EQMD) model, where width of wavepacket is dynamically treated based on variational principle. The time evolution of different energy components such as potential energy, kinetic energy, Coulomb energy and Pauli potential are analyzed when dynamical or fixed width is assumed in calculation. It is found that the dynamical wavepacket width can enhance the dissipation of incident energy and the fluctuations, which are important to form compound nuclei. Moreover, we compare the fusion barrier dependence on the incident energy when it is determined by both dynamical and fixed wavepacket width.

Cao, X. G.; Ma, Y. G.; Zhang, G. Q.; Wang, H. W.; Anastasi, A.; Curciarello, F.; De Leo, V.

2014-05-01

223

Electronic continuum model for molecular dynamics simulations

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

Leontyev, I. V.; Stuchebrukhov, A. A.

2009-01-01

224

DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA

Spectra and internal dynamics of highly excited molecules are essential to understanding processes of fundamental importance for combustion, including intramolecular energy transfer and isomerization reactions. The goal of our program is to develop new theoretical tools to unravel information about intramolecular dynamics encoded in highly excited experimental spectra. We want to understand the formations of ''new vibrational modes'' when the ordinary normal modes picture breaks down in highly excited vibrations. We use bifurcation analysis of semiclassical versions of the effective Hamiltonians used by spectroscopists to fit complex experimental spectra. Specific molecular systems are of interest for their relevance to combustion and the availability of high-quality experimental data. Because of its immense importance in combustion, the isomerizing acetylene/vinylidene system has been the object of long-standing experimental and theoretical research. We have made significant progress in systematically understanding the bending dynamics of the acetylene system. We have begun to make progress on extending our methodology to the full bend-stretch vibrational degrees of freedom, including dynamics with multiple wells and above barrier motion, and time-dependent dynamics. For this, development of our previous methods using spectroscopic fitting Hamiltonians is needed, for example, for systems with multiple barriers.

Michael E. Kellman

2005-06-17

225

Thermal decomposition of RDX from reactive molecular dynamics Alejandro Strachana)

Thermal decomposition of RDX from reactive molecular dynamics Alejandro Strachana) and Edward M field ReaxFF with molecular dynamics to study thermal induced chemistry in RDX cyclic- CH2N NO2 efficient way. Typical HE materials, such as TNT, RDX, HMX, TATB, and PETN, are complex organic molecular

Goddard III, William A.

226

Inhomogeneous dark states of atomic-molecular Bose-Einstein condensates in trapping potentials

We investigate possibilities of existence of inhomogeneous dark states of atomic-molecular Bose-Einstein condensates loaded in trap potentials. The system is described by three-coupled equations of the Gross-Pitaevskii type, which account for contributions of the kinetic energy, two-body interactions, and an external potential, and which govern the conversion between atoms and molecules in the stimulated Raman adiabatic passage. We report a class of trapping potentials allowing for the existence of localized stable dark states. The respective atomic and molecular distributions are computed, and their stability and dynamics are discussed.

Cruz, H. A.; Konotop, V. V. [Centro de Fisica Teorica e Computacional and Departamento de Fisica, Faculdade de Ciencias da Universidade de Lisboa, Avenida Professor Gama Pinto 2, P-1649-003 Lisbon (Portugal)

2011-03-15

227

Molecular Dynamics Simulations of Interface Failure

NASA Astrophysics Data System (ADS)

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.

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

2007-03-01

228

Bio-Molecular Dynamics Comes of Age

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Atomic force microscopy has recently been used to measure the binding force between two biomolecules; complementing the experiments are computational molecular dynamics studies that seek to reveal the details of the binding and unbinding mechanisms. In his Perspective, Berendsen discusses the results reported in the same issue by GrubmÃÂ¼ller et al. (p. 997) on numerical simulations of the binding and separation of biotin from streptavidin, which show excellent agreement with measurements of the rupture force.

Herman J. C. Berendsen (University of Groningen, Netherlands;Department of Biophysical Chemistry and the BIOSON Research Institute)

1996-02-16

229

Molecular Dynamics Simulation of Carbon Nanotube Based Gears

NASA Technical Reports Server (NTRS)

We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

230

Rotational and vibrational dynamics of interstitial molecular hydrogen T. Yildirim

Rotational and vibrational dynamics of interstitial molecular hydrogen T. Yildirim National. INTRODUCTION The study of rotational and vibrational dynamics of guest molecules i.e., CO, O2 , H2, etc develop a detailed analysis of coupled rotational and vibrational dynamics of a molecular hydrogen

Yildirim, Taner

231

-Value analysis by molecular dynamics simulations of reversible folding

-Value analysis by molecular dynamics simulations of reversible folding Giovanni Settanni dynamics (MD) simulations (total- ing 0.65 ms) have been performed for a large set of single-point mutants of conformations from the TS ensemble of several proteins (5Â9) and to bias molecular dynamics (MD) trajectories

Caflisch, Amedeo

232

Molecular dynamics simulation of hydration in myoglobin

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After salvation of the protein, energy minimization and equilibration of the system, 50 pico seconds of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water.

Gu, Wei [New Mexico Univ., Albuquerque, NM (United States). Dept. of Biochemistry; Schoenborn, B.P. [Los Alamos National Lab., NM (United States)

1995-09-01

233

MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000 Molecular Analysis of Human Spermatozoa: Potential for Infertility Research David Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...

234

Molecular dynamics simulation: a tool for exploration and discovery using simple models

Molecular dynamics simulation: a tool for exploration and discovery using simple models D, all studied by molecular dynamics (MD) simulation. The examples are taken from the disparate fields: molecular dynamics simulation, emergent phenomena, atomistic hydrodynamics, granular segregation, molecular

Rapaport, Dennis C.

235

Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations

Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations J 2004) An ad hoc thermostating procedure that couples a molecular dynamics (MD) simulation without the thermostat. Keywords: Molecular dynamics simulation; Molecular heat flow; Continuum

Brenner, Donald W.

236

Attosecond VUV Coherent Control of Molecular Dynamics

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

P. Ranitovic; C. W. Hogle; P. Riviere; A Palacios; X. M. Tong; N. Toshima; A. Gonzalez-Castrillo; L. Martin; F. Martin; M. M. Murnane; H. C. Kapteyn

2013-12-30

237

Multiple branched adaptive steered molecular dynamics

NASA Astrophysics Data System (ADS)

Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.

Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto

2014-08-01

238

Coarse-grained protein molecular dynamics simulations

NASA Astrophysics Data System (ADS)

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 A?16-22 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 A?16-22 peptides can form a three-stranded ? 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.

Derreumaux, Philippe; Mousseau, Normand

2007-01-01

239

Shock compression and spallation of tantalum: Molecular dynamics simulations

NASA Astrophysics Data System (ADS)

We perform large-scale molecular dynamics simulations of shock wave compression and spallation of Ta single crystals with different potentials including embedded-atom method (EAM), first-principles-based EAM (qEAM) and reactive forcefield (ReaxFF). Shock loading is applied along <100 >, <110> and <111>. Hugoniot states are obtained from direct shock or Hugoniostat simulations. Anisotropic behaviors are observed in plasticity (including twinning) during compression/tension and in spallation. We present detailed analysis of dislocations, twins and void nucleation and growth, and their implications for the mechanisms of plasticity and spall damage in Ta.

Luo, S. N.; An, Q.; Ravelo, R.; Germann, T. C.; Tonks, D. L.; Goddard, W. A., III

2011-06-01

240

Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

NASA Astrophysics Data System (ADS)

We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

Mugnai, Mauro L.; Elber, Ron

2015-01-01

241

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite

Hydrogen adsorption by graphite is examined by classical molecular dynamics simulation using a modified Brenner REBO potential. Such interactions are typical in chemical sputtering experiments, and knowledge of the fundamental behavior of hydrogen and graphene in collisional conditions is essential for modeling the sputtering mechanism. The hydrogen adsorption rate is found to be dependent on the incident hydrogen energy and not on graphene temperature. Rather than destroying the graphene, hydrogen incidence at energies of less than 100 eV can be classified into three regimes of adsorption, reflection and penetration through one or more graphene layers. Incidence at the lowest energies is shown to distort the graphene structure.

A. Ito; H. Nakamura

2006-04-24

242

Molecular dynamics simulations of shock-induced plasticity in tantalum

NASA Astrophysics Data System (ADS)

We present Non-Equilibrium Molecular Dynamics (NEMD) simulations of shock wave compression along the [001] direction in monocrystalline Tantalum, including pre-existing defects which act as dislocation sources. We use a new Embedded Atom Model (EAM) potential and study the nucleation and evolution of dislocations as a function of shock pressure and loading rise time. We find that the flow stress and dislocation density behind the shock front depend on strain rate. We find excellent agreement with recent experimental results on strength and recovered microstructure, which goes from dislocations to a mixture of dislocations and twins, to twinning dominated response, as the shock pressure increases.

Tramontina, Diego; Erhart, Paul; Germann, Timothy; Hawreliak, James; Higginbotham, Andrew; Park, Nigel; Ravelo, Ramón; Stukowski, Alexander; Suggit, Mathew; Tang, Yizhe; Wark, Justin; Bringa, Eduardo

2014-03-01

243

Isomers of Copper Clusters Obtained by a Molecular Dynamics Model

NASA Astrophysics Data System (ADS)

A molecular dynamics model was developed to search for stable copper clusters with up to 60 atoms by Gupts empirical potential based on the second-moment approximation to tight-binding model (TB-SMA). We found that isomers do not emerge until the clusters have more than 7 atoms, getting more for clusters with 30~52 atoms, and the magic number, 13, 19, 23, 26, 28, 32, 38, 43, 46, 49, and 55 have ground clusters with higher symmetry and have few isomers.

Wang, Ling; Ning, Xi-Jing

244

Molecular dynamics calculation of thermodynamic properties of iron solidification

NASA Astrophysics Data System (ADS)

The aim of this study is to identify the best available inter-atomic potentials for molecular dynamics (MD) calculation of solidification of iron and then to use the best potential to calculate thermodynamic properties such as equilibrium melting temperature, enthalpy, heat capacity and solid-liquid interfacial free energy. Our study reveals that embedded atom method (EAM) potential developed by Ackland et al. [2004 J. Phys.: Condens Matter. 16 S2629] appears to be the most accurate model for MD simulation of iron solidification. Simulations with the above EAM model predict the equilibrium melting temperature of iron is 1790K, the solid-liquid interfacial energy 214 mJ/m2. The difference with the experimental data is 1.2%, and 4.9% respectively.

Liu, J.; Dong, H. B.

2012-07-01

245

Molecular dynamics simulations of retinoblastoma protein.

Tumor suppressor proteins play a crucial role in cell cycle regulation. Retinoblastoma protein (pRB) is one among them which regulates G1-S transition by binding with transcription factors. The activity of pRB is deregulated by cyclin dependent kinases-mediated hyper-phosphorylation and also due to cancer-derived mutations. In addition, it is also deactivated by binding of viral onco-proteins such as large T antigen, E1A, and E7. These viral proteins initially recognize pRB through their conserved LxCxE motif and facilitate dissociation of preexisting pRB-E2F complex. Based on these features, molecular dynamics (MD) simulation is performed for four different states of pRB for which the crystal structure is available. The unliganded/apo form and complex forms with E2F and E7 peptides reveal the molecular mechanism behind the activation and inactivation of pRB. In addition, the ternary complex of pRB with both E7 and E2F (for which no crystal structure is available) is modeled and simulated to understand the influence of binding of one ligand on the other. The variations in the three major factors such as conformational changes, inter- and intra-molecular interactions, and binding free energies between the apo and complex forms confirm the possibility for designing a small molecule inhibitor to inhibit pRB-E7 interactions without altering the prebound E2F. The present study deals with the molecular modeling and MD simulations of pRB in free and ligand-bound forms and confirms that pRB could be a valid target for the anticancer drug design when the cancer is induced by the viral onco-proteins and forms a clear base for designing E7 antagonists. PMID:23157310

Ramakrishnan, C; Subramanian, V; Balamurugan, K; Velmurugan, D

2013-01-01

246

The Kinetic Theory Molecular Dynamics Method

NASA Astrophysics Data System (ADS)

We are interested in simulating plasmas under thermonuclear burn conditions relevant to NIF. As such, we have recently developed the Kinetic Theory Molecular Dynamics (KTMD) method, which takes advantage of the fact that the plasma electrons are typically moderately degenerate and weakly coupled, whereas the ions are classical and moderately to strongly coupled. The basic approach of KTMD is to describe the fully non-equilibrium electron dynamics with an appropriate kinetic equation while leaving the ion dynamics to MD. The current version of KTMD self-consistently follows the time evolution of a Fermi gas via the time-dependent, fully nonlinear Wigner-Poisson system. Our approach, its associated implementation, and preliminary physics benchmarking results, such as nonlinear plasma waves and instabilities, will be presented. We describe a Langevin approach designed to mitigate numerical errors causing the Fermi distribution to relax towards a Maxwellian during long simulations. Ideas for extending the current capability, such as extending the mean-field approach by including collisions and quantum mechanical smearing, will be outlined.

Fichtl, Chris; Murillo, Michael; Graziani, Frank

2011-11-01

247

Atomistic molecular dynamic simulations of multiferroics.

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

Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

2012-08-10

248

Shock compression of hydrocarbon polymer foam using molecular dynamics

NASA Astrophysics Data System (ADS)

Organic polymers and nanocomposites are increasingly being subjected to extreme environments. Molecular-scale modeling of these materials offers insight into failure mechanisms and response. In previously published work, we used classical molecular dynamics (MD) and density functional theory (DFT) simulations to determine the principal shock Hugoniot for two hydrocarbon polymers, polyethylene (PE) and poly(4-methyl-1-pentene) (PMP). DFT was in excellent agreement with experiment, and one of four classical MD potentials, ReaxFF, was found to be suitable for studies up to 50 GPa. Here, we extend these results to include low-density polymer foams using NEMD techniques. We find good quantitative agreement with both experiment and hydrocode simulations. Further, we have measured local temperatures to investigate the formation of hot spots and polymer dissociation near foam voids.

Lane, J. Matthew D.; Grest, Gary S.; Thompson, Aidan P.; Cochrane, Kyle R.; Desjarlais, Michael; Mattsson, Thomas R.

2012-03-01

249

A scheme to combine molecular dynamics and dislocation dynamics

NASA Astrophysics Data System (ADS)

Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake.

Brinckmann, Steffen; Mahajan, Dhiraj K.; Hartmaier, Alexander

2012-06-01

250

Molecular dynamics simulation of heat conduction through a molecular chain.

This work deals with a molecular dynamics simulation analysis of the intramolecular vibrational energy transfer in a system of two chromophores, azulene and anthracene, bridged by an aliphatic chain and is motivated by corresponding laser experiments. After selective excitation of the azulene chromophore, the subsequent intramolecular vibrational energy redistribution is monitored by analyzing the transient temperatures of the two chromophores and the chain between them. The main focus concerns the heat conduction process in the chain. Therefore, the chain length was varied from 0 to 19 CH(2) units. In addition, methoxymethyl, 1,2-dimethoxyethyl, and a thiomethoxymethyl chains were studied. The investigation of the intramolecular vibrational energy process was decomposed into a temporal analysis and a spatial analysis. For short alkyl chains, the time constant of energy relaxation increases proportionally to the chain length. However, for longer chains, the time constant characterizing the energy decay of the azulene chromophore saturates and becomes independent of the chain length. This behavior is consistent with experimental findings. The spatial analysis shows more or less exponential decay of the temperature along the chain near the excited chromophore. In additional simulations, the two chromophores were thermostatted at different temperatures to establish a constant heat flux from the azulene to the anthracene side. The steady-state temperature profiles for longer alkyl chains show strong gradients near the two chromophores and constant but weak gradients in the central part of the chain. Both simulation methods indicate that strong Kapitza effects at the boundaries between each chromophore and the molecular chain dominate the intramolecular energy flux. PMID:19928969

Schröder, Christian; Vikhrenko, Vyacheslav; Schwarzer, Dirk

2009-12-24

251

Nonequilibrium molecular dynamics: The first 25 years

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.

Hoover, W.G. [Univ. of California, Davis, CA (United States); [Lawrence Livermore National Lab., CA (United States)

1992-08-01

252

Molecular Dynamics Simulations of Hypervelocity Impacts

NASA Astrophysics Data System (ADS)

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.

Owens, Eli T.; Bachlechner, Martina E.

2007-03-01

253

Ion Mobility Analysis of Molecular Dynamics

NASA Astrophysics Data System (ADS)

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.

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

2014-04-01

254

Molecular dynamics simulations of silver nanocluster supported on carbon nanotube.

We carried out molecular dynamics simulations to examine the thermal, structural and dynamics properties of single walled carbon nanotube-supported silver nanoclusters with N=38, 108 and 256 atoms. The nanoclusters were simulated in two stages: first heated in 100-1700 K temperature range with steps of 100 K, then cooled to 100 K with the same steps. The number of Ag atoms in nanocluster layer in contact with the nanotube surface, the height of nanocluster and diameter of the lowest layer (layer in contact with nanotube) were calculated as a function of time. Also, the hysteresis in potential curves, surface melting, irreversibility of structural change with temperature, broaden interface structure and surface wetting were identified by analyzing the obtained data from simulations. PMID:24461833

Akbarzadeh, Hamed; Yaghoubi, Hamzeh

2014-03-15

255

Isobaric molecular dynamics simulations of hard sphere systems.

We describe an implementation of the Andersen algorithm for simulating the molecular dynamics in the isobaric isoenthalpic (NPH) ensemble for the hard sphere potential. The work is based on the adaptation of the Andersen algorithm to hard spheres by de Smedt et al. For a hard sphere system in the NPH ensemble, the particle velocities are not constant between collisions and we describe an efficient method for handling this part of the dynamics. The method is extended to give an NPT ensemble simulation of hard sphere systems by applying an ad hoc rescaling of the velocities. The accuracy of the algorithms is tested by comparison with traditional NVE simulation results for the structural, thermodynamic, and transport properties. PMID:11415067

Gruhn, T; Monson, P A

2001-06-01

256

Molecular Modeling and Molecular Dynamics Simulations of Recombinase Rad51

The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the ?-phosphate of ATP, K+ ions, H352, and D374; the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K+ ions was changed. The simulated structures suggested that K+ ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K+ ions function as glue between protomers. PMID:23561532

Kokabu, Yuichi; Ikeguchi, Mitsunori

2013-01-01

257

a Study of Hypervelocity Impacts Using Molecular Dynamics

NASA Astrophysics Data System (ADS)

Molecular Dynamics is used to conduct computer simulations of a hypervelocity impact where the impacting projectile and the target are composed of the same material. The potential is a truncated Lennard-Jones where the values of the parameters, varepsilon and sigma, selected are that of Argon. A target consisting of 4432 particles with a surface area of 625sigma^2 and a thickness of 6.25sigma is equilibrated at kT/ varepsilon = 0.1 under periodic boundary conditions. Three projectiles with length 6.25 sigma, 12.5sigma, and 75.0sigma are equilibrated with the same boundary conditions and temperature. The projectiles are placed at an initial distance from the target greater than the interaction distance of the potential and the periodic boundary is eliminated. Eight computer experiments using different impact velocities and aspect ratios are conducted. The time evolution of the pair and velocity distribution functions is examined for each of the experiments. An Eulerian grid is employed with the appropriate definitions to investigate the change over time in the density, pressure, and temperature for a system undergoing a hypervelocity event. Conclusions are presented and prospects for using Molecular Dynamics for further investigation of hypervelocity impact phenomena are discussed.

McDonald, Robert Allen

258

Molecular Dynamic Simulation of Failure of Ettringite

NASA Astrophysics Data System (ADS)

Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.

Sun, W.; Wang, D.; Wang, L.

2013-03-01

259

Molecular dynamics simulations of microscale fluid transport

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.

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

1998-02-01

260

Embryonic Forms of Nickel and Palladium: A Molecular Dynamics Computer Simulation

An empirical many Potential Energy Function (PEF) incorporating two-plus-three body atomistic potential derived by fitting experimental data per- taining to bulk nickel, and palladium has been applied to study the structural sta- bility and energetics of the trimers, tetramers, and pentamers microclusters of Ni and Pd. A constant temperature Molecular Dynamics (MD) technique is employed in the simulation. It has

Z. El-bayyari

261

Discrete Molecular Dynamics Study of Alzheimer Amyloid -protein (A) Folding

. INTRODUCTION Alzheimer's disease (AD) is a progressive neurological disorder that is estimated to affect 50 pathogenic events in Alzheimer's disease. We study A(1-42) folding by discrete molecular dynamics using. Keywords: Alzheimer's disease, amyloid -protein, protein folding, discrete molecular dynamics. I

Stanley, H. Eugene

262

Data mining of molecular dynamics trajectories of nucleic acids.

Analysis, storage, and transfer of molecular dynamic trajectories are becoming the bottleneck of computer simulations. In this paper we discuss different approaches for data mining and data processing of huge trajectory files generated from molecular dynamic simulations of nucleic acids. PMID:16363879

Noy, Agnes; Meyer, Tim; Rueda, Manuel; Ferrer, Carles; Valencia, Antonion; Pérez, Alberto; de la Cruz, Xavier; López-Bes, J M; Pouplana, R; Fernandez-Recio, J; Luque, F Javier; Orozco, Modesto

2006-02-01

263

Molecular Dynamics in Principal Component Space Servaas Michielssens,*,

Molecular Dynamics in Principal Component Space Servaas Michielssens,*, Titus S. van Erp,Â¶ Carsten dynamics algorithm in principal component space is presented. It is demonstrated that sampling can, is notoriously hard to probe experimentally. Therefore, molecular simulations are used routinely to study

de Groot, Bert

264

Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion

Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion Nanako Takahashi, Paulo C Propulsion Nanako Takahashi, Paulo C. Lozano June 2010 SSL # 6-10 This work is based on the unaltered text of Technology. 1 #12;2 #12;Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion by Nanako

265

Nonequilibrium Molecular Dynamics Simulation of Electric Conduction Tatsuro YUGE

Nonequilibrium Molecular Dynamics Simulation of Electric Conduction Tatsuro YUGE Ã? , Nobuyasu ITO1y for electric conduction, and study transport phenomena by molecular dynamics simulation. We observe. The electrical conductivity is almost independent of the impurity distribution and the system size

Shimizu, Akira

266

Molecular Dynamics Simulations of Silica Glass Ersan Demiralp 1 , Tahir

Molecular Dynamics Simulations of Silica Glass Ersan Demiralp 1 , Tahir Â¸ Ca~gin 1 , Norman T. Huff temperature (NPT) molecular dynamic (MD) simulations of silica glass to understand the effects 2 and William A. Goddard III 1 1 Materials and Process Simulation Center, Beckman Institute (139

Goddard III, William A.

267

WNDP (Wilson's disease protein) is a copper-transporting ATPase that plays an essential role in human physiology. Mutations in WNDP result in copper accumulation in tissues and cause a severe hepato-neurological disorder known as Wilson's disease. Several mutations were surmised to affect the nucleotide binding and hydrolysis by WNDP; however, how the nucleotides bind to normal and mutated WNDP remains unknown. To aid such studies, we performed the molecular modelling of the spatial structure and dynamics of the ATP-binding domain of WNDP and its interactions with ATP. The three-dimensional models of this domain in two conformations were built using the X-ray structures of the Ca2+-ATPase in the E1 and E2 states. To study the functional aspects of the models, they were subjected to long-term molecular dynamics simulations in an explicit solvent; similar calculations were performed for the ATP-binding domain of Ca2+-ATPase. In both cases, we found large-scale motions that lead to significant changes of distances between several functionally important residues. The ATP docking revealed two possible modes of ATP binding: via adenosine buried in the cleft near residues H1069, R1151 and D1164, and via phosphate moiety ‘anchored’ by H-bonds with residues in the vicinity of catalytic D1027. Furthermore, interaction of ATP with both sites occurs if they are spatially close to each other. This may be achieved after relative domain motions of the ‘closure’ type observed in molecular dynamics simulations. The results provide a framework for analysis of disease mutations and for future mutagenesis studies. PMID:15147237

2004-01-01

268

Molecular dynamics study for the thermal conductivity of diatomic liquid

NASA Astrophysics Data System (ADS)

The thermal conductivity of diatomic liquids was analyzed using a nonequilibrium molecular dynamics (NEMD) method. Five liquids, namely, O 2, CO, CS 2, Cl 2 and Br 2, were assumed. The two-center Lennard-Jones (2CLJ) model was used to express the intermolecular potential acting on liquid molecules. First, the equation of state of each liquid was obtained using MD simulation, and the critical temperature, density and pressure of each liquid were determined. Heat conduction of each liquid at various liquid states [metastable ( ?=1.9 ?cr), saturated ( ?=2.1 ?cr), and stable ( ?=2.3 ?cr)] at T=0.7 Tcr was simulated and the thermal conductivity was estimated. These values were compared with experimental results and it was confirmed that the simulated results were consistent with the experimental data within 10%. Obtained thermal conductivities at saturated state were reduced by the critical temperature, density and mass of molecules and these values were compared with each other. It was found that the reduced thermal conductivity increased with the increase in the molecular elongation. Detailed analysis of the molecular contribution to the thermal conductivity revealed that the contribution of the heat flux caused by energy transport and by translational energy transfer to the thermal conductivity is independent of the molecular elongation while the contribution of the heat flux caused by rotational energy transfer to the thermal conductivity increases with the increase in the molecular elongation. Moreover, by comparing the reduced thermal conductivity at various states, it was found that the increase of thermal conductivity with the increase in the density, or pressure, was caused by the increase of the contribution of energy transfer due to molecular interaction.

Tokumasu, Takashi; Kamijo, Kenjiro

2004-03-01

269

Molecular beam studies of reaction dynamics

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.

Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

270

Isomorphic phase transformation in shocked cerium using molecular dynamics

Cerium (Ce) undergoes a significant ({approx}16%) volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM) potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD) simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plastic wave. The plastic wave causes the expected fcc-fcc phase transformation. Comparisons to experiments and MD simulations on Cesium (Cs) indicate that three waves could be observed. The construction of the EAM potential may be the source of the difference.

Dupont, Virginie [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Chen, Shao - Ping [Los Alamos National Laboratory

2010-08-12

271

Statistical coarse-graining of molecular dynamics into peridynamics.

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.

Silling, Stewart Andrew; Lehoucq, Richard B.

2007-10-01

272

The MOLDY short-range molecular dynamics package

NASA Astrophysics Data System (ADS)

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as 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.

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

2011-12-01

273

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

NASA Astrophysics Data System (ADS)

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

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

2009-10-01

274

Hydration Effect on Temperature Dependence of Protein Dynamics Studied by Molecular Dynamics Simulation of Crystalline Protein Yasumasa JOTI and Akio KITAO Institute of Molecular and Cellular Biosciences, University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 1. Introduction Proteins are molecular

Katsumoto, Shingo

275

Seven-helix bundles: molecular modeling via restrained molecular dynamics.

Simulated annealing via restrained molecular dynamics (SA/MD) has been used to model compact bundles of seven approximately (anti)parallel alpha-helices. Seven such helix bundles occur, e.g., in bacteriorhodopsin, in rhodopsin, and in the channel-forming N-terminal domain of Bacillus thuringiensis delta-endotoxin. Two classes of model are considered: (a) those consisting of seven Ala20 peptide chains; and (b) those containing a single polypeptide chain, made up of seven Ala20 helices linked by GlyN interhelix loops (where N = 5 or 10). Three different starting C alpha templates for SA/MD are used, in which the seven helices are arranged (a) on a left-handed circular template, (b) on a bacteriorhodopsin-like template, or (c) on a zig-zag template. The ensembles of models generated by SA/MD are analyzed in terms of their geometry and energetics, and the most stable structures from each ensemble are examined in greater detail. Structures resembling bacteriorhodopsin and structures resembling delta-endotoxin are both represented among the most stable structures. delta-Endotoxin-like structures arise from both circular and bacteriorhodopsin-like C alpha templates. A third helix-packing mode occurs several times among the stable structures, regardless of the C alpha template and of the presence or absence of interhelix loops. It is characterized by a "4 + 1" core, in which four helices form a distorted left-handed supercoil around a central, buried helix. The remaining two helices pack onto the outside of the core. This packing mode is comparable with that proposed for rhodopsin on the basis of two-dimensional electron crystallographic and sequence analysis studies. Images FIGURE 1 FIGURE 4 FIGURE 6 PMID:7787019

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

1995-01-01

276

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

In this work we propose a straightforward and efficient approach to improve accuracy and convergence of free energy simulations in condensed-phase systems. We also introduce a new accelerated Molecular Dynamics (MD) approach in which molecular conformational transitions are accelerated by lowering the energy barriers while the potential surfaces near the minima are left unchanged. All free energy calculations were performed on the propane-to-propane model system. The accuracy of free energy simulations was significantly improved when sampling of internal degrees of freedom of solute was enhanced. However, accurate and converged results were only achieved when the solvent interactions were taken into account in the accelerated MD approaches. The analysis of the distribution of boost potential along the free energy simulations showed that the new accelerated MD approach samples efficiently both low- and high-energy regions of the potential surface. Since this approach also maintains substantial populations in regions near the minima, the statistics are not compromised in the thermodynamic integration calculations, and, as a result, the ensemble average can be recovered. PMID:19461868

2008-01-01

277

Accelerated molecular dynamics methods: introduction and recent developments

A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.

Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO

2009-01-01

278

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

NASA Astrophysics Data System (ADS)

Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the hydrocarbon "tail" and their hydrophilic head groups. We find that, for the surfactants, the aqueous solubility of anti-inflammatory molecules increases linearly with increasing surfactant concentration. In particular, we observed a 10-fold increase in the solubility of anti-inflammatory drugs relative to that in the aqueous buffer upon the addition of 100 mM dodecyltrimethyl ammonium bromide -DTAB.

Rakesh, L.

2009-09-01

279

Internal coordinate molecular dynamics: a foundation for multiscale dynamics.

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

Vaidehi, Nagarajan; Jain, Abhinandan

2015-01-29

280

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

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

281

Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution

Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.

Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy)] [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy)

2011-01-07

282

Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?

The ring polymer molecular dynamics (RPMD) method has gained popularity in recent years as a simple approximation for calculating real time quantum correlation functions in condensed media. However, the extent to which RPMD captures real dynamical quantum effects and why it fails under certain situations have not been clearly understood. Addressing this issue has been difficult in the absence of a genuine justification for the RPMD algorithm starting from the quantum Liouville equation. To this end, a new and exact path integral formalism for the calculation of real time quantum correlation functions is presented in this work, which can serve as a rigorous foundation for the analysis of the RPMD method as well as providing an alternative derivation of the well established centroid molecular dynamics method. The new formalism utilizes the cyclic symmetry of the imaginary time path integral in the most general sense and enables the expression of Kubo-transformed quantum time correlation functions as that of physical observables pre-averaged over the imaginary time path. Upon filtering with a centroid constraint function, the formulation results in the centroid dynamics formalism. Upon filtering with the position representation of the imaginary time path integral, we obtain an exact quantum dynamics formalism involving the same variables as the RPMD method. The analysis of the RPMD approximation based on this approach clarifies that an explicit quantum dynamical justification does not exist for the use of the ring polymer harmonic potential term (imaginary time kinetic energy) as implemented in the RPMD method. It is analyzed why this can cause substantial errors in nonlinear correlation functions of harmonic oscillators. Such errors can be significant for general correlation functions of anharmonic systems. We also demonstrate that the short time accuracy of the exact path integral limit of RPMD is of lower order than those for finite discretization of path. The present quantum dynamics formulation also serves as the basis for developing new quantum dynamical methods that utilize the cyclic nature of the imaginary time path integral.

Jang, Seogjoo, E-mail: sjang@qc.cuny.edu [Department of Chemistry and Biochemistry, Queens College and the Graduate Center, City University of New York, 65-30 Kissena Boulevard, Flushing, New York 11367 (United States)] [Department of Chemistry and Biochemistry, Queens College and the Graduate Center, City University of New York, 65-30 Kissena Boulevard, Flushing, New York 11367 (United States); Sinitskiy, Anton V.; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics and Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637 (United States)

2014-04-21

283

NASA Astrophysics Data System (ADS)

We study the phonon modes in single-walled MoS2 nanotubes via lattice dynamics calculation and molecular dynamics simulation. The phonon spectra for tubes of arbitrary chiralities are calculated from a dynamical matrix constructed by the combination of an empirical potential with the conserved helical quantum numbers (?, n). In particular, we show that the frequency (?) of the radial breathing mode is inversely proportional to the tube diameter (d) as ? = 665.3/d cm-1. The eigenvectors of the twenty lowest-frequency phonon modes are illustrated. Based on these eigenvectors, we demonstrate that the radial breathing oscillation is initially disturbed by phonon modes of three-fold symmetry, then eventually the tube is squashed by modes of two-fold symmetry . Our study provides fundamental knowledge for further investigations of the thermal and mechanical properties of MoS2 nanotubes.

Jiang, Jin-Wu; Wang, Bing-Shen; Rabczuk, Timon

2014-03-01

284

NASA Astrophysics Data System (ADS)

In this work we studied the temperature-induced changes in the structural and dynamical properties of liquid Ag using molecular dynamics (DM) computer simulation. The atomic interactions are modeled through a semiempirical potential function which incorporates n-body effects and is based on the second moments approximation of the density of states of a tight-binding Hamiltonian. The caloric curve was used to calculate the latent heat of fusion and the pair distribution function, g(r), was calculated from a set of atomic configurations collected at several time-steps. The dynamical properties are studied through the velocity autocorrelation function and the mean-square displacement. The self-diffusion coefficient and its behavior with the temperature, obtained from our simulations, shows the typical behavior of the simple liquids. Our results are compared to available experimental data.

Banuelos, E. U.; Amarillas, A. P.

2004-02-01

285

Molecular dynamics simulations of thermal conductivity of carbon nanotubes: Resolving the effects of many molecular dynamics (MD) simulation studies reported in the literature. The values of k obtained, atomistic molecular dynamics (MD) simulations present an attractive alternative. Indeed, atomistic

Zhigilei, Leonid V.

286

Molecular Dynamics Simulation of Site-Directed Spin Labeling: Experimental Validation in Muscle ABSTRACT We have developed a computational molecular dynamics technique to simulate the motions of spin determined molecular dynamics simulation conditions necessary for obtaining a convergent orientational

Thomas, David D.

287

Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations. PMID:25314544

Graziani, F R; Bauer, J D; Murillo, M S

2014-09-01

288

Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, “first principles” MD or “Car-Parrinello” method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics\\/chemistry (liquid phosphorus). Dynamical, finite

D. Hohl

1995-01-01

289

Experiments and Molecular Dynamics Simulations Ilya J. Finkelstein, Anne Goj, Brian L. McClain, Aaron M and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rateUltrafast Dynamics of Myoglobin without the Distal Histidine: Stimulated Vibrational Echo

Fayer, Michael D.

290

Dynamic Structure Factors from Lipid Membrane Molecular Dynamics Simulations

Dynamic structure factors for a lipid bilayer have been calculated from molecular dynamics simulations. From trajectories of a system containing 1024 lipids we obtain wave vectors down to 0.34 nm?1, which enables us to directly resolve the Rayleigh and Brillouin lines of the spectrum. The results confirm the validity of a model based on generalized hydrodynamics, but also improves the line widths and the position of the Brillouin lines. The improved resolution shows that the Rayleigh line is narrower than in earlier studies, which corresponds to a smaller thermal diffusivity. From a detailed analysis of the power spectrum, we can, in fact, distinguish two dispersive contributions to the elastic scattering. These translate to two exponential relaxation processes in separate time domains. Further, by including a first correction to the wave-vector-dependent position of the Brillouin lines, the results agree favorably to generalized hydrodynamics even up to intermediate wave vectors, and also yields a 20% higher adiabatic sound velocity. The width of the Brillouin lines shows a linear, not quadratic, dependence to low wave vectors. PMID:19254541

Brandt, Erik G.; Edholm, Olle

2009-01-01

291

Molecular dynamics simulation of radiation damage in bcc tungsten

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of collision cascades in pure tungsten are performed to assess the primary damage due to irradiation. For short-range interaction the universal potential is used [J.F. Ziegler, J.P. Biersack, U. Littmark, The Stopping and Range of Ions in Solids, Pergamon Press, 1985, p. 41], while for long-range interaction, three different embedded atom method potentials [M.W. Finnis, J.E. Sinclair, Phil. Mag. A 50 (1984) 45; G.J. Ackland, R. Thetford, Phil. Mag. A 56 (1987) 15; P.M. Derlet, D. Nguyen-Manh, S.L. Dudarev, Phys. Rev. B 76 (2007) 054107] are used, namely, Finnis-Sinclair, Ackland-Thetford and Derlet-Nguyen-Manh-Dudarev, the latter providing a more accurate formation energy for the <1 1 0> interstitial. The short-range and long-range potentials are smoothly connected. A new approach improving the reliability of such potential fits at short distances is presented. These potentials are then evaluated on the basis of displacement threshold, point defect formation and migration energies, thermal expansion and temperature of melting. Differences in the damage resulting from collision cascades are discussed.

Fikar, J.; Schäublin, R.

2009-04-01

292

Huge-scale molecular dynamics simulation of multibubble nuclei

NASA Astrophysics Data System (ADS)

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers.

Watanabe, Hiroshi; Suzuki, Masaru; Ito, Nobuyasu

2013-12-01

293

Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

294

Molecularly imprinted polymers—potential and challenges in analytical chemistry

Among the variety of biomimetic recognition schemes utilizing supramolecular approaches molecularly imprinted polymers (MIPs) have proven their potential as synthetic receptors in numerous applications ranging from liquid chromatography to assays and sensor technology. Their inherent advantages compared to biochemical\\/biological recognition systems include robustness, storage endurance and lower costs. However, until recently only few contributions throughout the relevant literature describe quantitative

J. O. Mahony; K. Nolan; M. R. Smyth; B. Mizaikoff

2005-01-01

295

Droplet evaporation: A molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations are used to model the evaporation of a Lennard-Jones argon nanodroplet into its own vapor for a wide range of ambient temperatures and ambient pressures. The transitions from (i) high to low Knudsen number evaporation and (ii) subcritical to supercritical evaporation are observed. At a low ambient pressure of 0.4 MPa, the initial droplet Knudsen number is 1 and the droplet diameter decreases linearly with time, consistent with kinetic theory predictions. For a moderate ambient pressure of 3.0 MPa, the initial droplet Knudsen number is 0.1 and the square of the droplet diameter decreases linearly with time. For a high ambient pressure of 6.1 MPa, the evaporation is supercritical and the number of atoms in the droplet decreases linearly for the majority of the droplet lifetime. A technique is introduced to maintain a constant ambient pressure over the droplet lifetime, allowing for the observation of the influence of the ambient conditions on the droplet surface temperature. When the ambient pressure is greater than or equal to 1.4 times the critical pressure, the droplet surface temperature reaches the critical temperature and the evaporation is supercritical. Below this ambient pressure, the droplet surface temperature reaches a pseudowet-bulb condition.

Landry, E. S.; Mikkilineni, S.; Paharia, M.; McGaughey, A. J. H.

2007-12-01

296

Molecular chaperone-mediated nuclear protein dynamics.

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

Echtenkamp, Frank J; Freeman, Brian C

2014-05-01

297

Integrating influenza antigenic dynamics with molecular evolution.

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

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

298

Molecular Dynamics Study of Helicobacter pylori Urease.

Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc. 2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine ?322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation. PMID:24839409

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

2014-05-13

299

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

300

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe. PMID:18271577

Furse, Kristina E; Lindquist, Beth A; Corcelli, Steven A

2008-03-13

301

DynamO: a free O(N) general event-driven molecular dynamics simulator.

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. PMID:21953566

Bannerman, M N; Sargant, R; Lue, L

2011-11-30

302

Nuclear molecular potentials based on a symplectic microscopic model

The symplectic model for single nuclei is extended to nuclear molecules. The authors construct the microscopic Hamiltonian. Rather than solving the Schroedinger equation in the microscopic space, they map the Hamiltonian to a potential in a phenomenological space with parameters related to the internuclear distance, deformation of the individual nuclei, and relative orientations. As examples they construct the potentials of the systems {sup 12}C-{sup 12}C and {sup 16}O-{sup 16}O and compare them to potentials obtained by other standard methods. The parameters of the potentials are fixed by experimental data of the individual nuclei. No further parameters are adjusted in the derivation of the internuclear potential. Using the microscope model they obtain better understanding of the structure of molecular potentials. 33 refs., 6 figs.

Hess, P.O.; Schmidt, J.; Scheid, W. [Institut fuer Theoretische Physik der Justus-Liebig-Universitaet, Gissen (Germany)] [Institut fuer Theoretische Physik der Justus-Liebig-Universitaet, Gissen (Germany)

1995-05-15

303

Multiscale molecular dynamics using the matched interface and boundary method

The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems. PMID:21088761

Geng, Weihua; Wei, G.W.

2010-01-01

304

Enhanced molecular dynamics for simulating porous interphase layers in batteries.

Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)

2009-10-01

305

Ab initio molecular dynamics of liquid hydrogen chloride

NASA Astrophysics Data System (ADS)

We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (?-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ?-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.

Dubois, Vincent; Pasquarello, Alfredo

2005-03-01

306

Molecular dynamics study of the mechanical loss in amorphous pure and doped silica

NASA Astrophysics Data System (ADS)

Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions.

Hamdan, Rashid; Trinastic, Jonathan P.; Cheng, H. P.

2014-08-01

307

Molecular-dynamics investigation of hydrogen hopping in palladium

Diffusive hopping of hydrogen in PdH/sub x/ has been reexamined with molecular-dynamics (MD) simulations in order to clarify earlier results of Gillan. We obtain the same values for the diffusion coefficient and width GAMMA/sub q/ of the quasielastic neutron scattering function when Gillan's potentials are used, but go beyond Gillan in performing a statistical analysis of the jumps. The analysis shows that over 95% of the jumps are uncorrelated and nearest neighbor, but the distribution of times between jumps is highly nonexponential. This latter feature accounts for the departure of GAMMA/sub q/, noted by Gillan, from the Chudley-Elliott (CE) theory based on simple one-step nearest-neighbor hopping. A simple physical model of the hopping as a two-step process can explain the results and suggests they are highly sensitive to the H-Pd potential at short distances. A new MD simulation with a harder-core potential gives a GAMMA/sub q/ in much better agreement with CE. We conclude that the non-CE behavior originally found by Gillan might be seen in real experiments on systems with suitably soft potentials.

Culvahouse, J.W.; Richards, P.M.

1988-11-15

308

Mechanical unfolding of a beta-hairpin using molecular dynamics

Single molecule mechanical unfolding experiments have the potential to provide insights into the details of protein folding pathways. To investigate the relationship between force-extension unfolding curves and microscopic events, we performed molecular dynamics simulations of the mechanical unfolding of the C-terminal hairpin of protein G. We have studied the dependence of the unfolding pathway on pulling speed, cantilever stiffness, and attachment points. Under conditions which generate low forces, the unfolding trajectory mimics the untethered, thermally accessible pathway previously proposed based on high temperature studies. In this stepwise pathway, complete breakdown of backbone hydrogen bonds precedes dissociation of the hydrophobic cluster. Under more extreme conditions, the cluster and hydrogen bonds break simultaneously. Transitions between folding intermediates can be identified in our simulations as features of the calculated force-extension curves.

Bryant, Zev; Pande, Vijay S.; Rokhsar, Daniel S.

1999-10-16

309

Study on C-W interactions by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

By means of molecular dynamics simulations using bond-order potential (BOP), we have investigated the interactions between carbon (C) atoms and bcc tungsten (W). At finite temperature ( T = 300 K) with incident energy of C atoms ranging from 0.5 to 100 eV at normal incidence, the projected range distribution as a function of incident energy and the average depth have been depicted. The properties of vacancy, vacancy migration, interstitial and substitutional C atoms in W have been determined. The most stable configuration for an interstitial C atom in W is in octahedral position and the lattice distortion around the C atom in octahedral interstitial configuration occurs along <1 0 0> and <1 1 0> directions. The mutual interaction between a vacancy and near interstitial C atom is also studied.

Yang, Zhongshi; Xu, Q.; Liao, Junqi; Li, Q.; Lu, G.-H.; Luo, G.-N.

2009-09-01

310

Effective interactions in molecular dynamics simulations of lysozyme solutions

NASA Astrophysics Data System (ADS)

In this article we explore a problem of effective interactions between two rotationally restrained lysozyme molecules forming a crystal contact in aqueous solution. We perform non-equilibrium molecular dynamics simulations in order to estimate the interaction energy as a function of the distance between the two proteins obtained from direct application of the Jarzynski equality (JE), and compare it with that calculated by means of another non-equilibrium approach (Forward-Reverse method) and constrained force methods. The performance of the JE equality when applied to solvated protein interactions is discussed. All of the equilibrium and non-equilibrium methods show clear evidence that the potentials of mean force (PMF) are short-ranged, do not exceed few kTs, and that there is an accumulation of anions in the presence of hydrophobic surfaces.

Pellicane, Giuseppe; Sarkisov, Lev

2014-09-01

311

Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.

We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide. PMID:25573551

Mugnai, Mauro L; Elber, Ron

2015-01-01

312

Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*

NASA Astrophysics Data System (ADS)

Results of recent experiments on polymer chains adsorbed from dilute solution at solid-liquid interface show the power scaling law dependence of the chain diffusivity, D, as a function of the degree of polymerization, N, D ˜ N^3/2. By contrast, DNA molecules bound to fluid cationic lipid bilayers follows Rouse dynamics with D ˜ N^1. We used molecular dynamics simulations to gain an understanding of these dissimilar scaling behaviors. Our model systems contain chains comprised of N monomers connected by anharmonic springs described by the finite extendible nonlinear elastic, FENE potential, embedded into a solvent of N=1 monomers. Two types of simulations we performed: (i) the chain is confined to two dimensions, (ii) the three dimensional chain in the solvent is confined between two solids plates. With randomly placed impenetrable obstacles on the surface, the diffusion of 2D chains exhibits, D ˜ N^3/2 behavior, when the chain radius of gyration, Rg, is larger than half the distance between obstacles, and D ˜ N^1 for shorter chains. In the presence of an athermal solvent, the scaling exponent is 0.75 due to hydrodynamic forces, for the two-dimensional system. We will also discuss the nature of dynamic adsorption transition and effects of hydrodynamics forces on chain diffusion for the three-dimensional simulations.

Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve

2004-05-01

313

CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS

This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.

Swanson, Jessica

2011-08-31

314

Can Dynamic Contact Angle Be Measured Using Molecular Modeling?

A method is presented for determining the dynamic contact angle at the three-phase contact between a solid, a liquid, and a vapor under an applied force, using molecular simulation. The method is demonstrated using a ...

Malani, Ateeque A. A. G.

315

Efficient Molecular Dynamics on a Network of Personal Computers

(PCs) connected by Fast Ethernet, GAMMA achieves much better communication performance compared lead to satisfactory performance. Keywords: Fast Ethernet; Molecular Dynamics; Network of workstations parallel applications in the scientific community. MD typically exhibits fairly good speedÂup figures

Ciaccio, Giuseppe

316

Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene

Using a realistic united-atom force field, molecular dynamics simulations were performed to study homogeneous nucleation of the crystal phase at about 30% supercooling from the melts of n-pentacontahectane (C150) and a ...

Yi, Peng

317

Molecular dynamics study of Cu-Pd ordered alloys

Purpose: The goal of the paper is to study the molecular dynamics of Cu-Pd ordered alloys. Design\\/methodology\\/approach: The thermal and mechanical properties of Cu, Pd pure metals and their ordered intermetallic alloys of Cu3Pd(L12) and CuPd3(L12) are studied by using the molecular dynamics simulation. The melting behavior of the metals considered in this work is studied by utilizing quantum Sutton-Chen

S. Özdemir Kart; A. Erbay; H. Kiliç; T. Cagin; M. Tomak

2008-01-01

318

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176

2013-01-01

319

Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding

Frederic Stahl; Daniel P. Berrar; Candida Silva; R. J. Rodrigues; Rui M. M. Brito; Werner Dubitzky

2005-01-01

320

Elucidation of molecular dynamics of invasive species of rice

Technology Transfer Automated Retrieval System (TEKTRAN)

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

321

NASA Astrophysics Data System (ADS)

This special section of Comments on Atomic, Molecular and Optical Physics (CAMOP) in Physica Scripta collects some of the papers that have been presented at the 18th European Conference on Dynamics of Molecular Systems MOLEC 2010 held in September 2010 in Curia, Portugal, as part of a series of biennial MOLEC conferences. This started in 1976 in Trento, Italy, and has continued, visiting 17 cities in 11 countries, namely Denmark, The Netherlands, Israel, France, Italy, Germany, Czech Republic, Spain, United Kingdom, Turkey and Russia. Following the MOLEC tradition, the scientific programme of the Curia meeting focused on experimental and theoretical studies of molecular interactions, collision dynamics, spectroscopy, and related fields. It included invited speakers from 22 countries, who were asked to summarize the problems reported in their presentations with the objective of revealing the current thinking of leading researchers in atomic, molecular and optical physics. It is hoped that their authoritative contributions presented in this CAMOP special section will also appeal to non-specialists through their clear and broad introductions to the field as well as references to the accessible literature. This CAMOP special section comprises ten contributions, which cover theoretical studies on the electronic structure of molecules and clusters as well as dynamics of elastic, inelastic and reactive encounters between atoms, molecules, ions, clusters and surfaces. Specifically, it includes electronic structure calculations using the traditional coupled-cluster method (Barreto et al 028111), the electron-attached equation-of-motion coupled cluster method (Hansen et al 028110), the diffusion Monte Carlo method (López-Durán et al 028107) and the path-integral Monte Carlo method (Barragán et al 028109). The contributions on molecular dynamics include on-the-fly quasi-classical trajectories on a five-atom molecule (Yu 028104), quantum reaction dynamics on triatomics (Bovino et al 028103, and Hankel et al 028102) and statistical reaction dynamics using a model based on the long-range interaction potential (McCarroll 028106). A contribution on gas-surface interactions is also included (Sahoo et al 028105) as well as first-principles ab initio calculations to explore the hydrogen-graphene interaction (Irving et al 028108). These articles reflect the recent progress made in this field and constructively build on work described in the previous three MOLEC special sections of CAMOP published in Physica Scripta. I thank, on behalf of the scientific organizing committee of MOLEC, all the authors who contributed and Physica Scripta for providing a platform for the publication of this special section dedicated to MOLEC 2010. A special thanks goes to the CAMOP Editor, Harold Linarz, for the excellent guidance in handling the editorial work. I hope that the articles catalyze the attention of the readers towards the topics covered and contribute in attracting them to attend MOLEC 2012 in Oxford, UK.

Varandas, A. J. C.

2011-08-01

322

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

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

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

323

The molecular dynamics of metabolites is structure dependent and vitally important for the interactive functions in their potential applications as natural materials. To understand the relationship between molecular structure and dynamics, the molecular motions of four structurally related ?-amino acids (?-alanine, ?-aminobutyric acid, 5-aminovaleric acid, and 6-aminocaproic acid) were investigated by measuring their proton spin-lattice relaxation times (T(1), T(1?)) as a function of temperature (180-440 K). (13)C CPMAS NMR and DSC analyses were performed to obtain complementary information. All of these ?-amino acids showed no phase transition in the temperature range studied but had outstandingly long proton T(1) at 300 MHz and even at 20 MHz for the deuterated forms. The molecular dynamics of all these ?-amino acids were dominated by the reorientation motions of amino groups and backbone motions except in ?-alanine. The activation energies for amino group reorientations were positively correlated with the strength of hydrogen bonds involving these groups in the crystals and the carbon-chain lengths, whereas such energies for the backbone motions were inversely correlated with the carbon-chain lengths. These findings provided essential information for the molecular dynamics of ?-amino acids and demonstrated the combined solid-state NMR methods as a useful approach for understanding the structural dependence of molecular dynamics. PMID:22251439

Huang, Jing; Zhang, Limin; Tang, Huiru

2012-02-23

324

Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics

Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322

M’Koma, Amosy E

2014-01-01

325

Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.

Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn's colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322

M'Koma, Amosy E

2014-11-27

326

Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination. PMID:21233509

Feng, Yaoyu; Xiao, Lihua

2011-01-01

327

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

Johnston, Jennifer M.

2014-01-01

328

Dynamic strength of molecularly bonded surfaces

NASA Astrophysics Data System (ADS)

This study reports a theoretical analysis of the forced separation of two adhesive surfaces linked via a large number of parallel noncovalent bonds. To describe the bond kinetics, we implement a three-state reaction model with kinetic rates obtained from a simple integral expression of the mean first passage time for diffusive barrier crossing in a pulled-distance-dependent potential. We then compute the rupture force for the separation of adhesive surfaces at a constant rate. The results correspond well with a Brownian dynamics simulation of the same system. The separation rate relative to the intrinsic relaxation time of the bonds defines three loading regimes and the general dependence of the adhesion on kinetic or thermodynamic parameters of the bonds. In the equilibrium regime, the rupture force asymptotically approaches the equilibrium rupture force, which increases linearly with the equilibrium bond energy. In the near-equilibrium regime, the rupture force increases with the separation rate and increasingly correlates with the bond rupture barrier. In the far-from-equilibrium regime where rebinding is irrelevant, the rupture force varies linearly with the rupture barrier.

Li, Fang; Leckband, Deborah

2006-11-01

329

Mechanical Properties of Palladium with Defects and Impurities: a Molecular Dynamics Study

Stress strain relations and failure strengths are determined for pure palladium, palladium with various sized helium bubbles, and palladium with hydrogen loading. The embedded atom method is used to model the potential in Parrinello-Rahman HtN molecular dynamics. The bubbles were found to be stable entities up to the point of failure. The failure strengths of the palladium crystals were lowered

Thomas Vincent Graham

1994-01-01

330

Molecular dynamics study on superheating of Pd at high heating rates

Molecular dynamics simulations are employed here to study the melting and superheating behaviors of bulk Palladium at high heating rates. Quantum Sutton-Chen many body potential is used for these simulations. Being heated, the superheating and melting behavior is found to be strongly affected by the heating rate, and heating rate induced randomization during non-equilibrium heating processes is found to be

Xin Liu; Changgong Meng; Changhou Liu

2006-01-01

331

Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations

Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics. The statistics of the main lipidÂlipid interactions, the charge density profiles, the electrostatic potential or neutral. Even in phospholipid bi- layers with neutral headgroups, the electrostatic interactions

Saiz, Leonor

332

Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes

Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes YASUSHI SHIBUTA, SHIGEO MARUYAMA Nucleation process of single-walled carbon nanotubes by the catalytic chemical on these potentials, interactions between catalytic metals and carbon atoms on formation process of single-walled

Maruyama, Shigeo

333

On the potential for molecular imaging with Cerenkov luminescence.

Recent observation of optical luminescence due to beta decay from suitable radiotracers has led to the possible development of new preclinical optical imaging methods. The generation of photons that can be detected using instrumentation optimized for bioluminescence imaging has been putatively associated with the Cerenkov effect. We describe the simultaneous utilization of fluorescence reporters to convert Cerenkov luminescence to longer wavelengths for better tissue penetration and also for modulating the luminescence spectrum for potential molecular imaging strategies. PMID:21124555

Lewis, Matthew A; Kodibagkar, Vikram D; Öz, Orhan K; Mason, Ralph P

2010-12-01

334

On the potential for molecular imaging with Cerenkov luminescence

Recent observation of optical luminescence due to beta decay from suitable radiotracers has led to the possible development of new preclinical optical imaging methods. The generation of photons that can be detected using instrumentation optimized for bioluminescence imaging has been putatively associated with the Cerenkov effect. We describe the simultaneous utilization of fluorescence reporters to convert the Cerenkov luminescence to longer wavelengths for better tissue penetration and also for modulating the luminescence spectrum for potential molecular imaging strategies. PMID:21124555

Lewis, Matthew A.; Kodibagkar, Vikram D.; Öz, Orhan K.; Mason, Ralph P.

2011-01-01

335

Molecular Dynamics Simulations of Protein Dynamics and their relevance to drug discovery

Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery. PMID:20971684

Salsbury, Freddie R.

2010-01-01

336

1 Dynamic viscosity estimation of hydrogen sulfide using a predictive scheme based on molecular on molecular dynamics results on Lennard-Jones spheres is proposed to model the viscosity of hydrogen sulfide is that the adjustment does not involve any viscosity data because only density values have been used in order

Boyer, Edmond

337

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

An increasing number of studies have reported computations of the absolute binding free energy of small ligands to proteins using molecular dynamics (MD) simulations with results that are in good agreement with experiments. This encouraging progress suggests that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future. Two types of approaches are principally used to compute binding free energies with MD simulations. The most widely known are based on alchemical free energy methods, in which the interaction of the ligand with its surrounding are progressively switched off. An alternative method is to use a potential of mean force (PMF), in which the ligand is physically separated from the protein receptor. For both of these computational approaches, restraining potentials affecting the translational, rotational and conformational freedom of the ligand and protein may be activated and released during the simulations to aid convergence and improve the sampling. Such restraining potentials add bias to the simulations, but their effects can be rigorously removed to yield a binding free energy that is properly unbiased with respect to the standard state. A review of recent results is presented. Examples of computations with T4-lysozyme mutants, FKBP12, SH2 domain, and cytochrome P450 are discussed and compared. Differences in computational methods are discussed and remaining difficulties and challenges are highlighted. PMID:19146384

Deng, Yuqing; Roux, Benoît

2013-01-01

338

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

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 ?-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26–27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K+ channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K+ and Na+ concentration gradients and the electrostatic potential difference of living cells. PMID:24081985

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

2013-01-01

339

NASA Astrophysics Data System (ADS)

We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we describe how nuclear quantum dynamics beyond the Born-Oppenheimer approximation can be performed using quantum trajectories. Finally, the coupling and control of an external electromagnetic field with mixed quantum/classical trajectory surface hopping is discussed.

Curchod, Basile F. E.; Penfold, Thomas J.; Rothlisberger, Ursula; Tavernelli, Ivano

2013-09-01

340

We use molecular dynamics simulations with the reactive potential ReaxFF to investigate the initial reactions and subsequent decomposition in the high-energy-density material ?-HMX excited thermally and via electric fields at various frequencies. We focus on the role of insult type and strength on the energy increase for initial decomposition and onset of exothermic chemistry. We find both of these energies increase with the increasing rate of energy input and plateau as the processes become athermal for high loading rates. We also find that the energy increase required for exothermic reactions and, to a lesser extent, that for initial chemical reactions depend on the insult type. Decomposition can be induced with relatively weak insults if the appropriate modes are targeted but increasing anharmonicities during heating lead to fast energy transfer and equilibration between modes that limit the effect of loading type. PMID:24400687

Wood, Mitchell A; van Duin, Adri C T; Strachan, Alejandro

2014-02-01

341

NASA Astrophysics Data System (ADS)

Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture, at neutral condition, the exterior residues folding back into interior would necessarily

Wu, Bin

342

227 The growing amount of high quality molecular dynamics simulations generated using the latest molecular dynamics MMD multiple molecular dynamics N number of particles constituting the system PME particle-mesh-Ewald rmsd root mean square deviation Introduction Since the first molecular dynamics (MD

Westhof, Eric

343

Quantitative FRAP in Analysis of Molecular Binding Dynamics In Vivo

Fluorescence recovery after photobleaching (FRAP) reveals the dynamics of fluorescently tagged molecules within live cells. These molecular dynamics are governed by diffusion of the molecule and its in vivo binding interactions. As a result, quantitative estimates of the association and dissociation rates of binding can be extracted from the FRAP. This chapter describes a systematic procedure to acquire the FRAP

James G. McNally

2008-01-01

344

Ideal Brittle Fracture of Silicon Studied with Molecular Dynamics

Dynamic fracture experiments measure crack velocity versus energy flux to the tip. We report here the first calculation of this quantity in a realistic setting, using molecular dynamics to study silicon. The results require relating the short length and time scales of simulations to the long length and time scales of experiments.

Dominic Holland; M. Marder

1998-01-01

345

Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.

Desai, Tapan; Keblinski, Pawel

2003-03-01

346

Molecular dynamics simulation of pervaporation in zeolite membranes

NASA Astrophysics Data System (ADS)

The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify intermolecular interactions between water, methanol, ethanol and the membrane surface that play a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial-and-error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems, including the hydrophobic or hydrophilic behaviour of zeolite membranes. The simulations showed that, for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor, as a consequence, increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.

Jia, W.; Murad, S.

347

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study.

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water. PMID:22713055

Bandyopadhyay, Dibyendu; Choudhury, Niharendu

2012-06-14

348

Molecular dynamics simulations of the mechanical properties of monoclinic hydroxyapatite.

Inorganic biomedical materials are of great interest in the biomedical field. One such material, hydroxyapatite (HAP), is the main inorganic substance in the hard tissue of bones and teeth in the human body. Until recently, studies of the mechanical properties of HAP by uniaxial tension testing and compression molecular dynamics (MD) simulation had remained difficult. In addition, electric charges used in such simulations alter the molecular structure of HAP. Here, we present the mechanical properties and new charges of the monoclinic form of HAP using the self-consistent charge equilibration (QEq) scheme proposed by Rappé and Goddard in 1991 (J Phys Chem 95:3358-3363), and a successful MD simulation of the uniaxially tensile and compressive properties of monoclinic HAP. Also presented is the change in potential energy in the cell and how temperature and strain rate affect the uniaxial tension and compressive properties of HAP. Additionally, we compare the mechanical properties of this substance along different directions, and some conclusions useful for further studies of the mechanical properties of HAP composite materials are discussed. PMID:25352517

Ou, Xiang; Han, Qiang

2014-11-01

349

Unfixed cryosections of striated muscle to study dynamic molecular events.

The structures of the actin and myosin filaments of striated muscle have been studied extensively in the past by sectioning of fixed specimens. However, chemical fixation alters molecular details and prevents biochemically induced structural changes. To overcome these problems, we investigate here the potential of cryosectioning unfixed muscle. In cryosections of relaxed, unfixed specimens, individual myosin filaments displayed the characteristic helical organization of detached cross-bridges, but the filament lattice had disintegrated. To preserve both the filament lattice and the molecular structure of the filaments, we decided to section unfixed rigor muscle, stabilized by actomyosin cross-bridges. The best sections showed periodic, angled cross-bridges attached to actin and their Fourier transforms displayed layer lines similar to those in x-ray diffraction patterns of rigor muscle. To preserve relaxed filaments in their original lattice, unfixed sections of rigor muscle were picked up on a grid and relaxed before negative staining. The myosin and actin filaments showed the characteristic helical arrangements of detached cross-bridges and actin subunits, and Fourier transforms were similar to x-ray patterns of relaxed muscle. We conclude that the rigor structure of muscle and the ability of the filament lattice to undergo the rigor-relaxed transformation can be preserved in unfixed cryosections. In the future, it should be possible to carry out dynamic studies of active sacromeres by cryo-electron microscopy. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 PMID:7819493

Ménétret, J F; Craig, R

1994-01-01

350

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials. PMID:21052521

Fonner, John M.; Schmidt, Christine E.; Ren, Pengyu

2010-01-01

351

Reactive Molecular Dynamics Simulations at the Petascale (Invited)

NASA Astrophysics Data System (ADS)

We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.

Nakano, A.

2013-12-01

352

Volume Determination of Globular Proteins by Molecular Dynamics

Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate aminotransferase is known to produce large volumetric changes in the enzyme, and this effect is demonstrated in simulation as well. This molecular dynamics approach, while more computationally expensive that extant computational methods of determining the apparent volume of biological systems, is quite feasible with modern computer hardware and is shown to yield accurate volumetric data with as little as several nanoseconds of dynamics.

Belof, Jonathan L; Larsen, Randy W; Space, Brian

2014-01-01

353

Volume Determination of Globular Proteins by Molecular Dynamics

Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate aminotransferase is known to produce large volumetric changes in the enzyme, and this effect is demonstrated in simulation as well. This molecular dynamics approach, while more computationally expensive that extant computational methods of determining the apparent volume of biological systems, is quite feasible with modern computer hardware and is shown to yield accurate volumetric data with as little as several nanoseconds of dynamics.

Jonathan L. Belof; Edward W. Lowe; Randy W. Larsen; Brian Space

2014-04-06

354

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. PMID:20440377

Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy

2010-01-01

355

dynamics simulation Ibrahim M. Moustafa Department of Biochemistry and Molecular Biology Eberly CollegeRole of dynamics in tuning fidelity of RNA-dependent RNA polymerase elucidated by molecular fidelity is not clear but suggested to be linked to dynamics of the enzyme [1]. By using molecular dynamics

BjÃ¸rnstad, Ottar Nordal

356

Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

NASA Astrophysics Data System (ADS)

We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

2015-01-01

357

A computational toy model for shallow landslides: Molecular Dynamics approach

The aim of this paper is to propose a 2D computational algorithm for modeling of the trigger and the propagation of shallow landslides caused by rainfall. We used a Molecular Dynamics (MD) inspired model, similar to discrete element method (DEM), that is suitable to model granular material and to observe the trajectory of single particle, so to identify its dynamical properties. We consider that the triggering of shallow landslides is caused by the decrease of the static friction along the sliding surface due to water infiltration by rainfall. Thence the triggering is caused by two following conditions: (a) a threshold speed of the particles and (b) a condition on the static friction, between particles and slope surface, based on the Mohr-Coulomb failure criterion. The latter static condition is used in the geotechnical model to estimate the possibility of landslide triggering. Finally the interaction force between particles is defined trough a potential that, in the absence of experimental data, we have mode...

Martelloni, Gianluca; Massaro, Emanuele

2012-01-01

358

Accelerated molecular dynamics of Co/Cu(001) heteroepitaxy

NASA Astrophysics Data System (ADS)

We extend the Bond-Boost Method [1] for accelerated molecular dynamics (MD) of rare events to handle processes occuring on widely separated timescales. In many systems, a small number of recurrent processes can be orders of magnitude faster than ordinary diffusion events such as adatom hopping, imposing severe limitations on the achievable simulation timescale. Our method addresses this problem via a special treatment of fast processes which preserves the correct coarse-grained dynamics yet allows the simulation timescale to be tuned to the slow events of interest. We apply the method to accelerated MD simulations of Co/Cu(001) heteroepitaxial growth using an empirical Tight-Binding (TBSMA) potential [2], and we are able to reach both the temperature (200-300K) and deposition flux (0.1 - 1 ML/s) ranges relevant to experimental conditions. We explain the experimentally observed bilayer island growth mode [3], and analyze the impact of high cluster mobility on the island density by comparing our results with DFT-KMC and experimental studies [4]. [1] R.A. Miron and K.A. Fichthorn, J. Chem. Phys. 119, 6210 (2003) [2] N.A. Levanov et.al., Phys. Rev. B 61, 2230 (2000) [3] J. Fassbender et.al., Surf. Sci. 383, L742 (1997) [4] R. Pentcheva et.al., Phys. Rev. Lett. 90, 076101 (2003)

Miron, Radu; Fichthorn, Kristen

2004-03-01

359

Molecular dynamics simulation of irradiation damage in tungsten

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations have been performed for the radiation damage of tungsten using a modified Finnis-Sinclair type many-body interatomic potential. The interstitial defects and vacancies are distinguished by the Wigner-Seitz cell method and the types of the interstitial dumbbells are also identified by the azimuth and polar angles of dumbbell line vectors. It is observed that the number of interstitial defects and vacancies initially sharply increases and passing through the peak position, relaxes to the steady state for all PKA energies and that all residual interstitial dumbbells at the steady state are the <1 1 1>-oriented. Based on the variation of the orientation angles of dumbbells during the radiation damage simulation, it is found that the recombination of the <1 1 1>-oriented dumbbells with the vacancies is much faster than that of two other types of dumbbells and that the population of the <1 0 0> dumbbells is much larger than that of the <1 1 0> ones in spite of its higher formation energy, the reason of which is explained with the dynamics of the individual dumbbell.

Park, Na-Young; Kim, Yu-Chan; Seok, Hyun-Kwang; Han, Seung-Hee; Cho, Seungyon; Cha, Pil-Ryung

2007-12-01

360

Molecular dynamics simulations were carried out for hydrogen absorption by palladium in various atomic ratios to identify the reason why hydrogen absorption heat changes from exothermic to endothermic at a high atomic ratio. Classical two-body interactions were used as interatomic potentials for these simulations in order to simplify the calculation. Pd-Pd and Pd-H interatomic potentials were determined empirically by fitting

Daigo Fukushi; Sotoji Hiragi; Takuya Honda

2000-01-01

361

Soliton dynamics in symmetric and non-symmetric complex potentials

NASA Astrophysics Data System (ADS)

Soliton propagation dynamics under the presence of a complex potential are investigated. A large variety of qualitatively different potentials, including periodic, semi-infinite periodic and localized potentials, is considered. Cases of both symmetric and non-symmetric potentials are studied in terms of their effect on soliton dynamics. The rich set of dynamical features of soliton propagation includes dynamical trapping, periodic and non-periodic soliton mass variation and non-reciprocal scattering dynamics. These features are systematically investigated with the utilization of an effective particle phase space approach which is shown in remarkable agreement with direct numerical simulations. The generality of the results enables the consideration of potential applications where the inhomogeneity of the gain and loss is appropriately engineered in order to provide desirable soliton dynamics.

Kominis, Yannis

2015-01-01

362

Application of molecular dynamics simulations for structural studies of carbon nanotubes.

Molecular dynamics studies based on the Brenner-Tersoff second-generation reactive empirical bond order potential and the Lennard-Jones carbon-carbon potential for intra- and inter-layer interactions have been performed for carbon nanotubes. These potentials reproduce reasonably the carbon-carbon distances and inter-layer spacing. The structure factors and the reduced radial distribution functions computed from the cartesian coordinates, resulting from energy minimisation and molecular dynamics simulations at 2 K and 300 K have been obtained for two models of two- and five-wall carbon nanotubes containing defects in the form of five and seven membered carbon rings. The results of computations have been compared with experimental data obtained from neutron and X-ray diffraction. The energy relaxation and the molecular dynamics simulations at 2 K and 300 K with appropriate values of the Debye-Waller factor lead practically to the same results which are in a good agreement with the experimental data indicating that molecular dynamics reproduce all structure features of the investigated carbon nanotubes together with thermal oscillations. Possible applications of this approach for other carbon nanotubes and related materials have been also discussed. PMID:17450918

Bródka, A; Ko?oczek, J; Burian, A

2007-01-01

363

Molecular dynamics simulation of clusters, liquid, and interface of carbon tetrachloride

A five-site polarizable carbon tetrachloride (CCl4) interaction potential model has been developed that reproduces reasonably well the structural and thermodynamic properties of bulk liquid CCl4. Molecular dynamics simulations with this potential are carried out to investigate the CCl4 vapor-liquid interface. The structure of the interface is characterized by the density profile and the molecular orientation analyses. A detailed study of salvation properties of Cs+ in small CCl4 clusters and bulk CCl4 will also be presented.

Chang, T.M.; Dang, L.X. [Pacific Northwest Lab., Richland, WA (United States)

1995-12-01

364

Molecular dynamics simulation of graphene bombardment with Si ion

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations with Tersoff-Ziegler-Biersack-Littmark (Tersoff-ZBL) potential and adaptive intermolecular reactive empirical bond order (AIREBO) potential are performed to study the effect of irradiated graphene with silicon ion at several positions and energy levels of 0.1-1000 eV. The simulations reveal four processes: absorption, replacement, transmission and damage. At energies below 110 eV, the dominant process is absorption. For atom in group (a), the process that takes place is replacement, in which the silicon ion removes one carbon atom and occupies the place of the eliminated atom at the incident energy of 72-370 eV. Transmission is present at energies above 100 eV for atom in group (d). Damage is a very important process in current bombardment, and there are four types of defects: single vacancy, replacement-single vacancy, double vacancy and nanopore. The simulations provide a fundamental understanding of the silicon bombardment of graphene, and the parameters required to develop graphene-based devices by controlling defect formation.

Qin, Xin-Mao; Gao, Ting-Hong; Yan, Wan-Jun; Guo, Xiao-Tian; Xie, Quan

2014-03-01

365

Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster

Timothy Campbell; Rajiv K. Kalia; Aiichiro Nakano; Priya Vashishta; Shuji Ogata; Stephen Rodgers

1999-01-01

366

Molecular dynamics study of the weakly solvent dependent relaxation dynamics following chlorine The solvation dynamics following photoexcitation of chlorine dioxide OClO in different solvents are investigated chemistry.1Â3 Representative of this group of compounds, chlorine dioxide OClO has been the subject of much

367

Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.

Wang, LiYa; Wang, FengChao; Yang, FuQian; Wu, HengAn

2014-11-01

368

Population Dynamics and Harvest Potential of Mountain

The understanding of population dynamics is a central issue for managing large mammals. Modeling has allowed population ecologists to increase their knowledge about complex systems and better predict population responses to diverse perturbations. Mountain goats (Oreamnos americanus) appear sensitive to harvest, but the relative influence of survival and reproductive rates on their population dynamics are not well understood. Using longitudinal

SANDRA HAMEL; STEEVE D. COTE; MARCO FESTA-BIANCHET

369

Molecular dynamics study of liquid methanol with a flexible three-site model

A new potential is presented which describes the methanol-methanol interactions on the basis of a flexible three-site model. The intramolecular part of the potential has been derived from spectroscopic data. A molecular dynamics study has been performed with this potential at 286 K. The structural properties of liquid methanol calculated from the simulations are in good agreement with X-ray measurements. The average geometrical arrangement of nearest neighbors and their hydrogen bonding are discussed. The potential describes correctly the gas-liquid frequency shifts of the intramolecular vibrations. Several thermodynamic properties calculated from the simulation compare favorably with experimental results.

Palinkas, G.; Hawlicka, E.; Heinzinger, K.

1987-07-30

370

Estimation of tangential momentum accommodation coefficient using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

The Tangential Momentum Accommodation Coefficient (TMAC) is used to improve the accuracy of fluid flow calculations in the slip flow regime. Under such conditions the continuum assumption that a fluid velocity at a solid surface is equal to the surface velocity is inaccurate because relatively significant fluid "slip" occurs at the surface. In this work, Molecular Dynamics techniques are used to study the impacts of individual gas atoms upon solid surfaces to understand how approach velocity, crystal geometry and interatomic forces affect the scattering of the gas atoms, specifically from the perspective of tangential momentum. The gas - solid impacts were modeled using Lennard Jones potentials. Solid surfaces were modeled with approximately 3 atoms wide by 3 atoms deep by 40 or more atoms long. The crystal surface was modeled as a Face Centered Cubic (100). The gas was modeled as individual free gas atoms. Gas approach angles were varied from 10° to 70° from normal. Gas speed was either specified directly or by way of a ratio relationship with the Lennard-Jones energy potential (Energy Ratio). For each impact the initial and final tangential momenta were determined and after a series of many impacts, a value of TMAC was calculated for those conditions. The modeling was validated with available experimental data for He gas atoms at 1770 m/s impacting Cu over angles ranging from 10° to 70°. The model agreed within 3% of the experimental values and correctly predicted that the coefficient changes with angle of approach. Molecular Dynamics results estimate TMAC values from a high of 1.2 to a low of 0.25, generally estimating a higher coefficient at the smaller angles. TMAC values above 1.0 indicate backscattering, which has been experimentally observed in numerous instances. Increasing the Energy Ratio above a value of 5 tends to decrease the coefficient at all angles. Adsorbed layers atop a surface influence the coefficient similar to their Energy Ratio. The results provide encouragement to develop the model further, so as to be able in the future to evaluate TMAC for gas flows with Maxwell temperature distributions involving numerous impact angles simultaneously.

Finger, George Wayne

371

Molecular Dynamics Simulations of a Liquid Droplet in Contact with a Solid Surface

Molecular Dynamics Simulations of a Liquid Droplet in Contact with a Solid Surface Shigeo MARUYAMA to predict the kinetic behavior of interfaces. Hence, an example of the molecular dynamics simulation molecular species, liquid-solid and vapor-solid interfaces of different species. Molecular dynamics

Maruyama, Shigeo

372

3358 J. Phys. Chem. 1991,95, 3358-3363 Charge Equilibration for Molecular Dynamics Simulations

3358 J. Phys. Chem. 1991,95, 3358-3363 Charge Equilibration for Molecular Dynamics Simulations and change during molecular dynamics calculations. We indicate how this approach can also be used to predict hy- drogen bonding) in molecular mechanics and molecular dynamics calculations.I4 Unfortunately

Goddard III, William A.

373

, prototyping tools based on molecular dynamics (MD) simulators should be developed in order to understandMicroelectronics Journal 39 (2008) 190Â201 Prototyping bio-nanorobots using molecular dynamics Abstract This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled

Mavroidis, Constantinos

374

State-to-state dynamics of molecular energy transfer

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

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01

375

Dynamic Nanodevices Based on Protein Molecular Motors

Most of the present micro\\/nano biodevices are designed for a single use, as opposed to ‘classical’ non-biodevices (e.g., from\\u000a the steam engine to the microchip). Once their function, be that simple molecular recognition like in microarrays or even\\u000a biomolecular computation as in DNA computation arrays, is fulfilled and the information is passed further to signal and information\\u000a processing systems, the

Dan V. Nicolau

376

Multimode Dynamics of a Coupled Ultracold Atomic-Molecular System

NASA Astrophysics Data System (ADS)

We analyze the coherent multimode dynamics of a system of coupled atomic and molecular Bose gases. Starting from an atomic Bose-Einstein condensate with a small thermal component, we observe a complete depletion of the atomic and molecular condensate modes on a short time scale due to a significant population of excited states. Giant coherent oscillations between the two condensates for typical parameters are almost completely suppressed. Our results cast serious doubts on the common use of the 2-mode model for the description of coupled ultracold atomic-molecular systems and should be considered when planning future experiments with ultracold molecules.

Góral, Krzysztof; Gajda, Mariusz; Rza?ewski, Kazimierz

2001-02-01

377

Snake venom metalloproteinase (SVMP) (Echis coloratus (Carpet viper) is a multifunctional enzyme that is involved in producing several symptoms that follow a snakebite, such as severe local hemorrhage, nervous system effects and tissue necrosis. Because the three-dimensional (3D) structure of SVMP is not known, models were constructed, and the best model was selected based on its stereo-chemical quality. The stability of the modeled protein was analyzed through molecular dynamics (MD) simulation studies. Structure-based virtual screening was performed, and 15 potential molecules with the highest binding energies were selected. Further analysis was carried out with induced fit docking, Prime/MM-GBSA (?GBind calculations), quantum-polarized ligand docking, and density functional theory calculations. Further, the stability of the lead molecules in the SVMP-active site was examined using MD simulation. The results showed that the selected lead molecules were highly stable in the active site of SVMP. Hence, these molecules could potentially be selective inhibitors of SVMP. These lead molecules can be experimentally validated, and their backbone structural scaffold could serve as building blocks in designing drug-like molecules for snake antivenom. PMID:25192471

Chinnasamy, Sathishkumar; Chinnasamy, Selvakkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan

2014-09-30

378

MOLECULAR DYNAMICS: Biomolecules See the Light

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Detailed knowledge of the dynamics of biomolecules is crucial for the treatment of human diseases, but is often hard to come by. In his Perspective, Pratt highlights the report of Dian et al., who have developed a method for manipulating the populations of different conformational states of small biomolecules that allows distinct folding pathways to be distinguished. If the method can be extended to larger molecules, it should provide important insights into their dynamics.

David W. Pratt (University of Pittsburgh;Department of Chemistry)

2002-06-28

379

VUV studies of molecular photofragmentation dynamics

State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01

380

Quantum dynamics of a molecular matter-wave amplifier

We study the quantum dynamics of a model of molecular matter-wave amplifier proposed by Search and Meystre [Phys. Rev. Lett. 93, 140405 (2004)], which employs a strongly damped optical cavity to convert an atomic Bose-Einstein condensate into vibrational ground-state molecules. By using the Monte Carlo wave-function method, we calculate the quantum evolution of the atomic and molecular matter waves. We find that the system always evolves into a pure ground-state molecular matter wave even if initially there was no ground-state molecules. Statistical properties of these atomic and molecular matter waves are also investigated. The final state of the molecular field is sub-Poissonian. Two-mode correlation functions exhibit anticorrelated properties.

Cheng, Jing [School of Physical Science and Technology, South China University of Technology, Guangzhou 510640 (China); Yan, YiJing [Department of Chemistry, Hong Kong University of Science and Technology, Kowloon (Hong Kong)

2007-03-15

381

Molecular Dynamics Simulations with IMD Johannes Roth, JÂ¨org Stadler, Marco Brunelli, Franz G Abstract. We describe IMD (ITAP Molecular Dynamics), a software package for classical molecular dynamics dynamics (MD) simulations in two or three dimensions. The basic implementation of IMD and a description

GÃ¤hler, Franz

382

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

Generalized Langevin models of molecular dynamics simulations with applications to ion channels Dan present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile

Krishnamurthy, Vikram

383

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations Arvind as molecular dynamics simulations progress. Our representation of MD simulations as a stream of continuously-dimensional structure, dynamics and function is underway. Molecular dynamics (MD) / Monte-Carlo (MC) simulations have

Langmead, Christopher James

384

Steered molecular dynamics simulations of protein-ligand interactions

Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational\\u000a drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques\\u000a in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and\\u000a kinetic processes of ligand-receptor binding and unbinding, which cannot be

Yechun Xu; Jianhua Shen; Xiaomin Luo; Xu Shen; Kaixian Chen; Hualiang Jiang

2004-01-01

385

Constrained molecular dynamics simulations of atomic ground states

The constrained molecular dynamics model, previously introduced for nuclear dynamics, has been extended to the atomic structure and collision calculations. Quantum effects, corresponding to the Pauli and Heisenberg principles, are enforced by constraints, following the idea of the Lagrange multiplier method. Our calculations for a small atomic system, H, He, Li, Be, and F reproduce the ground-state binding energies reasonably, compared with the experimental data. We discuss also the shell splitting due to e-e correlation.

Kimura, Sachie; Bonasera, Aldo [Laboratorio Nazionale del Sud, INFN, via Santa Sofia, 62, 95123 Catania (Italy)

2005-07-15

386

A fast recursive algorithm for molecular dynamics simulation

NASA Technical Reports Server (NTRS)

The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

Jain, A.; Vaidehi, N.; Rodriguez, G.

1993-01-01

387

Computation of molecular vibrational frequencies using anomalous harmoniclike potentials

NASA Astrophysics Data System (ADS)

The instabilities of Hartree-Fock (HF) solutions at or near the equilibrium geometry of symmetric molecular species imply the existence of broken-symmetry solutions having a lower energy than the corresponding symmetry-adapted ones. Moreover, the distortion of the nuclear framework along the normal modes that are implied by such broken-symmetry solutions results in an anomalous or even singular behavior in the corresponding cuts of the potential energy surface (PES). Using such HF solutions as a reference, these anomalies propagate to a post-HF level and make it impossible to determine reliable harmonic or fundamental vibrational frequencies for such modes by relying on either numerical or analytical differentiation of the PES, requiring instead a numerical integration of the Schrödinger equation for the nuclear motion. This, in turn, requires a detailed knowledge on the PES in a wide range of geometries, necessitating a computation of the potential energy function in a large number of points. We present an alternative approach to this problem, referred to as the integral averaging method (IAM), which facilitates this task by significantly reducing the number of geometries for which one has to compute the potential energy while yielding results of practically the same accuracy as the solution of the Schrödinger equation. The IAM is applied to several ABA-type triatomics and to the allyl radical, whose asymmetric stretching mode potential suffers from an anomalous behavior due to the spin-preserving instabilities in restricted open-shell HF solutions.

Li, Xiangzhu; Paldus, Josef

2009-07-01

388

NASA Astrophysics Data System (ADS)

The similarities among the molecular contours of three scalar fields, viz. electron density (ED), electrostatic potential (ESP) and bare nuclear potential (BNP) have been investigated. The topological resemblance between ESP and ED contour diagrams (as prompted by the Thomas-Fermi model) is more pronounced than that for BNP and ED contour diagrams (as predicted by the local density functional model of Parr, Gadre and Bartolotti) with three-membered ring systems as test cases. An analysis of critical points of these distributions has also been included. Thus it may be conjectured that ED maps may prove useful in predicting reactive sites in molecules.

Gadre, Shridhar R.; Bendale, Rajeev D.

1986-10-01

389

Molecular Dynamics Simulations of Supported Pt Nanoclusters

high activity Â· low energy consumption Â· long lifetime. Applications: Â· Catalytic converters for increasing catalytic activity. Increase surface area of catalyst. Objectives: Â· 100% selectivity Â· extremely of nanoscale catalytic processes Dynamic structure in supported Pt nanoclusters: Real-time density functional

Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group

390

NASA Astrophysics Data System (ADS)

Oxidation of a flat aluminum (111) surface and the reactive wetting of the aluminum (Al) droplet on a flat alumina (alpha-Al2O 3) surface are investigated by using parallel molecular-dynamics simulations with dynamic charge transfer among atoms on a microscopic length scale. The interatomic potential, based on the formalism of Streitz and Mintmire, allows atoms to vary their charges dynamically between anions and cations, when atoms move and their local environment is altered. We investigate the oxidation thickness as a function of time and the oxygen density which is 10--40 times that of the normal state (1 atm and 300 K). Stable amorphous oxide scales form around 51 A at 4.42 ns, 2.862 ns, and 2.524 ns, respectively, and molecular oxygen density 10--40 times the normal state. We also study structural correlations in the resulting final oxide scale. The structure of final oxide scales depend on depth, where density of aluminum (Al) and oxygen (0) atoms change. Reactive wetting of aluminum nanodroplet on alumina surface is also studied using parallel MD. We study heat transfer, diffusion within droplet, and the structure of the inter-metallic phases in the liquid-solid interface. Oxygen (0) atoms diffuse into the spherical aluminum (Al) droplet and form an interface between the flat solid substrate and the Al droplet. This diffusion of oxygen atoms may be the main source of adhesion between the Al drop and the flat alpha-Al 2O3 substrate. The temperature in the flat alpha-Al 2O3 bulk substrate rises from OK to 200 K at the end of the simulation, 8.5 ps, but the temperature becomes much higher at the reactive interface. We have examined which oxygen atoms from the substrate participate in the wetting and the formation of a solder joint at the Al/alpha-Al 2O3 interface.

Aral, Gurcan

391

NASA Astrophysics Data System (ADS)

A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum.

Kawamoto, Shuhei; Nakamura, Takenobu; Nielsen, Steven O.; Shinoda, Wataru

2013-07-01

392

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel ‘dual-resolution’ molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup–glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a ‘destabilizing’ tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed. PMID:21131331

Orsi, Mario; Noro, Massimo G.; Essex, Jonathan W.

2011-01-01

393

NASA Astrophysics Data System (ADS)

Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C.

2013-11-01

394

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

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

Holian, B.L.; Voter, A.F. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Ravelo, R. [Department of Physics, University of Texas, El Paso, Texas 79968 (United States)] [Department of Physics, University of Texas, El Paso, Texas 79968 (United States)

1995-09-01

395

Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics

NASA Astrophysics Data System (ADS)

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

Ehrlicher, Allen

2012-02-01

396

Soliton dynamics in a diffracting trapping potential AH Sheinfux1

Soliton dynamics in a diffracting trapping potential AH Sheinfux1 , MC Rechtsman1 , B Osting2 , J@technion.ac.il Abstract: We examine a novel regime of interaction between a soliton and a transient trapping potential experimentally and numerically. We find that a soliton can be guided by such a potential, and arrested at its

Marzuola, Jeremy

397

Molecular dynamics simulation of photodissociation of carbon monoxide from hemoglobin

A molecular dynamics simulation of the photodissociation of carbon monoxide from the alpha subunit of hemoglobin is described. To initiate photodissociation, trajectories of the liganded molecule were interrupted, the iron-carbon monoxide bond was broken, and the parameters of the iron-nitrogen bonds were simultaneously altered to produce a deoxyheme conformation. Heme potential functions were used that reproduce the energies and forces for the iron out-of-plane motion obtained from quantum mechanical calculations. The effect of the protein on the rate and extent of the displacement of the iron from the porphyrin plane was assessed by comparing the results with those obtained for an isolated complex of heme with imidazole and carbon monoxide. The half-time for the displacement of the iron from the porphyrin plane was found to be 50-150 fs for both the protein and the isolated complex. These results support the interpretation of optical absorption studies using 250-fs laser pulses that the iron is displaced from the porphyrin plane within 350 fs in both hemoglobin and a free heme complex in solution.

Henry, E.R.; Levitt, M.; Eaton, W.A.

1985-04-01

398

Molecular Dynamics Analysis of Temperature Dependence of Liquid Metal Diffusivity

NASA Astrophysics Data System (ADS)

The diffusivities of liquid Al, Co, Mg, Ni, and Pb have been calculated with molecular dynamics (MD)-based on semiempirical potentials derived from the second-moment approximation to the tight binding method (TBM-SMA). The liquid structure in terms of pair distribution function described in the present work agrees well with the available experimental data. The diffusion coefficients derived agree well with a limited number of experimental measurements. The calculated diffusivities were also compared with the predictions of available diffusion models, including the activated state model, the moving oscillator model, the density fluctuation model, the free volume model, and the scaling law proposed by Dzugutov. The present work substantiates the density fluctuation model, suggesting that diffusivity D possesses a square proportionality of temperature T 2. It is concluded that diffusion is materialized in liquid metals through continuous movements of individual atoms over a small distance as a result of local density fluctuations rather than through discrete jumps of atoms over an interatomic distance.

Yang, Sui; Su, Xuping; Wang, Jianhua; Yin, Fucheng; Tang, Nai-Yong

2009-12-01

399

RPMDRATE: Bimolecular chemical reaction rates from ring polymer molecular dynamics

NASA Astrophysics Data System (ADS)

We present RPMDRATE, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH4, OH+CH4 and H+C2H6 reactions. Catalogue identifier: AENW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 94512 No. of bytes in distributed program, including test data, etc.: 1395674 Distribution format: tar.gz Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). Computer: Not computer specific. Operating system: Any for which Python, Fortran 90/95 compiler and the required external routines are available. Has the code been vectorized or parallelized?: The program can efficiently utilize 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors are reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines.

Suleimanov, Yu. V.; Allen, J. W.; Green, W. H.

2013-03-01

400

A neural network approach to the study of dynamics and structure of molecular systems

Neural networks are used to study intramolecular energy flow in molecular systems (tetratomics to macromolecules), developing new techniques for efficient analysis of data obtained from molecular-dynamics and quantum mechanics calculations. Neural networks can map phase space points to intramolecular vibrational energies along a classical trajectory (example of complicated coordinate transformation), producing reasonably accurate values for any region of the multidimensional phase space of a tetratomic molecule. Neural network energy flow predictions are found to significantly enhance the molecular-dynamics method to longer time-scales and extensive averaging of trajectories for macromolecular systems. Pattern recognition abilities of neural networks can be used to discern phase space features. Neural networks can also expand model calculations by interpolation of costly quantum mechanical ab initio data, used to develop semiempirical potential energy functions.

Getino, C.; Sumpter, B.G.; Noid, D.W.

1994-10-01

401

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

centuries ago and an early competitor of the steam engine, continues to attract interest owing to itsSimulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine D 2009; published 30 April 2009 A nanoscale-sized Stirling engine with an atomistic working fluid has

Rapaport, Dennis C.

402

Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation

Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation S.J.V. Frankland *, D hydrogen in individual single-shell carbon nanotubes and nanotube ropes using a semiclassical model. The calculations predict that isolated hydrogen molecules inside of nanotubes have a Raman frequency that increases

Brenner, Donald W.

403

Phonon thermal conductivity in nanolaminated composite metals via molecular dynamics

We use nonequilibrium molecular dynamics to characterize the phonon contribution to thermal conduction of Al nanostructures and the role of interfaces in metallic nanocomposites. We characterize the lattice thermal conductivity of pure Al samples as a function of size and temperature from which we obtain, using kinetic theory, the temperature dependence of the phonon mean free path. We also calculated

Ya Zhou; Benjamin Anglin; Alejandro Strachan

2007-01-01

404

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems – ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a static bond structure for molecules, rendering them infeasible for reactive systems.

Hasan Metin Aktulga; Joseph C. Fogarty; Sagar A. Pandit; Ananth Y Grama

2009-01-01

405

Molecular dynamics modeling of stishovite Sheng-Nian Luo a;

with the molecular dynamics (MD) method. The equation of state, thermal expansivity and melting curve of stishovite of the solid along the Hugoniot in the shock melting experiments. MD simulations show that the thermal insulators such as minerals and ceramics. The proposed MS-Q FF for silica system de- scribes both the four

Stewart, Sarah T.

406

Multiconfigurational molecular dynamics with quantum transitions: Multiple proton transfer reactions

multiple proton transfer reactions. MC-MDQT is a mixed quantum/classical molecular dynamics method on the surface hopping method MDQT, which has already been applied to single proton transfer reactions mechanically. The direct extension of MDQT to multiple proton transfer reactions, where many hydrogen atoms

Hammes-Schiffer, Sharon

407

Molecular Cell Dynamic Basis for One-Dimensional DNA Scanning

Molecular Cell Article Dynamic Basis for One-Dimensional DNA Scanning by the Mismatch Repair: Center For Comparative Functional Genomics, Department of Biology, New York University, 1009 Silver how these pro- teins might function we used single-molecule optical microscopy to answer the following

Chowdhury, Arindam

408

Efficient stochastic thermostatting of path integral molecular dynamics

The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here

Michele Ceriotti; Michele Parrinello; Thomas E. Markland; David E. Manolopoulos

2010-01-01

409

Molecular dynamics study of atomic displacements in disordered solid alloys

The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity

Yevgeniy S. Puzyrev

2005-01-01

410

Molecular dynamics study of the mechanical properties of palladium nanocontacts

The mechanical properties of extended palladium nanocontacts have been investigated by the molecular dynamics method. The\\u000a characteristic interatomic distances in the contacts have been determined and the process of the formation of palladium atomic\\u000a contacts undergoing breaking has been studied for the (100), (110), and (111) orientations of the contact-surface interfaces.

A. L. Klavsyuk; S. V. Kolesnikov; E. M. Smelova; A. M. Saletsky

2010-01-01

411

Molecular dynamics study of the mechanical properties of palladium nanocontacts

The mechanical properties of extended palladium nanocontacts have been investigated by the molecular dynamics method. The characteristic interatomic distances in the contacts have been determined and the process of the formation of palladium atomic contacts undergoing breaking has been studied for the (100), (110), and (111) orientations of the contact-surface interfaces.

A. L. Klavsyuk; S. V. Kolesnikov; E. M. Smelova; A. M. Saletsky

2010-01-01

412

Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

NASA Technical Reports Server (NTRS)

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

Menon, Madhu

1998-01-01

413

NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par

Mark T. Nelson; William Humphrey; Attila Gursoy; Andrew Dalke; Laxmikant V. Kalé; Robert D. Skeel; Klaus Schulten

1996-01-01

414

Thermal conduction of carbon nanotubes using molecular dynamics Zhenhua Yao*

Thermal conduction of carbon nanotubes using molecular dynamics Zhenhua Yao* SingaporeÂMIT Alliance. The thermal conductance of CNT's is also calculated using the Green-Kubo formula from linear response theory conductance instead of conductivity in calculations and discussions. We find that the thermal conductance

Li, Baowen

415

CALCULATION OF VISCOSITY OF LIQUID NICKEL BY MOLECULAR DYNAMICS METHODS

CALCULATION OF VISCOSITY OF LIQUID NICKEL BY MOLECULAR DYNAMICS METHODS F.J. Cherne III and P) to calculating the viscosity of a liquid transition metal, namely Ni. For high temperature liquid metals of viscosity calculated from theoretical models might be as appropriate as the experimental value (1). To date

Deymier, Pierre

416

Ethanol and water capacities of alcohols: a molecular dynamics study

Technology Transfer Automated Retrieval System (TEKTRAN)

The extended hydrogen bond networks formed by alcohols are good indicators of their capacities to hold water. Results from molecular dynamics simulations on 24 linear alcohol isomers containing from 6 to 12 carbon atoms show the effects of the hydroxyl location on bulk hydrogen-bonded structures. ...

417

Molecular Dynamics Simulations on High-Performance Reconfigurable

23 Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems MATT CHIU and Applications (parts of Sections 4 and 5). Authors' address: M. Chiu and M. C. Herbordt, Computer Architecture: November 2010. #12;23: 2 Â· M. Chiu and M.C. Herbordt ACM Reference Format: Chiu, M. and Herbordt, M. C

Herbordt, Martin

418

A molecular dynamics `Maxwell Demon' experiment for granular mixtures

A molecular dynamics `Maxwell Demon' experiment for granular mixtures ALAIN BARRAT and EMMANUEL] has put forward an analytical approach to explain this apparent intrusion of a `Maxwell Demon, we revisit numerically the Maxwell Demon experiment in the latter case, and consider the specific

Barrat, Alain

419

Molecular dynamics simulation of ultrafast laser ablation of fused silica

is considered as "thermal" ablation because it is caused by the high temperature in the material. On the other" ablation. Both thermal and non-thermal (Coulomb explosion) ablation processes have been discussedMolecular dynamics simulation of ultrafast laser ablation of fused silica C Cheng, A Q Wu and X Xu

Xu, Xianfan

420

Growth mechanisms of silver nanoparticles: a molecular dynamics study

NASA Astrophysics Data System (ADS)

The shape control of metal nanoparticles allows one to finely tune their properties with great versatility. A self-seeding coreduction method has recently been developed for the synthesis of silver nanodiscs, triangular nanoplates and nanospheres. The addition of surfactants was found to be one of the most important factors in determining the final particle shape. In this paper, molecular dynamics simulations are performed to understand the growth mechanisms of silver nanoparticles for different surfactants (i.e. bis(2-ethylhexyl) sulfosuccinate, 1-dodecanethiol and cetyltrimethyl ammonium). The interaction energies between the surfactants and the silver crystal plane (i.e. (100), (110), (111)) are calculated. The molecular structural property of surfactants at the silver surface is also examined. It is demonstrated that the calculated interaction energies explain well the growth behaviour observed in the silver nanoparticle systems. Molecular dynamics simulation could provide a theoretical guideline for the choice of surfactants and hence the synthesis of various metal nanoparticles with controlled shape.

Zeng, Qinghua; Jiang, Xuchuan; Yu, Aibing; Lu, Gaoqing Max

2007-01-01

421

Molecular targets of HPV oncoproteins: potential biomarkers for cervical carcinogenesis.

Cervical cancer is the second most common cancer among women worldwide and is responsible for 275,000 deaths each year. Persistent infection with high-risk human papillomavirus (HR-HPV) is an essential factor for the development of cervical cancer. Although the process is not fully understood, molecular mechanisms caused by HPV infection are necessary for its development and reveal a large number of potential biomarkers for diagnosis and prognosis. These molecules are host genes and/or proteins, and cellular microRNAs involved in cell cycle regulation that result from disturbed expression of HR-HPV E5, E6 and E7 oncoproteins. One of the current challenges in medicine is to discover potent biomarkers that can correctly diagnose cervical premalignant lesions and standardize clinical management. Currently, studies are showing that some of these molecules are potential biomarkers of cervical carcinogenesis, and it is possible to carry out a more accurate diagnosis and provide more appropriate follow-up treatment for women with cervical dysplasia. In this paper, we review recent research studies on cell cycle molecules deregulated by HPV infections, as well as their potential use for cervical cancer screening. PMID:24388872

de Freitas, Antonio Carlos; Coimbra, Eliane Campos; Leitão, Maria da Conceição Gomes

2014-04-01

422

Large scale molecular dynamics simulations of homogeneous nucleation

NASA Astrophysics Data System (ADS)

We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between 1 × 109 and 8 × 109 Lennard-Jones (LJ) atoms, covering up to 1.2 ?s (56 × 106 time-steps). They cover a wide range of supersaturation ratios, S ? 1.55-104, and temperatures from kT = 0.3 to 1.0? (where ? is the depth of the LJ potential, and k is the Boltzmann constant). We have resolved nucleation rates as low as 1017 cm-3 s-1 (in the argon system), and critical cluster sizes as large as 100 atoms. Recent argon nucleation experiments probe nucleation rates in an overlapping range, making the first direct comparison between laboratory experiments and molecular dynamics simulations possible: We find very good agreement within the uncertainties, which are mainly due to the extrapolations of argon and LJ saturation curves to very low temperatures. The self-consistent, modified classical nucleation model of Girshick and Chiu [J. Chem. Phys. 93, 1273 (1990)], 10.1063/1.459191 underestimates the nucleation rates by up to 9 orders of magnitudes at low temperatures, and at kT = 1.0? it overestimates them by up to 105. The predictions from a semi-phenomenological model by Laaksonen et al. [Phys. Rev. E 49, 5517 (1994)], 10.1103/PhysRevE.49.5517 are much closer to our MD results, but still differ by factors of up to 104 in some cases. At low temperatures, the classical theory predicts critical clusters sizes, which match the simulation results (using the first nucleation theorem) quite well, while the semi-phenomenological model slightly underestimates them. At kT = 1.0?, the critical sizes from both models are clearly too small. In our simulations the growth rates per encounter, which are often taken to be unity in nucleation models, lie in a range from 0.05 to 0.24. We devise a new, empirical nucleation model based on free energy functions derived from subcritical cluster abundances, and find that it performs well in estimating nucleation rates.

Diemand, Jürg; Angélil, Raymond; Tanaka, Kyoko K.; Tanaka, Hidekazu

2013-08-01

423

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Liu, Qixin; Cai, Zhiyong

2014-01-01

424

Numerical methods for molecular dynamics. Progress report

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.

Skeel, R.D.

1991-12-31

425

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales

Shaw, David E.

426

Molecular Dynamics Simulations of RNA Systems

of the dynamics of such systems presents specific problems associated with the complex three-dimensional foldsRNA loop E 24 10.0 NaÃ¾ & Mg2Ã¾ 50 24 11.5 @0.2 and @1.0 M KCl and Mg2Ã¾ 38, 48, 49 HIV kissing loop complexes 46 7.5 NaÃ¾ and Mg2Ã¾ 52 16S rRNA 81 5.5 @0.1 M NaCl 120 Pseudoknot 26 5.0 NaÃ¾ CÃ¾ 34 Hammerhead

Westhof, Eric

427

Molecular Dynamics of a Water-Lipid Bilayer Interface

NASA Technical Reports Server (NTRS)

We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

Wilson, Michael A.; Pohorille, Andrew

1994-01-01

428

MOLECULAR ALTERATIONS IN GLIOBLASTOMA: POTENTIAL TARGETS FOR IMMUNOTHERAPY

Glioblastoma is the most common and deadly brain tumor, possibly arising from genetic and epigenetic alterations in normal astroglial cells. Multiple cytogenetic, chromosomal, and genetic alterations have been identified in glioblastoma, with distinct expression of antigens (Ags) and biomarkers that may alter therapeutic potential of this aggressive cancer. Current therapy consists of surgical resection, followed by radiation therapy and chemotherapy. In spite of these treatments, the prognosis for glioblastoma patients is poor. Although recent studies have focused on the development of novel immunotherapeutics against glioblastoma, little is known about glioblastoma specific immune responses. A better understanding of the molecular interactions among glioblastoma tumors, host immune cells, and the tumor microenvironment may give rise to novel integrated approaches for the simultaneous control of tumor escape pathways and the activation of antitumor immune responses. This review provides a detailed overview concerning genetic alterations in glioblastoma, their effects on Ag and biomarker expression and the future design of chemoimmunotherapeutics against glioblastoma. PMID:21199773

Haque, Azizul; Banik, Naren L.; Ray, Swapan K.

2015-01-01

429

Ab initio molecular dynamics: Concepts, recent developments, and future trends

The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed “on the fly” from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

Iftimie, Radu; Minary, Peter; Tuckerman, Mark E.

2005-01-01

430

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics July 2007; accepted 8 January 2008; published online 21 March 2008 We investigate the sensitivity-proline-alanine-leucine in explicit water. The sensitivity is quantified by varying the boundaries of the clusters and investigating

Nerukh, Dmitry

431

Self-consistent field theory based molecular dynamics with linear system-size scaling

We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany)] [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

2014-04-07

432

Molecular dynamics simulation of self-diffusion coefficients for liquid metals

NASA Astrophysics Data System (ADS)

The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature.

Ju, Yuan-Yuan; Zhang, Qing-Ming; Gong, Zi-Zheng; Ji, Guang-Fu

2013-08-01

433

The electric field dependence of the structure and dynamics of water at 77 K, i.e., below the glass transition temperature (136 K), is investigated using molecular dynamics simulations. Transitions are found at two critical field strengths, denoted E1 and E2. The transition around E1 3.5 V/nm is characterized by the onset of significant structural disorder, a rapid increase in the orientational polarization, and a maximum in the dynamical fluctuations. At E2 40 V/nm, the system crystallizes in discrete steps into a body-centered-cubic unit cell that minimizes the potential energy by simultaneous superpolarization of the water molecular dipoles and maximization of the intermolecular hydrogen bonds. The stepwise and discontinuous increase of the orientational polarization with the increasing electric field indicates that the dipole relaxation in the electric field is highly cooperative.

Hu, Xiaohu [ORNL; Elghobashi-Meinhardt, Nadia [Karlsruhe Institute of Technology, Karlsruhe, Germany; Gembris, Daniel [Bruker Bio-Spin MRI GmbH, Ettling, Germany; Smith, Jeremy C [ORNL

2011-01-01

434

Molecular dynamics simulation study of water adsorption on hydroxylated graphite surfaces.

In this paper, we present results from molecular dynamic simulations devoted to the characterization of the interaction between water molecules and hydroxylated graphite surfaces considered as models for surfaces of soot emitted by aircraft. The hydroxylated graphite surfaces are modeled by anchoring several OH groups on an infinite graphite plane. The molecular dynamics simulations are based on a classical potential issued from quantum chemical calculations. They are performed at three temperatures (100, 200, and 250 K) to provide a view of the structure and dynamics of water clusters on the model soot surface. These simulations show that the water-OH sites interaction is quite weak compared to the water-water interaction. This leads to the clustering of the water molecules above the surface, and the corresponding water aggregate can only be trapped by the OH sites when the temperature is sufficiently low, or when the density of OH sites is sufficiently high. PMID:16623525

Picaud, Sylvain; Collignon, B; Hoang, Paul N M; Rayez, J C

2006-04-27

435

Simulating electron spin resonance spectra of nitroxide spin labels from motional models is necessary for the quantitative analysis of experimental spectra. We present a framework for modeling the spin label dynamics by using trajectories such as those from molecular dynamics (MD) simulations combined with stochastic treatment of the global protein tumbling. This is achieved in the time domain after two efficient numerical integrators are developed: One for the quantal dynamics of the spins and the other for the classical rotational diffusion. For the quantal dynamics, we propagate the relevant part of the spin density matrix in Hilbert space. For the diffusional tumbling, we work with quaternions, which enables the treatment of anisotropic diffusion in a potential expanded as a sum of spherical harmonics. Time-averaging arguments are invoked to bridge the gap between the smaller time step of the MD trajectories and the larger time steps appropriate for the rotational diffusion and?or quantal spin dynamics. PMID:18447510

Sezer, Deniz; Freed, Jack H.; Roux, Benoît

2008-01-01

436

Laser-enhanced dynamics in molecular rate processes

NASA Technical Reports Server (NTRS)

The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.

1978-01-01

437

The density dependence of the local structure and of collective dynamics of a polar fluid fluoroform along an isotherm at a temperature of 1.03 T(c), in the near-critical (NC) region, were studied by classical molecular dynamics (MD) simulations. In the case of local structure we focus on local density inhomogeneities and on orientational pair correlations that are relevant to dielectric properties and light scattering intensities. Our results show that the density dependence of the frequency shifts of fluoroform ?(2) and ?(3) modes correlates well with that of intermolecular dipole-dipole interactions. Our study of collective dynamics deals with dipole and polarizability anisotropy relaxation, experimentally accessible through far-infrared absorption, depolarized light scattering, and optical Kerr effect. Our MD simulations were performed using an all-atom nonpolarizable potential model of fluoroform. Contributions of induced dipoles to dielectric properties were included using first-order perturbation theory, and this approach was also used to include interaction-induced contributions to polarizability anisotropy relaxation. For interactions involving induced dipoles, we calculated and compared the results of a distributed polarizability model to a model with a single polarizable site located at the center-of-mass. Using a projection scheme that allows us to identify the contributions from different relaxation mechanisms, we found that dipole relaxation is dominated by collective reorientation, while in the case of polarizability anisotropy, relaxation processes related to translational dynamics make a major contribution over most of the fluid density range. The dielectric properties of fluoroform in the NC region were calculated and compared to the corresponding measurements. We found the dielectric constant and the far-infrared absorption spectrum to be in good agreement with experiments. PMID:23259748

Ingrosso, Francesca; Ladanyi, Branka M

2013-01-17

438

Fluorescence Molecular Tomography: Principles and Potential for Pharmaceutical Research

Fluorescence microscopic imaging is widely used in biomedical research to study molecular and cellular processes in cell culture or tissue samples. This is motivated by the high inherent sensitivity of fluorescence techniques, the spatial resolution that compares favorably with cellular dimensions, the stability of the fluorescent labels used and the sophisticated labeling strategies that have been developed for selectively labeling target molecules. More recently, two and three-dimensional optical imaging methods have also been applied to monitor biological processes in intact biological organisms such as animals or even humans. These whole body optical imaging approaches have to cope with the fact that biological tissue is a highly scattering and absorbing medium. As a consequence, light propagation in tissue is well described by a diffusion approximation and accurate reconstruction of spatial information is demanding. While in vivo optical imaging is a highly sensitive method, the signal is strongly surface weighted, i.e., the signal detected from the same light source will become weaker the deeper it is embedded in tissue, and strongly depends on the optical properties of the surrounding tissue. Derivation of quantitative information, therefore, requires tomographic techniques such as fluorescence molecular tomography (FMT), which maps the three-dimensional distribution of a fluorescent probe or protein concentration. The combination of FMT with a structural imaging method such as X-ray computed tomography (CT) or Magnetic Resonance Imaging (MRI) will allow mapping molecular information on a high definition anatomical reference and enable the use of prior information on tissue's optical properties to enhance both resolution and sensitivity. Today many of the fluorescent assays originally developed for studies in cellular systems have been successfully translated for experimental studies in animals. The opportunity of monitoring molecular processes non-invasively in the intact organism is highly attractive from a diagnostic point of view but even more so for the drug developer, who can use the techniques for proof-of-mechanism and proof-of-efficacy studies. This review shall elucidate the current status and potential of fluorescence tomography including recent advances in multimodality imaging approaches for preclinical and clinical drug development. PMID:24310495

Stuker, Florian; Ripoll, Jorge; Rudin, Markus

2011-01-01

439

Molecular dynamics simulation of ultrafast laser ablation of fused silica film

NASA Astrophysics Data System (ADS)

Ultrafast laser ablation of fused silica is studied using molecular dynamics simulations. Ionization and generation of free electrons, absorption of the laser energy by free electrons and energy coupling between free electrons and ions are considered. The BKS potential is applied and modified to describe molecular interactions and the effect of free electrons. Smooth particle mesh of the Ewald method (SPME) is adopted to calculate the Coulomb force. It is found that the electrostatic Coulomb force, which is caused by the ionization, plays an important role in the laser ablation process.

Wang, Y.; Xu, X.; Zheng, L.

2008-09-01

440

Molecular Dynamics Simulation of MBE Growth of CdTe/ZnTe/Si

NASA Astrophysics Data System (ADS)

We simulate in three dimensions molecular beam epitaxial (MBE) growth of CdTe/ZnTe/Si using classical molecular dynamics. Atomic interactions are simulated with Stillinger-Weber potentials, whose parameters are obtained by fitting to experimental data or density function theory-calculated distortion energies of the component crystals. The effects of substrate temperature and atomic species flux ratios on epilayer morphology are investigated. The agreement between simulations and experiments suggests that this model has reasonable ability to predict the microstructures of CdTe/ZnTe/Si grown by MBE.

Zhang, Zhenli; Chatterjee, Alok; Grein, Christoph; Ciani, Anthony J.; Chung, Peter W.

2011-02-01

441

Molecular dynamics driven by ultrashort laser pulses: Interference effects due to rescattering

A time-dependent Schroedinger equation is integrated numerically to investigate the dynamics of a model molecular system driven by a high-intensity ultrashort laser pulse. Two-dimensional photoelectron momentum distributions are analyzed. Highly nonmonotonic electron angular distributions are obtained that cannot be explained by diffraction in the double-well potential of a molecular ion. The nonmonotonicity is also demonstrated for atomic ionization and is attributed to the interference that occurs between components of an electron wave packet after its rescattering from the parent ion. An analytical model explaining the observed effects is developed.

Burenkov, I. A.; Volkova, E. A.; Popov, A. M.; Tikhonova, O. V., E-mail: ovtikhonova@mail.r [Moscow State University, Skobeltsyn Institute of Nuclear Physics (Russian Federation)

2009-07-15

442

MOLECULAR DYNAMICS SIMULATION OF QUASI-BALLISTIC HEAT CONDUCTION IN CARBON NANOTUBES

MOLECULAR DYNAMICS SIMULATION OF QUASI-BALLISTIC HEAT CONDUCTION IN CARBON NANOTUBES J Shiomi. While experimental attempts to characterize heat conduction of carbon nanotubes encounter technical difficulties, the classical molecular dynamics (MD) simulations hold an advantage as the heat conduction

Maruyama, Shigeo

443

Molecular Dynamics Simulations of Sonic Hedgehog-Receptor and Inhibitor Complexes and Their

Molecular Dynamics Simulations of Sonic Hedgehog-Receptor and Inhibitor Complexes), Gyeongsang National University (GNU), Jinju, Republic of Korea Abstract The sonic hedgehog (Shh) signaling) Molecular Dynamics Simulations of Sonic Hedgehog-Receptor and Inhibitor Complexes and Their Applications

Lee, Keun Woo

444

Thermal conductivity of metal-organic framework 5 (MOF-5): Part I. Molecular dynamics simulations

The phonon thermal conductivity of MOF-5, a metal-organic framework crystal with a phenylene bridge, is predicted between temperatures of 200K and 400K using molecular dynamics simulations and the Green–Kubo method. The simulations are performed using interatomic potentials obtained using ab initio calculations and experimental results. The predicted thermal conductivity of MOF-5 is low for a crystal, 0.31W\\/mK at a temperature

B. L. Huang; A. J. H. McGaughey; M. Kaviany

2007-01-01

445

Initiation of PETN decomposition under shock compression: Reactive molecular dynamics simulation

The initial physical and chemical response of energetic materials under mechanical shock has been investigated for PETN by molecular dynamics method with ReaxFF reactive force field parameterized from first-principles calculations. We study the propagation of a shock wave and shock-induced chemical reactions created by moving piston mimicked by a potential wall. We simulate both the continuous and impulsive piston loading

Peng Xu; Sergey Zybin; Aidan Thompson; Joanne Budzien; William Goddard III

2009-01-01

446